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  • richardmitnick 7:55 pm on July 21, 2022 Permalink | Reply
    Tags: "Evolution-in-a-flask experiment moves but not the science", , Bacteriology, , , ,   

    From The Michigan State University College of Natural Science: “Evolution-in-a-flask experiment moves but not the science” 

    From The Michigan State University College of Natural Science

    At

    Michigan State Bloc

    Michigan State University

    7.5.22

    Michigan State University’s renowned Long-Term Evolution Experiment – a remarkable 34-year biological drama in flasks, with bacteria competing for resources and fighting for dominance – is itself evolving.

    1
    In June, the Lenski lab carefully packed up the latest samples from 75,000 generations of E. coli evolution to ship to the laboratory of Jeffrey Barrick, an evolutionary biologist at the University of Texas at Austin who first worked on the experiment as a postdoc in Lenski’s lab from 2006 to 2010. While the daily propagation of the LTEE is moving to Texas, copies of all of the samples remain at MSU. Lenski has lots of plans and ideas for studying them, both in his lab and with collaborators around the world. Credit: Harley J. Seeley.

    The bacteria’s main stage – frozen vials containing some 75,000 generations– has been moved from MSU’s Biomedical and Physical Sciences Building to Texas. Richard Lenski, its scientific founder and game master, is passing its care and feeding on to a former Michigan State postdoctoral researcher.

    Yet the bookends of news articles in high-profile international science magazines this month signal that MSU’s future with the LTEE is less about glowing obituaries and more about chapters still being written.

    Lenski wryly documented the migration of his microbial colleagues on his @RELenski Twitter account: “Bon voyage, #LTEE! Enjoy your new locale, even if your Erlenmeyer flask homes and DM25 diets are exactly the same as you’ve been evolving in and adapting to for the last 75,000 generations! Now keep on evolving, my friends — bacteria and humans alike!”

    The experiment was started in 1988 by Lenski, the John Hannah Distinguished Professor of Microbial Ecology in the MSU College of Natural Science. He began with 12 populations of Escherichia coli (E. coli) bacteria—identical ancestral strains placed into identical environments—to see how similarly or differently they would evolve. For years he and his team fed them and protected their tiny universes from disruptions. In return, the bacteria reproduced quickly, allowing evolutionary-minded scientists to ask questions about evolution that would take many human lifetimes to provide.

    The LTEE has resulted in the publication of more than 100 scientific papers documenting changes large and small in the bacteria – their competitive ability, size and shape, and the sequence of their genomes — findings now widely reported in textbooks, popular books by science writers, and in the media.

    This month, the Lenski lab carefully packed up the latest samples from 75,000 generations of evolution to ship to the laboratory of Jeffrey Barrick, an evolutionary biologist at the University of Texas at Austin who first worked on the experiment as a postdoc in Lenski’s lab from 2006 to 2010.

    Nature, a prestigious international science journal, covered the move [below] of what they termed a “legendary” experiment with a Q&A with Lenski and Barrick. A week later, New Scientist published [below] results by Lenski lab postdoctoral researcher Minako Izutsu, crediting a spin-off experiment with “settling (a) long-term evolution mystery.”

    The latest work addressed the long-standing debate in biology about the relative importance of existing variation versus new mutations in evolution. Izutsu and Lenski put that question to the test in a new evolution experiment with bacteria that ran for 2,000 generations. They found that new mutations began to dominate evolution after only about 50 generations – just a week or so for E. coli – and the effects of the initial variation on the bacteria’s competitiveness was erased by 500 generations.

    The New Scientist piece underscores that, while some of the day-to-day toiling to feed and care for the storied bacteria has been passed along to the next generation, the curiosity that is the scientists’ lifeblood remains strong.

    “While the daily propagation of the LTEE is moving to Texas, we’ve still got copies of all of the samples here, and lots of plans and ideas for studying them, both here in my lab as well as with collaborators around the world,” Lenski said.

    Then he picks up speed: after admitting to Nature that at 65 it seemed prudent to pass the baton to a younger group, it’s clear the ideas aren’t slowing.

    Lenski said he and MSU instructor Michael Wiser are planning to update their analyses of the fitness trajectories through the latest 75,000-generation samples of the LTEE. And they’ll be running computer simulations and analyzing mathematical models to better understand those fitness trajectories with PhD student Devin Lake.

    “And we’ve got lots of other projects going on as well,” he said. “We’re following up on Minako’s latest experiment by sequencing and analyzing the evolved genomes to dig deeper and better understand her exciting results.”

    Zachary Blount is a research assistant professor in MSU’s Department of Microbiology and Molecular Genetics. Blount is examining bacterial strains that use different transporters to take up citrate from the environment. One of the LTEE lines unexpectedly evolved the ability to consume citrate, and that discovery generated public interest as well as lots of new scientific questions.

    “Zack is using those strains to study the physiological and ecological effects of the bacteria consuming citrate, and how those effects would change if the bacteria had evolved to use citrate in a different way from the one that actually happened in the LTEE,” Lenski said.

    Lenski is a member of the Ecology, Evolution, and Behavior program at MSU, of which he previously served as director. Many in his lab – including Izutsu and Lake currently – have been members over the years as well.

    The long list of current projects and questions makes it easy to conclude that long-term evolutionary experiments never really go away, they simply keep on evolving.

    Science paper:
    Nature

    Science article:
    New Scientist

    See the full article here .


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    Please help promote STEM in your local schools.

    Stem Education Coalition

    About The College of Natural Science

    The College of Natural Science at Michigan State University is home to 27 departments and programs in the biological, physical and mathematical sciences.

    The college averages $57M in research expenditures annually while providing world-class educational opportunities to more than 5,500 undergraduate majors and 1,200 graduate and postdoc students. There are 800+ faculty and academic staff associated with NatSci and more than 63,000 living alumni worldwide.

    College of Natural Science Vision, Mission, Values

    The Michigan State University College of Natural Science is committed to creating a safe, collaborative and supportive environment in which differences are valued and all members of the NatSci community are empowered to grow and succeed.

    The following is the college’s vision, mission and values, as co-created and affirmed by the College of Natural Science community:

    Vision:

    A thriving planet and healthy communities through scientific discovery.

    Mission:

    To use discovery, innovation and our collective ingenuity to advance knowledge across the natural sciences. Through equitable, inclusive practices in research, education and service, we empower our students, staff and faculty to solve challenges in a complex and rapidly changing world.

    Core Values:

    Inclusiveness-

    Foster a safe, supportive, welcoming community that values diversity, respects difference and promotes belonging. We commit to providing equitable opportunity for all.

    Innovation-

    Cultivate creativity and imagination in the quest for new knowledge and insights. Through individual and collaborative endeavors, we seek novel solutions to current and emergent challenges in the natural sciences.

    Openness-

    Commit to honesty and transparency. By listening and being open to other perspectives, we create an environment of trust where ideas are freely shared and discussed.

    Professionalism-

    Strive for excellence, integrity and high ethical standards. We hold ourselves and each other accountable to these expectations in a respectful and constructive manner.

    Michigan State Campus

    Michigan State University is a public research university located in East Lansing, Michigan, United States. Michigan State University was founded in 1855 and became the nation’s first land-grant institution under the Morrill Act of 1862, serving as a model for future land-grant universities.

    The university was founded as the Agricultural College of the State of Michigan, one of the country’s first institutions of higher education to teach scientific agriculture. After the introduction of the Morrill Act, the college became coeducational and expanded its curriculum beyond agriculture. Today, Michigan State University is one of the largest universities in the United States (in terms of enrollment) and has approximately 634,300 living alumni worldwide.

    U.S. News & World Report ranks its graduate programs the best in the U.S. in elementary teacher’s education, secondary teacher’s education, industrial and organizational psychology, rehabilitation counseling, African history (tied), supply chain logistics and nuclear physics in 2019. Michigan State University pioneered the studies of packaging, hospitality business, supply chain management, and communication sciences. Michigan State University is a member of the Association of American Universities and is classified among “R1: Doctoral Universities – Very high research activity”. The university’s campus houses the National Superconducting Cyclotron Laboratory, the W. J. Beal Botanical Garden, the Abrams Planetarium, the Wharton Center for Performing Arts, the Eli and Edythe Broad Art Museum, the the Facility for Rare Isotope Beams, and the country’s largest residence hall system.

    Research

    The university has a long history of academic research and innovation. In 1877, botany professor William J. Beal performed the first documented genetic crosses to produce hybrid corn, which led to increased yields. Michigan State University dairy professor G. Malcolm Trout improved the process for the homogenization of milk in the 1930s, making it more commercially viable. In the 1960s, Michigan State University scientists developed cisplatin, a leading cancer fighting drug, and followed that work with the derivative, carboplatin. Albert Fert, an Adjunct professor at Michigan State University, was awarded the 2007 Nobel Prize in Physics together with Peter Grünberg.

    Today Michigan State University continues its research with facilities such as the Department of Energy -sponsored Plant Research Laboratory and a particle accelerator called the National Superconducting Cyclotron Laboratory [below]. The Department of Energy Office of Science named Michigan State University as the site for the Facility for Rare Isotope Beams (FRIB). The $730 million facility will attract top researchers from around the world to conduct experiments in basic nuclear science, astrophysics, and applications of isotopes to other fields.

    Michigan State University FRIB [Facility for Rare Isotope Beams] .

    In 2004, scientists at the Cyclotron produced and observed a new isotope of the element germanium, called Ge-60 In that same year, Michigan State University, in consortium with the University of North Carolina at Chapel Hill and the government of Brazil, broke ground on the 4.1-meter Southern Astrophysical Research Telescope (SOAR) in the Andes Mountains of Chile.

    The consortium telescope will allow the Physics & Astronomy department to study galaxy formation and origins. Since 1999, MSU has been part of a consortium called the Michigan Life Sciences Corridor, which aims to develop biotechnology research in the State of Michigan. Finally, the College of Communication Arts and Sciences’ Quello Center researches issues of information and communication management.


    The Michigan State University Spartans compete in the NCAA Division I Big Ten Conference. Michigan State Spartans football won the Rose Bowl Game in 1954, 1956, 1988 and 2014, and the university claims a total of six national football championships. Spartans men’s basketball won the NCAA National Championship in 1979 and 2000 and has attained the Final Four eight times since the 1998–1999 season. Spartans ice hockey won NCAA national titles in 1966, 1986 and 2007. The women’s cross country team was named Big Ten champions in 2019. In the fall of 2019, MSU student-athletes posted all-time highs for graduation success rates and federal graduation rates, according to NCAA statistics.

     
  • richardmitnick 8:32 am on July 19, 2022 Permalink | Reply
    Tags: "Stanford researchers show how geological activity rapidly changes deep microbial communities", , Bacteriology, , , , , , , , SURF-Sanford Underground Research Facility at Lead in South Dakota.   

    From Stanford University: “Stanford researchers show how geological activity rapidly changes deep microbial communities” 

    Stanford University Name

    From Stanford University

    July 14, 2022
    Danielle Torrent Tucker

    New research reveals that, rather than being influenced only by environmental conditions, deep subsurface microbial communities can transform because of geological movements. The findings advance our understanding of subsurface microorganisms, which comprise up to half of all living material on the planet.

    In the deep subsurface that plunges into the Earth for miles, microscopic organisms inhabit vast bedrock pores and veins. Below ground microorganisms, or microbes, comprise up to half of all living material on the planet and support the existence of all life forms up the food chain. They are essential for realizing an environmentally sustainable future and can change the chemical makeup of minerals, break down pollutants, and alter the composition of groundwater.

    1
    Lead study author Yuran Zhang working deep underground at the field site in South Dakota. Zhang and her colleagues used samples collected from the facility to show that microbial community changes can be driven by geological activity. (Image credit: Courtesy of Yuran Zhang)

    While the significance of bacteria and archaea is undeniable, the only evidence of their existence in the deep subsurface comes from traces of biological material that seep through mine walls, cave streams, and drill holes that tap into aquifers.

    Many scientists have assumed that the composition of microbial communities in the deep subsurface is primarily shaped by local environmental pressures on microbial survival such as temperature, acidity, and oxygen concentration. This process, environmental selection, can take years to millennia to cause significant community-level changes in slow-growing communities like the subsurface.

    Now, with data collected nearly 5,000 feet below ground, Stanford University researchers have shown that deep subsurface microbial communities can change in a matter of days, and the shifts can be driven by geological activity – not only by environmental pressures.

    “In the deep subsurface, we can no longer understand environmental selection to be the dominant driver in community dynamics – it could be just a changing flow rate or movement of the groundwater through the crevices and cracks in the subsurface that’s driving what we observe,” said lead study author Yuran Zhang, PhD ’20, who conducted the research as a PhD student in energy resources engineering.

    Filling in gaps

    Like reading a random page of someone’s 1000-word biography, previous studies on deep subsurface microbes have only offered glimpses into the chronicles of their existence. By collecting water samples from multiple geothermal wells weekly over 10 months, the Stanford researchers showed how these populations can change over space and time, demonstrating the first evidence of geological activity as a driver for microbial community change – and therefore evolution.

    “There is previous research on the composition of microbial communities in the deep subsurface, but it’s almost always using samples from a single time point,” said geomicrobiologist Anne Dekas, a senior study author and assistant professor of Earth system science. “To have a time series over 10 months – especially at a weekly resolution – is a really different perspective that allowed us to ask different questions about how and why these communities change with time.”

    Dekas said that while microbial ecologists might have guessed that geological activity was at play, she was surprised by the extent of the community shifts that occurred after a change in the flow network.

    Boreholes and test tubes

    The technique used in the study involved processing samples from a flow test conducted at the Sanford Underground Research Facility (SURF), formerly the Homestake Gold Mine, in South Dakota.

    Zhang said the experience of moving from a borehole sample setting to a test-tube-filled lab with a PCR machine on campus was “like connecting two totally different worlds,” referring to how this work unites the distinct fields of microbial ecology and geothermal engineering.

    In analyzing the properties of the water samples, the researchers identified microbial DNA fingerprints. Each of the 132 water samples supplied tens of thousands of unique sequencing IDs. Those data were used to show that when geological activity occurred, it could quickly mix disparate biological communities – and from locations that weren’t previously known to be connected.

    “One of the additional pieces of information from this microbiology study is that we’ve seen populations of microbes that have moved not just directly from place to place, but as a consequence of the network in between,” said senior study author Roland Horne, the Thomas Davies Barrow Professor of Earth Sciences. “That’s so important from the reservoir point of view because it reveals something that isn’t revealed by normal geothermal analytical methods.

    Geology meets biology

    The level of data collected by current geothermal techniques is like only having access to highways that are cut off from the side roads that will take you all the way home. Investigation of microorganism populations opens the potential for mapping the complex intricacies of the deep subsurface in more detail, Horne said.

    Being able to use biology as a tool may also bring insights into the deep subsurface as a frontier for geological storage, such as nuclear waste and carbon sequestration. But combining biology and geology requires fundamental knowledge of both subjects.

    “On the geothermal underground project, I realized that reservoir engineers or geologists or geophysicists usually aren’t that familiar with microbiology,” said Zhang, who was co-advised by Horne and Dekas. “There is common knowledge about geochemistry, but not so much in geomicrobiology.”

    This work could even be meaningful beyond Earth-based disciplines: If some of the oldest life forms in the deep subsurface of Earth can change and diversify because of geological activity, maybe we can have similar expectations for the origin and diversification of life on other tectonic planetary bodies.

    “What we observe could potentially connect to the early story of life’s evolution,” Zhang said. “If geological activity is a driver for early life formation or diversification, then maybe we should look for extraterrestrial life on planets that are geologically active.”

    The findings were published last month in PNAS.

