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  • richardmitnick 8:24 am on January 9, 2023 Permalink | Reply
    Tags: "Entrepreneurial Milestones in Life Sciences", , , Life Sciences, , Measuring the many proteins in a tumor sample in high resolution., , Quantitative Biomedicine, Spatial single-cell proteomics, The field of "image-based systems biology",   

    From The University of Zürich (Universität Zürich) (CH): “Entrepreneurial Milestones in Life Sciences” 

    From The University of Zürich (Universität Zürich) (CH)

    Nathalie Huber
    English translations by Philip Isler

    UZH Spin-Offs in 2022

    Three new spin-offs were founded at UZH in 2022, transferring scientific findings into industry practice. The business ventures explore new perspectives in the fight against cancer, space factories to produce human tissue, and ways to accelerate the development of novel drugs.

    The goal of the UZH spin-off Navignostics is to enable a more precise cancer diagnosis for patients. (Image: iStock / utah778)

    At UZH, new ideas evolve into pioneering technologies of the future. Last year, three groups of business founders with roots at UZH took the entrepreneurial leap and signed a licensing agreement with UZH. Their spin-offs emerged from life sciences research conducted at the Faculty of Medicine and the Faculty of Science. 

    Precision diagnostics, bespoke therapies

    Despite a wide variety of available drugs and treatment options, many people still succumb to cancer. Every tumor is unique, making it difficult to find the ideal treatment for each patient. The spin-off Navignostics develops novel diagnostic methods to perform advanced tumor sample analyses. “We want to help specialists find targeted immuno-oncology therapies that are tailored to the individual cancer patient’s tumor phenotype,” says Bernd Bodenmiller, professor of Quantitative Biomedicine.

    Navignostics leverages spatial single-cell proteomics, an approach that was developed by Bodenmiller and his research group. Their approach involves measuring the many proteins in a tumor sample in high resolution. This enables clinicians to use algorithms to determine the cell types present in the tumor as well as which of the cells’ processes are deregulated and how the tumor cells affect the surrounding cells. The aim is to use these data and artificial intelligence to recommend therapies that are tailored to the individual cancer patient.

    Navignostics is currently providing pharmaceutics companies with various services to support them in developing cancer drugs and companion diagnostics or to increase the chances of their clinical trials. Thanks to its successful round of seed financing (CHF 7.5 million), the spin-off can accelerate the development of its first diagnostic product and step up its cooperation with clinical, pharma and biotech partners.

    Human tissue from space

    The ambitious goal of Prometheus Life Technologies AG is to set up a factory that can produce human tissue – in space, no less. The spin-off wants to use the microgravity environment in space to manufacture three-dimensional organ-like tissues – dubbed organoids – using human stem cells. These tissues only grow three-dimensionally in zero gravity. On Earth and in labs, they require highly complicated auxiliary structures to do so. “At the moment, there’s an unmet demand for 3D organoids,” says Oliver Ullrich, director of the UZH Space Hub and co-inventor.

    These tissues are particularly popular among pharmaceutical companies, as they enable them to carry out toxicological trials on human tissue without first having to use animal models. Organoids produced from a patient’s stem cells could also one day be used as the building blocks for transplants to treat damaged organs, as the number of donated organs is nowhere near enough to meet the worldwide demand. Further opportunities for growth arise from replacing 2D with the more in-vivo-like 3D cell cultures.

    The spin-off’s technology is based on a previous joint project of UZH and Airbus. The research and development phase included comprehensive experiments on the ground as well as two successful production tests aboard the International Space Station (ISS). The whole process, from idea to commercialization, originated, developed and matured in the UZH Space Hub. Prometheus Life Technologies AG already won a high-ranking international award last month. The spin-off was selected as the winner of the Reef Starter Innovation Challenge, an innovation engine powered by Orbital Reef, a mixed-use space station to be built in the Earth’s lower orbit.

    Mapping drug activity contexts

    Just as statements shouldn’t be considered out of context, the effects of drugs need to be seen in a bigger picture. Founded by Lucas Pelkmans, professor of molecular biology, Apricot Therapeutics specializes in mapping drug activity contexts, or DACs. “We’re the first pharmaceutical company worldwide that focuses on DACs, and our goal is to drive forward the development of novel and innovative drugs,” Pelkmans says. The technology used by the spin-off is based on Pelkmans’ pioneering discovery that it is possible to predict the behavior of individual cells by mapping their surroundings using multi-scale microscopy and imaging technology. DACs capture how the various spatial organizations of our individual cells cause drugs to have variable effects.

    Apricot Therapeutics’ technology platform is based on methods in the field of “image-based systems biology”, for which the spin-off is currently evaluating two patent applications. The goal of the spin-off is to develop a procedure to measure all DACs relevant for drug activity and use machine learning to predict cellular responses to drugs with unprecedented accuracy. The company is the first to apply novel genomics 3.0 technologies to predict drug activity and treatment outcomes. Future clients include pharmaceutical companies, biotech and medtech start-ups, diagnostic centers, clinicians and research laboratories.

