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  • richardmitnick 11:36 am on November 8, 2022 Permalink | Reply
    Tags: "Study reveals how ancient fish colonized the deep sea", , Aquaculture, , Climate changes alone don’t explain how fish came to colonize the deep sea in the first place., , , , , , , , , Scientists have long thought the explanation for this was intuitive — shallow ocean waters are warm and full of resources., The College of the Environment, The deep sea contains more than 90% of the water in our oceans but only about a third of all fish species., The earliest fish that were able to transition into the deep sea tended to have large jaws. These likely gave them more opportunities to catch food., The new study reveals that throughout Earth’s ancient history there were several periods of time when many fish actually favored the cold and dark and barren waters of the deep sea., The researchers found that much later in history fish that had longer tapered tails tended to be most successful at making the transition to deep water. This allowed them to conserve energy., The study identified three major events that likely played a role: the breakup of Pangea; the Cretaceous Hot Greenhouse period; the middle Miocene climatic transition., , There were periods lasting tens of millions of years when new species were evolving faster in the deep sea than in more shallow areas.   

    From The College of the Environment At The University of Washington : “Study reveals how ancient fish colonized the deep sea” 


    From The College of the Environment


    The University of Washington


    A lanternfish, which is a deep-water fish that gets its name from its ability to produce light. Credit: Steven Haddock/Monterey Bay Aquarium Research Institute.

    The deep sea contains more than 90% of the water in our oceans, but only about a third of all fish species. Scientists have long thought the explanation for this was intuitive — shallow ocean waters are warm and full of resources, making them a prime location for new species to evolve and thrive. But a new University of Washington study [PNAS (below)] led by Elizabeth Miller reports that throughout Earth’s ancient history, there were several periods of time when many fish actually favored the cold, dark, barren waters of the deep sea.

    “It’s easy to look at shallow habitats like coral reefs, which are very diverse and exciting, and assume that they’ve always been that way,” said Miller, who completed the study as a postdoctoral researcher in the UW School of Aquatic and Fishery Sciences and is now a postdoctoral fellow at the University of Oklahoma. “These results really challenge that assumption, and help us understand how fish species have adapted to major changes to the climate.”

    The deep sea is typically defined as anything below about 650 feet, the depth at which there is no longer enough sunlight for photosynthesis to occur. That means there is far less food and warmth than in the shallows, making it a difficult place to live. But by analyzing the relationships of fish using their genetic records going back 200 million years, Miller was able to identify a surprising evolutionary pattern: the speciation rates — that is, how quickly new species evolved — flip-flopped over time. There were periods lasting tens of millions of years when new species were evolving faster in the deep sea than in more shallow areas.

    In some ways, this discovery raised more questions than it answered. What was causing fish to prefer one habitat over another? What made some fish able to move into the deep sea more easily than others? And how did these ancient shifts help create the diversity of species we have today?

    A deep-sea bristlemouth fish. Credit: Steven Haddock/Monterey Bay Aquarium Research Institute.

    When Miller mapped these flip-flopping speciation rates onto a timeline of Earth’s history, she was able to identify three major events that likely played a role.

    “The first was the breakup of Pangea, which occurred between 200 and 150 million years ago,” said Miller. “That created new coastlines and new oceans, which meant there were more opportunities for fishes to move from shallow to deep water. There were suddenly a lot more access points.”

    Next was the Cretaceous Hot Greenhouse period, which occurred approximately 100 million years ago and marked one of the warmest eras in Earth’s history. During this time, many continents were flooded due to sea-level rise, creating a large number of new, shallow areas across the earth.

    “It was around this period that we really see shallow-water fishes take off and diversify,” said Miller. “We can trace a lot of the species diversity we see in the shallows today to this time.”

    The third event was yet another major climatic change about 15 million years ago, known as the middle Miocene climatic transition. This was caused by further shifting of the continents, which caused major changes in ocean circulation and cooled the planet — all the way down to the deep sea.

    “Around this time we see deep-sea speciation rates really speed up,” Miller said. “This was especially driven by cold-water fishes. A lot of the species you see today off the coasts of Washington and Alaska diversified during this time.”

    But climate changes alone don’t explain how fish came to colonize the deep sea in the first place. Not every species has the right combination of traits to survive in deeper water and make use of the relatively limited resources beyond the reach of sunlight.

    “To evolve into a new species in the deep sea, first you have to get there,” said Miller. “What we found was that not only were the speciation rates flip-flopping through time, but what the deep-sea fishes looked like was as well.”

    The earliest fish that were able to transition into the deep sea tended to have large jaws. These likely gave them more opportunities to catch food, which can be scarce at depth. The researchers found that much later in history, fish that had longer, tapered tails tended to be most successful at making the transition to deep water. This allowed them to conserve energy by scooting along the seafloor instead of swimming in the water column.

    “If you look at who lives in the deep sea today, some species have a tapered body and others have big, scary, toothy jaws,” Miller said. “Those two body plans represent ancestors that colonized the deep sea millions of years apart.”

    While these events might seem like ancient history, they may be able to teach us about how today’s changing climate will affect life in our oceans. Miller hopes that future research can build on these findings and investigate how modern deep-sea fish will respond to climate change, and potentially inform conservation efforts.

    “What we learned from this study is that deep-sea fishes tend to do well when oceans are colder, but with climate change, oceans are getting warmer,” she said. “We can expect that this is really going to impact fish in the deep-sea in the coming years.”

    Science paper:

    See the full article here .


    Please help promote STEM in your local schools.
    Stem Education Coalition


    The University of Washington College of the Environment

    Diversity, equity and inclusion at the Program on the Environment

    How do we accomplish change that lasts, especially with complex issues such as diversity, equity and inclusion? That question lies at the heart of conversations that have been occurring over the past two years in University of Washington’s Program on the Environment (PoE). PoE is an interdisciplinary undergraduate program where students study and reflect upon intersections of the environment and human societies, and the primary unit in the College of the Environment offering a Bachelor of Arts degree. Their unit’s size (5 core faculty, 2 staff, plus several pre- and post-doctoral instructors) allows everyone in PoE to meet as a whole and to focus regularly on discussions about diversity, equity and inclusion, rather than delegating DEI work to a committee.

