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  • richardmitnick 9:15 am on October 4, 2021 Permalink | Reply
    Tags: "David Julius ’77 shares the Nobel Prize in physiology or medicine", 2021 Nobel Prize in Physiology or Medicine, , , DNA, ,   

    From The Massachusetts Institute of Technology (US) : “David Julius ’77 shares the Nobel Prize in physiology or medicine” 

    MIT News

    From The Massachusetts Institute of Technology (US)

    October 4, 2021
    Anne Trafton

    1
    David Julius, a 1977 graduate of MIT, will share the 2021 Nobel Prize in physiology or medicine
    Credit: Steve Babuljak, UCSF

    David Julius ’77 will share the 2021 Nobel Prize in Physiology or Medicine, the Royal Swedish Academy of Sciences announced this morning in Stockholm.

    Julius, a professor at The University of California-San Francisco (US), shares the prize with Ardem Patapoutian, a professor at The Scripps Research Institute (US), for their discoveries in how the body senses touch and temperature.

    Both scientists helped to answer a fundamental question regarding how the nervous system interprets our environment: How are temperature and mechanical stimuli converted into electrical impulses in the nervous system?

    Using capsaicin, a compound that gives chili peppers their distinctive burning sensation, Julius was able to identify a receptor in the nerve endings of skin that responds to heat. His experiments revealed that this receptor, which he called TRPV1, is an ion channel that is activated by painful heat.

    “David Julius’ discovery of TRPV1 was the breakthrough that allowed us to understand how differences in temperature can induce electrical signals in the nervous system,” according to today’s announcement by the Nobel committee.

    Later, Julius and Patapoutian independently discovered a receptor called TRPM8, which responds to cold. Patapoutian was also honored for his discovery of receptors that respond to mechanical force in the skin and other organs. Their work on how the body senses temperature and mechanical stimuli is now being harnessed to develop treatments for a variety of diseases, including chronic pain.

    Julius, who was born in New York, earned his bachelor’s degree in biology from MIT in 1977. He received a PhD in 1984 from University of California at Berkeley and was a postdoc at Columbia University before joining the faculty of the University of California at San Francisco in 1989.

    He is the 39th MIT graduate to win a Nobel Prize.

    See the full article here .


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

    Stem Education Coalition

    MIT Seal

    USPS “Forever” postage stamps celebrating Innovation at MIT.

    MIT Campus

    The Massachusetts Institute of Technology (US) 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 (US), the MIT Bates Research and Engineering Center (US), and the Haystack Observatory (US), as well as affiliated laboratories such as the Broad Institute of MIT and Harvard(US) and Whitehead Institute (US).

    Founded in 1861 in response to the increasing industrialization of the United States, Massachusetts Institute of Technology (US) 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 (US) . The university also has a strong entrepreneurial culture and MIT alumni have founded or co-founded many notable companies. Massachusetts Institute of Technology (US) 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 (US), 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 Massachusetts Institute of Technology (US) 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 (US)). In 1866, the proceeds from land sales went toward new buildings in the Back Bay.

    Massachusetts Institute of Technology (US) 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 (US) faculty and alumni rebuffed Harvard University (US) 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 (US) 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 (US) 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 (US)in 1934.

    Still, as late as 1949, the Lewis Committee lamented in its report on the state of education at Massachusetts Institute of Technology (US) 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.

    Massachusetts Institute of Technology (US)‘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 (US)’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, Massachusetts Institute of Technology (US) 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 Massachusetts Institute of Technology (US) 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 Massachusetts Institute of Technology (US) 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, Massachusetts Institute of Technology (US) 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 Massachusetts Institute of Technology (US)’s defense research. In this period Massachusetts Institute of Technology (US)’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. Massachusetts Institute of Technology (US) ultimately divested itself from the Instrumentation Laboratory and moved all classified research off-campus to the MIT (US) 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 (US) 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 Massachusetts Institute of Technology (US) over its involvement in SDI (space weaponry) and CBW (chemical and biological warfare) research. More recently, Massachusetts Institute of Technology (US)’s research for the military has included work on robots, drones and ‘battle suits’.

    Recent history

    Massachusetts Institute of Technology (US) 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 (US) 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.

    Massachusetts Institute of Technology (US) 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, Massachusetts Institute of Technology (US) 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, Massachusetts Institute of Technology (US) 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 (US) faculty adopted an open-access policy to make its scholarship publicly accessible online.

    Massachusetts Institute of Technology (US) 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 (US) community with thousands of police officers from the New England region and Canada. On November 25, 2013, Massachusetts Institute of Technology (US) 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 (US) 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 (US) was designed and constructed by a team of scientists from California Institute of Technology (US), Massachusetts Institute of Technology (US), and industrial contractors, and funded by the National Science Foundation (US) .

    MIT/Caltech 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 (US) physicist Rainer Weiss won the Nobel Prize in physics in 2017. Weiss, who is also an Massachusetts Institute of Technology (US) graduate, designed the laser interferometric technique, which served as the essential blueprint for the LIGO.

    The mission of Massachusetts Institute of Technology (US) 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 11:24 am on September 16, 2021 Permalink | Reply
    Tags: "New programmable gene editing proteins found outside of CRISPR systems", , , , , DNA, IscB; IsrB; and TnpB are found in mobile genetic elements called transposons., IscBs and TnpBs appear to be predecessors of Cas9 and Cas12 CRISPR systems., , Programmable DNA modifying systems called OMEGAs (Obligate Mobile Element Guided Activity), Programmable enzymes-particularly those that use an RNA guide-can be rapidly adapted for different uses., , The first hints that OMEGA proteins might be directed by RNA came from the genes for proteins called IscBs., Two other classes of small proteins known as IsrBs and TnpBs-one of the most abundant genes in bacteria-also use ωRNAs that act as guides to direct the cleavage of DNA.   

    From Massachusetts Institute of Technology (US) : “New programmable gene editing proteins found outside of CRISPR systems” 

    MIT News

    From Massachusetts Institute of Technology (US)

    September 15, 2021
    Jennifer Michalowski | McGovern Institute for Brain Research

    1
    Soumya Kannan is a 2021-22 Yang-Tan Center for Molecular Therapeutics Graduate Student Fellow in the lab of MIT Professor Feng Zhang and co-first author with Han Altae-Tran of a study reporting a new class of programmable DNA modifying systems known as OMEGAs. Credit: Caitlin Cunningham.

    Within the last decade, scientists have adapted CRISPR systems from microbes into gene editing technology, a precise and programmable system for modifying DNA. Now, scientists at MIT’s McGovern Institute for Brain Research and the Broad Institute of MIT and Harvard have discovered a new class of programmable DNA modifying systems called OMEGAs (Obligate Mobile Element Guided Activity), which may naturally be involved in shuffling small bits of DNA throughout bacterial genomes.

    These ancient DNA-cutting enzymes are guided to their targets by small pieces of RNA. While they originated in bacteria, they have now been engineered to work in human cells, suggesting they could be useful in the development of gene editing therapies, particularly as they are small (about 30 percent of the size of Cas9), making them easier to deliver to cells than bulkier enzymes. The discovery, reported Sept. 9 in the journal Science, provides evidence that natural RNA-guided enzymes are among the most abundant proteins on Earth, pointing toward a vast new area of biology that is poised to drive the next revolution in genome editing technology.

    The research was led by McGovern Investigator Feng Zhang, who is the James and Patricia Poitras Professor of Neuroscience at MIT, a Howard Hughes Medical Institute (US) investigator, and a Core Institute Member of the Broad Institute. Zhang’s team has been exploring natural diversity in search of new molecular systems that can be rationally programmed.

    “We are super excited about the discovery of these widespread programmable enzymes, which have been hiding under our noses all along,” says Zhang. “These results suggest the tantalizing possibility that there are many more programmable systems that await discovery and development as useful technologies.”

    Natural adaptation

    Programmable enzymes-particularly those that use an RNA guide-can be rapidly adapted for different uses. For example, CRISPR enzymes naturally use an RNA guide to target viral invaders, but biologists can direct Cas9 to any target by generating their own RNA guide. “It’s so easy to just change a guide sequence and set a new target,” says Soumya Kannan, MIT graduate student in biological engineering and co-first author of the paper. “So one of the broad questions that we’re interested in is trying to see if other natural systems use that same kind of mechanism.”

    The first hints that OMEGA proteins might be directed by RNA came from the genes for proteins called IscBs. The IscBs are not involved in CRISPR immunity and were not known to associate with RNA, but they looked like small, DNA-cutting enzymes. The team discovered that each IscB had a small RNA encoded nearby and it directed IscB enzymes to cut specific DNA sequences. They named these RNAs “ωRNAs.”

    The team’s experiments showed that two other classes of small proteins known as IsrBs and TnpBs-one of the most abundant genes in bacteria-also use ωRNAs that act as guides to direct the cleavage of DNA.

    IscB; IsrB; and TnpB are found in mobile genetic elements called transposons. Han Altae-Tran, MIT graduate student in biological engineering and co-first author on the paper, explains that each time these transposons move, they create a new guide RNA, allowing the enzyme they encode to cut somewhere else.

    It’s not clear how bacteria benefit from this genomic shuffling — or whether they do at all. Transposons are often thought of as selfish bits of DNA, concerned only with their own mobility and preservation, Kannan says. But if hosts can “co-opt” these systems and repurpose them, hosts may gain new abilities, as with CRISPR systems that confer adaptive immunity.

    IscBs and TnpBs appear to be predecessors of Cas9 and Cas12 CRISPR systems. The team suspects they, along with IsrB, likely gave rise to other RNA-guided enzymes, too — and they are eager to find them. They are curious about the range of functions that might be carried out in nature by RNA-guided enzymes, Kannan says, and suspect evolution likely already took advantage of OMEGA enzymes like IscBs and TnpBs to solve problems that biologists are keen to tackle.

    “A lot of the things that we have been thinking about may already exist naturally in some capacity,” says Altae-Tran. “Natural versions of these types of systems might be a good starting point to adapt for that particular task.”

    The team is also interested in tracing the evolution of RNA-guided systems further into the past. “Finding all these new systems sheds light on how RNA-guided systems have evolved, but we don’t know where RNA-guided activity itself comes from,” Altae-Tran says. Understanding those origins, he says, could pave the way to developing even more classes of programmable tools.

    This work was made possible with support from the Simons Center for the Social Brain at MIT, the National Institutes of Health and its Intramural Research Program, Howard Hughes Medical Institute, Open Philanthropy, G. Harold and Leila Y. Mathers Charitable Foundation, Edward Mallinckrodt, Jr. Foundation, Poitras Center for Psychiatric Disorders Research at MIT, Hock E. Tan and K. Lisa Yang Center for Autism Research at MIT, Yang-Tan Center for Molecular Therapeutics at MIT, Lisa Yang, Phillips family, R. Metcalfe, and J. and P. Poitras.

    See the full article here .


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

    Stem Education Coalition

    MIT Seal

    USPS “Forever” postage stamps celebrating Innovation at MIT.

    MIT Campus

    Massachusetts Institute of Technology (US) 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 (US), the MIT Bates Research and Engineering Center (US), and the Haystack Observatory (US), as well as affiliated laboratories such as the Broad Institute of MIT and Harvard(US) and Whitehead Institute (US).