    Here are some of the milestones: 

    Successful cooperation

    Biotech company Molecular Partners concluded a licensing agreement with Novartis for Ensovibep, a drug against Covid-19. Molecular Partners sold the drug’s worldwide rights to Novartis for a one-time payment of CHF 150 million and a 22 percent royalty on sales. 
    Neuroimmune entered into a licensing agreement with AstraZeneca subsidiary Alexion to develop and market the NI006 heart drug. The spin-off also stepped up its cooperation with Japanese company Ono Pharmaceutical in the field of neurodegenerative diseases with the aim of co-developing new drugs.

    Medtech firsts

    Clemedi rolled out Tuberculini in 2022. The molecular test for drug-resistant tuberculosis can deliver results within 48 hours. 
    CUTISS AG received certification from Swissmedic that allows the UZH spin-off to manufacture personalized human skin transplants in its Schlieren facilities. On-site production increases the company’s flexibility and production capacity. In addition, CUTISS was awarded a tissue graft patent by the European Patent Office. 
    Oncobit AG obtained CE marking for its first product, oncobit™ PM. This marking, granted by European regulatory authorities, guarantees that the product can be used without restrictions throughout Europe. oncobit™ PM can be used to monitor treatment response, minimal residual disease, and disease recurrence in melanoma patients.

    New capital

    ImmunOs Therapeutics AG completed a highly successful financing round, raising over CHF 72 million. The biopharmaceutical company develops novel therapeutics for the treatment of cancer and autoimmune diseases.  
    Schlieren-based Kuros Biosciences AG announced a capital increase of CHF 6 million. The spin-off develops spinal fusion technologies that ease the burden of back pain.
    Invasight AG successfully raised CHF 4.5 million. Founded in 2020, the biotech spin-off develops protein-protein interaction antagonists (PPIAs) against invasive cancers.

    KOVE Medical and OxyPrem were each awarded an EIC Accelerator Grant funded by the State Secretariat for Education, Research and Innovation (SERI) to promote groundbreaking innovations by Swiss start-ups. KOVE is developing a method to make prenatal surgical interventions, while OxyPrem is producing a device to monitor oxygen supply to the brain.

    See the full article here .

    Comments are invited and will be appreciated, especially if the reader finds any errors which I can correct. Use “Reply”.


    Please help promote STEM in your local schools.

    Stem Education Coalition

    The University of Zürich (Universität Zürich) (CH), located in the city of Zürich, is the largest university in Switzerland, with over 26,000 students. It was founded in 1833 from the existing colleges of theology, law, medicine and a new faculty of philosophy.

    Currently, the university has seven faculties: Philosophy, Human Medicine, Economic Sciences, Law, Mathematics and Natural Sciences, Theology and Veterinary Medicine. The university offers the widest range of subjects and courses of any Swiss higher education institutions.

    As a member of the League of European Research Universities (EU) (LERU) and Universitas 21 (U21) network, a global network of 27 research universities from around the world, promoting research collaboration and exchange of knowledge.

    Numerous distinctions highlight the University’s international renown in the fields of medicine, immunology, genetics, neuroscience and structural biology as well as in economics. To date, the Nobel Prize has been conferred on twelve UZH scholars.

    Sharing Knowledge

    The academic excellence of the University of Zürich brings benefits to both the public and the private sectors not only in the Canton of Zürich, but throughout Switzerland. Knowledge is shared in a variety of ways: in addition to granting the general public access to its twelve museums and many of its libraries, the University makes findings from cutting-edge research available to the public in accessible and engaging lecture series and panel discussions.

    1. Identity of the University of Zürich


    The University of Zürich (UZH) is an institution with a strong commitment to the free and open pursuit of scholarship.

    Scholarship is the acquisition, the advancement and the dissemination of knowledge in a methodological and critical manner.

    Academic freedom and responsibility

    To flourish, scholarship must be free from external influences, constraints and ideological pressures. The University of Zürich is committed to unrestricted freedom in research and teaching.

    Academic freedom calls for a high degree of responsibility, including reflection on the ethical implications of research activities for humans, animals and the environment.


    Work in all disciplines at the University is based on a scholarly inquiry into the realities of our world

    As Switzerland’s largest university, the University of Zürich promotes wide diversity in both scholarship and in the fields of study offered. The University fosters free dialogue, respects the individual characteristics of the disciplines, and advances interdisciplinary work.

    2. The University of Zurich’s goals and responsibilities

    Basic principles

    UZH pursues scholarly research and teaching, and provides services for the benefit of the public.

    UZH has successfully positioned itself among the world’s foremost universities. The University attracts the best researchers and students, and promotes junior scholars at all levels of their academic career.

    UZH sets priorities in research and teaching by considering academic requirements and the needs of society. These priorities presuppose basic research and interdisciplinary methods.