    “One of the advantages of a small community is that we can all meet to talk about diversity initiatives at least quarterly,” said PoE Director Gary Handwerk. “The common university committee structure and bureaucracy itself can be impediments to real change.”

    Some of the changes so far have included major revisions to the curriculum that introduce new course requirements in sustainability and environmental justice, and embedding and threading DEI concepts throughout all courses, deeply weaving it into the fabric of environmental awareness.

    PoE also collaborated with Program on Climate Change’s Becky Alexander in creating a workshop for faculty to collaborate on integrating climate justice concepts into an array of courses across the College. These conversations among faculty from seven different units helped extend the “embed and thread” model across the College. Based on positive feedback from participants, this workshop will be offered again in winter 2022 and 2023, with participation expanded to faculty from across the University. Handwerk is “optimistic that this workshop will have long-term effects and create a framework for probing and transformative conversations across the College.”

    In fall of 2021, PoE members launched an annual Autumn Seminar Series focused on Environmental Justice. Students enrolled in an associated one-credit course and participated in live sessions with speakers on Zoom, while UW and community members could tune into a livestream (later archived on the PoE YouTube page). This dual format allowed students and attendees to converse beyond the walls of a classroom and university. Enrolled students also actively participated in an online discussion forum following each presentation. This year’s series, “Indigenous Perspectives on the Environment,” brought in Indigenous voices representing a number of tribes from across the United States and Canada.

    “I liked being able to hear different people’s experiences that I might not otherwise have been able to hear,” said student Tia Vontver. “The opportunity to hear from voices not through research papers or in a textbook, but directly from them was invaluable. Traditional ecological knowledge is passed down through stories, so I’ve been able to hear many different perspectives through these speakers.”

    Larger challenges, however, remain. It is one thing to feature marginalized voices weekly at a seminar, and quite another to shift the demographic diversity of the faculty or student body as a whole. Handwerk acknowledges that difficult and crucial goals like these remain ahead, but he is optimistic that efforts like those described above will help to create an infrastructure and climate conducive to recruiting and retaining a robustly diverse group of faculty and students.


    The University of Washington is one of the world’s preeminent public universities. Our impact on individuals, on our region, and on the world is profound — whether we are launching young people into a boundless future or confronting the grand challenges of our time through undaunted research and scholarship. Ranked number 10 in the world in Shanghai Jiao Tong University rankings and educating more than 54,000 students annually, our students and faculty work together to turn ideas into impact and in the process transform lives and our world. For more about our impact on the world, every day.

    So what defines us —the students, faculty and community members at the University of Washington? Above all, it’s our belief in possibility and our unshakable optimism. It’s a connection to others, both near and far. It’s a hunger that pushes us to tackle challenges and pursue progress. It’s the conviction that together we can create a world of good. Join us on the journey.

    The University of Washington is a public research university in Seattle, Washington, United States. Founded in 1861, University of Washington is one of the oldest universities on the West Coast; it was established in downtown Seattle approximately a decade after the city’s founding to aid its economic development. Today, the university’s 703-acre main Seattle campus is in the University District above the Montlake Cut, within the urban Puget Sound region of the Pacific Northwest. The university has additional campuses in Tacoma and Bothell. Overall, University of Washington encompasses over 500 buildings and over 20 million gross square footage of space, including one of the largest library systems in the world with more than 26 university libraries, as well as the UW Tower, lecture halls, art centers, museums, laboratories, stadiums, and conference centers. The university offers bachelor’s, master’s, and doctoral degrees through 140 departments in various colleges and schools, sees a total student enrollment of roughly 46,000 annually, and functions on a quarter system.

    University of Washington is a member of the Association of American Universities and is classified among “R1: Doctoral Universities – Very high research activity”. According to the National Science Foundation, UW spent $1.41 billion on research and development in 2018, ranking it 5th in the nation. As the flagship institution of the six public universities in Washington state, it is known for its medical, engineering and scientific research as well as its highly competitive computer science and engineering programs. Additionally, University of Washington continues to benefit from its deep historic ties and major collaborations with numerous technology giants in the region, such as Amazon, Boeing, Nintendo, and particularly Microsoft. Paul G. Allen, Bill Gates and others spent significant time at Washington computer labs for a startup venture before founding Microsoft and other ventures. The University of Washington’s 22 varsity sports teams are also highly competitive, competing as the Huskies in the Pac-12 Conference of the NCAA Division I, representing the United States at the Olympic Games, and other major competitions.

    The university has been affiliated with many notable alumni and faculty, including 21 Nobel Prize laureates and numerous Pulitzer Prize winners, Fulbright Scholars, Rhodes Scholars and Marshall Scholars.

    In 1854, territorial governor Isaac Stevens recommended the establishment of a university in the Washington Territory. Prominent Seattle-area residents, including Methodist preacher Daniel Bagley, saw this as a chance to add to the city’s potential and prestige. Bagley learned of a law that allowed United States territories to sell land to raise money in support of public schools. At the time, Arthur A. Denny, one of the founders of Seattle and a member of the territorial legislature, aimed to increase the city’s importance by moving the territory’s capital from Olympia to Seattle. However, Bagley eventually convinced Denny that the establishment of a university would assist more in the development of Seattle’s economy. Two universities were initially chartered, but later the decision was repealed in favor of a single university in Lewis County provided that locally donated land was available. When no site emerged, Denny successfully petitioned the legislature to reconsider Seattle as a location in 1858.

    In 1861, scouting began for an appropriate 10 acres (4 ha) site in Seattle to serve as a new university campus. Arthur and Mary Denny donated eight acres, while fellow pioneers Edward Lander, and Charlie and Mary Terry, donated two acres on Denny’s Knoll in downtown Seattle. More specifically, this tract was bounded by 4th Avenue to the west, 6th Avenue to the east, Union Street to the north, and Seneca Streets to the south.