    Founded in 1861 in response to the increasing industrialization of the United States, Massachusetts Institute of Technology (US) 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 Massachusetts Institute of Technology (US) . The university also has a strong entrepreneurial culture and MIT alumni have founded or co-founded many notable companies. Massachusetts Institute of Technology (US) 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 (US), 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 Massachusetts Institute of Technology (US) 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 (US)). In 1866, the proceeds from land sales went toward new buildings in the Back Bay.

    Massachusetts Institute of Technology (US) 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 (US) faculty and alumni rebuffed Harvard University (US) 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 (US) 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 (US) 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 (US)in 1934.

    Still, as late as 1949, the Lewis Committee lamented in its report on the state of education at Massachusetts Institute of Technology (US) 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.

    Massachusetts Institute of Technology (US)‘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 (US)’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, Massachusetts Institute of Technology (US) 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 Massachusetts Institute of Technology (US) 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 Massachusetts Institute of Technology (US) 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, Massachusetts Institute of Technology (US) 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 Massachusetts Institute of Technology (US)’s defense research. In this period Massachusetts Institute of Technology (US)’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. Massachusetts Institute of Technology (US) ultimately divested itself from the Instrumentation Laboratory and moved all classified research off-campus to the MIT (US) 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 (US) 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 Massachusetts Institute of Technology (US) over its involvement in SDI (space weaponry) and CBW (chemical and biological warfare) research. More recently, Massachusetts Institute of Technology (US)’s research for the military has included work on robots, drones and ‘battle suits’.

    Recent history

    Massachusetts Institute of Technology (US) 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 (US) 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.

    Massachusetts Institute of Technology (US) 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, Massachusetts Institute of Technology (US) 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, Massachusetts Institute of Technology (US) 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 (US) faculty adopted an open-access policy to make its scholarship publicly accessible online.

    Massachusetts Institute of Technology (US) 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 (US) community with thousands of police officers from the New England region and Canada. On November 25, 2013, Massachusetts Institute of Technology (US) 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 (US) 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 (US) was designed and constructed by a team of scientists from California Institute of Technology (US), Massachusetts Institute of Technology (US), and industrial contractors, and funded by the National Science Foundation (US) .

    MIT/Caltech 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 (US) physicist Rainer Weiss won the Nobel Prize in physics in 2017. Weiss, who is also an Massachusetts Institute of Technology (US) graduate, designed the laser interferometric technique, which served as the essential blueprint for the LIGO.

    The mission of Massachusetts Institute of Technology (US) 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 (US) community the ability and passion to work wisely, creatively, and effectively for the betterment of humankind.

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

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

    From MIT Technology Review (US)

    August 24, 2021
    Leigh Buchanan

    1
    Credit: Sasha Israel.

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

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

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

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

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

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

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

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

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

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

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

    From East Texas to MIT

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

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

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

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

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

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

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

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

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

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

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

    Finding the production switch

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

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

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

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

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

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

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

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

    Mentoring young scientists

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

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

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

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

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

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

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

    On being Black at MIT-Bearing witness to racism

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

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

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

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

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

    See the full article here .


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    Stem Education Coalition

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

     
  • richardmitnick 2:39 pm on September 3, 2021 Permalink | Reply
    Tags: According to the “RNA world” hypothesis primordial living systems were based on self-replicating RNA molecules., , , , , DNA, , RNA is of particular interest in the context of the origin of life as a promising candidate for the first functional biopolymer.   

    From Ludwig Maximilian University of Munich [Ludwig-Maximilians-Universität München] (DE) : “The right mixture of salts to get life started” 

    From Ludwig Maximilian University of Munich [Ludwig-Maximilians-Universität München] (DE)

    26 Aug 2021

    A new study shows how a blend of salts in the presence of heat flows may have contributed to the formation of the first self-replicating biomolecules.

    1
    Basaltic glass is produced when melted basalt is rapidly cooled, e.g. when it comes into contact with ocean water. In combination with convection currents, suitable conditions for RNA folding are created. © IMAGO / ingimage.

    In modern organisms, the hereditary material DNA encodes the instructions for the synthesis of proteins – the versatile nanomachines that enable modern cells to function and replicate. But how was this functional linkage between DNA and proteins established? According to the “RNA world” hypothesis primordial living systems were based on self-replicating RNA molecules. Chemically speaking, RNA is closely related to DNA. However, in addition to storing information, RNA can fold into complex structures that have catalytic activity, similar to the protein nanomachines that catalyze chemical reactions in cells. These properties suggest that RNA molecules should be capable of catalyzing the replication of other RNA strands, and initiating self-sustaining evolutionary processes. Hence, RNA is of particular interest in the context of the origin of life as a promising candidate for the first functional biopolymer.

    In order to fold correctly, RNA requires a relatively high concentration of doubly charged magnesium ions and a minimal concentration of singly charged sodium, since the latter leads to misfolding of RNA strands. Drying alone alters the salt concentration, but not the relative amounts of the different ions. Therefore, researchers led by LMU biophysicists Dieter Braun and Christof Mast, in collaboration with colleagues at the MPG Institute of Biochemistry [MPG Institut für Biochemie](DE), the Technical University of Dortmund [Technische Universität Dortmund](DE) and LMU Geosciences, have now asked how the relevant salt balance might have been achieved under the conditions that prevailed on Earth some 4 billion years ago. “We have shown that a combination of basaltic rocks and simple convection currents can give rise to the optimal relationship between Mg and Na ions under natural conditions,” Mast explains.

    Basaltic glass und heat currents

    For this purpose, LMU geoscientists led by Donald Dingwell and Bettina Scheu first synthesized basaltic glass, and characterized the basalt in its various forms, as both rock and glass. Basaltic glass is produced when melted basalt is rapidly cooled, e.g. when it comes into contact with ocean water – a natural process that occurs continuously on the Earth. In the second step, the LMU biophysicists analyzed the amounts of magnesium and sodium that were extracted from the glass, under diverse conditions – such as temperature or the grain size of the geological material. They always found significantly more sodium than magnesium in the water, and the latter was present in much lower concentrations than those required by the prebiotic RNA nanomachines.

    “However, this situation changed considerably when heat currents – which are very likely to have been present, owing to the high levels of geological activity expected in prebiotic environments – were added,” says Mast. In the narrow pores and cracks that are a feature of basaltic glasses, temperature gradients not only induce convective flows, they also result in the net movement of ions against the direction of the current. The magnitude of this effect, which is known as thermophoresis, is strongly dependent on the size and electrical charge of the ions concerned. This combination of convection and thermophoresis eventually results in the local accumulation of magnesium ions in much higher local concentrations than sodium ions. Furthermore, the magnitude of this concentration effect increases with the size of the system involved.

    Using as a benchmark system catalytic RNA strands that were provided by Hannes Mutschler (MPG Institute for Biochemistry/ Technical University of Dortmund [Technische Universität Dortmund](DE)), the team went on to confirm that ligation of RNA strands and ribozyme self-replication and are more efficient under thermophoretic conditions. In fact, the new study shows that the presence of heat flows permits RNA activity to take place even when the medium contains a large excess (1000:1) of sodium over magnesium ions, i.e. under conditions which are assumed in some prebiotic scenarios but are otherwise incompatible with RNA-based catalytic processes.

    Science paper:
    Nature Chemistry

    See the full article here.

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

    Please help promote STEM in your local schools.

    Stem Education Coalition

    Welcome to Ludwig Maximilian University of Munich [Ludwig-Maximilians-Universität München] (DE) – the University in the heart of Munich. LMU is recognized as one of Europe’s premier academic and research institutions. Since our founding in 1472, LMU has attracted inspired scholars and talented students from all over the world, keeping the University at the nexus of ideas that challenge and change our complex world.

    Ludwig Maximilian University of Munich [Ludwig-Maximilians-Universität München] (DE) is a public research university located in Munich, Germany.

    The University of Munich is Germany’s sixth-oldest university in continuous operation. Originally established in Ingolstadt in 1472 by Duke Ludwig IX of Bavaria-Landshut, the university was moved in 1800 to Landshut by King Maximilian I of Bavaria when Ingolstadt was threatened by the French, before being relocated to its present-day location in Munich in 1826 by King Ludwig I of Bavaria. In 1802, the university was officially named Ludwig-Maximilians-Universität by King Maximilian I of Bavaria in his as well as the university’s original founder’s honour.

    The University of Munich is associated with 43 Nobel laureates (as of October 2020). Among these were Wilhelm Röntgen, Max Planck, Werner Heisenberg, Otto Hahn and Thomas Mann. Pope Benedict XVI was also a student and professor at the university. Among its notable alumni, faculty and researchers are inter alia Rudolf Peierls, Josef Mengele, Richard Strauss, Walter Benjamin, Joseph Campbell, Muhammad Iqbal, Marie Stopes, Wolfgang Pauli, Bertolt Brecht, Max Horkheimer, Karl Loewenstein, Carl Schmitt, Gustav Radbruch, Ernst Cassirer, Ernst Bloch, Konrad Adenauer. The LMU has recently been conferred the title of “University of Excellence” under the German Universities Excellence Initiative.

    LMU is currently the second-largest university in Germany in terms of student population; in the winter semester of 2018/2019, the university had a total of 51,606 matriculated students. Of these, 9,424 were freshmen while international students totalled 8,875 or approximately 17% of the student population. As for operating budget, the university records in 2018 a total of 734,9 million euros in funding without the university hospital; with the university hospital, the university has a total funding amounting to approximately 1.94 billion euros.

    Faculties

    LMU’s Institute of Systematic Botany is located at Botanischer Garten München-Nymphenburg
    Faculty of chemistry buildings at the Martinsried campus of LMU Munich

    The university consists of 18 faculties which oversee various departments and institutes. The official numbering of the faculties and the missing numbers 06 and 14 are the result of breakups and mergers of faculties in the past. The Faculty of Forestry Operations with number 06 has been integrated into the Technical University of Munich [Technische Universität München] (DE) in 1999 and faculty number 14 has been merged with faculty number 13.

    01 Faculty of Catholic Theology
    02 Faculty of Protestant Theology
    03 Faculty of Law
    04 Faculty of Business Administration
    05 Faculty of Economics
    07 Faculty of Medicine
    08 Faculty of Veterinary Medicine
    09 Faculty for History and the Arts
    10 Faculty of Philosophy, Philosophy of Science and Study of Religion
    11 Faculty of Psychology and Educational Sciences
    12 Faculty for the Study of Culture
    13 Faculty for Languages and Literatures
    15 Faculty of Social Sciences
    16 Faculty of Mathematics, Computer Science and Statistics
    17 Faculty of Physics
    18 Faculty of Chemistry and Pharmacy
    19 Faculty of Biology
    20 Faculty of Geosciences and Environmental Sciences

    Research centres

    In addition to its 18 faculties, the University of Munich also maintains numerous research centres involved in numerous cross-faculty and transdisciplinary projects to complement its various academic programmes. Some of these research centres were a result of cooperation between the university and renowned external partners from academia and industry; the Rachel Carson Center for Environment and Society, for example, was established through a joint initiative between LMU Munich and the Deutsches Museum, while the Parmenides Center for the Study of Thinking resulted from the collaboration between the Parmenides Foundation and LMU Munich’s Human Science Center.

