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  • richardmitnick 8:31 am on November 30, 2022 Permalink | Reply
    Tags: "New CRISPR-based tool inserts large DNA sequences at desired sites in cells", "PASTE": Programmable Addition via Site-specific Targeting Elements, , , , , For this study the researchers focused on "serine integrases" which can insert huge chunks of DNA-as large as 50000 base pairs., , Genomics, , The ability to site-specifically make large genomic integrations is of huge value to both basic science and biotechnology studies., The CRISPR-Cas9 gene editing system consists of a DNA-cutting enzyme called Cas9 and a short RNA strand that guides the enzyme to a specific area of the genome directing Cas9 where to make its cut., The DNA sequences that the researchers inserted in this study were up to 36000 base pairs long but they believe even longer sequences could also be used., , The MIT team wanted to develop a tool that could cut out a defective gene and replace it with a new one without inducing any double-stranded DNA breaks.   

    From The Massachusetts Institute of Technology: “New CRISPR-based tool inserts large DNA sequences at desired sites in cells” 

    From The Massachusetts Institute of Technology

    11.24.22
    Anne Trafton

    1
    Building on the CRISPR gene-editing system, MIT researchers designed a new tool that can snip out faulty genes and replace them with new ones. Image: MIT News, with images from iStockphoto.

    Building on the CRISPR gene-editing system, MIT researchers have designed a new tool that can snip out faulty genes and replace them with new ones, in a safer and more efficient way.

    Using this system, the researchers showed that they could deliver genes as long as 36,000 DNA base pairs to several types of human cells, as well as to liver cells in mice. The new technique, known as PASTE, could hold promise for treating diseases that are caused by defective genes with a large number of mutations, such as cystic fibrosis.

    “It’s a new genetic way of potentially targeting these really hard to treat diseases,” says Omar Abudayyeh, a McGovern Fellow at MIT’s McGovern Institute for Brain Research. “We wanted to work toward what gene therapy was supposed to do at its original inception, which is to replace genes, not just correct individual mutations.”

    The new tool combines the precise targeting of CRISPR-Cas9, a set of molecules originally derived from bacterial defense systems, with enzymes called integrases, which viruses use to insert their own genetic material into a bacterial genome.

    “Just like CRISPR, these integrases come from the ongoing battle between bacteria and the viruses that infect them,” says Jonathan Gootenberg, also a McGovern Fellow. “It speaks to how we can keep finding an abundance of interesting and useful new tools from these natural systems.”

    Gootenberg and Abudayyeh are the senior authors of the new study, which appears today in Nature Biotechnology [below]. The lead authors of the study are MIT technical associates Matthew Yarnall and Rohan Krajeski, former MIT graduate student Eleonora Ioannidi, and MIT graduate student Cian Schmitt-Ulms.

    DNA insertion

    The CRISPR-Cas9 gene editing system consists of a DNA-cutting enzyme called Cas9 and a short RNA strand that guides the enzyme to a specific area of the genome, directing Cas9 where to make its cut. When Cas9 and the guide RNA targeting a disease gene are delivered into cells, a specific cut is made in the genome, and the cells’ DNA repair processes glue the cut back together, often deleting a small portion of the genome.

    If a DNA template is also delivered, the cells can incorporate a corrected copy into their genomes during the repair process. However, this process requires cells to make double-stranded breaks in their DNA, which can cause chromosomal deletions or rearrangements that are harmful to cells. Another limitation is that it only works in cells that are dividing, as nondividing cells don’t have active DNA repair processes.

    The MIT team wanted to develop a tool that could cut out a defective gene and replace it with a new one without inducing any double-stranded DNA breaks. To achieve this goal, they turned to a family of enzymes called integrases, which viruses called bacteriophages use to insert themselves into bacterial genomes.

    For this study, the researchers focused on “serine integrases”, which can insert huge chunks of DNA, as large as 50,000 base pairs. These enzymes target specific genome sequences known as attachment sites, which function as “landing pads.” When they find the correct landing pad in the host genome, they bind to it and integrate their DNA payload.

    In past work, scientists have found it challenging to develop these enzymes for human therapy because the landing pads are very specific, and it’s difficult to reprogram integrases to target other sites. The MIT team realized that combining these enzymes with a CRISPR-Cas9 system that inserts the correct landing site would enable easy reprogramming of the powerful insertion system.

    The new tool, PASTE (Programmable Addition via Site-specific Targeting Elements), includes a Cas9 enzyme that cuts at a specific genomic site, guided by a strand of RNA that binds to that site. This allows them to target any site in the genome for insertion of the landing site, which contains 46 DNA base pairs. This insertion can be done without introducing any double-stranded breaks by adding one DNA strand first via a fused reverse transcriptase, then its complementary strand.

    Once the landing site is incorporated, the integrase can come along and insert its much larger DNA payload into the genome at that site. 

    “We think that this is a large step toward achieving the dream of programmable insertion of DNA,” Gootenberg says. “It’s a technique that can be easily tailored both to the site that we want to integrate as well as the cargo.”

    Gene replacement

    In this study, the researchers showed that they could use PASTE to insert genes into several types of human cells, including liver cells, T cells, and lymphoblasts (immature white blood cells). They tested the delivery system with 13 different payload genes, including some that could be therapeutically useful, and were able to insert them into nine different locations in the genome.

    In these cells, the researchers were able to insert genes with a success rate ranging from 5 to 60 percent. This approach also yielded very few unwanted “indels” (insertions or deletions) at the sites of gene integration.

    “We see very few indels, and because we’re not making double-stranded breaks, you don’t have to worry about chromosomal rearrangements or large-scale chromosome arm deletions,” Abudayyeh says.

    The researchers also demonstrated that they could insert genes in “humanized” livers in mice. Livers in these mice consist of about 70 percent human hepatocytes, and PASTE successfully integrated new genes into about 2.5 percent of these cells.

    The DNA sequences that the researchers inserted in this study were up to 36,000 base pairs long, but they believe even longer sequences could also be used. A human gene can range from a few hundred to more than 2 million base pairs, although for therapeutic purposes only the coding sequence of the protein needs to be used, drastically reducing the size of the DNA segment that needs to be inserted into the genome.

    “The ability to site-specifically make large genomic integrations is of huge value to both basic science and biotechnology studies. This toolset will, I anticipate, be very enabling for the research community,” says Prashant Mali, a professor of bioengineering at the University of California at San Diego, who was not involved in the study.

    The researchers are now further exploring the possibility of using this tool as a possible way to replace the defective cystic fibrosis gene. This technique could also be useful for treating blood diseases caused by faulty genes, such as hemophilia and G6PD deficiency, or Huntington’s disease, a neurological disorder caused by a defective gene that has too many gene repeats.

    The researchers have also made their genetic constructs available online for other scientists to use.

    “One of the fantastic things about engineering these molecular technologies is that people can build on them, develop and apply them in ways that maybe we didn’t think of or hadn’t considered,” Gootenberg says. “It’s really great to be part of that emerging community.”

    The research was funded by a Swiss National Science Foundation Postdoc Mobility Fellowship, the U.S. National Institutes of Health, the McGovern Institute Neurotechnology Program, the K. Lisa Yang and Hock E. Tan Center for Molecular Therapeutics in Neuroscience, the G. Harold and Leila Y. Mathers Charitable Foundation, the MIT John W. Jarve Seed Fund for Science Innovation, Impetus Grants, a Cystic Fibrosis Foundation Pioneer Grant, Google Ventures, Fast Grants, the Harvey Family Foundation, and the McGovern Institute.

    Science paper:
    Nature Biotechnology

    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”.


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    Please help promote STEM in your local schools.

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    MIT Seal

    USPS “Forever” postage stamps celebrating Innovation at MIT.

    MIT Campus

    The Massachusetts Institute of Technology is a private land-grant research university in Cambridge, Massachusetts. The institute has an urban campus that extends more than a mile (1.6 km) alongside the Charles River. The institute also encompasses a number of major off-campus facilities such as the MIT Lincoln Laboratory , the MIT Bates Research and Engineering Center , and the Haystack Observatory , as well as affiliated laboratories such as the Broad Institute of MIT and Harvard and Whitehead Institute.

    Massachusettes Institute of Technology-Haystack Observatory Westford, Massachusetts, USA, Altitude 131 m (430 ft).

    Founded in 1861 in response to the increasing industrialization of the United States, Massachusetts Institute of Technology adopted a European polytechnic university model and stressed laboratory instruction in applied science and engineering. It has since played a key role in the development of many aspects of modern science, engineering, mathematics, and technology, and is widely known for its innovation and academic strength. It is frequently regarded as one of the most prestigious universities in the world.

    As of December 2020, 97 Nobel laureates, 26 Turing Award winners, and 8 Fields Medalists have been affiliated with MIT as alumni, faculty members, or researchers. In addition, 58 National Medal of Science recipients, 29 National Medals of Technology and Innovation recipients, 50 MacArthur Fellows, 80 Marshall Scholars, 3 Mitchell Scholars, 22 Schwarzman Scholars, 41 astronauts, and 16 Chief Scientists of the U.S. Air Force have been affiliated with The Massachusetts Institute of Technology. The university also has a strong entrepreneurial culture and MIT alumni have founded or co-founded many notable companies. Massachusetts Institute of Technology is a member of the Association of American Universities.

    Foundation and vision

    In 1859, a proposal was submitted to the Massachusetts General Court to use newly filled lands in Back Bay, Boston for a “Conservatory of Art and Science”, but the proposal failed. A charter for the incorporation of the Massachusetts Institute of Technology, proposed by William Barton Rogers, was signed by John Albion Andrew, the governor of Massachusetts, on April 10, 1861.

    Rogers, a professor from the University of Virginia , wanted to establish an institution to address rapid scientific and technological advances. He did not wish to found a professional school, but a combination with elements of both professional and liberal education, proposing that:

    “The true and only practicable object of a polytechnic school is, as I conceive, the teaching, not of the minute details and manipulations of the arts, which can be done only in the workshop, but the inculcation of those scientific principles which form the basis and explanation of them, and along with this, a full and methodical review of all their leading processes and operations in connection with physical laws.”

    The Rogers Plan reflected the German research university model, emphasizing an independent faculty engaged in research, as well as instruction oriented around seminars and laboratories.

    Early developments

    Two days after The Massachusetts Institute of Technology was chartered, the first battle of the Civil War broke out. After a long delay through the war years, MIT’s first classes were held in the Mercantile Building in Boston in 1865. The new institute was founded as part of the Morrill Land-Grant Colleges Act to fund institutions “to promote the liberal and practical education of the industrial classes” and was a land-grant school. In 1863 under the same act, the Commonwealth of Massachusetts founded the Massachusetts Agricultural College, which developed as the University of Massachusetts Amherst ). In 1866, the proceeds from land sales went toward new buildings in the Back Bay.