    UZH strives to uphold the highest quality in all its activities.
    To secure and improve quality, the University regularly monitors and evaluates its performance.


    UZH contributes to the increase of knowledge through the pursuit of cutting-edge research.

    UZH is primarily a research institution. As such, it enables and expects its members to conduct research, and supports them in doing so.

    While basic research is the core focus at UZH, the University also pursues applied research.

  • richardmitnick 11:36 am on November 8, 2022 Permalink | Reply
    Tags: "Study reveals how ancient fish colonized the deep sea", , , , Climate changes alone don’t explain how fish came to colonize the deep sea in the first place., , , , , , , Life Sciences, , 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 7:28 pm on October 4, 2022 Permalink | Reply
    Tags: "DNA reference library a game-changer for environmental monitoring", , , , , , , Life Sciences   

    From CSIRO (AU)-Commonwealth Scientific and Industrial Research Organization: “DNA reference library a game-changer for environmental monitoring” 

    CSIRO bloc

    From CSIRO (AU)-Commonwealth Scientific and Industrial Research Organization

    Ms Andrea Wild
    Communication Advisor, National Research Collections Australia

    CSIRO is building a National Biodiversity DNA Library which aims to deliver a complete collection of DNA reference sequences for all known Australian animal and plant species.

    A new DNA reference library which is set to transform how Australia monitors biodiversity was announced today by CSIRO, Australia’s national science agency, along with the library’s first campaign which is supported by founding partner, Minderoo Foundation.

    The National Biodiversity DNA Library (NBDL) aims to create a complete collection of DNA reference sequences for all known Australian animal and plant species. Just like COVID wastewater testing, it will enable DNA detected in the environment to be assigned to the species to which it belongs.

    CSIRO Director of the NBDL Jenny Giles said environmental DNA (eDNA) analysis has the potential to create a revolution in biodiversity monitoring.

    “Monitoring biodiversity and detecting pests is extremely important, but it’s hard to do and is expensive in a country as large as Australia. eDNA surveys could change that by allowing us to detect animals, plants and other organisms from traces of DNA left behind in the environment, but only if we can reliably assign this DNA to species,” Dr Giles said.

    “People may be surprised to realize that there are tiny pieces of DNA shed by animals, plants, and other life forms left in the air, soil, and water around us.

    “eDNA surveys are increasingly being used to detect and monitor species, but only a tiny fraction of Australian species have sufficient reference data available to support this approach. This means most eDNA we collect can’t currently be assigned to a species.

    “Our National Biodiversity DNA Library aims to provide this missing data through an open access online portal, that will allow Australian state and federal governments, industry, researchers and citizen scientists to take full advantage of this powerful technique to describe and detect changes in our environment,” she said.

    Minderoo Foundation is partnering with CSIRO to fund the first part of this DNA reference library, focusing on all species of Australian marine vertebrates, including fishes, whales, dolphins, seals, turtles, sea snakes and inshore sea and aquatic birds.

    Minderoo Foundation Director of the OceanOmics program Steve Burnell said eDNA approaches will transform how we monitor marine biodiversity and help manage and conserve marine species.

    “The NBDL will help our program and other researchers to detect and map marine vertebrate species around Australia, improving the speed, scale and precision at which we can provide information to resource managers,” Dr Burnell said.

    “We’re proud to support this powerful conservation tool – the surveillance of marine ecosystems using eDNA provides an exciting and non-invasive means to measure biodiversity and monitor the health of our oceans.”

    Dr Giles said the library will be built using unique laboratory techniques developed by CSIRO.

    “This technology enables the large-scale generation of DNA reference sequences from preserved specimens of any organism. This miniaturized, high-throughput approach can unlock genetic information from the millions of scientific specimens preserved in Australian research collections,” she said.

    CSIRO will work with Bioplatforms Australia, enabled by the Commonwealth Government National Collaborative Research Infrastructure Strategy, and Australian natural history collections to rapidly increase the DNA reference sequences available for Australian marine vertebrates. These data will be generated from expertly identified specimens held in collections including CSIRO’s Australian National Fish Collection and Australian National Wildlife Collection.

    The NBDL collaboration between CSIRO, its partners, and our nation’s vast research collections will result in greater understanding of Australia’s animal and plant species and will support industries across fisheries, agriculture, environmental management and tourism.

    The library’s first online data release is expected to occur by early 2024.

    Stag and Plate coral. PHOTO: Minderoo OceanOmics Centre

    Sea lion (Neophoca cinerea). PHOTO: Minderoo OceanOmics Centre

    See the full article here .


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    Stem Education Coalition

    CSIRO campus

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

    CSIRO works with leading organizations 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 organization 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 organized 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 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., , Bar-Ilan University [ אוניברסיטת בר-אילן‎](IL), , , Everything that is true of coral reefs is also true in humans., Life Sciences, , , 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)



    May 31, 2022

    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 .


    Please help promote STEM in your local schools.