    John Pike, for whom Pike Street is named, was the university’s architect and builder. It was opened on November 4, 1861, as the Territorial University of Washington. The legislature passed articles incorporating the University, and establishing its Board of Regents in 1862. The school initially struggled, closing three times: in 1863 for low enrollment, and again in 1867 and 1876 due to funds shortage. University of Washington awarded its first graduate Clara Antoinette McCarty Wilt in 1876, with a bachelor’s degree in science.

    19th century relocation

    By the time Washington state entered the Union in 1889, both Seattle and the University had grown substantially. University of Washington’s total undergraduate enrollment increased from 30 to nearly 300 students, and the campus’s relative isolation in downtown Seattle faced encroaching development. A special legislative committee, headed by University of Washington graduate Edmond Meany, was created to find a new campus to better serve the growing student population and faculty. The committee eventually selected a site on the northeast of downtown Seattle called Union Bay, which was the land of the Duwamish, and the legislature appropriated funds for its purchase and construction. In 1895, the University relocated to the new campus by moving into the newly built Denny Hall. The University Regents tried and failed to sell the old campus, eventually settling with leasing the area. This would later become one of the University’s most valuable pieces of real estate in modern-day Seattle, generating millions in annual revenue with what is now called the Metropolitan Tract. The original Territorial University building was torn down in 1908, and its former site now houses the Fairmont Olympic Hotel.

    The sole-surviving remnants of Washington’s first building are four 24-foot (7.3 m), white, hand-fluted cedar, Ionic columns. They were salvaged by Edmond S. Meany, one of the University’s first graduates and former head of its history department. Meany and his colleague, Dean Herbert T. Condon, dubbed the columns as “Loyalty,” “Industry,” “Faith”, and “Efficiency”, or “LIFE.” The columns now stand in the Sylvan Grove Theater.

    20th century expansion

    Organizers of the 1909 Alaska-Yukon-Pacific Exposition eyed the still largely undeveloped campus as a prime setting for their world’s fair. They came to an agreement with Washington’s Board of Regents that allowed them to use the campus grounds for the exposition, surrounding today’s Drumheller Fountain facing towards Mount Rainier. In exchange, organizers agreed Washington would take over the campus and its development after the fair’s conclusion. This arrangement led to a detailed site plan and several new buildings, prepared in part by John Charles Olmsted. The plan was later incorporated into the overall University of Washington campus master plan, permanently affecting the campus layout.

    Both World Wars brought the military to campus, with certain facilities temporarily lent to the federal government. In spite of this, subsequent post-war periods were times of dramatic growth for the University. The period between the wars saw a significant expansion of the upper campus. Construction of the Liberal Arts Quadrangle, known to students as “The Quad,” began in 1916 and continued to 1939. The University’s architectural centerpiece, Suzzallo Library, was built in 1926 and expanded in 1935.

    After World War II, further growth came with the G.I. Bill. Among the most important developments of this period was the opening of the School of Medicine in 1946, which is now consistently ranked as the top medical school in the United States. It would eventually lead to the University of Washington Medical Center, ranked by U.S. News and World Report as one of the top ten hospitals in the nation.

    In 1942, all persons of Japanese ancestry in the Seattle area were forced into inland internment camps as part of Executive Order 9066 following the attack on Pearl Harbor. During this difficult time, university president Lee Paul Sieg took an active and sympathetic leadership role in advocating for and facilitating the transfer of Japanese American students to universities and colleges away from the Pacific Coast to help them avoid the mass incarceration. Nevertheless, many Japanese American students and “soon-to-be” graduates were unable to transfer successfully in the short time window or receive diplomas before being incarcerated. It was only many years later that they would be recognized for their accomplishments during the University of Washington’s Long Journey Home ceremonial event that was held in May 2008.

    From 1958 to 1973, the University of Washington saw a tremendous growth in student enrollment, its faculties and operating budget, and also its prestige under the leadership of Charles Odegaard. University of Washington student enrollment had more than doubled to 34,000 as the baby boom generation came of age. However, this era was also marked by high levels of student activism, as was the case at many American universities. Much of the unrest focused around civil rights and opposition to the Vietnam War. In response to anti-Vietnam War protests by the late 1960s, the University Safety and Security Division became the University of Washington Police Department.

    Odegaard instituted a vision of building a “community of scholars”, convincing the Washington State legislatures to increase investment in the University. Washington senators, such as Henry M. Jackson and Warren G. Magnuson, also used their political clout to gather research funds for the University of Washington. The results included an increase in the operating budget from $37 million in 1958 to over $400 million in 1973, solidifying University of Washington as a top recipient of federal research funds in the United States. The establishment of technology giants such as Microsoft, Boeing and Amazon in the local area also proved to be highly influential in the University of Washington’s fortunes, not only improving graduate prospects but also helping to attract millions of dollars in university and research funding through its distinguished faculty and extensive alumni network.

    21st century

    In 1990, the University of Washington opened its additional campuses in Bothell and Tacoma. Although originally intended for students who have already completed two years of higher education, both schools have since become four-year universities with the authority to grant degrees. The first freshman classes at these campuses started in fall 2006. Today both Bothell and Tacoma also offer a selection of master’s degree programs.

    In 2012, the University began exploring plans and governmental approval to expand the main Seattle campus, including significant increases in student housing, teaching facilities for the growing student body and faculty, as well as expanded public transit options. The University of Washington light rail station was completed in March 2015, connecting Seattle’s Capitol Hill neighborhood to the University of Washington Husky Stadium within five minutes of rail travel time. It offers a previously unavailable option of transportation into and out of the campus, designed specifically to reduce dependence on private vehicles, bicycles and local King County buses.

    University of Washington has been listed as a “Public Ivy” in Greene’s Guides since 2001, and is an elected member of the American Association of Universities. Among the faculty by 2012, there have been 151 members of American Association for the Advancement of Science, 68 members of the National Academy of Sciences, 67 members of the American Academy of Arts and Sciences, 53 members of the National Academy of Medicine, 29 winners of the Presidential Early Career Award for Scientists and Engineers, 21 members of the National Academy of Engineering, 15 Howard Hughes Medical Institute Investigators, 15 MacArthur Fellows, 9 winners of the Gairdner Foundation International Award, 5 winners of the National Medal of Science, 7 Nobel Prize laureates, 5 winners of Albert Lasker Award for Clinical Medical Research, 4 members of the American Philosophical Society, 2 winners of the National Book Award, 2 winners of the National Medal of Arts, 2 Pulitzer Prize winners, 1 winner of the Fields Medal, and 1 member of the National Academy of Public Administration. Among UW students by 2012, there were 136 Fulbright Scholars, 35 Rhodes Scholars, 7 Marshall Scholars and 4 Gates Cambridge Scholars. UW is recognized as a top producer of Fulbright Scholars, ranking 2nd in the US in 2017.