    See the full article here .


    five-ways-keep-your-child-safe-school-shootings
    Please help promote STEM in your local schools.

    Stem Education Coalition

    Stanford University campus

    Leland and Jane Stanford founded Stanford 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 (originally named the Stanford Linear Accelerator Center), established in 1962, performs research in particle physics.

    Land

    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, the University of Texas System, and Yale University 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
    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 and UC San Francisco, 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 University of California- 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.

    Athletics

    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.

    Traditions

    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 3:11 pm on July 4, 2022 Permalink | Reply
    Tags: "Microbes support adaptation to climate change", , Bacteriology, , , Heinrich Heine University Düsseldorf, ,   

    From The Kiel University [Christian-Albrechts-Universität zu Kiel] (DE): “Microbes support adaptation to climate change” 

    From The Kiel University [Christian-Albrechts-Universität zu Kiel] (DE)

    7.4.22
    Science Contact
    Prof. Sebastian Fraune,
    Zoology and Organismic Interactions, Department Biology,
    Heinrich Heine University Düsseldorf (HHU):
    +49 (0) 211 81-14991
    fraune@hhu.de

    Press contact:
    Christian Urban
    Science communication “Kiel Life Science”,
    Kiel University:
    +49 (0) 431-880-1974
    curban@uv.uni-kiel.de

    Researchers from Kiel and Düsseldorf use the example of the sea anemone Nematostella vectensis to investigate the contribution of the microbiome to thermal adaptation of living organisms.

    1
    The offspring of the sea anemone Nematostella vectensis, shown here laying eggs, can directly inherit the temperature tolerance of the parent generation by passing on certain bacteria. © Hanna Domin.

    All multicellular organisms are colonized by an unimaginably large number of microorganisms and have co-evolved with them from the very beginning of life’s evolutionary history. The natural microbiome, i.e. the totality of these bacteria, viruses and fungi living in and on a body, is of fundamental importance for the organism as a whole: it performs vital tasks for the host, for example, it assists in nutrient uptake and it helps defend against pathogens. A research team from Heinrich Heine University Düsseldorf (HHU) and Kiel University has now investigated how the microbiome assists an organism in the adaptation to changing environmental conditions. In a study within the Collaborative Research Center (CRC) 1182 “Origin and Function of Metaorganisms”, they have investigated the involvement of the microbiome in thermal adaptation of anemones in a so-called acclimation experiment. The researchers led by Professor Sebastian Fraune of the HHU Institute of Zoology and Organismic Interactions, who is also project leader in the Kiel CRC 1182, were able to show that the bacterial colonization of the animals changes as a result of acclimation. Furthermore, the organism of the sea anemone becomes more resistant to heat stress. In addition, the research team succeeded in proving a causal relationship: If they transferred the microbiome of heat-adapted to non-acclimated anemones, the latter also became less sensitive to higher temperatures. The CRC 1182 research team published the results, which are particularly significant with regard to changing environmental conditions as a result of climate change, recently in the journal Nature Communications.

    Long-term acclimation experiment

    The new work is based on a long-term study funded by the Human Frontier Science Program (HFSP), in which the researchers have been studying the adaptation of anemones to changing environmental conditions for more than four years. To do this, they worked with clones of a single original animal and compared 50 genetically identical anemones in each of 15 different colonies. The researchers divided these colonies into three groups that were kept at 15, 20 and 25 degrees Celsius in order to analyze their acclimation to different temperatures. In the course of the long observation period, characteristic changes in the so-called phenotype of the anemones, i.e. in their external shape including physiological features, became apparent: among other things, the animals grow significantly larger at lower temperatures and they changed their reproductive mode. Changes in temperature tolerance were also particularly interesting. “The anemones differed very significantly in their stress resistance to high temperatures. If we exposed them to a very high temperature stress of 40 degrees Celsius for six hours, the animals acclimated at 25 degrees Celsius almost exclusively survived,” says Laura Baldassarre, former member of Fraune’s group and lead author of the study.

    Previous research suggested that adaptation to temperature stress may be related to changes in the microbiome composition of the animals. Analysis of the bacterial colonization of the different colonies in the acclimation experiment again supported this hypothesis, as the microbiome of the acclimated animals also changed compared to their non-acclimated conspecifics. “That acclimation, the so-called phenotypic plasticity, can be partly controlled by bacteria seems very plausible. Their much shorter generation times allow a much faster adaptation than would be possible via genetic recombination of the host organism,” emphasizes Fraune. The fact that there is indeed a causal relationship between the change in the microbiome and temperature adaptation has now been proven.

    Microbiome transplantation provides confirmation

    “In a transplantation experiment, we transferred the microbiomes from anemones acclimated to 15, 20 and 25 degrees Celsius to non-adapted but genetically identical animals. It turned out that these animals, which received the microbiome of the anemones acclimated at 25 degrees Celsius, subsequently adopted tolerance to high temperatures as well,” says Baldassarre. Thus, when the entire microbiome of an animal is transferred, the phenotype with its altered temperature tolerance can also be transplanted. Fraune: “We were able to establish a causal relationship between microbiome composition and environmental adaptations. Thus, we experimentally confirm the so-called hologenome concept, which defines evolution as the development of host organisms with their colonizing microorganisms toward shared fitness benefits for the entire metaorganism.”

    The research team then analyzed whether the altered microbiome due to thermal acclimation can be passed on between anemones – a prerequisite for a lasting adaptation process. In previous work, the scientists already showed that in Nematostella, certain bacteria can be passed on from the parent generation to the offspring. The evolutionary advantage of thermal adaptation can therefore in principle be inherited directly and the related bacteria must not necessarily be taken up from the environment. The current study provides further evidence of the transmission of maternal bacteria to the offspring: Like their genetically identical parents, the offspring also showed a higher probability of survival under temperature stress when the maternal animals were acclimated at 25 degrees Celsius.

    Investigating mechanisms at the species level

    With their findings, the researchers are helping to better understand the role of the interplay between host organisms and microbes in adaption processes to rapidly changing environmental conditions. “Our results offer new explanations for the mechanisms of rapid thermal adaptation mediated by the microbiome and how they are transmitted to subsequent generations,” Fraune said.

    In further research, the scientists in Düsseldorf and Kiel now want to explore the mechanisms of acclimation in detail, with a particular focus on the role of individual bacterial species involved. To this end, detailed bacterial genomic analyses are in preparation for a planned third funding phase of the CRC 1182 by the German Research Foundation (DFG). They will shed light on possible individual relationships between bacteria and certain metabolic processes of the host cells and their influence on the temperature tolerance of the organism as a whole.

    “Overall, it is important to understand the bacterial component of thermal acclimation in more detail. It likely plays a fundamental role in many other living organisms from various animals and plants to overall ecosystems such as coral reefs. Deeper knowledge of the underlying processes is therefore crucial to better assess or possibly mitigate the effects of global change on species and habitats”, Fraune summarizes.

    See the full article here .

    five-ways-keep-your-child-safe-school-shootings

    Please help promote STEM in your local schools.

    Stem Education Coalition

    The Kiel University [ Christian-Albrechts-Universität zu Kiel ] (DE) was founded back in 1665. It is Schleswig-Holstein’s oldest, largest and best-known university, with over 26,000 students and around 3,000 members of staff. It is also the only fully-fledged university in the state. Seven Nobel prize winners have worked here. The CAU has been successfully taking part in the Excellence Initiative since 2006. The Cluster of Excellence The Future Ocean, which was established in cooperation with the GEOMAR [Helmholtz-Zentrum für Ozeanforschung Kiel](DE) in 2006, is internationally recognized. The second Cluster of Excellence “Inflammation at Interfaces” deals with chronic inflammatory diseases. The Kiel Institute for the World Economy is also affiliated with Kiel University. The university has a great reputation for its focus on public international law. The oldest public international law institution in Germany and Europe – the Walther Schuecking Institute for International Law – is based in Kiel.

    History

    The University of Kiel was founded under the name Christiana Albertina on 5 October 1665 by Christian Albert, Duke of Holstein-Gottorp. The citizens of the city of Kiel were initially quite sceptical about the upcoming influx of students, thinking that these could be “quite a pest with their gluttony, heavy drinking and their questionable character” (German: mit Fressen, Sauffen und allerley leichtfertigem Wesen sehr ärgerlich seyn). But those in the city who envisioned economic advantages of a university in the city won, and Kiel thus became the northernmost university in the German Holy Roman Empire.

    After 1773, when Kiel had come under Danish rule, the university began to thrive, and when Kiel became part of Prussia in the year 1867, the university grew rapidly in size. The university opened one of the first botanical gardens in Germany (now the Alter Botanischer Garten Kiel), and Martin Gropius designed many of the new buildings needed to teach the growing number of students.

    The Christiana Albertina was one of the first German universities to obey the Gleichschaltung in 1933 and agreed to remove many professors and students from the school, for instance Ferdinand Tönnies or Felix Jacoby. During World War II, the University of Kiel suffered heavy damage, therefore it was later rebuilt at a different location with only a few of the older buildings housing the medical school.

    In 2019, it was announced it has banned full-face coverings in classrooms, citing the need for open communication that includes facial expressions and gestures.

    Faculties

    Faculty of Theology
    Faculty of Law
    Faculty of Business, Economics and Social Sciences
    Faculty of Medicine
    Faculty of Arts and Humanities
    Faculty of Mathematics and Natural Sciences
    Faculty of Agricultural Science and Nutrition
    Faculty of Engineering

     
  • richardmitnick 4:03 pm on June 30, 2022 Permalink | Reply
    Tags: "Bacteria for Blastoff:: Using Microbes to Make Supercharged New Rocket Fuel", "POP-FAMEs": Polycylcopropanated fatty acid methyl esters, "Streptomyces" bacteria, A group of biofuel experts led by Lawrence Berkeley National Laboratory developed a totally new type of fuel with energy density greater than fuels used today by NASA., A quest for the ring(s), , Bacteria have been producing carbon-based energy molecules for billions of years., Bacteriology, , , , Cyclopropane molecules, Energy density is everything when it comes to aviation and rocketry and this is where biology can really shine., Higher energy densities allow for lower fuel volumes which in a rocket can allow for increased payloads and decreased overall emissions., , Polycylcopropanated molecules contain multiple triangle-shaped three-carbon rings that force each carbon-carbon bond into a sharp 60-degree angle., Scientists turned to an oddball bacterial molecule that looks like a jaw full of sharp teeth to create a new type of fuel that could be used for all types of vehicles including rockets., , , The potential energy in this strained bond translates into more energy for combustion than can be achieved with the larger ring structures or carbon-carbon chains typically found in fuels., The simulation data suggest that POP fuel candidates are safe and stable at room temperature and will have energy density values of more than 50 megajoules per liter after chemical processing., The team discovered that their POP-FAMEs are very close in structure to an experimental petroleum-based rocket fuel called Syntin developed in the 1960s by the Soviet Union space agency., The team hoped to remix existing bacterial machinery to create a new molecule with ready-to-burn fuel properties., These fuels would be produced from bacteria fed with plant matter – which is made from carbon dioxide pulled from the atmosphere., These structures enable fuel molecules to pack tightly together in a small volume increasing the mass – and therefore the total energy – of fuel that fits in any given tank., This biosynthetic pathway provides a clean route to highly energy-dense fuels., This process reduces the amount of added greenhouse gas relative to any fuel generated from petroleum., What kinds of interesting structures can biology make that petrochemistry can’t make?   

    From The DOE’s Lawrence Berkeley National Laboratory: “Bacteria for Blastoff:: Using Microbes to Make Supercharged New Rocket Fuel” 

    From The DOE’s Lawrence Berkeley National Laboratory

    June 30, 2022
    Aliyah Kovner
    akovner@lbl.gov

    1
    Scientists turned to an oddball bacterial molecule that looks like a jaw full of sharp teeth to create a new type of fuel that could be used for all types of vehicles including rockets. (Credit: Jenny Nuss/Berkeley Lab)

    Converting petroleum into fuels involves crude chemistry first invented by humans in the 1800s. Meanwhile, bacteria have been producing carbon-based energy molecules for billions of years. Which do you think is better at the job?

    Well aware of the advantages biology has to offer, a group of biofuel experts led by Lawrence Berkeley National Laboratory took inspiration from an extraordinary antifungal molecule made by Streptomyces bacteria to develop a totally new type of fuel that has projected energy density greater than the most advanced heavy-duty fuels used today, including the rocket fuels used by NASA.

    “This biosynthetic pathway provides a clean route to highly energy-dense fuels that, prior to this work, could only be produced from petroleum using a highly toxic synthesis process,” said project leader Jay Keasling, a synthetic biology pioneer and CEO of the Department of Energy’s Joint BioEnergy Institute (JBEI). “As these fuels would be produced from bacteria fed with plant matter – which is made from carbon dioxide pulled from the atmosphere – burning them in engines will significantly reduce the amount of added greenhouse gas relative to any fuel generated from petroleum.”

    The incredible energy potential of these fuel candidate molecules, called POP-FAMEs (for polycylcopropanated fatty acid methyl esters), comes from the fundamental chemistry of their structures. Polycylcopropanated molecules contain multiple triangle-shaped three-carbon rings that force each carbon-carbon bond into a sharp 60-degree angle. The potential energy in this strained bond translates into more energy for combustion than can be achieved with the larger ring structures or carbon-carbon chains typically found in fuels. In addition, these structures enable fuel molecules to pack tightly together in a small volume increasing the mass – and therefore the total energy – of fuel that fits in any given tank.

    With petrochemical fuels, you get kind of a soup of different molecules and you don’t have a lot of fine control over those chemical structures. But that’s what we used for a long time and we designed all of our engines to run on petroleum derivatives,” said Eric Sundstrom, an author on the paper describing POP fuel candidates published in the journal Joule and a research scientist at Berkeley Lab’s Advanced Biofuels and Bioproducts Process Development Unit (ABPDU).

    “The larger consortium behind this work, Co-Optima, was funded to think about not just recreating the same fuels from biobased feedstocks, but how we can make new fuels with better properties,” said Sundstrom. “The question that led to this is: ‘What kinds of interesting structures can biology make that petrochemistry can’t make?’”

    A quest for the ring(s)

    Keasling, who is also a professor at UC Berkeley, had his eye on cyclopropane molecules for a long time. He had scoured the scientific literature for organic compounds with three-carbon rings and found just two known examples, both made by Streptomyces bacteria that are nearly impossible to grow in a lab environment. Fortunately, one of the molecules had been studied and genetically analyzed due to interest in its antifungal properties. Discovered in 1990, the natural product is named jawsamycin, because its unprecedented five cyclopropane rings make it look like a jaw filled with pointy teeth.

    4
    A culture of the Streptomyces bacteria that makes the jawsamycin. (Credit: Pablo Morales-Cruz)

    Keasling’s team, comprised of JBEI and ABPDU scientists, studied the genes from the original strain (S. roseoverticillatus) that encode the jawsamycin-building enzymes and took a deep dive into the genomes of related Streptomyces, looking for a combination of enzymes that could make a molecule with jawsamycin’s toothy rings while skipping the other parts of the structure. Like a baker rewriting recipes to invent the perfect dessert, the team hoped to remix existing bacterial machinery to create a new molecule with ready-to-burn fuel properties.

    First author Pablo Cruz-Morales was able to assemble all the necessary ingredients to make POP-FAMEs after discovering new cyclopropane-making enzymes in a strain called S. albireticuli. “We searched in thousands of genomes for pathways that naturally make what we needed. That way we avoided the engineering that may or may not work and used nature’s best solution,” said Cruz-Morales, a senior researcher at the Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark and the co-principal investigator of the yeast natural products lab with Keasling.

