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  • richardmitnick 1:23 pm on July 23, 2021 Permalink | Reply
    Tags: "Stanford researchers develop tool to drastically speed up the study of enzymes", A chemical reaction that would take longer than the lifetime of the universe to happen on its own can occur in seconds with the aid of enzymes., A new tool that enables thousands of tiny experiments to run simultaneously on a single polymer chip will let scientists study enzymes faster and more comprehensively than ever before., , Because each tiny chamber contains only a thousandth of a millionth of a liter of material the scientists can engineer thousands of variants of an enzyme in a single device and study them in parallel., Biology, , Enzyme experiments on a chip, , Google-funded AlphaFold project: designed to deduce an enzyme’s complicated 3D shape from its amino acid sequence alone., HT-MEK combines two existing technologies: microfluidics and cell-free protein synthesis [explained in the blog post.], HT-MEK could also accelerate an approach to drug development called allosteric targeting which aims to increase drug specificity by targeting beyond an enzyme’s active site., HT-MEK may even allow scientists to reverse-engineer enzymes and design bespoke varieties of their own., HT-MEK: High-Throughput Microfluidic Enzyme Kinetics, If widely adopted HT-MEK could not only improve our basic understanding of enzyme function but also catalyze advances in medicine and industry.,   

    From Stanford University (US) : “Stanford researchers develop tool to drastically speed up the study of enzymes” 

    Stanford University Name

    From Stanford University (US)

    July 22, 2021
    Ker Than

    A new tool that enables thousands of tiny experiments to run simultaneously on a single polymer chip will let scientists study enzymes faster and more comprehensively than ever before.

    1
    HT-MEK – short for High-Throughput Microfluidic Enzyme Kinetics – combines microfluidics and cell-free protein synthesis technologies to dramatically speed up the study of enzymes. Credit: Daniel Mokhtari.

    For much of human history, animals and plants were perceived to follow a different set of rules than rest of the universe. In the 18th and 19th centuries, this culminated in a belief that living organisms were infused by a non-physical energy or “life force” that allowed them to perform remarkable transformations that couldn’t be explained by conventional chemistry or physics alone.

    Scientists now understand that these transformations are powered by enzymes – protein molecules comprised of chains of amino acids that act to speed up, or catalyze, the conversion of one kind of molecule (substrates) into another (products). In so doing, they enable reactions such as digestion and fermentation – and all of the chemical events that happen in every one of our cells – that, left alone, would happen extraordinarily slowly.

    “A chemical reaction that would take longer than the lifetime of the universe to happen on its own can occur in seconds with the aid of enzymes,” said Polly Fordyce, an assistant professor of bioengineering and of genetics at Stanford University.

    While much is now known about enzymes, including their structures and the chemical groups they use to facilitate reactions, the details surrounding how their forms connect to their functions, and how they pull off their biochemical wizardry with such extraordinary speed and specificity are still not well understood.

    A new technique, developed by Fordyce and her colleagues at Stanford and detailed this week in the journal Science, could help change that. Dubbed HT-MEK — short for High-Throughput Microfluidic Enzyme Kinetics — the technique can compress years of work into just a few weeks by enabling thousands of enzyme experiments to be performed simultaneously. “Limits in our ability to do enough experiments have prevented us from truly dissecting and understanding enzymes,” said study co-leader Dan Herschlag, a professor of biochemistry at Stanford’s School of Medicine.

    2
    Closeup image of the HT-MEK device shows the individual nanoliter-sized chambers where enzyme experiments are performed. Credit: Daniel Mokhtari.

    By allowing scientists to deeply probe beyond the small “active site” of an enzyme where substrate binding occurs, HT-MEK could reveal clues about how even the most distant parts of enzymes work together to achieve their remarkable reactivity.

    “It’s like we’re now taking a flashlight and instead of just shining it on the active site we’re shining it over the entire enzyme,” Fordyce said. “When we did this, we saw a lot of things we didn’t expect.”

    Enzymatic tricks

    HT-MEK is designed to replace a laborious process for purifying enzymes that has traditionally involved engineering bacteria to produce a particular enzyme, growing them in large beakers, bursting open the microbes and then isolating the enzyme of interest from all the other unwanted cellular components. To piece together how an enzyme works, scientists introduce intentional mistakes into its DNA blueprint and then analyze how these mutations affect catalysis.

    This process is expensive and time consuming, however, so like an audience raptly focused on the hands of a magician during a conjuring trick, researchers have mostly limited their scientific investigations to the active sites of enzymes. “We know a lot about the part of the enzyme where the chemistry occurs because people have made mutations there to see what happens. But that’s taken decades,” Fordyce said.

    But as any connoisseur of magic tricks knows, the key to a successful illusion can lie not just in the actions of the magician’s fingers, but might also involve the deft positioning of an arm or the torso, a misdirecting patter or discrete actions happening offstage, invisible to the audience. HT-MEK allows scientists to easily shift their gaze to parts of the enzyme beyond the active site and to explore how, for example, changing the shape of an enzyme’s surface might affect the workings of its interior.

    “We ultimately would like to do enzymatic tricks ourselves,” Fordyce said. “But the first step is figuring out how it’s done before we can teach ourselves to do it.”

    Enzyme experiments on a chip

    The technology behind HT-MEK was developed and refined over six years through a partnership between the labs of Fordyce and Herschlag. “This is an amazing case of engineering and enzymology coming together to — we hope — revolutionize a field,” Herschlag said. “This project went beyond your typical collaboration — it was a group of people working jointly to solve a very difficult problem — and continues with the methodologies in place to try to answer difficult questions.”

    HT-MEK combines two existing technologies to rapidly speed up enzyme analysis. The first is microfluidics, which involves molding polymer chips to create microscopic channels for the precise manipulation of fluids. “Microfluidics shrinks the physical space to do these fluidic experiments in the same way that integrated circuits reduced the real estate needed for computing,” Fordyce said. “In enzymology, we are still doing things in these giant liter-sized flasks. Everything is a huge volume and we can’t do many things at once.”

    The second is cell-free protein synthesis, a technology that takes only those crucial pieces of biological machinery required for protein production and combines them into a soupy extract that can be used to create enzymes synthetically, without requiring living cells to serve as incubators.

    “We’ve automated it so that we can use printers to deposit microscopic spots of synthetic DNA coding for the enzyme that we want onto a slide and then align nanoliter-sized chambers filled with the protein starter mix over the spots,” Fordyce explained.

    3
    The scientists used HT-MEK to study how mutations to different parts of a well-studied enzyme called PafA affected its catalytic ability. Credit: Daniel Mokhtari.

    Because each tiny chamber contains only a thousandth of a millionth of a liter of material the scientists can engineer thousands of variants of an enzyme in a single device and study them in parallel. By tweaking the DNA instructions in each chamber, they can modify the chains of amino acid molecules that comprise the enzyme. In this way, it’s possible to systematically study how different modifications to an enzyme affects its folding, catalytic ability and ability to bind small molecules and other proteins.

    When the team applied their technique to a well-studied enzyme called PafA, they found that mutations well beyond the active site affected its ability to catalyze chemical reactions — indeed, most of the amino acids, or “residues,” making up the enzyme had effects.

    The scientists also discovered that a surprising number of mutations caused PafA to misfold into an alternate state that was unable to perform catalysis. “Biochemists have known for decades that misfolding can occur but it’s been extremely difficult to identify these cases and even more difficult to quantitatively estimate the amount of this misfolded stuff,” said study co-first author Craig Markin, a research scientist with joint appointments in the Fordyce and Herschlag labs.

    “This is one enzyme out of thousands and thousands,” Herschlag emphasized. “We expect there to be more discoveries and more surprises.”

    Accelerating advances

    If widely adopted HT-MEK could not only improve our basic understanding of enzyme function but also catalyze advances in medicine and industry, the researchers say. “A lot of the industrial chemicals we use now are bad for the environment and are not sustainable. But enzymes work most effectively in the most environmentally benign substance we have — water,” said study co-first author Daniel Mokhtari, a Stanford graduate student in the Herschlag and Fordyce labs.


    Movie shows fluorescence buildup denoting catalytic reactions in a portion of the HT-MEK device over time. Credit: Craig Markin and Daniel Mokhtari.

    HT-MEK could also accelerate an approach to drug development called allosteric targeting which aims to increase drug specificity by targeting beyond an enzyme’s active site. Enzymes are popular pharmaceutical targets because of the key role they play in biological processes. But some are considered “undruggable” because they belong to families of related enzymes that share the same or very similar active sites, and targeting them can lead to side effects. The idea behind allosteric targeting is to create drugs that can bind to parts of enzymes that tend to be more differentiated, like their surfaces, but still control particular aspects of catalysis. “With PafA, we saw functional connectivity between the surface and the active site, so that gives us hope that other enzymes will have similar targets,” Markin said. “If we can identify where allosteric targets are, then we’ll be able to start on the harder job of actually designing drugs for them.”

    The sheer amount of data that HT-MEK is expected to generate will also be a boon to computational approaches and machine learning algorithms, like the Google-funded AlphaFold project designed to deduce an enzyme’s complicated 3D shape from its amino acid sequence alone. “If machine learning is to have any chance of accurately predicting enzyme function, it will need the kind of data HT-MEK can provide to train on,” Mokhtari said.

    Much further down the road, HT-MEK may even allow scientists to reverse-engineer enzymes and design bespoke varieties of their own. “Plastics are a great example,” Fordyce said. “We would love to create enzymes that can degrade plastics into nontoxic and harmless pieces. If it were really true that the only part of an enzyme that matters is its active site, then we’d be able to do that and more already. Many people have tried and failed, and it’s thought that one reason why we can’t is because the rest of the enzyme is important for getting the active site in just the right shape and to wiggle in just the right way.”

    Herschlag hopes that adoption of HT-MEK among scientists will be swift. “If you’re an enzymologist trying to learn about a new enzyme and you have the opportunity to look at 5 or 10 mutations over six months or 100 or 1,000 mutants of your enzyme over the same period, which would you choose?” he said. “This is a tool that has the potential to supplant traditional methods for an entire community.”

    See the full article here .


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    Stanford University campus. No image credit

    Stanford University (US)

    Leland and Jane Stanford founded the University to “promote the public welfare by exercising an influence on behalf of humanity and civilization.” Stanford opened its doors in 1891, and more than a century later, it remains dedicated to finding solutions to the great challenges of the day and to preparing our students for leadership in today’s complex world. Stanford, is an American private research university located in Stanford, California on an 8,180-acre (3,310 ha) campus near Palo Alto. Since 1952, more than 54 Stanford faculty, staff, and alumni have won the Nobel Prize, including 19 current faculty members.

    Stanford University, officially Leland Stanford Junior University, is a private research university located in Stanford, California. Stanford was founded in 1885 by Leland and Jane Stanford in memory of their only child, Leland Stanford Jr., who had died of typhoid fever at age 15 the previous year. Stanford is consistently ranked as among the most prestigious and top universities in the world by major education publications. It is also one of the top fundraising institutions in the country, becoming the first school to raise more than a billion dollars in a year.

    Leland Stanford was a U.S. senator and former governor of California who made his fortune as a railroad tycoon. The school admitted its first students on October 1, 1891, as a coeducational and non-denominational institution. Stanford University struggled financially after the death of Leland Stanford in 1893 and again after much of the campus was damaged by the 1906 San Francisco earthquake. Following World War II, provost Frederick Terman supported faculty and graduates’ entrepreneurialism to build self-sufficient local industry in what would later be known as Silicon Valley.

    The university is organized around seven schools: three schools consisting of 40 academic departments at the undergraduate level as well as four professional schools that focus on graduate programs in law, medicine, education, and business. All schools are on the same campus. Students compete in 36 varsity sports, and the university is one of two private institutions in the Division I FBS Pac-12 Conference. It has gained 126 NCAA team championships, and Stanford has won the NACDA Directors’ Cup for 24 consecutive years, beginning in 1994–1995. In addition, Stanford students and alumni have won 270 Olympic medals including 139 gold medals.

    As of October 2020, 84 Nobel laureates, 28 Turing Award laureates, and eight Fields Medalists have been affiliated with Stanford as students, alumni, faculty, or staff. In addition, Stanford is particularly noted for its entrepreneurship and is one of the most successful universities in attracting funding for start-ups. Stanford alumni have founded numerous companies, which combined produce more than $2.7 trillion in annual revenue, roughly equivalent to the 7th largest economy in the world (as of 2020). Stanford is the alma mater of one president of the United States (Herbert Hoover), 74 living billionaires, and 17 astronauts. It is also one of the leading producers of Fulbright Scholars, Marshall Scholars, Rhodes Scholars, and members of the United States Congress.

    Stanford University was founded in 1885 by Leland and Jane Stanford, dedicated to Leland Stanford Jr, their only child. The institution opened in 1891 on Stanford’s previous Palo Alto farm.

    Jane and Leland Stanford modeled their university after the great eastern universities, most specifically Cornell University. Stanford opened being called the “Cornell of the West” in 1891 due to faculty being former Cornell affiliates (either professors, alumni, or both) including its first president, David Starr Jordan, and second president, John Casper Branner. Both Cornell and Stanford were among the first to have higher education be accessible, nonsectarian, and open to women as well as to men. Cornell is credited as one of the first American universities to adopt this radical departure from traditional education, and Stanford became an early adopter as well.

