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  • richardmitnick 8:00 am on June 23, 2022 Permalink | Reply
    Tags: "BGCs": biosynthetic gene clusters, "Tapping the ocean as a source of natural products", , DNA, , , , , Ocean Microbiome, , , Using DNA data ETH researchers have examined seawater to find not only new species of bacteria but also previously unknown natural products that may one day prove beneficial.   

    From The Swiss Federal Institute of Technology in Zürich [ETH Zürich] [Eidgenössische Technische Hochschule Zürich] (CH): “Tapping the ocean as a source of natural products” 

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

    6.22.22
    Peter Rüegg

    Using DNA data ETH researchers have examined seawater to find not only new species of bacteria but also previously unknown natural products that may one day prove beneficial.

    1
    Marine bacteria are a significant reservoir of undiscovered chemical compounds that could be of interest to humans.
    Credit: Helena Klein.

    The oceans are teeming with countless forms of life, from the world’s largest creature – the blue whale – to miniscule microorganisms. In addition to their vast numbers, these microorganisms are also crucial for ensuring that the entire eco-​ and climate system work properly. For instance, there are photosynthetically active varieties such as cyanobacteria that produce around 50 percent of the oxygen in the atmosphere. Moreover, by removing carbon dioxide from the atmosphere, microorganisms help counter global warming.

    Despite this significant role, research into the diversity of microorganisms found in the ocean has thus far been only rudimentary. So, a group of researchers led by Shinichi Sunagawa, Professor of Microbiome Research, is working closely with Jörn Piel’s group to investigate this diversity. Both groups are at the Institute of Microbiology at ETH Zürich.

    To detect new natural products made by bacteria, Sunagawa and his team examined publicly available DNA data from 1,000 water samples collected at different depths from every ocean region in the world. The data came from such sources as ocean expeditions and observation platforms positioned out at sea.

    Thanks to modern technologies like environmental DNA (eDNA) analysis, it has become easier to search for new species and discover which known organisms can be found where. But what is hardly known at all is what special effects the marine microorganisms offer – in other words, what chemical compounds they make that are important for interactions between organisms. In the best-​case scenario, such compounds would benefit humans as well. Underpinning the research is the assumption that the ocean microbiome harbours great potential for natural products that could prove beneficial, for instance for their antibiotic properties.

    The extracted eDNA present in the samples was sequenced by the original researchers of the various expeditions. By reconstructing entire genomes on the computer, the scientists succeeded in decrypting the encoded information – the blueprints for proteins. Finally, they consolidated this new data together with the existing 8,500 genome data sets for marine microorganisms in a single database.

    This gave them 35,000 genomes to draw on when searching for new microbial species and, in particular, for promising biosynthetic gene clusters (BGCs). A BGC is a group of genes that provide the synthetic pathway for a natural product.

    New species and new molecules discovered

    In this genome data, the researchers detected not only many potentially useful BGCs – some 40,000 in all – but also previously undiscovered species of bacteria belonging to the phylum Eremiobacterota. This group of bacteria had been known to exist only in terrestrial environments and didn’t exhibit any special biosynthetic diversity.

    Sunagawa and his team named a new family of these bacteria as Eudoremicrobiaceae, and also were able to demonstrate that these bacteria are common and widespread: one species belonging to this family, Eudoremicrobium malaspinii, accounts for up to 6 percent of all bacteria present in certain areas of the ocean.

    “The relatives in the ocean possess what for bacteria is a giant genome. Fully decrypting it was technically challenging because the organisms had not been cultivated before,” Sunagawa says. Moreover, the new bacteria turned out to belong to the group of microorganisms that boasts the highest BGC diversity of all the samples examined. “As things stand, they are the most biosynthetically diverse family in the oceanic water column,” he says.

    The researchers looked at two Eudoremicrobiaceae BGCs in detail. One was a gene cluster containing the genetic code for enzymes that, according to Sunagawa, have never been found in this constellation in a bacterial BGC before. The other examined example was a bioactive natural product that inhibits a proteolytic enzyme.

    Validating experiments led to a surprise

    In collaboration with the group led by Jörn Piel, the researchers used experiments to validate the structure and function of both natural products. Since E. malaspinii could not be cultivated, Piel’s team had to graft genes into a model bacterium so they would act as blueprints for the natural products. This bacterium then produced the corresponding substances. Lastly, the researchers isolated the molecules from the cells, determined the structure and validated the biological activity.

    This was necessary because in one case, the enzymatic activity predicted by computer programs did not tally with the results of the experiments. “Computer predictions for what chemical reactions an enzyme will trigger have their limitations,” Sunagawa says. “This is why such predictions have to be validated in the lab if there’s any doubt.”

    Doing so is an expensive and time-​consuming endeavour that’s simply not viable for a database of 40,000 potential natural products. “However, our database has plenty to offer, and it’s accessible to all researchers who wish to use it,” Sunagawa says.

    Beyond the continued collaboration with Piel’s group to discover new natural products, Sunagawa wants to investigate unresolved questions in the evolution and ecology of oceanic microorganisms. These include how microorganisms are dispersed in the ocean given that they can spread over great distances only passively. He also wants to discover what ecological or evolutionary benefits certain genes create for microbes. Sunagawa suspects the BGCs may play a major role.

    Science paper:
    Nature

    See the full article here .

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    Please help promote STEM in your local schools.

    Stem Education Coalition

    ETH Zurich campus

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

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

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

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

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

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

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

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

    Reputation and ranking

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

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

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

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

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

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

     
  • richardmitnick 11:44 am on June 8, 2022 Permalink | Reply
    Tags: "What the humble planarian teaches us about the building blocks of life", , , , , DNA, , New technologies developed in the past decade make it easier than ever to manipulate DNA and insert it into a living cell., Planarians have an ability of which humans could only dream: regrowing wounded body parts., , The worms’ bodies are filled with pluripotent stem cells-a type of “universal” cell that can grow into any type of tissue.   

    From Stanford University Engineering: “What the humble planarian teaches us about the building blocks of life” 

    From Stanford University Engineering

    at

    Stanford University Name

    Stanford University

    May 26, 2022
    David Levin

    A bioengineer studies the flatworms’ ability to regenerate nerves, muscle, and other tissue. “One of the big questions we want to answer is how it does this on a genetic level?”

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    As unremarkable as planarians may seem, they have an ability of which humans could only dream. | iStock/tonaquatic

    At first glance, planarians aren’t exactly awe-inspiring. These brownish flatworms, each less than half an inch long, have few defining features: At one end, a tail comes to a rounded point; at the other, a head is punctuated by a pair of large, cartoonish eyes.

    As unremarkable as the worms may seem, however, they have an ability we could only dream of. Cut off a planarian’s head, and it’ll sprout a new one. Lop off its tail, and it’ll soon be replaced. Even rending its body into tiny pieces is no big deal. Each chunk, regrowing from its wounded edges, replaces nerves, muscle, and other tissue until it becomes a separate, fully formed, individual worm in just a couple weeks.

    “One of the big questions we want to answer is how it does this on a genetic level,” says Bo Wang, assistant professor of bioengineering at Stanford. “What’s in the worm’s DNA that lets it choose which body parts to grow, how much they’re going to grow, where to stop, and when to stop?”

    Wang studies planarians’ alien-like regeneration. Part of what drives this astonishing ability, he says, is the fact that the worms’ bodies are filled with pluripotent stem cells-a type of “universal” cell that can grow into any type of tissue. When a worm is sliced in half, biochemical signals radiate outward from the damaged site, kicking those stem cells into action. Gradually, the cells differentiate into muscle, nerves, and other structures, forming a new head or tail over several days.

    Although this sort of research is his primary focus today, Wang says he never expected to wind up in the field. Originally trained as a physicist, he spent much of his early career studying Brownian motion, the random movement of tiny particles suspended in a liquid or gas. Then, by chance, he saw a video of the worm C. elegans developing from a fertilized egg.

    “As a physicist, I thought that when you’re dealing with things at the microscopic scale, all movement should be random, propelled by thermal energy and probability—but cells in these worm embryos could divide and move synchronously in a programmed manner even though they were just a few microns in size,” he says. “That blew me away. I think it’s what really converted me from working on physics to working on biology.”

    Today, Wang is digging into some of the most fundamental building blocks of life: the various types of cells that make up an organism. His lab is sequencing the DNA and messenger RNA, the linear molecules that guide protein synthesis, within individual cells of several animals, including planarians, and is developing computational methods to compare them with cell types in other animals ranging from sponge to human in order to find commonalities and differences.

    In the process, they’re learning how each of these organisms has developed unique and powerful ways to use conserved cell types for building new structures and has invented new cell types to survive in its environment.

    Wang doesn’t want to stop at just cataloging those cell types, however. He’s got his sights set on bigger goals. With a deeper understanding of how cell types make tissues and how DNA in a cell nucleus controls the fate and identity of that cell, he says, it may one day be possible to harness the power of biology for our own purposes.

    “As a bioengineer, I’m constantly thinking about that. Once we know the novel functions of a piece of DNA, we can transfer them to other cells—it’s really a matter of shifting the knowledge we get from one system to another,” he says. “I think we could eventually use them to program ‘living machines’ that do a specific job.”

    It’s not so far-fetched. New technologies developed in the past decade make it easier than ever to manipulate DNA and insert it into a living cell. Biologists do it every day with microbes and human cell lines, reprogramming them into tiny “factories” that spit out drugs or other products. In theory, constructing entirely new cells, or even new organisms, in the lab could be right around the corner. Wang thinks it’s just a matter of imagination.

    “We really don’t know the possibilities ahead of us yet,” he says. “But that’s the most exciting aspect of being a scientist. We’re constantly searching for new things, new surprises. That’s what gets me up each day.”

    See the full article here .

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    Please help promote STEM in your local schools.

    Stem Education Coalition

    Stanford Engineering has been at the forefront of innovation for nearly a century, creating pivotal technologies that have transformed the worlds of information technology, communications, health care, energy, business and beyond.

    The school’s faculty, students and alumni have established thousands of companies and laid the technological and business foundations for Silicon Valley. Today, the school educates leaders who will make an impact on global problems and seeks to define what the future of engineering will look like.
    Mission

    Our mission is to seek solutions to important global problems and educate leaders who will make the world a better place by using the power of engineering principles, techniques and systems. We believe it is essential to educate engineers who possess not only deep technical excellence, but the creativity, cultural awareness and entrepreneurial skills that come from exposure to the liberal arts, business, medicine and other disciplines that are an integral part of the Stanford experience.

    Our key goals are to:

    Conduct curiosity-driven and problem-driven research that generates new knowledge and produces discoveries that provide the foundations for future engineered systems
    Deliver world-class, research-based education to students and broad-based training to leaders in academia, industry and society
    Drive technology transfer to Silicon Valley and beyond with deeply and broadly educated people and transformative ideas that will improve our society and our world.

    The Future of Engineering

    The engineering school of the future will look very different from what it looks like today. So, in 2015, we brought together a wide range of stakeholders, including mid-career faculty, students and staff, to address two fundamental questions: In what areas can the School of Engineering make significant world‐changing impact, and how should the school be configured to address the major opportunities and challenges of the future?

    One key output of the process is a set of 10 broad, aspirational questions on areas where the School of Engineering would like to have an impact in 20 years. The committee also returned with a series of recommendations that outlined actions across three key areas — research, education and culture — where the school can deploy resources and create the conditions for Stanford Engineering to have significant impact on those challenges.

    Stanford University

    Stanford University campus
    Stanford University

    Leland and Jane Stanford founded Stanford 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(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. 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, the University of Texas System, and Yale University 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,
    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 -Stanford Engineering, 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 University of California-Berkeley and University of California-San Francisco, 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.

    RISC [Reduced Instruction Set Computer microprocessor architecture] – DARPA funded VLSI project of microprocessor design. Stanford and The University of California-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 SPARC. Another success from this era were IBM’s efforts that eventually led to the IBM POWER instruction set architecture, the 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 Systems, 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.
    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.The University of California-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 10:17 am on June 7, 2022 Permalink | Reply
    Tags: "Convenience-sized RNA editing", , , CRISPR-Cas gene editing systems, DNA, , MIT neuroscientists expand CRISPR toolkit with new compact Cas7-11 enzyme., The CRISPR-Cas9 genome editing technology has given researchers the ability to modify the genes inside human cells., The discovery of Cas7-11 opened the doors to a more precise form of RNA editing analogous to the Cas9 enzyme for DNA., , The team is now planning future studies on other proteins that interact with Cas7-11 in the bacteria that from which it originates., There are lots of positives about being able to permanently change DNA especially when it comes to treating an inherited genetic disease.   