    Stem Education Coalition


    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 11:26 am on January 2, 2021 Permalink | Reply
    Tags: "Comb of a Lifetime- A New Method for Fluorescence Microscopy", An optical frequency comb is essentially a light signal composed of the sum of many discrete optical frequencies with a constant spacing in between them., , , , , Conventional fluorescence microscopy provides poor quantitative information of the sample because it only captures fluorescence intensity which changes frequently and depends on external factors., Life Sciences, One of the main pillars of their new method is the use of an optical frequency comb as the excitation light for the sample., Scientists from Japan have developed a new fluorescence microscopy technique to measure both fluorescence intensity and lifetime., Thanks to its superior speed and high spatial resolution the microscopy method developed in this study will make it easier to exploit the advantages of fluorescence lifetime measurements., Tokushima University [徳島大学; Tokushima Daigaku] (JP)   

    From Tokushima University [徳島大学; Tokushima Daigaku] (JP): “Comb of a Lifetime- A New Method for Fluorescence Microscopy” 

    From Tokushima University [徳島大学, Tokushima Daigaku] (JP)

    1 Jan 2021

    Scientists develop a fluorescence “lifetime” microscopy technique that uses frequency combs and no mechanical parts to observe dynamic biological phenomena.

    Conventional fluorescence microscopy provides poor quantitative information of the sample because it only captures fluorescence intensity, which changes frequently and depends on external factors. Now, scientists from Japan have developed a new fluorescence microscopy technique to measure both fluorescence intensity and lifetime. Their method does not require mechanical scanning of a focal point; instead, it produces images from all points in the sample simultaneously, enabling a more quantitative study of dynamic biological and chemical processes.

    Fluorescence microscopy is widely used in biochemistry and life sciences because it allows scientists to directly observe cells and certain compounds in and around them. Fluorescent molecules absorb light within a specific wavelength range and then re-emit it at the longer wavelength range. However, the major limitation of conventional fluorescence microscopy techniques is that the results are very difficult to evaluate quantitatively; fluorescence intensity is significantly affected by both experimental conditions and the concentration of the fluorescent substance. Now, a new study by scientists from Japan is set to revolutionize the field of fluorescence lifetime microscopy. Read on to understand how!

    A way around the conventional problem is to focus on fluorescence lifetime instead of intensity. When a fluorescent substance is irradiated with a short burst of light, the resulting fluorescence does not disappear immediately but actually “decays” over time in a way that is specific to that substance. The “fluorescence lifetime microscopy” technique leverages this phenomenon—which is independent of experimental conditions—to accurately quantify fluorescent molecules and changes in their environment. However, fluorescence decay is extremely fast, and ordinary cameras cannot capture it. While a single-point photodetector can be used instead, it has to be scanned throughout the sample’s area to be able to reconstruct a complete 2D picture from each measured point. This process involves movement of mechanical pieces, which greatly limits the speed of image capture.

    Fortunately, in this recent study published in Science Advances, the aforementioned team of scientists developed a novel approach to acquire fluorescence lifetime images without necessitating mechanical scanning. Professor Takeshi Yasui, from Institute of Post-LED Photonics (pLED), Tokushima University, Japan, who led the study, explains, “Our method can be interpreted as simultaneously mapping 44,400 ‘light stopwatches’ over a 2D space to measure fluorescence lifetimes—all in a single shot and without scanning.” So, how was this achieved?

    2D arrangement of 44,400 light stopwatches enables scan-less fluorescence lifetime imaging.

    One of the main pillars of their method is the use of an optical frequency comb as the excitation light for the sample. An optical frequency comb is essentially a light signal composed of the sum of many discrete optical frequencies with a constant spacing in between them. The word “comb” in this context refers to how the signal looks when plotted against optical frequency: a dense cluster of equidistant “spikes” rising from the optical frequency axis and resembling a hair comb. Using special optical equipment, a pair of excitation frequency comb signals is decomposed into individual optical beat signals (dual-comb optical beats) with different intensity-modulation frequencies, each carrying a single modulation frequency, and irradiated on the target sample. The key here is that each light beam hits the sample on a spatially distinct location, creating a one-to-one correspondence between each point on the 2D surface of the sample (pixel) and each modulation frequency of the dual-comb optical beats.

    Because of its fluorescence properties, the sample re-emits part of the captured radiation while still preserving the aforementioned frequency–position correspondence. The fluorescence emitted from the sample is then simply focused using a lens onto a high-speed single-point photodetector. Finally, the measured signal is mathematically transformed into the frequency domain, and the fluorescence lifetime at each “pixel” is easily calculated from the relative phase delay that exists between the excitation signal at that modulation frequency versus the one measured.

    Principle of operation. Manga courtesy: Suana Science YMY.

    Thanks to its superior speed and high spatial resolution, the microscopy method developed in this study will make it easier to exploit the advantages of fluorescence lifetime measurements. “Because our technique does not require scanning, a simultaneous measurement over the entire sample is guaranteed in each shot,” remarks Prof. Yasui, “This will be helpful in life sciences where dynamic observations of living cells are needed.” In addition to providing deeper insight into biological processes, this new approach could be used for simultaneous imaging of multiple samples for antigen testing, which is already being used for the diagnosis of COVID-19.