    The Massachusetts Institute of Technology was informally called “Boston Tech”. The institute adopted the European polytechnic university model and emphasized laboratory instruction from an early date. Despite chronic financial problems, the institute saw growth in the last two decades of the 19th century under President Francis Amasa Walker. Programs in electrical, chemical, marine, and sanitary engineering were introduced, new buildings were built, and the size of the student body increased to more than one thousand.

    The curriculum drifted to a vocational emphasis, with less focus on theoretical science. The fledgling school still suffered from chronic financial shortages which diverted the attention of the MIT leadership. During these “Boston Tech” years, Massachusetts Institute of Technology faculty and alumni rebuffed Harvard University president (and former MIT faculty) Charles W. Eliot’s repeated attempts to merge MIT with Harvard College’s Lawrence Scientific School. There would be at least six attempts to absorb MIT into Harvard. In its cramped Back Bay location, MIT could not afford to expand its overcrowded facilities, driving a desperate search for a new campus and funding. Eventually, the MIT Corporation approved a formal agreement to merge with Harvard, over the vehement objections of MIT faculty, students, and alumni. However, a 1917 decision by the Massachusetts Supreme Judicial Court effectively put an end to the merger scheme.

    In 1916, The Massachusetts Institute of Technology administration and the MIT charter crossed the Charles River on the ceremonial barge Bucentaur built for the occasion, to signify MIT’s move to a spacious new campus largely consisting of filled land on a one-mile-long (1.6 km) tract along the Cambridge side of the Charles River. The neoclassical “New Technology” campus was designed by William W. Bosworth and had been funded largely by anonymous donations from a mysterious “Mr. Smith”, starting in 1912. In January 1920, the donor was revealed to be the industrialist George Eastman of Rochester, New York, who had invented methods of film production and processing, and founded Eastman Kodak. Between 1912 and 1920, Eastman donated $20 million ($236.6 million in 2015 dollars) in cash and Kodak stock to MIT.

    Curricular reforms

    In the 1930s, President Karl Taylor Compton and Vice-President (effectively Provost) Vannevar Bush emphasized the importance of pure sciences like physics and chemistry and reduced the vocational practice required in shops and drafting studios. The Compton reforms “renewed confidence in the ability of the Institute to develop leadership in science as well as in engineering”. Unlike Ivy League schools, Massachusetts Institute of Technology catered more to middle-class families, and depended more on tuition than on endowments or grants for its funding. The school was elected to the Association of American Universities in 1934.

    Still, as late as 1949, the Lewis Committee lamented in its report on the state of education at The Massachusetts Institute of Technology that “the Institute is widely conceived as basically a vocational school”, a “partly unjustified” perception the committee sought to change. The report comprehensively reviewed the undergraduate curriculum, recommended offering a broader education, and warned against letting engineering and government-sponsored research detract from the sciences and humanities. The School of Humanities, Arts, and Social Sciences and the MIT Sloan School of Management were formed in 1950 to compete with the powerful Schools of Science and Engineering. Previously marginalized faculties in the areas of economics, management, political science, and linguistics emerged into cohesive and assertive departments by attracting respected professors and launching competitive graduate programs. The School of Humanities, Arts, and Social Sciences continued to develop under the successive terms of the more humanistically oriented presidents Howard W. Johnson and Jerome Wiesner between 1966 and 1980.

    The Massachusetts Institute of Technology‘s involvement in military science surged during World War II. In 1941, Vannevar Bush was appointed head of the federal Office of Scientific Research and Development and directed funding to only a select group of universities, including MIT. Engineers and scientists from across the country gathered at Massachusetts Institute of Technology ‘s Radiation Laboratory, established in 1940 to assist the British military in developing microwave radar. The work done there significantly affected both the war and subsequent research in the area. Other defense projects included gyroscope-based and other complex control systems for gunsight, bombsight, and inertial navigation under Charles Stark Draper’s Instrumentation Laboratory; the development of a digital computer for flight simulations under Project Whirlwind; and high-speed and high-altitude photography under Harold Edgerton. By the end of the war, The Massachusetts Institute of Technology became the nation’s largest wartime R&D contractor (attracting some criticism of Bush), employing nearly 4000 in the Radiation Laboratory alone and receiving in excess of $100 million ($1.2 billion in 2015 dollars) before 1946. Work on defense projects continued even after then. Post-war government-sponsored research at MIT included SAGE and guidance systems for ballistic missiles and Project Apollo.

    These activities affected The Massachusetts Institute of Technology profoundly. A 1949 report noted the lack of “any great slackening in the pace of life at the Institute” to match the return to peacetime, remembering the “academic tranquility of the prewar years”, though acknowledging the significant contributions of military research to the increased emphasis on graduate education and rapid growth of personnel and facilities. The faculty doubled and the graduate student body quintupled during the terms of Karl Taylor Compton, president of The Massachusetts Institute of Technology between 1930 and 1948; James Rhyne Killian, president from 1948 to 1957; and Julius Adams Stratton, chancellor from 1952 to 1957, whose institution-building strategies shaped the expanding university. By the 1950s, The Massachusetts Institute of Technology no longer simply benefited the industries with which it had worked for three decades, and it had developed closer working relationships with new patrons, philanthropic foundations and the federal government.

    In late 1960s and early 1970s, student and faculty activists protested against the Vietnam War and The Massachusetts Institute of Technology ‘s defense research. In this period Massachusetts Institute of Technology’s various departments were researching helicopters, smart bombs and counterinsurgency techniques for the war in Vietnam as well as guidance systems for nuclear missiles. The Union of Concerned Scientists was founded on March 4, 1969 during a meeting of faculty members and students seeking to shift the emphasis on military research toward environmental and social problems. The Massachusetts Institute of Technology ultimately divested itself from the Instrumentation Laboratory and moved all classified research off-campus to the MIT Lincoln Laboratory facility in 1973 in response to the protests. The student body, faculty, and administration remained comparatively unpolarized during what was a tumultuous time for many other universities. Johnson was seen to be highly successful in leading his institution to “greater strength and unity” after these times of turmoil. However, six Massachusetts Institute of Technology students were sentenced to prison terms at this time and some former student leaders, such as Michael Albert and George Katsiaficas, are still indignant about MIT’s role in military research and its suppression of these protests. (Richard Leacock’s film, November Actions, records some of these tumultuous events.)

    In the 1980s, there was more controversy at The Massachusetts Institute of Technology over its involvement in SDI (space weaponry) and CBW (chemical and biological warfare) research. More recently, The Massachusetts Institute of Technology’s research for the military has included work on robots, drones and ‘battle suits’.

    Recent history

    The Massachusetts Institute of Technology has kept pace with and helped to advance the digital age. In addition to developing the predecessors to modern computing and networking technologies, students, staff, and faculty members at Project MAC, the Artificial Intelligence Laboratory, and the Tech Model Railroad Club wrote some of the earliest interactive computer video games like Spacewar! and created much of modern hacker slang and culture. Several major computer-related organizations have originated at MIT since the 1980s: Richard Stallman’s GNU Project and the subsequent Free Software Foundation were founded in the mid-1980s at the AI Lab; the MIT Media Lab was founded in 1985 by Nicholas Negroponte and Jerome Wiesner to promote research into novel uses of computer technology; the World Wide Web Consortium standards organization was founded at the Laboratory for Computer Science in 1994 by Tim Berners-Lee; the MIT OpenCourseWare project has made course materials for over 2,000 Massachusetts Institute of Technology classes available online free of charge since 2002; and the One Laptop per Child initiative to expand computer education and connectivity to children worldwide was launched in 2005.

    The Massachusetts Institute of Technology was named a sea-grant college in 1976 to support its programs in oceanography and marine sciences and was named a space-grant college in 1989 to support its aeronautics and astronautics programs. Despite diminishing government financial support over the past quarter century, MIT launched several successful development campaigns to significantly expand the campus: new dormitories and athletics buildings on west campus; the Tang Center for Management Education; several buildings in the northeast corner of campus supporting research into biology, brain and cognitive sciences, genomics, biotechnology, and cancer research; and a number of new “backlot” buildings on Vassar Street including the Stata Center. Construction on campus in the 2000s included expansions of the Media Lab, the Sloan School’s eastern campus, and graduate residences in the northwest. In 2006, President Hockfield launched the MIT Energy Research Council to investigate the interdisciplinary challenges posed by increasing global energy consumption.

    In 2001, inspired by the open source and open access movements, The Massachusetts Institute of Technology launched “OpenCourseWare” to make the lecture notes, problem sets, syllabi, exams, and lectures from the great majority of its courses available online for no charge, though without any formal accreditation for coursework completed. While the cost of supporting and hosting the project is high, OCW expanded in 2005 to include other universities as a part of the OpenCourseWare Consortium, which currently includes more than 250 academic institutions with content available in at least six languages. In 2011, The Massachusetts Institute of Technology announced it would offer formal certification (but not credits or degrees) to online participants completing coursework in its “MITx” program, for a modest fee. The “edX” online platform supporting MITx was initially developed in partnership with Harvard and its analogous “Harvardx” initiative. The courseware platform is open source, and other universities have already joined and added their own course content. In March 2009 the Massachusetts Institute of Technology faculty adopted an open-access policy to make its scholarship publicly accessible online.

    The Massachusetts Institute of Technology has its own police force. Three days after the Boston Marathon bombing of April 2013, MIT Police patrol officer Sean Collier was fatally shot by the suspects Dzhokhar and Tamerlan Tsarnaev, setting off a violent manhunt that shut down the campus and much of the Boston metropolitan area for a day. One week later, Collier’s memorial service was attended by more than 10,000 people, in a ceremony hosted by the Massachusetts Institute of Technology community with thousands of police officers from the New England region and Canada. On November 25, 2013, The Massachusetts Institute of Technology announced the creation of the Collier Medal, to be awarded annually to “an individual or group that embodies the character and qualities that Officer Collier exhibited as a member of The Massachusetts Institute of Technology community and in all aspects of his life”. The announcement further stated that “Future recipients of the award will include those whose contributions exceed the boundaries of their profession, those who have contributed to building bridges across the community, and those who consistently and selflessly perform acts of kindness”.