    Some of the research centres which have been established include:

    Center for Integrated Protein Science Munich (CIPSM)
    Graduate School of Systemic Neurosciences (GSN)
    Helmholtz Zentrum München – German Research Center for Environmental Health
    Nanosystems Initiative Munich (NIM)
    Parmenides Center for the Study of Thinking
    Rachel Carson Center for Environment and Society

     
  • richardmitnick 11:51 am on August 12, 2021 Permalink | Reply
    Tags: "Shining Light on the Dark Matter of Biology", , , , , Disordered regions are extremely abundant in proteomes—the collection of proteins within a cell or organism., Disordered regions are known to play important roles in DNA transcription and misregulation in transcription is linked to many diseases., DNA, , Intrinsically disordered proteins are flexible in nature and do not have a stable structure., Labeling proteins expressed by the cells with fluorescent tags using CRISPR., , Shasha Chong, The dark proteome is another name for these intrinsically disordered regions., The regulation of transcription is extremely complicated.   

    From California Institute of Technology (US) : “Shasha Chong-Shining Light on the Dark Matter of Biology” 

    Caltech Logo

    From California Institute of Technology (US)

    August 09, 2021
    Emily Velasco
    (626) 372‑0067
    evelasco@caltech.edu

    1
    Shasha Chong. Credit: Caltech.

    It is tempting to think we understand cells. They are small. They have DNA. They consume nutrients and make proteins. They grow and divide. Simple, right?

    Actually, no. Researchers may have a broad understanding about the biology and chemistry of cells, but there is much that they do not know. For example, while many of the functions that keep cells alive and ticking are conducted by proteins with clearly defined shapes, many other functions are governed by a structureless class of proteins known as intrinsically disordered regions.

    The proteins we are most familiar with can be thought of as being analogous to a tool like a wrench. A wrench has a certain shape that makes it ideal for turning nuts and bolts, and it is always in that shape. Intrinsically disordered proteins are not like that at all. They are dynamic. They are floppy. They wiggle around in space and change their shape. And because these proteins do not have a consistent shape, they have been hard to study and characterize.

    Shasha Chong, who has recently joined Caltech’s faculty in the Division of Chemistry and Chemical Engineering after receiving her PhD in chemistry and chemical biology from Harvard University (US) and conducting postdoctoral research at University of California-Berkeley (US), wants to understand these proteins. We sat down with her to talk about her work.

    Describe your work for us.

    I have been studying how gene expression is regulated. Gene expression is fundamental to all the processes happening in our cells. How your tissues work, how an organism survives, and how it reproduces—it’s all reliant on gene expression.

    The first step of gene expression is transcription, which is where the DNA is copied into RNA. Regulation of transcription is important for every healthy cell. And, of course, when transcription goes wrong, it can lead to diseases.

    I’m particularly interested in mammals. And in mammalian cells, the regulation of transcription is extremely complicated. We are still pretty far away from understanding how transcription is regulated. One important reason is that much of the regulation is mediated by intrinsically disordered regions, which are proteins that do not have clear shapes. These proteins are so difficult to understand because they don’t fold into well-defined protein structures and cannot be understood by conventional analytic methods.

    My way of studying them is to visualize and track these protein molecules one at a time in live cells. To observe their behaviors in the native state, I label proteins expressed by the cells with fluorescent tags using CRISPR, the genome-editing method. Single-molecule imaging is uniquely powerful for understanding biomolecular transactions. This method can provide in-depth insights that no other method is capable of providing. Using high-resolution single-molecule imaging, I have discovered a new type of interaction between the intrinsically disordered regions in transcription regulatory proteins. Such interactions mean a molecule can bind to a variable number of partners depending on surrounding conditions. Such interactions play an essential role in transcription.

    Long term, I will be developing new imaging methods and combining them with other approaches to achieve two primary goals. I want to understand the fundamental rules that govern the interaction behaviors of intrinsically disordered regions and I want to elucidate the detailed mechanisms by which disordered regions mediate gene transcription under normal and disease conditions.

    Can you talk more about intrinsically disordered regions and why they are important?

    Given the recent advances of structural biology, lots of proteins have gotten their atomic structures solved. And by knowing those structures, we can learn lots of useful information, like which partners the proteins interact with and how they interact. But the methods used for understanding these proteins only work for proteins with one stable structure. Intrinsically disordered regions, or intrinsically disordered proteins are flexible in nature and do not have a stable structure. Therefore, they cannot be described by classical structural description methods such as X-ray crystallography and cryo-electron microscopy.

    These disordered regions are extremely abundant in proteomes—the collection of proteins within a cell or organism. For example, they constitute nearly half of the human proteome. They are involved in virtually every cellular process and perform many critical functions. But the mechanisms underlying these functions are largely unknown.

    What are the big-picture questions you want to solve?

    A lot of these disordered regions are known to play important roles in DNA transcription and misregulation in transcription is linked to many diseases. More importantly, mutations in transcription-related disordered regions are directly implicated in many human diseases. By understanding intrinsically disordered regions and how they regulate transcription, we may learn more about treating different types of cancer, neurodegenerative diseases, and diabetes.

    You also study the dark proteome. What is the dark proteome?

    The dark proteome is another name for these intrinsically disordered regions. They can be thought of as the dark matter of biology because they make up a large portion of our bodies’ proteins and play many roles in our bodies, but we know very little about them.

    What are you looking forward to most in joining Caltech?

    Caltech has really impressed me by having so many successful faculty members who are friendly and approachable even though they are giants in their fields. I’m looking forward to working with extremely brilliant colleagues and very motivated students. Everybody here seems to be really excited about their science and their career. That’s really convinced me that Caltech is the best place for me to be.

    What do you like to do with your free time?

    I enjoy spending my time with my family—for example, with my toddler boy. Even just sitting with him watching him play with his toy cars is very relaxing.

    See the full article here .


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    Please help promote STEM in your local schools.

    Stem Education Coalition

    Caltech campus

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

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

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

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

    Research

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

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

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

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

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

     
  • richardmitnick 9:06 am on August 2, 2021 Permalink | Reply
    Tags: "Study links autism to new set of rare gene variants", , ASD affects about 1 in 59 children in the United States., , DNA, , , The effects of these newly identified genes are unknown but some are associated with protein networks known to play a role in autism., University of Washington (US) School of Medicine   

    From University of Washington (US) School of Medicine : “Study links autism to new set of rare gene variants” 

    From University of Washington (US) School of Medicine

    July 26, 2021

    Brian Donohue
    206.543.7856
    bdonohue@uw.edu

    The effects of these newly identified genes are unknown but some are associated with protein networks known to play a role in autism.

    1
    A child with autism plays with blocks. Credit: University of Washington (US) School of Medicine./Getty Images.

    “These ultra-rare variants involve a set of genes that have not been associated with autism before,” said Amy B. Wilfert, a senior research fellow in the Department of Genome Sciences at the University of Washington School of Medicine. She was the lead author of the report published July 26 in the journal Nature Genetics. Evan Eichler, UW professor of genome sciences, led the team that conducted the study.

    The findings should help researchers better understand how the genetic risk of developing autism is inherited and how mutations in these variants might contribute to the disorder.

    Autism, or autism spectrum disorder (ASD), affects about 1 in 59 children in the United States. The exact cause is unknown, but certain genes with deleterious mutation are known to increase the risk of developing the disorder.

    To date, most research has focused on genes with mutations not found in the parents’ genomes but which originate in the sperm, the egg, or very early in the development of the fertilized egg. Such “de novo” variants have been shown to greatly increase a child’s risk of developing ASD, but account for a relatively small percentage of cases.

    To better understand how children might inherit mutations in genes from a parent that put them at risk of developing ASD, the Seattle researchers and their collaborators looked for variants in genes so rare that they appeared in only one parent in a study group involving thousands of families. Such variants are called ultra-rare or private variants.

    To find these ultra-rare variants, the researchers examined the genome sequences of nearly 3,500 families that had at least one child with ASD. They limited their search to changes in the genes that would likely disable the gene, called likely-gene disruptive (LGD) variants. They then repeated the analysis in a larger dataset of nearly 6,000 families. Overall, they analyzed nearly 35,000 genomes.

    In the end, they identified 163 candidate genes with private LGD variants that collectively increase the risk of ASD. These genes had not been previously identified as ASD-risk genes by studies of de novo variants. The researchers estimate these mutations in these genes may account for as much as 4.5% of autism cases. That’s on par with the percentage ascribed to the more intensely studied de novo variants.

    Inheriting one or more of these variants is not enough to cause ASD as none of the parents who carried the variants had ASD, the researchers found. Some additional factors, either genetic or environmental, must therefore have to be present for the child to go on to develop ASD. This finding supports the theory that changes in multiple genes must be present for a child to develop ASD, known as the “multi-hit” model. “Our study suggests that one inherited mutation is not enough,” said Wilfert. “You need at least one other mutation to push a child over the threshold required to be diagnosed with autism.”

    One reason why these variants are so rare is that they appear to be relatively short-lived, persisting in a family for only a few generations, perhaps because those children that inherit them are less likely to go on to have children of their own, the researchers said.

    Just how these ultra-rare variants increase a child’s risk of ASD is unknown, Wilfert said, but many of the genes are involved in protein networks that play a role in biochemical pathways that have been previously linked to the development of ASD.

    “The availability of large whole genome and exome datasets made it possible to identify such rare variants. Without the sequencing efforts by our collaborators at the Centers for Common Disease Genomics, and the study coordination efforts from Simons Foundation this study would have been impossible,” she said. “Our findings won’t be brought into the clinic tomorrow,” Wilfert said, “but they do give researchers new areas to focus on and may lead to clinically relevant knowledge in the future.”

    Study collaborators included researchers from the Allen Institute for Brain Science in Seattle, the New York Genome Center in New York, and the Center for Medical Genetic & Hunan Key Laboratory of Medical Genetics, Central South University, in Changsha, China.

    This work was supported in part by grants from the National Institutes of Health (US) (R01 MH101221, R01 MH100047, K99 MH117165, K99 HG011041, UM1 HG008901); The National Human Genome Research Institute (US); The National Heart, Lung, and Blood Institute (US); The Genome Sequencing Program Coordinating Center (U24 HG008956); The National Institute of Mental Health (US) via Autism Speaks (1U24MH081810); The Howard Hughes Medical Institute (US); and The Simons Foundation (US).

    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-washington-campus

    The University of Washington School of Medicine (UWSOM) is a large public medical school in the northwest United States, located in Seattle and affiliated with the University of Washington. According to U.S. News & World Report’s 2022 Best Graduate School rankings, University of Washington School of Medicine ranked #1 in the nation for primary care education, and #7 for research.

    UWSOM is the first public medical school in the states of Washington, Wyoming, Alaska, Montana, and Idaho. The school maintains a network of teaching facilities in more than 100 towns and cities across the five-state region. As part of this “WWAMI” partnership, medical students from Wyoming, Alaska, Montana, and Idaho spend their first year and a half at The University of Wyoming (US), The University of Alaska-Anchorage (US), Montana State University (US), or The University of Idaho (US), respectively. In addition, sixty first-year students and forty second-year students from Washington are based at Gonzaga University (US) in Spokane. Preference is given to residents of the WWAMI states.