    Perhaps most importantly, this study showcases how optical frequency combs, which were only being used as “frequency rulers,” can find a place in microscopy techniques to push the envelope in life sciences. It holds promise for the development of novel therapeutic options to treat intractable diseases and enhance life expectancy, thereby benefitting the whole of humanity.

    See the full article here.


    Please help promote STEM in your local schools.

    Stem Education Coalition

    Tokushima University [徳島大学; Tokushima Daigaku] is a national university in the city of Tokushima, Japan, with seven graduate schools and five undergraduate faculties. The university was founded in 1949, by merging six national education facilities into one. The 2014 Nobel Prize Laureate in Physics, Shuji Nakamura graduated from Tokushima.

    On April 1, 2015 the name of the university was changed from the University of Tokushima to Tokushima University.

    Tokushima University is organized into seven graduate schools: School of Human and Natural Environment Sciences, School of Medical Sciences, School of Oral Sciences, School of Pharmaceutical Sciences, School of Nutrition and Bioscience, School of Health Sciences and School of Advanced Technology and Science. As for undergraduate faculties, there are Faculty of Integrated Arts and Sciences, Faculty of Medicine, Faculty of Dentistry, Faculty of Pharmaceutical Sciences and Faculty of Engineering.

    One unique feature is the large number of affiliated institutes and research centers representing a wide range of interests and disciplines.

    Urologist Susumu Kagawa has been the president of the university since 2010.

    Tokushima University operates on three campuses: Shinkura (with the administrative head office), Jōsanjima, and Kuramoto.

  • richardmitnick 1:58 pm on March 17, 2014 Permalink | Reply
    Tags: , , , Life Sciences   

    From Berkeley Lab: “Vast Gene-Expression Map Yields Neurological and Environmental Stress Insights” 

    Berkeley Lab

    March 16, 2014
    Dan Krotz 510-486-4019 dakrotz@lbl.gov

    A consortium led by scientists from the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) has conducted the largest survey yet of how information encoded in an animal genome is processed in different organs, stages of development, and environmental conditions. Their findings paint a new picture of how genes function in the nervous system and in response to environmental stress.

    They report their research this week in the Advance Online Publication of the journal Nature.

    The scientists studied the fruit fly, an important model organism in genetics research. Seventy percent of known human disease genes have closely related genes in the fly, yet the fly genome is one-thirtieth the size of ours. Previous fruit fly research has provided insights on cancer, birth defects, addictive behavior, and neurological diseases. It has also advanced our understanding of processes common to all animals such as body patterning and synaptic transmission.

    The remarkable complexity of the fruit fly transcriptome comes to life in this fruit fly embryo. Blue dye indicates the presence of RNA molecules in the brain from a previously uncharacterized gene (CG42748) that encodes hundreds of different proteins. No image credit.

    In the latest scientific fruit from the fruit fly, the consortium, led by Susan Celniker of Berkeley Lab’s Life Sciences Division, generated the most comprehensive map of gene expression in any animal to date. Scientists from the University of California at Berkeley, Indiana University at Bloomington, the University of Connecticut Health Center, and several other institutions contributed to the research.

    In all organisms, the information encoded in genomes is transcribed into RNA molecules that are either translated into proteins, or utilized to perform functions in the cell. The collection of RNA molecules expressed in a cell is known as its transcriptome, which can be thought of as the “read out” of the genome.

    While the genome is essentially the same in every cell in our bodies, the transcriptome is different in each cell type and constantly changing. Cells in cardiac tissue are radically different from those in the gut or the brain, for example.

    The transcriptome also changes rapidly in response to environmental challenges. These dynamics in gene expression allow our bodies to adapt to changes such as temperature or exposure to chemicals.

    The broad range of genes that respond to environmental stress is evident in this genome-wide map of genes that are up or down-regulated when fruit flies are exposed to the heavy metal cadmium. Labeled genes are those that showed a 20-fold change in response. No image credit.

    To map the transcriptome, the scientists used deep sequencing technology to generate 1.2 trillion bases of RNA sequence data. They analyzed RNA in 29 fruit fly tissue types, 25 cell lines, and “environmental challenge” scenarios including heat, cold, heavy metal poisoning, and acute exposure to pesticides.

    The combination of extremely deep sequencing and a diverse array of tissues and conditions resulted in a full-body map of RNA activity, which revealed new genes and rare RNAs that are expressed in only one tissue type. Among the discoveries are the unexpected complexity and diversity of the RNAs present in tissues of the nervous system, and previously unknown genes implicated in stress response.

    In samples of the fly’s nervous system, the scientists found about 100 genes that can encode hundreds or even thousands of different types of proteins. Many of these proteins are made in the developing embryo during the early formation of the nervous system. This hints at a previously unknown source of the complexity of the brain, given that most genes express five or fewer types of transcripts, and half encode just one protein.