    Despite being impacted by earthquakes in both 1906 and 1989, the campus was rebuilt each time. In 1919, The Hoover Institution on War, Revolution and Peace was started by Herbert Hoover to preserve artifacts related to World War I. The Stanford Medical Center, completed in 1959, is a teaching hospital with over 800 beds. The DOE’s SLAC National Accelerator Laboratory(US)(originally named the Stanford Linear Accelerator Center), established in 1962, performs research in particle physics.

    Land

    Most of Stanford is on an 8,180-acre (12.8 sq mi; 33.1 km^2) campus, one of the largest in the United States. It is located on the San Francisco Peninsula, in the northwest part of the Santa Clara Valley (Silicon Valley) approximately 37 miles (60 km) southeast of San Francisco and approximately 20 miles (30 km) northwest of San Jose. In 2008, 60% of this land remained undeveloped.

    Stanford’s main campus includes a census-designated place within unincorporated Santa Clara County, although some of the university land (such as the Stanford Shopping Center and the Stanford Research Park) is within the city limits of Palo Alto. The campus also includes much land in unincorporated San Mateo County (including the SLAC National Accelerator Laboratory and the Jasper Ridge Biological Preserve), as well as in the city limits of Menlo Park (Stanford Hills neighborhood), Woodside, and Portola Valley.

    Non-central campus

    Stanford currently operates in various locations outside of its central campus.

    On the founding grant:

    Jasper Ridge Biological Preserve is a 1,200-acre (490 ha) natural reserve south of the central campus owned by the university and used by wildlife biologists for research.
    SLAC National Accelerator Laboratory is a facility west of the central campus operated by the university for the Department of Energy. It contains the longest linear particle accelerator in the world, 2 miles (3.2 km) on 426 acres (172 ha) of land.
    Golf course and a seasonal lake: The university also has its own golf course and a seasonal lake (Lake Lagunita, actually an irrigation reservoir), both home to the vulnerable California tiger salamander. As of 2012 Lake Lagunita was often dry and the university had no plans to artificially fill it.

    Off the founding grant:

    Hopkins Marine Station, in Pacific Grove, California, is a marine biology research center owned by the university since 1892.
    Study abroad locations: unlike typical study abroad programs, Stanford itself operates in several locations around the world; thus, each location has Stanford faculty-in-residence and staff in addition to students, creating a “mini-Stanford”.

    Redwood City campus for many of the university’s administrative offices located in Redwood City, California, a few miles north of the main campus. In 2005, the university purchased a small, 35-acre (14 ha) campus in Midpoint Technology Park intended for staff offices; development was delayed by The Great Recession. In 2015 the university announced a development plan and the Redwood City campus opened in March 2019.

    The Bass Center in Washington, DC provides a base, including housing, for the Stanford in Washington program for undergraduates. It includes a small art gallery open to the public.

    China: Stanford Center at Peking University, housed in the Lee Jung Sen Building, is a small center for researchers and students in collaboration with Beijing University [北京大学](CN) (Kavli Institute for Astronomy and Astrophysics at Peking University(CN) (KIAA-PKU).

    Administration and organization

    Stanford is a private, non-profit university that is administered as a corporate trust governed by a privately appointed board of trustees with a maximum membership of 38. Trustees serve five-year terms (not more than two consecutive terms) and meet five times annually.[83] A new trustee is chosen by the current trustees by ballot. The Stanford trustees also oversee the Stanford Research Park, the Stanford Shopping Center, the Cantor Center for Visual Arts, Stanford University Medical Center, and many associated medical facilities (including the Lucile Packard Children’s Hospital).

    The board appoints a president to serve as the chief executive officer of the university, to prescribe the duties of professors and course of study, to manage financial and business affairs, and to appoint nine vice presidents. The provost is the chief academic and budget officer, to whom the deans of each of the seven schools report. Persis Drell became the 13th provost in February 2017.

    As of 2018, the university was organized into seven academic schools. The schools of Humanities and Sciences (27 departments), Engineering (nine departments), and Earth, Energy & Environmental Sciences (four departments) have both graduate and undergraduate programs while the Schools of Law, Medicine, Education and Business have graduate programs only. The powers and authority of the faculty are vested in the Academic Council, which is made up of tenure and non-tenure line faculty, research faculty, senior fellows in some policy centers and institutes, the president of the university, and some other academic administrators, but most matters are handled by the Faculty Senate, made up of 55 elected representatives of the faculty.

    The Associated Students of Stanford University (ASSU) is the student government for Stanford and all registered students are members. Its elected leadership consists of the Undergraduate Senate elected by the undergraduate students, the Graduate Student Council elected by the graduate students, and the President and Vice President elected as a ticket by the entire student body.

    Stanford is the beneficiary of a special clause in the California Constitution, which explicitly exempts Stanford property from taxation so long as the property is used for educational purposes.

    Endowment and donations

    The university’s endowment, managed by the Stanford Management Company, was valued at $27.7 billion as of August 31, 2019. Payouts from the Stanford endowment covered approximately 21.8% of university expenses in the 2019 fiscal year. In the 2018 NACUBO-TIAA survey of colleges and universities in the United States and Canada, only Harvard University(US), the University of Texas System(US), and Yale University(US) had larger endowments than Stanford.

    In 2006, President John L. Hennessy launched a five-year campaign called the Stanford Challenge, which reached its $4.3 billion fundraising goal in 2009, two years ahead of time, but continued fundraising for the duration of the campaign. It concluded on December 31, 2011, having raised a total of $6.23 billion and breaking the previous campaign fundraising record of $3.88 billion held by Yale. Specifically, the campaign raised $253.7 million for undergraduate financial aid, as well as $2.33 billion for its initiative in “Seeking Solutions” to global problems, $1.61 billion for “Educating Leaders” by improving K-12 education, and $2.11 billion for “Foundation of Excellence” aimed at providing academic support for Stanford students and faculty. Funds supported 366 new fellowships for graduate students, 139 new endowed chairs for faculty, and 38 new or renovated buildings. The new funding also enabled the construction of a facility for stem cell research; a new campus for the business school; an expansion of the law school; a new Engineering Quad; a new art and art history building; an on-campus concert hall; a new art museum; and a planned expansion of the medical school, among other things. In 2012, the university raised $1.035 billion, becoming the first school to raise more than a billion dollars in a year.

    Research centers and institutes

    DOE’s SLAC National Accelerator Laboratory(US)
    Stanford Research Institute, a center of innovation to support economic development in the region.
    Hoover Institution, a conservative American public policy institution and research institution that promotes personal and economic liberty, free enterprise, and limited government.
    Hasso Plattner Institute of Design, a multidisciplinary design school in cooperation with the Hasso Plattner Institute of University of Potsdam [Universität Potsdam](DE) that integrates product design, engineering, and business management education).
    Martin Luther King Jr. Research and Education Institute, which grew out of and still contains the Martin Luther King Jr. Papers Project.
    John S. Knight Fellowship for Professional Journalists
    Center for Ocean Solutions
    Together with UC Berkeley(US) and UC San Francisco(US), Stanford is part of the Biohub, a new medical science research center founded in 2016 by a $600 million commitment from Facebook CEO and founder Mark Zuckerberg and pediatrician Priscilla Chan.

    Discoveries and innovation

    Natural sciences

    Biological synthesis of deoxyribonucleic acid (DNA) – Arthur Kornberg synthesized DNA material and won the Nobel Prize in Physiology or Medicine 1959 for his work at Stanford.
    First Transgenic organism – Stanley Cohen and Herbert Boyer were the first scientists to transplant genes from one living organism to another, a fundamental discovery for genetic engineering. Thousands of products have been developed on the basis of their work, including human growth hormone and hepatitis B vaccine.
    Laser – Arthur Leonard Schawlow shared the 1981 Nobel Prize in Physics with Nicolaas Bloembergen and Kai Siegbahn for his work on lasers.
    Nuclear magnetic resonance – Felix Bloch developed new methods for nuclear magnetic precision measurements, which are the underlying principles of the MRI.

    Computer and applied sciences

    ARPANETStanford Research Institute, formerly part of Stanford but on a separate campus, was the site of one of the four original ARPANET nodes.

    Internet—Stanford was the site where the original design of the Internet was undertaken. Vint Cerf led a research group to elaborate the design of the Transmission Control Protocol (TCP/IP) that he originally co-created with Robert E. Kahn (Bob Kahn) in 1973 and which formed the basis for the architecture of the Internet.

    Frequency modulation synthesis – John Chowning of the Music department invented the FM music synthesis algorithm in 1967, and Stanford later licensed it to Yamaha Corporation.

    Google – Google began in January 1996 as a research project by Larry Page and Sergey Brin when they were both PhD students at Stanford. They were working on the Stanford Digital Library Project (SDLP). The SDLP’s goal was “to develop the enabling technologies for a single, integrated and universal digital library” and it was funded through the National Science Foundation, among other federal agencies.

    Klystron tube – invented by the brothers Russell and Sigurd Varian at Stanford. Their prototype was completed and demonstrated successfully on August 30, 1937. Upon publication in 1939, news of the klystron immediately influenced the work of U.S. and UK researchers working on radar equipment.

    RISCARPA funded VLSI project of microprocessor design. Stanford and UC Berkeley are most associated with the popularization of this concept. The Stanford MIPS would go on to be commercialized as the successful MIPS architecture, while Berkeley RISC gave its name to the entire concept, commercialized as the SPARC. Another success from this era were IBM’s efforts that eventually led to the IBM POWER instruction set architecture, PowerPC, and Power ISA. As these projects matured, a wide variety of similar designs flourished in the late 1980s and especially the early 1990s, representing a major force in the Unix workstation market as well as embedded processors in laser printers, routers and similar products.
    SUN workstation – Andy Bechtolsheim designed the SUN workstation for the Stanford University Network communications project as a personal CAD workstation, which led to Sun Microsystems.

    Businesses and entrepreneurship

    Stanford is one of the most successful universities in creating companies and licensing its inventions to existing companies; it is often held up as a model for technology transfer. Stanford’s Office of Technology Licensing is responsible for commercializing university research, intellectual property, and university-developed projects.

    The university is described as having a strong venture culture in which students are encouraged, and often funded, to launch their own companies.

    Companies founded by Stanford alumni generate more than $2.7 trillion in annual revenue, equivalent to the 10th-largest economy in the world.

    Some companies closely associated with Stanford and their connections include:

    Hewlett-Packard, 1939, co-founders William R. Hewlett (B.S, PhD) and David Packard (M.S).
    Silicon Graphics, 1981, co-founders James H. Clark (Associate Professor) and several of his grad students.
    Sun Microsystems, 1982, co-founders Vinod Khosla (M.B.A), Andy Bechtolsheim (PhD) and Scott McNealy (M.B.A).
    Cisco, 1984, founders Leonard Bosack (M.S) and Sandy Lerner (M.S) who were in charge of Stanford Computer Science and Graduate School of Business computer operations groups respectively when the hardware was developed.[163]
    Yahoo!, 1994, co-founders Jerry Yang (B.S, M.S) and David Filo (M.S).
    Google, 1998, co-founders Larry Page (M.S) and Sergey Brin (M.S).
    LinkedIn, 2002, co-founders Reid Hoffman (B.S), Konstantin Guericke (B.S, M.S), Eric Lee (B.S), and Alan Liu (B.S).
    Instagram, 2010, co-founders Kevin Systrom (B.S) and Mike Krieger (B.S).
    Snapchat, 2011, co-founders Evan Spiegel and Bobby Murphy (B.S).
    Coursera, 2012, co-founders Andrew Ng (Associate Professor) and Daphne Koller (Professor, PhD).

    Student body

    Stanford enrolled 6,996 undergraduate and 10,253 graduate students as of the 2019–2020 school year. Women comprised 50.4% of undergraduates and 41.5% of graduate students. In the same academic year, the freshman retention rate was 99%.

    Stanford awarded 1,819 undergraduate degrees, 2,393 master’s degrees, 770 doctoral degrees, and 3270 professional degrees in the 2018–2019 school year. The four-year graduation rate for the class of 2017 cohort was 72.9%, and the six-year rate was 94.4%. The relatively low four-year graduation rate is a function of the university’s coterminal degree (or “coterm”) program, which allows students to earn a master’s degree as a 1-to-2-year extension of their undergraduate program.

    As of 2010, fifteen percent of undergraduates were first-generation students.

    Athletics

    As of 2016 Stanford had 16 male varsity sports and 20 female varsity sports, 19 club sports and about 27 intramural sports. In 1930, following a unanimous vote by the Executive Committee for the Associated Students, the athletic department adopted the mascot “Indian.” The Indian symbol and name were dropped by President Richard Lyman in 1972, after objections from Native American students and a vote by the student senate. The sports teams are now officially referred to as the “Stanford Cardinal,” referring to the deep red color, not the cardinal bird. Stanford is a member of the Pac-12 Conference in most sports, the Mountain Pacific Sports Federation in several other sports, and the America East Conference in field hockey with the participation in the inter-collegiate NCAA’s Division I FBS.

    Its traditional sports rival is the University of California, Berkeley, the neighbor to the north in the East Bay. The winner of the annual “Big Game” between the Cal and Cardinal football teams gains custody of the Stanford Axe.