    From The Massachusetts Institute of Technology: “Convenience-sized RNA editing” 

    From The Massachusetts Institute of Technology

    May 31, 2022
    Sarah CP Williams | McGovern Institute for Brain Research

    MIT neuroscientists expand CRISPR toolkit with new compact Cas7-11 enzyme.

    1
    Artistic rendering of the CRISPR Cas 7-11S enzyme. Image: Steve Dixon.

    Last year, researchers at MIT’s McGovern Institute for Brain Research discovered and characterized Cas7-11, the first CRISPR enzyme capable of making precise, guided cuts to strands of RNA without harming cells in the process. Now, working with collaborators at the University of Tokyo, the same team has revealed that Cas7-11 can be shrunk to a more compact version, making it an even more viable option for editing the RNA inside living cells. The new, compact Cas7-11 was described May 27 in the journal Cell along with a detailed structural analysis of the original enzyme.

    “When we looked at the structure, it was clear there were some pieces that weren’t needed, which we could actually remove,” says Research Scientist and McGovern Fellow Omar Abudayyeh, who led the new work with Research Scientist and McGovern Fellow Jonathan Gootenberg and collaborator Hiroshi Nishimasu from the University of Tokyo. “This makes the enzyme small enough that it fits into a single viral vector for therapeutic applications.”

    The authors, who also include former McGovern Institute postdoc Nathan Zhou and Kazuki Kato from the University Tokyo, see the new three-dimensional structure of Cas7-11 as a rich resource to answer questions about the basic biology of the enzymes and reveal other ways to tweak its function in the future.

    Targeting RNA

    Over the past decade, the CRISPR-Cas9 genome editing technology has given researchers the ability to modify the genes inside human cells — a boon for both basic research and the development of therapeutics to reverse disease-causing genetic mutations. But CRISPR-Cas9 only works to alter DNA, and for some research and clinical purposes, editing RNA is more effective or useful.

    A cell retains its DNA for life, and passes an identical copy to daughter cells as it duplicates, so any changes to DNA are relatively permanent. However, RNA is a more transient molecule, transcribed from DNA and degraded not long after.

    “There are lots of positives about being able to permanently change DNA especially when it comes to treating an inherited genetic disease,” Gootenberg says. “But for an infection, an injury, or some other temporary disease, being able to temporarily modify a gene through RNA targeting makes more sense.”

    Until Abudayyeh, Gootenberg, and their colleagues discovered and characterized Cas7-11, the only enzyme that could target RNA had a messy side effect; when it recognized a particular gene, the enzyme — Cas13 — began cutting up all the RNA around it. This property makes Cas13 effective for diagnostic tests, where it is used to detect the presence of a piece of RNA, but not very useful for therapeutics, where targeted cuts are required.

    The discovery of Cas7-11 opened the doors to a more precise form of RNA editing analogous to the Cas9 enzyme for DNA. However, the massive Cas7-11 protein was too big to fit inside a single viral vector — the empty shell of a virus that researchers typically use to deliver gene editing machinery into patient’s cells.

    Structural insight

    To determine the overall structure of Cas7-11, Abudayyeh, Gootenberg, and Nishimasu used cryo-electron microscopy, which shines beams of electrons on frozen protein samples and measures how the beams are transmitted. The researchers knew that Cas7-11 was like an amalgamation of five separate Cas enzymes, fused into one single gene, but were not sure exactly how those parts folded and fit together.

    “The really fascinating thing about Cas7-11, from a fundamental biology perspective, is that it should be all these separate pieces that come together, but instead you have a fusion into one gene,” Gootenberg says. “We really didn’t know what that would look like.”

    The structure of Cas7-11, caught in the act of binding both its target tRNA strand and the guide RNA, which directs that binding, revealed how the pieces assembled and which parts of the protein were critical to recognizing and cutting RNA. This kind of structural insight is critical to figuring out how to make Cas7-11 carry out targeted jobs inside human cells.

    The structure also illuminated a section of the protein that wasn’t serving any apparent functional role. This finding suggested the researchers could remove it, re-engineering Cas7-11 to make it smaller without taking away its ability to target RNA. Abudayyeh and Gootenberg tested the impact of removing different bits of this section, resulting in a new compact version of the protein, dubbed Cas7-11S. With Cas7-11S in hand, they packaged the system inside a single viral vector, delivered it into mammalian cells, and efficiently targeted RNA.

    The team is now planning future studies on other proteins that interact with Cas7-11 in the bacteria from which it originates, and also hopes to continue working towards the use of Cas7-11 for therapeutic applications.

    “Imagine you could have an RNA gene therapy, and when you take it, it modifies your RNA, but when you stop taking it, that modification stops,” Abudayyeh says. “This is really just the beginning of enabling that tool set.”

    This research was funded, in part, by the McGovern Institute Neurotechnology Program, K. Lisa Yang and Hock E. Tan Center for Molecular Therapeutics in Neuroscience, G. Harold and Leila Y. Mathers Charitable Foundation, MIT John W. Jarve (1978) Seed Fund for Science Innovation, FastGrants, Basis for Supporting Innovative Drug Discovery and Life Science Research Program, JSPS KAKENHI, Takeda Medical Research Foundation, and Inamori Research Institute for Science.

    See the full article here .


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

    Stem Education Coalition

    MIT Seal

    USPS “Forever” postage stamps celebrating Innovation at MIT.

    MIT Campus

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

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

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

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

    Foundation and vision

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

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

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

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

    Early developments

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

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

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

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

    Curricular reforms

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

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

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

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

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

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

    Recent history

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

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

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

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

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

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

    Caltech /MIT Advanced aLigo

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

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

     
  • richardmitnick 4:27 pm on May 31, 2022 Permalink | Reply
    Tags: "Decoding how a protein on the move keeps cells healthy", Ago helps cut off protein production by finding and destroying molecules called mRNA., , , Cells control production with a process called RNA interference (RNAi)., Cells produce proteins like little factories. But if they make too much at the wrong times it can lead to diseases like cancer., , DNA, , How RNAi’s workhorse protein Argonaute (Ago) leverages limited resources., , RNAi doesn’t make permanent changes to cells and can be reversed., The scientists discovered how cells use a process called "phosphorylation" to break Ago’s grip on a mRNA target.   

    From Cold Spring Harbor Laboratory: “Decoding how a protein on the move keeps cells healthy” 

    From Cold Spring Harbor Laboratory

    31 May 2022

    Nick Wurm,
    Communications Specialist
    wurm@cshl.edu
    516-367-8455

    1
    The protein Argonaute, which helps cells control protein production in a process called RNA interference. Image: In conjunction with Scripps Research.

    Cells produce proteins like little factories. But if they make too much at the wrong times it can lead to diseases like cancer, so they control production with a process called RNA interference (RNAi). As of July 2021, several drugs already take advantage of RNAi to treat painful kidney and liver diseases—with another seven in clinical trials. There is a lot of potential for RNAi therapeutics, and Cold Spring Harbor Laboratory (CSHL) researchers are working hard to paint a complete picture of the process, to improve therapies today and make better ones tomorrow.

    CSHL Professor & HHMI Investigator Leemor Joshua-Tor and recent CSHL School of Biological Sciences graduate Brianna Bibel are filling in some of the blanks. They recently discovered how RNAi’s workhorse protein Argonaute (Ago) leverages limited resources to keep protein production on track.

    It’s important to understand exactly how RNAi works because it’s such a basic and heavily used process, Joshua-Tor said. It also offers a kind of safety net for therapeutics because it doesn’t make permanent changes to cells and can be reversed. Joshua-Tor says:

    “For therapeutics, you would maybe not want to mess around with the genome so much. In all these kinds of things, you want to know exactly what’s happening, and if something isn’t working, then you know what to do and where to look. The more information you have, the better it is—you get a complete picture of what’s happening.”

    Ago helps cut off protein production by finding, binding, and destroying molecules called mRNA—which tell cells to make proteins. But the amount of Ago in the body pales in comparison to the amount of mRNA it must target. After destroying one, the protein is still capable of finding another but it can’t move on without help. Bibel discovered how cells use a process called phosphorylation to break Ago’s grip on a mRNA target, allowing it to commute to the next. Bibel explains:

    “Our theory is that having phosphorylation promote release is a way that you could free up Argonaute because when the target gets released, the guide’s still there and it’s super duper stable. So our thinking is that by phosphorylating it, you’re going to free it to go repress other targets—because it’s still totally capable of doing that work.”

    Bibel hopes her discovery will come in handy as research into RNAi continues. “A lot of great advances in science come from just doing basic research,” she said. “And this is one of those basic research questions, trying to figure out how this is working.”

    Science paper:
    eLife

    See the full article here.

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

    Please help promote STEM in your local schools.

    Stem Education Coalition

    Advancing the frontiers of biology through research & education

    Founded in 1890, Cold Spring Harbor Laboratory has shaped contemporary biomedical research and education with programs in cancer, neuroscience, plant biology and quantitative biology. Home to eight Nobel Prize winners, the private, not-for-profit Laboratory employs 1,100 people including 600 scientists, students and technicians. The Meetings & Courses Program hosts more than 12,000 scientists from around the world each year on its campuses in Long Island and in Suzhou, China. The Laboratory’s education arm also includes an academic publishing house, a graduate school and programs for middle and high school students and teachers.

     
  • richardmitnick 12:50 pm on May 31, 2022 Permalink | Reply
    Tags: "An arms race that plays out in a single genome", "Coevolution theory", , , DNA, DNA damage, ,   

    From Penn Today: “An arms race that plays out in a single genome” 

    From Penn Today

    at

    U Penn bloc

    University of Pennsylvania

    May 27, 2022
    Katherine Unger Baillie

    1
    Like Alice furiously running to keep up with the Red Queen, but remaining in one place, two genetic elements in the fruit fly genome are engaged in an evolutionary arms race to simply keep the biological status quo, according to new research by Penn scientists. (Image: John Tenniel in Lewis Carroll’s Through the Looking Glass)

    Biological arms races are commonplace in nature. Cheetahs, for example, have evolved a sleek body form that lends itself to rapid running, enabling them to feast upon similarly speedy gazelles, the fastest of which may evade predation. On the molecular level, immune cells produce proteins to conquer pathogens, which may in turn evolve mutations to evade detection.

    Though less well known, other games of one-upmanship unfold within the genome. In a new study, biologists at the University of Pennsylvania show, for the first time, evidence of a two-sided genomic arms race involving stretches of repetitive DNA called satellites. “Opposing” the rapidly evolving satellites in the arms race are similarly fast-evolving proteins that bind those satellites.

    While satellite DNA does not encode genes, it can contribute to essential biological functions, such as formation of molecular machines that process and maintain chromosomes. When satellite repeats are improperly regulated, impairments to these crucial processes can result. Such disruptions are hallmarks of cancer and infertility.

    Using two closely related species of fruit flies, researchers probed this arms race by purposefully introducing a species mismatch, pitting, for example, one species’ satellite DNA against the other species’ satellite-binding protein. Severe impairments to fertility were a result, underscoring evolution’s delicate balance, even at the level of a single genome.

    “We typically think of our genome as a cohesive community of elements that make or regulate proteins to build a fertile and viable individual,” says Mia Levine, an assistant professor of biology in Penn’s School of Arts & Sciences and the senior author on the work, published in Current Biology. “This evokes the idea of a collaboration between our genomic elements, and that’s largely true.

    “But some of these elements, we think, actually harm us,” she says. “This disquieting idea suggests that there needs to be a mechanism to keep them in check.”

    The researchers’ findings, likely to also be relevant in humans, suggest that when satellite DNA occasionally escapes the management of satellite-binding proteins, significant costs to fitness can occur, including impacts on molecular pathways required for fertility and perhaps even those relevant in the development of cancer.