    Unfortunately, the bacteria weren’t as cooperative when it came to productivity. Ubiquitous in soils on every continent, Streptomyces are famous for their ability to make unusual chemicals. “A lot of the drugs used today, such as immunosuppressants, antibiotics, and anti-cancer drugs, are made by engineered Streptomyces,” said Cruz-Morales. “But they are very capricious and they’re not nice to work with in the lab. They’re talented, but they’re divas.” When two different engineered Streptomyces failed to make POP-FAMEs in sufficient quantities, he and his colleagues had to copy their newly arranged gene cluster into a more “tame” relative.

    The resulting fatty acids contain up to seven cyclopropane rings chained on a carbon backbone, earning them the name fuelimycins. In a process similar to biodiesel production, these molecules require only one additional chemical processing step before they can serve as a fuel.

    Now we’re cooking with cyclopropane

    Though they still haven’t produced enough fuel candidate molecules for field tests – “you need 10 kilograms of fuel to do a test in a real rocket engine, and we’re not there yet,” Cruz-Morales explained with a laugh – they were able to evaluate Keasling’s predictions about energy density.

    Colleagues at The DOE’s Pacific Northwest National Laboratory analyzed the POP-FAMEs with nuclear magnetic resonance spectroscopy to prove the presence of the elusive cyclopropane rings. And collaborators at The DOE’s Sandia National Laboratories used computer simulations to estimate how the compounds would perform compared to conventional fuels.

    The simulation data suggest that POP fuel candidates are safe and stable at room temperature and will have energy density values of more than 50 megajoules per liter after chemical processing. Regular gasoline has a value of 32 megajoules per liter, JetA, the most common jet fuel, and RP-1, a popular kerosene-based rocket fuel, have around 35.

    During the course of their research, the team discovered that their POP-FAMEs are very close in structure to an experimental petroleum-based rocket fuel called Syntin developed in the 1960s by the Soviet Union space agency and used for several successful Soyuz rocket launches in the 70s and 80s. Despite its powerful performance, Syntin manufacturing was halted due to high costs and the unpleasant process involved: a series of synthetic reactions with toxic byproducts and an unstable, explosive intermediate.

    “Although POP-FAMEs share similar structures to Syntin, many have superior energy densities. Higher energy densities allow for lower fuel volumes which in a rocket can allow for increased payloads and decreased overall emissions,” said author Alexander Landera, a staff scientist at Sandia. One of the team’s next goals to create a process to remove the two oxygen atoms on each molecule, which add weight but no combustion benefit. “When blended into a jet fuel, properly deoxygenated versions of POP-FAMEs may provide a similar benefit,” Landera added.

    Since publishing their proof-of-concept paper, the scientists have begun work to increase the bacteria’s production efficiency even further to generate enough for combustion testing. They are also investigating how the multi-enzyme production pathway could be modified to create polycyclopropanated molecules of different lengths. “We’re working on tuning the chain length to target specific applications,” said Sundstrom. “Longer chain fuels would be solids, well-suited to certain rocket fuel applications, shorter chains might be better for jet fuel, and in the middle might be a diesel-alternative molecule.”

    Author Corinne Scown, JBEI’s Director of Technoeconomic Analysis, added: “Energy density is everything when it comes to aviation and rocketry and this is where biology can really shine. The team can make fuel molecules tailored to the applications we need in those rapidly evolving sectors.”

    Eventually, the scientists hope to engineer the process into a workhorse bacteria strain that could produce large quantities of POP molecules from plant waste food sources (like inedible agricultural residue and brush cleared for wildfire prevention), potentially making the ultimate carbon-neutral fuel.

    See the full article here .

    five-ways-keep-your-child-safe-school-shootings

    Please help promote STEM in your local schools.

    Stem Education Coalition

    LBNL campus

    LBNL Molecular Foundry

    Bringing Science Solutions to the World

    In the world of science, The Lawrence Berkeley National Laboratory (Berkeley Lab) is synonymous with “excellence.” Thirteen Nobel prizes are associated with Berkeley Lab. Seventy Lab scientists are members of the The National Academy of Sciences, one of the highest honors for a scientist in the United States. Thirteen of our scientists have won the National Medal of Science, our nation’s highest award for lifetime achievement in fields of scientific research. Eighteen of our engineers have been elected to the The National Academy of Engineering, and three of our scientists have been elected into the Institute of Medicine. In addition, Berkeley Lab has trained thousands of university science and engineering students who are advancing technological innovations across the nation and around the world.

    Berkeley Lab is a member of the national laboratory system supported by the U.S. Department of Energy through its Office of Science. It is managed by the University of California and is charged with conducting unclassified research across a wide range of scientific disciplines. Located on a 202-acre site in the hills above the University of California- Berkeley campus that offers spectacular views of the San Francisco Bay, Berkeley Lab employs approximately 3,232 scientists, engineers and support staff. The Lab’s total costs for FY 2014 were $785 million. A recent study estimates the Laboratory’s overall economic impact through direct, indirect and induced spending on the nine counties that make up the San Francisco Bay Area to be nearly $700 million annually. The Lab was also responsible for creating 5,600 jobs locally and 12,000 nationally. The overall economic impact on the national economy is estimated at $1.6 billion a year. Technologies developed at Berkeley Lab have generated billions of dollars in revenues, and thousands of jobs. Savings as a result of Berkeley Lab developments in lighting and windows, and other energy-efficient technologies, have also been in the billions of dollars.

    Berkeley Lab was founded in 1931 by Ernest Orlando Lawrence, a University of California-Berkeley physicist who won the 1939 Nobel Prize in physics for his invention of the cyclotron, a circular particle accelerator that opened the door to high-energy physics. It was Lawrence’s belief that scientific research is best done through teams of individuals with different fields of expertise, working together. His teamwork concept is a Berkeley Lab legacy that continues today.

    History

    1931–1941

    The laboratory was founded on August 26, 1931, by Ernest Lawrence, as the Radiation Laboratory of the University of California, Berkeley, associated with the Physics Department. It centered physics research around his new instrument, the cyclotron, a type of particle accelerator for which he was awarded the Nobel Prize in Physics in 1939.

    LBNL 88 inch cyclotron.

    LBNL 88 inch cyclotron.

    Throughout the 1930s, Lawrence pushed to create larger and larger machines for physics research, courting private philanthropists for funding. He was the first to develop a large team to build big projects to make discoveries in basic research. Eventually these machines grew too large to be held on the university grounds, and in 1940 the lab moved to its current site atop the hill above campus. Part of the team put together during this period includes two other young scientists who went on to establish large laboratories; J. Robert Oppenheimer founded DOE’s Los Alamos Laboratory, and Robert Wilson founded Fermi National Accelerator Laborator.

    1942–1950

    Leslie Groves visited Lawrence’s Radiation Laboratory in late 1942 as he was organizing the Manhattan Project, meeting J. Robert Oppenheimer for the first time. Oppenheimer was tasked with organizing the nuclear bomb development effort and founded today’s Los Alamos National Laboratory to help keep the work secret. At the RadLab, Lawrence and his colleagues developed the technique of electromagnetic enrichment of uranium using their experience with cyclotrons. The “calutrons” (named after the University) became the basic unit of the massive Y-12 facility in Oak Ridge, Tennessee. Lawrence’s lab helped contribute to what have been judged to be the three most valuable technology developments of the war (the atomic bomb, proximity fuse, and radar). The cyclotron, whose construction was stalled during the war, was finished in November 1946. The Manhattan Project shut down two months later.

    1951–2018

    After the war, the Radiation Laboratory became one of the first laboratories to be incorporated into the Atomic Energy Commission (AEC) (now Department of Energy . The most highly classified work remained at Los Alamos, but the RadLab remained involved. Edward Teller suggested setting up a second lab similar to Los Alamos to compete with their designs. This led to the creation of an offshoot of the RadLab (now the Lawrence Livermore National Laboratory) in 1952. Some of the RadLab’s work was transferred to the new lab, but some classified research continued at Berkeley Lab until the 1970s, when it became a laboratory dedicated only to unclassified scientific research.

    Shortly after the death of Lawrence in August 1958, the UC Radiation Laboratory (both branches) was renamed the Lawrence Radiation Laboratory. The Berkeley location became the Lawrence Berkeley Laboratory in 1971, although many continued to call it the RadLab. Gradually, another shortened form came into common usage, LBNL. Its formal name was amended to Ernest Orlando Lawrence Berkeley National Laboratory in 1995, when “National” was added to the names of all DOE labs. “Ernest Orlando” was later dropped to shorten the name. Today, the lab is commonly referred to as “Berkeley Lab”.

    The Alvarez Physics Memos are a set of informal working papers of the large group of physicists, engineers, computer programmers, and technicians led by Luis W. Alvarez from the early 1950s until his death in 1988. Over 1700 memos are available on-line, hosted by the Laboratory.

    The lab remains owned by the Department of Energy , with management from the University of California. Companies such as Intel were funding the lab’s research into computing chips.

    Science mission

    From the 1950s through the present, Berkeley Lab has maintained its status as a major international center for physics research, and has also diversified its research program into almost every realm of scientific investigation. Its mission is to solve the most pressing and profound scientific problems facing humanity, conduct basic research for a secure energy future, understand living systems to improve the environment, health, and energy supply, understand matter and energy in the universe, build and safely operate leading scientific facilities for the nation, and train the next generation of scientists and engineers.

    The Laboratory’s 20 scientific divisions are organized within six areas of research: Computing Sciences; Physical Sciences; Earth and Environmental Sciences; Biosciences; Energy Sciences; and Energy Technologies. Berkeley Lab has six main science thrusts: advancing integrated fundamental energy science; integrative biological and environmental system science; advanced computing for science impact; discovering the fundamental properties of matter and energy; accelerators for the future; and developing energy technology innovations for a sustainable future. It was Lawrence’s belief that scientific research is best done through teams of individuals with different fields of expertise, working together. His teamwork concept is a Berkeley Lab tradition that continues today.

    Berkeley Lab operates five major National User Facilities for the DOE Office of Science:

    The Advanced Light Source (ALS) is a synchrotron light source with 41 beam lines providing ultraviolet, soft x-ray, and hard x-ray light to scientific experiments.

    LBNL/ALS

    DOE’s Lawrence Berkeley National Laboratory Advanced Light Source .
    The ALS is one of the world’s brightest sources of soft x-rays, which are used to characterize the electronic structure of matter and to reveal microscopic structures with elemental and chemical specificity. About 2,500 scientist-users carry out research at ALS every year. Berkeley Lab is proposing an upgrade of ALS which would increase the coherent flux of soft x-rays by two-three orders of magnitude.

    The DOE Joint Genome Institute supports genomic research in support of the DOE missions in alternative energy, global carbon cycling, and environmental management. The JGI’s partner laboratories are Berkeley Lab, DOE’s Lawrence Livermore National Laboratory, DOE’s Oak Ridge National Laboratory (ORNL), DOE’s Pacific Northwest National Laboratory (PNNL), and the HudsonAlpha Institute for Biotechnology . The JGI’s central role is the development of a diversity of large-scale experimental and computational capabilities to link sequence to biological insights relevant to energy and environmental research. Approximately 1,200 scientist-users take advantage of JGI’s capabilities for their research every year.

    The LBNL Molecular Foundry [above] is a multidisciplinary nanoscience research facility. Its seven research facilities focus on Imaging and Manipulation of Nanostructures; Nanofabrication; Theory of Nanostructured Materials; Inorganic Nanostructures; Biological Nanostructures; Organic and Macromolecular Synthesis; and Electron Microscopy. Approximately 700 scientist-users make use of these facilities in their research every year.

    The DOE’s NERSC National Energy Research Scientific Computing Center is the scientific computing facility that provides large-scale computing for the DOE’s unclassified research programs. Its current systems provide over 3 billion computational hours annually. NERSC supports 6,000 scientific users from universities, national laboratories, and industry.

    DOE’s NERSC National Energy Research Scientific Computing Center at Lawrence Berkeley National Laboratory.

    Cray Cori II supercomputer at National Energy Research Scientific Computing Center at DOE’s Lawrence Berkeley National Laboratory, named after Gerty Cori, the first American woman to win a Nobel Prize in science.

    NERSC Hopper Cray XE6 supercomputer.

    NERSC Cray XC30 Edison supercomputer.

    NERSC GPFS for Life Sciences.

    The Genepool system is a cluster dedicated to the DOE Joint Genome Institute’s computing needs. Denovo is a smaller test system for Genepool that is primarily used by NERSC staff to test new system configurations and software.

    NERSC PDSF computer cluster in 2003.

    PDSF is a networked distributed computing cluster designed primarily to meet the detector simulation and data analysis requirements of physics, astrophysics and nuclear science collaborations.

    Cray Shasta Perlmutter SC18 AMD Epyc Nvidia pre-exascale supercomputer.

    NERSC is a DOE Office of Science User Facility.

    The DOE’s Energy Science Network is a high-speed network infrastructure optimized for very large scientific data flows. ESNet provides connectivity for all major DOE sites and facilities, and the network transports roughly 35 petabytes of traffic each month.

    Berkeley Lab is the lead partner in the DOE’s Joint Bioenergy Institute (JBEI), located in Emeryville, California. Other partners are the DOE’s Sandia National Laboratory, the University of California (UC) campuses of Berkeley and Davis, the Carnegie Institution for Science , and DOE’s Lawrence Livermore National Laboratory (LLNL). JBEI’s primary scientific mission is to advance the development of the next generation of biofuels – liquid fuels derived from the solar energy stored in plant biomass. JBEI is one of three new U.S. Department of Energy (DOE) Bioenergy Research Centers (BRCs).

    Berkeley Lab has a major role in two DOE Energy Innovation Hubs. The mission of the Joint Center for Artificial Photosynthesis (JCAP) is to find a cost-effective method to produce fuels using only sunlight, water, and carbon dioxide. The lead institution for JCAP is the California Institute of Technology and Berkeley Lab is the second institutional center. The mission of the Joint Center for Energy Storage Research (JCESR) is to create next-generation battery technologies that will transform transportation and the electricity grid. DOE’s Argonne National Laboratory leads JCESR and Berkeley Lab is a major partner.

     
  • richardmitnick 7:39 pm on June 28, 2022 Permalink | Reply
    Tags: "Discovery Paves Way for More Sustainable Crop Cultivation Methods", , Bacteria in non-photosynthetic leaf cells of seed plants can naturally provide nitrogen to plants., Bacteriology, Currently inorganic nitrogen fertilizers such as ammonia or nitrate are commonly applied to soils and damaging them., If this becomes a successful methodology it would help with a reduction of global warming by cutting the release of greenhouse gasses and environmental degradation., Nitrogen-fixing bacteria discovered hidden within leaf cells., , This discovery will pay dividends in preservation of the environment and regeneration of agricultural soils., This finding could dramatically change how we cultivate crops.   

    From Rutgers University: “Discovery Paves Way for More Sustainable Crop Cultivation Methods” 

    Rutgers smaller
    Our Great Seal.

    From Rutgers University

    June 7, 2022

    Megan Schumann
    848-445-1907
    megan.schumann@rutgers.edu

    1
    Confocal microscope images of clover leaves showing red-stained bacteria (arrows) within leaf cells.
    James F. White and Qiuwei Zhang/Rutgers University-New Brunswick

    Rutgers researchers have discovered that nitrogen-fixing bacteria hidden within leaf cells could lead to more efficient and sustainable methods of crop cultivation.

    The study, recently published in the journal Biology, investigated how bacteria in non-photosynthetic leaf cells of seed plants can naturally provide nitrogen to plants. Currently inorganic nitrogen fertilizers such as ammonia or nitrate are commonly applied to soils and damaging them, and causing nitrogen runoff that contaminates streams, rivers, and other water bodies.