    Stanford has had at least one NCAA team champion every year since the 1976–77 school year and has earned 126 NCAA national team titles since its establishment, the most among universities, and Stanford has won 522 individual national championships, the most by any university. Stanford has won the award for the top-ranked Division 1 athletic program—the NACDA Directors’ Cup, formerly known as the Sears Cup—annually for the past twenty-four straight years. Stanford athletes have won medals in every Olympic Games since 1912, winning 270 Olympic medals total, 139 of them gold. In the 2008 Summer Olympics, and 2016 Summer Olympics, Stanford won more Olympic medals than any other university in the United States. Stanford athletes won 16 medals at the 2012 Summer Olympics (12 gold, two silver and two bronze), and 27 medals at the 2016 Summer Olympics.

    Traditions

    The unofficial motto of Stanford, selected by President Jordan, is Die Luft der Freiheit weht. Translated from the German language, this quotation from Ulrich von Hutten means, “The wind of freedom blows.” The motto was controversial during World War I, when anything in German was suspect; at that time the university disavowed that this motto was official.
    Hail, Stanford, Hail! is the Stanford Hymn sometimes sung at ceremonies or adapted by the various University singing groups. It was written in 1892 by mechanical engineering professor Albert W. Smith and his wife, Mary Roberts Smith (in 1896 she earned the first Stanford doctorate in Economics and later became associate professor of Sociology), but was not officially adopted until after a performance on campus in March 1902 by the Mormon Tabernacle Choir.
    “Uncommon Man/Uncommon Woman”: Stanford does not award honorary degrees, but in 1953 the degree of “Uncommon Man/Uncommon Woman” was created to recognize individuals who give rare and extraordinary service to the University. Technically, this degree is awarded by the Stanford Associates, a voluntary group that is part of the university’s alumni association. As Stanford’s highest honor, it is not conferred at prescribed intervals, but only when appropriate to recognize extraordinary service. Recipients include Herbert Hoover, Bill Hewlett, Dave Packard, Lucile Packard, and John Gardner.
    Big Game events: The events in the week leading up to the Big Game vs. UC Berkeley, including Gaieties (a musical written, composed, produced, and performed by the students of Ram’s Head Theatrical Society).
    “Viennese Ball”: a formal ball with waltzes that was initially started in the 1970s by students returning from the now-closed Stanford in Vienna overseas program. It is now open to all students.
    “Full Moon on the Quad”: An annual event at Main Quad, where students gather to kiss one another starting at midnight. Typically organized by the Junior class cabinet, the festivities include live entertainment, such as music and dance performances.
    “Band Run”: An annual festivity at the beginning of the school year, where the band picks up freshmen from dorms across campus while stopping to perform at each location, culminating in a finale performance at Main Quad.
    “Mausoleum Party”: An annual Halloween Party at the Stanford Mausoleum, the final resting place of Leland Stanford Jr. and his parents. A 20-year tradition, the “Mausoleum Party” was on hiatus from 2002 to 2005 due to a lack of funding, but was revived in 2006. In 2008, it was hosted in Old Union rather than at the actual Mausoleum, because rain prohibited generators from being rented. In 2009, after fundraising efforts by the Junior Class Presidents and the ASSU Executive, the event was able to return to the Mausoleum despite facing budget cuts earlier in the year.
    Former campus traditions include the “Big Game bonfire” on Lake Lagunita (a seasonal lake usually dry in the fall), which was formally ended in 1997 because of the presence of endangered salamanders in the lake bed.

    Award laureates and scholars

    Stanford’s current community of scholars includes:

    19 Nobel Prize laureates (as of October 2020, 85 affiliates in total)
    171 members of the National Academy of Sciences
    109 members of National Academy of Engineering
    76 members of National Academy of Medicine
    288 members of the American Academy of Arts and Sciences
    19 recipients of the National Medal of Science
    1 recipient of the National Medal of Technology
    4 recipients of the National Humanities Medal
    49 members of American Philosophical Society
    56 fellows of the American Physics Society (since 1995)
    4 Pulitzer Prize winners
    31 MacArthur Fellows
    4 Wolf Foundation Prize winners
    2 ACL Lifetime Achievement Award winners
    14 AAAI fellows
    2 Presidential Medal of Freedom winners

    Stanford University Seal

     
  • richardmitnick 12:18 pm on July 23, 2021 Permalink | Reply
    Tags: "U.S. Department of Energy Awards $127 Million to Bring Innovative Clean Energy Technologies to Market", , Biology, , , DOE Bioenergy Technologies Office, DOE Office of Energy Efficiency & Renewable Energy (US), , Phase II funding is based on the initial success of their phase I awards., The U.S. Department of Energy’s (DOE's) Office of Energy and Efficiency and Renewable Energy (EERE) will award $57 million to 53 projects by 51 American small businesses and entrepreneurs.   

    From Department of Energy (US)-DOE Office of Energy Efficiency & Renewable Energy (US) : “U.S. Department of Energy Awards $127 Million to Bring Innovative Clean Energy Technologies to Market” 

    From Department of Energy (US)

    July 23, 2021

    1
    More than $57 million will be awarded to American small businesses and entrepreneurs. Photo courtesy of National Renewable Energy Laboratory (US).

    The U.S. Department of Energy’s (DOE’s) Office of Energy and Efficiency and Renewable Energy (EERE) will award $57 million to 53 projects by 51 American small businesses and entrepreneurs with phase II funding based on the initial success of their phase I awards. This includes follow-on awards to support projects closer to market.

    Through DOE’s Small Business Innovation Research (SBIR) and Small Business Technology Transfer (STTR) programs, the phase II awards support the research and development of innovative clean energy technologies toward commercialization. EERE phase II awards are awarded for a two-year project duration, with initial funding up to $1.1 million, and two potential follow-on awards of up to $1.1 million each.

    The six projects funded through the DOE Bioenergy Technologies Office are:

    Near Infrared Biomass Probe and Deployment Methods for Real-time, Field-based, Biomass Quality Measurement by ANTARES Group Inc. in Edgewater, MD: This project will help further develop a novel way to identify and measure the quality of biomass. This new probe will provide more rapid assessment of biomass quality than traditional testing, thereby guiding real-time decisions on the need for additional quality improvements to produce conversion-ready feedstocks.

    Conversion of Biogas to Liquid Fuels on Superior Catalysts by NexTech Materials, Ltd. Dba Nexceris, LLC in Lewis Center, OH: New CO2 reduction processes are required to efficiently convert biogas, biomass and stored CO2 to usable fuels. The Nexceris/WSU/Tonkomo team is developing a system to convert bio-methane and carbon dioxide into diesel fuel, jet fuel, and Fischer-Tropsch wax a valuable feedstock for chemicals, lubricants, and fuels production.

    Removing Ammonia Contamination from Biogas Feedstock by Pancopia, Inc. in Hampton, VA: Ammonia emissions from swine farms decrease swine productivity, harm the health of surrounding communities, significantly increase pollution, and threaten the production of biogas. This project will develop low-cost, reliable treatment technology to eliminate 90% of ammonia emissions from farms thus resolving these pressing issues which are preventing the implementation of biogas projects.

    Biorecovery of Nutrients from Municipal Wastewaters with Co-production of Biofuels and other Bioproducts by MicroBio Engineering in San Luis Obispo, CA: Development of technology is needed to remove phosphorus from wastewater at low-cost to very low levels to fight environmental pollution triggering harmful algal blooms. This project will reduce phosphorus contents to essentially zero level by applying conditioned filamentous algae in controlled systems allowing removal in secondary or tertiary wastewater within hours.

    Advancing Optical Imaging and Classification to Enhance Biodiversity Monitoring by OceanSpace, LLC in St. Petersburg, FL: Biofuel production requires cost reduction coupled with enhanced benefits, and an important potential benefit is reduction in impacts to biodiversity. Evaluating biodiversity impacts requires a modern sampling technology that is practical and cost-effective, an excellent solution being a sensor system that is easy to use, cost-efficient, and enhances decision-making capabilities.

    Upcycling Ocean-based Plastics for Sustainable Feedstock Supply Chain by RiKarbon, Inc. in Newark, DE: RiKarbon, Inc. is commercializing an enabling technology to produce low-cost waste plastic feedstock and waste plastic’s selective depolymerization to plastic’s building block chemicals for manufacturing renewable plastics. This project will mitigate health risks to ocean life and humans, improve the environment eco-system, promote future energy security and develop a circular economy.

    Read more about the SBIR and SBTT programs, and read the full list of selected projects here.

    See the full article here.

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

    Please help promote STEM in your local schools.

    Stem Education Coalition

    The Department of Energy (US) is a cabinet-level department of the United States Government concerned with the United States’ policies regarding energy and safety in handling nuclear material. Its responsibilities include the nation’s nuclear weapons program; nuclear reactor production for the United States Navy; energy conservation; energy-related research; radioactive waste disposal; and domestic energy production. It also directs research in genomics. the Human Genome Project originated in a DOE initiative. DOE sponsors more research in the physical sciences than any other U.S. federal agency, the majority of which is conducted through its system of National Laboratories. The agency is led by the United States Secretary of Energy, and its headquarters are located in Southwest Washington, D.C., on Independence Avenue in the James V. Forrestal Building, named for James Forrestal, as well as in Germantown, Maryland.

    Formation and consolidation

    In 1942, during World War II, the United States started the Manhattan Project, a project to develop the atomic bomb, under the eye of the U.S. Army Corps of Engineers. After the war in 1946, the Atomic Energy Commission (AEC) was created to control the future of the project. The Atomic Energy Act of 1946 also created the framework for the first National Laboratories. Among other nuclear projects, the AEC produced fabricated uranium fuel cores at locations such as Fernald Feed Materials Production Center in Cincinnati, Ohio. In 1974, the AEC gave way to the Nuclear Regulatory Commission, which was tasked with regulating the nuclear power industry and the Energy Research and Development Administration, which was tasked to manage the nuclear weapon; naval reactor; and energy development programs.

    The 1973 oil crisis called attention to the need to consolidate energy policy. On August 4, 1977, President Jimmy Carter signed into law The Department of Energy Organization Act of 1977 (Pub.L. 95–91, 91 Stat. 565, enacted August 4, 1977), which created the Department of Energy(US). The new agency, which began operations on October 1, 1977, consolidated the Federal Energy Administration; the Energy Research and Development Administration; the Federal Power Commission; and programs of various other agencies. Former Secretary of Defense James Schlesinger, who served under Presidents Nixon and Ford during the Vietnam War, was appointed as the first secretary.

    President Carter created the Department of Energy with the goal of promoting energy conservation and developing alternative sources of energy. He wanted to not be dependent on foreign oil and reduce the use of fossil fuels. With international energy’s future uncertain for America, Carter acted quickly to have the department come into action the first year of his presidency. This was an extremely important issue of the time as the oil crisis was causing shortages and inflation. With the Three-Mile Island disaster, Carter was able to intervene with the help of the department. Carter made switches within the Nuclear Regulatory Commission in this case to fix the management and procedures. This was possible as nuclear energy and weapons are responsibility of the Department of Energy.

    Recent

    On March 28, 2017, a supervisor in the Office of International Climate and Clean Energy asked staff to avoid the phrases “climate change,” “emissions reduction,” or “Paris Agreement” in written memos, briefings or other written communication. A DOE spokesperson denied that phrases had been banned.

    In a May 2019 press release concerning natural gas exports from a Texas facility, the DOE used the term ‘freedom gas’ to refer to natural gas. The phrase originated from a speech made by Secretary Rick Perry in Brussels earlier that month. Washington Governor Jay Inslee decried the term “a joke”.

    Facilities

    The Department of Energy operates a system of national laboratories and technical facilities for research and development, as follows:

    Ames Laboratory
    Argonne National Laboratory
    Brookhaven National Laboratory
    Fermi National Accelerator Laboratory
    Idaho National Laboratory
    Lawrence Berkeley National Laboratory
    Lawrence Livermore National Laboratory
    Los Alamos National Laboratory
    National Energy Technology Laboratory
    National Renewable Energy Laboratory
    Oak Ridge National Laboratory
    Pacific Northwest National Laboratory
    Princeton Plasma Physics Laboratory
    Sandia National Laboratories
    Savannah River National Laboratory
    SLAC National Accelerator Laboratory
    Thomas Jefferson National Accelerator Facility

    Other major DOE facilities include:
    Albany Research Center
    Bannister Federal Complex
    Bettis Atomic Power Laboratory – focuses on the design and development of nuclear power for the U.S. Navy
    Kansas City Plant
    Knolls Atomic Power Laboratory – operates for Naval Reactors Program Research under the DOE (not a National Laboratory)
    National Petroleum Technology Office
    Nevada Test Site
    New Brunswick Laboratory
    Office of Fossil Energy
    Office of River Protection
    Pantex
    Radiological and Environmental Sciences Laboratory
    Y-12 National Security Complex
    Yucca Mountain nuclear waste repository
    Other:

    Pahute Mesa Airstrip – Nye County, Nevada, in supporting Nevada National Security Site

     
  • richardmitnick 1:12 pm on July 21, 2021 Permalink | Reply
    Tags: "New imaging technique may boost biology and neuroscience research", , Biology, , , , , The system called De-scattering with Excitation Patterning (or DEEP) is believed to be the first of its kind .   