    The Academic Ranking of World Universities (ARWU) has consistently ranked University of Washington as one of the top 20 universities worldwide every year since its first release. In 2019, University of Washington ranked 14th worldwide out of 500 by the ARWU, 26th worldwide out of 981 in the Times Higher Education World University Rankings, and 28th worldwide out of 101 in the Times World Reputation Rankings. Meanwhile, QS World University Rankings ranked it 68th worldwide, out of over 900.

    U.S. News & World Report ranked University of Washington 8th out of nearly 1,500 universities worldwide for 2021, with University of Washington’s undergraduate program tied for 58th among 389 national universities in the U.S. and tied for 19th among 209 public universities.

    In 2019, it ranked 10th among the universities around the world by SCImago Institutions Rankings. In 2017, the Leiden Ranking, which focuses on science and the impact of scientific publications among the world’s 500 major universities, ranked University of Washington 12th globally and 5th in the U.S.

    In 2019, Kiplinger Magazine’s review of “top college values” named University of Washington 5th for in-state students and 10th for out-of-state students among U.S. public colleges, and 84th overall out of 500 schools. In the Washington Monthly National University Rankings University of Washington was ranked 15th domestically in 2018, based on its contribution to the public good as measured by social mobility, research, and promoting public service.

  • richardmitnick 3:12 pm on October 14, 2022 Permalink | Reply
    Tags: "Engineering Duckweed to Produce Oil for Biofuels and Bioproducts", , , Aquaculture, As an aquatic plant oil-producing duckweed wouldn’t compete with food crops for prime agricultural land., , , , , , , , This engineered plant could potentially clean up agricultural waste streams as it produces oil.   

    From The DOE’s Brookhaven National Laboratory: “Engineering Duckweed to Produce Oil for Biofuels and Bioproducts” 

    From The DOE’s Brookhaven National Laboratory

    Karen McNulty Walsh
    (631) 344-8350

    Peter Genzer
    (631) 344-3174

    Brookhaven biochemists engineered duckweed, an aquatic plant, to produce large quantities of oil. If scaled up the approach could produce sustainable bio-based fuel without competing for high-value croplands while also potentially cleaning up agricultural wastewater.

    Scientists at the U.S. Department of Energy’s Brookhaven National Laboratory and collaborators at Cold Spring Harbor Laboratory (CSHL) have engineered duckweed to produce high yields of oil. The team added genes to one of nature’s fastest growing aquatic plants to “push” the synthesis of fatty acids, “pull” those fatty acids into oils, and “protect” the oil from degradation. As the scientists explain in a paper published in Plant Biotechnology Journal [below], such oil-rich duckweed could be easily harvested to produce biofuels or other bioproducts.

    The paper describes how the scientists engineered a strain of duckweed, Lemna japonica, to accumulate oil at close to 10 percent of its dry weight biomass. That’s a dramatic, 100-fold increase over such plants growing in the wild—with yields more than seven times higher than soybeans, today’s largest source of biodiesel.

    “Duckweed grows fast,” said Brookhaven Lab biochemist John Shanklin, who led the team. “It has only tiny stems and roots—so most of its biomass is in leaf-like fronds that grow on the surface of ponds worldwide. Our engineering creates high oil content in all that biomass.

    “Growing and harvesting this engineered duckweed in batches and extracting its oil could be an efficient pathway to renewable and sustainable oil production,” he said.

    Two added benefits: As an aquatic plant, oil-producing duckweed wouldn’t compete with food crops for prime agricultural land. It can even grow on runoff from pig and poultry farms.

    “That means this engineered plant could potentially clean up agricultural waste streams as it produces oil,” Shanklin said.

    Leveraging two Long Island research institutions

    The current project has roots in Brookhaven Lab research on duckweeds from the 1970s, led by William S. Hillman in the Biology Department. Later, other members of the Biology Department worked with the Martienssen group at Cold Spring Harbor to develop a highly efficient method for expressing genes from other species in duckweeds, along with approaches to suppress expression of duckweeds’ own genes, as desired.

    As Brookhaven researchers led by Shanklin and Jorg Schwender over the past two decades identified the key biochemical factors that drive oil production and accumulation in plants, one goal was to leverage that knowledge and the genetic tools to try to modify plant oil production. The latest research, reported here, tested this approach by engineering duckweed with the genes that control these oil-production factors to study their combined effects.

    “The current project brings together Brookhaven Lab’s expertise in the biochemistry and regulation of plant oil biosynthesis with Cold Spring Harbor’s cutting-edge genomics and genetics capabilities,” Shanklin said.

    One of the oil-production genes identified by the Brookhaven researchers pushes the production of the basic building blocks of oil, known as fatty acids. Another pulls, or assembles, those fatty acids into molecules called triacylglycerols (TAG)—combinations of three fatty acids that link up to form the hydrocarbons we call oils. The third gene produces a protein that coats oil droplets in plant tissues, protecting them from degradation.

    From preliminary work, the scientists found that increased fatty acid levels triggered by the “push” gene can have detrimental effects on plant growth. To avoid those effects, Brookhaven Lab postdoctoral researcher Yuanxue Liang paired that gene with a promoter that can be turned on by the addition of a tiny amount of a specific chemical inducer.

    “Adding this promoter keeps the push gene turned off until we add the inducer, which allows the plants to grow normally before we turn on fatty acid/oil production,” Shanklin said.

    Liang then created a series of gene combinations to express the improved push, pull, and protect factors singly, in pairs, and all together. In the paper these are abbreviated as W, D, and O for their biochemical/genetic names, where W=push, D=pull, and O=protect.