    “Development of new crop varieties or agricultural technologies based on rebuilding and supporting native nitrogen-fixing endosymbiosis could dramatically change how we cultivate crops,” said James White, a principal investigator of the study and professor of plant biology at the School of Environmental and Biological Sciences (SEBS) at Rutgers University-New Brunswick. “This discovery will pay dividends in preservation of the environment and regeneration of agricultural soils and reduction of global warming by cutting the release of greenhouse gasses and environmental degradation that results from fertilizer runoff.”

    Prior to this study, it was commonly understood that nitrogen-fixing symbioses were limited to roots of legumes and a few other families of plants that form root nodules containing nitrogen-fixing bacteria. But by examining more than 30 species of seed plants in 18 families of monocots and dicots, the study investigators found that bacteria in leaf cells can exchange nitrogen for plant sugars.

    This discovery shows how non-domesticated plants, such as wild or weed plants, grow in non-fertile soils without the addition of nitrogen fertilizers. Instead, plants harvest nitrogen from the air using intracellular bacteria that they absorb into their cells from soils and carry in seeds.

    The most efficient of these cryptic nitrogen-transfer endosymbiosis was seen in the glandular trichomes (also known as leaf hairs) of dicot plants like hops (Humulus lupulus) and hemp (Cannabis sativa). Glandular trichomes contain terpenoids, cannabinoids, essential oils or other antioxidants that may increase efficiency of endosymbiotic nitrogen fixation by scavenging or excluding oxygen that inhibits nitrogen fixation.

    White said expanding our knowledge of how plants extract nitrogen from endosymbiotic bacteria within leaves could help growers find more efficient and sustainable ways to fertilize crops.

    “This research shows that it may be possible to support nitrogen-fixing activities by endosymbiotic bacteria in leaves by breeding plants to preserve native endosymbiosis or by applications of microbes to plant seedlings to re-establish nitrogen-fixation endosymbiosis,” he said. “Our hope is that this study will open doors to the development of new methods of crop cultivation that are more efficient and sustainable than what is currently practiced.”

    In addition to Rutgers researchers, the study involved collaborators at the U.S. Geological Survey, University of the Sacred Heart in Puerto Rico and University of the Valley in Colombia.

    See the full article here .


    five-ways-keep-your-child-safe-school-shootings

    Please help promote STEM in your local schools.

    Stem Education Coalition

    rutgers-campus

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

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

    Rutgers University is a public land-grant research university based in New Brunswick, New Jersey. Chartered in 1766, Rutgers was originally called Queen’s College, and today it is the eighth-oldest college in the United States, the second-oldest in New Jersey (after Princeton University), and one of the nine U.S. colonial colleges that were chartered before the American War of Independence. In 1825, Queen’s College was renamed Rutgers College in honor of Colonel Henry Rutgers, whose substantial gift to the school had stabilized its finances during a period of uncertainty. For most of its existence, Rutgers was a private liberal arts college but it has evolved into a coeducational public research university after being designated The State University of New Jersey by the New Jersey Legislature via laws enacted in 1945 and 1956.

    Rutgers today has three distinct campuses, located in New Brunswick (including grounds in adjacent Piscataway), Newark, and Camden. The university has additional facilities elsewhere in the state, including oceanographic research facilities at the New Jersey shore. Rutgers is also a land-grant university, a sea-grant university, and the largest university in the state. Instruction is offered by 9,000 faculty members in 175 academic departments to over 45,000 undergraduate students and more than 20,000 graduate and professional students. The university is accredited by the Middle States Association of Colleges and Schools and is a member of the Big Ten Academic Alliance, the Association of American Universities and the Universities Research Association. Over the years, Rutgers has been considered a Public Ivy.

    Research

    Rutgers is home to the Rutgers University Center for Cognitive Science, also known as RUCCS. This research center hosts researchers in psychology, linguistics, computer science, philosophy, electrical engineering, and anthropology.

    It was at Rutgers that Selman Waksman (1888–1973) discovered several antibiotics, including actinomycin, clavacin, streptothricin, grisein, neomycin, fradicin, candicidin, candidin, and others. Waksman, along with graduate student Albert Schatz (1920–2005), discovered streptomycin—a versatile antibiotic that was to be the first applied to cure tuberculosis. For this discovery, Waksman received the Nobel Prize for Medicine in 1952.

    Rutgers developed water-soluble sustained release polymers, tetraploids, robotic hands, artificial bovine insemination, and the ceramic tiles for the heat shield on the Space Shuttle. In health related field, Rutgers has the Environmental & Occupational Health Science Institute (EOHSI).

    Rutgers is also home to the RCSB Protein Data bank, “…an information portal to Biological Macromolecular Structures’ cohosted with the San Diego Supercomputer Center. This database is the authoritative research tool for bioinformaticists using protein primary, secondary and tertiary structures worldwide….”

    Rutgers is home to the Rutgers Cooperative Research & Extension office, which is run by the Agricultural and Experiment Station with the support of local government. The institution provides research & education to the local farming and agro industrial community in 19 of the 21 counties of the state and educational outreach programs offered through the New Jersey Agricultural Experiment Station Office of Continuing Professional Education.

    Rutgers University Cell and DNA Repository (RUCDR) is the largest university based repository in the world and has received awards worth more than $57.8 million from the National Institutes of Health. One will fund genetic studies of mental disorders and the other will support investigations into the causes of digestive, liver and kidney diseases, and diabetes. RUCDR activities will enable gene discovery leading to diagnoses, treatments and, eventually, cures for these diseases. RUCDR assists researchers throughout the world by providing the highest quality biomaterials, technical consultation, and logistical support.

    Rutgers–Camden is home to the nation’s PhD granting Department of Childhood Studies. This department, in conjunction with the Center for Children and Childhood Studies, also on the Camden campus, conducts interdisciplinary research which combines methodologies and research practices of sociology, psychology, literature, anthropology and other disciplines into the study of childhoods internationally.

    Rutgers is home to several National Science Foundation IGERT fellowships that support interdisciplinary scientific research at the graduate-level. Highly selective fellowships are available in the following areas: Perceptual Science, Stem Cell Science and Engineering, Nanotechnology for Clean Energy, Renewable and Sustainable Fuels Solutions, and Nanopharmaceutical Engineering.

    Rutgers also maintains the Office of Research Alliances that focuses on working with companies to increase engagement with the university’s faculty members, staff and extensive resources on the four campuses.

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

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

     
  • richardmitnick 12:56 pm on June 27, 2022 Permalink | Reply
    Tags: , After the "Great Oxidation Event" more than 2 billion years ago Earth’s atmosphere began to experience a rise in the amount of oxygen., , , Bacteria and archaea figured out how to use the plentiful energy from the sun without the complex biomolecules required for photosynthesis., Bacteriology, , Early Earth is an alien environment compared to our world today., Earth of billions of years ago illuminated by light-capturing proteins., , It’s like taking the DNA of many grandchildren to reproduce the DNA of their grandparents., Life as we know it is as much an expression of the conditions on our planet as it is of life itself., , Our study demonstrates for the first time that the behavioral histories of enzymes are amenable to evolutionary reconstruction in ways that conventional molecular biosignatures are not., Rhodopsins are related to rods and cones in human eyes that enable us to distinguish between light and dark and see colors., Rhodopsins today are able to absorb colors of light that chlorophyll pigments in plants cannot., The earliest living things-archaea-inhabited a primarily oceanic planet without an ozone layer to protect them from the sun’s radiation., The research team theorizes that billions-of-years-old microbes lived many meters down in the water column to shield themselves from intense UVB radiation at the surface., The scientists created a type of family tree that allowed them to reconstruct rhodopsins from 2.5 to 4 billion years ago., , , These microbes evolved rhodopsins — proteins with the ability to turn sunlight into energy using them to power cellular processes., This suggests co-evolution in that one group of organisms is exploiting light not absorbed by the other., Understanding how organisms here have changed with time and in different environments is going to teach us crucial things about how to search for and recognize life elsewhere., Using light-capturing proteins in living microbes scientists have reconstructed what life was like for some of Earth’s earliest organisms.,   

    From The University of California-Riverside: “Ancient microbes may help us find extraterrestrial life forms” 

    UC Riverside bloc

    From The University of California-Riverside

    June 27, 2022

    Jules L Bernstein
    Senior Public Information Officer
    jules.bernstein@ucr.edu
    (951) 827-4580

    1
    Rendering of the process by which ancient microbes captured light with rhodopsin proteins. (Credit: Sohail Wasif/UCR)

    Earth of billions of years ago illuminated by light-capturing proteins.

    Using light-capturing proteins in living microbes scientists have reconstructed what life was like for some of Earth’s earliest organisms. These efforts could help us recognize signs of life on other planets, whose atmospheres may more closely resemble our pre-oxygen planet.

    The earliest living things, including bacteria and single-celled organisms called archaea, inhabited a primarily oceanic planet without an ozone layer to protect them from the sun’s radiation. These microbes evolved rhodopsins — proteins with the ability to turn sunlight into energy using them to power cellular processes.

    “On early Earth, energy may have been very scarce. Bacteria and archaea figured out how to use the plentiful energy from the sun without the complex biomolecules required for photosynthesis,” said UC Riverside astrobiologist Edward Schwieterman, who is co-author of a study describing the research.

    Rhodopsins are related to rods and cones in human eyes that enable us to distinguish between light and dark and see colors. They are also widely distributed among modern organisms and environments like saltern ponds, which present a rainbow of vibrant colors.

    Using machine learning the research team analyzed rhodopsin protein sequences from all over the world and tracked how they evolved over time. Then, they created a type of family tree that allowed them to reconstruct rhodopsins from 2.5 to 4 billion years ago, and the conditions that they likely faced.

    Their findings are detailed in a paper published in the journal Molecular Biology and Evolution.

    2
    Aerial view of saltern ponds in Namibia, southwest Africa. (R.M. Nunes/iStock/Getty)

    “Life as we know it is as much an expression of the conditions on our planet as it is of life itself. We resurrected ancient DNA sequences of one molecule, and it allowed us to link to the biology and environment of the past,” said University of Wisconsin-Madison astrobiologist and study lead Betul Kacar.

    “It’s like taking the DNA of many grandchildren to reproduce the DNA of their grandparents. Only, it’s not grandparents, but tiny things that lived billions of years ago, all over the world,” Schwieterman said.

    Modern rhodopsins absorb blue, green, yellow and orange light, and can appear pink, purple or red by virtue of the light they are not absorbing or complementary pigments. However, according to the team’s reconstructions, ancient rhodopsins were tuned to absorb mainly blue and green light.

    Since ancient Earth did not yet have the benefit of an ozone layer, the research team theorizes that billions-of-years-old microbes lived many meters down in the water column to shield themselves from intense UVB radiation at the surface.

    Blue and green light best penetrates water, so it is likely that the earliest rhodopsins primarily absorbed these colors. “This could be the best combination of being shielded and still being able to absorb light for energy,” Schwieterman said.

    After the Great Oxidation Event, more than 2 billion years ago Earth’s atmosphere began to experience a rise in the amount of oxygen. With additional oxygen and ozone in the atmosphere, rhodopsins evolved to absorb additional colors of light.

    Rhodopsins today are able to absorb colors of light that chlorophyll pigments in plants cannot. Though they represent completely unrelated and independent light capture mechanisms, they absorb complementary areas of the spectrum.

    3
    Illustration of photosynthesis in a plant, an alternative method of capturing light to create energy. (Viacheslav Besputin/iStock/Getty)

    “This suggests co-evolution in that one group of organisms is exploiting light not absorbed by the other,” Schwieterman said. “This could have been because rhodopsins developed first and screened out the green light, so chlorophylls later developed to absorb the rest. Or it could have happened the other way around.”

    Moving forward, the team is hoping to resurrect model rhodopsins in a laboratory using synthetic biology techniques.

    “We engineer the ancient DNA inside modern genomes and reprogram the bugs to behave how we believe they did millions of years ago. Rhodopsin is a great candidate for laboratory time-travel studies,” Kacar said.

    Ultimately, the team is pleased about the possibilities for research opened up by techniques they used for this study. Since other signs of life from the deep geologic past need to be physically preserved and only some molecules are amenable to long-term preservation, there are many aspects of life’s history that have not been accessible to researchers until now.

    “Our study demonstrates for the first time that the behavioral histories of enzymes are amenable to evolutionary reconstruction in ways that conventional molecular biosignatures are not,” Kacar said.

    The team also hopes to take what they learned about the behavior of early Earth organisms and use it to search the skies for signs of life on other planets.

    “Early Earth is an alien environment compared to our world today. Understanding how organisms here have changed with time and in different environments is going to teach us crucial things about how to search for and recognize life elsewhere,” Schwieterman said.

    See the full article here .

    five-ways-keep-your-child-safe-school-shootings

    Please help promote STEM in your local schools.

    Stem Education Coalition

    University of California-Riverside Campus

    The University of California-Riverside is a public land-grant research university in Riverside, California. It is one of the 10 campuses of The University of California system. The main campus sits on 1,900 acres (769 ha) in a suburban district of Riverside with a branch campus of 20 acres (8 ha) in Palm Desert. In 1907, the predecessor to The University of California-Riverside was founded as the UC Citrus Experiment Station, Riverside which pioneered research in biological pest control and the use of growth regulators responsible for extending the citrus growing season in California from four to nine months. Some of the world’s most important research collections on citrus diversity and entomology, as well as science fiction and photography, are located at Riverside.

    The University of California-Riverside ‘s undergraduate College of Letters and Science opened in 1954. The Regents of the University of California declared The University of California-Riverside a general campus of the system in 1959, and graduate students were admitted in 1961. To accommodate an enrollment of 21,000 students by 2015, more than $730 million has been invested in new construction projects since 1999. Preliminary accreditation of the The University of California-Riverside School of Medicine was granted in October 2012 and the first class of 50 students was enrolled in August 2013. It is the first new research-based public medical school in 40 years.

    The University of California-Riverside is classified among “R1: Doctoral Universities – Very high research activity.” The 2019 U.S. News & World Report Best Colleges rankings places UC-Riverside tied for 35th among top public universities and ranks 85th nationwide. Over 27 of The University of California-Riverside ‘s academic programs, including the Graduate School of Education and the Bourns College of Engineering, are highly ranked nationally based on peer assessment, student selectivity, financial resources, and other factors. Washington Monthly ranked The University of California-Riverside 2nd in the United States in terms of social mobility, research and community service, while U.S. News ranks The University of California-Riverside as the fifth most ethnically diverse and, by the number of undergraduates receiving Pell Grants (42 percent), the 15th most economically diverse student body in the nation. Over 70% of all The University of California-Riverside students graduate within six years without regard to economic disparity. The University of California-Riverside ‘s extensive outreach and retention programs have contributed to its reputation as a “university of choice” for minority students. In 2005, The University of California-Riverside became the first public university campus in the nation to offer a gender-neutral housing option. The University of California-Riverside’s sports teams are known as the Highlanders and play in the Big West Conference of the National Collegiate Athletic Association (NCAA) Division I. Their nickname was inspired by the high altitude of the campus, which lies on the foothills of Box Springs Mountain. The University of California-Riverside women’s basketball team won back-to-back Big West championships in 2006 and 2007. In 2007, the men’s baseball team won its first conference championship and advanced to the regionals for the second time since the university moved to Division I in 2001.

    History

    At the turn of the 20th century, Southern California was a major producer of citrus, the region’s primary agricultural export. The industry developed from the country’s first navel orange trees, planted in Riverside in 1873. Lobbied by the citrus industry, the University of California Regents established the UC Citrus Experiment Station (CES) on February 14, 1907, on 23 acres (9 ha) of land on the east slope of Mount Rubidoux in Riverside. The station conducted experiments in fertilization, irrigation and crop improvement. In 1917, the station was moved to a larger site, 475 acres (192 ha) near Box Springs Mountain.