    From Harvard Gazette (US) : “New imaging technique may boost biology and neuroscience research” 

    From Harvard Gazette (US)

    At

    Harvard University (US)

    July 7, 2021
    Juan Siliezar

    Scientists hope it will let them see inner workings of complex systems.

    1
    Dushan Wadduwage works with a laser in his Northwest lab where he does research on deep tissue imaging. Credit: Jon Chase/Harvard Staff Photographer.

    Microscopists have long sought a way to produce high-quality, deep-tissue imaging of living subjects in a timely fashion. To date, they have had to choose between image quality or speed when looking into the inner workings of complex biological systems.

    A better imaging system would have a powerful impact on researchers in biology and in neuroscience, experts say. Now Dushan N. Wadduwage, a John Harvard Distinguished Science Fellow in imaging at the FAS Center of Advanced Imaging, along with a team from MIT, has detailed a new technique that would make that possible in a report in Science Advances.

    In the paper, the team presents a new process that uses computational imaging to get high-resolution images 100 to 1,000 times faster than other state-of-the-art technologies using complex algorithms and machine learning. The method can shorten a process that often takes months into a matter of days.

    3
    TFM and DEEP-TFM images of a mouse muscle specimen at a 190-um-deep imaging plane. The blue and red channels are respectively nucleus (stained with Hoechst 33342) and F-actin (stained with Alexa Fluor 568 Phalloidin). Courtesy of Dushan N. Wadduwage.

    The system called De-scattering with Excitation Patterning (or DEEP) is believed to be the first of its kind and may one day lead to new understanding of how complicated processes, such as those in the brain, function, because DEEP can capture images other microscopes cannot.

    Because the new system has the potential to actually speed up what they can image along with how fast they can do it, “scientists will be able to image fast processes they haven’t been able to capture before, like what happens when a neuron fires or how the signals move around in the brain,” Wadduwage said. “Also, because it’s technically faster, you can image a larger volume of area at one time, not just a small field of view as you would with a slower imaging system. It’s like being able to look at a much larger picture, and this is very important for neuroscientists and other biologists to actually get better statistics as well as to see what’s happening around the area being imaged.”

    The system works like many other animal-imaging techniques. Near-infrared laser light is used to penetrate deep through biological tissue that scatters the light. That light excites the fluorescent molecules the researchers want to image, and these emit signals that the microscope captures to form an image.

    There have been two main ways these types of images are taken. Point-scanning multiphoton microscopy can penetrate deep into a specimen and capture high-quality images, but this process is extremely slow because the image is formed one point at a time. Capturing a centimeter-sized image, for example, can take months. It also limits studies of fast biological dynamics, such as neurons firing. The other method is called temporal focusing microscopy. This is much faster and can capture images at a wider scale, but it is unable to capture high-resolution images at anything deeper than a few millionths of a meter. The fluorescent light scatters too much, causing the image to degrade when the camera detects it.

    DEEP, however, allows for wide-scale and quick tissue penetration, and produces high-resolution images. The system projects a wide light into the subject as in the temporal microscopy method, but that laser light is in a specific pattern. The computational-imaging algorithm that knows the initial pattern takes in the information gathered to reverse the process when it gets scattered and then reconstructs it, de-scattering the image. This is especially notable since it takes the reconstruction of structural features from millions of measurements to tens and hundreds. DEEP can image hundreds of microns deep through scattering tissue comparable to point-scanning techniques.

    DEEP is still in its early years of development, but is emerging from its proof-of-concept phase.

    “We showed that we can image about 300 microns into the brains of live mice,” Wadduwage said. “But since this is only the first demonstration, almost all aspects of the technique have room for improvement.”

    See the full article here .

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

    Please help promote STEM in your local schools.

    Stem Education Coalition

    Harvard University campus

    Harvard University (US) is the oldest institution of higher education in the United States, established in 1636 by vote of the Great and General Court of the Massachusetts Bay Colony. It was named after the College’s first benefactor, the young minister John Harvard of Charlestown, who upon his death in 1638 left his library and half his estate to the institution. A statue of John Harvard stands today in front of University Hall in Harvard Yard, and is perhaps the University’s bestknown landmark.

    Harvard University (US) has 12 degree-granting Schools in addition to the Radcliffe Institute for Advanced Study. The University has grown from nine students with a single master to an enrollment of more than 20,000 degree candidates including undergraduate, graduate, and professional students. There are more than 360,000 living alumni in the U.S. and over 190 other countries.

    The Massachusetts colonial legislature, the General Court, authorized Harvard University (US)’s founding. In its early years, Harvard College primarily trained Congregational and Unitarian clergy, although it has never been formally affiliated with any denomination. Its curriculum and student body were gradually secularized during the 18th century, and by the 19th century, Harvard University (US) had emerged as the central cultural establishment among the Boston elite. Following the American Civil War, President Charles William Eliot’s long tenure (1869–1909) transformed the college and affiliated professional schools into a modern research university; Harvard became a founding member of the Association of American Universities in 1900. James B. Conant led the university through the Great Depression and World War II; he liberalized admissions after the war.

    The university is composed of ten academic faculties plus the Radcliffe Institute for Advanced Study. Arts and Sciences offers study in a wide range of academic disciplines for undergraduates and for graduates, while the other faculties offer only graduate degrees, mostly professional. Harvard has three main campuses: the 209-acre (85 ha) Cambridge campus centered on Harvard Yard; an adjoining campus immediately across the Charles River in the Allston neighborhood of Boston; and the medical campus in Boston’s Longwood Medical Area. Harvard University (US)’s endowment is valued at $41.9 billion, making it the largest of any academic institution. Endowment income helps enable the undergraduate college to admit students regardless of financial need and provide generous financial aid with no loans The Harvard Library is the world’s largest academic library system, comprising 79 individual libraries holding about 20.4 million items.

    Harvard University (US) has more alumni, faculty, and researchers who have won Nobel Prizes (161) and Fields Medals (18) than any other university in the world and more alumni who have been members of the U.S. Congress, MacArthur Fellows, Rhodes Scholars (375), and Marshall Scholars (255) than any other university in the United States. Its alumni also include eight U.S. presidents and 188 living billionaires, the most of any university. Fourteen Turing Award laureates have been Harvard affiliates. Students and alumni have also won 10 Academy Awards, 48 Pulitzer Prizes, and 108 Olympic medals (46 gold), and they have founded many notable companies.

    Colonial

    Harvard University (US) was established in 1636 by vote of the Great and General Court of the Massachusetts Bay Colony. In 1638, it acquired British North America’s first known printing press. In 1639, it was named Harvard College after deceased clergyman John Harvard, an alumnus of the University of Cambridge(UK) who had left the school £779 and his library of some 400 volumes. The charter creating the Harvard Corporation was granted in 1650.

    A 1643 publication gave the school’s purpose as “to advance learning and perpetuate it to posterity, dreading to leave an illiterate ministry to the churches when our present ministers shall lie in the dust.” It trained many Puritan ministers in its early years and offered a classic curriculum based on the English university model—many leaders in the colony had attended the University of Cambridge—but conformed to the tenets of Puritanism. Harvard University (US) has never affiliated with any particular denomination, though many of its earliest graduates went on to become clergymen in Congregational and Unitarian churches.

    Increase Mather served as president from 1681 to 1701. In 1708, John Leverett became the first president who was not also a clergyman, marking a turning of the college away from Puritanism and toward intellectual independence.

    19th century

    In the 19th century, Enlightenment ideas of reason and free will were widespread among Congregational ministers, putting those ministers and their congregations in tension with more traditionalist, Calvinist parties. When Hollis Professor of Divinity David Tappan died in 1803 and President Joseph Willard died a year later, a struggle broke out over their replacements. Henry Ware was elected to the Hollis chair in 1805, and the liberal Samuel Webber was appointed to the presidency two years later, signaling the shift from the dominance of traditional ideas at Harvard to the dominance of liberal, Arminian ideas.

    Charles William Eliot, president 1869–1909, eliminated the favored position of Christianity from the curriculum while opening it to student self-direction. Though Eliot was the crucial figure in the secularization of American higher education, he was motivated not by a desire to secularize education but by Transcendentalist Unitarian convictions influenced by William Ellery Channing and Ralph Waldo Emerson.

    20th century

    In the 20th century, Harvard University (US)’s reputation grew as a burgeoning endowment and prominent professors expanded the university’s scope. Rapid enrollment growth continued as new graduate schools were begun and the undergraduate college expanded. Radcliffe College, established in 1879 as the female counterpart of Harvard College, became one of the most prominent schools for women in the United States. Harvard University (US) became a founding member of the Association of American Universities in 1900.

    The student body in the early decades of the century was predominantly “old-stock, high-status Protestants, especially Episcopalians, Congregationalists, and Presbyterians.” A 1923 proposal by President A. Lawrence Lowell that Jews be limited to 15% of undergraduates was rejected, but Lowell did ban blacks from freshman dormitories.

    President James B. Conant reinvigorated creative scholarship to guarantee Harvard University (US)’s preeminence among research institutions. He saw higher education as a vehicle of opportunity for the talented rather than an entitlement for the wealthy, so Conant devised programs to identify, recruit, and support talented youth. In 1943, he asked the faculty to make a definitive statement about what general education ought to be, at the secondary as well as at the college level. The resulting Report, published in 1945, was one of the most influential manifestos in 20th century American education.

    Between 1945 and 1960, admissions were opened up to bring in a more diverse group of students. No longer drawing mostly from select New England prep schools, the undergraduate college became accessible to striving middle class students from public schools; many more Jews and Catholics were admitted, but few blacks, Hispanics, or Asians. Throughout the rest of the 20th century, Harvard became more diverse.

    Harvard University (US)’s graduate schools began admitting women in small numbers in the late 19th century. During World War II, students at Radcliffe College (which since 1879 had been paying Harvard University (US) professors to repeat their lectures for women) began attending Harvard University (US) classes alongside men. Women were first admitted to the medical school in 1945. Since 1971, Harvard University (US) has controlled essentially all aspects of undergraduate admission, instruction, and housing for Radcliffe women. In 1999, Radcliffe was formally merged into Harvard University (US).

    21st century

    Drew Gilpin Faust, previously the dean of the Radcliffe Institute for Advanced Study, became Harvard University (US)’s first woman president on July 1, 2007. She was succeeded by Lawrence Bacow on July 1, 2018.

     
  • richardmitnick 9:28 am on July 18, 2021 Permalink | Reply
    Tags: "Neurons Unexpectedly Encode Information in the Timing of Their Firing", , Artificial Intelligence researchers typically have to train artificial neural networks on hundreds or thousands of examples of a pattern or concept before the synapse strengthens., , Biology, , , Information seems to be encoded through the strengthening of synapses only when two neurons fire within tens of milliseconds of each other., It’s really important not just how many [neuron activations] occur but when exactly they occur., Phase precession: a relationship between the continuous rhythm of a brain wave and the specific moments that neurons in that brain area activate., , Place cells: each of which is tuned to a specific region or “place field.”, , The closer you get to the center of a place field the faster the corresponding place cell fires., The pattern of phase precession was elusive in humans until now., There are other theories about our rapid learning abilities. And researchers stressed that it’s difficult to draw conclusions about any widespread role for phase precession., These studies suggest that phase precession allows the brain to link sequences of times; images; and events in the same way as it does spatial positions.   

    From Quanta Magazine : “Neurons Unexpectedly Encode Information in the Timing of Their Firing” 

    From Quanta Magazine

    July 7, 2021
    Elena Renken

    1
    Samuel Velasco/Quanta Magazine.

    For decades, neuroscientists have treated the brain somewhat like a Geiger counter: The rate at which neurons fire is taken as a measure of activity, just as a Geiger counter’s click rate indicates the strength of radiation. But new research suggests the brain may be more like a musical instrument. When you play the piano, how often you hit the keys matters, but the precise timing of the notes is also essential to the melody.

    “It’s really important not just how many [neuron activations] occur but when exactly they occur,” said Joshua Jacobs, a neuroscientist and biomedical engineer at Columbia University (US) who reported new evidence for this claim last month in Cell.

    For the first time, Jacobs and two coauthors spied neurons in the human brain encoding spatial information through the timing, rather than rate, of their firing. This temporal firing phenomenon is well documented in certain brain areas of rats, but the new study and others suggest it might be far more widespread in mammalian brains. “The more we look for it, the more we see it,” Jacobs said.

    Some researchers think the discovery might help solve a major mystery: how brains can learn so quickly.

    The phenomenon is called phase precession. It’s a relationship between the continuous rhythm of a brain wave — the overall ebb and flow of electrical signaling in an area of the brain — and the specific moments that neurons in that brain area activate. A theta brain wave, for instance, rises and falls in a consistent pattern over time, but neurons fire inconsistently, at different points on the wave’s trajectory. In this way, brain waves act like a clock, said one of the study’s coauthors, Salman Qasim, also of Columbia. They let neurons time their firings precisely so that they’ll land in range of other neurons’ firing — thereby forging connections between neurons.