    The key findings

    Overexpression of each gene modification alone did not significantly increase fatty acid levels in Lemna japonica fronds. But plants engineered with all three modifications accumulated up to 16 percent of their dry weight as fatty acids and 8.7 percent as oil when results were averaged across several different transgenic lines. The best plants accumulated up to 10 percent TAG—more than 100 times the level of oil that accumulates in unmodified wild type plants.

    Some combinations of two modifications (WD and DO) increased fatty acid content and TAG accumulation dramatically relative to their individual effects. These results are called synergistic, where the combined effect of two genes increased production more than the sum of the two separate modifications.

    These results were also revealed in images of lipid droplets in the plants’ fronds, produced using a confocal microscope at the Center for Functional Nanomaterials (CFN) [below], a DOE Office of Science user facility at Brookhaven Lab. When the duckweed fronds were stained with a chemical that binds to oil, the images showed that plants with each two-gene combination (OD, OW, WD) had enhanced accumulation of lipid droplets relative to plants where these genes were expressed singly—and also when compared to control plants with no genetic modification. Plants from the OD and OWD lines both had large oil droplets, but the OWD line had more of them, producing the strongest signals.

    “Future work will focus on testing push, pull, and protect factors from a variety of different sources, optimizing the levels of expression of the three oil-inducing genes, and refining the timing of their expression,” Shanklin said. “Beyond that we are working on how to scale up production from laboratory to industrial levels.”

    That scale-up work has several main thrusts: 1) designing the types of large-scale culture vessels for growing the modified plants, 2) optimizing large-scale growth conditions, and 3) developing methods to efficiently extract oil at high levels.

    This work was funded by the DOE Office of Science (BER). CFN is also supported by the Office of Science (BES).

    Science paper:
    Plant Biotechnology Journal

    See the full article here .


    Please help promote STEM in your local schools.

    Stem Education Coalition

    Brookhaven Campus

    One of ten national laboratories overseen and primarily funded by the The DOE Office of Science, The DOE’s Brookhaven National Laboratory conducts research in the physical, biomedical, and environmental sciences, as well as in energy technologies and national security. Brookhaven Lab also builds and operates major scientific facilities available to university, industry and government researchers. The Laboratory’s almost 3,000 scientists, engineers, and support staff are joined each year by more than 5,000 visiting researchers from around the world. Brookhaven is operated and managed for DOE’s Office of Science by Brookhaven Science Associates, a limited-liability company founded by Stony Brook University the largest academic user of Laboratory facilities, and Battelle, a nonprofit, applied science and technology organization.

    Research at BNL specializes in nuclear and high energy physics, energy science and technology, environmental and bioscience, nanoscience and national security. The 5300 acre campus contains several large research facilities, including the Relativistic Heavy Ion Collider [below] and National Synchrotron Light Source II [below]. Seven Nobel prizes have been awarded for work conducted at Brookhaven lab.

    BNL is staffed by approximately 2,750 scientists, engineers, technicians, and support personnel, and hosts 4,000 guest investigators every year. The laboratory has its own police station, fire department, and ZIP code (11973). In total, the lab spans a 5,265-acre (21 km^2) area that is mostly coterminous with the hamlet of Upton, New York. BNL is served by a rail spur operated as-needed by the New York and Atlantic Railway. Co-located with the laboratory is the Upton, New York, forecast office of the National Weather Service.

    Major programs

    Although originally conceived as a nuclear research facility, Brookhaven Lab’s mission has greatly expanded. Its foci are now:

    Nuclear and high-energy physics
    Physics and chemistry of materials
    Environmental and climate research
    Energy research
    Structural biology
    Accelerator physics


    Brookhaven National Lab was originally owned by the Atomic Energy Commission and is now owned by that agency’s successor, the United States Department of Energy (DOE). DOE subcontracts the research and operation to universities and research organizations. It is currently operated by Brookhaven Science Associates LLC, which is an equal partnership of Stony Brook University and Battelle Memorial Institute. From 1947 to 1998, it was operated by Associated Universities, Inc. (AUI), but AUI lost its contract in the wake of two incidents: a 1994 fire at the facility’s high-beam flux reactor that exposed several workers to radiation and reports in 1997 of a tritium leak into the groundwater of the Long Island Central Pine Barrens on which the facility sits.


    Following World War II, the US Atomic Energy Commission was created to support government-sponsored peacetime research on atomic energy. The effort to build a nuclear reactor in the American northeast was fostered largely by physicists Isidor Isaac Rabi and Norman Foster Ramsey Jr., who during the war witnessed many of their colleagues at Columbia University leave for new remote research sites following the departure of the Manhattan Project from its campus. Their effort to house this reactor near New York City was rivalled by a similar effort at the Massachusetts Institute of Technology to have a facility near Boston, Massachusetts. Involvement was quickly solicited from representatives of northeastern universities to the south and west of New York City such that this city would be at their geographic center. In March 1946 a nonprofit corporation was established that consisted of representatives from nine major research universities — Columbia University, Cornell University, Harvard University, Johns Hopkins University, Massachusetts Institute of Technology, Princeton University, University of Pennsylvania, University of Rochester, and Yale University.

    Out of 17 considered sites in the Boston-Washington corridor, Camp Upton on Long Island was eventually chosen as the most suitable in consideration of space, transportation, and availability. The camp had been a training center from the US Army during both World War I and World War II. After the latter war, Camp Upton was deemed no longer necessary and became available for reuse. A plan was conceived to convert the military camp into a research facility.

    On March 21, 1947, the Camp Upton site was officially transferred from the U.S. War Department to the new U.S. Atomic Energy Commission (AEC), predecessor to the U.S. Department of Energy (DOE).

    Research and facilities

    Reactor history

    In 1947 construction began on the first nuclear reactor at Brookhaven, the Brookhaven Graphite Research Reactor. This reactor, which opened in 1950, was the first reactor to be constructed in the United States after World War II. The High Flux Beam Reactor operated from 1965 to 1999. In 1959 Brookhaven built the first US reactor specifically tailored to medical research, the Brookhaven Medical Research Reactor, which operated until 2000.