    The 1944 passage of the GI Bill during World War II set in motion a rise in college enrollments that necessitated an expansion of the state university system in California. A local group of citrus growers and civic leaders, including many University of California-Berkeley alumni, lobbied aggressively for a University of California -administered liberal arts college next to the CES. State Senator Nelson S. Dilworth authored Senate Bill 512 (1949) which former Assemblyman Philip L. Boyd and Assemblyman John Babbage (both of Riverside) were instrumental in shepherding through the State Legislature. Governor Earl Warren signed the bill in 1949, allocating $2 million for initial campus construction.

    Gordon S. Watkins, dean of the College of Letters and Science at The University of California-Los Angeles, became the first provost of the new college at Riverside. Initially conceived of as a small college devoted to the liberal arts, he ordered the campus built for a maximum of 1,500 students and recruited many young junior faculty to fill teaching positions. He presided at its opening with 65 faculty and 127 students on February 14, 1954, remarking, “Never have so few been taught by so many.”

    The University of California-Riverside’s enrollment exceeded 1,000 students by the time Clark Kerr became president of the University of California system in 1958. Anticipating a “tidal wave” in enrollment growth required by the baby boom generation, Kerr developed the California Master Plan for Higher Education and the Regents designated Riverside a general university campus in 1959. The University of California-Riverside’s first chancellor, Herman Theodore Spieth, oversaw the beginnings of the school’s transition to a full university and its expansion to a capacity of 5,000 students. The University of California-Riverside’s second chancellor, Ivan Hinderaker led the campus through the era of the free speech movement and kept student protests peaceful in Riverside. According to a 1998 interview with Hinderaker, the city of Riverside received negative press coverage for smog after the mayor asked Governor Ronald Reagan to declare the South Coast Air Basin a disaster area in 1971; subsequent student enrollment declined by up to 25% through 1979. Hinderaker’s development of innovative programs in business administration and biomedical sciences created incentive for enough students to enroll at University of California-Riverside to keep the campus open.

    In the 1990s, The University of California-Riverside experienced a new surge of enrollment applications, now known as “Tidal Wave II”. The Regents targeted The University of California-Riverside for an annual growth rate of 6.3%, the fastest in The University of California system, and anticipated 19,900 students at The University of California-Riverside by 2010. By 1995, African American, American Indian, and Latino student enrollments accounted for 30% of The University of California-Riverside student body, the highest proportion of any University of California campus at the time. The 1997 implementation of Proposition 209—which banned the use of affirmative action by state agencies—reduced the ethnic diversity at the more selective UC campuses but further increased it at The University of California-Riverside.

    With The University of California-Riverside scheduled for dramatic population growth, efforts have been made to increase its popular and academic recognition. The students voted for a fee increase to move The University of California-Riverside athletics into NCAA Division I standing in 1998. In the 1990s, proposals were made to establish a law school, a medical school, and a school of public policy at The University of California-Riverside, with The University of California-Riverside School of Medicine and the School of Public Policy becoming reality in 2012. In June 2006, The University of California-Riverside received its largest gift, 15.5 million from two local couples, in trust towards building its medical school. The Regents formally approved The University of California-Riverside’s medical school proposal in 2006. Upon its completion in 2013, it was the first new medical school built in California in 40 years.

    Academics

    As a campus of The University of California system, The University of California-Riverside is governed by a Board of Regents and administered by a president University of California-Riverside ‘s academic policies are set by its Academic Senate, a legislative body composed of all UC-Riverside faculty members.

    The University of California-Riverside is organized into three academic colleges, two professional schools, and two graduate schools. The University of California-Riverside’s liberal arts college, the College of Humanities, Arts and Social Sciences, was founded in 1954, and began accepting graduate students in 1960. The College of Natural and Agricultural Sciences, founded in 1960, incorporated the CES as part of the first research-oriented institution at The University of California-Riverside; it eventually also incorporated the natural science departments formerly associated with the liberal arts college to form its present structure in 1974. The University of California-Riverside ‘s newest academic unit, the Bourns College of Engineering, was founded in 1989. Comprising the professional schools are the Graduate School of Education, founded in 1968, and The University of California-Riverside School of Business, founded in 1970. These units collectively provide 81 majors and 52 minors, 48 master’s degree programs, and 42 Doctor of Philosophy (PhD) programs. The University of California-Riverside is the only UC campus to offer undergraduate degrees in creative writing and public policy and one of three UCs (along with The University of California-Berkeley and The University of California-Irvine) to offer an undergraduate degree in business administration. Through its Division of Biomedical Sciences, founded in 1974, The University of California-Riverside offers the Thomas Haider medical degree program in collaboration with The University of California-Los Angeles. The University of California-Riverside ‘s doctoral program in the emerging field of dance theory, founded in 1992, was the first program of its kind in the United States, and The University of California-Riverside ‘s minor in lesbian, gay and bisexual studies, established in 1996, was the first undergraduate program of its kind in the University of California system. A new BA program in bagpipes was inaugurated in 2007.

    Research and economic impact

    The University of California-Riverside operated under a $727 million budget in fiscal year 2014–15. The state government provided $214 million, student fees accounted for $224 million and $100 million came from contracts and grants. Private support and other sources accounted for the remaining $189 million. Overall, monies spent at The University of California-Riverside have an economic impact of nearly $1 billion in California. The University of California-Riverside research expenditure in FY 2018 totaled $167.8 million. Total research expenditures at The University of California-Riverside are significantly concentrated in agricultural science, accounting for 53% of total research expenditures spent by the university in 2002. Top research centers by expenditure, as measured in 2002, include the Agricultural Experiment Station; the Center for Environmental Research and Technology; the Center for Bibliographical Studies; the Air Pollution Research Center; and the Institute of Geophysics and Planetary Physics.

    Throughout The University of California-Riverside ‘s history, researchers have developed more than 40 new citrus varieties and invented new techniques to help the $960 million-a-year California citrus industry fight pests and diseases. In 1927, entomologists at the CES introduced two wasps from Australia as natural enemies of a major citrus pest, the citrophilus mealybug, saving growers in Orange County $1 million in annual losses. This event was pivotal in establishing biological control as a practical means of reducing pest populations. In 1963, plant physiologist Charles Coggins proved that application of gibberellic acid allows fruit to remain on citrus trees for extended periods. The ultimate result of his work, which continued through the 1980s, was the extension of the citrus-growing season in California from four to nine months. In 1980, The University of California-Riverside released the Oroblanco grapefruit, its first patented citrus variety. Since then, the citrus breeding program has released other varieties such as the Melogold grapefruit, the Gold Nugget mandarin (or tangerine), and others that have yet to be given trademark names.

    To assist entrepreneurs in developing new products, The University of California-Riverside is a primary partner in the Riverside Regional Technology Park, which includes the City of Riverside and the County of Riverside. It also administers six reserves of the University of California Natural Reserve System. UC-Riverside recently announced a partnership with China Agricultural University[中国农业大学](CN) to launch a new center in Beijing, which will study ways to respond to the country’s growing environmental issues. University of California-Riverside can also boast the birthplace of two-name reactions in organic chemistry, the Castro-Stephens coupling and the Midland Alpine Borane Reduction.

     
  • richardmitnick 8:00 am on June 23, 2022 Permalink | Reply
    Tags: "BGCs": biosynthetic gene clusters, "Tapping the ocean as a source of natural products", Bacteriology, , , , , , Ocean Microbiome, , , Using DNA data ETH researchers have examined seawater to find not only new species of bacteria but also previously unknown natural products that may one day prove beneficial.   

    From The Swiss Federal Institute of Technology in Zürich [ETH Zürich] [Eidgenössische Technische Hochschule Zürich] (CH): “Tapping the ocean as a source of natural products” 

    From The Swiss Federal Institute of Technology in Zürich [ETH Zürich] [Eidgenössische Technische Hochschule Zürich] (CH)

    6.22.22
    Peter Rüegg

    Using DNA data ETH researchers have examined seawater to find not only new species of bacteria but also previously unknown natural products that may one day prove beneficial.

    1
    Marine bacteria are a significant reservoir of undiscovered chemical compounds that could be of interest to humans.
    Credit: Helena Klein.

    The oceans are teeming with countless forms of life, from the world’s largest creature – the blue whale – to miniscule microorganisms. In addition to their vast numbers, these microorganisms are also crucial for ensuring that the entire eco-​ and climate system work properly. For instance, there are photosynthetically active varieties such as cyanobacteria that produce around 50 percent of the oxygen in the atmosphere. Moreover, by removing carbon dioxide from the atmosphere, microorganisms help counter global warming.

    Despite this significant role, research into the diversity of microorganisms found in the ocean has thus far been only rudimentary. So, a group of researchers led by Shinichi Sunagawa, Professor of Microbiome Research, is working closely with Jörn Piel’s group to investigate this diversity. Both groups are at the Institute of Microbiology at ETH Zürich.

    To detect new natural products made by bacteria, Sunagawa and his team examined publicly available DNA data from 1,000 water samples collected at different depths from every ocean region in the world. The data came from such sources as ocean expeditions and observation platforms positioned out at sea.

    Thanks to modern technologies like environmental DNA (eDNA) analysis, it has become easier to search for new species and discover which known organisms can be found where. But what is hardly known at all is what special effects the marine microorganisms offer – in other words, what chemical compounds they make that are important for interactions between organisms. In the best-​case scenario, such compounds would benefit humans as well. Underpinning the research is the assumption that the ocean microbiome harbours great potential for natural products that could prove beneficial, for instance for their antibiotic properties.

    The extracted eDNA present in the samples was sequenced by the original researchers of the various expeditions. By reconstructing entire genomes on the computer, the scientists succeeded in decrypting the encoded information – the blueprints for proteins. Finally, they consolidated this new data together with the existing 8,500 genome data sets for marine microorganisms in a single database.

    This gave them 35,000 genomes to draw on when searching for new microbial species and, in particular, for promising biosynthetic gene clusters (BGCs). A BGC is a group of genes that provide the synthetic pathway for a natural product.

    New species and new molecules discovered

    In this genome data, the researchers detected not only many potentially useful BGCs – some 40,000 in all – but also previously undiscovered species of bacteria belonging to the phylum Eremiobacterota. This group of bacteria had been known to exist only in terrestrial environments and didn’t exhibit any special biosynthetic diversity.

    Sunagawa and his team named a new family of these bacteria as Eudoremicrobiaceae, and also were able to demonstrate that these bacteria are common and widespread: one species belonging to this family, Eudoremicrobium malaspinii, accounts for up to 6 percent of all bacteria present in certain areas of the ocean.

    “The relatives in the ocean possess what for bacteria is a giant genome. Fully decrypting it was technically challenging because the organisms had not been cultivated before,” Sunagawa says. Moreover, the new bacteria turned out to belong to the group of microorganisms that boasts the highest BGC diversity of all the samples examined. “As things stand, they are the most biosynthetically diverse family in the oceanic water column,” he says.

    The researchers looked at two Eudoremicrobiaceae BGCs in detail. One was a gene cluster containing the genetic code for enzymes that, according to Sunagawa, have never been found in this constellation in a bacterial BGC before. The other examined example was a bioactive natural product that inhibits a proteolytic enzyme.

    Validating experiments led to a surprise

    In collaboration with the group led by Jörn Piel, the researchers used experiments to validate the structure and function of both natural products. Since E. malaspinii could not be cultivated, Piel’s team had to graft genes into a model bacterium so they would act as blueprints for the natural products. This bacterium then produced the corresponding substances. Lastly, the researchers isolated the molecules from the cells, determined the structure and validated the biological activity.

    This was necessary because in one case, the enzymatic activity predicted by computer programs did not tally with the results of the experiments. “Computer predictions for what chemical reactions an enzyme will trigger have their limitations,” Sunagawa says. “This is why such predictions have to be validated in the lab if there’s any doubt.”

    Doing so is an expensive and time-​consuming endeavour that’s simply not viable for a database of 40,000 potential natural products. “However, our database has plenty to offer, and it’s accessible to all researchers who wish to use it,” Sunagawa says.

    Beyond the continued collaboration with Piel’s group to discover new natural products, Sunagawa wants to investigate unresolved questions in the evolution and ecology of oceanic microorganisms. These include how microorganisms are dispersed in the ocean given that they can spread over great distances only passively. He also wants to discover what ecological or evolutionary benefits certain genes create for microbes. Sunagawa suspects the BGCs may play a major role.

    Science paper:
    Nature

    See the full article here .

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    ETH Zurich campus

    The Swiss Federal Institute of Technology in Zürich [ETH Zürich] [Eidgenössische Technische Hochschule Zürich] (CH) is a public research university in the city of Zürich, Switzerland. Founded by the Swiss Federal Government in 1854 with the stated mission to educate engineers and scientists, the school focuses exclusively on science, technology, engineering and mathematics. Like its sister institution The Swiss Federal Institute of Technology in Lausanne [EPFL-École Polytechnique Fédérale de Lausanne](CH) , it is part of The Swiss Federal Institutes of Technology Domain (ETH Domain)) , part of the The Swiss Federal Department of Economic Affairs, Education and Research [EAER][Eidgenössisches Departement für Wirtschaft, Bildung und Forschung] [Département fédéral de l’économie, de la formation et de la recherche] (CH).

    The university is an attractive destination for international students thanks to low tuition fees of 809 CHF per semester, PhD and graduate salaries that are amongst the world’s highest, and a world-class reputation in academia and industry. There are currently 22,200 students from over 120 countries, of which 4,180 are pursuing doctoral degrees. In the 2021 edition of the QS World University Rankings ETH Zürich is ranked 6th in the world and 8th by the Times Higher Education World Rankings 2020. In the 2020 QS World University Rankings by subject it is ranked 4th in the world for engineering and technology (2nd in Europe) and 1st for earth & marine science.

    As of November 2019, 21 Nobel laureates, 2 Fields Medalists, 2 Pritzker Prize winners, and 1 Turing Award winner have been affiliated with the Institute, including Albert Einstein. Other notable alumni include John von Neumann and Santiago Calatrava. It is a founding member of the IDEA League and the International Alliance of Research Universities (IARU) and a member of the CESAER network.

    ETH Zürich was founded on 7 February 1854 by the Swiss Confederation and began giving its first lectures on 16 October 1855 as a polytechnic institute (eidgenössische polytechnische schule) at various sites throughout the city of Zurich. It was initially composed of six faculties: architecture, civil engineering, mechanical engineering, chemistry, forestry, and an integrated department for the fields of mathematics, natural sciences, literature, and social and political sciences.

    It is locally still known as Polytechnikum, or simply as Poly, derived from the original name eidgenössische polytechnische schule, which translates to “federal polytechnic school”.

    ETH Zürich is a federal institute (i.e., under direct administration by the Swiss government), whereas The University of Zürich [Universität Zürich ] (CH) is a cantonal institution. The decision for a new federal university was heavily disputed at the time; the liberals pressed for a “federal university”, while the conservative forces wanted all universities to remain under cantonal control, worried that the liberals would gain more political power than they already had. In the beginning, both universities were co-located in the buildings of the University of Zürich.

    From 1905 to 1908, under the presidency of Jérôme Franel, the course program of ETH Zürich was restructured to that of a real university and ETH Zürich was granted the right to award doctorates. In 1909 the first doctorates were awarded. In 1911, it was given its current name, Eidgenössische Technische Hochschule. In 1924, another reorganization structured the university in 12 departments. However, it now has 16 departments.