    In September 2017, the school announced the creation of an artificial intelligence research lab called the MIT-IBM Watson AI Lab. IBM will spend $240 million over the next decade, and the lab will be staffed by MIT and IBM scientists. In October 2018 MIT announced that it would open a new Schwarzman College of Computing dedicated to the study of artificial intelligence, named after lead donor and The Blackstone Group CEO Stephen Schwarzman. The focus of the new college is to study not just AI, but interdisciplinary AI education, and how AI can be used in fields as diverse as history and biology. The cost of buildings and new faculty for the new college is expected to be $1 billion upon completion.

    The Caltech/MIT Advanced aLIGO was designed and constructed by a team of scientists from California Institute of Technology , Massachusetts Institute of Technology, and industrial contractors, and funded by the National Science Foundation .

    Caltech /MIT Advanced aLigo

    It was designed to open the field of gravitational-wave astronomy through the detection of gravitational waves predicted by general relativity. Gravitational waves were detected for the first time by the LIGO detector in 2015. For contributions to the LIGO detector and the observation of gravitational waves, two Caltech physicists, Kip Thorne and Barry Barish, and Massachusetts Institute of Technology physicist Rainer Weiss won the Nobel Prize in physics in 2017. Weiss, who is also a Massachusetts Institute of Technology graduate, designed the laser interferometric technique, which served as the essential blueprint for the LIGO.

    The mission of The Massachusetts Institute of Technology is to advance knowledge and educate students in science, technology, and other areas of scholarship that will best serve the nation and the world in the twenty-first century. We seek to develop in each member of The Massachusetts Institute of Technology community the ability and passion to work wisely, creatively, and effectively for the betterment of humankind.

     
  • richardmitnick 6:49 pm on November 28, 2022 Permalink | Reply
    Tags: "Predicting the Structures of Proteins", , , , , Computer programming, DeepMind’s AlphaFold, , Genomics, Kathryn Tunyasuvunakool, , ,   

    From “Physics” : “Predicting the Structures of Proteins” Kathryn Tunyasuvunakool 

    About Physics

    From “Physics”

    11.28.22
    Katherine Wright

    1
    K. Tunyasuvunakool.

    Kathryn Tunyasuvunakool grew up surrounded by scientific activities carried out at home by her mother—who went to university a few years after Tunyasuvunakool was born. One day a pendulum hung from a ceiling in her family’s home, Tunyasuvunakool’s mother standing next to it, timing the swings for a science assignment. Another day, fossil samples littered the dining table, her mother scrutinizing their patterns for a report. This early exposure to science imbued Tunyasuvunakool with the idea that science was fun and that having a career in science was an attainable goal. “From early on I was desperate to go to university and be a scientist,” she says.

    Tunyasuvunakool fulfilled that ambition, studying math as an undergraduate, and computational biology as a graduate student. During her PhD work she helped create a model that captured various elements of the development of a soil-inhabiting roundworm called Caenorhabditis elegans, a popular organism for both biologists and physicists to study. She also developed a love for programming, which, she says, lent itself naturally to a jump into software engineering. Today Tunyasuvunakool is part of the team behind DeepMind’s AlphaFold—a protein-structure-prediction tool. Physics Magazine spoke to her to find out more about this software, which recently won two of its makers a Breakthrough Prize, and about why she’s excited for the potential discoveries it could enable.

    What is AlphaFold and what can it be used for?

    2
    DeepMind puts the entire human proteome online, as folded by AlphaFold. Image Credit: DeepMind.

    AlphaFold is a machine-learning model that can predict a protein’s structure from its amino-acid sequence. Protein sequences are relativity easy to obtain, with many experiments now able to quickly determine a given protein’s 1D amino-acid chain. But this sequence doesn’t explain how the protein will fold up into a 3D structure, which determines how the protein functions. Folded structures can be experimentally obtained but doing so is time consuming. AlphaFold can predict the structures in a fraction of the time, accelerating the understanding of these systems.

    What is your role on the AlphaFold team?

    When I first joined the team, I worked as a software engineer, writing data pipelines that take existing experimental protein-structure data and turn them into features we can use to train the model. While doing that, I became really interested in how useful AlphaFold’s predictions were. I started to scrutinize the predictions, performing detailed comparisons with literature findings. I then moved into doing that full time, evaluating model performance and finding applications for the software.

    So, how good are AlphaFold’s predictions?

    In 2020 I compared AlphaFold’s predictions to the structures found in experimental studies reported in the highest-impact journals, mostly those published in Nature. At the time we were trying to predict single-chain protein structures, and AlphaFold did really rather well. But I noticed that many of the papers weren’t looking at single chains, they were studying more complex systems that contained multiple chains.

    That motivated us to start working on AlphaFold Multimer, a version of the model specifically trained for multichain protein complexes.

    Have AlphaFold’s predictions ever disagreed with experimentally derived structures, which were then found to be wrong?

    There have been a few cases; but they weren’t ones that I found. Since AlphaFold became available for anyone to use, researchers have carried out an enormous number of investigations with the software. One finding that came out of that effort is, in some instances, AlphaFold predicts more accurate structures than have been experimentally found with nuclear magnetic resonance (NMR) techniques. In NMR, the experimental data need quite a lot of processing to turn them into a structure. And there have been instances where AlphaFold’s predicted structure has fit the data better than the original NMR-derived one.

    How many structures has AlphaFold predicted to date?

    Over 200 million.

    Any notable proteins whose structures you have worked on?

    With the version of AlphaFold evaluated in CASP14 (the 14th iteration of a biennial assessment of protein-structure-prediction models), the first sequence I worked on was for one of the proteins of SARS-CoV-2, the virus that causes COVID-19. That was a sad way to start testing the system, but people were obviously interested in what that protein’s structure looked like.

    What’s on the horizon for AlphaFold?

    I can’t share many details, but I can say that the team behind AlphaFold is committed to working on protein-related problems for the long-term. There are still lots of things AlphaFold can’t do, such as modeling the nonprotein components bound to the system of interest or the influence of water molecules or ligands on how a given protein behaves. The 3D structure of a protein is also just one of its properties. It would be cool to be able to predict other things, such as how a protein’s shape is affected by point mutations.

    There are about 20 people working on updates to AlphaFold—its success is really a team effort—and the team is constantly collaborating with researchers to make sure we are looking at problems that are of interest to scientists. We have a constant stream of follow-up problems to investigate.

    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”.

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    Please help promote STEM in your local schools.

    Stem Education Coalition

    Physicists are drowning in a flood of research papers in their own fields and coping with an even larger deluge in other areas of physics. How can an active researcher stay informed about the most important developments in physics? Physics highlights a selection of papers from the Physical Review journals. In consultation with expert scientists, the editors choose these papers for their importance and/or intrinsic interest. To highlight these papers, Physics features three kinds of articles: Viewpoints are commentaries written by active researchers, who are asked to explain the results to physicists in other subfields. Focus stories are written by professional science writers in a journalistic style and are intended to be accessible to students and non-experts. Synopses are brief editor-written summaries. Physics provides a much-needed guide to the best in physics, and we welcome your comments.

     
  • richardmitnick 8:55 am on November 22, 2022 Permalink | Reply
    Tags: "In search of the principles of life", , , Breaking stereotypes about academics - like that they all come from elite schools and affluent families., Ecosystems, Genomics, , MIT Associate Professor Otto Cordero, Studying fundamental questions of life using Computational Biology, The Department of Civil and Environmental Engineering, , Understanding microbial ecosystems through the broad factors that dictate their composition and behavior., Why are things the way they are?, Why do species divide labor in nature?   

    From The Department of Civil and Environmental Engineering At The Massachusetts Institute of Technology: “In search of the principles of life” MIT Associate Professor Otto Cordero 

    2

    From The Department of Civil and Environmental Engineering

    at

    The Massachusetts Institute of Technology

    11.22.22
    Zach Winn

    1
    MIT Associate Professor Otto Cordero studies microbial ecosystems to research the fundamental factors and constraints that shape living communities. Photo: Jodi Hilton.

    2
    “Trying to make sense of the diversity of microorganisms, or any organism, in an environment is really complex, so the natural instinct is to start with little things — to see what one organism does,” Cordero says. Photo: Jodi Hilton.

    MIT Associate Professor Otto Cordero has always gravitated toward the most basic questions of life. How do ecosystems assemble? Why do species divide labor in nature? He believes these are some of the most central questions for understanding life.

    “The challenge is discovering something that applies across organisms and across environments — now we’re talking about a fundamental constraint of life,” says Cordero, who recently earned tenure in the MIT Department of Civil and Environmental Engineering. “I really care about that type of thing. That’s where it ends for me. Why are things the way they are? Why do they look the way they do and function the way they do? It’s because there are constraints. It’s evolution. It’s how the world works. Discovering those principals is the ultimate prize.”

    Cordero’s search has led him into areas of research he never could have imagined. Along the way, he’s made progress toward understanding microbial ecosystems through the broad factors that dictate their composition and behavior.

    “I talk to a lot of physicists, and they all tell the same story,” Cordero says, smiling. “Many years ago, there were people looking at the molecules of a gas, trying to predict where each one will be, and then somebody at some point figured out there were master variables: pressure, volume, and temperature, and they all relate to each other very nicely. Now they have the gas law, and everything makes sense once you understand those variables. It’s unclear if master variables like that exist in biology, and even more so in microbial ecology, but it’s certainly worth looking for them.”

    Embracing chance

    Cordero was raised by his mother in Guayaquil, Ecuador, where he says scientific activity was sparse.

    “I never met a scientist in my life,” Cordero says. “At my university in Ecuador, there was one teacher who had a PhD, and everybody called him doctor.”

    Although no one in Cordero’s family had gone to college, his mother prioritized his education, and Cordero gained an appreciation for reading and learning from his grandfather. Those influences led him to a technical college for his undergraduate degree.

    Cordero’s childhood was humble — there were days he had to borrow 25 cents just to catch a bus to campus. But a pivotal moment came when he received a scholarship to attend Utrecht University for graduate school in the Netherlands.

    “Everything is serendipitous,” Cordero says. “I tell my students when I look back, I could never have predicted where I’d be in three to five years.”

    Up to that point, Cordero hadn’t met many people outside of Ecuador, but he jokes that he met someone from every country in Europe within a week. He’d go on to make friends from around the world.

    While majoring in artificial intelligence as a master’s student, Cordero became interested in algorithms that described the organization of organisms like insects. One day he was searching through papers on the subject when a Dutch name caught his eye. It turned out to be a professor in the building next to him. He hurried over and met the professor, Paulien Hogeweg, who was studying fundamental questions of life using computational biology. Cordero fell in love with the subject, and Hogeweg would become his PhD advisor.