    Accelerator history

    In 1952 Brookhaven began using its first particle accelerator, the Cosmotron. At the time the Cosmotron was the world’s highest energy accelerator, being the first to impart more than 1 GeV of energy to a particle.

    BNL Cosmotron 1952-1966.

    The Cosmotron was retired in 1966, after it was superseded in 1960 by the new Alternating Gradient Synchrotron (AGS).

    BNL Alternating Gradient Synchrotron (AGS).

    The AGS was used in research that resulted in 3 Nobel prizes, including the discovery of the muon neutrino, the charm quark, and CP violation.

    In 1970 in BNL started the ISABELLE project to develop and build two proton intersecting storage rings.

    The groundbreaking for the project was in October 1978. In 1981, with the tunnel for the accelerator already excavated, problems with the superconducting magnets needed for the ISABELLE accelerator brought the project to a halt, and the project was eventually cancelled in 1983.

    The National Synchrotron Light Source operated from 1982 to 2014 and was involved with two Nobel Prize-winning discoveries. It has since been replaced by the National Synchrotron Light Source II. [below].

    BNL National Synchrotron Light Source.

    After ISABELLE’S cancellation, physicist at BNL proposed that the excavated tunnel and parts of the magnet assembly be used in another accelerator. In 1984 the first proposal for the accelerator now known as the Relativistic Heavy Ion Collider (RHIC)[below] was put forward. The construction got funded in 1991 and RHIC has been operational since 2000. One of the world’s only two operating heavy-ion colliders, RHIC is as of 2010 the second-highest-energy collider after the Large Hadron Collider (CH). RHIC is housed in a tunnel 2.4 miles (3.9 km) long and is visible from space.

    On January 9, 2020, it was announced by Paul Dabbar, undersecretary of the US Department of Energy Office of Science, that the BNL eRHIC design has been selected over the conceptual design put forward by DOE’s Thomas Jefferson National Accelerator Facility [Jlab] as the future Electron–ion collider (EIC) in the United States.

    In addition to the site selection, it was announced that the BNL EIC had acquired CD-0 from the Department of Energy. BNL’s eRHIC design proposes upgrading the existing Relativistic Heavy Ion Collider, which collides beams light to heavy ions including polarized protons, with a polarized electron facility, to be housed in the same tunnel.

    Other discoveries

    In 1958, Brookhaven scientists created one of the world’s first video games, Tennis for Two. In 1968 Brookhaven scientists patented Maglev, a transportation technology that utilizes magnetic levitation.

    Major facilities

    Relativistic Heavy Ion Collider (RHIC), which was designed to research quark–gluon plasma and the sources of proton spin. Until 2009 it was the world’s most powerful heavy ion collider. It is the only collider of spin-polarized protons.

    Center for Functional Nanomaterials (CFN), used for the study of nanoscale materials.

    BNL National Synchrotron Light Source II, Brookhaven’s newest user facility, opened in 2015 to replace the National Synchrotron Light Source (NSLS), which had operated for 30 years. NSLS was involved in the work that won the 2003 and 2009 Nobel Prize in Chemistry.

    Alternating Gradient Synchrotron, a particle accelerator that was used in three of the lab’s Nobel prizes.
    Accelerator Test Facility, generates, accelerates and monitors particle beams.
    Tandem Van de Graaff, once the world’s largest electrostatic accelerator.

    Computational Science resources, including access to a massively parallel Blue Gene series supercomputer that is among the fastest in the world for scientific research, run jointly by Brookhaven National Laboratory and Stony Brook University-SUNY.

    Interdisciplinary Science Building, with unique laboratories for studying high-temperature superconductors and other materials important for addressing energy challenges.
    NASA Space Radiation Laboratory, where scientists use beams of ions to simulate cosmic rays and assess the risks of space radiation to human space travelers and equipment.

    Off-site contributions

    It is a contributing partner to the ATLAS experiment, one of the four detectors located at the The European Organization for Nuclear Research [La Organización Europea para la Investigación Nuclear][Organization européenne pour la recherche nucléaire] [Europäische Organization für Kernforschung](CH)[CERN] Large Hadron Collider(LHC).

    The European Organization for Nuclear Research [La Organización Europea para la Investigación Nuclear][Organization européenne pour la recherche nucléaire] [Europäische Organization für Kernforschung](CH)[CERN] map.

    Iconic view of the European Organization for Nuclear Research [La Organización Europea para la Investigación Nuclear] [Organization européenne pour la recherche nucléaire] [Europäische Organization für Kernforschung](CH) [CERN] ATLAS detector.

    It is currently operating at The European Organization for Nuclear Research [La Organización Europea para la Investigación Nuclear][Organization européenne pour la recherche nucléaire] [Europäische Organization für Kernforschung](CH) [CERN] near Geneva, Switzerland.

    Brookhaven was also responsible for the design of the Spallation Neutron Source at DOE’s Oak Ridge National Laboratory, Tennessee.

    DOE’s Oak Ridge National Laboratory Spallation Neutron Source annotated.

    Brookhaven plays a role in a range of neutrino research projects around the world, including the Daya Bay Neutrino Experiment (CN) nuclear power plant, approximately 52 kilometers northeast of Hong Kong and 45 kilometers east of Shenzhen, China.

    Daya Bay Neutrino Experiment (CN) nuclear power plant, approximately 52 kilometers northeast of Hong Kong and 45 kilometers east of Shenzhen, China .

    BNL Center for Functional Nanomaterials.

    BNL National Synchrotron Light Source II.


    BNL Relative Heavy Ion Collider Campus.

    BNL/RHIC Phenix detector.

  • richardmitnick 12:38 pm on September 26, 2022 Permalink | Reply
    Tags: "Can engineering biology feed more people with fewer resources?", , , Aquaculture, , ,   

    From CSIRO (AU) ECOS : “Can engineering biology feed more people with fewer resources?” 

    From CSIRO (AU) ECOS

    Sibel Korhaliller

    A changing climate, declining arable lands and an increasing demand for more environmentally friendly products is making us think outside the box when it comes to food production and traditional agricultural production. How can we produce more food with fewer resources?