    Researchers began noticing phase precession decades ago among the neurons in rat brains that encode information about spatial position. Human brains and rat brains both contain these so-called place cells, each of which is tuned to a specific region or “place field.” Our brains seem to scale these place fields to cover our current surroundings, whether that’s miles of freeway or the rooms of one’s home, said Kamran Diba, a neuroscientist at the University of Michigan (US). The closer you get to the center of a place field the faster the corresponding place cell fires. As you leave one place field and enter another, the firing of the first place cell peters out, while that of the second picks up.

    But along with rate, there’s also timing: As the rat passes through a place field, the associated place cell fires earlier and earlier with respect to the cycle of the background theta wave. As the rat crosses from one place field into another, the very early firing of the first place cell occurs close in time with the late firing of the next place cell. Their near-coincident firings cause the synapse, or connection, between them to strengthen, and this coupling of the place cells ingrains the rat’s trajectory into the brain. (Information seems to be encoded through the strengthening of synapses only when two neurons fire within tens of milliseconds of each other.)

    Phase precession is obvious in rats. “It’s so prominent and prevalent in the rodent brain that it makes you want to assume it’s a generalizable mechanism,” Qasim said. Scientists had also identified phase precession in the spatial processing of bats and marmosets, but the pattern was elusive in humans until now.

    Monitoring individual neurons is too invasive to do on the average human study participant, but the Columbia team took advantage of data collected years ago from 13 epilepsy patients who had already had electrodes implanted to map the electrical signals of their seizures. The electrodes recorded the firings of individual neurons while patients steered their way through a virtual-reality simulation using a joystick. As the patients maneuvered themselves around, the researchers identified phase precession in 12% of the neurons they were monitoring.

    Pulling out these signals required sophisticated statistical analysis, because humans exhibit a more complicated pattern of overlapping brain waves than rodents do — and because less of our neural activity is devoted to navigation. But the researchers could say definitively that phase precession is there.

    Other research suggests that phase precession may be crucial beyond navigation. In animals, the phenomenon has been tied to non-spatial perceptions, including processing sounds and smell. And in humans, research co-authored by Jacobs last year found phase precession in time-sensitive brain cells NIH-NLB-PNAS. A not-yet-peer-reviewed preprint [bioRxiv] by cognitive scientists in France and the Netherlands indicated that processing serial images involved phase precession, too. Finally, in Jacobs’ new study, it was found not just in literal navigation, but also as the humans progressed toward abstract goals in the simulation.

    These studies suggest that phase precession allows the brain to link sequences of times; images; and events in the same way as it does spatial positions. “Finding that first evidence really opens the door for it to be some sort of universal coding mechanism in the brain — across mammalian species, possibly,” Qasim said. “You might be missing a whole lot of information coding if you’re not tracking the relative timing of neural activity.”

    Neuroscientists are, in fact, on the lookout for a new kind of coding in the brain to answer the longstanding question: How does the brain encode information so quickly? It’s understood that patterns in external data become ingrained in the firing patterns of the network through the strengthening and weakening of synaptic connections. But artificial intelligence researchers typically have to train artificial neural networks on hundreds or thousands of examples of a pattern or concept before the synapse strengths adjust enough for the network to learn the pattern. Mysteriously, humans can typically learn from just one or a handful of examples.

    Phase precession could play a role in that disparity. One hint of this comes from a study [Journal of Neuroscience] by Johns Hopkins University (US) researchers who found that phase precession showed up in rats learning an unfamiliar track — on their first lap. “As soon as you’re learning something, this pattern for learning sequences is already in place,” Qasim added. “That might facilitate very rapid learning of sequences.”

    Phase precession organizes the timing so that learning happens more often than it could otherwise. It arranges for neurons activated by related information to fire in quick-enough succession for the synapse between them to strengthen. “It would point to this notion that the brain is basically computing faster than you would imagine from rate coding alone,” Diba said.

    There are other theories about our rapid learning abilities. And researchers stressed that it’s difficult to draw conclusions about any widespread role for phase precession in the brain from the limited studies so far.

    Still, a thorough search for the phenomenon may be in order. Bradley Lega, a neurologist at the UTexas Southwestern Medical Center(US), said, “There’s a lot of problems that phase precession can solve.”

    See the full article here .


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

    Please help promote STEM in your local schools.

    Stem Education Coalition

    Formerly known as Simons Science News, Quanta Magazine is an editorially independent online publication launched by the Simons Foundation to enhance public understanding of science. Why Quanta? Albert Einstein called photons “quanta of light.” Our goal is to “illuminate science.” At Quanta Magazine, scientific accuracy is every bit as important as telling a good story. All of our articles are meticulously researched, reported, edited, copy-edited and fact-checked.

     
  • richardmitnick 3:21 pm on July 17, 2021 Permalink | Reply
    Tags: "The paradox of a free-electron laser without the laser: a new source of coherent radiation", , , Biology, , Common electron-beam based light sources-known as fourth-generation light sources-are based on the free-electron laser (FEL) which uses an undulator to convert electron beam energy into X-rays., , , , The scientists have developed a type of ultra-short wavelength coherent light source that does not require laser action to produce coherence., University of Strathclyde [Oilthigh Shrath Chluaidh] (SCT),   

    From University of Strathclyde [Oilthigh Shrath Chluaidh] (SCT): “The paradox of a free-electron laser without the laser: a new source of coherent radiation” 

    From University of Strathclyde [Oilthigh Shrath Chluaidh] (SCT)

    16 July 2021

    1

    A new way of producing coherent light in the ultra-violet spectral region, which points the way to developing brilliant table-top x-ray sources, has been produced in research led at the University of Strathclyde.

    The scientists have developed a type of ultra-short wavelength coherent light source that does not require laser action to produce coherence. Common electron-beam based light sources-known as fourth-generation light sources-are based on the free-electron laser (FEL) which uses an undulator to convert electron beam energy into X-rays.

    Coherent light sources are powerful tools that enable research in many areas of medicine, biology, material sciences, chemistry and physics.

    Making ultraviolet and X-ray coherent light sources more widely available would transform the way science is done; a university could have one of the devices in a single room, on a table top, for a reasonable price.

    The group is now planning a proof-of-principle experiment in the ultraviolet spectral range to demonstrate this new way of producing coherent light. If successful, it should dramatically accelerate the development of even shorter wavelength coherent sources based on the same principle. The Strathclyde group has set up a facility to investigate these types of sources: the Scottish Centre for the Application of Plasma-based Accelerators (SCAPA), which hosts one of the highest power lasers in the UK.

    The new research has been published in Scientific Reports.

    Professor Dino Jaroszynski, of Strathclyde’s Department of Physics, led the research. He said: “This work significantly advances the state-of-the-art of synchrotron sources by proposing a new method of producing short-wavelength coherent radiation, using a short undulator and attosecond duration electron bunches.

    “This is more compact and less demanding on the electron beam quality than free-electron lasers and could provide a paradigm shift in light sources, which would stimulate a new direction of research. It proposes to use bunch compression – as in chirped pulse amplification lasers – within the undulator to significantly enhance the radiation brightness.

    “The new method presented would be of wide interest to a diverse community developing and using light sources.”

    In FELs, as in all lasers, the intensity of light is amplified by a feedback mechanism that locks the phases of individual radiators, which in this case are “free” electrons. In the FEL, this is achieved by passing a high energy electron beam through the undulator, which is an array of alternating polarity magnets.

    Light emitted from the electrons as they wiggle through the undulator creates a force called the ponderomotive force that bunches the electrons – some are slowed down, some are sped up, which causes bunching, similar to traffic on a motorway periodically slowing and speeding up.

    Electrons passing through the undulator radiate incoherent light if they are uniformly distributed – for every electron that emits light, there is another electron that partially cancels out the light because they radiate out of phase. An analogy of this partial cancelling out is rain on the sea: it produces many small ripples that partially cancel each other out, effectively quelling the waves – reducing their amplitude. In contrast, steady or pulsating wind will cause the waves to amplify through the mutual interaction of the wind with the sea.

    In the FEL, electron bunching causes amplification of the light and the increase in its coherence, which usually takes a long time – thus very long undulators are required. In an X-ray FEL, the undulators can be more than a hundred metres long. The accelerators driving these X-ray FELs are kilometres long, which makes these devices very expensive and some of the largest instruments in the world.

    However, using a free-electron laser to produce coherent radiation is not the only way; a “pre-bunched” beam or ultra-short electron bunch can also be used to achieve exactly the same coherence in a very short undulator that is less than a metre in length. As long as the electron bunch is shorter than the wavelength of the light produced by the undulator, it will automatically produce coherent light – all the light waves will add up or interfere constructively, which leads to very brilliant light with exactly the same properties of light from a laser.

    The researchers have demonstrated theoretically that this can be achieved using a laser-plasma wakefield accelerator, which produces electron bunches that can have a length of a few tens of nanometres. They show that if these ultra-short bunches of high energy electrons pass through a short undulator, they can produce as may photons as a very expensive FEL can produce. Moreover, they have also shown that by producing an electron bunch that has an energy “chirp”, they can ballistically compress the bunch to a very short duration inside the undulator, which provides a unique way of going to even shorter electron bunches and therefore produce even shorter wavelength light.

    The research collaboration also involved the University of Manchester (UK), Pulsar Physics (NL) and the STFC ASTeC group at Daresbury Laboratories. The study has received funding from the EPSRC (Engineering and Physical Sciences Research Council), to support a project named “Lab in a Bubble”.

    See the full article here.

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

    Please help promote STEM in your local schools.

    Stem Education Coalition

    The University of Strathclyde [Oilthigh Shrath Chluaidh] (SCT)) is a public research university located in Glasgow, Scotland. Founded in 1796 as the Andersonian Institute, it is Glasgow’s second-oldest university, having received its royal charter in 1964 as the first technological university in the United Kingdom. Taking its name from the historic Kingdom of Strathclyde, it is Scotland’s third-largest university by number of students, with students and staff from over 100 countries.

    The institution was named University of the Year 2012 by Times Higher Education and again in 2019, becoming the first university to receive this award twice. The annual income of the institution for 2019–20 was £334.8 million of which £81.2 million was from research grants and contracts, with an expenditure of £298.8 million. It is one of the 39 old universities in the UK comprising the distinctive second cluster of elite universities after Oxbridge.

    Research

    In 2011 the University’s Advanced Forming Research Centre was announced as a leading partner in the first UK-wide Technology Strategy Board Catapult Centre. The Government also announced that the University is to lead the UK-wide EPSRC Centre for Innovative Manufacturing in Continuous Manufacturing and Crystallisation.

    The University has become the base for the first Fraunhofer Centre to be established in the UK. Fraunhofer-Gesellschaft, Europe’s largest organisation for contract research, is creating the new Fraunhofer Centre for Applied Photonics in collaboration with Strathclyde, for research in sectors including healthcare, security, energy and transport.

    Strathclyde was chosen in 2012 as the exclusive European partner university for South Korea’s global research and commercialisation programme – the Global Industry-Academia Cooperation Programme, funded by South Korea’s Ministry of Knowledge and Economics.

    In 2012 the University became a key partner in its second UK Catapult Centre. Plans for the Catapult Centre for Offshore Renewable Energy were announced at Strathclyde by Business Secretary Vince Cable. The University has also become a partner in the Industrial Doctorate Centre for Offshore Renewable Energy, which is one of 11 doctoral centres at Strathclyde.

    Engineers at the University are leading the €4 million, Europe-wide Stardust project, a research-based training network investigating the removal of space debris and the deflection of asteroids.

    Strathclyde has become part of the new ESRC Enterprise Research Centre, a £2.9 million venture generating world-class research to help stimulate growth for small and medium-sized enterprises.

    The University has centres in pharmacy, drug delivery and development, micro and ultrasonic engineering, biophotonics and photonics, biomedical engineering, medical devices, new therapies,prosthetics and orthotics, public health history, law, crime and justice and social work. The University is involved in 11 partnerships with other universities through the Scottish Funding Councils’ Research Pooling Programme, covering areas such as engineering, life sciences, energy, marine science and technology, physics, chemistry, computer sciences and economics.

    Several Strathclyde staff have been elected to Fellowships in the Royal Societies of Edinburgh and London.

     
  • richardmitnick 8:23 am on July 13, 2021 Permalink | Reply
    Tags: "Scientists Discover The First Known Algae Species With Three Distinct Sexes", , Biology, , , ,   

    From University of Tokyo [(東京大学](JP) via Science Alert (US) : “Scientists Discover The First Known Algae Species With Three Distinct Sexes” 

    From University of Tokyo [(東京大学](JP)

    via

    ScienceAlert

    Science Alert (US)

    13 JULY 2021
    JACINTA BOWLER

    1
    Credit: Kohei Takahashi.

    Although we might think of ourselves as far removed from blobby green algae, we’re not really that different.

    An algae explosion a few hundred million years ago is thought to have been what allowed all human and animal life to evolve, and all told there’s only about one and a half billion years between us in terms of evolution.

    Plus, according to a Japanese team of researchers, algae could actually help us to understand how different sex systems – like male and female – evolved in the first place.

    Researchers from the University of Tokyo and a number of other Japanese universities have discovered that a type of green algae called Pleodorina starrii has three distinct sexes – ‘male’, ‘female’, and a third sex that the team have called ‘bisexual’. This is the first time any species of algae has been discovered with three sexes.