    “Our study indicates that the total information output of an animal transcriptome is heavily weighted by the needs of the developing nervous system,” says Ben Brown, a Berkeley Lab staff scientist in the Life Sciences Division who led the data analysis team.

    The scientists also discovered a much broader response to stress than previously recognized. Exposure to heavy metals like cadmium resulted in the activation of known stress-response pathways that prevent damage to DNA and proteins. It also revealed several new genes of completely unknown function.

    “To better understand how cells fight stress, we have to figure out what these mysterious genes do,” says Celniker.

    The research was funded by the National Human Genome Research Institute modENCODE Project.

    Other institutions involved in this research include the Sloan-Kettering Institute, Japan’s RIKEN Yokohama Institute, Cold Spring Harbor Laboratory, and Harvard Medical School.

    See the full article here.

    A U.S. Department of Energy National Laboratory Operated by the University of California

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  • richardmitnick 5:01 pm on February 3, 2014 Permalink | Reply
    Tags: , , , , Life Sciences,   

    From Berkeley Lab: “How a Shape-shifting DNA-repair Machine Fights Cancer” 

    Berkeley Lab

    February 03, 2014
    Dan Krotz 510-484-5956 dakrotz@lbl.gov

    Maybe you’ve seen the movies or played with toy Transformers, those shape-shifting machines that morph in response to whatever challenge they face. It turns out that DNA-repair machines in your cells use a similar approach to fight cancer and other diseases, according to research led by scientists from the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab).

    One protein complex, two very different shapes and functions: In the top image, the scientists created an Mre11-Rad50 mutation that speeds up hydrolysis, yielding an open state that favors a high-fidelity way to repair DNA. In the bottom image, the scientists slowed down hydrolysis, resulting in a closed ATP-bound state that favors low-fidelity DNA repair. (Credit: Tainer lab)

    As reported in a pair of new studies, the scientists gained new insights into how a protein complex called Mre11-Rad50 reshapes itself to take on different DNA-repair tasks.

    Their research sheds light on how this molecular restructuring leads to different outcomes in a cell. It could also guide the development of better cancer-fighting therapies and more effective gene therapies.

    As reported in a pair of new studies, the scientists gained new insights into how a protein complex called Mre11-Rad50 reshapes itself to take on different DNA-repair tasks.

    Their research sheds light on how this molecular restructuring leads to different outcomes in a cell. It could also guide the development of better cancer-fighting therapies and more effective gene therapies.

    Mre11-Rad50’s job is the same in your cells, your pet’s cells, or any organism’s. It detects and helps fix the gravest kind of DNA breaks in which both strands of a DNA double helix are cut. The protein complex binds to the broken DNA ends, sends out a signal that stops the cell from dividing, and uses its shape-shifting ability to choose which DNA repair process is launched to fix the broken DNA. If unrepaired, double strand breaks are lethal to the cell. In addition, a repair job gone wrong can lead to the proliferation of cancer cells.

    Little is known about how the protein’s Transformer-like capabilities relate to its DNA-repair functions, however.

    To learn more, the scientists modified the protein complex in ways that were designed to affect just one of the many activities it undertakes. They then used structural biology, biochemistry, and genomic tools to study the impacts of these modifications.

    “By targeting a single activity, we can make the protein complex go down a different pathway and learn how its dynamic structure changes,” says John Tainer of Berkeley Lab’s Life Sciences Division. He conducted the research with fellow Berkeley Lab scientist Gareth Williams and scientists from several other institutions.

    Adds Williams, “In some cases, we sped up or slowed down the protein complex’s movements, and by doing so we changed its biological outcomes.”

    Much of the research was conducted at the SIBYLS beamline at the Advanced Light Source. SIBYLS stands for Structurally Integrated Biology for Life Sciences.

    Much of the research was conducted at the Advanced Light Source (ALS), a synchrotron located at Berkeley Lab that generates intense X-rays to probe the fundamental properties of substances. They used an ALS beamline called SYBILS, which combines X-ray scattering with X-ray diffraction capabilities. It yields atomic-resolution images of the crystal structures of proteins. It can also watch the transformation of the protein as it undergoes conformational changes.

    In one study published in the journal Molecular Cell, the scientists studied Mre11 from microbial cells. They developed two molecular inhibitors that block Mre11’s ability to cut DNA, a critical initial step in the repair process.

    They tested the effect of these inhibitors in human cells. They found that Mre11 first makes a nick away from the broken DNA strand it is repairing. Mre11 then works back toward the broken end. Previously, scientists thought that Mre11 always starts at the broken DNA end. They also found that when Mre11 cuts in the middle of a DNA strand, it initiates a high-precision DNA-repair pathway called homologous recombination repair.

    In another study published in EMBO Journal, the scientists created Rad50 mutations that either promote or destabilize the shape formed when the Rad50 subunit binds with ATP, a chemical that fuels the protein complex’s movements.