    One way this can be achieved is through what is known as engineering biology. It combines the fields of biology and engineering to create safer, more sustainable, and in time, potentially cheaper products. These include feed ingredients, agricultural chemicals and even biofuels.

    Last year we released a Synthetic Biology Roadmap that estimated products made using engineering biology could generate more than $19.2 billion for Australia’s food and agricultural industry by 2040.

    While there has been a lot of research in this space over the past two decades, commercialization opportunities are still in their infancy. But understanding what these are can help the sector prioritize their efforts in the short to medium term.

    Engineering biology techniques could benefit Australia’s agriculture, aquaculture (pictured) and forestry industries over the next 10 years.

    Revolutionizing agriculture

    To feed everyone on the planet, we need to revolutionise agriculture in the next 30 years.

    Greg Williams is Associate Director for Health and Biosecurity in the CSIRO Futures team, CSIRO’s strategic consulting arm. He says engineering biology can help us address the increasing pressures that global agriculture producers face.

    “Engineering biology solutions are one way we can help keep our food systems resilient to future demand. However, we still have a lot to learn to move the science out of the lab and onto farms for real-world impact,” he says.

    Engineering biology opportunities on farm

    We recently explored eight key engineering biology opportunities for the agriculture industry as part of research funded by AgriFutures Australia, who invest in research, innovation and learning across Australian rural industries.

    “We explored both research and commercial applications of this technology globally to assess what Australia’s agriculture and aquaculture sectors could start to prepare for,” Greg says.

    “The applications range from biosensors that detect pathogens in livestock or disease in crops, to biomanufacturing sustainable proteins and additives that can be added to animal feed, to creating agricultural chemicals, such as insecticides or fertilisers.”

    One of these opportunities involves engineering biological agricultural treatments to create new crops that can fix their own nitrogen for growth. In doing so, this helps to overcome environmental challenges in conventional agricultural practices, such as the overuse of nitrogen fertilizer.

    On the Sunshine Coast, we have also supported a local company, Provectus Algae through the Australian Government’s Innovation Connections program to synthetically produce algae for several applications, including food and beverage (natural and sustainable food flavourings, fragrances and colourings), aquaculture feed, natural pesticides and also therapeutics (such as medicines).

    Biofungicides are new microbial-derived tools for protecting crops such as canola.

    CSIRO researcher Louise Thatcher says a collaboration with Melbourne-based business Nufarm is helping to develop and run a pre-commercial pilot trial of a novel biofungicide to prevent sclerotina outbreaks.

    “Fungal diseases of crops cause billions of dollars of losses globally,” Louise says.

    “Part of what I do at CSIRO is to find alternative solutions to the use of synthetic agrichemicals. These chemicals contribute to increased yields but can have negative impacts on the environment.

    “We’re screening and researching a collection of beneficial microbes that could kill fungal diseases that affect crops such as canola.

    “A product from this research would be engineered to maximise effectiveness against sclerotinia whilst minimising off target effects to the environment and people.

    “We were able to successfully isolate a new biocontrol microbe that is found naturally in West Australia soils. We engineered a new biofungicide formulation and tested its application to treat sclerotinia outbreaks, with very positive results to far.”

    We are evaluating biofungicides to supress sclerotinia in canola.

    See the full article here.


    Please help promote STEM in your local schools.

    Stem Education Coalition

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

    CSIRO works with leading organisations around the world. From its headquarters in Canberra, CSIRO maintains more than 50 sites across Australia and in France, Chile and the United States, employing about 5,500 people.

    Federally funded scientific research began in Australia 104 years ago. The Advisory Council of Science and Industry was established in 1916 but was hampered by insufficient available finance. In 1926 the research effort was reinvigorated by establishment of the Council for Scientific and Industrial Research (CSIR), which strengthened national science leadership and increased research funding. CSIR grew rapidly and achieved significant early successes. In 1949 further legislated changes included renaming the organisation as CSIRO.

    Notable developments by CSIRO have included the invention of atomic absorption spectroscopy; essential components of Wi-Fi technology; development of the first commercially successful polymer banknote; the invention of the insect repellent in Aerogard and the introduction of a series of biological controls into Australia, such as the introduction of myxomatosis and rabbit calicivirus for the control of rabbit populations.

    Research and focus areas

    Research Business Units

    As at 2019, CSIRO’s research areas are identified as “Impact science” and organised into the following Business Units:

    Agriculture and Food
    Health and Biosecurity
    Data 61
    Land and Water
    Mineral Resources
    Oceans and Atmosphere

    National Facilities

    CSIRO manages national research facilities and scientific infrastructure on behalf of the nation to assist with the delivery of research. The national facilities and specialized laboratories are available to both international and Australian users from industry and research. As at 2019, the following National Facilities are listed:
    Australian Animal Health Laboratory (AAHL)
    Australia Telescope National Facility – radio telescopes included in the Facility include the Australia Telescope Compact Array, the Parkes Observatory, Mopra Radio Telescope Observatory and the Australian Square Kilometre Array Pathfinder.

    STCA CSIRO Australia Compact Array (AU), six radio telescopes at the Paul Wild Observatory, is an array of six 22-m antennas located about twenty five kilometres (16 mi) west of the town of Narrabri in Australia.

    CSIRO-Commonwealth Scientific and Industrial Research Organization (AU) Parkes Observatory [Murriyang, the traditional Indigenous name], located 20 kilometres north of the town of Parkes, New South Wales, Australia, 414.80m above sea level.

    NASA Canberra Deep Space Communication Complex, AU, Deep Space Network. Credit: NASA.

    CSIRO Canberra campus.

    ESA DSA 1, hosts a 35-metre deep-space antenna with transmission and reception in both S- and X-band and is located 140 kilometres north of Perth, Western Australia, near the town of New Norcia.

    CSIRO-Commonwealth Scientific and Industrial Research Organisation (AU)CSIRO R/V Investigator.

    UK Space NovaSAR-1 satellite (UK) synthetic aperture radar satellite.