    “It seems very uncommon to find a species with three sexes, but in natural conditions, I think it may not be so rare,” said one of the researchers, University of Tokyo[(東京大] (JP) biologist Hisayoshi Nozaki.

    Algae isn’t a very specific scientific classification. It’s an informal term for a huge collection of different eukaryotic creatures that use photosynthesis to get energy. They’re not plants, as they lack many plant features; they’re not bacteria (despite cyanobacteria sometimes being called blue-green algae); and they’re not fungi.

    Everything from many-celled giant kelp species, all the way down to cute single-celled dinoflagellates can be classed as algae.

    Because algae are such a big, diverse group, there’s lots of variation in the way that they get it on, but generally algae are able to reproduce asexually (by cloning themselves) or sexually (with a partner), depending on the life cycle stage they’re in. This can be either haploid (with a single set of chromosomes), or diploid (with two sets).

    There’s also hermaphroditic algae that can change depending on the gene expression of the organism. Having three sexes, including hermaphrodites, is called ‘trioecy’.

    But the volvocine green algae P. starrii is different from this again. The bisexual form of this haploid algae has both male and female reproductive cells. The team describe it as a “new haploid mating system” completely unique to algae.

    P. starrii form either 32 or 64 same-sex celled vegetative colonies and have small mobile (male) and large immobile (female) sex cells similar to humans. The male sex cells are sent out in the world in sperm packets to find a female colony to attach to.

    Bisexual P. starrii have both, can form either male or female colonies, and therefore can mate with either a male, a female, or another bisexual.

    2
    Sexually induced male colony of algae (left). Female colony with male sperm packet (center). Female colony with dissociated male gametes (right). Credit: Kohei Takahashi.

    The researchers are particularly excited because other closely related algae have different sex systems, meaning the discovery might be able to tell us more about how these sexual changes evolve.

    “Mixed mating systems such as trioecy may represent intermediate states of evolutionary transitions between dioecious (with male and female) and monoecious (with only hermaphrodites) mating systems in diploid organisms,” the team write in their new paper.

    “However, haploid mating systems with three sex phenotypes within a single biological species have not been previously reported.”

    For 30 years, Nozaki had been collecting algae samples from the Sagami River outside of Tokyo. Samples that were taken from lakes along that river in 2007 and 2013 were used by the team for the new finding.

    The team separated the algal colonies and induced them to reproduce sexually by depriving them of nutrients, discovering that the bisexual algae had a ‘bisexual factor’ gene that was separate to previously discovered male and female specific genes.

    The bisexual cells had the male gene as well, but can produce either male or female offspring.

    “Co-existence of three sex phenotypes in a single biological species may not be an unusual phenomenon in wild populations,” the researchers conclude.

    “The continued field-collection studies may reveal further existence of three sex phenotypes in other volvocine species.”

    The research has been published in Evolution.

    See the full article here .

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

    Please help promote STEM in your local schools.

    Stem Education Coalition

    The University of Tokyo [(東京大学](JP) aims to be a world-class platform for research and education, contributing to human knowledge in partnership with other leading global universities. The University of Tokyo aims to nurture global leaders with a strong sense of public responsibility and a pioneering spirit, possessing both deep specialism and broad knowledge. The University of Tokyo aims to expand the boundaries of human knowledge in partnership with society. Details about how the University is carrying out this mission can be found in the University of Tokyo Charter and the Action Plans.

    The university has ten faculties, 15 graduate schools and enrolls about 30,000 students, 2,100 of whom are international students. Its five campuses are in Hongō, Komaba, Kashiwa, Shirokane and Nakano. It is among the top echelon of the select Japanese universities assigned additional funding under the MEXT’s Top Global University Project to enhance Japan’s global educational competitiveness.

    University of Tokyo (Todai) is considered to be the most selective and prestigious university in Japan and is counted as one of the best universities in the world. As of 2018, University of Tokyo’s alumni, faculty members and researchers include seventeen Prime Ministers, sixteen Nobel Prize laureates, three Pritzker Prize laureates, three astronauts, and a Fields Medalist.

    The university was chartered by the Meiji government in 1877 under its current name by amalgamating older government schools for medicine, various traditional scholars and modern learning. It was renamed “the Imperial University [帝國大學; Teikoku daigaku]” in 1886, and then Tokyo Imperial University [東京帝國大學; Tōkyō teikoku daigaku] in 1897 when the Imperial University system was created. In September 1923, an earthquake and the following fires destroyed about 700,000 volumes of the Imperial University Library. The books lost included the Hoshino Library [星野文庫; Hoshino bunko], a collection of about 10,000 books. The books were the former possessions of Hoshino Hisashi before becoming part of the library of the university and were mainly about Chinese philosophy and history.

    In 1947 after Japan’s defeat in World War II it re-assumed its original name. With the start of the new university system in 1949, Todai swallowed up the former First Higher School (today’s Komaba campus) and the former Tokyo Higher School, which thenceforth assumed the duty of teaching first- and second-year undergraduates, while the faculties on Hongo main campus took care of third- and fourth-year students.

    Although the university was founded during the Meiji period, it has earlier roots in the Astronomy Agency (天文方; 1684), Shoheizaka Study Office (昌平坂学問所; 1797), and the Western Books Translation Agency (蕃書和解御用; 1811). These institutions were government offices established by the 徳川幕府 Tokugawa shogunate (1603–1867), and played an important role in the importation and translation of books from Europe.

    In the fall of 2012 and for the first time, the University of Tokyo started two undergraduate programs entirely taught in English and geared toward international students—Programs in English at Komaba (PEAK)—the International Program on Japan in East Asia and the International Program on Environmental Sciences. In 2014, the School of Science at the University of Tokyo introduced an all-English undergraduate transfer program called Global Science Course (GSC).

    Research

    The University of Tokyo is considered a top research institution of Japan. It receives the largest amount of national grants for research institutions, Grants-in-Aid for Scientific Research, receiving 40% more than the University with 2nd largest grants and 90% more than the University with 3rd largest grants. This massive financial investment from the Japanese government directly affects Todai’s research outcomes. According to Thomson Reuters, Todai is the best research university in Japan. Its research excellence is especially distinctive in Physics (1st in Japan, 2nd in the world); Biology & Biochemistry (1st in Japan, 3rd in the world); Pharmacology & Toxicology (1st in Japan, 5th in the world); Materials Science (3rd in Japan, 19th in the world); Chemistry (2nd in Japan, 5th in the world); and Immunology (2nd in Japan, 20th in the world).

    In another ranking, Nikkei Shimbun on 16 February 2004 surveyed about the research standards in Engineering studies based on Thomson Reuters, Grants in Aid for Scientific Research and questionnaires to heads of 93 leading Japanese Research Centers. Todai was placed 4th (research planning ability 3rd/informative ability of research outcome; 10th/ability of business-academia collaboration 3rd) in this ranking. Weekly Diamond also reported that Todai has the 3rd highest research standard in Japan in terms of research fundings per researchers in COE Program. In the same article, it is also ranked 21st in terms of the quality of education by GP funds per student.

    Todai also has been recognized for its research in the social sciences and humanities. In January 2011, Repec ranked Todai’s Economics department as Japan’s best economics research university. And it is the only Japanese university within world top 100. Todai has produced 9 presidents of the Japanese Economic Association, the largest number in the association. Asahi Shimbun summarized the number of academic papers in Japanese major legal journals by university, and Todai was ranked top during 2005–2009.

    Research institutes

    Institute of Medical Science
    Earthquake Research Institute
    Institute of Advanced Studies on Asia
    Institute of Social Science
    Institute of Industrial Science
    Historiographical Institute
    Institute of Molecular and Cellular Biosciences
    Institute for Cosmic Ray Research
    Institute for Solid State Physics
    Atmosphere and Ocean Research Institute
    Research Center for Advanced Science and Technology

    The University’s School of Science and the Earthquake Research Institute are both represented on the national Coordinating Committee for Earthquake Prediction.

     
  • richardmitnick 3:30 pm on July 4, 2021 Permalink | Reply
    Tags: , As a human cell begins division its 23 chromosomes duplicate into identical copies that remain joined at a region called the centromere., Biology, Kinetochore: the engine of the mitosis machinery., Mitosis: the mechanism of cell division that is so important for life., Questions about how the kinetochore works are still open., The kinetochore is a beautiful flawless machine: You almost never lose a chromosome in a normal cell!   

    MPG Institute for Molecular Physiology [MPG Institut für molekulare Physiologie ](DE): “Manufacturing the core engine of cell division” 

    Max Planck Institute of Molecular Physiology bloc

    MPG Institute for Molecular Physiology [MPG Institut für molekulare Physiologie](DE)

    June 30, 2021

    Prof. Dr. Andrea Musacchio
    Max Planck Institute of Molecular Physiology, Dortmund
    +49 231 133-2100
    andrea.musacchio@mpi-dortmund.mpg.de

    Johann Jarzombek
    Press and Public Relations
    Max Planck Institute of Molecular Physiology, Dortmund
    +49 231 133-2252
    johann.jarzombek@mpi-dortmund.mpg.de

    Manufacturing the core engine of cell division.

    It´s a cellular process going on since one billion years, yet we are not able to replicate it, nor to fully understand it. Mitosis, the mechanism of cell division that is so important for life, involves more than 100 proteins at its core. Now, the group of Andrea Musacchio from the MPG Institute of Molecular Physiology in Dortmund has been able to fully reconstitute the engine of the mitosis machinery, called kinetochore. Being able to model a functioning kinetochore is the first step towards the making of artificial chromosomes that may one day be used to restore missing functions in cells.

    1
    Scheme of the reconstituted kinetochore binding the centromere (yellow) of the chromosome (blue) on one side and a microtubule (green) on the other side. © MPG Insititute of Molecular Physiology.

    As a human cell begins division its 23 chromosomes duplicate into identical copies that remain joined at a region called the centromere. Here lies the kinetochore, a complicated assembly of proteins that binds to thread-like structures, the microtubules. As mitosis progresses, the kinetochore gives green light to the microtubules to tear the DNA copies apart, towards the new forming cells. “The kinetochore is a beautiful flawless machine: You almost never lose a chromosome in a normal cell!”, says Musacchio. “We already know the proteins that constitute it, yet important questions about how the kinetochore works are still open: How does it rebuild itself during chromosome replication? How does it bind to the microtubules? And how does it control them?”

    Musacchio´s quest for answers started more than 20 years ago and has been guided by a simple motto: “Before we understand how things go wrong, we better understand why and how things work”. He therefore embarked in the mission of rebuilding the kinetochore in vitro. In 2016 he could synthesize a partial kinetochore made of 21 proteins.

    In the new publication, Musacchio, his Postdoc Kai Walstein, and their colleagues at MPG Institute in Dortmund have been able to fully reconstruct the system: All subunits, from the ones that bind the centromere to the ones that bind the microtubules, are now present in the right numbers and stoichiometry. Scientists proved that the new system functions properly, by successfully substituting parts of the original kinetochore in the cell with artificial ones. “This is a real milestone in the reconstruction of an object that exists, unaltered, in all eukaryotic cells since more than one billion years!”, says Musacchio. This breakthrough paves the way towards the making of synthetic chromosomes carrying functions that can be replicated in organisms. “The potential for biotech applications could be huge”, he says.

    In the protein factory
    3
    First Author Kai Walstein in the “protein factory”.

    Max Planck scientists had to overcome a major hurdle to rebuild the kinetochore, namely to fully reconstruct the highly flexible Centromeric Protein C (CENP-C). This is an essential protein that bridges the centromeric region to the outer proteins of the kinetochore. Researchers rebuilt CENP-C by “gluing” together the two ends of it.

    A highly organised laboratory, similar to a factory, is fundamental for the reconstitution of complex protein assemblies. For each protein of the kinetochore, Max Planck scientists built a production pipeline to isolate the genes, express them in insects’ cells, and collect them. “When we put them together in vitro, these proteins click-in to form the kinetochore, just like Lego pieces following the instructions”, he says. Other than the famous toys though, each kinetochore protein has a different interface and interaction with closer proteins. The group will now step up to the next level of complexity: Investigating how the kinetochore functions and interacts in the presence of microtubules and supplied energy (in the form of ATP). The project has been recently granted an ERC Synergy Grant and will be carried out by an international team comprising Musacchio’s group and researchers from Cambridge, UK, and Barcelona, Spain.

    Science paper:
    Science Advances

    See the full article here .

    Please help promote STEM in your local schools.

    Stem Education Coalition

    Max Planck Institute of Molecular Physiology campus

    About the Institute

    MPG Institute for Molecular Physiology [MPG Institut für molekulare Physiologie] DE is an international team of cell biologists, structural biologists, physicist and chemists engaged in a young, future-oriented research field: systems biology.

    The goal of our work is not to investigate individual elements of cells or tissues, but rather to obtain an integrated picture of all processes which regulate the metabolism, growth and proliferation of living organisms.

    The reason: Genes and proteins are not static building blocks of life. Rather, they are more like capricious divas: How they behave depends to a great extent on their surroundings and their respective contacts. And it is precisely this social behavior of the molecules which determines whether a cell stays healthy or not.

    To unravel these networks, researchers from different disciplines are venturing together into the nanocosmos and are exploring at the atomic level. This includes elucidating the structure of individual molecules, live imaging of the cell interior, and even the synthesis of chemical substances, which can influence the dynamics of specific molecules.