    “These findings indicate that there is antagonistic evolution between these elements that can impact these seemingly conserved and essential molecular pathways,” says Cara Brand, a postdoc in Levine’s lab and first author on the work. “It means that, over evolutionary time, constant innovation is required to maintain the status quo.”

    Evolutionary paradox

    It’s long been known that the genome is not composed solely of genes. In between genes that give rise to proteins one can find long stretches of what Levine calls “gobbledygook.”

    “If genes are words and you were to read the story of our genome, these other parts are incoherent,” she says. “For a long time, it was ignored as genomic junk.”

    Satellite DNA is part of this so-called “junk.” In Drosophila melanogaster, the fruit fly species often used as a scientific model organism, satellite repeats make up roughly half the genome. Because they evolve so rapidly without any apparent functional consequence, however, scientists used to believe satellite repeats were unlikely to be doing anything useful in the body.

    But more recent work has revised this “junk DNA” theory, revealing that the “gobbledygook,” satellite repeats included, plays a variety of roles, many related to maintaining genome integrity and structure in the nucleus.

    “So this presents a paradox,” Levine says. “If these regions of the genome that are highly repetitive actually do important jobs, or, if not managed properly, can be harmful, it suggests that we need keep them in check.”

    In 2001, a group of scientists put forward a theory, suggesting that coevolution was taking place, with the satellites rapidly evolving and satellite binding proteins evolving to keep up. In the two decades since, scientists have offered support to the theory. With genetic manipulation, these studies have introduced a satellite-binding protein from one species into the genome of a closely related species and observed what happens as a result of the mismatch.

    “Often these gene swaps cause dysfunction,” says Brand, “particularly disrupting a process that is usually mediated by regions of the genome that are enriched with repetitive DNA.”

    New tools to prove the case

    These investigations lent support to “coevolution theory”. But until researchers could experimentally manipulate both the satellite-binding protein and the satellite DNA, it would be impossible to prove that the disruption they observed arose because of an interaction between the two elements.

    In the current work, Levine and Brand found a way to do just that. Another fruit fly species, Drosophila simulans, lacks a satellite repeat that spans a whopping 11 million nucleotide base pairs found in its close relative, D. melanogaster. This satellite was known to occupy the same cellular location as a protein called Maternal Haploid (MH). The researchers also had access to a mutant strain of D. melanogaster that lack the 11 million base pair repeat.

    “It turns out the fly can live and reproduce just fine without this repeat,” Levine says. “So it gave us a unique opportunity to manipulate both sides of the arms race.”

    To first investigate the satellite-binding protein side, the researchers used the CRISPR/Cas9 gene editing system to remove the original MH gene from D. melanogaster and add back the D. simulans version of the gene. Compared to control females, female flies with the D. simulans MH gene had significantly reduced fertility, producing substantially fewer eggs.

    Flies that lacked MH altogether, however, were unable to produce any offspring; the embryos were not viable.

    “This was interesting because it showed that these satellite-binding proteins are essential, even though they’re rapidly evolving,” says Brand. “Doing the gene swap showed us that we could rescue the ability to make embryos. But another function, related to the ovary and egg production, was impaired.”

    Looking closely at the ovaries, Brand and Levine discovered that the apparent cause of reduced egg formation and atrophied ovaries was DNA damage. Such damage often triggers a checkpoint protein to stop developmental pathways. When the researchers repeated the experiments in a fly with a broken checkpoint protein, egg production levels were restored to a higher level.

    Levine and Brand were then ready to test the other side of the coevolutionary arms race, to find evidence that the problems that arose with the swapped MH protein were due to an incompatibility with the 11 million base pair satellite, or if they were acting on a different genetic element. Here they relied on the D. melanogaster strain that was missing the repeat and found that the gene swap now had no effect on these flies. DNA damage levels, egg production, and ovary size were all normal.

    Looking to the closest relative of the MH protein in humans, a protein called Spartan, gave the scientists a clue as to the mechanism behind these results. In humans, Spartan is understood to digest proteins that can get stuck on DNA, posing an obstacle to various processes and packaging that DNA must undergo. “After everything we’d discovered thus far,” Levine says, “we thought, maybe this wrong species version of the protein is chewing up something it shouldn’t.”

    One of the proteins often targeted by Spartan is Topoisomerase II, or Top2, an enzyme that can help resolve tangles in tightly wound and entangled DNA. To see whether the negative effects of the MH gene mismatch owed to inappropriate degradation of Top2, they overexpressed Top2 and found fertility was restored. Reducing Top2, on the other hand, exacerbated the reduction in fertility.

    “This repair process that MH is involved in happens in yeast, in flies, in humans, across the tree of life,” says Brand. “Yet we’re seeing rapid or adaptive evolution of these proteins involved. That suggests that this seemingly conserved and essential pathway requires evolutionary innovation.” In other words, coevolution must proceed apace, just to maintain this essential pathway.

    Implications beyond flies

    In future work, Brand and Levine will be looking to see if segments of the genome beyond satellites are involved and will be looking in other organisms, including mammals, to drill down into the molecular players of these evolutionary arms races.

    “There’s no reason to believe that these arms races are playing out only in flies,” Levine says. “The same types of proteins and satellites in primates also evolve rapidly and that tells us that what we are studying is broadly relevant.”

    The focal genes involved in this study have important roles in human health. Spartan mutations have been associated with cancer and ineffective regulation of satellite DNA could shed light on infertility and miscarriage.

    “The number of miscarriages is remarkably high, and certainly satellite DNA is an unprobed source of aneuploidy and genome instability,” Levine says.

    See the full article here .

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    Please help promote STEM in your local schools.

    Stem Education Coalition

    U Penn campus

    Academic life at University of Pennsylvania is unparalleled, with 100 countries and every U.S. state represented in one of the Ivy League’s most diverse student bodies. Consistently ranked among the top 10 universities in the country, Penn enrolls 10,000 undergraduate students and welcomes an additional 10,000 students to our world-renowned graduate and professional schools.

    Penn’s award-winning educators and scholars encourage students to pursue inquiry and discovery, follow their passions, and address the world’s most challenging problems through an interdisciplinary approach.

    The University of Pennsylvania is a private Ivy League research university in Philadelphia, Pennsylvania. The university claims a founding date of 1740 and is one of the nine colonial colleges chartered prior to the U.S. Declaration of Independence. Benjamin Franklin, Penn’s founder and first president, advocated an educational program that trained leaders in commerce, government, and public service, similar to a modern liberal arts curriculum.

    Penn has four undergraduate schools as well as twelve graduate and professional schools. Schools enrolling undergraduates include the College of Arts and Sciences; the School of Engineering and Applied Science; the Wharton School; and the School of Nursing. Penn’s “One University Policy” allows students to enroll in classes in any of Penn’s twelve schools. Among its highly ranked graduate and professional schools are a law school whose first professor wrote the first draft of the United States Constitution, the first school of medicine in North America (Perelman School of Medicine, 1765), and the first collegiate business school (Wharton School, 1881).

    Penn is also home to the first “student union” building and organization (Houston Hall, 1896), the first Catholic student club in North America (Newman Center, 1893), the first double-decker college football stadium (Franklin Field, 1924 when second deck was constructed), and Morris Arboretum, the official arboretum of the Commonwealth of Pennsylvania. The first general-purpose electronic computer (ENIAC) was developed at Penn and formally dedicated in 1946. In 2019, the university had an endowment of $14.65 billion, the sixth-largest endowment of all universities in the United States, as well as a research budget of $1.02 billion. The university’s athletics program, the Quakers, fields varsity teams in 33 sports as a member of the NCAA Division I Ivy League conference.

    As of 2018, distinguished alumni and/or Trustees include three U.S. Supreme Court justices; 32 U.S. senators; 46 U.S. governors; 163 members of the U.S. House of Representatives; eight signers of the Declaration of Independence and seven signers of the U.S. Constitution (four of whom signed both representing two-thirds of the six people who signed both); 24 members of the Continental Congress; 14 foreign heads of state and two presidents of the United States, including Donald Trump. As of October 2019, 36 Nobel laureates; 80 members of the American Academy of Arts and Sciences; 64 billionaires; 29 Rhodes Scholars; 15 Marshall Scholars and 16 Pulitzer Prize winners have been affiliated with the university.

    History

    The University of Pennsylvania considers itself the fourth-oldest institution of higher education in the United States, though this is contested by Princeton University and Columbia University. The university also considers itself as the first university in the United States with both undergraduate and graduate studies.

    In 1740, a group of Philadelphians joined together to erect a great preaching hall for the traveling evangelist George Whitefield, who toured the American colonies delivering open-air sermons. The building was designed and built by Edmund Woolley and was the largest building in the city at the time, drawing thousands of people the first time it was preached in. It was initially planned to serve as a charity school as well, but a lack of funds forced plans for the chapel and school to be suspended. According to Franklin’s autobiography, it was in 1743 when he first had the idea to establish an academy, “thinking the Rev. Richard Peters a fit person to superintend such an institution”. However, Peters declined a casual inquiry from Franklin and nothing further was done for another six years. In the fall of 1749, now more eager to create a school to educate future generations, Benjamin Franklin circulated a pamphlet titled Proposals Relating to the Education of Youth in Pensilvania, his vision for what he called a “Public Academy of Philadelphia”. Unlike the other colonial colleges that existed in 1749—Harvard University, William & Mary, Yale Unversity, and The College of New Jersey—Franklin’s new school would not focus merely on education for the clergy. He advocated an innovative concept of higher education, one which would teach both the ornamental knowledge of the arts and the practical skills necessary for making a living and doing public service. The proposed program of study could have become the nation’s first modern liberal arts curriculum, although it was never implemented because Anglican priest William Smith (1727-1803), who became the first provost, and other trustees strongly preferred the traditional curriculum.

    Franklin assembled a board of trustees from among the leading citizens of Philadelphia, the first such non-sectarian board in America. At the first meeting of the 24 members of the board of trustees on November 13, 1749, the issue of where to locate the school was a prime concern. Although a lot across Sixth Street from the old Pennsylvania State House (later renamed and famously known since 1776 as “Independence Hall”), was offered without cost by James Logan, its owner, the trustees realized that the building erected in 1740, which was still vacant, would be an even better site. The original sponsors of the dormant building still owed considerable construction debts and asked Franklin’s group to assume their debts and, accordingly, their inactive trusts. On February 1, 1750, the new board took over the building and trusts of the old board. On August 13, 1751, the “Academy of Philadelphia”, using the great hall at 4th and Arch Streets, took in its first secondary students. A charity school also was chartered on July 13, 1753 by the intentions of the original “New Building” donors, although it lasted only a few years. On June 16, 1755, the “College of Philadelphia” was chartered, paving the way for the addition of undergraduate instruction. All three schools shared the same board of trustees and were considered to be part of the same institution. The first commencement exercises were held on May 17, 1757.

    The institution of higher learning was known as the College of Philadelphia from 1755 to 1779. In 1779, not trusting then-provost the Reverend William Smith’s “Loyalist” tendencies, the revolutionary State Legislature created a University of the State of Pennsylvania. The result was a schism, with Smith continuing to operate an attenuated version of the College of Philadelphia. In 1791, the legislature issued a new charter, merging the two institutions into a new University of Pennsylvania with twelve men from each institution on the new board of trustees.

    Penn has three claims to being the first university in the United States, according to university archives director Mark Frazier Lloyd: the 1765 founding of the first medical school in America made Penn the first institution to offer both “undergraduate” and professional education; the 1779 charter made it the first American institution of higher learning to take the name of “University”; and existing colleges were established as seminaries (although, as detailed earlier, Penn adopted a traditional seminary curriculum as well).

    After being located in downtown Philadelphia for more than a century, the campus was moved across the Schuylkill River to property purchased from the Blockley Almshouse in West Philadelphia in 1872, where it has since remained in an area now known as University City. Although Penn began operating as an academy or secondary school in 1751 and obtained its collegiate charter in 1755, it initially designated 1750 as its founding date; this is the year that appears on the first iteration of the university seal. Sometime later in its early history, Penn began to consider 1749 as its founding date and this year was referenced for over a century, including at the centennial celebration in 1849. In 1899, the board of trustees voted to adjust the founding date earlier again, this time to 1740, the date of “the creation of the earliest of the many educational trusts the University has taken upon itself”. The board of trustees voted in response to a three-year campaign by Penn’s General Alumni Society to retroactively revise the university’s founding date to appear older than Princeton University, which had been chartered in 1746.