    CSIRO Pawsey Supercomputing Centre AU)

    Magnus Cray XC40 supercomputer at Pawsey Supercomputer Centre Perth Australia.

    Galaxy Cray XC30 Series Supercomputer at at Pawsey Supercomputer Centre Perth Australia.

    Pausey Supercomputer CSIRO Zeus SGI Linux cluster.

    Others not shown


    SKA- Square Kilometer Array.

    SKA Square Kilometre Array low frequency at Murchison Widefield Array, Boolardy station in outback Western Australia on the traditional lands of the Wajarri peoples.

    EDGES telescope in a radio quiet zone at the Murchison Radio-astronomy Observatory in Western Australia, on the traditional lands of the Wajarri peoples.

  • richardmitnick 7:04 am on January 23, 2020 Permalink | Reply
    Tags: , Aquaculture, , , Ocean Resources, Ocean Twilight Zone,   

    From Woods Hole Oceanographic Institution: “Report reveals ‘unseen’ human benefits from ocean twilight zone” 

    From Woods Hole Oceanographic Institution

    January 22, 2020
    Media Relations Office
    (508) 289-3340


    Did you know that there’s a natural carbon sink—even bigger than the Amazon rainforest—that helps regulate Earth’s climate by sucking up to six billion tons of carbon from the air each year?

    A new report from researchers at Woods Hole Oceanographic Institution (WHOI) reveals for the first time the unseen—and somewhat surprising—benefits that people receive from the ocean’s twilight zone. Also known as the “mesopelagic,” this is the ocean layer just beyond the sunlit surface.

    The ocean twilight zone is a mysterious place filled with alien-looking creatures. The nightly, massive migration of animals from the zone to the surface waters to find food helps to cycle carbon through the ocean’s depths, down into the deep ocean and even to the seabed, where it can remain sequestered indefinitely.

    “We knew that the ocean’s twilight zone played an important role in climate, but we are uncertain about how much carbon it is sequestering, or trapping, annually,” says Porter Hoagland, a WHOI marine policy analyst and lead author of the report. “This massive migration of tiny creatures is happening all over the world, helping to remove an enormous amount of carbon from the atmosphere.”

    Exactly how much carbon is difficult to pinpoint because the ocean twilight zone is challenging to get to and is understudied. The WHOI Ocean Twilight Zone project, which launched in April 2018, is focused on changing that with the development of new technologies.

    It’s estimated that two to six billion metric tons of carbon are sequestered through the ocean’s twilight zone annually. By comparison, the world’s largest rain forest sucks in only about 544 million metric tons of carbon a year—five percent of the world’s annual 10 billion metric tons of carbon emissions.

    NYT A transparent hatchetfish, retrieved by researchers from the Woods Hole Oceanographic Institution, which is seeking to understand better the creatures that occupy the sea from 600 to 3,300 feet deep.Credit Paul Caiger/Woods Hole Oceanographic Institution

    A variety of myctophids, or lantern fish. The twilight zone contains about 250 different species of myctophids.Credit Paul Caiger/Woods Hole Oceanographic Institution

    The photophores of a transparent hatchetfish. Credit Paul Caiger/Woods Hole Oceanographic Institution

    Silver hatchetfish. Credit Paul Caiger/Woods Hole Oceanographic Institution

    Glass squid Credit Paul Caiger/Woods Hole Oceanographic Institution

    Common fangtooth Credit Paul Caiger/Woods Hole Oceanographic Institution

    Value Beyond View: The Ocean Twilight Zone

    From NYT
    Daily journeys between the ocean’s layers


    Using a range of prices for carbon, reflecting future damages expected as a consequence of a changing climate, this “regulating” service has an estimated value of $300 to $900 billion annually, Hoagland notes. Without the ocean’s ability to sequester carbon, atmospheric carbon dioxide levels could be as much as 200 parts per million higher than they are today (about 415 ppm), which would result in a temperature increase of about six degrees Celsius or 10.8 degrees Fahrenheit.

    In addition to its role in the carbon cycle, the twilight zone likely harbors more fish biomass than the rest of the ocean combined, and it is home to the most abundant vertebrate species on the planet— the bristlemouth. While twilight zone fish are unlikely to ever end up on peoples’ dinner plates because of their small size and strange appearance, they do provide meals for larger, economically important fish, like tuna and swordfish, and for other top predators, including sharks, whales, seals, penguins, and seabirds.

    The twilight zone’s biological abundance makes it an attractive target for commercial fishing operations. Ocean twilight zone animals could be harvested to produce fish meal to support the rapidly growing aquaculture industry and to provide fish oils for nutraceutical markets. Because the twilight zone is situated largely in unregulated international waters, there is concern that its potential resources could be subject to unsustainable exploitation.

    The research team hopes that the report will be useful for decision makers, such as the United Nations delegates who will meet this spring in New York to continue developing a new international agreement governing the conservation and sustainable management of marine life on the high seas, in areas beyond the coastal waters managed by individual member States.

    “We need to think carefully about what we stand to gain or lose from future actions that could affect the animals of the twilight zone and their valuable ecosystem services,” says Hoagland. “Increasing scientific understanding is essential if we are going to move toward a goal of the sustainable use of the resources.”

    See the full article here .


    Please help promote STEM in your local schools.

    Stem Education Coalition

    Woods Hole Oceanographic Institute

    Vision & Mission

    The ocean is a defining feature of our planet and crucial to life on Earth, yet it remains one of the planet’s last unexplored frontiers. For this reason, WHOI scientists and engineers are committed to understanding all facets of the ocean as well as its complex connections with Earth’s atmosphere, land, ice, seafloor, and life—including humanity. This is essential not only to advance knowledge about our planet, but also to ensure society’s long-term welfare and to help guide human stewardship of the environment. WHOI researchers are also dedicated to training future generations of ocean science leaders, to providing unbiased information that informs public policy and decision-making, and to expanding public awareness about the importance of the global ocean and its resources.
    Mission Statement

    The Woods Hole Oceanographic Institution is dedicated to advancing knowledge of the ocean and its connection with the Earth system through a sustained commitment to excellence in science, engineering, and education, and to the application of this knowledge to problems facing society.

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