    Our focus is on basic research – with a clear objective: We are striving to understand the collective behavior of the involved molecules, because this is crucial to understanding complex diseases like cancer.

    MPG Society for the Advancement of Science [MPG Gesellschaft zur Förderung der Wissenschaften e. V.] (DE) is a formally independent non-governmental and non-profit association of German research institutes founded in 1911 as the Kaiser Wilhelm Society and renamed the Max Planck Society in 1948 in honor of its former president, theoretical physicist Max Planck. The society is funded by the federal and state governments of Germany as well as other sources.
    According to its primary goal, the Max Planck Society supports fundamental research in the natural, life and social sciences, the arts and humanities in its 83 (as of January 2014) Max Planck Institutes. The society has a total staff of approximately 17,000 permanent employees, including 5,470 scientists, plus around 4,600 non-tenured scientists and guests. Society budget for 2015 was about €1.7 billion.
    The Max Planck Institutes focus on excellence in research. The Max Planck Society has a world-leading reputation as a science and technology research organization, with 33 Nobel Prizes awarded to their scientists, and is generally regarded as the foremost basic research organization in Europe and the world. In 2013, the Nature Publishing Index placed the Max Planck institutes fifth worldwide in terms of research published in Nature journals (after Harvard University (US), Massachusetts Institute of Technology (US), Stanford University (US) and the National Institutes of Health (US) ). In terms of total research volume (unweighted by citations or impact), the Max Planck Society is only outranked by the Chinese Academy of Sciences [中国科学院](CN), the Russian Academy of Sciences [Росси́йская акаде́мия нау́к; (РАН) Rossíiskaya akadémiya naúk](RU) and Harvard University. The Thomson Reuters-Science Watch website placed the Max Planck Society as the second leading research organization worldwide following Harvard University, in terms of the impact of the produced research over science fields.
    The Max Planck Society and its predecessor Kaiser Wilhelm Society hosted several renowned scientists in their fields, including Otto Hahn, Werner Heisenberg, and Albert Einstein.

    History

    The organization was established in 1911 as the Kaiser Wilhelm Society, or Kaiser-Wilhelm-Gesellschaft (KWG), a non-governmental research organization named for the then German emperor. The KWG was one of the world’s leading research organizations; its board of directors included scientists like Walther Bothe, Peter Debye, Albert Einstein, and Fritz Haber. In 1946, Otto Hahn assumed the position of President of KWG, and in 1948, the society was renamed the Max Planck Society (MPG) after its former President (1930–37) Max Planck, who died in 1947.
    The Max Planck Society has a world-leading reputation as a science and technology research organization. In 2006, the Times Higher Education Supplement rankings of non-university research institutions (based on international peer review by academics) placed the Max Planck Society as No.1 in the world for science research, and No.3 in technology research (behind AT&T Corporation and the DOE’s Argonne National Laboratory (US).
    The domain mpg.de attracted at least 1.7 million visitors annually by 2008 according to a Compete.com study.
    Max Planck Institutes and research groups
    The Max Planck Society consists of over 80 research institutes. In addition, the society funds a number of Max Planck Research Groups (MPRG) and International Max Planck Research Schools (IMPRS). The purpose of establishing independent research groups at various universities is to strengthen the required networking between universities and institutes of the Max Planck Society.
    The research units are primarily located across Europe with a few in South Korea and the U.S. In 2007, the Society established its first non-European centre, with an institute on the Jupiter campus of Florida Atlantic University (US) focusing on neuroscience.
    The Max Planck Institutes operate independently from, though in close cooperation with, the universities, and focus on innovative research which does not fit into the university structure due to their interdisciplinary or transdisciplinary nature or which require resources that cannot be met by the state universities.
    Internally, Max Planck Institutes are organized into research departments headed by directors such that each MPI has several directors, a position roughly comparable to anything from full professor to department head at a university. Other core members include Junior and Senior Research Fellows.
    In addition, there are several associated institutes:

    International Max Planck Research Schools
    Together with the Association of Universities and other Education Institutions in Germany, the Max Planck Society established numerous International Max Planck Research Schools (IMPRS) to promote junior scientists:
    Cologne Graduate School of Ageing Research, Cologne
    International Max Planck Research School for Intelligent Systems, at the MPG Institute for Intelligent Systems (DE) located in Tübingen and Stuttgart
    International Max Planck Research School on Adapting Behavior in a Fundamentally Uncertain World (Uncertainty School), at the Max Planck Institutes for Economics, for Human Development, and/or Research on Collective Goods
    International Max Planck Research School for Analysis, Design and Optimization in Chemical and Biochemical Process Engineering, Magdeburg
    International Max Planck Research School for Astronomy and Cosmic Physics, Heidelberg at the MPG for Astronomy
    International Max Planck Research School for Astrophysics, Garching at the MPG Institute for Astrophysics
    International Max Planck Research School for Complex Surfaces in Material Sciences, Berlin
    International Max Planck Research School for Computer Science, Saarbrücken
    International Max Planck Research School for Earth System Modeling, Hamburg
    International Max Planck Research School for Elementary Particle Physics, Munich, at the MPG Institute for Physics
    International Max Planck Research School for Environmental, Cellular and Molecular Microbiology, Marburg at the MPG Institute for Terrestrial Microbiology
    International Max Planck Research School for Evolutionary Biology, Plön at the Max Planck Institute for Evolutionary Biology
    International Max Planck Research School “From Molecules to Organisms”, Tübingen at the MPG Institute for Developmental Biology
    International Max Planck Research School for Global Biogeochemical Cycles, Jena at the Max Planck Institute for Biogeochemistry
    International Max Planck Research School on Gravitational Wave Astronomy, Hannover and Potsdam MPG Institute for Gravitational Physics
    International Max Planck Research School for Heart and Lung Research, Bad Nauheim at the MPG Institute for Heart and Lung Research
    International Max Planck Research School for Infectious Diseases and Immunity, Berlin at the Max Planck Institute for Infection Biology
    International Max Planck Research School for Language Sciences, Nijmegen
    International Max Planck Research School for Neurosciences, Göttingen
    International Max Planck Research School for Cognitive and Systems Neuroscience, Tübingen
    International Max Planck Research School for Marine Microbiology (MarMic), joint program of the MPG Institute for Marine Microbiology in Bremen, the University of Bremen (DE), the Alfred Wegener Institute for Polar and Marine Research in Bremerhaven, and the Jacobs University Bremen
    International Max Planck Research School for Maritime Affairs, Hamburg
    International Max Planck Research School for Molecular and Cellular Biology, Freiburg
    International Max Planck Research School for Molecular and Cellular Life Sciences, Munich[
    International Max Planck Research School for Molecular Biology, Göttingen
    International Max Planck Research School for Molecular Cell Biology and Bioengineering, Dresden
    International Max Planck Research School Molecular Biomedicine, program combined with the ‘Graduate Programm Cell Dynamics And Disease’ at the University of Münster (DE) and the MPG Institute for Molecular Biomedicine (DE)
    International Max Planck Research School on Multiscale Bio-Systems, Potsdam
    International Max Planck Research School for Organismal Biology, at the University of Konstanz (DE) and the MPG Institute for Ornithology (DE)
    International Max Planck Research School on Reactive Structure Analysis for Chemical Reactions (IMPRS RECHARGE), Mülheim an der Ruhr, at the Max Planck Institute for Chemical Energy Conversion (DE)
    International Max Planck Research School for Science and Technology of Nano-Systems, Halle at MPG Institute of Microstructure Physics (DE)
    International Max Planck Research School for Solar System Science[49] at theUniversity of Göttingen – Georg-August-Universität Göttingen (DE) hosted by MPG Institute for Solar System Research [Max-Planck-Institut für Sonnensystemforschung] (DE)
    International Max Planck Research School for Astronomy and Astrophysics, Bonn, at the MPG Institute for Radio Astronomy [MPG Institut für Radioastronomie](DE) (formerly the International Max Planck Research School for Radio and Infrared Astronomy)
    International Max Planck Research School for the Social and Political Constitution of the Economy, Cologne
    International Max Planck Research School for Surface and Interface Engineering in Advanced Materials, Düsseldorf at MPG Institute for Iron Research [MPG Institut für Eisenforschung] (DE)
    International Max Planck Research School for Ultrafast Imaging and Structural Dynamics, Hamburg

     
  • richardmitnick 10:15 pm on July 1, 2021 Permalink | Reply
    Tags: "Making Citizen Science Inclusive Will Require More Than Rebranding", , , Biology, , , ,   

    From North Carolina State University (US) : “Making Citizen Science Inclusive Will Require More Than Rebranding” 

    NC State bloc

    From North Carolina State University (US)

    June 24, 2021
    Laura Oleniacz

    1
    A tree in the Court of North Carolina, tagged with a QR code, allows people to answer questions for a citizen science project as part of a College of Natural Resources research project. Credit: North Carolina State University.

    Scientists need to focus on tangible efforts to boost equity, diversity and inclusion in citizen science, researchers from North Carolina State University argued in a new perspective.

    Published in the journal Science, the perspective is a response to a debate about rebranding “citizen science,” the movement to use crowdsourced data collection, analysis or design in research. Researchers said that while the motivation for rebranding is in response to a real concern, there will be a cost to it, and efforts to make projects more inclusive should go deeper than that. Their recommendations speak to a broader discussion about how to ensure science is responsive to the needs of a diverse audience.

    “At its heart, citizen science is a system of knowledge production that doesn’t block entry based on credentials,” said first author Caren Cooper, associate professor of forestry and environmental resources at NC State. “Those of us in citizen science have been saying ‘science is for everyone, you don’t need a degree or special training.’ But, the sad irony is that it hasn’t been for everyone. The overwhelming majority of participants resemble their academic counterparts, who are often white, affluent and have advanced degrees. We want to take the good intentions that are driving rebranding, and commit to long-term, sustained efforts to reimagine an inclusive citizen science.”

    The term “citizen science” was coined in the 1990s, researchers said, to describe science led by institutions that use volunteers to collect data. It has evolved to encompass many types of projects with public involvement in design, leadership or data collection and analysis. As a “citizen science campus,” there are projects underway at NC State in which undergraduates, faculty, staff and the general public can help collect data. Examples include projects that rely on volunteers to help figure out the microbial content of sourdough bread or detect the presence of lead pipes in homes around the state.

    In an effort to resolve concerns that the term is exclusionary to people who do not have citizenship status in a given nation, some organizations have moved toward using the term “community science,” among other names. But researchers said community science is a distinct and existing research movement led and designed by communities, rather than institutions, to address environmental or social justice problems.

    “It’s a huge dis to community science to flippantly change the name like it isn’t already being utilized, and could be considered disrespectful to people who are doing this work and have been for many years,” said co-author Zakiya Leggett, assistant professor of forestry and environmental resources. “If you have a citizen science project, but you advertise it as ‘community science,’ it does a disservice to both practices.”

    In addition, there is a cost to losing the term “citizen science,” they said, since the term has gained momentum globally. In the United States, the term is used in a federal law authorizing the government to include volunteers in scientific research irrespective of their credentials and citizenship status.

    “There is a lot of work that has gone toward incorporating ‘citizen science’ as a part of policy, as well as being accepted into mainstream science,” said co-author Madhusudan Katti, associate professor of forestry and environmental resources at NC State. “The name has been caught up in politicization of citizenship and nationalist politics, and rebranding is a little bit reactive. The concern is genuine, but the fix is not deep enough. Renaming something doesn’t make it different from what it’s been all along.”

    The researchers argued for strategic planning to advance accessibility, justice, equity, diversity and inclusion in citizen science.

    “One approach that could work for citizen science is ‘centering in the margins.’ That can include centering research agendas based on the areas that are underserved by science,” Cooper said.

    Other tactics could involve ensuring there are diverse perspectives in project leadership, or overcoming economic barriers to participation. They also said there is a need for funding to support science that addresses interests, concerns and needs of people who have historically or are currently underserved by science.

    They said rebranding, if needed, should only happen if it is called for as part of a broader strategic plan. They also said rebranding efforts should refrain from co-opting existing terminology, avoid exporting issues in the United States to the rest of the world, and identify terminology to help further clarify distinctions for different types of projects.

    “We wanted the fact that diversity and inclusion in citizen science remains elusive to serve as a canary in the coal mine to the rest of the scientific community – it takes far more than words and good intentions to be inclusive,” Cooper said. “We can learn from community science without co-opting it. We need to figure this out without expecting quick-fix solutions, because those can do more harm than good.”

    The perspective, “Inclusion in citizen science: The conundrum of rebranding,” was published online in Science [above]. In addition to Cooper, Katti and Leggett, other authors included Chris L. Hawn, Lincoln R. Larson, Julia K. Parrish, Gillian Bowser, Darlene Cavalier, Robert R. Dunn, Mordechai (Muki) Haklay, Kaberia Kar Gupta, Na’Taki Osborne Jelks, Valerie A. Johnson, Omega R. Wilson and Sacoby Wilson. Researchers reported funding from the National Science Foundation (US), through grant No. 1713562, to Cooper and Larson.

    Interested in a participation in Citizen Science? Here are some ideas:

    All of these will use your device without any interruption in your use of your device.