    ETH Zürich, EPFL (Swiss Federal Institute of Technology in Lausanne) [École polytechnique fédérale de Lausanne](CH), and four associated research institutes form The Domain of the Swiss Federal Institutes of Technology (ETH Domain) [ETH-Bereich; Domaine des Écoles polytechniques fédérales] (CH) with the aim of collaborating on scientific projects.

    Reputation and ranking

    ETH Zürich is ranked among the top universities in the world. Typically, popular rankings place the institution as the best university in continental Europe and ETH Zürich is consistently ranked among the top 1-5 universities in Europe, and among the top 3-10 best universities of the world.

    Historically, ETH Zürich has achieved its reputation particularly in the fields of chemistry, mathematics and physics. There are 32 Nobel laureates who are associated with ETH Zürich, the most recent of whom is Richard F. Heck, awarded the Nobel Prize in chemistry in 2010. Albert Einstein is perhaps its most famous alumnus.

    In 2018, the QS World University Rankings placed ETH Zürich at 7th overall in the world. In 2015, ETH Zürich was ranked 5th in the world in Engineering, Science and Technology, just behind the Massachusetts Institute of Technology, Stanford University and University of Cambridge (UK). In 2015, ETH Zürich also ranked 6th in the world in Natural Sciences, and in 2016 ranked 1st in the world for Earth & Marine Sciences for the second consecutive year.

    In 2016, Times Higher Education World University Rankings ranked ETH Zürich 9th overall in the world and 8th in the world in the field of Engineering & Technology, just behind the Massachusetts Institute of Technology, Stanford University, California Institute of Technology, Princeton University, University of Cambridge(UK), Imperial College London(UK) and University of Oxford(UK) .

    In a comparison of Swiss universities by swissUP Ranking and in rankings published by CHE comparing the universities of German-speaking countries, ETH Zürich traditionally is ranked first in natural sciences, computer science and engineering sciences.

    In the survey CHE Excellence Ranking on the quality of Western European graduate school programs in the fields of biology, chemistry, physics and mathematics, ETH Zürich was assessed as one of the three institutions to have excellent programs in all the considered fields, the other two being Imperial College London (UK) and the University of Cambridge (UK), respectively.

     
  • richardmitnick 3:49 pm on May 31, 2022 Permalink | Reply
    Tags: "How diverse microbial communities remain stable", , An ecosystem can become unstable and collapse if it contains too many species., Bacteria play a vital role in creating the living conditions of larger organisms., Bacteriology, Bar-Ilan University [ אוניברסיטת בר-אילן‎](IL), , , Everything that is true of coral reefs is also true in humans., , , , The microbiome is of great importance to our health., The number of different species of bacteria that can survive in the same ecological environment is limited by the strength of their interactions., The scientists analyzed data from thousands of samples of bacterial populations in the human body and from bacterial populations that live on marine sponges in coral reefs., Understanding the stability principles of bacterial communities: stability principles dictate the evolution of the ecosystem; ecosystems may collapse as a result of human intervention.   

    From Bar-Ilan University [ אוניברסיטת בר-אילן‎](IL) via phys.org : “How diverse microbial communities remain stable” 

    From Bar-Ilan University [ אוניברסיטת בר-אילן‎](IL)

    via

    phys.org

    May 31, 2022

    1
    Observing complexity–stability patterns in natural microbial communities without network reconstruction. Credit: Nature Ecology & Evolution (2022). DOI: 10.1038/s41559-022-01745-8

    Government coalitions often dissolve when too many parties disagree on too many issues. Even if a coalition seems stable for some time, a small crisis can cause a chain reaction that eventually causes the system to collapse. A study conducted in the Department of Physics at Bar-Ilan University demonstrates that this principle also holds true for ecosystems, particularly bacterial ecosystems.

    In an ecosystem, different species can have a negative effect on one another. The cheetah, for example, preys on the zebra and trees in the jungle compete with one another for sunlight. Conversely, species can positively affect one another, like the bee that pollinates flowers. In the 1970s, the renowned mathematician and biologist Robert May predicted the collapse of coalitions in ecosystems, such as trees in rainforests, animals in savannahs, or fish in coral reefs. According to May, an ecosystem can become unstable and collapse if it contains too many species, or if the networks of connections between them are too intense. In other words, according to May’s theory, small ecosystems in nature are generally characterized by strong bonds, while large systems are characterized by weak bonds. Until now May’s theory has been difficult to prove due to the difficulty of measuring these networks.

    In the new study, published in Nature Ecology & Evolution, Yogev Yonatan and Guy Amit from the research group of Dr. Amir Bashan of Bar-Ilan University’s Department of Physics, in collaboration with Dr. Yonatan Friedman of the Hebrew University, demonstrated the first evidence of May’s theory in microbial ecosystems.

    The microbiome is of great importance to our health—such as digestion and absorption of nutrients and training of our immune system. Disruptions in the ecological balance is associated with many ill-effects on our physical and mental well-being, from obesity to mental and various psychiatric conditions, and the risk of chronic diseases such as diabetes and cancer. Some interventions have been introduced to maintain a healthy balance include dietary elements, probiotic intake, antibiotics and fecal transplantation. Outside the human body, bacteria play a vital role in creating the living conditions of larger organisms. They are necessary for nutrient decomposition, regulation of production and decomposition of gases in the atmosphere, including greenhouse gases, methane, carbon dioxide, and more.

    The researchers developed a novel computational method that allows the level of connectivity in the ecosystem (a measure of the number of connections in the network and their strength) to be estimated by analyzing large amounts of data from a variety of microbial communities without having to create a detailed map of all the interactions—analogous to how the temperature of a glass of water can be measured without complete knowledge of the velocity and position of each water molecule.

    Initially, the researchers tested the new method on simulated data of ecological dynamics. Later on, they analyzed data from thousands of samples of bacterial populations from various organs in the human body and from bacterial populations that live on marine sponges in coral reefs in various sites around the world. In each ecological environment, they compared the number of different species in the bacterial population and the level of connectivity of the ecological network, and found initial evidence of the existence of Robert May’s principle of stability in these systems.

    Understanding the stability principles of bacterial communities is important for two reasons. Stability principles are the rules of the game that dictate the evolution of the ecosystem in a particular environment and help answer scientific questions such as why different bacterial populations develop in different places, or why the number of species differs between places. A second reason is that ecosystems may collapse as a result of disturbing the ecological balance following human intervention. This is true of coral reefs in Australia and rainforests in Brazil, and it is also true of bacterial populations in humans and in the environment. It is important to assess how close these systems are to collapse so that we know how to avoid damaging them and how they can be rehabilitated.

    The results show that the number of different species of bacteria that can survive in the same ecological environment is limited by the strength of the interactions between them. For example, in the gut, where there is an abundance of food for bacteria and less intense competition for resources, we find dozens to hundreds of different types of bacteria. The opposite occurs in other places where competition is fierce and the number of species is small. Understanding the stability principles of bacterial populations is especially important when we are interested in developing treatments that include attempts to influence, change and control their composition. Therefore, understanding the ecological laws that govern the bacterial populations in man and the world is very important both for the development of medical treatments and for preservation of the environment.

    The topic of this research, which is generally studied by life sciences researchers, is an example of a growing trend in recent years toward multidisciplinary research, in which complex problems are explored by experts from various disciplines. In this study physicists used tools from the fields of statistical physics, nonlinear dynamics, network science, and data science to study problems characterized by large amounts of data, of which networks in bacterial populations or diverse human interactions are only a part.

    See the full article here .

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    Stem Education Coalition

    DCIM100MEDIADJI_0015.JPG

    Bar-Ilan University (IL) [ אוניברסיטת בר-אילן ] is a public research university in the city of Ramat Gan in the Tel Aviv District, Israel. Established in 1955, Bar Ilan is Israel’s second-largest academic institution. It has some 33,000 students (including 9,000 students in its affiliated regional colleges) and 1,350 faculty members.

    The university aims to “blend tradition with modern technologies and scholarship, and teach the compelling ethics of Jewish heritage to all … to synthesize the ancient and modern, the sacred and the material, the spiritual and the scientific”.

    The university was named for Rabbi Meir Bar-Ilan (originally Meir Berlin), a Religious Zionist leader who served as the inspiration for its establishment. Although he was trained in Orthodox seminaries in Berlin, he believed there was a need for an institution providing a dual curriculum of secular academic studies and religious Torah studies.

    BIU’s student population is diverse and includes both Jewish and non-Jewish students.

    At least ten courses in Jewish studies are required for graduation. These are available as academic Jewish studies courses, as well as through more traditional Torah study, offered primarily by the Machon HaGavoah LeTorah, established in the 1970s. The “Machon” operates a kollel / bet midrash for men, and a midrasha for women. The kollel offers traditional yeshiva studies with an emphasis on Talmud and Halakha (Jewish law), while the midrasha offers courses in Tanakh, practical Halakha, and Machshavah (Jewish philosophy). The midrasha is the largest in Israel. These programs are open to all students free of charge.

    Yitzhak Rabin’s convicted assassin, Yigal Amir, was a student of law and computer science at Bar-Ilan, prompting charges that the university had become a hotbed of political extremism. One of the steps taken by the university following the 1995 assassination was to encourage dialogue between left-wing and right-wing students.

    Under university president Moshe Kaveh (1996-2013), Bar-Ilan underwent a major expansion, with new buildings added on the northern side of the campus. New science programs have been introduced, including a multidisciplinary brain research center and a center for nanotechnology. The university has placed archaeology as one of its priorities, and this includes excavations such as the Tell es-Safi/Gath archaeological excavations and the recently opened Bar-Ilan University/Weizmann Institute of Science joint program in Archaeological Sciences.

    Bar-Ilan’s Faculty of Law made headlines in 2008 by achieving the highest average Israeli Bar Exam grade of 81.9 by its graduates.

    Bar-Ilan University has eight faculties: Exact Sciences, Life Sciences, Social Sciences, Humanities, Jewish Studies, Medicine, Engineering, and Law. There are also interdisciplinary studies. At the undergraduate level, as mentioned, ten courses in Jewish studies related subjects are required from all students.

    Bar-Ilan offers several special programs, including its International B.A. Program, taught entirely in English, and is the first university in Israel to offer a full undergraduate program taught entirely in English. Currently students can choose between a B.A. degree in interdisciplinary social sciences, where students can choose between a macro track in economics, political sciences, and sociology, or the Micro Track in Criminology, Psychology, and Sociology, or a major in communications, with a minor in either English literature or political science. The degrees are internationally recognized and are open to students from all over the world.

    In addition, Bar-Ilan offers a preparatory program that readies new immigrants for Israeli colleges. The university also runs a one-year overseas program called Tochnit Torah Im Derech Eretz, which combines traditional kollel Torah studies in the morning, separate for men and women, as well as co-ed general university studies and Jewish history classes in the afternoon. Many American students enrolled in regular programs of study in the university also take these Jewish history classes to fulfill their Jewish studies requirements.

    Bar-Ilan also houses several research institutions such as the Gonda Multidisciplinary Brain Research Center, focused on neuroscience.

     
  • richardmitnick 8:55 pm on May 17, 2022 Permalink | Reply
    Tags: "Using Bacteria to Accelerate CO2 Capture in Oceans", Bacteriology, , , , , Gene manipulation, Removing CO2 from the oceans will enable them to continue to do their job of absorbing excess CO2 from the atmosphere., , The oceans have been acting as an important carbon sink for our planet., The path to capturing excess CO2 lays in being able to engineer a microbe.   

    From The DOE’s Lawrence Berkeley National Laboratory: “Using Bacteria to Accelerate CO2 Capture in Oceans” 

    From The DOE’s Lawrence Berkeley National Laboratory

    May 16, 2022
    Julie Chao

    1
    Berkeley Lab researcher Peter Agbo was awarded a grant for a carbon capture project under the Lab’s Carbon Negative Initiative. (Credit: Marilyn Sargent/Berkeley Lab)

    You may be familiar with direct air capture, or DAC, in which carbon dioxide is removed from the atmosphere in an effort to slow the effects of climate change. Now a scientist at Lawrence Berkeley National Laboratory has proposed a scheme for direct ocean capture. Removing CO2 from the oceans will enable them to continue to do their job of absorbing excess CO2 from the atmosphere.

    Experts mostly agree that combating climate change will take more than halting emissions of climate-warming gases. We must also remove the carbon dioxide and other greenhouse gases that have already been emitted, to the tune of gigatons of CO2 removed each year by 2050 in order to achieve net zero emissions. The oceans contain significantly more CO2 than the atmosphere and have been acting as an important carbon sink for our planet.

    Peter Agbo is a Berkeley Lab staff scientist in the Chemical Sciences Division, with a secondary appointment in the Molecular Biophysics and Integrated Bioimaging Division. He was awarded a grant through Berkeley Lab’s Carbon Negative Initiative, which is aiming to develop breakthrough negative emissions technologies, for his ocean capture proposal. His co-investigators on this project are Steven Singer at the Joint BioEnergy Institute and Ruchira Chatterjee, a scientist in the Molecular Biophysics and Integrated Bioimaging Division of Berkeley Lab.

    Q. Can you explain how you envision your technology to work?

    What I’m essentially trying to do is convert CO2 to limestone, and one way to do this is to use seawater. The reason you can do this is because limestone is composed of magnesium, or what’s called magnesium and calcium carbonates. There’s a lot of magnesium and calcium naturally resident in seawater. So if you have free CO2 floating around in seawater, along with that magnesium and calcium, it will naturally form limestone to a certain extent, but the process is very slow – borderline geologic time scales.

    It turns out that the bottleneck in the conversion of CO2 to these magnesium and calcium carbonates in seawater is a process that is naturally catalyzed by an enzyme called carbonic anhydrase. It’s not important to know the enzyme name; it’s just important to know that when you add carbonic anhydrase to this seawater mixture, you can basically accelerate the conversion of CO2 to these limestones under suitable conditions.

    And so the idea is to scale this up – drawing CO2 out of the atmosphere into the ocean and ultimately into some limestone product that you could sequester.

    Q. Fascinating. So you want to turn carbon dioxide into rock using a process that occurs naturally in seawater, but accelerating it. This sounds almost like science fiction. What are the challenges in getting this to work?

    To absorb CO2 from the air quick enough for the technology to work, you have to solve the problem of how to provide enough of this enzyme that you could deploy this process at a meaningful scale. If we were to simply try to supply the enzyme as a pure product, you couldn’t do it in an economically viable way. So the question I’m trying to answer here is, how would you do this? You also have to find ways of stabilizing the pH and mixing in enough air to raise and maintain your CO2 concentration in water.

    The solution that occurred to me was, okay, given that we know carbonic anhydrase is a protein, and proteins are naturally synthesized by biochemical systems, such as bacteria, which we can manipulate, then we could take bacteria and then engineer them to make carbonic anhydrase for us. And you can just keep growing these bacteria as long as you feed them. One problem, though, is that now you’ve shifted the cost burden onto supplying enough food to produce enough bacteria to produce enough enzyme.

    One way around this issue would be to use bacteria that can grow using energy and nutrients that are readily available in the natural environment. So this pointed towards photosynthetic bacteria. They can use sunlight as their energy source, and they can also use CO2 as their carbon source to feed on. And certain photosynthetic bacteria can also use the minerals that naturally occur in seawater essentially as vitamins.

    Q. Interesting. So the path to capturing excess CO2 lays in being able to engineer a microbe?

    Potentially one way, yes. What I’ve been working on in this project is to develop a genetically modified bacterium that is photosynthetic and is engineered to produce a lot of carbon anhydrase on its surface. Then, if you were to put it in seawater, where you have a lot of magnesium and calcium, and also CO2 present, you would see a rapid formation of limestone. That’s the basic idea.