    Serendipity struck again when Cordero began his postdoctoral work at MIT, where he worked under longtime MIT professor Martin Polz, who is now a professor at the University of Vienna.

    “I ended up opening this area of research for myself that I never imagined before,” Cordero says. “I started to study microbial interactions — essentially how different strains or species of bacteria interact in the environment.”

    Through that work, Cordero uncovered mechanisms microbes use to work together or kill off competing species, which have major implications for microbial ecosystems and perhaps also large biogeochemical processes like the carbon cycle.

    “From there, I was an expert in microbial interactions and evolution,” Cordero says. “I was working on exciting projects, and when that happens at MIT the environment lifts you up. Everybody wants to talk to you about the next idea. It’s stimulating. I enjoy that very much. The dynamics and exposure here are unrivaled. I feel like I go to a talk and I know what the next big-impact paper is going to be.”

    Cordero joined the faculty at MIT in 2015, and he’s continued studying microbes to explore how biological systems function and evolve.

    In keeping with that mission, in 2017 Cordero helped assemble an interdisciplinary group of researchers from around the world to look for universal principles of biology that could help explain and predict the behavior of microbial systems. The resulting collaboration, called Principles of Microbial Ecosystems (PRIME), has made progress identifying environmental factors and constraints that help shape all ecosystems.

    For instance, PRIME researchers have profiled the metabolic processes of hundreds of species of microbes to place them into broader metabolic classes that can be used to accurately model and predict the behavior of ecosystems.

    “Trying to make sense of the diversity of microorganisms, or any organism, in an environment is really complex, so the natural instinct is to start with little things — to see what one organism does,” Cordero says. “I wanted to look for things that could be generalized. Is there some sort of principal that helps explain or predict why communities assemble this way, or what we should expect in this environment or that environment? We see these broad patterns, and it begs the question of what the right variables are to study. Things become much simpler and more predictable when you identify those right variables.”

    Focusing on the bigger picture

    Cordero says he wants to break stereotypes about academics, like that they all come from elite schools and affluent families.

    He also wants to show students that researchers can have fun while working hard. Before the pandemic, Cordero played in a band with students from his department that featured two PhD students on guitar, a postdoctoral drummer, an MBA on the trumpet, and a master’s student singing.

    “That was the highlight of the week for me,” Cordero says. “Hopefully we bring it back!”

    Cordero’s personal life has also gotten a bit busier since the start of the pandemic — he now has a 2-year-old and 5-month-old.

    Overall, whether in his personal life or work, Cordero tries to focus on the big picture.

    “When you sequence [the genome] of something, you get this long list of taxa with Latin names, but that’s not really the most important information,” Cordero says. “The vision is that one day — hopefully not too far into the future — we can transform that information into more functional variables. [This goes back to] the pressure-volume-temperature analogy. Maybe these ecosystems can be understood with simple models, and maybe we can predict what they will do in the future. That would be a huge game-changer.”

    See the full article here .


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    Please help promote STEM in your local schools.

    Stem Education Coalition

    Our Mission

    In The MIT Department of Civil and Environmental Engineering, we are driven by a simple truth: we only have one Earth to call home. Our intellectual focus is on the human-built environment and the complex infrastructure systems that it entails, as well as the man-made effect on the natural world. We seek to foster an inclusive community that pushes the boundaries of what is possible to shape the future of civil and environmental engineering. Our goal is to educate and train the next generation of researchers and engineers, driven by a passion to positively impact our society, economy, and our planet.

    Our faculty and students work in tandem to develop and apply pioneering approaches that range from basic scientific principles to complex engineering design, with a focus on translating fundamental advances to real-world impact. We offer undergraduate and graduate degree programs in the broad areas of infrastructure and environment, in order to advance the frontiers of knowledge for a sustainable civilization.

    Our Vision

    Bold solutions for sustainability across scales.

    MIT CEE is creating a new era of sustainable and resilient infrastructure and systems from the nanoscale to the global scale.

    We are pioneering a bold transformation of civil and environmental engineering as a field, fostering collaboration across disciplines to drive meaningful change. Our research and educational programs challenge the status quo, advance the frontier of knowledge and expand the limit of what is possible.

    MIT Seal

    USPS “Forever” postage stamps celebrating Innovation at MIT.

    MIT Campus

    The Massachusetts Institute of Technology is a private land-grant research university in Cambridge, Massachusetts. The institute has an urban campus that extends more than a mile (1.6 km) alongside the Charles River. The institute also encompasses a number of major off-campus facilities such as the MIT Lincoln Laboratory , the MIT Bates Research and Engineering Center , and the Haystack Observatory , as well as affiliated laboratories such as the Broad Institute of MIT and Harvard and Whitehead Institute.

    Massachusettes Institute of Technology-Haystack Observatory Westford, Massachusetts, USA, Altitude 131 m (430 ft).

    Founded in 1861 in response to the increasing industrialization of the United States, Massachusetts Institute of Technology adopted a European polytechnic university model and stressed laboratory instruction in applied science and engineering. It has since played a key role in the development of many aspects of modern science, engineering, mathematics, and technology, and is widely known for its innovation and academic strength. It is frequently regarded as one of the most prestigious universities in the world.

    As of December 2020, 97 Nobel laureates, 26 Turing Award winners, and 8 Fields Medalists have been affiliated with MIT as alumni, faculty members, or researchers. In addition, 58 National Medal of Science recipients, 29 National Medals of Technology and Innovation recipients, 50 MacArthur Fellows, 80 Marshall Scholars, 3 Mitchell Scholars, 22 Schwarzman Scholars, 41 astronauts, and 16 Chief Scientists of the U.S. Air Force have been affiliated with The Massachusetts Institute of Technology. The university also has a strong entrepreneurial culture and MIT alumni have founded or co-founded many notable companies. Massachusetts Institute of Technology is a member of the Association of American Universities (AAU).

    Foundation and vision

    In 1859, a proposal was submitted to the Massachusetts General Court to use newly filled lands in Back Bay, Boston for a “Conservatory of Art and Science”, but the proposal failed. A charter for the incorporation of the Massachusetts Institute of Technology, proposed by William Barton Rogers, was signed by John Albion Andrew, the governor of Massachusetts, on April 10, 1861.

    Rogers, a professor from the University of Virginia , wanted to establish an institution to address rapid scientific and technological advances. He did not wish to found a professional school, but a combination with elements of both professional and liberal education, proposing that:

    “The true and only practicable object of a polytechnic school is, as I conceive, the teaching, not of the minute details and manipulations of the arts, which can be done only in the workshop, but the inculcation of those scientific principles which form the basis and explanation of them, and along with this, a full and methodical review of all their leading processes and operations in connection with physical laws.”

    The Rogers Plan reflected the German research university model, emphasizing an independent faculty engaged in research, as well as instruction oriented around seminars and laboratories.

    Early developments

    Two days after The Massachusetts Institute of Technology was chartered, the first battle of the Civil War broke out. After a long delay through the war years, MIT’s first classes were held in the Mercantile Building in Boston in 1865. The new institute was founded as part of the Morrill Land-Grant Colleges Act to fund institutions “to promote the liberal and practical education of the industrial classes” and was a land-grant school. In 1863 under the same act, the Commonwealth of Massachusetts founded the Massachusetts Agricultural College, which developed as the University of Massachusetts Amherst ). In 1866, the proceeds from land sales went toward new buildings in the Back Bay.

    The Massachusetts Institute of Technology was informally called “Boston Tech”. The institute adopted the European polytechnic university model and emphasized laboratory instruction from an early date. Despite chronic financial problems, the institute saw growth in the last two decades of the 19th century under President Francis Amasa Walker. Programs in electrical, chemical, marine, and sanitary engineering were introduced, new buildings were built, and the size of the student body increased to more than one thousand.

    The curriculum drifted to a vocational emphasis, with less focus on theoretical science. The fledgling school still suffered from chronic financial shortages which diverted the attention of the MIT leadership. During these “Boston Tech” years, Massachusetts Institute of Technology faculty and alumni rebuffed Harvard University president (and former MIT faculty) Charles W. Eliot’s repeated attempts to merge MIT with Harvard College’s Lawrence Scientific School. There would be at least six attempts to absorb MIT into Harvard. In its cramped Back Bay location, MIT could not afford to expand its overcrowded facilities, driving a desperate search for a new campus and funding. Eventually, the MIT Corporation approved a formal agreement to merge with Harvard, over the vehement objections of MIT faculty, students, and alumni. However, a 1917 decision by the Massachusetts Supreme Judicial Court effectively put an end to the merger scheme.

    In 1916, The Massachusetts Institute of Technology administration and the MIT charter crossed the Charles River on the ceremonial barge Bucentaur built for the occasion, to signify MIT’s move to a spacious new campus largely consisting of filled land on a one-mile-long (1.6 km) tract along the Cambridge side of the Charles River. The neoclassical “New Technology” campus was designed by William W. Bosworth and had been funded largely by anonymous donations from a mysterious “Mr. Smith”, starting in 1912. In January 1920, the donor was revealed to be the industrialist George Eastman of Rochester, New York, who had invented methods of film production and processing, and founded Eastman Kodak. Between 1912 and 1920, Eastman donated $20 million ($236.6 million in 2015 dollars) in cash and Kodak stock to MIT.

    Curricular reforms

    In the 1930s, President Karl Taylor Compton and Vice-President (effectively Provost) Vannevar Bush emphasized the importance of pure sciences like physics and chemistry and reduced the vocational practice required in shops and drafting studios. The Compton reforms “renewed confidence in the ability of the Institute to develop leadership in science as well as in engineering”. Unlike Ivy League schools, Massachusetts Institute of Technology catered more to middle-class families, and depended more on tuition than on endowments or grants for its funding. The school was elected to the Association of American Universities in 1934.

    Still, as late as 1949, the Lewis Committee lamented in its report on the state of education at The Massachusetts Institute of Technology that “the Institute is widely conceived as basically a vocational school”, a “partly unjustified” perception the committee sought to change. The report comprehensively reviewed the undergraduate curriculum, recommended offering a broader education, and warned against letting engineering and government-sponsored research detract from the sciences and humanities. The School of Humanities, Arts, and Social Sciences and the MIT Sloan School of Management were formed in 1950 to compete with the powerful Schools of Science and Engineering. Previously marginalized faculties in the areas of economics, management, political science, and linguistics emerged into cohesive and assertive departments by attracting respected professors and launching competitive graduate programs. The School of Humanities, Arts, and Social Sciences continued to develop under the successive terms of the more humanistically oriented presidents Howard W. Johnson and Jerome Wiesner between 1966 and 1980.