    Research, innovations and discoveries

    Penn is classified as an “R1” doctoral university: “Highest research activity.” Its economic impact on the Commonwealth of Pennsylvania for 2015 amounted to $14.3 billion. Penn’s research expenditures in the 2018 fiscal year were $1.442 billion, the fourth largest in the U.S. In fiscal year 2019 Penn received $582.3 million in funding from the National Institutes of Health.

    In line with its well-known interdisciplinary tradition, Penn’s research centers often span two or more disciplines. In the 2010–2011 academic year alone, five interdisciplinary research centers were created or substantially expanded; these include the Center for Health-care Financing; the Center for Global Women’s Health at the Nursing School; the $13 million Morris Arboretum’s Horticulture Center; the $15 million Jay H. Baker Retailing Center at Wharton; and the $13 million Translational Research Center at Penn Medicine. With these additions, Penn now counts 165 research centers hosting a research community of over 4,300 faculty and over 1,100 postdoctoral fellows, 5,500 academic support staff and graduate student trainees. To further assist the advancement of interdisciplinary research President Amy Gutmann established the “Penn Integrates Knowledge” title awarded to selected Penn professors “whose research and teaching exemplify the integration of knowledge”. These professors hold endowed professorships and joint appointments between Penn’s schools.

    Penn is also among the most prolific producers of doctoral students. With 487 PhDs awarded in 2009, Penn ranks third in the Ivy League, only behind Columbia University and Cornell University (Harvard University did not report data). It also has one of the highest numbers of post-doctoral appointees (933 in number for 2004–2007), ranking third in the Ivy League (behind Harvard and Yale University) and tenth nationally.

    In most disciplines Penn professors’ productivity is among the highest in the nation and first in the fields of epidemiology, business, communication studies, comparative literature, languages, information science, criminal justice and criminology, social sciences and sociology. According to the National Research Council nearly three-quarters of Penn’s 41 assessed programs were placed in ranges including the top 10 rankings in their fields, with more than half of these in ranges including the top five rankings in these fields.

    Penn’s research tradition has historically been complemented by innovations that shaped higher education. In addition to establishing the first medical school; the first university teaching hospital; the first business school; and the first student union Penn was also the cradle of other significant developments. In 1852, Penn Law was the first law school in the nation to publish a law journal still in existence (then called The American Law Register, now the Penn Law Review, one of the most cited law journals in the world). Under the deanship of William Draper Lewis, the law school was also one of the first schools to emphasize legal teaching by full-time professors instead of practitioners, a system that is still followed today. The Wharton School was home to several pioneering developments in business education. It established the first research center in a business school in 1921 and the first center for entrepreneurship center in 1973 and it regularly introduced novel curricula for which BusinessWeek wrote, “Wharton is on the crest of a wave of reinvention and change in management education”.

    Several major scientific discoveries have also taken place at Penn. The university is probably best known as the place where the first general-purpose electronic computer (ENIAC) was born in 1946 at the Moore School of Electrical Engineering.

    ENIAC UPenn

    It was here also where the world’s first spelling and grammar checkers were created, as well as the popular COBOL programming language. Penn can also boast some of the most important discoveries in the field of medicine. The dialysis machine used as an artificial replacement for lost kidney function was conceived and devised out of a pressure cooker by William Inouye while he was still a student at Penn Med; the Rubella and Hepatitis B vaccines were developed at Penn; the discovery of cancer’s link with genes; cognitive therapy; Retin-A (the cream used to treat acne), Resistin; the Philadelphia gene (linked to chronic myelogenous leukemia) and the technology behind PET Scans were all discovered by Penn Med researchers. More recent gene research has led to the discovery of the genes for fragile X syndrome, the most common form of inherited mental retardation; spinal and bulbar muscular atrophy, a disorder marked by progressive muscle wasting; and Charcot–Marie–Tooth disease, a progressive neurodegenerative disease that affects the hands, feet and limbs.

    Conductive polymer was also developed at Penn by Alan J. Heeger, Alan MacDiarmid and Hideki Shirakawa, an invention that earned them the Nobel Prize in Chemistry. On faculty since 1965, Ralph L. Brinster developed the scientific basis for in vitro fertilization and the transgenic mouse at Penn and was awarded the National Medal of Science in 2010. The theory of superconductivity was also partly developed at Penn, by then-faculty member John Robert Schrieffer (along with John Bardeen and Leon Cooper). The university has also contributed major advancements in the fields of economics and management. Among the many discoveries are conjoint analysis, widely used as a predictive tool especially in market research; Simon Kuznets’s method of measuring Gross National Product; the Penn effect (the observation that consumer price levels in richer countries are systematically higher than in poorer ones) and the “Wharton Model” developed by Nobel-laureate Lawrence Klein to measure and forecast economic activity. The idea behind Health Maintenance Organizations also belonged to Penn professor Robert Eilers, who put it into practice during then-President Nixon’s health reform in the 1970s.

    International partnerships

    Students can study abroad for a semester or a year at partner institutions such as the London School of Economics(UK), University of Barcelona [Universitat de Barcelona](ES), Paris Institute of Political Studies [Institut d’études politiques de Paris](FR), University of Queensland(AU), University College London(UK), King’s College London(UK), Hebrew University of Jerusalem(IL) and University of Warwick(UK).

     
  • richardmitnick 9:09 am on May 14, 2022 Permalink | Reply
    Tags: "The origin of life- a paradigm shift", According to a new concept by LMU chemists led by Thomas Carell it was a novel molecular species composed out of RNA and peptides that set in motion the evolution of life into more complex forms., Amino acids and peptides linked to the RNA then react with each other to form ever larger and more complex peptides., , , , DNA, , Investigating the question as to how life could emerge long ago on the early Earth is one of the most fascinating challenges for science., , Non-canonical nucleosides are the key ingredient that allows the RNA world to link up with the world of proteins., Non-information-coding nucleotides are very important for the functioning of RNA molecules., , Single-stranded RNA molecules could combine into double strands giving rise to the theoretical possibility that the molecules could replicate themselves – i.e. reproduce., The most important RNA catalyst is the ribosome which still links amino acids into long peptide chains today., The so-called “RNA world idea’ from molecular biology pioneer Walter Gilbert formulated in 1986.   

    From Ludwig Maximilian University of Munich [Ludwig-Maximilians-Universität München] (DE) : “The origin of life- a paradigm shift” 

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

    11 May 2022

    According to a new concept by LMU chemists led by Thomas Carell it was a novel molecular species composed out of RNA and peptides that set in motion the evolution of life into more complex forms.

    1
    LMU-chemists Felix Müller (left) and Luis Escobar discussing a new prebiotic molecular design | © Markus Müller / LMU.

    Investigating the question as to how life could emerge long ago on the early Earth is one of the most fascinating challenges for science. Which conditions must have prevailed for the basic building blocks of more complex life to form? One of the main answers is based upon the so-called RNA world idea, which molecular biology pioneer Walter Gilbert formulated in 1986. The hypothesis holds that nucleotides – the basic building blocks of the nucleic acids A, C, G, and U – emerged out of the primordial soup, and that short RNA molecules then formed out of the nucleotides. These so-called oligonucleotides were already capable of encoding small amounts of genetic information.

    As such single-stranded RNA molecules could also combine into double strands, however, this gave rise to the theoretical possibility that the molecules could replicate themselves – i.e. reproduce. Only two nucleotides fit together in each case, meaning that one strand is the exact counterpart of another and thus forms the template for another strand.

    In the course of evolution, this replication could have improved and at some stage yielded more complex life. “The RNA world idea has the big advantage that it sketches out a pathway whereby complex biomolecules such as nucleic acids with optimized catalytic and, at the same time, information-coding properties can emerge,” says LMU chemist Thomas Carell. Genetic material, as we understand it today, is made up of double strands of DNA, a slightly modified, durable form of macromolecule composed of nucleotides.

    However, the hypothesis is not without its issues. For example, RNS is a very fragile molecule, especially when it gets longer. Furthermore, it is not clear how the linking of RNA molecules with the world of proteins could have come about, for which the genetic material, as we know, supplies the blueprints. As laid out in a new paper published in Nature, Carell’s working group has discovered a way in which this linking could have occurred.

    2
    Luis Escobar from the Carell Group in his laboratory. | © Markus Müller / LMU.

    To understand, we must take another, closer look at RNA. In itself, RNA is a complicated macromolecule. In addition to the four canonical bases A, C, G, and U, which encode genetic information, it also contains non-canonical bases, some of which have very unusual structures. These non-information-coding nucleotides are very important for the functioning of RNA molecules. We currently have knowledge of more than 120 such modified RNA nucleosides, which nature incorporates into RNA molecules. It is highly probable that they are relicts of the former RNA world.

    The Carell group has now discovered that these non-canonical nucleosides are the key ingredient, as it were, that allows the RNA world to link up with the world of proteins. Some of these molecular fossils can, when located in RNA, “adorn” themselves with individual amino acids or even small chains of them (peptides), according to Carell. This results in small chimeric RNA-peptide structures when amino acids or peptides happen to be present in a solution simultaneously alongside the RNA. In such structures, the amino acids and peptides linked to the RNA then even react with each other to form ever larger and more complex peptides. “In this way, we created RNA-peptide particles in the lab that could encode genetic information and even formed lengthening peptides,” says Carell.

    The ancient fossil nucleosides are therefore somewhat akin to nuclei in RNA, forming a core upon which long peptide chains can grow. On some strands of RNA, the peptides were even growing at several points. “That was a very surprising discovery,” says Carell. “It’s possible that there never was a pure RNA world, but that RNA and peptides co-existed from the beginning in a common molecule.” As such, we should expand the concept of an RNA world to that of an RNA-peptide world. The peptides and the RNA mutually supported each other in their evolution, the new idea proposes.

    According to the new theory, a decisive element at the beginning was the presence of RNA molecules that could adorn themselves with amino acids and peptides and so join them into larger peptide structures. “RNA developed slowly into a constantly improving amino acid linking catalyst,” says Carell. This relationship between RNA and peptides or proteins has remained to this day. The most important RNA catalyst is the ribosome, which still links amino acids into long peptide chains today. One of the most complicated RNA machines, it is responsible in every cell for translating genetic information into functional proteins. “The RNA-peptide world thus solves the chicken-and-egg problem,” says Carell. “The new idea creates a foundation upon which the origin of life gradually becomes explicable.”

    See the full article here.

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

    Please help promote STEM in your local schools.

    Stem Education Coalition

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

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

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

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

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

    Faculties

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

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

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

    Research centres

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

    Some of the research centres which have been established include:

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

     
  • richardmitnick 9:51 am on May 11, 2022 Permalink | Reply
    Tags: "Study finds cells take out the trash before they divide", , , , Cells may use this strategy to clear out toxic byproducts and give their offspring a clean slate., DNA, Lysosomal exocytosis, Quantitative Phase Microscopy,   

    From The Massachusetts Institute of Technology: “Study finds cells take out the trash before they divide” 

    From The Massachusetts Institute of Technology

    May 10, 2022
    Anne Trafton

    1
    MIT researchers have discovered that before cells start to divide, they toss waste products. In this image, the magenta represents DNA, and the green represents a lysosomal marker on the surface of the cells, which is an indicator of lysosomal exocytosis. Image courtesy of the researchers.

    Cells may use this strategy to clear out toxic byproducts and give their offspring a clean slate.

    MIT researchers have discovered that before cells start to divide, they do a little cleanup, tossing out molecules that they appear not to need anymore.

    Using a new method they developed for measuring the dry mass of cells, the researchers found that cells lose about 4 percent of their mass as they enter cell division. The researchers believe that this emptying of trash helps cells to give their offspring a “fresh start,” without the accumulated junk of the parent cell.

    “Our hypothesis is that cells might be throwing out things that are building up, toxic components or just things that don’t function properly that you don’t want to have there. It could allow the newborn cells to be born with more functional contents,” says Teemu Miettinen, an MIT research scientist and the lead author of the new study.