    Biochemical and functional assays conducted by Tanya Paull of the University of Texas at Austin revealed how these changes affect microbial, yeast, and human Mre11-Rad50 activities. Paul Russell at the Scripps Research Institute helped the scientists learn how these Rad50 mutations affect yeast cells.

    They found that some mutations slowed down ATP hydrolysis, which is how Rad50 and other enzymes use ATP as fuel. Other mutations sped it up. Both changes affected Mre11-Rad50’s workflow, and its biological outcomes, in a big way.

    “When we slowed down hydrolysis and favored the ATP-bound state, Rad50 favored a non-homologous end joining pathway, which is a low-fidelity way to repair DNA,” says Williams. “When we sped it up, the subunit favored homologous repair, which is the high-fidelity pathway.”

    This approach, in which scientists start with a specific protein mechanism and learn how it affects the entire organism, will help researchers develop a predictive understanding of how Mre11-Rad50 works.

    “It’s a ‘bottom up’ way to study proteins such as Mre11-Rad50, and it could guide the development of better cancer therapies and other applications,” says Tainer.

    See the full article, with further material, here.

    A U.S. Department of Energy National Laboratory Operated by the University of California

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  • richardmitnick 2:58 pm on September 16, 2013 Permalink | Reply
    Tags: , , Life Sciences,   

    From Livermore Lab: “It’s a shock: Life on Earth may have come from out of this world” 

    Lawrence Livermore National Laboratory

    Anne M Stark, LLNL, (925) 422-9799, stark8@llnl.gov

    A group of international scientists including a Lawrence Livermore National Laboratory researcher have confirmed that life really could have come from out of this world. The team shock compressed an icy mixture, similar to what is found in comets, which then created a number of amino acids – the building blocks of life. The research appears in advanced online publication Sept. 15 on the Nature Geoscience journal website.

    Comets contain elements such as water, ammonia, methanol and carbon dioxide that could have supplied the raw materials, in which upon impact on early Earth would have yielded an abundant supply of energy to produce amino acids and jump start life.

    This is the first experimental confirmation of what LLNL scientist Nir Goldman first predicted in 2010 and again in 2013 using computer simulations performed on LLNL’s supercomputers, including Rzcereal and Aztec.

    Goldman’s initial research found that the impact of icy comets crashing into Earth billions of years ago could have produced a variety of prebiotic or life-building compounds, including amino acids. Amino acids are critical to life and serve as the building blocks of proteins. His work predicted that the simple molecules found in comets (such as water, ammonia, methanol and carbon dioxide) could have supplied the raw materials, and the impact with early Earth would have yielded an abundant supply of energy to drive this prebiotic chemistry.

    In the new work, collaborators from Imperial College in London and University of Kent conducted a series of experiments very similar to Goldman’s previous simulations in which a projectile was fired using a light gas gun into a typical cometary ice mixture. The result: Several different types of amino acids formed.

    “These results confirm our earlier predictions of impact synthesis of prebiotic material, where the impact itself can yield life-building compounds,” Goldman said. “Our work provides a realistic additional synthetic production pathway for the components of proteins in our solar system, expanding the inventory of locations where life could potentially originate.”

    See the full article here.

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  • richardmitnick 11:05 am on September 13, 2013 Permalink | Reply
    Tags: , , , , Life Sciences   

    From Berkeley Lab: “Radiotherapy in Girls and the Risk of Breast Cancer Later in Life” 

    Berkeley Lab

    September 11, 2013
    Lynn Yarris (510) 486-5375 lcyarris@lbl.gov

    Exposing young women and girls under the age of 20 to ionizing radiation can substantially raise the risk of their developing breast cancer later in life. Scientists may now know why. A collaborative study, in which Berkeley Lab researchers played a pivotal role, points to increased stem cell self-renewal and subsequent mammary stem cell enrichment as the culprits. Breasts enriched with mammary stem cells as a result of ionizing irradiation during puberty show a later-in-life propensity for developing ER negative tumors – cells that do not have the estrogen receptor. Estrogen receptors – proteins activated by the estrogen hormone – are critical to the normal development of the breast and other female sexual characteristics during puberty.

    This mammary gland agent-based model depicts the network structure at week three formed by cell agents that come together to form duct agents. In turn, duct agents organize into a network similar to the branched structure of the mammary gland. No image credit.

    “Our results are in agreement with epidemiology studies showing that radiation-induced human breast cancers are more likely to be ER negative than are spontaneous breast cancers,” says Sylvain Costes, a biophysicist with Berkeley Lab’s Life Sciences Division. “This is important because ER negative breast cancers are less differentiated, more aggressive, and often have a poor prognosis compared to the other breast cancer subtypes.”