    The Massachusetts Institute of Technology‘s involvement in military science surged during World War II. In 1941, Vannevar Bush was appointed head of the federal Office of Scientific Research and Development and directed funding to only a select group of universities, including MIT. Engineers and scientists from across the country gathered at Massachusetts Institute of Technology ‘s Radiation Laboratory, established in 1940 to assist the British military in developing microwave radar. The work done there significantly affected both the war and subsequent research in the area. Other defense projects included gyroscope-based and other complex control systems for gunsight, bombsight, and inertial navigation under Charles Stark Draper’s Instrumentation Laboratory; the development of a digital computer for flight simulations under Project Whirlwind; and high-speed and high-altitude photography under Harold Edgerton. By the end of the war, The Massachusetts Institute of Technology became the nation’s largest wartime R&D contractor (attracting some criticism of Bush), employing nearly 4000 in the Radiation Laboratory alone and receiving in excess of $100 million ($1.2 billion in 2015 dollars) before 1946. Work on defense projects continued even after then. Post-war government-sponsored research at MIT included SAGE and guidance systems for ballistic missiles and Project Apollo.

    These activities affected The Massachusetts Institute of Technology profoundly. A 1949 report noted the lack of “any great slackening in the pace of life at the Institute” to match the return to peacetime, remembering the “academic tranquility of the prewar years”, though acknowledging the significant contributions of military research to the increased emphasis on graduate education and rapid growth of personnel and facilities. The faculty doubled and the graduate student body quintupled during the terms of Karl Taylor Compton, president of The Massachusetts Institute of Technology between 1930 and 1948; James Rhyne Killian, president from 1948 to 1957; and Julius Adams Stratton, chancellor from 1952 to 1957, whose institution-building strategies shaped the expanding university. By the 1950s, The Massachusetts Institute of Technology no longer simply benefited the industries with which it had worked for three decades, and it had developed closer working relationships with new patrons, philanthropic foundations and the federal government.

    In late 1960s and early 1970s, student and faculty activists protested against the Vietnam War and The Massachusetts Institute of Technology ‘s defense research. In this period Massachusetts Institute of Technology’s various departments were researching helicopters, smart bombs and counterinsurgency techniques for the war in Vietnam as well as guidance systems for nuclear missiles. The Union of Concerned Scientists was founded on March 4, 1969 during a meeting of faculty members and students seeking to shift the emphasis on military research toward environmental and social problems. The Massachusetts Institute of Technology ultimately divested itself from the Instrumentation Laboratory and moved all classified research off-campus to the MIT Lincoln Laboratory facility in 1973 in response to the protests. The student body, faculty, and administration remained comparatively unpolarized during what was a tumultuous time for many other universities. Johnson was seen to be highly successful in leading his institution to “greater strength and unity” after these times of turmoil. However, six Massachusetts Institute of Technology students were sentenced to prison terms at this time and some former student leaders, such as Michael Albert and George Katsiaficas, are still indignant about MIT’s role in military research and its suppression of these protests. (Richard Leacock’s film, November Actions, records some of these tumultuous events.)

    In the 1980s, there was more controversy at The Massachusetts Institute of Technology over its involvement in SDI (space weaponry) and CBW (chemical and biological warfare) research. More recently, The Massachusetts Institute of Technology’s research for the military has included work on robots, drones and ‘battle suits’.

    Recent history

    The Massachusetts Institute of Technology has kept pace with and helped to advance the digital age. In addition to developing the predecessors to modern computing and networking technologies, students, staff, and faculty members at Project MAC, the Artificial Intelligence Laboratory, and the Tech Model Railroad Club wrote some of the earliest interactive computer video games like Spacewar! and created much of modern hacker slang and culture. Several major computer-related organizations have originated at MIT since the 1980s: Richard Stallman’s GNU Project and the subsequent Free Software Foundation were founded in the mid-1980s at the AI Lab; the MIT Media Lab was founded in 1985 by Nicholas Negroponte and Jerome Wiesner to promote research into novel uses of computer technology; the World Wide Web Consortium standards organization was founded at the Laboratory for Computer Science in 1994 by Tim Berners-Lee; the MIT OpenCourseWare project has made course materials for over 2,000 Massachusetts Institute of Technology classes available online free of charge since 2002; and the One Laptop per Child initiative to expand computer education and connectivity to children worldwide was launched in 2005.

    The Massachusetts Institute of Technology was named a sea-grant college in 1976 to support its programs in oceanography and marine sciences and was named a space-grant college in 1989 to support its aeronautics and astronautics programs. Despite diminishing government financial support over the past quarter century, MIT launched several successful development campaigns to significantly expand the campus: new dormitories and athletics buildings on west campus; the Tang Center for Management Education; several buildings in the northeast corner of campus supporting research into biology, brain and cognitive sciences, genomics, biotechnology, and cancer research; and a number of new “backlot” buildings on Vassar Street including the Stata Center. Construction on campus in the 2000s included expansions of the Media Lab, the Sloan School’s eastern campus, and graduate residences in the northwest. In 2006, President Hockfield launched the MIT Energy Research Council to investigate the interdisciplinary challenges posed by increasing global energy consumption.

    In 2001, inspired by the open source and open access movements, The Massachusetts Institute of Technology launched OpenCourseWare to make the lecture notes, problem sets, syllabi, exams, and lectures from the great majority of its courses available online for no charge, though without any formal accreditation for coursework completed. While the cost of supporting and hosting the project is high, OCW expanded in 2005 to include other universities as a part of the OpenCourseWare Consortium, which currently includes more than 250 academic institutions with content available in at least six languages. In 2011, The Massachusetts Institute of Technology announced it would offer formal certification (but not credits or degrees) to online participants completing coursework in its “MITx” program, for a modest fee. The “edX” online platform supporting MITx was initially developed in partnership with Harvard and its analogous “Harvardx” initiative. The courseware platform is open source, and other universities have already joined and added their own course content. In March 2009 the Massachusetts Institute of Technology faculty adopted an open-access policy to make its scholarship publicly accessible online.

    The Massachusetts Institute of Technology has its own police force. Three days after the Boston Marathon bombing of April 2013, MIT Police patrol officer Sean Collier was fatally shot by the suspects Dzhokhar and Tamerlan Tsarnaev, setting off a violent manhunt that shut down the campus and much of the Boston metropolitan area for a day. One week later, Collier’s memorial service was attended by more than 10,000 people, in a ceremony hosted by the Massachusetts Institute of Technology community with thousands of police officers from the New England region and Canada. On November 25, 2013, The Massachusetts Institute of Technology announced the creation of the Collier Medal, to be awarded annually to “an individual or group that embodies the character and qualities that Officer Collier exhibited as a member of The Massachusetts Institute of Technology community and in all aspects of his life”. The announcement further stated that “Future recipients of the award will include those whose contributions exceed the boundaries of their profession, those who have contributed to building bridges across the community, and those who consistently and selflessly perform acts of kindness”.

    In September 2017, the school announced the creation of an artificial intelligence research lab called the MIT-IBM Watson AI Lab. IBM will spend $240 million over the next decade, and the lab will be staffed by MIT and IBM scientists. In October 2018 MIT announced that it would open a new Schwarzman College of Computing dedicated to the study of artificial intelligence, named after lead donor and The Blackstone Group CEO Stephen Schwarzman. The focus of the new college is to study not just AI, but interdisciplinary AI education, and how AI can be used in fields as diverse as history and biology. The cost of buildings and new faculty for the new college is expected to be $1 billion upon completion.

    The Caltech/MIT Advanced aLIGO was designed and constructed by a team of scientists from California Institute of Technology , Massachusetts Institute of Technology, and industrial contractors, and funded by the National Science Foundation .

    Caltech /MIT Advanced aLigo

    It was designed to open the field of gravitational-wave astronomy through the detection of gravitational waves predicted by general relativity. Gravitational waves were detected for the first time by the LIGO detector in 2015. For contributions to the LIGO detector and the observation of gravitational waves, two Caltech physicists, Kip Thorne and Barry Barish, and Massachusetts Institute of Technology physicist Rainer Weiss won the Nobel Prize in physics in 2017. Weiss, who is also a Massachusetts Institute of Technology graduate, designed the laser interferometric technique, which served as the essential blueprint for the LIGO.

    The mission of The Massachusetts Institute of Technology is to advance knowledge and educate students in science, technology, and other areas of scholarship that will best serve the nation and the world in the twenty-first century. We seek to develop in each member of The Massachusetts Institute of Technology community the ability and passion to work wisely, creatively, and effectively for the betterment of humankind.

     
  • 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., , , , , , Genomics, , , 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” 

    1

    From The College of the Environment

    at

    The University of Washington

    11.2.22

    1
    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?

    2
    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:
    PNAS

    See the full article here .


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

    4

    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.

    u-washington-campus

    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 7:38 pm on November 1, 2022 Permalink | Reply
    Tags: "Ancient genomes reveal hidden history of human adaptation", , , , Evidence for this type of adaptive genetic change has been inconsistent in humans. This discovery consequently challenges the prevailing view of human adaptation., Genomics, , Paleogenomics, , The use of ancient DNA including samples of human remains around 45000 years old has shed light on a previously unknown aspect of human evolution., The use of ancient genomes was crucial because they preceded major historical mixing events that have radically reshaped modern European genetic ancestry., This gives us a new and exciting insight into how humans have adapted to the novel environmental pressures they encountered as we spread across the planet.   

    From The University of Adelaide (AU) : “Ancient genomes reveal hidden history of human adaptation” 

    u-adelaide-bloc

    From The University of Adelaide (AU)

    11.1.22
    Media contacts

    Dr Yassine Souilmi, Ph.D.
    Group Leader, Australian Centre for Ancient DNA
    The University of Adelaide
    +61 (0)466 632 395
    Yassine.souilmi@adelaide.edu.au

    Dr Ray Tobler
    Adjunct Fellow
    The University of Adelaide
    +61 (0)424 533 046
    ray.tobler@adelaide.edu.au

    Professor Christian Huber
    Assistant Professor
    The Pennsylvania State University
    +1 814 863 6634.
    cdh5313@psu.edu

    Lee Gaskin,
    Media Coordinator
    The University of Adelaide
    +61 (0)415 747 075
    lee.gaskin@adelaide.edu.au

    The use of ancient DNA, including samples of human remains around 45,000 years old, has shed light on a previously unknown aspect of human evolution.