    Scott Manalis, the David H. Koch Professor of Engineering in the departments of Biological Engineering and Mechanical Engineering, and a member of the Koch Institute for Integrative Cancer Research, is the senior author of the paper, which appears today in eLife. MIT biological engineering undergraduates Kevin Ly and Alice Lam are also authors of the paper.

    Measuring mass

    Measuring the dry mass of a cell — the weight of its contents not including the water — is commonly done using a microscopy technique called quantitative phase microscopy. This technique can measure cell growth, but it does not reveal information about the molecular content of the dry mass and it is difficult to use with cells that grow in suspension.

    Manalis’ lab has previously developed a technique for measuring the buoyant mass of cells, which is their mass as they float in a fluid such as water. This method measures buoyant mass by flowing cells through a channel embedded in a vibrating cantilever, which can be done repeatedly to track changes in a particular cell’s mass over many hours or days.

    For their new study, the researchers wanted to adapt the technique so that it could be used to calculate the dry mass of cells, as well as the density of the dry mass. About 10 years ago, they had discovered that they could calculate a cell’s dry mass if they first measured the cell in normal water and then in heavy water (which contains deuterium instead of ordinary hydrogen). These two measurements can be used to calculate the cell’s dry mass.

    However, heavy water is toxic to cells, so they were only able to obtain a single measurement per cell. Last year, Miettinen set out to see if he could design a system in which cells could be measured repeatedly with minimal exposure to heavy water.

    In the system he came up with, cells are exposed to heavy water very briefly as they flow through microfluidic channels. It takes only one second for a cell to completely exchange its water content, so the researchers could measure the cell’s mass when it was full of heavy water, compare it to the mass in normal water, and then calculate the dry mass.

    “Our idea was that if we minimize the cells’ exposure to the heavy water, we could engineer the system so that we could repeat this measurement over extended time periods without hurting the cell,” Miettinen says. “That enabled us for the first time to track not just the dry mass of a cell, which is what others do using microscopic methods, but also the density of the dry mass, which informs us of the cell’s biomolecular composition.”

    The researchers showed that their dry mass measurements qualitatively agreed with previous work using quantitative phase microscopy. And, in addition to providing density of the dry mass, the MIT team’s method enables higher temporal resolution, which proved to be useful for revealing dynamics during mitosis (cell division).

    Taking out the trash

    In cells undergoing mitosis, the researchers used their new technique to study what happens to cell mass and composition during that process. In a 2019 paper, Miettinen and Manalis found that buoyant mass increases slightly as mitosis begins. However, other studies that used quantitative phase microscopy suggested that cells might retain or lose dry mass early in cell division.

    In the new study, the MIT team measured three types of cancer cells, which are easier to study because they divide more frequently than healthy cells. To their surprise, the researchers found that the dry mass of cells actually decreases when they enter the cell division cycle. This mass is regained later on, before division is complete.

    Further experiments revealed that as cells enter mitosis, they ramp up activity of a process called lysosomal exocytosis. Lysosomes are cell organelles that break down or recycle cellular waste products, and exocytosis is the process they use to jettison any molecules that aren’t needed any more.

    The researchers also found that the density of the dry mass increases as the cells lose dry mass, leading them to believe that the cells are losing low-density molecules such as lipids or lipoproteins. They hypothesize that cells use this process to clear out toxic molecules before dividing. “What we are seeing is that cells might be trying to throw out damaged components before dividing,” Miettinen says.

    The researchers speculate that their findings may help explain why neurons, which do not divide, are more likely to accumulate toxic proteins such as Tau or amyloid beta, which are linked to the development of Alzheimer’s disease.

    The findings could also be relevant to cancer: Cancer cells can expel some chemotherapy drugs using exocytosis, helping them to become resistant to the drugs. In theory, preventing exocytosis from occurring before cell division could help to make cancer cells more susceptible to such drugs.

    “There are diseases where we might want upregulate exocytosis, for example in neurodegenerative diseases, but then there are diseases like cancer where maybe we want to dial it down,” Miettinen says. “In the future, if we could better understand the molecular mechanism behind this, and find a way to trigger it outside of mitosis or prevent it during mitosis, we could really have a new toggle to use when treating disease.”

    The research was funded by the MIT Center for Cancer Precision Medicine, the Virginia and D.K. Ludwig Fund for Cancer Research, the Cancer Systems Biology Consortium, and the Koch Institute Support (core) Grant from the National Cancer Institute.

    See the full article here .


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    Please help promote STEM in your local schools.

    Stem Education Coalition

    MIT Seal

    USPS “Forever” postage stamps celebrating Innovation at MIT.

    MIT Campus

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

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

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

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

    Foundation and vision

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

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

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

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

    Early developments

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

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

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

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

    Curricular reforms

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

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

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

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

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

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

    Recent history

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

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

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

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

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

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

    Caltech /MIT Advanced aLigo

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

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

     
  • richardmitnick 11:51 am on April 26, 2022 Permalink | Reply
    Tags: "Could the Blueprint for Life Have Been Generated in Asteroids?", , , , DNA, Five informational components called nucleobases., ,   

    From The NASA Goddard Space Flight Center: “Could the Blueprint for Life Have Been Generated in Asteroids?” 

    NASA Goddard Banner

    From The NASA Goddard Space Flight Center

    Apr 26, 2022
    By: Anil Oza

    Editor and Media Contact: Bill Steigerwald
    NASA Goddard Space Flight Center, Greenbelt, Maryland
    william.a.steigerwald@nasa.gov

    Using new analyses, scientists have just found the last two of the five informational units of DNA and RNA that had yet to be discovered in samples from meteorites. While it is unlikely that DNA could be formed in a meteorite, this discovery demonstrates that these genetic parts are available for delivery and could have contributed to the development of the instructional molecules on early Earth. The discovery, by an international team with NASA researchers, gives more evidence that chemical reactions in asteroids can make some of life’s ingredients, which could have been delivered to ancient Earth by meteorite impacts or perhaps the infall of dust.

    1
    Conceptual image of meteoroids delivering nucleobases to ancient Earth. The nucleobases are represented by structural diagrams with hydrogen atoms as white spheres, carbon as black, nitrogen as blue and oxygen as red.
    Credits: Dan Gallagher/NASA Goddard/CI Lab/.

    All DNA and RNA, which contains the instructions to build and operate every living being on Earth, contains five informational components called nucleobases. Until now, scientists scouring extraterrestrial samples had only found three of the five. However, a recent analysis by a team of scientists led by Associate Professor Yasuhiro Oba of Hokkaido University [北海道大学](JP), identified the final two nucleobases that have eluded scientists.

    Nucleobases belong to classes of organic molecules called purines and pyrimidines, which have a wide variety. However, it remains a mystery why more types haven’t been discovered in meteorites so far.

    “I wonder why purines and pyrimidines are exceptional in that they do not show structural diversity in carbonaceous meteorites unlike other classes of organic compounds such as amino acids and hydrocarbons,” said Oba, lead author of a paper about the research published April 26 in Nature Communications. “Since purines and pyrimidines can be synthesized in extraterrestrial environments, as has been demonstrated by our own study, one would expect to find a wide diversity of these organic molecules in meteorites.”

    “We now have evidence that the complete set of nucleobases used in life today could have been available on Earth when life emerged,” said Danny Glavin, a co-author of the paper at NASA’s Goddard Space Flight Center in Greenbelt, Maryland.

    This newly discovered pair of nucleobases, cytosine and thymine, have been elusive in previous analyses likely because of their more delicate structure, which may have degraded when scientists previously extracted samples. In the earlier experiments, scientists created something of a “meteorite tea,” placing grains of meteorite in a hot bath to let the molecules on the sample extract into the solution and then analyzed the molecular makeup of the extraterrestrial broth.

    “We study these water extracts since they contain the good stuff, ancient organic molecules that could have been key building blocks for the origin of life on Earth,” said Glavin.

    Because of how delicate these two nucleobases are, the team was initially skeptical to see them in the samples. But two factors may have contributed to the new discovery: first, the team used cool water to extract the compounds instead of hot formic acid — which is very reactive and could have destroyed these fragile molecules in previous samples. Second, more sensitive analytics were employed that could pick up on smaller amounts of these molecules.

    “This group has managed a technique that is more like cold brew than hot tea and is able to pull out more delicate compounds,” said Jason Dworkin, a co-author of the paper at NASA Goddard. “I was amazed that they had seen cytosine, which is very fragile.”

    The finding doesn’t provide a smoking gun as to whether life on Earth got an assist from space or came about exclusively in the prebiotic soup in the planet’s infancy. But completing the set of nucleobases that make up life today, in addition to other molecules found in the sample, gives scientists who are trying to understand the beginning of life more compounds to experiment with in the lab.

    “This is adding more and more pieces; meteorites have been found to have sugars and bases now,” Dworkin said. “It’s exciting to see progress in the making of the fundamental molecules of biology from space.”

    Not only did this analysis add to the kit for those modeling the inception of life on Earth, it also provides a proof of concept for a more effective technique to extract information from asteroids in the future, especially from the samples of Bennu making their way to Earth in the next year via NASA’s OSIRIS-REx mission.

    See the full article here.


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

    Please help promote STEM in your local schools.


    Stem Education Coalition


    NASA/Goddard Campus

    NASA’s Goddard Space Flight Center, Greenbelt, MD is home to the nation’s largest organization of combined scientists, engineers and technologists that build spacecraft, instruments and new technology to study the Earth, the sun, our solar system, and the universe.

    Named for American rocketry pioneer Dr. Robert H. Goddard, the center was established in 1959 as NASA’s first space flight complex. Goddard and its several facilities are critical in carrying out NASA’s missions of space exploration and scientific discovery.

    GSFC also operates two spaceflight tracking and data acquisition networks (the NASA Deep Space Network and the Near Earth Network); develops and maintains advanced space and Earth science data information systems, and develops satellite systems for the National Oceanic and Atmospheric Administration .

    GSFC manages operations for many NASA and international missions including the NASA/ESA Hubble Space Telescope; the Explorers Program; the Discovery Program; the Earth Observing System; INTEGRAL; MAVEN; OSIRIS-REx; the Solar and Heliospheric Observatory ; the Solar Dynamics Observatory; Tracking and Data Relay Satellite System ; Fermi; and Swift. Past missions managed by GSFC include the Rossi X-ray Timing Explorer (RXTE), Compton Gamma Ray Observatory, SMM, COBE, IUE, and ROSAT. Typically, unmanned Earth observation missions and observatories in Earth orbit are managed by GSFC, while unmanned planetary missions are managed by the Jet Propulsion Laboratory (JPL) in Pasadena, California.

    Goddard is one of four centers built by NASA since its founding on July 29, 1958. It is NASA’s first, and oldest, space center. Its original charter was to perform five major functions on behalf of NASA: technology development and fabrication; planning; scientific research; technical operations; and project management. The center is organized into several directorates, each charged with one of these key functions.

    Until May 1, 1959, NASA’s presence in Greenbelt, MD was known as the Beltsville Space Center. It was then renamed the Goddard Space Flight Center (GSFC), after Robert H. Goddard. Its first 157 employees transferred from the United States Navy’s Project Vanguard missile program, but continued their work at the Naval Research Laboratory in Washington, D.C., while the center was under construction.

    Goddard Space Flight Center contributed to Project Mercury, America’s first manned space flight program. The Center assumed a lead role for the project in its early days and managed the first 250 employees involved in the effort, who were stationed at Langley Research Center in Hampton, Virginia. However, the size and scope of Project Mercury soon prompted NASA to build a new Manned Spacecraft Center, now the Johnson Space Center, in Houston, Texas. Project Mercury’s personnel and activities were transferred there in 1961.

    The Goddard network tracked many early manned and unmanned spacecraft.

    Goddard Space Flight Center remained involved in the manned space flight program, providing computer support and radar tracking of flights through a worldwide network of ground stations called the Spacecraft Tracking and Data Acquisition Network (STDN). However, the Center focused primarily on designing unmanned satellites and spacecraft for scientific research missions. Goddard pioneered several fields of spacecraft development, including modular spacecraft design, which reduced costs and made it possible to repair satellites in orbit. Goddard’s Solar Max satellite, launched in 1980, was repaired by astronauts on the Space Shuttle Challenger in 1984. The Hubble Space Telescope, launched in 1990, remains in service and continues to grow in capability thanks to its modular design and multiple servicing missions by the Space Shuttle.