    The University of Washington (US) 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 (US) 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(US) and is classified among “R1: Doctoral Universities – Very high research activity”. According to the National Science Foundation(US), 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(US), 67 members of the American Academy of Arts and Sciences, 53 members of the National Academy of Medicine(US), 29 winners of the Presidential Early Career Award for Scientists and Engineers, 21 members of the National Academy of Engineering(US), 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 11:47 am on July 29, 2021 Permalink | Reply
    Tags: "Biology through the Eyes of a Physicist", , , , , , Cissé and his team use cutting-edge microscopy tools to study the real-time behaviors of individual molecules in cells as a way to understand the fundamental nature of life itself., Cissé specializes in visualizing single molecules inside living cells using a technique called super-resolution imaging., DNA, One distinguishing trait of physicists is the drive to quantify and measure processes in nature., , Physics professor Ibrahim Cissé, Rob Phillips-Fred and Nancy Morris Professor of Biophysics Biology and Physics takes a by-the-numbers approach to biology-exemplified by reports that describe the COVID-19 virus and Earth’s biomass., Shu-ou Shan-Altair Professor of Chemistry at Caltech-sees quantitative modeling as part of the mindset of a biophysicist.   

    From California Institute of Technology (US) : “Biology through the Eyes of a Physicist” 

    Caltech Logo

    From California Institute of Technology (US)

    Summer 2021
    Whitney Clavin

    1
    Illustration: Lance Hayashida.

    A look at the multifaceted, interdisciplinary world of biophysics.

    DNA, the quintessential molecule of all living beings, is composed of two twisted strands that wind around each other in the shape of a helix. The structure was famously discovered in 1953 by Francis Crick and James Watson; prior to that, scientists knew of the existence of DNA but could not crack the mystery of its 3-D structure, nor were they even sure that it was the storehouse of genetic information. One integral piece of the puzzle came in the form of X-ray diffraction images of DNA strands, meticulously captured by Rosalind Franklin and Maurice Wilkins. The images revealed a cross-shaped pattern suggestive of a helix and ultimately helped Watson and Crick solve the mystery as well as propose how DNA’s ability to unwind allows for it to be copied and passed on.

    The discovery of the double helix exemplifies the multifaceted field of biophysics, in which biology is viewed and better understood through the lens of physics. In this case, the X-ray-based tools of physicists were applied to living matter; in fact, Franklin began her career as a physical chemist, and Wilkins and Crick as physicists.

    Recently, Caltech’s Division of Physics, Mathematics and Astronomy (PMA), which traditionally includes professors and students who study everything from subatomic particles to exploding stars, hired physics professor Ibrahim Cissé, who is an expert in the imaging of single molecules in living cells.

    2
    Physics professor Ibrahim Cissé, who uses super-resolution microscopy to study protein dynamics, recently joined Caltech’s Division of Physics, Mathematics and Astronomy (PMA). His arrival, says Fiona Harrison, Kent and Joyce Kresa Leadership Chair of PMA, will help advance the growing interdisciplinary field of biophysics across the Institute. Photo courtesy of the Vilcek Foundation.

    “The questions the physicist will ask, even if they are studying the exact same material as a biologist, are going to be different,” says Cissé. “I am a physicist whose subject is living matter.” Cissé and his team use cutting-edge microscopy tools to study the real-time behaviors of individual molecules in cells as a way to understand the fundamental nature of life itself. Having Cissé in the division, says Fiona Harrison, the Kent and Joyce Kresa Leadership Chair of PMA, will help further catalyze the growing interdisciplinary field of biophysics across Caltech.

    “Physicists approach problems using fundamental, quantitative principles,” says Harrison. “PMA sees the expansion of our efforts in biophysics as an opportunity to apply this approach to issues in biology. This kind of fundamental look at scientific problems is well suited to Caltech, which focuses on basic research.”

    In the same spirit, chemists and biologists across the Caltech campus use the tools and approaches of biophysics to probe the mysteries of life, including everything from the mechanics of the living cell to the structure of biomolecules. As Cissé explains, there is a lot of overlap among the various fields of science.

    “The cell doesn’t care if your training is in chemistry, biology, or physics,” he says. “It uses all of them. And to understand the cell, we really have to integrate all these different disciplines and bodies of knowledge together.”

    Condensation in Cells

    Cissé specializes in visualizing single molecules inside living cells using a technique called super-resolution imaging, in which the limits of optical light itself, specifically the diffraction limit, are surpassed and cellular structures on the scale of a few nanometers can be resolved.

    Cissé and his team have adapted and further developed the tool of super-resolution microscopy to study clusters of molecules that are not static but rapidly assemble and disassemble in living mammalian cells. “We want to push super-resolution microscopy to detect clusters that form in very crowded environments and that are highly dynamic,” he says.

    One bustling environment of interest is the nucleus of a cell. There, DNA is transcribed into messenger RNA, which ultimately provides the building instructions for the proteins that run the daily business of a cell. In order for the DNA to be transcribed, proteins called RNA polymerases, along with a host of associated proteins, must sit down on, or attach themselves to, the DNA strands and go to work. But how do the proteins gather together?

    Using their super-resolution microscopy tools, Cissé and his team were able to see what was actually happening. They learned that the proteins come together in clusters like workers quickly gathering at a construction site. “There is a level of cooperation between the proteins,” he says. What triggers this sudden condensation? From a physicist’s point of view, you can quickly condense things with a phase transition, for example when vapor spontaneously condenses into a liquid droplet. “Phase transitions have been thoroughly studied in the realm of physics, and now we are able to study their role in regulating biological processes in the living cell.”

    Ultimately, Cissé says, understanding a process as complex as DNA transcription requires an integration of physics with biology and chemistry. “We are studying how the cell works and discovering that living matter exhibits some of the same emergent phenomena, like phase transitions, that we also see in nonliving matter. There may even be a new physical understanding of how nature works that comes out of this line of investigation. Through biology, we are gaining new insights about physics.”

    By the Numbers

    5
    Rob Phillips, Fred and Nancy Morris Professor of Biophysics, Biology, and Physics (seen here pre-pandemic), takes a by-the-numbers approach to biology, exemplified by quantitative reports that describe the COVID-19 virus and Earth’s biomass. Photo: Lance Hayashida.

    One distinguishing trait of physicists is the drive to quantify and measure processes in nature. Rob Phillips, Fred and Nancy Morris Professor of Biophysics, Biology, and Physics, exemplifies this with his by-the-numbers approach to the study of biology. For instance, in 2018, he and his longtime collaborators Ron Milo and Yinon Bar-On of the Weizmann Institute of Science (IL) made quantitative estimates of the amount of biological matter, or biomass, covering our planet, including everything from bacteria to humans. Their research revealed, among other factoids, that humans and their livestock outweigh all wild animals by a factor of 20.

    More recently, the trio, along with Avi Flamholz, a postdoctoral scholar at Caltech, published a similar by-the-numbers report, this time detailing those numbers that describe the COVID-19 virus, such as average concentrations throughout the body, number of genes, infection rate, and more.

    “My approach to biophysics involves coming up with principles and theories first. It’s a certain style of inquiry, and it’s about quantifying and measuring things at all scales,” says Phillips, who is also co-author, along with Ron Milo, of the popular book Cell Biology by the Numbers. “It is physics unleashed on the nature of living organisms. That runs the gamut from very specific questions about the nature of proteins that interact with DNA all the way up to giant ecosystems.

    “Astrophysicists study the cosmos, condensed matter physicists study nonliving matter, and biological physicists study living matter,” he says. “Personally, you will have a hard time convincing me that you and I and other living creatures are not the most interesting matter in the universe.”

    Of course, an integral tool for quantifying nature is math. Phillips says that math is front and center in more or less every discussion in his group. “The language we speak in my lab,” he jokes, “is not English but math.” He recalls his graduate school teacher who had a blackboard on his door: “When I would come into his office, he would shut the door and tell me that if I had something to say, I needed to write it down in equations. I’m a devotee of mathematics now. We want to observe and measure.”

    3
    Shu-ou Shan, Altair Professor of Chemistry at Caltech, sees quantitative modeling as part of the mindset of a biophysicist. One of her areas of research focuses on how proteins in cells are sorted to the proper locations as well as folded into the correct 3-D structures. Photo: Max Gerber.

    Shu-ou Shan, Altair Professor of Chemistry at Caltech, also sees math and quantitative modeling as part of the mindset of a biophysicist. One of Shan’s areas of research focuses on how proteins in cells are sorted to the proper locations as well as folded into the correct 3-D structures. Though her work lies in the field of biochemistry, she says her methods are rooted in both physics and chemistry.

    “The biophysical side of our work involves making quantitative measurements, modeling molecular events based on first principles, and making predictions,” she says. “We also use microscopy and spectroscopy tools that have been developed by physicists.” In fact, Shan is leaving this month for a sabbatical at University of California-San Francisco (US), where she plans to learn the powerful tool of cryogenic electron microscopy (cryo-EM) for visualizing the structures of biomolecules. “Tools like cryo-EM and NMR [nuclear magnetic resonance] spectroscopy involve math, principles of light scattering, Fourier transforms, and so on. Physics helps us improve these techniques.”

    Simplicity First

    Biophysics is also not the primary field in which Michael Elowitz, professor of biology and bioengineering at Caltech, works. But, he says, his experiences with the principles of physics have given him a taste for a different type of questioning.

    “Physicists seek the minimal set of components and assumptions that can explain a phenomenon and then develop models that one can understand as deeply as possible,” he says. “Even though, or perhaps because, biological systems are incredibly complex, it is critical to try to identify simplifying underlying principles.”

    Elowitz and his lab use this approach to create and study synthetic cellular systems. For example, he and his graduate student Ronghui Zhu, along with other collaborators, recently asked what minimal biological-circuit designs could account for the ability of our own cells to take on many different “fates”: becoming liver cells, neurons, or other cell types. To find out, they designed a synthetic gene circuit in living cells based on mathematical models and inspired by aspects of natural cell-fate control circuits. The synthetic system establishes multiple stable cell fates and allows researchers to switch a cell from one fate to another. Built “from scratch,” as Elowitz says, the system provides insight into critical biological processes and could eventually play a role in the emerging paradigm of engineered-cell therapy, in which researchers design cells, rather than drugs, to target cancer and other disease states.

    Elowitz says the approach of building biological systems as a means to understand them takes inspiration from a quote, often cited in the field of synthetic biology, by the late Caltech physicist and Nobel laureate Richard Feynman. The quote, discovered in the upper corner of Feynman’s blackboard after his death in 1988, read: “What I cannot create, I do not understand.”

    A Tradition of Crossing Disciplines

    4
    Michael Elowitz, professor of biology and bioengineering at Caltech, seeks to identify the underlying principles behind biological systems. The image above shows a synthetic cellular system created in his lab that maintains cell colonies in distinct cell “fates,” indicated by different colors. Photo: Jon Nalick.

    Feynman himself dabbled in biology; in addition to other pursuits, he spent a year in the laboratory of the late Max Delbrück, a Nobel laureate and longtime Caltech professor who helped launch the modern field of molecular biology. While Feynman’s interests largely lay in pure physics, Delbrück is a prime example of a physicist turning an eye toward biology.

    Delbrück, who was born in Germany in 1906, studied quantum mechanics with some of the great physicists of his time, including Niels Bohr, who reportedly piqued Delbrück’s interest in biology. Ultimately, Delbrück and his colleagues Alfred Hershey and Salvador Luria, in the 1940s, would learn the secrets of viral genetics through their studies of bacteriophages, viruses that infect bacteria. According to the press release for their 1969 Nobel Prize in Physiology or Medicine, the scientists “worked out rigorous quantitative methods and this turned bacteriophage research into an exact science.”