    1
    A new study co-led by a University of Adelaide researcher has used ancient DNA to challenge the prevailing view of human adaptation. Credit: iStock.

    Dr Yassine Souilmi, Group Leader at the University of Adelaide’s Australian Centre for Ancient DNA, co-led the new study published in Nature Ecology and Evolution [below] .

    “It was widely believed the genetics of our human ancestors didn’t change due to environmental pressures as much as other animals, due to our enhanced communication skills and ability to make and use tools,” Dr Souilmi said.

    “However, by comparing modern genomes with ancient DNA, we discovered more than 50 cases of an initially rare beneficial genetic variant becoming prevalent across all members of ancient human groups.

    “In contrast to many other species, evidence for this type of adaptive genetic change has been inconsistent in humans. This discovery consequently challenges the prevailing view of human adaptation, and gives us a new and exciting insight into how humans have adapted to the novel environmental pressures they encountered as we spread across the planet.”

    Co-lead author Dr Ray Tobler – an Adjunct Fellow at the University of Adelaide and a DECRA fellow at the Australian National University – said examining ancient DNA has been critical in unlocking the secrets of human evolution.

    “We believed historical mixing events between human groups might have hidden signs of genetic changes in modern human genomes,” Dr Tobler said.

    “We examined DNA from more than 1,000 ancient genomes, the oldest which was around 45,000 years old, to see if certain types of genetic adaptation had been more common in our history than studies of modern genomes had suggested.”

    Professor Christian Huber, a senior author of the research paper, is an Adjunct Fellow at the University of Adelaide and an Assistant Professor at Penn State University.

    “The use of ancient genomes was crucial because they preceded major historical mixing events that have radically reshaped modern European genetic ancestry,” Professor Huber said.

    “This allowed the recovery of historical signs of adaptation that are invisible to standard analysis of modern genomes.”

    Established in 2005, the Australian Centre for Ancient DNA is a world leader in the research and development of advanced ancient DNA approaches for evolutionary, environmental and conservation applications.

    Researchers based at the Mayo Clinic, the Garvan Institute of Medical Research, the Max Planck Institute for the Science of Human History in Germany, the University of New South Wales, and Massey University in New Zealand also contributed to the research paper.

    Science paper:
    Nature Ecology and Evolution
    See the science paper for detailed material with images.

    See the full article here.

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

    Please help promote STEM in your local schools.

    Stem Education Coalition

    u-adelaide-campus

    The University of Adelaide is a public research university located in Adelaide, South Australia. Established in 1874, it is the third-oldest university in Australia. The university’s main campus is located on North Terrace in the Adelaide city centre, adjacent to the Art Gallery of South Australia, the South Australian Museum and the State Library of South Australia.

    The university has four campuses, three in South Australia: North Terrace campus in the city, Roseworthy campus at Roseworthy and Waite campus at Urrbrae, and one in Melbourne, Victoria. The university also operates out of other areas such as Thebarton, the National Wine Centre in the Adelaide Park Lands, and in Singapore through the Ngee Ann-Adelaide Education Centre.

    The University of Adelaide is composed of five faculties, with each containing constituent schools. These include the Faculty of Engineering, Computer, and Mathematical Sciences (ECMS), the Faculty of Health and Medical Sciences, the Faculty of Arts, the Faculty of the Professions, and the Faculty of Sciences. It is a member of The Group of Eight and The Association of Commonwealth Universities. The university is also a member of the Sandstone universities, which mostly consist of colonial-era universities within Australia.

    The university is associated with five Nobel laureates, constituting one-third of Australia’s total Nobel Laureates, and 110 Rhodes scholars. The university has had a considerable impact on the public life of South Australia, having educated many of the state’s leading business people, lawyers, medical professionals and politicians. The university has been associated with many notable achievements and discoveries, such as the discovery and development of penicillin, the development of space exploration, sunscreen, the military tank, Wi-Fi, polymer banknotes and X-ray crystallography, and the study of viticulture and oenology.

    Research

    The University of Adelaide is one of the most research-intensive universities in Australia, securing over $180 million in research funding annually. Its researchers are active in both basic and commercially oriented research across a broad range of fields including agriculture, psychology, health sciences, and engineering.

    Research strengths include engineering, mathematics, science, medical and health sciences, agricultural sciences, artificial intelligence, and the arts.

    The university is a member of Academic Consortium 21, an association of 20 research intensive universities, mainly in Oceania, though with members from the US and Europe. The university held the Presidency of AC 21 for the period 2011–2013 as host the biennial AC21 International Forum in June 2012.

    The Centre for Automotive Safety Research (CASR), based at the University of Adelaide, was founded in 1973 as the Road Accident Research Unit and focuses on road safety and injury control.

     
  • richardmitnick 3:12 pm on October 14, 2022 Permalink | Reply
    Tags: "Engineering Duckweed to Produce Oil for Biofuels and Bioproducts", , , , As an aquatic plant oil-producing duckweed wouldn’t compete with food crops for prime agricultural land., , , , , , Genomics, , 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

    10.11.22
    Karen McNulty Walsh
    kmcnulty@bnl.gov
    (631) 344-8350

    Peter Genzer
    genzer@bnl.gov
    (631) 344-3174

    1
    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 .


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

    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
    Nanomaterials
    Energy research
    Nonproliferation
    Structural biology
    Accelerator physics

    Operation

    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.

    Foundations

    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 NSLS II.

    BNL Relative Heavy Ion Collider Campus.

    BNL/RHIC Phenix detector.


     
  • richardmitnick 1:32 pm on October 7, 2022 Permalink | Reply
    Tags: "New route to evolution - how DNA from our mitochondria gets into our genomes", , , Each mitochondrion has its own DNA distinct to the rest of the human genome which is comprised of nuclear DNA., , Genomics, It is not clear exactly how the mitochondrial DNA inserts itself., Mitochondrial DNA also appears in some cancer DNA suggesting that it acts as a sticking plaster to try and repair damage to our genetic code., Mitochondrial DNA is passed down the maternal line., Scientists have shown that in one in every 4000 births some of the genetic code from our mitochondria – the ‘batteries’ that power our cells – inserts itself into our DNA.,   

    From The University of Cambridge (UK): “New route to evolution – how DNA from our mitochondria gets into our genomes” 

    U Cambridge bloc

    From The University of Cambridge (UK)

    10.5.22
    Craig Brierley

    1
    Mitochondria surrounded by cytoplasm. Credit: Dr David Furness.

    Scientists have shown that in one in every 4,000 births, some of the genetic code from our mitochondria – the ‘batteries’ that power our cells – inserts itself into our DNA, revealing a surprising new insight into how humans evolve.

    In a study published today in Nature [below], researchers at the University of Cambridge and Queen Mary University of London show that mitochondrial DNA also appears in some cancer DNA suggesting that it acts as a sticking plaster to try and repair damage to our genetic code.

    Mitochondria are tiny ‘organelles’ that sit within our cells, where they act like batteries, providing energy in the form of the molecule ATP to power the cells. Each mitochondrion has its own DNA – mitochondrial DNA – that is distinct to the rest of the human genome which is comprised of nuclear DNA.

    Mitochondrial DNA is passed down the maternal line – that is, we inherit it from our mothers, not our fathers. However, a study published in PNAS [below] in 2018 from researchers at the Cincinnati Children’s Hospital Medical Center in the USA reported evidence that suggested some mitochondrial DNA had been passed down the paternal line.

    To investigate these claims, the Cambridge team looked at the DNA from over 11,000 families recruited to Genomics England’s 100,000 Genomes Project, searching for patterns that looked like paternal inheritance. The Cambridge team found mitochondrial DNA ‘inserts’ in the nuclear DNA of some children that were not present in that of their parents. This meant that the US team had probably reached the wrong conclusions: what they had observed were not paternally-inherited mitochondrial DNA, but rather these inserts.

    Now, extending this work to over 66,000 people, the team showed that the new inserts are actually happening all the time, showing a new way our genome evolves.

    Professor Patrick Chinnery, from the Medical Research Council Mitochondrial Biology Unit and Department of Clinical Neurosciences at the University of Cambridge, explained: “Billions of years ago, a primitive animal cell took in a bacterium that became what we now call mitochondria. These supply energy to the cell to allow it to function normally, while removing oxygen, which is toxic at high levels. Over time, bits of these primitive mitochondria have passed into the cell nucleus, allowing their genomes to talk to each other.

    “This was all thought to have happened a very long time ago, mostly before we had even formed as a species, but what we’ve discovered is that that’s not true. We can see this happening right now, with bits of our mitochondrial genetic code transferring into the nuclear genome in a measurable way.”

    The team estimate that mitochondrial DNA transfers to nuclear DNA in around one in every 4,000 births. If that individual has children of their own, they will pass these inserts on – the team found that most of us carry five of the new inserts, and one in seven of us (14%) carry very recent ones. Once in place, the inserts can occasionally lead to very rare diseases, including a rare genetic form of cancer.

    It is not clear exactly how the mitochondrial DNA inserts itself – whether it does so directly or via an intermediary, such as RNA – but Professor Chinnery says it is likely to occur within the mother’s egg cells.

    When the team looked at sequences taken from 12,500 tumour samples, they found that mitochondrial DNA was even more common in tumour DNA, arising in around one in 1,000 cancers, and in some cases, the mitochondrial DNA inserts actually causes the cancer.

    “Our nuclear genetic code is breaking and being repaired all the time,” said Professor Chinnery. “Mitochondrial DNA appears to act almost like a Band-Aid, a sticking plaster to help the nuclear genetic code repair itself. And sometimes this works, but on rare occasions if might make things worse or even trigger the development of tumours.”

    More than half (58%) of the insertions were in regions of the genome that code for proteins. In the majority of cases, the body recognizes the invading mitochondrial DNA and silences it in a process known as methylation, whereby a molecule attaches itself to the insert and switches it off. A similar process occurs when viruses manage to insert themselves into our DNA. However, this method of silencing is not perfect, as some of the mitochondrial DNA inserts go on to be copied and move around the nucleus itself.

    The team looked for evidence that the reverse might happen – that mitochondrial DNA absorbs parts of our nuclear DNA – but found none. There are likely to be several reasons why this should be the case.

    Firstly, cells only have two copies of nuclear DNA, but thousands of copies of mitochondrial DNA, so the chances of mitochondrial DNA being broken and passing into the nucleus are much greater than the other way around.

    Secondly, the DNA in mitochondria is packaged inside two membranes and there are no holes in the membrane, so it would be difficult for nuclear DNA to get in. By contrast, if mitochondrial DNA manages to get out, holes in the membrane surrounding nuclear DNA would allow it pass through with relative ease.