    Today, the center remains involved in each of NASA’s key programs. Goddard has developed more instruments for planetary exploration than any other organization, among them scientific instruments sent to every planet in the Solar System. The center’s contribution to the Earth Science Enterprise includes several spacecraft in the Earth Observing System fleet as well as EOSDIS, a science data collection, processing, and distribution system. For the manned space flight program, Goddard develops tools for use by astronauts during extra-vehicular activity, and operates the Lunar Reconnaissance Orbiter, a spacecraft designed to study the Moon in preparation for future manned exploration.

    The National Aeronautics and Space Administration (NASA) is the agency of the United States government that is responsible for the nation’s civilian space program and for aeronautics and aerospace research.

    President Dwight D. Eisenhower established the National Aeronautics and Space Administration (NASA) in 1958 with a distinctly civilian (rather than military) orientation encouraging peaceful applications in space science. The National Aeronautics and Space Act was passed on July 29, 1958, disestablishing NASA’s predecessor, the National Advisory Committee for Aeronautics (NACA). The new agency became operational on October 1, 1958.

    Since that time, most U.S. space exploration efforts have been led by NASA, including the Apollo moon-landing missions, the Skylab space station, and later the Space Shuttle. Currently, NASA is supporting the International Space Station and is overseeing the development of the Orion Multi-Purpose Crew Vehicle and Commercial Crew vehicles. The agency is also responsible for the Launch Services Program (LSP) which provides oversight of launch operations and countdown management for unmanned NASA launches. Most recently, NASA announced a new Space Launch System that it said would take the agency’s astronauts farther into space than ever before and lay the cornerstone for future human space exploration efforts by the U.S.

    NASA science is focused on better understanding Earth through the Earth Observing System, advancing heliophysics through the efforts of the Science Mission Directorate’s Heliophysics Research Program, exploring bodies throughout the Solar System with advanced robotic missions such as New Horizons, and researching astrophysics topics, such as the Big Bang, through the Great Observatories [Hubble, Chandra, Spitzer, and associated programs.] NASA shares data with various national and international organizations such as from the [JAXA]Greenhouse Gases Observing Satellite.

     
  • richardmitnick 12:36 pm on April 1, 2022 Permalink | Reply
    Tags: "Johns Hopkins scientists contribute to first complete sequence of human genome", , , Being able to track changes over time in these newly accessible genome regions will allow researchers to make more rigorous comparisons of people of different origins or from species to species., , Clinical labs will need to transition from the previous genome mapping to the new complete version-no small undertaking requiring that they adjust the information they already have., DNA, Finally from tip to tip; telomere to telomere we have an assembly of the genome we can look at., , , Having a single complete genome improves the ability of scientists to understand variations in the genomes of individuals from different populations., More sophisticated sequencing technology now enables scientists to make better sense of the once inscrutable region using long reads., More than a million genetic variants that were not previously known were revealed., Of particular interest to the researchers was an enigmatic component of the genome known as centromeres.,   

    From The Johns Hopkins University HUB : “Johns Hopkins scientists contribute to first complete sequence of human genome” 

    From The Johns Hopkins University HUB

    3.31.22
    Randy Rieland

    1
    Credit: Will Kirk / Johns Hopkins University.

    The Hopkins team contributed key research to the effort, which will provide a clearer picture of how DNA affects the risks of diseases and how genes are expressed and regulated.

    A group of Johns Hopkins University scientists has collaborated with more than 100 researchers around the world to assemble and analyze the first complete sequence of a human genome, two decades after the Human Genome Project produced the first draft.

    The work is part of the Telomere to Telomere (T2T) consortium, led by researchers at The National Human Genome Research Institute; The University of California-Santa Cruz; and The University of Washington, Seattle.

    Johns Hopkins contributed key research to the effort to decipher our DNA—which has remained a mystery despite the initial progress 20 years ago. The revelations are expected to open new lines of molecular and genetic exploration while providing scientists with a clearer picture of how DNA affects the risks of diseases, and how genes are expressed and regulated.

    A package of six papers reporting the achievement appears in today’s issue of Science, along with companion papers in several other journals.

    2

    https://doi.org/10.1126/science.abj6987
    https://doi.org/10.1126/science.abj5089
    https://doi.org/10.1126/science.abj6965
    https://doi.org/10.1126/science.abk3112
    https://doi.org/10.1126/science.abl3533
    https://doi.org/10.1126/science.abl4178

    “Opening up these new parts of the genome, we think there will be genetic variation contributing to many different traits and disease risk,” said Rajiv McCoy, an assistant professor in the university’s Department of Biology in the Krieger School of Arts and Sciences whose research focuses on human genetics and evolution. “There’s an aspect of this that’s like, we don’t know yet what we don’t know.”

    McCoy and 12 Johns Hopkins researchers worked on different aspects of the international initiative, contributing to the main genome assembly project and to several companion works analyzing what can be learned about patterns of genetic and epigenetic variation from person to person through the newly sequenced sections of the genome.

    Winston Timp, associate professor of biomedical engineering in the Whiting School of Engineering, and his graduate student, Ariel Gershman, worked on a part of the project that focused on how the completed genome will enhance understanding of gene regulation and expression–the process of turning genes “on” and “off.”

    Johns Hopkins researchers, led by PhD students Samantha Zarate, Stephanie Yan, and Melanie Kirsche, along with postdoctoral researcher Sergey Aganezov, specifically helped demonstrate how having a single complete genome improves the ability of scientists to understand variations in the genomes of individuals from different populations. By analyzing data from more than 3,200 people from around the world, they revealed more than a million genetic variants that were not previously known. To do so, the Hopkins team used the NHGRI Analysis, Visualization, and Informatics Labspace (AnVIL), a cloud-based platform co-lead by Bloomberg Distinguished Professor Michael Schatz, who was also an author of the T2T papers.

    The study found that because the previous model, known as the reference genome, was a composite of multiple individuals’ genomes essentially “stitched together,” it created artificial “seams” where the model switches from the genome of one person to another. The new, complete version eliminates those seams and is more representative of what an individual’s actual genome looks like.

    Using the new human genome model, the Johns Hopkins contributors also quantified how frequently different versions of the same gene occur in diverse human populations. That serves as an evolutionary record of both random fluctuations and potential natural selection affecting certain parts of the genome.

    Coordinating their research during the COVID-19 pandemic through the messaging platform Slack, scientists from 30 different institutions added or corrected more than 200 million DNA base pairs, increasing the total number in the human genome to 3.05 billion. A base pair is two chemical bases bonded to one another to form a “rung” of the DNA ladder. Through the process, they also discovered more than 100 new genes able to produce proteins.

    According to Schatz, the sequencing has made accessible a segment of the genome about the same size as one of the larger human chromosomes.

    “We’ve effectively added an entirely new human chromosome to our knowledge,” he said. “There’s a lot to be gained and learned from it. There’s this whole new opportunity for discovery.”

    At the same time, he said, because errors in the previous sequencing were identified and corrected, scientists now have a more precise view of “clinically relevant genes,” a potential boon to personalized medicine.

    Of particular interest to the researchers was an enigmatic component of the genome known as centromeres. They are dense bundles of DNA that hold chromosomes together and play a key role in cell division. Previously, however, they had been considered unmappable because they contain thousands of stretches of DNA sequences that repeat over and over.

    Timp explained how this work was empowered by long read sequencing, analogous to jigsaw puzzle pieces. Previously these regions were unresolved because they were so repetitive, so all of the pieces were a single color and shape. “It’s like all you have are pieces that look like blue sky. They’re identical. So, how do you put that together? It becomes almost an impossible problem” he said.

    But more sophisticated sequencing technology now enables scientists to make better sense of the once inscrutable region using long reads. “It’s like the puzzle pieces are now really big, like a toddler puzzle,” Timp said. “And we discovered there are some objects in the pieces, say some grass or the sun. It’s not just blue sky.”

    Being able to track changes over time in these newly accessible genome regions will allow researchers to make more rigorous comparisons from one generation to the next, of people of different origins, or from species to species.

    “Finally from tip to tip; telomere to telomere we have an assembly of the genome we can look at,” Timp said.

    One immediate challenge McCoy identified is that clinical labs will need to transition from the previous genome mapping to the new complete version-no small undertaking requiring that they adjust the information they have about the links between genes and diseases.

    “There are all sorts of databases and resources that have been built around the previous version, and it can be hard to get people to shift over,” he said. “So one goal of our work now is to encourage these important resources to move over to the new mapping to really empower the community.”

    For Schatz, who switched careers from cybersecurity to genomics in 2002 after being inspired by the original Human Genome Project, the comprehensive assembly of the human genome, and his being able to contribute to it, is particularly gratifying.

    “I always believed this could be done,” he said. “But I don’t think anyone really knew when it could be done and what it would really take. I thought it was going to take many more years. It really was a surprise to me how quickly we could get through it.

    See the full article here .

    See also the article from University of Washington Medicine here.

    See also the full article from University of California-Santa Cruz here.

    See also the full article from The National Institutes of Health here .


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    Please help promote STEM in your local schools.

    Stem Education Coalition

    About the The Johns Hopkins University HUB

    We’ve been doing some thinking — quite a bit, actually — about all the things that go on at Johns Hopkins. Discovering the glue that holds the universe together, for example. Or unraveling the mysteries of Alzheimer’s disease. Or studying butterflies in flight to fine-tune the construction of aerial surveillance robots. Heady stuff, and a lot of it.

    In fact, Johns Hopkins does so much, in so many places, that it’s hard to wrap your brain around it all. It’s too big, too disparate, too far-flung.

    We created the Hub to be the news center for all this diverse, decentralized activity, a place where you can see what’s new, what’s important, what Johns Hopkins is up to that’s worth sharing. It’s where smart people (like you) can learn about all the smart stuff going on here.

    At the Hub, you might read about cutting-edge cancer research or deep-trench diving vehicles or bionic arms. About the psychology of hoarders or the delicate work of restoring ancient manuscripts or the mad motor-skills brilliance of a guy who can solve a Rubik’s Cube in under eight seconds.

    There’s no telling what you’ll find here because there’s no way of knowing what Johns Hopkins will do next. But when it happens, this is where you’ll find it.

    The Johns Hopkins University opened in 1876, with the inauguration of its first president, Daniel Coit Gilman. “What are we aiming at?” Gilman asked in his installation address. “The encouragement of research … and the advancement of individual scholars, who by their excellence will advance the sciences they pursue, and the society where they dwell.”

    The mission laid out by Gilman remains the university’s mission today, summed up in a simple but powerful restatement of Gilman’s own words: “Knowledge for the world.”

    What Gilman created was a research university, dedicated to advancing both students’ knowledge and the state of human knowledge through research and scholarship. Gilman believed that teaching and research are interdependent, that success in one depends on success in the other. A modern university, he believed, must do both well. The realization of Gilman’s philosophy at Johns Hopkins, and at other institutions that later attracted Johns Hopkins-trained scholars, revolutionized higher education in America, leading to the research university system as it exists today.

    The Johns Hopkins University is a private research university in Baltimore, Maryland. Founded in 1876, the university was named for its first benefactor, the American entrepreneur and philanthropist Johns Hopkins. His $7 million bequest (approximately $147.5 million in today’s currency)—of which half financed the establishment of the Johns Hopkins Hospital—was the largest philanthropic gift in the history of the United States up to that time. Daniel Coit Gilman, who was inaugurated as the institution’s first president on February 22, 1876, led the university to revolutionize higher education in the U.S. by integrating teaching and research. Adopting the concept of a graduate school from Germany’s historic Ruprecht Karl University of Heidelberg, [Ruprecht-Karls-Universität Heidelberg] (DE), Johns Hopkins University is considered the first research university in the United States. Over the course of several decades, the university has led all U.S. universities in annual research and development expenditures. In fiscal year 2016, Johns Hopkins spent nearly $2.5 billion on research. The university has graduate campuses in Italy, China, and Washington, D.C., in addition to its main campus in Baltimore.