    Today, a strong current of biophysics runs through the Institute, crossing numerous divisions and sparking collaborations among a wide range of scientists. “That’s one of the beautiful things about Caltech: we can be in more than one department and have our collaborations be meaningful and real,” says Phillips.

    “There are no barriers to integrating all of this science,” says Cissé. “Once you get a critical mass of people, you can really work together and nucleate new and exciting ideas.”

    See the full article here .


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    Please help promote STEM in your local schools.

    Stem Education Coalition

    Caltech campus

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

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

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

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

    Research

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

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

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

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

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

     
  • richardmitnick 9:23 am on April 7, 2021 Permalink | Reply
    Tags: "Shaking the foundations of life", , , , DNA, , Evolution never stops – and disruptions can speed up the process. Now ETH researchers are delving deeper into the secrets of evolutionary change., It’s now clear that microbes far from being isolated loners are actually highly social 
organisms., Microbes cooperate with deceive and fight other microbes., , Success through cooperation   

    From ETH Zürich [Eidgenössische Technische Hochschule Zürich] (CH): “Shaking the foundations of life” 

    From ETH Zürich [Eidgenössische Technische Hochschule Zürich] (CH)

    06.04.2021
    Peter Rüegg

    Evolution never stops – and disruptions can speed up the process. Now ETH researchers are delving deeper into the secrets of evolutionary change.

    1
    Soil bacterium Myxococcus xanthus Credit: Gregory J. Velicer.

    The evolution of life on Earth has taken a long, long time. Protocells – the precursors of today’s unicellular organisms – formed around four billion years ago, eventually evolving into bacteria and 
archaea. The first eukaryotes emerged two billion years ago, providing the basis for more complex, multicellular organisms. As life evolved, it faced numerous disruptions in the form of meteorites, volcanic eruptions, ice ages and periods of great heat. Our planet has experienced at least five mass extinction events over its long history – yet still life has continued, undaunted.

    Change is one of the driving forces behind evolution: all organisms, from bacteria to elephants, must constantly change and adapt to deal with challenges such as increasing competition for food and space, food scarcity, environmental changes and climate change. Failure to adapt means extinction.

    Success through cooperation

    Bacteria are ideal for investigating evolutionary processes because they are small and have very short generation times. ETH professor Greg Velicer opted for the soil bacterium Myxococcus xanthus as a model organism because it forms cooperative groups and hunts other microorganisms. When food becomes scarce, thousands of Myxococcus cells aggregate into a fruiting body and produce spores, which can survive in the soil for long periods of time under stressful conditions.

    “It’s now clear that microbes far from being isolated loners are actually highly social 
organisms. Microbes cooperate with deceive and fight other microbes, both within their own 
intra-​specific social groups and within extremely complex multi-​species communities,” says Velicer, Professor of Evolutionary Biology at the Institute of Integrative Biology. These findings also apply to pathogens. For example, cells of the dreaded hospital bug Pseudomonas aeruginosa or the cholera pathogen Vibrio cholerae communicate with one another in order to form resistant biofilms and in producing cytotoxic agents.

    “One of the key questions for evolutionary biologists is how cooperation evolves over time, and especially how it persists in the face of selfish, non-​cooperative behaviour,” says Velicer.

    A while back, he and his colleagues were able to show that some individual bacteria in groups of Myxococcus cells exhibit cheating behaviour towards other cells in the same group: these mutant cells – or cheats – do not themselves produce fruiting bodies or spores. Mix these cheats with cooperative, spore-​forming cells, however, and they benefit from this work without making any contribution of their own – in other words, without providing the required energy in the form of chemical messengers and enzymes. This enables the cheats to increase their frequency in a population at virtually no cost to themselves, thus threatening the survival of the cooperative system. “We’ve even seen cases of cheating that have driven entire populations of cooperators and cheats to extinction,” says Velicer.

    Nevertheless, cooperation continues to be a successful evolutionary strategy that has proven to be evolutionarily stable against such cheating across many biological systems. For example, cooperative Myxococcus bacteria can quickly give rise to social adaptations, as Velicer discovered in a further study. He observed how a strain that began by exhibiting cooperative behaviours evolved first to become a cheat and then later evolved back into a cooperating strain – in fact, a new, better-​adapted form of cooperating strain that was highly resistant to its own progenitors’ attempts at cheating. A subsequent study by one of Velicer’s colleagues showed that cooperation was restored thanks to a single mutation in a previously unknown small RNA (sRNA). It emerged that this sRNA plays an essential role in the regulation of fruiting-​body formation.

    Dramatic doubling of the genome

    Mutations in DNA occur spontaneously and randomly, yet they are fundamental to evolution. While most are inconsequential and have no effect on the organism, some genetic changes are more profound and affect the entire genome. One example of such a sudden and dramatic event is the duplication of the entire set of chromosomes. During meiosis – the cell division of germ cells – the chromosomes do not split into the daughter cells evenly. Chromosomes are threads of DNA wrapped around a protein scaffold. A normal human cell has 46 chromosomes: two sex chromosomes and 22 pairs of non-​sex chromosomes.

    When meiosis goes wrong, one of the daughter cells gets all the chromosomes and thus all the genetic material of the parent cell. It remains diploid, while the other cell receives nothing and dies. If two diploid germ cells then fuse, this produces an organism with cells that have four sets of chromosomes. The organism is now polyploid, which poses significant challenges in regard to cell biology and the organism’s physiology.

    Kirsten Bomblies, Professor of Plant Evolutionary Genetics at ETH Zürich’s Department of Biology, has been investigating this phenomenon: “Polyploidy can occur randomly or due to environmental changes such as drought, cold or salt stress.” It is common among plants, though less frequent in fish and amphibians. There is only one example of a polyploid mammal – though even this case is heavily disputed. Most polyploids are evolutionary dead ends but some acquire an advantage. “Plants with multiple sets of chromosomes are far more resistant to drought and salt than their predecessors,” she explains. Polyploid plants also have larger fruits and seeds, which makes them an interesting model for breeding new varieties of crops with higher yields and resilience. In fact, many important food crops have already been bred to be polyploid: wheat, potatoes, maize and coffee all have multiple sets of chromosomes.

    In one of her projects, Bomblies is investigating why polyploid plants are so stress-​tolerant. One reason is cell size. Polyploid cells are larger than diploid cells, and this affects their interactions with the environment, such as the exchange of gases and water. “For an evolutionary biologist, polyploidy is as an absolutely fascinating example of disruption,” Bomblies says. “It’s a profound evolutionary force because it changes everything in an organism’s biology.”

    See the full article here .

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    Please help promote STEM in your local schools.

    Stem Education Coalition

    ETH Zurich campus
    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 EPFL[École polytechnique fédérale de Lausanne](CH), it is part of the Swiss Federal Institutes of Technology Domain (ETH Domain), part of the Swiss Federal Department of Economic Affairs, Education and Research.
    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 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 “ETH Domain” 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 Rankingsplaced 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(US), Stanford University(US) 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(US), Stanford University(US), California Institute of Technology(US), Princeton University(US), University of Cambridge(UK), Imperial College London(UK) and

     
  • richardmitnick 10:47 am on March 12, 2021 Permalink | Reply
    Tags: "Researchers reveal 3D structure responsible for gene expression", , , DNA, , Med-PIC: Mediator-bound pre-initiation complex, Mediator helps position the rest of the complex — RNA polymerase II and the general transcription factors — at the beginning of genes that the cell wants to transcribe.,   

    From Northwestern University: “Researchers reveal 3D structure responsible for gene expression” 

    Northwestern U bloc
    From Northwestern University

    March 11, 2021
    Amanda Morris

    Study marks first time the structure has been visualized in 3D for human cells.

    1
    Image of the human Mediator-bound pre-initiation complex. Credit: Yuan He.

    For the first time ever, a Northwestern University-led research team has peered inside a human cell to view a multi-subunit machine responsible for regulating gene expression.

    Called the Mediator-bound pre-initiation complex (Med-PIC), the structure is a key player in determining which genes are activated and which are suppressed. Mediator helps position the rest of the complex — RNA polymerase II and the general transcription factors — at the beginning of genes that the cell wants to transcribe.

    The researchers visualized the complex in high resolution using cryogenic electron microscopy (cryo-EM), enabling them to better understand how it works. Because this complex plays a role in many diseases, including cancer, neurodegenerative diseases, HIV and metabolic disorders, researchers’ new understanding of its structure could potentially be leveraged to treat disease.

    “This machine is so basic to every branch of modern molecular biology in the context of gene expression,” said Northwestern’s Yuan He, senior author of the study. “Visualizing the structure in 3D will help us answer basic biological questions, such as how DNA is copied to RNA.”

    “Seeing this structure allows us to understand how it works,” added Ryan Abdella, the paper’s co-first author. “It’s like taking apart a common household appliance to see how everything fits together. Now we can understand how the proteins in the complex come together to perform their function.”

    The study was published March 11 in the journal Science. This marks the first time the human Mediator complex has been visualized in 3D in the human cell.

    He is an assistant professor of molecular biosciences in Northwestern’s Weinberg College of Arts and Sciences. Abdella and Anna Talyzina, both graduate students in the He lab, are co-first authors of the paper.

    Famed biochemist Roger Kornberg discovered the Mediator complex in yeast in 1990, a project for which he won the 2006 Nobel Prize in Chemistry. But Mediator comprises a daunting 26 subunits — 56 total when combined with the pre-initiation complex — it’s taken researchers until now to obtain high-resolution images of the human version.

    “It’s a technically quite challenging project,” He said. “These complexes are scarce. It takes hundreds of liters of human cells, which are very hard to grow, to obtain small amounts of the protein complexes.”

    A breakthrough came when He’s team put the sample on a single layer of graphene oxide. By providing this support, the graphene sheet minimized the amount of sample needed for imaging. And compared to the typical support used — amorphous carbon — graphene improved the signal-to-noise ratio for higher-resolution imaging.

    After preparing the sample, the team used cryo-EM, a relatively new technique that won the 2017 Nobel Prize in Chemistry, to determine the 3D shape of proteins, which are often thousands of times smaller than the width of a human hair. The technique works by blasting a stream of electrons at a flash-frozen sample to take many 2D images.

    For this study, He’s team captured hundreds of thousands of images of the Med-PIC complex. They then used computational methods to reconstruct a 3D image.

    “Solving this complex was like assembling a puzzle,” Talyzina said. “Some of those subunits were already known from other experiments, but we had no idea how the pieces assembled together or interacted with each other. With our final structure, we were finally able to see this whole complex and understand its organization.”

    The resulting image shows the Med-PIC complex as a flat, elongated structure, measuring 45 nanometers in length. The researchers also were surprised to discover that the Mediator moves relative to the rest of the complex, binding to RNA polymerase II at a hinge point.

    “Mediator moves like a pendulum,” Abdella said. “Next, we want to understand what this flexibility means. We think it might have an impact on the activity of a key enzyme within the complex.”

    See the full article here .

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    Please help promote STEM in your local schools.

    Stem Education Coalition

    Northwestern South Campus
    South Campus

    Northwestern University(US) is a private research university in Evanston, Illinois. Founded in 1851 to serve the former Northwest Territory, the university is a founding member of the Big Ten Conference.

    On May 31, 1850, nine men gathered to begin planning a university that would serve the Northwest Territory.