    Professor Sir Mark Caulfield, Vice Principal for Health at Queen Mary University of London, said: “I am so delighted that the 100,000 Genomes Project has unlocked the dynamic interplay between mitochondrial DNA and our genome in the cell’s nucleus. This defines a new role in DNA repair, but also one that could occasionally trigger rare disease, or even malignancy.”

    The research was mainly funded by the Medical Research Council, Wellcome, and the National Institute for Health Research.

    Science papers:
    Nature
    PNAS 2018
    See the science papers for instructive material.

    See the full article here .

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    Please help promote STEM in your local schools.

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    U Cambridge Campus

    The University of Cambridge (UK) [legally The Chancellor, Masters, and Scholars of the University of Cambridge] is a collegiate public research university in Cambridge, England. Founded in 1209 Cambridge is the second-oldest university in the English-speaking world and the world’s fourth-oldest surviving university. It grew out of an association of scholars who left the University of Oxford (UK) after a dispute with townsfolk. The two ancient universities share many common features and are often jointly referred to as “Oxbridge”.

    Cambridge is formed from a variety of institutions which include 31 semi-autonomous constituent colleges and over 150 academic departments, faculties and other institutions organized into six schools. All the colleges are self-governing institutions within the university, each controlling its own membership and with its own internal structure and activities. All students are members of a college. Cambridge does not have a main campus and its colleges and central facilities are scattered throughout the city. Undergraduate teaching at Cambridge is organized around weekly small-group supervisions in the colleges – a feature unique to the Oxbridge system. These are complemented by classes, lectures, seminars, laboratory work and occasionally further supervisions provided by the central university faculties and departments. Postgraduate teaching is provided predominantly centrally.

    Cambridge University Press a department of the university is the oldest university press in the world and currently the second largest university press in the world. Cambridge Assessment also a department of the university is one of the world’s leading examining bodies and provides assessment to over eight million learners globally every year. The university also operates eight cultural and scientific museums, including the Fitzwilliam Museum, as well as a botanic garden. Cambridge’s libraries – of which there are 116 – hold a total of around 16 million books, around nine million of which are in Cambridge University Library, a legal deposit library. The university is home to – but independent of – the Cambridge Union – the world’s oldest debating society. The university is closely linked to the development of the high-tech business cluster known as “Silicon Fe”. It is the central member of Cambridge University Health Partners, an academic health science centre based around the Cambridge Biomedical Campus.

    By both endowment size and consolidated assets Cambridge is the wealthiest university in the United Kingdom. In the fiscal year ending 31 July 2019, the central university – excluding colleges – had a total income of £2.192 billion of which £592.4 million was from research grants and contracts. At the end of the same financial year the central university and colleges together possessed a combined endowment of over £7.1 billion and overall consolidated net assets (excluding “immaterial” historical assets) of over £12.5 billion. It is a member of numerous associations and forms part of the ‘golden triangle’ of English universities.

    Cambridge has educated many notable alumni including eminent mathematicians; scientists; politicians; lawyers; philosophers; writers; actors; monarchs and other heads of state. As of October 2020, 121 Nobel laureates; 11 Fields Medalists; 7 Turing Award winners; and 14 British prime ministers have been affiliated with Cambridge as students; alumni; faculty or research staff. University alumni have won 194 Olympic medals.

    History

    By the late 12th century, the Cambridge area already had a scholarly and ecclesiastical reputation due to monks from the nearby bishopric church of Ely. However, it was an incident at Oxford which is most likely to have led to the establishment of the university: three Oxford scholars were hanged by the town authorities for the death of a woman without consulting the ecclesiastical authorities who would normally take precedence (and pardon the scholars) in such a case; but were at that time in conflict with King John. Fearing more violence from the townsfolk scholars from the University of Oxford started to move away to cities such as Paris; Reading; and Cambridge. Subsequently enough scholars remained in Cambridge to form the nucleus of a new university when it had become safe enough for academia to resume at Oxford. In order to claim precedence, it is common for Cambridge to trace its founding to the 1231 charter from Henry III granting it the right to discipline its own members (ius non-trahi extra) and an exemption from some taxes; Oxford was not granted similar rights until 1248.

    A bull in 1233 from Pope Gregory IX gave graduates from Cambridge the right to teach “everywhere in Christendom”. After Cambridge was described as a studium generale in a letter from Pope Nicholas IV in 1290 and confirmed as such in a bull by Pope John XXII in 1318 it became common for researchers from other European medieval universities to visit Cambridge to study or to give lecture courses.

    Foundation of the colleges

    The colleges at the University of Cambridge were originally an incidental feature of the system. No college is as old as the university itself. The colleges were endowed fellowships of scholars. There were also institutions without endowments called hostels. The hostels were gradually absorbed by the colleges over the centuries; but they have left some traces, such as the name of Garret Hostel Lane.

    Hugh Balsham, Bishop of Ely, founded Peterhouse – Cambridge’s first college in 1284. Many colleges were founded during the 14th and 15th centuries but colleges continued to be established until modern times. There was a gap of 204 years between the founding of Sidney Sussex in 1596 and that of Downing in 1800. The most recently established college is Robinson built in the late 1970s. However, Homerton College only achieved full university college status in March 2010 making it the newest full college (it was previously an “Approved Society” affiliated with the university).

    In medieval times many colleges were founded so that their members would pray for the souls of the founders and were often associated with chapels or abbeys. The colleges’ focus changed in 1536 with the Dissolution of the Monasteries. Henry VIII ordered the university to disband its Faculty of Canon Law and to stop teaching “scholastic philosophy”. In response, colleges changed their curricula away from canon law and towards the classics; the Bible; and mathematics.

    Nearly a century later the university was at the centre of a Protestant schism. Many nobles, intellectuals and even commoners saw the ways of the Church of England as too similar to the Catholic Church and felt that it was used by the Crown to usurp the rightful powers of the counties. East Anglia was the centre of what became the Puritan movement. In Cambridge the movement was particularly strong at Emmanuel; St Catharine’s Hall; Sidney Sussex; and Christ’s College. They produced many “non-conformist” graduates who, greatly influenced by social position or preaching left for New England and especially the Massachusetts Bay Colony during the Great Migration decade of the 1630s. Oliver Cromwell, Parliamentary commander during the English Civil War and head of the English Commonwealth (1649–1660), attended Sidney Sussex.

    Modern period

    After the Cambridge University Act formalized the organizational structure of the university the study of many new subjects was introduced e.g. theology, history and modern languages. Resources necessary for new courses in the arts architecture and archaeology were donated by Viscount Fitzwilliam of Trinity College who also founded the Fitzwilliam Museum. In 1847 Prince Albert was elected Chancellor of the University of Cambridge after a close contest with the Earl of Powis. Albert used his position as Chancellor to campaign successfully for reformed and more modern university curricula, expanding the subjects taught beyond the traditional mathematics and classics to include modern history and the natural sciences. Between 1896 and 1902 Downing College sold part of its land to build the Downing Site with new scientific laboratories for anatomy, genetics, and Earth sciences. During the same period the New Museums Site was erected including the Cavendish Laboratory which has since moved to the West Cambridge Site and other departments for chemistry and medicine.

    The University of Cambridge began to award PhD degrees in the first third of the 20th century. The first Cambridge PhD in mathematics was awarded in 1924.

    In the First World War 13,878 members of the university served and 2,470 were killed. Teaching and the fees it earned came almost to a stop and severe financial difficulties followed. As a consequence, the university first received systematic state support in 1919 and a Royal Commission appointed in 1920 recommended that the university (but not the colleges) should receive an annual grant. Following the Second World War the university saw a rapid expansion of student numbers and available places; this was partly due to the success and popularity gained by many Cambridge scientists.

     
  • richardmitnick 10:52 am on August 21, 2022 Permalink | Reply
    Tags: "See How Scientists Put Together the Complete Human Genome?", , , , , For the first time researchers have sequenced all 3117275501 bases of our genetic code., Genomics,   

    From “Scientific American” : “See How Scientists Put Together the Complete Human Genome” 

    From “Scientific American”

    8.1.22
    Clara Moskowitz
    Martin Krzywinski

    For the first time researchers have sequenced all 3117275501 bases of our genetic code.

    1
    Credit: Martin Krzywinski.

    The human genome is at last complete. Researchers have been working for decades toward this goal, and the Human Genome Project claimed victory in 2001, when it had read almost all of a person’s DNA. But the stubborn remaining 8 percent of the genome took another two decades to decipher. These final sections were highly repetitive and highly variable among individuals, making them the hardest parts to sequence. Yet they revealed hundreds of new genes, including genes involved in immune responses and those responsible for humans developing larger brains than our primate ancestors. “Now that we have one complete reference, we can understand human variation and how we changed with respect to our closest related species on the planet,” says geneticist Evan Eichler of the University of Washington, one of the co-chairs of the Telomere-to-Telomere consortium at The National Human Genome Research Institute that finished the genome.


    Credit: Martin Krzywinski; Sources: The University of California-Santa Cruz Genome Browser; “The Complete Sequence of a Human Genome,” by Sergey Nurk et al., in Science April 2022.

    See the full article here .


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    Please help promote STEM in your local schools.

    Stem Education Coalition

    Scientific American, the oldest continuously published magazine in the U.S., has been bringing its readers unique insights about developments in science and technology for more than 160 years.

     
  • richardmitnick 6:56 am on July 6, 2022 Permalink | Reply
    Tags: "Making CRISPR hype more of a reality", , , , , Genomics, ,   

    From The Swiss Federal Institute of Technology in Zürich [ETH Zürich] [Eidgenössische Technische Hochschule Zürich] (CH): “Making CRISPR hype more of a reality” 

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

    7.6.22
    Dr. Eric Aird

    This year we celebrate 10 years of genome editing with CRISPR.

    1
    Scientific American/ Credit: Getty Images

    The system is often referred to as molecular scissors, and this designation is quite accurate for its first applications. These short 10 years were marked by stunningly swift development and a great promise to cure thousands of genetic diseases with relative ease – with a single treatment dose that specifically corrects disease-​causing DNA mutations in the body’s cells. Sickle cell anemia and muscular dystrophy are two such diseases. And indeed, a decade later, we are now delivering on that promise in the form of many therapies currently being tested in human clinical trials.

    Parallel to the development of the first such therapies, scientists have further evolved genome editing technologies. Recently developed molecular CRISPR tools have little in common with molecular scissors and are poised to make medical applications even safer.