    Johns Hopkins is organized into 10 divisions on campuses in Maryland and Washington, D.C., with international centers in Italy and China. The two undergraduate divisions, the Zanvyl Krieger School of Arts and Sciences and the Whiting School of Engineering, are located on the Homewood campus in Baltimore’s Charles Village neighborhood. The medical school, nursing school, and Bloomberg School of Public Health, and Johns Hopkins Children’s Center are located on the Medical Institutions campus in East Baltimore. The university also consists of the Peabody Institute, Applied Physics Laboratory, Paul H. Nitze School of Advanced International Studies, School of Education, Carey Business School, and various other facilities.

    Johns Hopkins was a founding member of the American Association of Universities. As of October 2019, 39 Nobel laureates and 1 Fields Medalist have been affiliated with Johns Hopkins. Founded in 1883, the Blue Jays men’s lacrosse team has captured 44 national titles and plays in the Big Ten Conference as an affiliate member as of 2014.

    Research

    The opportunity to participate in important research is one of the distinguishing characteristics of Hopkins’ undergraduate education. About 80 percent of undergraduates perform independent research, often alongside top researchers. In FY 2013, Johns Hopkins received $2.2 billion in federal research grants—more than any other U.S. university for the 35th consecutive year. Johns Hopkins has had seventy-seven members of the Institute of Medicine, forty-three Howard Hughes Medical Institute Investigators, seventeen members of the National Academy of Engineering, and sixty-two members of the National Academy of Sciences. As of October 2019, 39 Nobel Prize winners have been affiliated with the university as alumni, faculty members or researchers, with the most recent winners being Gregg Semenza and William G. Kaelin.

    Between 1999 and 2009, Johns Hopkins was among the most cited institutions in the world. It attracted nearly 1,222,166 citations and produced 54,022 papers under its name, ranking No. 3 globally [after Harvard University and the Max Planck Society (DE)] in the number of total citations published in Thomson Reuters-indexed journals over 22 fields in America.

    In FY 2000, Johns Hopkins received $95.4 million in research grants from the National Aeronautics and Space Administration, making it the leading recipient of NASA research and development funding. In FY 2002, Hopkins became the first university to cross the $1 billion threshold on either list, recording $1.14 billion in total research and $1.023 billion in federally sponsored research. In FY 2008, Johns Hopkins University performed $1.68 billion in science, medical and engineering research, making it the leading U.S. academic institution in total R&D spending for the 30th year in a row, according to a National Science Foundation ranking. These totals include grants and expenditures of JHU’s Applied Physics Laboratory in Laurel, Maryland.

    The Johns Hopkins University also offers the “Center for Talented Youth” program—a nonprofit organization dedicated to identifying and developing the talents of the most promising K-12 grade students worldwide. As part of the Johns Hopkins University, the “Center for Talented Youth” or CTY helps fulfill the university’s mission of preparing students to make significant future contributions to the world. The Johns Hopkins Digital Media Center (DMC) is a multimedia lab space as well as an equipment, technology and knowledge resource for students interested in exploring creative uses of emerging media and use of technology.

    In 2013, the Bloomberg Distinguished Professorships program was established by a $250 million gift from Michael Bloomberg. This program enables the university to recruit fifty researchers from around the world to joint appointments throughout the nine divisions and research centers. Each professor must be a leader in interdisciplinary research and be active in undergraduate education. Directed by Vice Provost for Research Denis Wirtz, there are currently thirty two Bloomberg Distinguished Professors at the university, including three Nobel Laureates, eight fellows of the American Association for the Advancement of Science, ten members of the American Academy of Arts and Sciences, and thirteen members of the National Academies.

     
  • richardmitnick 12:44 am on March 26, 2022 Permalink | Reply
    Tags: "UCI scientists make leap forward for genetic sequencing", , , DNA, Every scientific field that relies on accurate DNA sequencing stands to benefit from a better understanding of how Taq works., , If scientists understand how Taq functions then they can better understand just how accurate a person’s sequenced genome truly is., It’s well-known that Taq rejects any wrong items that land into its proverbial shopping cart., Taq replicates DNA., The find is a leap toward revolutionizing medical care., The take-home message: Taq is much less efficient at doing its job than it could be., , This work could be used to develop improved versions of Taq that waste less time while making copies of DNA., What’s surprising in the new work is just how frequently Taq rejects correct bases.   

    From The University of California-Irvine: “UCI scientists make leap forward for genetic sequencing” 

    UC Irvine bloc

    From The University of California-Irvine

    March 11, 2022

    Lucas Van Wyk Joel
    925-918-2060
    ljoel@uci.edu

    Research can lead to improved personalized medicine and understanding of evolution.

    1
    This image shows the Taq enzyme in its open configuration waiting for a new chemical base to arrive so it can try to fit it to a DNA chain. Max Strul / UCI and Lorena Beese laboratory / Duke University

    In a paper published today in Sciences Advances, researchers in the Department of Chemistry and the Department of Physics & Astronomy at the University of California, Irvine revealed new details about a key enzyme that makes DNA sequencing possible. The finding is a leap forward into the era of personalized medicine when doctors will be able to design treatments based on the genomes of individual patients.

    “Enzymes make life possible by catalyzing chemical transformations that otherwise would just take too long for an organism,” said Greg Weiss, UCI professor of chemistry and a co-corresponding author of the new study. “One of the transformations we’re really interested in is essential for all life on the planet – it’s the process by which DNA is copied and repaired.”

    The molecule the UCI-led team studied is an enzyme called Taq, a name derived from the microorganism it was first discovered in, Thermos aquaticus. The molecule the UCI-led team studied is an enzyme called Taq, a name derived from the microorganism it was first discovered in, Thermos aquaticus. Taq replicates DNA. Polymerase chain reaction, the technique with thousands of uses from forensics to PCR tests to detect COVID-19, takes advantage of Taq.

    The UCI-led team found that Taq, as it helps make new copies of DNA, behaves completely unlike what scientists previously thought. Instead of behaving like a well-oiled, efficient machine continuously churning out DNA copies, the enzyme, Weiss explained, acts like an indiscriminate shopper who cruises the aisles of a store, throwing everything they see into the shopping cart.

    “Instead of carefully selecting each piece to add to the DNA chain, the enzyme grabs dozens of misfits for each piece added successfully,” said Weiss. “Like a shopper checking items off a shopping list, the enzyme tests each part against the DNA sequence it’s trying to replicate.”

    It’s well-known that Taq rejects any wrong items that land into its proverbial shopping cart – that rejection is the key, after all, to successfully duplicating a DNA sequence. What’s surprising in the new work is just how frequently Taq rejects correct bases. “It’s the equivalent of a shopper grabbing half a dozen identical cans of tomatoes, putting them in the cart, and testing all of them when only one can is needed.”

    The take-home message: Taq is much less efficient at doing its job than it could be.

    The find is a leap toward revolutionizing medical care, explained Philip Collins, a professor in the UCI Department of Physics & Astronomy who’s a co-corresponding author of the new research. That’s because if scientists understand how Taq functions then they can better understand just how accurate a person’s sequenced genome truly is.

    “Every single person has a slightly different genome,” said Collins, “with different mutations in different places. Some of those are responsible for diseases, and others are responsible for absolutely nothing. To really get at whether these differences are important or healthcare – for properly prescribing medicines – you need to know the differences accurately.”

    “Scientists don’t know how these enzymes achieve their accuracy,” said Collins, whose lab created the nano-scale devices for studying Taq’s behavior. “How do you guarantee to a patient that you’ve accurately sequenced their DNA when it’s different from the accepted human genome? Does the patient really have a rare mutation,” asks Collins, “or did the enzyme simply make a mistake?”

    “This work could be used to develop improved versions of Taq that waste less time while making copies of DNA,” Weiss said.

    The impacts of the work don’t stop at medicine; every scientific field that relies on accurate DNA sequencing stands to benefit from a better understanding of how Taq works. In interpreting evolutionary histories using ancient DNA, for example, scientists rely on assumptions about how DNA changes over time, and those assumptions rely on accurate genetic sequencing.

    “We’ve entered the century of genomic data,” said Collins. “At the beginning of the century we unraveled the human genome for the very first time, and we’re starting to understand organisms and species and human history with this newfound information from genomics, but that genomic information is only useful if it’s accurate.”

    Co-authors on this study include Mackenzie Turvey, Ph.D., a former UCI graduate student in physics & astronomy, and Kristin Gabriel, Ph.D., a former UCI graduate student in molecular biology & biochemistry. This research was funded by the National Human Genome Research Institute of the NIH.

    See the full article here .

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    Please help promote STEM in your local schools.

    Stem Education Coalition

    UC Irvine Campus.


    Since 1965, the University of California-Irvine (US) has combined the strengths of a major research university with the bounty of an incomparable Southern California location. UCI’s unyielding commitment to rigorous academics, cutting-edge research, and leadership and character development makes the campus a driving force for innovation and discovery that serves our local, national and global communities in many ways.

    With more than 29,000 undergraduate and graduate students, 1,100 faculty and 9,400 staff, UCI is among the most dynamic campuses in the University of California system. Increasingly a first-choice campus for students, UCI ranks among the top 10 U.S. universities in the number of undergraduate applications and continues to admit freshmen with highly competitive academic profiles.

    UCI fosters the rigorous expansion and creation of knowledge through quality education. Graduates are equipped with the tools of analysis, expression and cultural understanding necessary for leadership in today’s world.

    Consistently ranked among the nation’s best universities – public and private – UCI excels in a broad range of fields, garnering national recognition for many schools, departments and programs. Times Higher Education ranked UCI No. 1 among universities in the U.S. under 50 years old. Three UCI researchers have won Nobel Prizes – two in chemistry and one in physics.

    The university is noted for its top-rated research and graduate programs, extensive commitment to undergraduate education, and growing number of professional schools and programs of academic and social significance. Recent additions include highly successful programs in public health, pharmaceutical sciences and nursing science; an expanding education school; and a law school already ranked among the nation’s top 10 for its scholarly impact.

    The University of California

    The University of California is a public land-grant research university system in the U.S. state of California. The system is composed of the campuses at Berkeley, Davis, Irvine, Los Angeles, Merced, Riverside, San Diego, San Francisco, Santa Barbara, and Santa Cruz, along with numerous research centers and academic abroad centers. The system is the state’s land-grant university.

    The University of California was founded on March 23, 1868, and operated in Oakland before moving to Berkeley in 1873. Over time, several branch locations and satellite programs were established. In March 1951, the University of California began to reorganize itself into something distinct from its campus in Berkeley, with University of California President Robert Gordon Sproul staying in place as chief executive of the University of California system, while Clark Kerr became the first chancellor of The University of California-Berkeley and Raymond B. Allen became the first chancellor of The University of California-Los Angeles. However, the 1951 reorganization was stalled by resistance from Sproul and his allies, and it was not until Kerr succeeded Sproul as University of California President that University of California was able to evolve into a university system from 1957 to 1960. At that time, chancellors were appointed for additional campuses and each was granted some degree of greater autonomy.

    The University of California currently has 10 campuses, a combined student body of 285,862 students, 24,400 faculty members, 143,200 staff members and over 2.0 million living alumni. Its newest campus in Merced opened in fall 2005. Nine campuses enroll both undergraduate and graduate students; one campus, The University of California-San Francisco, enrolls only graduate and professional students in the medical and health sciences. In addition, the University of California Hastings College of the Law, located in San Francisco, is legally affiliated with University of California, but other than sharing its name is entirely autonomous from the rest of the system. Under the California Master Plan for Higher Education, the University of California is a part of the state’s three-system public higher education plan, which also includes the California State University system and the California Community Colleges system. University of California is governed by a Board of Regents whose autonomy from the rest of the state government is protected by the state constitution. The University of California also manages or co-manages three national laboratories for the U.S. Department of Energy: The DOE’s Lawrence Berkeley National Laboratory , The DOE’s Lawrence Livermore National Laboratory , and The Doe’s Los Alamos National Laboratory.