    Given that they had little money, no land and limited higher education experience, their vision was ambitious. But through a combination of creative financing, shrewd politicking, religious inspiration and an abundance of hard work, the founders of Northwestern University were able to make that dream a reality.

    In 1853, the founders purchased a 379-acre tract of land on the shore of Lake Michigan 12 miles north of Chicago. They established a campus and developed the land near it, naming the surrounding town Evanston in honor of one of the University’s founders, John Evans. After completing its first building in 1855, Northwestern began classes that fall with two faculty members and 10 students.
    Twenty-one presidents have presided over Northwestern in the years since. The University has grown to include 12 schools and colleges, with additional campuses in Chicago and Doha, Qatar.

    Northwestern is known for its focus on interdisciplinary education, extensive research output, and student traditions. The university provides instruction in over 200 formal academic concentrations, including various dual degree programs. The university is composed of eleven undergraduate, graduate, and professional schools, which include the Kellogg School of Management, the Pritzker School of Law, the Feinberg School of Medicine, the Weinberg College of Arts and Sciences, the Bienen School of Music, the McCormick School of Engineering and Applied Science, the Medill School of Journalism, the School of Communication, the School of Professional Studies, the School of Education and Social Policy, and The Graduate School. As of fall 2019, the university had 21,946 enrolled students, including 8,327 undergraduates and 13,619 graduate students.

    Valued at $12.2 billion, Northwestern’s endowment is among the largest university endowments in the United States. Its numerous research programs bring in nearly $900 million in sponsored research each year.

    Northwestern’s main 240-acre (97 ha) campus lies along the shores of Lake Michigan in Evanston, 12 miles north of Downtown Chicago. The university’s law, medical, and professional schools, along with its nationally ranked Northwestern Memorial Hospital, are located on a 25-acre (10 ha) campus in Chicago’s Streeterville neighborhood. The university also maintains a campus in Doha, Qatar and locations in San Francisco, California, Washington, D.C. and Miami, Florida.

    As of October 2020, Northwestern’s faculty and alumni have included 1 Fields Medalist, 22 Nobel Prize laureates, 40 Pulitzer Prize winners, 6 MacArthur Fellows, 17 Rhodes Scholars, 27 Marshall Scholars, 23 National Medal of Science winners, 11 National Humanities Medal recipients, 84 members of the American Academy of Arts and Sciences, 10 living billionaires, 16 Olympic medalists, and 2 U.S. Supreme Court Justices. Northwestern alumni have founded notable companies and organizations such as the Mayo Clinic, The Blackstone Group, Kirkland & Ellis, U.S. Steel, Guggenheim Partners, Accenture, Aon Corporation, AQR Capital, Booz Allen Hamilton, and Melvin Capital.

    The foundation of Northwestern University can be traced to a meeting on May 31, 1850, of nine prominent Chicago businessmen, Methodist leaders, and attorneys who had formed the idea of establishing a university to serve what had been known from 1787 to 1803 as the Northwest Territory. On January 28, 1851, the Illinois General Assembly granted a charter to the Trustees of the North-Western University, making it the first chartered university in Illinois. The school’s nine founders, all of whom were Methodists (three of them ministers), knelt in prayer and worship before launching their first organizational meeting. Although they affiliated the university with the Methodist Episcopal Church, they favored a non-sectarian admissions policy, believing that Northwestern should serve all people in the newly developing territory by bettering the economy in Evanston.

    John Evans, for whom Evanston is named, bought 379 acres (153 ha) of land along Lake Michigan in 1853, and Philo Judson developed plans for what would become the city of Evanston, Illinois. The first building, Old College, opened on November 5, 1855. To raise funds for its construction, Northwestern sold $100 “perpetual scholarships” entitling the purchaser and his heirs to free tuition. Another building, University Hall, was built in 1869 of the same Joliet limestone as the Chicago Water Tower, also built in 1869, one of the few buildings in the heart of Chicago to survive the Great Chicago Fire of 1871. In 1873 the Evanston College for Ladies merged with Northwestern, and Frances Willard, who later gained fame as a suffragette and as one of the founders of the Woman’s Christian Temperance Union (WCTU), became the school’s first dean of women (Willard Residential College, built in 1938, honors her name). Northwestern admitted its first female students in 1869, and the first woman was graduated in 1874.

    Northwestern fielded its first intercollegiate football team in 1882, later becoming a founding member of the Big Ten Conference. In the 1870s and 1880s, Northwestern affiliated itself with already existing schools of law, medicine, and dentistry in Chicago. Northwestern University Pritzker School of Law is the oldest law school in Chicago. As the university’s enrollments grew, these professional schools were integrated with the undergraduate college in Evanston; the result was a modern research university combining professional, graduate, and undergraduate programs, which gave equal weight to teaching and research. By the turn of the century, Northwestern had grown in stature to become the third largest university in the United States after Harvard University(US) and the University of Michigan(US).

    Under Walter Dill Scott’s presidency from 1920 to 1939, Northwestern began construction of an integrated campus in Chicago designed by James Gamble Rogers, noted for his design of the Yale University(US) campus, to house the professional schools. The university also established the Kellogg School of Management and built several prominent buildings on the Evanston campus, including Dyche Stadium, now named Ryan Field, and Deering Library among others. In the 1920s, Northwestern became one of the first six universities in the United States to establish a Naval Reserve Officers Training Corps (NROTC). In 1939, Northwestern hosted the first-ever NCAA Men’s Division I Basketball Championship game in the original Patten Gymnasium, which was later demolished and relocated farther north, along with the Dearborn Observatory, to make room for the Technological Institute.

    After the golden years of the 1920s, the Great Depression in the United States (1929–1941) had a severe impact on the university’s finances. Its annual income dropped 25 percent from $4.8 million in 1930-31 to $3.6 million in 1933-34. Investment income shrank, fewer people could pay full tuition, and annual giving from alumni and philanthropists fell from $870,000 in 1932 to a low of $331,000 in 1935. The university responded with two salary cuts of 10 percent each for all employees. It imposed hiring and building freezes and slashed appropriations for maintenance, books, and research. Having had a balanced budget in 1930-31, the university now faced deficits of roughly $100,000 for the next four years. Enrollments fell in most schools, with law and music suffering the biggest declines. However, the movement toward state certification of school teachers prompted Northwestern to start a new graduate program in education, thereby bringing in new students and much needed income. In June 1933, Robert Maynard Hutchins, president of the University of Chicago(US), proposed a merger of the two universities, estimating annual savings of $1.7 million. The two presidents were enthusiastic, and the faculty liked the idea; many Northwestern alumni, however, opposed it, fearing the loss of their Alma Mater and its many traditions that distinguished Northwestern from Chicago. The medical school, for example, was oriented toward training practitioners, and alumni feared it would lose its mission if it were merged into the more research-oriented University of Chicago Medical School. The merger plan was ultimately dropped. In 1935, the Deering family rescued the university budget with an unrestricted gift of $6 million, bringing the budget up to $5.4 million in 1938-39. This allowed many of the previous spending cuts to be restored, including half of the salary reductions.

    Like other American research universities, Northwestern was transformed by World War II (1939–1945). Regular enrollment fell dramatically, but the school opened high-intensity, short-term programs that trained over 50,000 military personnel, including future president John F. Kennedy. Northwestern’s existing NROTC program proved to be a boon to the university as it trained over 36,000 sailors over the course of the war, leading Northwestern to be called the “Annapolis of the Midwest.” Franklyn B. Snyder led the university from 1939 to 1949, and after the war, surging enrollments under the G.I. Bill drove dramatic expansion of both campuses. In 1948, prominent anthropologist Melville J. Herskovits founded the Program of African Studies at Northwestern, the first center of its kind at an American academic institution. J. Roscoe Miller’s tenure as president from 1949 to 1970 saw an expansion of the Evanston campus, with the construction of the Lakefill on Lake Michigan, growth of the faculty and new academic programs, and polarizing Vietnam-era student protests. In 1978, the first and second Unabomber attacks occurred at Northwestern University. Relations between Evanston and Northwestern became strained throughout much of the post-war era because of episodes of disruptive student activism, disputes over municipal zoning, building codes, and law enforcement, as well as restrictions on the sale of alcohol near campus until 1972. Northwestern’s exemption from state and municipal property-tax obligations under its original charter has historically been a source of town-and-gown tension.

    Although government support for universities declined in the 1970s and 1980s, President Arnold R. Weber was able to stabilize university finances, leading to a revitalization of its campuses. As admissions to colleges and universities grew increasingly competitive in the 1990s and 2000s, President Henry S. Bienen’s tenure saw a notable increase in the number and quality of undergraduate applicants, continued expansion of the facilities and faculty, and renewed athletic competitiveness. In 1999, Northwestern student journalists uncovered information exonerating Illinois death-row inmate Anthony Porter two days before his scheduled execution. The Innocence Project has since exonerated 10 more men. On January 11, 2003, in a speech at Northwestern School of Law’s Lincoln Hall, then Governor of Illinois George Ryan announced that he would commute the sentences of more than 150 death-row inmates.

    In the 2010s, a 5-year capital campaign resulted in a new music center, a replacement building for the business school, and a $270 million athletic complex. In 2014, President Barack Obama delivered a seminal economics speech at the Evanston campus.

    Organization and administration

    Governance

    Northwestern is privately owned and governed by an appointed Board of Trustees, which is composed of 70 members and, as of 2011, has been chaired by William A. Osborn ’69. The board delegates its power to an elected president who serves as the chief executive officer of the university. Northwestern has had sixteen presidents in its history (excluding interim presidents). The current president, economist Morton O. Schapiro, succeeded Henry Bienen whose 14-year tenure ended on August 31, 2009. The president maintains a staff of vice presidents, directors, and other assistants for administrative, financial, faculty, and student matters. Kathleen Haggerty assumed the role of interim provost for the university in April 2020.

    Students are formally involved in the university’s administration through the Associated Student Government, elected representatives of the undergraduate students, and the Graduate Student Association, which represents the university’s graduate students.

    The admission requirements, degree requirements, courses of study, and disciplinary and degree recommendations for each of Northwestern’s 12 schools are determined by the voting members of that school’s faculty (assistant professor and above).

    Undergraduate and graduate schools

    Evanston Campus:

    Weinberg College of Arts and Sciences (1851)
    School of Communication (1878)
    Bienen School of Music (1895)
    McCormick School of Engineering and Applied Science (1909)
    Medill School of Journalism (1921)
    School of Education and Social Policy (1926)
    School of Professional Studies (1933)

    Graduate and professional

    Evanston Campus

    Kellogg School of Management (1908)
    The Graduate School

    Chicago Campus

    Feinberg School of Medicine (1859)
    Kellogg School of Management (1908)
    Pritzker School of Law (1859)
    School of Professional Studies (1933)

    Northwestern University had a dental school from 1891 to May 31, 2001, when it closed.

    Endowment

    In 1996, Princess Diana made a trip to Evanston to raise money for the university hospital’s Robert H. Lurie Comprehensive Cancer Center at the invitation of then President Bienen. Her visit raised a total of $1.5 million for cancer research.

    In 2003, Northwestern finished a five-year capital campaign that raised $1.55 billion, exceeding its fundraising goal by $550 million.

    In 2014, Northwestern launched the “We Will” campaign with a fundraising goal of $3.75 billion. As of December 31, 2019, the university has received $4.78 billion from 164,026 donors.