    Let’s take a brief look back: “first generation” CRISPR genetic scissors dock at specific sites in the genome and cut the DNA molecule. The cell generates short, arbitrary mutations at the break site to, for example, disrupt gene function. However, unintended genetic alterations to the cell are possible, and the scope of diseases treatable with this methodology are relatively small. An ill-​intended cut in the genome might manifest itself as a trigger for cancer decades later. Additionally, these scissors cause DNA damage, and such damage is inherently toxic and potentially lethal for cells. Stem cells, a primary target for clinical uses of CRISPR, react particularly sensitively to DNA damage.

    A broad application of this first generation of CRISPR in humans is therefore not entirely risk-​free. This is also a major reason why scientists have developed molecular tools to generate genomic modifications without using scissors.

    In the past few years, researchers across the globe have developed a host of such “next generation” CRISPR technologies. A more appropriate analogy for these innovative systems would that be of a molecular taxi. Such platforms can be used to shuttle, for example, specialized proteins to specific destinations in the genome. These proteins can directly change the DNA code without the same deleterious consequences caused by scissors.

    Reduced toxicity

    Not only does this approach reduce toxicity for cells, but it also vastly expands the range of treatable genetic diseases. Instead of simply cutting a gene to render it non-​functional, these CRISPR genome editors1 can be used to correct individual genetic mutations to restore gene function. It is estimated that more than 100,000 DNA mutations in our genome cause disease, a vast majority of which could be treated with such new technologies.

    Next generation genome editing systems are expected to be used in human trials for the first time later this year. An American biotech company recently received approval to begin human trials to cure sickle cell disease and beta-​thalassemia.2 Treatments for high cholesterol and a form of blindness are also on the verge of moving into humans as well, not to mention the plethora of projects to treat a range of genetic disorders that are currently being tested in animals and could one day benefit humans. In all cases, these diseases can be cured by reverting the mutated genetic code back to the “normal” sequence, reversions which were not possible with the traditional CRISPR scissor-​based approach.

    One-​time therapy

    CRISPR-​based technologies have an enormous upside. Today, patients suffering from hemophilia need multiple infusions per week. A CRISPR treatment, on the other hand, would ideally take place once, and the cells modified with CRISPR would persist for the rest of the patient’s life.

    This also means, however, that once the treatment has been started, it can no longer be discontinued. But would you choose a treatment where you can never stop taking the drug? This question arises with CRISPR-​based therapies.

    Safety concerns about unintended editing have mostly, but not entirely, been alleviated with next generation CRISPR molecular taxis. It must be stressed that the first generation treatments currently being clinically tested have underwent extensive studies to determine and limit detrimental effects. Nevertheless, the safety of CRISPR-​based systems must be kept in mind. It is important that the long-​term safety profiles of CRISPR technologies are established, and therefore I expect the first CRISPR-​treated patients will be monitored for life.

    A cure for previously incurable diseases

    Given all the safety considerations, one must also consider the therapeutic alternatives. Take progeria for example, a genetic disease in which children rapidly age and medication only exists to marginally extend lifespan. A next generation CRISPR technology currently under development has the potential to revolutionize progeria therapy: it doubled the lifespan in mouse models. For a fatal disease like progeria, for which there is no or inadequate therapy, many patients are likely to opt for a CRISPR treatment, even if there is some residual risk of potentially negative outcomes in the long term.

    The speed at which CRISPR technologies have advanced over the past decade has been tremendous. Regulatory agencies, which are required to assess the safety of these technologies, have sometimes failed to keep up with this pace. Urgently needed guidelines for the approval of the new technologies are not yet mature. This must change. There is a great need for action on the part of the regulatory authorities.

    The first decade of CRISPR has brought immense potential, rapid technological development, and the first patients treated. As we look to the next 10 years, both first and next generation CRISPR systems are poised to deliver on its potential and provide life-​long cures to patients of both rare and more common genetic disorders.

    See the full article here .

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    Please help promote STEM in your local schools.

    Stem Education Coalition

    ETH Zurich campus

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

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

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

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

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

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

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

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

    Reputation and ranking

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

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

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

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

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

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

     
  • richardmitnick 11:56 am on July 1, 2022 Permalink | Reply
    Tags: "The beauty and benefits of biodiversity", Adaptability lies at the very heart of speciation., , As well as working with living organisms the researchers also study the genetic material of specimens held in collections., , , , , , , , , Genomics, One of the most beautiful aspects of biodiversity is how species co-​evolve and exist together., , Species diversity is only one aspect of biodiversity-the others being habitat diversity and genetic diversity., Species diversity makes ecosystems resilient., The beauty of the world’s coral reefs never fails to amaze., , Time is of the essence because biodiversity is under threat and declining rapidly., Unfertilized minimally cultivated meadows and dry grasslands are incredibly diverse which makes them not just beautiful but essential., Using the eDNA method it took the researchers less than two years to confirm the presence of more fish species and families than experts had managed to identify during 13 years of reef dives.   

    From The Swiss Federal Institute of Technology in Zürich [ETH Zürich] [Eidgenössische Technische Hochschule Zürich] (CH): “The beauty and benefits of biodiversity” 

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

    01.07.2022
    Peter Rüegg

    1

    Biodiversity is beautiful, but it’s also vitally important. ETH researchers are getting to the heart of how species diversity and genetic diversity evolve – and why we must fight to preserve them.

    Spring is synonymous with bright yellow dandelions, lush green fields and cloudless blue skies, a captivating combination of colours that sends many people into raptures of delight. Yet biodiversity researchers such as Alex Widmer, Professor of Plant Ecological Genetics in the Department of Environmental Systems Science, take a rather different view: “I know too much about ecosystems to take any pleasure in something so monotonous,” he says. His notion of beauty tends more towards dry grasslands and natural meadows rich in different species. “A far cry,” he says, “from the picture-​postcard idyll.” He argues that such areas are beautiful in much less obvious ways. Unfertilized, minimally cultivated meadows and dry grasslands are incredibly diverse, he says, which makes them not just beautiful, but essential.

    “Species diversity makes ecosystems resilient,” says Widmer, “and at the core of that resilience is genetic diversity.” Without genetic diversity, he explains, species and organisms cannot adapt to existing and evolving environmental conditions. And it’s this adaptability that lies at the very heart of speciation.

    2
    Natural meadows exhibit high levels of diversity. (Photograph: Peter Rüegg)

    Loïc Pellissier, Professor of Ecosystems and Landscape Evolution in the Department of Environmental Systems Science, agrees that much of the beauty of biodiversity is hidden from view. One of the most beautiful aspects of biodiversity, he says, is how species co-​evolve and exist together. “All organisms have evolved to interact with each other, as anyone who works in species diversity will tell you. To me, ecosystems are like huge jigsaw puzzles, in which all the pieces fit together more or less perfectly.” His research focuses on how species diversity arises and evolves. Because this occurs over the course of millions of years, Pellissier relies on computer models to simulate geological processes and the evolutionary forces that lead to the formation of new species.

    Genetic diversity

    Pellissier also conducts numerous field projects to unlock the secrets of species diversity. He favours a new and increasingly popular method that enables ecologists to detect species and organisms from the DNA they leave behind in the environment – known for short as environmental DNA, or eDNA. Researchers simply collect water and soil samples and analyse them to see what genetic material they contain. They then match whatever DNA they find to the corresponding organisms, provided a reference is available for this. This method provides a relatively quick way to determine whether a species is present in an ecosystem or not – and it works for a wide variety of organisms. “eDNA gives us a new insight into an ecosystem’s diversity,” he says.

    Recently, Pellissier co-​authored a study on the diversity of reef fish worldwide. Researchers collected over 200 seawater samples from various tropical coral reefs and then “fished out” whatever fish DNA they could find. Using the eDNA method it took the researchers less than two years to confirm the presence of more fish species and families than experts had managed to identify during 13 years of reef dives.

    Yet species diversity is only one aspect of biodiversity, the others being habitat diversity and genetic diversity. “Of the three, genetic diversity is the one that has been most neglected,” says Widmer. “Studying and monitoring genetic diversity is much more difficult and time-​consuming than monitoring habitats or species numbers.” Hence the numerous inventories of Swiss plants, animals and habitats – from forests and wetlands to dry grasslands. “Yet there isn’t a single monitoring project in Switzerland that focuses on the genetic diversity of living things,” says Widmer, “This is despite the fact that genetic diversity is fundamental for species diversity and adaptability.”

    To fill this gap, Widmer has joined forces with the Swiss Federal Institute for Forest, Snow and Landscape Research WSL on a project that aims to add this crucial element to Switzerland’s existing biodiversity monitoring systems. With the support of the Swiss Federal Office for the Environment (FOEN), Widmer and his colleagues have already launched a pilot study of five different species, including two plant species, a butterfly and a toad. The fifth species in their study is the yellowhammer, a songbird commonly found in cultivated areas of Switzerland. The researchers have already sequenced the genomes of one hundred individual yellowhammers from right across the country.

    4
    The beauty of the world’s coral reefs never fails to amaze. Yet behind such splendour, there lies much more – namely, a diverse habitat for a host of marine life. (Photograph: Stocksy)

    As well as working with living organisms, the researchers also study the genetic material of specimens held in collections. “This tells us whether populations from over 100 years ago were as diverse as today’s, or whether some of that genetic diversity has been lost,” says Widmer. Research into biodiversity in Switzerland has already revealed a sharp decline in species diversity, he notes: “We’d like to find out whether the same applies to genetic diversity.” Once the pilot study is complete, Widmer’s goal is to set up a large-​scale monitoring project encompassing up to 50 species. These would be examined at regular intervals to detect changes in their genetic diversity. However, it is still unclear whether this complex and ambitious project will receive the necessary funding.

    Fragile and endangered beauty

    Time is of the essence because biodiversity is under threat and declining rapidly. It is only by firmly fitting together the many different pieces of the biodiversity puzzle that we can slow the extinction of individual species. Reduce this network by half, and species will die out a thousand times faster – and when external pressures such as climate change are factored in, species extinction will occur a thousand times faster again.

    “Biodiversity is essential to our lives,” says Widmer. “It impacts everything from our mental well-​being to whether we have food on the table.” Diverse ecosystems are much more stable and better geared for the future than monotonous, species-​poor habitats. Pellissier nods in agreement: “Biodiversity is like classical art in the sense that it can’t be replaced. If the earth loses its biological riches, it will lose its magic.”

    See the full article here .

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

    Please help promote STEM in your local schools.

    Stem Education Coalition

    ETH Zurich campus

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

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

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

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

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

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

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

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

    Reputation and ranking

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

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

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

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

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

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

     
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