    World Community Grid [WCG] is the home for many projects which depend on a community of “crunchers” to process data on home computers, cell phones, etc. You sign up here, you look at the projects and you attach to those in which you are interested. Here are some examples:

    WCG Help Stop TB
    2

    WCG Mapping Cancer Markers
    3

    WCG Smash Childhood Cancer
    4

    WCG Microbiome Immunity Project
    5

    WCG OpenPandemics – COVID-19
    1

    WCG Africa Rainfall Project
    6

    World Community Grid is a philanthropic initiative of IBM Corporate Citizenship

    Another great place to start in BOINC– The Berkeley Open Infrastructure for Network Computing.

    There are many projects in Basic and Applied Science available at the BOINC website. Visit the site, download the software to your device, use BOINC directives to configure your computer for optimal usage and attach to those projects which you would like to help.

    My BOINC stats

    See the full article here .

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

    Please help promote STEM in your local schools.

    Stem Education Coalition

    NC State campus

    North Carolina State University (US) was founded with a purpose: to create economic, societal and intellectual prosperity for the people of North Carolina and the country. We began as a land-grant institution teaching the agricultural and mechanical arts. Today, we’re a pre-eminent research enterprise that excels in science, technology, engineering, math, design, the humanities and social sciences, textiles and veterinary medicine.

    North Carolina State University (US) students, faculty and staff take problems in hand and work with industry, government and nonprofit partners to solve them. Our 34,000-plus high-performing students apply what they learn in the real world by conducting research, working in internships and co-ops, and performing acts of world-changing service. That experiential education ensures they leave here ready to lead the workforce, confident in the knowledge that NC State consistently rates as one of the best values in higher education.

     
  • richardmitnick 4:33 pm on July 1, 2021 Permalink | Reply
    Tags: "Department of Energy Awards 22 Million Node-Hours of Computing Time to Support Cutting-Edge Research", Advanced Scientific Computing Research (ASCR) Leadership Computing Challenge (ALCC) program, , , , Biology, , , , , ,   

    From U.S. Department of Energy Office of Science: “Department of Energy Awards 22 Million Node-Hours of Computing Time to Support Cutting-Edge Research” 

    DOE Main

    From U.S. Department of Energy Office of Science

    Department of Energy Awards 22 Million Node-Hours of Computing Time to Support Cutting-Edge Research
    The U.S. Department of Energy’s (DOE) Office of Science today announced that 22 million node-hours for 41 scientific projects under the Advanced Scientific Computing Research (ASCR) Leadership Computing Challenge (ALCC) program. The projects, with applications ranging from nuclear forensics to advanced energy systems to climate change, will use DOE supercomputers to uncover unique insights about scientific problems that would otherwise be impossible to solve using other experimental approaches.

    Selected projects will receive computational time, also known as node-hours, on one or multiple DOE supercomputers to conduct research that would take years to complete on a standard desktop computer. A node-hour is the usage of one node (or computing unit) on a supercomputer for one hour. A project allocated 1,000,000 node-hours could run a simulation on 1,000 compute nodes for 1,000 hours – vastly reducing the total amount of time required to complete the simulation. These three supercomputers – The Oak Ridge Leadership Computing Facility’s “Summit” system at DOE’s Oak Ridge National Laboratory (US), The Argonne Leadership Computing Facility’s “Theta” system at DOE’s Argonne National Laboratory (US), and the DOE’s National Energy Research Scientific Computing Center’s “Cori” system at DOE’s Lawrence Berkeley National Laboratory (US) – are among the fastest computers in the nation. Oak Ridge National Laboratory’s “Summit” currently performs as the second fastest computer in the world.

    “The Department of Energy is committed to providing the advanced scientific tools needed to move U.S. science forward. Supercomputers allow us to explore scientific problems in ways we haven’t been able to in the past – modeling dangerous, large, or costly experiments, safely and quickly,” said Barb Helland, DOE Associate Director for DOE Office of Science Advanced Scientific Computing Research (US). “The ALCC awards are just one example of how the DOE’s investments in supercomputing benefit researchers all across our nation to advance our nation’s scientific competitiveness, accelerate clean energy options, and to understand and mitigate the impacts of climate change.”

    The ASCR Leadership Computing Challenge (ALCC) program supports efforts to broaden community access to DOE’s computing facilities. ALCC focuses on high-risk, high-payoff simulations in areas directly related to the DOE mission and seeks to broaden the community of researchers who use DOE’s advanced computing resources. The 2021 awardees are awarded compute time at DOE’s high-performance computing facilities at Oak Ridge National Laboratory in Tennessee, Argonne National Laboratory in Illinois, and the National Energy Research Scientific Computing Center (US) at Lawrence Berkeley National Laboratory in California. Of the 41 projects, 3 are from industry, 19 are led by universities and 19 are led by national laboratories.
    The projects cover a variety of topics, including:
    • Climate change research, including improving climate models, studying the effects of turbulence in oceans, characterizing the impact of low-level jets on wind farms, improving the simulation of biochemical processes, and simulating clouds on a global scale.
    • Energy research, including AI and deep learning prediction for fusion energy systems, modeling materials for energy storage, studying wind turbine mechanics, and research into the properties of lithium battery electrolytes.
    • Medical research, such as deep learning for medical natural language processing, modeling cancer screening strategies, and modeling cancer initiation pathways.
    Learn more about the 2021 ALCC awardees by visiting the ASCR website. The ALCC application period will re-open for the 2022-23 allocation cycle in Fall 2021.

    See the full article here .

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

    Please help promote STEM in your local schools.

    Stem Education Coalition
    The mission of the Energy Department is to ensure America’s security and prosperity by addressing its energy, environmental and nuclear challenges through transformative science and technology solutions.

    Science Programs Organization

    The Office of Science manages its research portfolio through six program offices:

    Advanced Scientific Computing Research
    Basic Energy Sciences
    Biological and Environmental Research
    Fusion Energy Sciences
    High Energy Physics
    Nuclear Physics

    The Science Programs organization also includes the following offices:

    The Department of Energy’s Small Business Innovation Research and Small Business Technology Transfer Programs, which the Office of Science manages for the Department;
    The Workforce Development for Teachers and Students program sponsors programs helping develop the next generation of scientists and engineers to support the DOE mission, administer programs, and conduct research; and
    The Office of Project Assessment provides independent advice to the SC leadership regarding those activities essential to constructing and operating major research facilities.

     
  • richardmitnick 11:09 am on July 1, 2021 Permalink | Reply
    Tags: "The power of two", , , , Biology, , , , Ellen Zhong, , , , Software called cryoDRGN   

    From Massachusetts Institute of Technology (US) : “The power of two” 

    MIT News

    From Massachusetts Institute of Technology (US)

    June 30, 2021
    Saima Sidik | Department of Biology

    Graduate student Ellen Zhong helped biologists and mathematicians reach across departmental lines to address a longstanding problem in electron microscopy.

    1
    Ellen Zhong, a graduate student from the Computational and Systems Biology Program, is using a computational pattern-recognition tool called a neural network to study the shapes of molecular machines.
    Credit: Matthew Brown.

    MIT’s Hockfield Court is bordered on the west by the ultramodern Stata Center, with its reflective, silver alcoves that jut off at odd angles, and on the east by Building 68, which is a simple, window-lined, cement rectangle. At first glance, Bonnie Berger’s mathematics lab in the Stata Center and Joey Davis’s biology lab in Building 68 are as different as the buildings that house them. And yet, a recent collaboration between these two labs shows how their disciplines complement each other. The partnership started when Ellen Zhong, a graduate student from the Computational and Systems Biology (CSB) Program, decided to use a computational pattern-recognition tool called a neural network to study the shapes of molecular machines. Three years later, Zhong’s project is letting scientists see patterns that run beneath the surface of their data, and deepening their understanding of the molecules that shape life.

    Zhong’s work builds on a technique from the 1970s called cryo-electron microscopy (cryo-EM), which lets researchers take high-resolution images of frozen protein complexes. Over the past decade, better microscopes and cameras have led to a “resolution revolution” in cryo-EM that’s allowed scientists to see individual atoms within proteins. But, as good as these images are, they’re still only static snapshots. In reality, many of these molecular machines are constantly changing shape and composition as cells carry out their normal functions and adjust to new situations.

    Along with former Berger lab member Tristan Belper, Zhong devised software called cryoDRGN. The tool uses neural nets to combine hundreds of thousands of cryo-EM images, and shows scientists the full range of three-dimensional conformations that protein complexes can take, letting them reconstruct the proteins’ motion as they carry out cellular functions. Understanding the range of shapes that protein complexes can take helps scientists develop drugs that block viruses from entering cells, study how pests kill crops, and even design custom proteins that can cure disease. Covid-19 vaccines, for example, work partly because they include a mutated version of the virus’s spike protein that’s stuck in its active conformation, so vaccinated people produce antibodies that block the virus from entering human cells. Scientists needed to understand the variety of shapes that spike proteins can take in order to figure out how to force spike into its active conformation.

    Getting off the computer and into the lab

    Zhong’s interest in computational biology goes back to 2011 when, as a chemical engineering undergrad at the University of Virginia (US), she worked with Professor Michael Shirts to simulate how proteins fold and unfold. After college, Zhong took her skills to a company called D. E. Shaw Research, where, as a scientific programmer, she took a computational approach to studying how proteins interact with small-molecule drugs.

    “The research was very exciting,” Zhong says, “but all based on computer simulations. To really understand biological systems, you need to do experiments.”

    This goal of combining computation with experimentation motivated Zhong to join MIT’s CSB PhD program, where students often work with multiple supervisors to blend computational work with bench work. Zhong “rotated” in both the Davis and Berger labs, then decided to combine the Davis lab’s goal of understanding how protein complexes form with the Berger lab’s expertise in machine learning and algorithms. Davis was interested in building up the computational side of his lab, so he welcomed the opportunity to co-supervise a student with Berger, who has a long history of collaborating with biologists.

    Davis himself holds a dual bachelor’s degree in computer science and biological engineering, so he’s long believed in the power of combining complementary disciplines. “There are a lot of things you can learn about biology by looking in a microscope,” he says. “But as we start to ask more complicated questions about entire systems, we’re going to require computation to manage the high-dimensional data that come back.”


    Reconstructing Molecules in Motion.

    Before rotating in the Davis lab, Zhong had never performed bench work before — or even touched a pipette. She was fascinated to find how streamlined some very powerful molecular biology techniques can be. Still, Zhong realized that physical limitations mean that biology is much slower when it’s done at the bench instead of on a computer. “With computational research, you can automate experiments and run them super quickly, whereas in the wet lab, you only have two hands, so you can only do one experiment at a time,” she says.

    Zhong says that synergizing the two different cultures of the Davis and Berger labs is helping her become a well-rounded, adaptable scientist. Working around experimentalists in the Davis lab has shown her how much labor goes into experimental results, and also helped her to understand the hurdles that scientists face at the bench. In the Berger lab, she enjoys having coworkers who understand the challenges of computer programming.

    “The key challenge in collaborating across disciplines is understanding each other’s ‘languages,’” Berger says. “Students like Ellen are fortunate to be learning both biology and computing dialects simultaneously.”

    Bringing in the community

    Last spring revealed another reason for biologists to learn computational skills: these tools can be used anywhere there’s a computer and an internet connection. When the Covid-19 pandemic hit, Zhong’s colleagues in the Davis lab had to wind down their bench work for a few months, and many of them filled their time at home by using cryo-EM data that’s freely available online to help Zhong test her cryoDRGN software. The difficulty of understanding another discipline’s language quickly became apparent, and Zhong spent a lot of time teaching her colleagues to be programmers. Seeing the problems that nonprogrammers ran into when they used cryoDRGN was very informative, Zhong says, and helped her create a more user-friendly interface.

    Although the paper announcing cryoDRGN was just published in February, the tool created a stir as soon as Zhong posted her code online, many months prior. The cryoDRGN team thinks this is because leveraging knowledge from two disciplines let them visualize the full range of structures that protein complexes can have, and that’s something researchers have wanted to do for a long time. For example, the cryoDRGN team recently collaborated with researchers from Harvard and Washington universities to study locomotion of the single-celled organism Chlamydomonas reinhardtii. The mechanisms they uncovered could shed light on human health conditions, like male infertility, that arise when cells lose the ability to move. The team is also using cryoDRGN to study the structure of the SARS-CoV-2 spike protein, which could help scientists design treatments and vaccines to fight coronaviruses.

    Zhong, Berger, and Davis say they’re excited to continue using neural nets to improve cryo-EM analysis, and to extend their computational work to other aspects of biology. Davis cited mass spectrometry as “a ripe area to apply computation.” This technique can complement cryo-EM by showing researchers the identities of proteins, how many of them are bound together, and how cells have modified them.

    “Collaborations between disciplines are the future,” Berger says. “Researchers focused on a single discipline can take it only so far with existing techniques. Shining a different lens on the problem is how advances can be made.”

    Zhong says it’s not a bad way to spend a PhD, either. Asked what she’d say to incoming graduate students considering interdisciplinary projects, she says: “Definitely do it.”

    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, the Bates Center, and the Haystack Observatory, as well as affiliated laboratories such as the Broad and Whitehead Institutes.

    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.

     
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