    Costes and Jonathan Tang, also with Berkeley Lab’s Life Sciences Division, were part of a collaboration led by Mary Helen Barcellos-Hoff, formerly with Berkeley Lab and now at the New York University School of Medicine, that investigated the so-called “window of susceptibility” known to exist between radiation treatments at puberty and breast cancer risk in later adulthood. The key to their success were two mammary lineage agent-based models (ABMs) they developed in which a system is modeled as a collection of autonomous decision-making entities called agents. One ABM simulated the effects of radiation on the mammary gland during either the developmental stages or during adulthood. The other simulated the growth dynamics of human mammary epithelial cells in culture after irradiation.

    This mammary gland agent-based model depicts the network structure at week three formed by cell agents that come together to form duct agents. In turn, duct agents organize into a network similar to the branched structure of the mammary gland.

    “Our mammary gland ABM consisted of millions of agents, with each agent representing either a mammary stem cell, a progenitor cell or a differentiated cell in the breast,” says Tang. “We ran thousands of simulations on Berkeley Lab’s Lawrencium supercomputer during which each agent continually assessed its situation and made decisions on the basis of a set of rules that correspond to known or hypothesized biological properties of mammary cells. The advantage of this approach is that it allows us to view the global consequences to the system that emerge over time from our assumptions about the individual agents. To our knowledge, our mammary gland model is the first multi-scale model of the development of full glands starting from the onset of puberty all the way to adulthood.”

    Epidemiological studies have shown that girls under 20 given radiotherapy treatment for disorders such as Hodgkin’s lymphoma run about the same risk of developing breast cancer in their 40s as women who were born with a BRCA gene mutation. From their study, Costes, Tang and their collaboration partners concluded that self-renewal of stem cells was the most likely responsible mechanism.

    “Stem cell self-renewal was the only mechanism in the mammary gland model that led to predictions that were consistent with data from both our in vivo mouse work and our in vitro experiments with MCF10A, a human mammary epithelial cell line,” Tang says. “Additionally, our model predicts that this mechanism would only generate more stem cells during puberty while the gland is developing and considerable cell proliferation is taking place.”

    Costes and Tang are now looking for genetic or phenotypic biomarkers that would identify young girls who are at the greatest breast cancer risk from radiation therapy. The results of their study with Barcellos-Hoff and her research group show that the links between ionizing radiation and breast cancer extend beyond DNA damage and mutations.

    “Essentially, exposure of the breast to ionizing radiation generates an overall biochemical signal that tells the system something bad happened,” Costes says. “If exposure takes place during puberty, this signal triggers a regenerative response leading to a larger pool of stem cells, thereby increasing the chance of developing aggressive ER negative breast cancers later in life.”

    See the full article here.

    A U.S. Department of Energy National Laboratory Operated by the University of California

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  • richardmitnick 2:11 pm on August 12, 2013 Permalink | Reply
    Tags: , , Life Sciences, ,   

    From Livermore Lab: "Lawrence Livermore scientists make new discoveries in the transmission of viruses between animals and humans" 

    Lawrence Livermore National Laboratory

    Kenneth K Ma

    “Outbreaks such as the severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome coronavirus (MERS) have afflicted people around the world, yet many people think these trends are on the decline. Quite the opposite is true.

    SARS coronavirus (SARS-CoV) is causative of the syndrome.

    MERS-CoV particles as seen by negative stain electron microscopy. Virions contain characteristic club-like projections emanating from the viral membrane.

    The efforts to combat this epidemic are being spearheaded by a team of Lawrence Livermore National Laboratory (LLNL) scientists. Led by Monica Borucki of LLNL’s Biosciences and Biotechnology Division, the Lab researchers have made promising new discoveries that provide insight into the emergence of inter-species transmittable viruses.

    They discovered that the genetic diversity of a viral population within a host animal could allow a virus to adapt to certain conditions, which could help it reach a human host. This discovery advances the scientific understanding of how new viruses produced from animal reservoirs can infect people. An animal reservoir is an animal species that harbors an infectious agent, which then goes on to potentially infect humans or other species. Borucki’s team is investigating viruses related to SARS and MERS, but not the actual viruses themselves.

    ‘The team’s findings are the first steps in developing methods for predicting which viral species are most likely to jump from animals to humans and potentially cause outbreaks of diseases,’ Borucki said.

    Borucki’s LLNL multidisciplinary research team includes Jonathan Allen, Tom Slezak, Clinton Torres and Adam Zemla from the Computation Directorate; Haiyin Chen from the Engineering Directorate; and Pam Hullinger, Gilda Vanier and Shalini Mabery from the Physical and Life Sciences Directorate.


    Coronaviruses are one of the groups of viruses that most commonly jump to new host species as evidenced by SARS and MERS, according to Borucki. These viruses appear to have jumped from animals to humans and are capable of causing severe diseases in humans.

    ‘Our discoveries indicate that the next generation of genetic sequencing technology, combined with advance computational analysis, can be used to characterize the dynamics of certain viral populations,’ she said.”

    See the full article here.

    Operated by Lawrence Livermore National Security, LLC, for the Department of Energy’s National Nuclear Security
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