    Sustainability

    In January 2009, the Green Power Partnership (sponsored by the EPA) listed Northwestern as one of the top 10 universities in the country in purchasing energy from renewable sources. The university matches 74 million kilowatt hours (kWh) of its annual energy use with Green-e Certified Renewable Energy Certificates (RECs). This green power commitment represents 30 percent of the university’s total annual electricity use and places Northwestern in the EPA’s Green Power Leadership Club. The Initiative for Sustainability and Energy at Northwestern (ISEN), supporting research, teaching and outreach in these themes, was launched in 2008.

    Northwestern requires that all new buildings be LEED-certified. Silverman Hall on the Evanston campus was awarded Gold LEED Certification in 2010; Wieboldt Hall on the Chicago campus was awarded Gold LEED Certification in 2007, and the Ford Motor Company Engineering Design Center on the Evanston campus was awarded Silver LEED Certification in 2006. New construction and renovation projects will be designed to provide at least a 20% improvement over energy code requirements where feasible. At the beginning of the 2008–09 academic year, the university also released the Evanston Campus Framework Plan, which outlines plans for future development of the university’s Evanston campus. The plan not only emphasizes sustainable building construction, but also focuses on reducing the energy costs of transportation by optimizing pedestrian and bicycle access. Northwestern has had a comprehensive recycling program in place since 1990. The university recycles over 1,500 tons of waste, or 30% of all waste produced on campus, each year. All landscape waste at the university is composted.

    Academics

    Education and rankings

    Northwestern is a large, residential research university, and is frequently ranked among the top universities in the United States. The university is a leading institution in the fields of materials engineering, chemistry, business, economics, education, journalism, and communications. It is also prominent in law and medicine. Accredited by the Higher Learning Commission and the respective national professional organizations for chemistry, psychology, business, education, journalism, music, engineering, law, and medicine, the university offers 124 undergraduate programs and 145 graduate and professional programs. Northwestern conferred 2,190 bachelor’s degrees, 3,272 master’s degrees, 565 doctoral degrees, and 444 professional degrees in 2012–2013. Since 1951, Northwestern has awarded 520 honorary degrees. Northwestern also has chapters of academic honor societies such as Phi Beta Kappa (Alpha of Illinois), Eta Kappa Nu, Tau Beta Pi, Eta Sigma Phi (Beta Chapter), Lambda Pi Eta, and Alpha Sigma Lambda (Alpha Chapter).

    The four-year, full-time undergraduate program comprises the majority of enrollments at the university. Although there is no university-wide core curriculum, a foundation in the liberal arts and sciences is required for all majors; individual degree requirements are set by the faculty of each school. The university heavily emphasizes interdisciplinary learning, with 72% of undergrads combining two or more areas of study. Northwestern’s full-time undergraduate and graduate programs operate on an approximately 10-week academic quarter system with the academic year beginning in late September and ending in early June. Undergraduates typically take four courses each quarter and twelve courses in an academic year and are required to complete at least twelve quarters on campus to graduate. Northwestern offers honors, accelerated, and joint degree programs in medicine, science, mathematics, engineering, and journalism. The comprehensive doctoral graduate program has high coexistence with undergraduate programs.

    Despite being a mid-sized university, Northwestern maintains a relatively low student to faculty ratio of 6:1.

    Research

    Northwestern was elected to the Association of American Universities in 1917 and is classified as an R1 university, denoting “very high” research activity. Northwestern’s schools of management, engineering, and communication are among the most academically productive in the nation. The university received $887.3 million in research funding in 2019 and houses over 90 school-based and 40 university-wide research institutes and centers. Northwestern also supports nearly 1,500 research laboratories across two campuses, predominately in the medical and biological sciences.

    Northwestern is home to the Center for Interdisciplinary Exploration and Research in Astrophysics, Northwestern Institute for Complex Systems, Nanoscale Science and Engineering Center, Materials Research Center, Center for Quantum Devices, Institute for Policy Research, International Institute for Nanotechnology, Center for Catalysis and Surface Science, Buffet Center for International and Comparative Studies, the Initiative for Sustainability and Energy at Northwestern, and the Argonne/Northwestern Solar Energy Research Center among other centers for interdisciplinary research.

    Student body

    Northwestern enrolled 8,186 full-time undergraduate, 9,904 full-time graduate, and 3,856 part-time students in the 2019–2020 academic year. The freshman retention rate for that year was 98%. 86% of students graduated after four years and 92% graduated after five years. These numbers can largely be attributed to the university’s various specialized degree programs, such as those that allow students to earn master’s degrees with a one or two year extension of their undergraduate program.

    The undergraduate population is drawn from all 50 states and over 75 foreign countries. 20% of students in the Class of 2024 were Pell Grant recipients and 12.56% were first-generation college students. Northwestern also enrolls the 9th-most National Merit Scholars of any university in the nation.

    In Fall 2014, 40.6% of undergraduate students were enrolled in the Weinberg College of Arts and Sciences, 21.3% in the McCormick School of Engineering and Applied Science, 14.3% in the School of Communication, 11.7% in the Medill School of Journalism, 5.7% in the Bienen School of Music, and 6.4% in the School of Education and Social Policy. The five most commonly awarded undergraduate degrees are economics, journalism, communication studies, psychology, and political science. The Kellogg School of Management’s MBA, the School of Law’s JD, and the Feinberg School of Medicine’s MD are the three largest professional degree programs by enrollment. With 2,446 students enrolled in science, engineering, and health fields, the largest graduate programs by enrollment include chemistry, integrated biology, material sciences, electrical and computer engineering, neuroscience, and economics.

    Athletics

    Northwestern is a charter member of the Big Ten Conference. It is the conference’s only private university and possesses the smallest undergraduate enrollment (the next-smallest member, the University of Iowa, is roughly three times as large, with almost 22,000 undergraduates).

    Northwestern fields 19 intercollegiate athletic teams (8 men’s and 11 women’s) in addition to numerous club sports. 12 of Northwestern’s varsity programs have had NCAA or bowl postseason appearances. Northwestern is one of five private AAU members to compete in NCAA Power Five conferences (the other four being Duke, Stanford, USC, and Vanderbilt) and maintains a 98% NCAA Graduation Success Rate, the highest among Football Bowl Subdivision schools.

    In 2018, the school opened the Walter Athletics Center, a $270 million state of the art lakefront facility for its athletics teams.

    Nickname and mascot

    Before 1924, Northwestern teams were known as “The Purple” and unofficially as “The Fighting Methodists.” The name Wildcats was bestowed upon the university in 1924 by Wallace Abbey, a writer for the Chicago Daily Tribune, who wrote that even in a loss to the University of Chicago, “Football players had not come down from Evanston; wildcats would be a name better suited to “[Coach Glenn] Thistletwaite’s boys.” The name was so popular that university board members made “Wildcats” the official nickname just months later. In 1972, the student body voted to change the official nickname to “Purple Haze,” but the new name never stuck.

    The mascot of Northwestern Athletics is “Willie the Wildcat”. Prior to Willie, the team mascot had been a live, caged bear cub from the Lincoln Park Zoo named Furpaw, who was brought to the playing field on game days to greet the fans. After a losing season however, the team decided that Furpaw was to blame for its misfortune and decided to select a new mascot. “Willie the Wildcat” made his debut in 1933, first as a logo and then in three dimensions in 1947, when members of the Alpha Delta fraternity dressed as wildcats during a Homecoming Parade.

    Traditions

    Northwestern’s official motto, “Quaecumque sunt vera,” was adopted by the university in 1890. The Latin phrase translates to “Whatsoever things are true” and comes from the Epistle of Paul to the Philippians (Philippians 4:8), in which St. Paul admonishes the Christians in the Greek city of Philippi. In addition to this motto, the university crest features a Greek phrase taken from the Gospel of John inscribed on the pages of an open book, ήρης χάριτος και αληθείας or “the word full of grace and truth” (John 1:14).
    Alma Mater is the Northwestern Hymn. The original Latin version of the hymn was written in 1907 by Peter Christian Lutkin, the first dean of the School of Music from 1883 to 1931. In 1953, then Director-of-Bands John Paynter recruited an undergraduate music student, Thomas Tyra (’54), to write an English version of the song, which today is performed by the Marching Band during halftime at Wildcat football games and by the orchestra during ceremonies and other special occasions.
    Purple became Northwestern’s official color in 1892, replacing black and gold after a university committee concluded that too many other universities had used these colors. Today, Northwestern’s official color is purple, although white is something of an official color as well, being mentioned in both the university’s earliest song, Alma Mater (1907) (“Hail to purple, hail to white”) and in many university guidelines.
    The Rock, a 6-foot high quartzite boulder donated by the Class of 1902, originally served as a water fountain. It was painted over by students in the 1940s as a prank and has since become a popular vehicle of self-expression on campus.
    Armadillo Day, commonly known as Dillo Day, is the largest student-run music festival in the country. The festival is hosted every Spring on Northwestern’s Lakefront.
    Primal Scream is held every quarter at 9 p.m. on the Sunday before finals week. Students lean out of windows or gather in courtyards and scream to help relieve stress.
    In the past, students would throw marshmallows during football games, but this tradition has since been discontinued.

    Philanthropy

    One of Northwestern’s most notable student charity events is Dance Marathon, the most established and largest student-run philanthropy in the nation. The annual 30-hour event is among the most widely-attended events on campus. It has raised over $1 million for charity ever year since 2011 and has donated a total of $13 million to children’s charities since its conception.

    The Northwestern Community Development Corps (NCDC) is a student-run organization that connects hundreds of student volunteers to community development projects in Evanston and Chicago throughout the year. The group also holds a number of annual community events, including Project Pumpkin, a Halloween celebration that provides over 800 local children with carnival events and a safe venue to trick-or-treat each year.

    Many Northwestern students participate in the Freshman Urban Program, an initiative for students interested in community service to work on addressing social issues facing the city of Chicago, and the university’s Global Engagement Studies Institute (GESI) programs, including group service-learning expeditions in Asia, Africa, or Latin America in conjunction with the Foundation for Sustainable Development.

    Several internationally recognized non-profit organizations were established at Northwestern, including the World Health Imaging, Informatics and Telemedicine Alliance, a spin-off from an engineering student’s honors thesis.