    It’s a small project for now, so I decided to focus on getting the engineered organism. Right now, I’m simply trying to develop the primary catalyst system, which are the enzyme-modified bacteria to drive the mineralization. The other non-trivial pieces of this approach – how to appropriately design the reactor to stabilize CO2 concentrations and pH needed for this scheme to work – are future challenges. But I’ve been using simulations to inform my approaches to those problems.

    It’s a fun project because on any given day my co-PIs and I could be doing either physical electrochemistry or gene manipulation in the lab.

    Q. How would this look once it’s scaled up? And how much carbon would it be able to sequester?

    What I have envisioned is, the bacterium would be grown in a plant-scaled bioreactor. You basically flow seawater into this bioreactor while actively mixing in air, and it processes the seawater, converting it to limestone. Ideally, you probably have some type of downstream centrifugation process to extract the solids, which maybe could be driven by the flow of water itself, which then helps to pull out the limestone carbonates before you then eject the depleted seawater. An alternative that could possibly resolve the pH constraints of mineralization would be to implement this instead as a reversible process, where you also use the enzyme to reconvert the carbon you’ve captured in seawater back to a more concentrated CO2 stream (carbonic anhydrase behavior is reversible).

    What I’ve calculated for this system, assuming that the protein carbonic anhydrase behaves on the bacterial surface, more or less, the way it does in free solution, would suggest that you would need a plant that has only about a 1-million-liter volume, which is actually quite small. One of those could get you to roughly 1 megaton of CO2 captured per year. A lot of assumptions are built into that sort of estimate though, and it’s likely to change as work advances.

    Erecting 1,000 such facilities globally, which is a small number compared to the 14,000 water treatment facilities in the United States alone, would permit the annual, gigaton-scale capture of atmospheric CO2.

    See the full article here .

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    LBNL campus

    LBNL Molecular Foundry

    Bringing Science Solutions to the World

    In the world of science, The Lawrence Berkeley National Laboratory (Berkeley Lab) is synonymous with “excellence.” Thirteen Nobel prizes are associated with Berkeley Lab. Seventy Lab scientists are members of the The National Academy of Sciences, one of the highest honors for a scientist in the United States. Thirteen of our scientists have won the National Medal of Science, our nation’s highest award for lifetime achievement in fields of scientific research. Eighteen of our engineers have been elected to the The National Academy of Engineering, and three of our scientists have been elected into the Institute of Medicine. In addition, Berkeley Lab has trained thousands of university science and engineering students who are advancing technological innovations across the nation and around the world.

    Berkeley Lab is a member of the national laboratory system supported by the U.S. Department of Energy through its Office of Science. It is managed by the University of California and is charged with conducting unclassified research across a wide range of scientific disciplines. Located on a 202-acre site in the hills above the University of California- Berkeley campus that offers spectacular views of the San Francisco Bay, Berkeley Lab employs approximately 3,232 scientists, engineers and support staff. The Lab’s total costs for FY 2014 were $785 million. A recent study estimates the Laboratory’s overall economic impact through direct, indirect and induced spending on the nine counties that make up the San Francisco Bay Area to be nearly $700 million annually. The Lab was also responsible for creating 5,600 jobs locally and 12,000 nationally. The overall economic impact on the national economy is estimated at $1.6 billion a year. Technologies developed at Berkeley Lab have generated billions of dollars in revenues, and thousands of jobs. Savings as a result of Berkeley Lab developments in lighting and windows, and other energy-efficient technologies, have also been in the billions of dollars.

    Berkeley Lab was founded in 1931 by Ernest Orlando Lawrence, a University of California-Berkeley physicist who won the 1939 Nobel Prize in physics for his invention of the cyclotron, a circular particle accelerator that opened the door to high-energy physics. It was Lawrence’s belief that scientific research is best done through teams of individuals with different fields of expertise, working together. His teamwork concept is a Berkeley Lab legacy that continues today.

    History

    1931–1941

    The laboratory was founded on August 26, 1931, by Ernest Lawrence, as the Radiation Laboratory of the University of California, Berkeley, associated with the Physics Department. It centered physics research around his new instrument, the cyclotron, a type of particle accelerator for which he was awarded the Nobel Prize in Physics in 1939.

    LBNL 88 inch cyclotron.

    LBNL 88 inch cyclotron.

    Throughout the 1930s, Lawrence pushed to create larger and larger machines for physics research, courting private philanthropists for funding. He was the first to develop a large team to build big projects to make discoveries in basic research. Eventually these machines grew too large to be held on the university grounds, and in 1940 the lab moved to its current site atop the hill above campus. Part of the team put together during this period includes two other young scientists who went on to establish large laboratories; J. Robert Oppenheimer founded DOE’s Los Alamos Laboratory, and Robert Wilson founded Fermi National Accelerator Laborator.

    1942–1950

    Leslie Groves visited Lawrence’s Radiation Laboratory in late 1942 as he was organizing the Manhattan Project, meeting J. Robert Oppenheimer for the first time. Oppenheimer was tasked with organizing the nuclear bomb development effort and founded today’s Los Alamos National Laboratory to help keep the work secret. At the RadLab, Lawrence and his colleagues developed the technique of electromagnetic enrichment of uranium using their experience with cyclotrons. The “calutrons” (named after the University) became the basic unit of the massive Y-12 facility in Oak Ridge, Tennessee. Lawrence’s lab helped contribute to what have been judged to be the three most valuable technology developments of the war (the atomic bomb, proximity fuse, and radar). The cyclotron, whose construction was stalled during the war, was finished in November 1946. The Manhattan Project shut down two months later.

    1951–2018

    After the war, the Radiation Laboratory became one of the first laboratories to be incorporated into the Atomic Energy Commission (AEC) (now Department of Energy . The most highly classified work remained at Los Alamos, but the RadLab remained involved. Edward Teller suggested setting up a second lab similar to Los Alamos to compete with their designs. This led to the creation of an offshoot of the RadLab (now the Lawrence Livermore National Laboratory) in 1952. Some of the RadLab’s work was transferred to the new lab, but some classified research continued at Berkeley Lab until the 1970s, when it became a laboratory dedicated only to unclassified scientific research.

    Shortly after the death of Lawrence in August 1958, the UC Radiation Laboratory (both branches) was renamed the Lawrence Radiation Laboratory. The Berkeley location became the Lawrence Berkeley Laboratory in 1971, although many continued to call it the RadLab. Gradually, another shortened form came into common usage, LBNL. Its formal name was amended to Ernest Orlando Lawrence Berkeley National Laboratory in 1995, when “National” was added to the names of all DOE labs. “Ernest Orlando” was later dropped to shorten the name. Today, the lab is commonly referred to as “Berkeley Lab”.

    The Alvarez Physics Memos are a set of informal working papers of the large group of physicists, engineers, computer programmers, and technicians led by Luis W. Alvarez from the early 1950s until his death in 1988. Over 1700 memos are available on-line, hosted by the Laboratory.

    The lab remains owned by the Department of Energy , with management from the University of California. Companies such as Intel were funding the lab’s research into computing chips.

    Science mission

    From the 1950s through the present, Berkeley Lab has maintained its status as a major international center for physics research, and has also diversified its research program into almost every realm of scientific investigation. Its mission is to solve the most pressing and profound scientific problems facing humanity, conduct basic research for a secure energy future, understand living systems to improve the environment, health, and energy supply, understand matter and energy in the universe, build and safely operate leading scientific facilities for the nation, and train the next generation of scientists and engineers.

    The Laboratory’s 20 scientific divisions are organized within six areas of research: Computing Sciences; Physical Sciences; Earth and Environmental Sciences; Biosciences; Energy Sciences; and Energy Technologies. Berkeley Lab has six main science thrusts: advancing integrated fundamental energy science; integrative biological and environmental system science; advanced computing for science impact; discovering the fundamental properties of matter and energy; accelerators for the future; and developing energy technology innovations for a sustainable future. It was Lawrence’s belief that scientific research is best done through teams of individuals with different fields of expertise, working together. His teamwork concept is a Berkeley Lab tradition that continues today.

    Berkeley Lab operates five major National User Facilities for the DOE Office of Science:

    The Advanced Light Source (ALS) is a synchrotron light source with 41 beam lines providing ultraviolet, soft x-ray, and hard x-ray light to scientific experiments.

    LBNL/ALS

    DOE’s Lawrence Berkeley National Laboratory Advanced Light Source .
    The ALS is one of the world’s brightest sources of soft x-rays, which are used to characterize the electronic structure of matter and to reveal microscopic structures with elemental and chemical specificity. About 2,500 scientist-users carry out research at ALS every year. Berkeley Lab is proposing an upgrade of ALS which would increase the coherent flux of soft x-rays by two-three orders of magnitude.

    The DOE Joint Genome Institute supports genomic research in support of the DOE missions in alternative energy, global carbon cycling, and environmental management. The JGI’s partner laboratories are Berkeley Lab, DOE’s Lawrence Livermore National Laboratory, DOE’s Oak Ridge National Laboratory (ORNL), DOE’s Pacific Northwest National Laboratory (PNNL), and the HudsonAlpha Institute for Biotechnology . The JGI’s central role is the development of a diversity of large-scale experimental and computational capabilities to link sequence to biological insights relevant to energy and environmental research. Approximately 1,200 scientist-users take advantage of JGI’s capabilities for their research every year.

    The LBNL Molecular Foundry [above] is a multidisciplinary nanoscience research facility. Its seven research facilities focus on Imaging and Manipulation of Nanostructures; Nanofabrication; Theory of Nanostructured Materials; Inorganic Nanostructures; Biological Nanostructures; Organic and Macromolecular Synthesis; and Electron Microscopy. Approximately 700 scientist-users make use of these facilities in their research every year.

    The DOE’s NERSC National Energy Research Scientific Computing Center is the scientific computing facility that provides large-scale computing for the DOE’s unclassified research programs. Its current systems provide over 3 billion computational hours annually. NERSC supports 6,000 scientific users from universities, national laboratories, and industry.

    DOE’s NERSC National Energy Research Scientific Computing Center at Lawrence Berkeley National Laboratory.

    Cray Cori II supercomputer at National Energy Research Scientific Computing Center at DOE’s Lawrence Berkeley National Laboratory, named after Gerty Cori, the first American woman to win a Nobel Prize in science.

    NERSC Hopper Cray XE6 supercomputer.

    NERSC Cray XC30 Edison supercomputer.

    NERSC GPFS for Life Sciences.

    The Genepool system is a cluster dedicated to the DOE Joint Genome Institute’s computing needs. Denovo is a smaller test system for Genepool that is primarily used by NERSC staff to test new system configurations and software.

    NERSC PDSF computer cluster in 2003.

    PDSF is a networked distributed computing cluster designed primarily to meet the detector simulation and data analysis requirements of physics, astrophysics and nuclear science collaborations.

    Cray Shasta Perlmutter SC18 AMD Epyc Nvidia pre-exascale supercomputer.

    NERSC is a DOE Office of Science User Facility.

    The DOE’s Energy Science Network is a high-speed network infrastructure optimized for very large scientific data flows. ESNet provides connectivity for all major DOE sites and facilities, and the network transports roughly 35 petabytes of traffic each month.

    Berkeley Lab is the lead partner in the DOE’s Joint Bioenergy Institute (JBEI), located in Emeryville, California. Other partners are the DOE’s Sandia National Laboratory, the University of California (UC) campuses of Berkeley and Davis, the Carnegie Institution for Science , and DOE’s Lawrence Livermore National Laboratory (LLNL). JBEI’s primary scientific mission is to advance the development of the next generation of biofuels – liquid fuels derived from the solar energy stored in plant biomass. JBEI is one of three new U.S. Department of Energy (DOE) Bioenergy Research Centers (BRCs).

    Berkeley Lab has a major role in two DOE Energy Innovation Hubs. The mission of the Joint Center for Artificial Photosynthesis (JCAP) is to find a cost-effective method to produce fuels using only sunlight, water, and carbon dioxide. The lead institution for JCAP is the California Institute of Technology and Berkeley Lab is the second institutional center. The mission of the Joint Center for Energy Storage Research (JCESR) is to create next-generation battery technologies that will transform transportation and the electricity grid. DOE’s Argonne National Laboratory leads JCESR and Berkeley Lab is a major partner.

     
  • richardmitnick 7:11 am on April 26, 2022 Permalink | Reply
    Tags: "Newly Discovered Bacterial Enzyme Produces Useful Biopolymer", , Bacteriology, ,   

    From The DOE’s Lawrence Berkeley National Laboratory: “Newly Discovered Bacterial Enzyme Produces Useful Biopolymer” 

    From The DOE’s Lawrence Berkeley National Laboratory

    April 14, 2022

    1
    The 3D structure of the biosynthetic enzyme that produces acholetin, with key domains highlighted. Credit: Jose Henrique Pereira/Berkeley Lab.

    Researchers at the Joint BioEnergy Institute (JBEI) and the DOE Joint Genome Institute (JGI), both located at Lawrence Berkeley National Laboratory, collaborated on a University of British Columbia-led study that identified a bacterial enzyme that produces a novel biopolymer. Described in a recent ACS Central Science article, the polymer, dubbed acholetin, is a chain of sugar molecules known as a polysaccharide. Acholetin is similar in structure to chitin, the major component of insect exoskeletons, and holds promise as a useful biomaterial because of its biodegradability and biocompatibility.

    In work facilitated by the JGI team members, the enzyme was discovered by combing through the genome of a common laboratory contaminant, a bacterium called Acholeplasma laidlawii. The structure of the acholetin-producing enzyme was visualized by JBEI research scientist Jose H. Pereira via X-ray crystallography in the Berkeley Center for Structural Biology at the Advanced Light Source (ALS).

    Armed with a deep understanding of how the enzyme makes acholetin, scientists now have a target for preventing bacterial contamination and the means to produce acholetin for a variety of purposes.

    See the full article here .

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    LBNL campus

    LBNL Molecular Foundry

    Bringing Science Solutions to the World

    In the world of science, The Lawrence Berkeley National Laboratory (Berkeley Lab) is synonymous with “excellence.” Thirteen Nobel prizes are associated with Berkeley Lab. Seventy Lab scientists are members of the The National Academy of Sciences, one of the highest honors for a scientist in the United States. Thirteen of our scientists have won the National Medal of Science, our nation’s highest award for lifetime achievement in fields of scientific research. Eighteen of our engineers have been elected to the The National Academy of Engineering, and three of our scientists have been elected into the Institute of Medicine. In addition, Berkeley Lab has trained thousands of university science and engineering students who are advancing technological innovations across the nation and around the world.

    Berkeley Lab is a member of the national laboratory system supported by the U.S. Department of Energy through its Office of Science. It is managed by the University of California and is charged with conducting unclassified research across a wide range of scientific disciplines. Located on a 202-acre site in the hills above the University of California- Berkeley campus that offers spectacular views of the San Francisco Bay, Berkeley Lab employs approximately 3,232 scientists, engineers and support staff. The Lab’s total costs for FY 2014 were $785 million. A recent study estimates the Laboratory’s overall economic impact through direct, indirect and induced spending on the nine counties that make up the San Francisco Bay Area to be nearly $700 million annually. The Lab was also responsible for creating 5,600 jobs locally and 12,000 nationally. The overall economic impact on the national economy is estimated at $1.6 billion a year. Technologies developed at Berkeley Lab have generated billions of dollars in revenues, and thousands of jobs. Savings as a result of Berkeley Lab developments in lighting and windows, and other energy-efficient technologies, have also been in the billions of dollars.

    Berkeley Lab was founded in 1931 by Ernest Orlando Lawrence, a University of California-Berkeley physicist who won the 1939 Nobel Prize in physics for his invention of the cyclotron, a circular particle accelerator that opened the door to high-energy physics. It was Lawrence’s belief that scientific research is best done through teams of individuals with different fields of expertise, working together. His teamwork concept is a Berkeley Lab legacy that continues today.