    Media
    Print

    Established in 1881, The Daily Northwestern is the university’s main student newspaper and is published on weekdays during the academic year. It is directed entirely by undergraduate students and owned by the Students Publishing Company. Although it serves the Northwestern community, the Daily has no business ties to the university and is supported wholly by advertisers.
    North by Northwestern is an online undergraduate magazine established in September 2006 by students at the Medill School of Journalism. Published on weekdays, it consists of updates on news stories and special events throughout the year. It also publishes a quarterly print magazine.
    Syllabus is the university’s undergraduate yearbook. It is distributed in late May and features a culmination of the year’s events at Northwestern. First published in 1885, the yearbook is published by Students Publishing Company and edited by Northwestern students.
    Northwestern Flipside is an undergraduate satirical magazine. Founded in 2009, it publishes a weekly issue both in print and online.
    Helicon is the university’s undergraduate literary magazine. Established in 1979, it is published twice a year: a web issue is released in the winter and a print issue with a web complement is released in the spring.
    The Protest is Northwestern’s quarterly social justice magazine.
    The Northwestern division of Student Multicultural Affairs supports a number of publications for particular cultural groups including Ahora, a magazine about Hispanic and Latino/a culture and campus life; Al Bayan, published by the Northwestern Muslim-cultural Student Association; BlackBoard Magazine, a magazine centered around African-American student life; and NUAsian, a magazine and blog on Asian and Asian-American culture and issues.
    The Northwestern University Law Review is a scholarly legal publication and student organization at Northwestern University School of Law. Its primary purpose is to publish a journal of broad legal scholarship. The Law Review publishes six issues each year. Student editors make the editorial and organizational decisions and select articles submitted by professors, judges, and practitioners, as well as student pieces. The Law Review also publishes scholarly pieces weekly on the Colloquy.
    The Northwestern Journal of Technology and Intellectual Property is a law review published by an independent student organization at Northwestern University School of Law.
    The Northwestern Interdisciplinary Law Review is a scholarly legal publication published annually by an editorial board of Northwestern undergraduates. Its mission is to publish interdisciplinary legal research, drawing from fields such as history, literature, economics, philosophy, and art. Founded in 2008, the journal features articles by professors, law students, practitioners, and undergraduates. It is funded by the Buffett Center for International and Comparative Studies and the Office of the Provost.

    Web-based

    Established in January 2011, Sherman Ave is a humor website that often publishes content on Northwestern student life. Most of its staff writers are current Northwestern undergraduates writing under various pseudonyms. The website is popular among students for its interviews of prominent campus figures, Freshman Guide, and live-tweeting coverage of football games. In Fall 2012, the website promoted a satiric campaign to end the Vanderbilt University football team’s custom of clubbing baby seals.
    Politics & Policy is dedicated to the analysis of current events and public policy. Established in 2010 by students at the Weinberg College of Arts and Sciences, School of Communication, and Medill School of Journalism, the publication reaches students on more than 250 college campuses around the world. Run entirely by undergraduates, it is published several times a week and features material ranging from short summaries of events to extended research pieces. The publication is financed in part by the Buffett Center.
    Northwestern Business Review is a campus source for business news. Founded in 2005, it has an online presence as well as a quarterly print schedule.
    TriQuarterly Online (formerly TriQuarterly) is a literary magazine published twice a year featuring poetry, fiction, nonfiction, drama, literary essays, reviews, blog posts, and art.
    The Queer Reader is Northwestern’s first radical feminist and LGBTQ+ publication.

    Radio, film, and television

    WNUR (89.3 FM) is a 7,200-watt radio station that broadcasts to the city of Chicago and its northern suburbs. WNUR’s programming consists of music (jazz, classical, and rock), literature, politics, current events, varsity sports (football, men’s and women’s basketball, baseball, softball, and women’s lacrosse), and breaking news on weekdays.
    Studio 22 is a student-run production company that produces roughly ten films each year. The organization financed the first film Zach Braff directed, and many of its films have featured students who would later go into professional acting, including Zach Gilford of Friday Night Lights.
    Applause for a Cause is currently the only student-run production company in the nation to create feature-length films for charity. It was founded in 2010 and has raised over $5,000 to date for various local and national organizations across the United States.
    Northwestern News Network is a student television news and sports network, serving the Northwestern and Evanston communities. Its studios and newsroom are located on the fourth floor of the McCormick Tribune Center on Northwestern’s Evanston campus. NNN is funded by the Medill School of Journalism.

     
  • richardmitnick 8:52 am on December 28, 2020 Permalink | Reply
    Tags: "2020 Was a Breakout Year for Crispr", , , DNA, For thousands of years humans have been modifying the DNA by breeding animals to produce the most desirable traits. With Crispr one no longer has to wait generations to make significant genetic change, , , On December 21 the US Department of Agriculture which regulates changes made to crops announced a proposal to take charge of overseeing gene editing in animals bred for food as well., Scientists in Seattle and Boston published a study showing they had discovered a way to harness a strange enzyme in biofilm-forming bacteria to make precise changes to mitochondrial DNA., The FDA authorized two Crispr-based tests both for detecting SARS-CoV-2., The Nobel Prize, The pandemic sped up the need to develop commercial diagnostics without the need for expensive lab instruments., The US Food and Drug Administration decided in 2017 to regulate changes made by Crispr and other molecular tools as animal drugs.,   

    From WIRED: “2020 Was a Breakout Year for Crispr” 


    From WIRED

    12.28.2020
    Megan Molteni

    Between glimpses of a medical cure and winning science’s shiniest prize, this proved to the gene-editing technology’s biggest year yet.

    1
    Credit: Tracy J. Lee; Elena Lacey; Getty Images.

    It will be difficult to remember 2020 as anything other than the year Covid-19 drew the world to a socially distanced standstill. But while thousands of life scientists pivoted to trying to understand how the novel coronavirus wreaks havoc on the human body, and others transformed their labs into pop-up testing facilities, the field of Crispr gene editing nevertheless persisted. In fact, it triumphed. Here are five of the (mostly coronavirus-free) breakthroughs in the Crisprsphere that you might have missed in 2020.

    1. Crispr takes on blood diseases

    Last summer, doctors in Tennessee injected Victoria Gray—a 34-year-old sickle cell disease patient—with billions of her own stem cells that scientists in Massachusetts had reprogrammed with Crispr to produce healthy blood cells. The hours-long infusion made her the first American with a heritable disease to be treated with the experimental gene-editing technology. And it appears to be working.

    This July, Gray celebrated a year of being symptom-free. In December, a team that includes researchers from the two companies that developed the treatment—CRISPR Therapeutics and Vertex Pharmaceuticals—published promising results from a clinical trial, which is also treating patients in Germany who suffer from a related disease called ß-thalassaemia. In both groups of patients, the treatment seems to be safe, and it so far has eliminated the need for regular blood transfusions. It’s still too soon to say how long the effects will last, so don’t call it a cure just yet. But the consequences could be huge. Sickle cell disease and ß-thalassaemia are among the most common genetic disorders caused by mutations to a single gene, affecting millions of people worldwide.

    2. The stable of gene-edited animals grows

    For thousands of years, humans have been modifying the DNA of our closest furry and feathered friends by breeding animals to produce the most desirable traits. With Crispr, one no longer has to wait generations to make significant genetic changes. This year, researchers welcomed a raft of world-first barnyard creatures. Among them are pandemic-proof pigs, whose cells have been edited to remove the molecular lock-and-key mechanism that a variety of respiratory viruses use to infect them, and chickens Crispr’d to make them impervious to a common bird disease caused by the avian leukosis virus.

    In April, scientists at UC Davis birthed Cosmo, a black bull calf whose genome had been altered so that 75 percent of his future offspring—rather than the natural 50 percent—will be male. He’s the first Crispr knock-in bovine, and proof that one day making all-male beef herds might be possible. (Female beef cattle convert feed to protein less efficiently, so in theory, the approach could mean fewer animals on the land, making it a win both for ranchers and the environment.)

    For years, the future of gene editing in agricultural animals has been uncertain, since the US Food and Drug Administration decided in 2017 to regulate changes made by Crispr and other molecular tools as animal drugs. But on December 21, the US Department of Agriculture, which (much more leniently) regulates similar changes made to crops, announced a proposal to take charge of overseeing gene editing in animals bred for food as well. The move, if it goes through, could make it much easier for breeders to bring Crispr’d cows, chickens, pigs, and sheep to market in the US.

    3. Disease detectors hit the market

    For the past few years, startups spun out of Crispr patent rivals UC Berkeley and the Broad Institute have been sprinting to develop commercial diagnostics without the need for expensive lab instruments. The idea is to use Crispr’s programmable gene-seeking capabilities to pick up bits of foreign genetic material—from a virus, bacteria, or fungus—circulating in a sick person’s bodily fluids, and deliver those results via something that looks like a pregnancy test. Tests made with disposable paper strips are cheap and can go into the field or into people’s homes, greatly expanding their reach.

    The pandemic sped up the need for such tests. This summer, the FDA authorized two Crispr-based tests, both for detecting SARS-CoV-2. Boston-based Sherlock Biosciences received the green light for its test in May, and the Bay Area’s Mammoth Biosciences followed in August. It marked the first time the FDA has allowed a Crispr-based diagnostic tool to be used on patients. The tests still need to be analyzed in a lab, but they are faster than the standard method for detecting SARS-CoV-2, called PCR, which typically takes four to eight hours to run. The new tests return results in about one hour. Both companies are currently working toward versions of the test that can be conducted at home.

    “Before the pandemic, there was a lot of general excitement about the potential of next-generation diagnostics to decentralize the testing industry, but there was still a lot of inertia,” Mammoth Bioscience CEO Trevor Martin told WIRED this summer. The coronavirus, he says, shocked the industry out of it. “Things that would have taken years are now things that must be done in months.”

    4. Mitochondria join the genome-editing party

    Crispr can make precise cuts to the genomes of pretty much any organism on the planet. But mitochondria—cells’ energy-producing nanofactories—have their own DNA separate from the rest of the genome. Until recently, this DNA-targeting tool couldn’t manage to make changes to the genetic code coiled inside them.

    And unlike chromosomes, which you inherit from both parents, mitochondrial DNA comes only from your maternal side. Mutations in mitochondrial DNA can cripple the cell’s ability to generate energy and lead to debilitating, often fatal conditions that affect about one in 6,500 people worldwide. Up until now, scientists have tried preventing mitochondrial disease by swapping out one egg’s mitochondria for another, a procedure commonly known as three-person IVF, which is currently banned in the US.

    But this summer, scientists in Seattle and Boston published a study [Nature] showing they had discovered a way to harness a strange enzyme found in biofilm-forming bacteria to make precise changes to mitochondrial DNA.

    3
    A mitochondrion, as seen through a transmission electron microscope. The membranes (in pink) prevent CRISPR–Cas9 genome editing.Credit: CNRI/SPL.

    The work was led by David Liu, whose evolution-hacking lab at the Broad Institute and Harvard University has churned out a series of groundbreaking DNA-altering tools over the last few years. The new system has not yet been tested in humans, and clinical trials are still a long way off, but the discovery opens up another promising avenue for treating mitochondrial disease.

    5. Crispr’s Nobel victory

    Last but certainly not least, in October, the 2020 Nobel Prize in Chemistry was awarded to Emmanuelle Charpentier and Jennifer Doudna for Crispr genome editing. It was both a stunning choice (as a DNA-altering tool, Crispr has only been around for 8 years) and a completely expected one. Crispr has completely revolutionized biological research since its arrival in 2012; scientists have since published more than 300,000 studies using the tool to manipulate the genomes of organisms across every kingdom, including mosquitoes, tomatoes, King Charles Spaniels, and even humans. It’s cheap, fast, and easy enough for almost anyone to use. Today, scientists can order custom-made Crispr components with the click of a button.

    The win also broke barriers of another sort. Doudna and Charpentier are the first women to win a Nobel Prize in the sciences together. And there had been much speculation about who the prize would actually go to, since credit for the creation story of Crispr is still a matter of hot debate (and litigation). “Many women think that, no matter what they do, their work will never be recognized the way it would be if they were a man,” said Doudna upon learning the news. “And I think [this prize] refutes that. It makes a strong statement that women can do science, women can do chemistry, and that great science is recognized and honored.” In other words, she continued, “women rock.” We couldn’t agree more.

    See the full article here .

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    Please help promote STEM in your local schools.

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