    History

    1931–1941

    The laboratory was founded on August 26, 1931, by Ernest Lawrence, as the Radiation Laboratory of the University of California, Berkeley, associated with the Physics Department. It centered physics research around his new instrument, the cyclotron, a type of particle accelerator for which he was awarded the Nobel Prize in Physics in 1939.

    LBNL 88 inch cyclotron.

    LBNL 88 inch cyclotron.

    Throughout the 1930s, Lawrence pushed to create larger and larger machines for physics research, courting private philanthropists for funding. He was the first to develop a large team to build big projects to make discoveries in basic research. Eventually these machines grew too large to be held on the university grounds, and in 1940 the lab moved to its current site atop the hill above campus. Part of the team put together during this period includes two other young scientists who went on to establish large laboratories; J. Robert Oppenheimer founded DOE’s Los Alamos Laboratory, and Robert Wilson founded Fermi National Accelerator Laborator.

    1942–1950

    Leslie Groves visited Lawrence’s Radiation Laboratory in late 1942 as he was organizing the Manhattan Project, meeting J. Robert Oppenheimer for the first time. Oppenheimer was tasked with organizing the nuclear bomb development effort and founded today’s Los Alamos National Laboratory to help keep the work secret. At the RadLab, Lawrence and his colleagues developed the technique of electromagnetic enrichment of uranium using their experience with cyclotrons. The “calutrons” (named after the University) became the basic unit of the massive Y-12 facility in Oak Ridge, Tennessee. Lawrence’s lab helped contribute to what have been judged to be the three most valuable technology developments of the war (the atomic bomb, proximity fuse, and radar). The cyclotron, whose construction was stalled during the war, was finished in November 1946. The Manhattan Project shut down two months later.

    1951–2018

    After the war, the Radiation Laboratory became one of the first laboratories to be incorporated into the Atomic Energy Commission (AEC) (now Department of Energy . The most highly classified work remained at Los Alamos, but the RadLab remained involved. Edward Teller suggested setting up a second lab similar to Los Alamos to compete with their designs. This led to the creation of an offshoot of the RadLab (now the Lawrence Livermore National Laboratory) in 1952. Some of the RadLab’s work was transferred to the new lab, but some classified research continued at Berkeley Lab until the 1970s, when it became a laboratory dedicated only to unclassified scientific research.

    Shortly after the death of Lawrence in August 1958, the UC Radiation Laboratory (both branches) was renamed the Lawrence Radiation Laboratory. The Berkeley location became the Lawrence Berkeley Laboratory in 1971, although many continued to call it the RadLab. Gradually, another shortened form came into common usage, LBNL. Its formal name was amended to Ernest Orlando Lawrence Berkeley National Laboratory in 1995, when “National” was added to the names of all DOE labs. “Ernest Orlando” was later dropped to shorten the name. Today, the lab is commonly referred to as “Berkeley Lab”.

    The Alvarez Physics Memos are a set of informal working papers of the large group of physicists, engineers, computer programmers, and technicians led by Luis W. Alvarez from the early 1950s until his death in 1988. Over 1700 memos are available on-line, hosted by the Laboratory.

    The lab remains owned by the Department of Energy , with management from the University of California. Companies such as Intel were funding the lab’s research into computing chips.

    Science mission

    From the 1950s through the present, Berkeley Lab has maintained its status as a major international center for physics research, and has also diversified its research program into almost every realm of scientific investigation. Its mission is to solve the most pressing and profound scientific problems facing humanity, conduct basic research for a secure energy future, understand living systems to improve the environment, health, and energy supply, understand matter and energy in the universe, build and safely operate leading scientific facilities for the nation, and train the next generation of scientists and engineers.

    The Laboratory’s 20 scientific divisions are organized within six areas of research: Computing Sciences; Physical Sciences; Earth and Environmental Sciences; Biosciences; Energy Sciences; and Energy Technologies. Berkeley Lab has six main science thrusts: advancing integrated fundamental energy science; integrative biological and environmental system science; advanced computing for science impact; discovering the fundamental properties of matter and energy; accelerators for the future; and developing energy technology innovations for a sustainable future. It was Lawrence’s belief that scientific research is best done through teams of individuals with different fields of expertise, working together. His teamwork concept is a Berkeley Lab tradition that continues today.

    Berkeley Lab operates five major National User Facilities for the DOE Office of Science:

    The Advanced Light Source (ALS) is a synchrotron light source with 41 beam lines providing ultraviolet, soft x-ray, and hard x-ray light to scientific experiments.

    LBNL/ALS

    DOE’s Lawrence Berkeley National Laboratory Advanced Light Source .
    The ALS is one of the world’s brightest sources of soft x-rays, which are used to characterize the electronic structure of matter and to reveal microscopic structures with elemental and chemical specificity. About 2,500 scientist-users carry out research at ALS every year. Berkeley Lab is proposing an upgrade of ALS which would increase the coherent flux of soft x-rays by two-three orders of magnitude.

    The DOE Joint Genome Institute supports genomic research in support of the DOE missions in alternative energy, global carbon cycling, and environmental management. The JGI’s partner laboratories are Berkeley Lab, DOE’s Lawrence Livermore National Laboratory, DOE’s Oak Ridge National Laboratory (ORNL), DOE’s Pacific Northwest National Laboratory (PNNL), and the HudsonAlpha Institute for Biotechnology . The JGI’s central role is the development of a diversity of large-scale experimental and computational capabilities to link sequence to biological insights relevant to energy and environmental research. Approximately 1,200 scientist-users take advantage of JGI’s capabilities for their research every year.

    The LBNL Molecular Foundry [above] is a multidisciplinary nanoscience research facility. Its seven research facilities focus on Imaging and Manipulation of Nanostructures; Nanofabrication; Theory of Nanostructured Materials; Inorganic Nanostructures; Biological Nanostructures; Organic and Macromolecular Synthesis; and Electron Microscopy. Approximately 700 scientist-users make use of these facilities in their research every year.

    The DOE’s NERSC National Energy Research Scientific Computing Center is the scientific computing facility that provides large-scale computing for the DOE’s unclassified research programs. Its current systems provide over 3 billion computational hours annually. NERSC supports 6,000 scientific users from universities, national laboratories, and industry.

    DOE’s NERSC National Energy Research Scientific Computing Center at Lawrence Berkeley National Laboratory.

    Cray Cori II supercomputer at National Energy Research Scientific Computing Center at DOE’s Lawrence Berkeley National Laboratory, named after Gerty Cori, the first American woman to win a Nobel Prize in science.

    NERSC Hopper Cray XE6 supercomputer.

    NERSC Cray XC30 Edison supercomputer.

    NERSC GPFS for Life Sciences.

    The Genepool system is a cluster dedicated to the DOE Joint Genome Institute’s computing needs. Denovo is a smaller test system for Genepool that is primarily used by NERSC staff to test new system configurations and software.

    NERSC PDSF computer cluster in 2003.

    PDSF is a networked distributed computing cluster designed primarily to meet the detector simulation and data analysis requirements of physics, astrophysics and nuclear science collaborations.

    Cray Shasta Perlmutter SC18 AMD Epyc Nvidia pre-exascale supercomputer.

    NERSC is a DOE Office of Science User Facility.

    The DOE’s Energy Science Network is a high-speed network infrastructure optimized for very large scientific data flows. ESNet provides connectivity for all major DOE sites and facilities, and the network transports roughly 35 petabytes of traffic each month.

    Berkeley Lab is the lead partner in the DOE’s Joint Bioenergy Institute (JBEI), located in Emeryville, California. Other partners are the DOE’s Sandia National Laboratory, the University of California (UC) campuses of Berkeley and Davis, the Carnegie Institution for Science , and DOE’s Lawrence Livermore National Laboratory (LLNL). JBEI’s primary scientific mission is to advance the development of the next generation of biofuels – liquid fuels derived from the solar energy stored in plant biomass. JBEI is one of three new U.S. Department of Energy (DOE) Bioenergy Research Centers (BRCs).

    Berkeley Lab has a major role in two DOE Energy Innovation Hubs. The mission of the Joint Center for Artificial Photosynthesis (JCAP) is to find a cost-effective method to produce fuels using only sunlight, water, and carbon dioxide. The lead institution for JCAP is the California Institute of Technology and Berkeley Lab is the second institutional center. The mission of the Joint Center for Energy Storage Research (JCESR) is to create next-generation battery technologies that will transform transportation and the electricity grid. DOE’s Argonne National Laboratory leads JCESR and Berkeley Lab is a major partner.

    The University of California-Berkeley is a public land-grant research university in Berkeley, California. Established in 1868 as the state’s first land-grant university, it was the first campus of the University of California system and a founding member of the Association of American Universities . Its 14 colleges and schools offer over 350 degree programs and enroll some 31,000 undergraduate and 12,000 graduate students. Berkeley is ranked among the world’s top universities by major educational publications.

    Berkeley hosts many leading research institutes, including the Mathematical Sciences Research Institute and the Space Sciences Laboratory. It founded and maintains close relationships with three national laboratories at DOE’s Lawrence Berkeley National Laborator, DOE’s Lawrence Livermore National Laboratory and DOE’s Los Alamos National Lab, and has played a prominent role in many scientific advances, from the Manhattan Project and the discovery of 16 chemical elements to breakthroughs in computer science and genomics. Berkeley is also known for student activism and the Free Speech Movement of the 1960s.

    Berkeley alumni and faculty count among their ranks 110 Nobel laureates (34 alumni), 25 Turing Award winners (11 alumni), 14 Fields Medalists, 28 Wolf Prize winners, 103 MacArthur “Genius Grant” recipients, 30 Pulitzer Prize winners, and 19 Academy Award winners. The university has produced seven heads of state or government; five chief justices, including Chief Justice of the United States Earl Warren; 21 cabinet-level officials; 11 governors; and 25 living billionaires. It is also a leading producer of Fulbright Scholars, MacArthur Fellows, and Marshall Scholars. Berkeley alumni, widely recognized for their entrepreneurship, have founded many notable companies.

    Berkeley’s athletic teams compete in Division I of the NCAA, primarily in the Pac-12 Conference, and are collectively known as the California Golden Bears. The university’s teams have won 107 national championships, and its students and alumni have won 207 Olympic medals.

    Made possible by President Lincoln’s signing of the Morrill Act in 1862, the University of California was founded in 1868 as the state’s first land-grant university by inheriting certain assets and objectives of the private College of California and the public Agricultural, Mining, and Mechanical Arts College. Although this process is often incorrectly mistaken for a merger, the Organic Act created a “completely new institution” and did not actually merge the two precursor entities into the new university. The Organic Act states that the “University shall have for its design, to provide instruction and thorough and complete education in all departments of science, literature and art, industrial and professional pursuits, and general education, and also special courses of instruction in preparation for the professions”.

    Ten faculty members and 40 students made up the fledgling university when it opened in Oakland in 1869. Frederick H. Billings, a trustee of the College of California, suggested that a new campus site north of Oakland be named in honor of Anglo-Irish philosopher George Berkeley. The university began admitting women the following year. In 1870, Henry Durant, founder of the College of California, became its first president. With the completion of North and South Halls in 1873, the university relocated to its Berkeley location with 167 male and 22 female students.

    Beginning in 1891, Phoebe Apperson Hearst made several large gifts to Berkeley, funding a number of programs and new buildings and sponsoring, in 1898, an international competition in Antwerp, Belgium, where French architect Émile Bénard submitted the winning design for a campus master plan.

    20th century

    In 1905, the University Farm was established near Sacramento, ultimately becoming the University of California-Davis. In 1919, Los Angeles State Normal School became the southern branch of the University, which ultimately became the University of California-Los Angeles. By 1920s, the number of campus buildings had grown substantially and included twenty structures designed by architect John Galen Howard.

    In 1917, one of the nation’s first ROTC programs was established at Berkeley and its School of Military Aeronautics began training pilots, including Gen. Jimmy Doolittle. Berkeley ROTC alumni include former Secretary of Defense Robert McNamara and Army Chief of Staff Frederick C. Weyand as well as 16 other generals. In 1926, future fleet admiral Chester W. Nimitz established the first Naval ROTC unit at Berkeley.

    In the 1930s, Ernest Lawrence helped establish the Radiation Laboratory (now DOE’s Lawrence Berkeley National Laboratory) and invented the cyclotron, which won him the Nobel physics prize in 1939. Using the cyclotron, Berkeley professors and Berkeley Lab researchers went on to discover 16 chemical elements—more than any other university in the world. In particular, during World War II and following Glenn Seaborg’s then-secret discovery of plutonium, Ernest Orlando Lawrence’s Radiation Laboratory began to contract with the U.S. Army to develop the atomic bomb. Physics professor J. Robert Oppenheimer was named scientific head of the Manhattan Project in 1942. Along with the Lawrence Berkeley National Laboratory, Berkeley founded and was then a partner in managing two other labs, Los Alamos National Laboratory (1943) and Lawrence Livermore National Laboratory (1952).

    By 1942, the American Council on Education ranked Berkeley second only to Harvard University in the number of distinguished departments.

    In 1952, the University of California reorganized itself into a system of semi-autonomous campuses, with each campus given its own chancellor, and Clark Kerr became Berkeley’s first Chancellor, while Sproul remained in place as the President of the University of California.

    Berkeley gained a worldwide reputation for political activism in the 1960s. In 1964, the Free Speech Movement organized student resistance to the university’s restrictions on political activities on campus—most conspicuously, student activities related to the Civil Rights Movement. The arrest in Sproul Plaza of Jack Weinberg, a recent Berkeley alumnus and chair of Campus CORE, in October 1964, prompted a series of student-led acts of formal remonstrance and civil disobedience that ultimately gave rise to the Free Speech Movement, which movement would prevail and serve as precedent for student opposition to America’s involvement in the Vietnam War.

    In 1982, the Mathematical Sciences Research Institute (MSRI) was established on campus with support from the National Science Foundation and at the request of three Berkeley mathematicians — Shiing-Shen Chern, Calvin Moore and Isadore M. Singer. The institute is now widely regarded as a leading center for collaborative mathematical research, drawing thousands of visiting researchers from around the world each year.

    21st century

    In the current century, Berkeley has become less politically active and more focused on entrepreneurship and fundraising, especially for STEM disciplines.

    Modern Berkeley students are less politically radical, with a greater percentage of moderates and conservatives than in the 1960s and 70s. Democrats outnumber Republicans on the faculty by a ratio of 9:1. On the whole, Democrats outnumber Republicans on American university campuses by a ratio of 10:1.

    In 2007, the Energy Biosciences Institute was established with funding from BP and Stanley Hall, a research facility and headquarters for the California Institute for Quantitative Biosciences, opened. The next few years saw the dedication of the Center for Biomedical and Health Sciences, funded by a lead gift from billionaire Li Ka-shing; the opening of Sutardja Dai Hall, home of the Center for Information Technology Research in the Interest of Society; and the unveiling of Blum Hall, housing the Blum Center for Developing Economies. Supported by a grant from alumnus James Simons, the Simons Institute for the Theory of Computing was established in 2012. In 2014, Berkeley and its sister campus, University of California-San Francisco, established the Innovative Genomics Institute, and, in 2020, an anonymous donor pledged $252 million to help fund a new center for computing and data science.

    Since 2000, Berkeley alumni and faculty have received 40 Nobel Prizes, behind only Harvard and Massachusetts Institute of Technology among US universities; five Turing Awards, behind only MIT and Stanford; and five Fields Medals, second only to Princeton University. According to PitchBook, Berkeley ranks second, just behind Stanford University, in producing VC-backed entrepreneurs.

    UC Berkeley Seal

     
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