    Collectively, the colleges, institutions, and alumni of the University of California make it the most comprehensive and advanced post-secondary educational system in the world, responsible for nearly $50 billion per year of economic impact. Major publications generally rank most University of California campuses as being among the best universities in the world. Eight of the campuses, Berkeley, Davis, Irvine, Los Angeles, Santa Barbara, San Diego, Santa Cruz, and Riverside, are considered Public Ivies, making California the state with the most universities in the nation to hold the title. University of California campuses have large numbers of distinguished faculty in almost every academic discipline, with University of California faculty and researchers having won 71 Nobel Prizes as of 2021.

    In 1849, the state of California ratified its first constitution, which contained the express objective of creating a complete educational system including a state university. Taking advantage of the Morrill Land-Grant Acts, the California State Legislature established an Agricultural, Mining, and Mechanical Arts College in 1866. However, it existed only on paper, as a placeholder to secure federal land-grant funds.

    Meanwhile, Congregational minister Henry Durant, an alumnus of Yale University, had established the private Contra Costa Academy, on June 20, 1853, in Oakland, California. The initial site was bounded by Twelfth and Fourteenth Streets and Harrison and Franklin Streets in downtown Oakland (and is marked today by State Historical Plaque No. 45 at the northeast corner of Thirteenth and Franklin). In turn, the academy’s trustees were granted a charter in 1855 for a College of California, though the college continued to operate as a college preparatory school until it added college-level courses in 1860. The college’s trustees, educators, and supporters believed in the importance of a liberal arts education (especially the study of the Greek and Roman classics), but ran into a lack of interest in liberal arts colleges on the American frontier (as a true college, the college was graduating only three or four students per year).

    In November 1857, the college’s trustees began to acquire various parcels of land facing the Golden Gate in what is now Berkeley for a future planned campus outside of Oakland. But first, they needed to secure the college’s water rights by buying a large farm to the east. In 1864, they organized the College Homestead Association, which borrowed $35,000 to purchase the land, plus another $33,000 to purchase 160 acres (650,000 m^2) of land to the south of the future campus. The Association subdivided the latter parcel and started selling lots with the hope it could raise enough money to repay its lenders and also create a new college town. But sales of new homesteads fell short.

    Governor Frederick Low favored the establishment of a state university based upon The University of Michigan plan, and thus in one sense may be regarded as the founder of the University of California. At the College of California’s 1867 commencement exercises, where Low was present, Benjamin Silliman Jr. criticized Californians for creating a state polytechnic school instead of a real university. That same day, Low reportedly first suggested a merger of the already-functional College of California (which had land, buildings, faculty, and students, but not enough money) with the nonfunctional state college (which had money and nothing else), and went on to participate in the ensuing negotiations. On October 9, 1867, the college’s trustees reluctantly agreed to join forces with the state college to their mutual advantage, but under one condition—that there not be simply an “Agricultural, Mining, and Mechanical Arts College”, but a complete university, within which the assets of the College of California would be used to create a College of Letters (now known as the College of Letters and Science). Accordingly, the Organic Act, establishing the University of California, was introduced as a bill by Assemblyman John W. Dwinelle on March 5, 1868, and after it was duly passed by both houses of the state legislature, it was signed into state law by Governor Henry H. Haight (Low’s successor) on March 23, 1868. However, as legally constituted, the new university was not an actual merger of the two colleges, but was an entirely new institution which merely inherited certain objectives and assets from each of them. The University of California’s second president, Daniel Coit Gilman, opened its new campus in Berkeley in September 1873.

    Section 8 of the Organic Act authorized the Board of Regents to affiliate the University of California with independent self-sustaining professional colleges. “Affiliation” meant University of California and its affiliates would “share the risk in launching new endeavors in education.” The affiliates shared the prestige of the state university’s brand, and University of California agreed to award degrees in its own name to their graduates on the recommendation of their respective faculties, but the affiliates were otherwise managed independently by their own boards of trustees, charged their own tuition and fees, and maintained their own budgets separate from the University of California budget. It was through the process of affiliation that University of California was able to claim it had medical and law schools in San Francisco within a decade of its founding.

    In 1879, California adopted its second and current constitution, which included unusually strong language to ensure University of California’s independence from the rest of the state government. This had lasting consequences for the Hastings College of the Law, which had been separately chartered and affiliated in 1878 by an act of the state legislature at the behest of founder Serranus Clinton Hastings. After a falling out with his own handpicked board of directors, the founder persuaded the state legislature in 1883 and 1885 to pass new laws to place his law school under the direct control of the Board of Regents. In 1886, the Supreme Court of California declared those newer acts to be unconstitutional because the clause protecting University of California’s independence in the 1879 state constitution had stripped the state legislature of the ability to amend the 1878 act. To this day, the Hastings College of the Law remains an affiliate of University of California, maintains its own board of directors, and is not governed by the Regents.

    In contrast, Toland Medical College (founded in 1864 and affiliated in 1873) and later, the dental, pharmacy, and nursing schools in SF were affiliated with University of California through written agreements, and not statutes invested with constitutional importance by court decisions. In the early 20th century, the Affiliated Colleges (as they came to be called) began to agree to submit to the Regents’ governance during the term of President Benjamin Ide Wheeler, as the Board of Regents had come to recognize the problems inherent in the existence of independent entities that shared the University of California brand but over which University of California had no real control. While Hastings remained independent, the Affiliated Colleges were able to increasingly coordinate their operations with one another under the supervision of the University of California President and Regents, and evolved into the health sciences campus known today as the University of California-San Francisco.

    In August 1882, the California State Normal School (whose original normal school in San Jose is now San Jose State University) opened a second school in Los Angeles to train teachers for the growing population of Southern California. In 1887, the Los Angeles school was granted its own board of trustees independent of the San Jose school, and in 1919, the state legislature transferred it to University of California control and renamed it the Southern Branch of the University of California. In 1927, it became The University of California-Los Angeles; the “at” would be replaced with a comma in 1958.

    Los Angeles surpassed San Francisco in the 1920 census to become the most populous metropolis in California. Because Los Angeles had become the state government’s single largest source of both tax revenue and votes, its residents felt entitled to demand more prestige and autonomy for their campus. Their efforts bore fruit in March 1951, when UCLA became the first University of California site outside of Berkeley to achieve de jure coequal status with the Berkeley campus. That month, the Regents approved a reorganization plan under which both the Berkeley and Los Angeles campuses would be supervised by chancellors reporting to the University of California President. However, the 1951 plan was severely flawed; it was overly vague about how the chancellors were to become the “executive heads” of their campuses. Due to stubborn resistance from President Sproul and several vice presidents and deans—who simply carried on as before—the chancellors ended up as glorified provosts with limited control over academic affairs and long-range planning while the President and the Regents retained de facto control over everything else.

    Upon becoming president in October 1957, Clark Kerr supervised University of California’s rapid transformation into a true public university system through a series of proposals adopted unanimously by the Regents from 1957 to 1960. Kerr’s reforms included expressly granting all campus chancellors the full range of executive powers, privileges, and responsibilities which Sproul had denied to Kerr himself, as well as the radical decentralization of a tightly knit bureaucracy in which all lines of authority had always run directly to the President at Berkeley or to the Regents themselves. In 1965, UCLA Chancellor Franklin D. Murphy tried to push this to what he saw as its logical conclusion: he advocated for authorizing all chancellors to report directly to the Board of Regents, thereby rendering the University of California President redundant. Murphy wanted to transform University of California from one federated university into a confederation of independent universities, similar to the situation in Kansas (from where he was recruited). Murphy was unable to develop any support for his proposal, Kerr quickly put down what he thought of as “Murphy’s rebellion”, and therefore Kerr’s vision of University of California as a university system prevailed: “one university with pluralistic decision-making”.

    During the 20th century, University of California acquired additional satellite locations which, like Los Angeles, were all subordinate to administrators at the Berkeley campus. California farmers lobbied for University of California to perform applied research responsive to their immediate needs; in 1905, the Legislature established a “University Farm School” at Davis and in 1907 a “Citrus Experiment Station” at Riverside as adjuncts to the College of Agriculture at Berkeley. In 1912, University of California acquired a private oceanography laboratory in San Diego, which had been founded nine years earlier by local business promoters working with a Berkeley professor. In 1944, University of California acquired Santa Barbara State College from the California State Colleges, the descendants of the State Normal Schools. In 1958, the Regents began promoting these locations to general campuses, thereby creating The University of California-Santa Barbara (1958), The University of California-Davis (1959), The University of California-Riverside (1959), The University of California-San Diego (1960), and The University of California-San Francisco (1964). Each campus was also granted the right to have its own chancellor upon promotion. In response to California’s continued population growth, University of California opened two additional general campuses in 1965, with The University of California-Irvine opening in Irvine and The University of California-Santa Cruz opening in Santa Cruz. The youngest campus, The University of California-Merced opened in fall 2005 to serve the San Joaquin Valley.

    After losing campuses in Los Angeles and Santa Barbara to the University of California system, supporters of the California State College system arranged for the state constitution to be amended in 1946 to prevent similar losses from happening again in the future.

    The California Master Plan for Higher Education of 1960 established that University of California must admit undergraduates from the top 12.5% (one-eighth) of graduating high school seniors in California. Prior to the promulgation of the Master Plan, University of California was to admit undergraduates from the top 15%. University of California does not currently adhere to all tenets of the original Master Plan, such as the directives that no campus was to exceed total enrollment of 27,500 students (in order to ensure quality) and that public higher education should be tuition-free for California residents. Five campuses, Berkeley, Davis, Irvine, Los Angeles, and San Diego each have current total enrollment at over 30,000.

    After the state electorate severely limited long-term property tax revenue by enacting Proposition 13 in 1978, University of California was forced to make up for the resulting collapse in state financial support by imposing a variety of fees which were tuition in all but name. On November 18, 2010, the Regents finally gave up on the longstanding legal fiction that University of California does not charge tuition by renaming the Educational Fee to “Tuition.” As part of its search for funds during the 2000s and 2010s, University of California quietly began to admit higher percentages of highly accomplished (and more lucrative) students from other states and countries, but was forced to reverse course in 2015 in response to the inevitable public outcry and start admitting more California residents.

    As of 2019, University of California controls over 12,658 active patents. University of California researchers and faculty were responsible for 1,825 new inventions that same year. On average, University of California researchers create five new inventions per day.

    Seven of University of California’s ten campuses (UC Berkeley, UC Davis, UC Irvine, UCLA, UC San Diego, UC Santa Barbara, and UC Santa Cruz) are members of the Association of American Universities, an alliance of elite American research universities founded in 1900 at University of California’s suggestion. Collectively, the system counts among its faculty (as of 2002):

    389 members of the Academy of Arts and Sciences
    5 Fields Medal recipients
    19 Fulbright Scholars
    25 MacArthur Fellows
    254 members of the National Academy of Sciences
    91 members of the National Academy of Engineering
    13 National Medal of Science Laureates
    61 Nobel laureates.
    106 members of the Institute of Medicine

    Davis, Los Angeles, Riverside, and Santa Barbara all followed Berkeley’s example by aggregating the majority of arts, humanities, and science departments into a relatively large College of Letters and Science. Therefore, at Berkeley, Davis, Los Angeles, and Santa Barbara, their respective College of Letters and Science is by far the single largest academic unit on each campus. The College of Letters and Science at Los Angeles is the largest academic unit in the entire University of California system.

    Finally, Irvine is organized into 13 schools and San Francisco is organized into four schools, all of which are relatively narrow in scope.

    In 2006 the Scholarly Publishing and Academic Resources Coalition awarded the University of California the SPARC Innovator Award for its “extraordinarily effective institution-wide vision and efforts to move scholarly communication forward”, including the 1997 founding (under then University of California President Richard C. Atkinson) of the California Digital Library (CDL) and its 2002 launching of CDL’s eScholarship, an institutional repository. The award also specifically cited the widely influential 2005 academic journal publishing reform efforts of University of California faculty and librarians in “altering the marketplace” by publicly negotiating contracts with publishers, as well as their 2006 proposal to amend University of California’s copyright policy to allow open access to University of California faculty research. On July 24, 2013, the University of California Academic Senate adopted an Open Access Policy, mandating that all University of California faculty produced research with a publication agreement signed after that date be first deposited in University of California’s eScholarship open access repository.

    University of California system-wide research on the SAT exam found that, after controlling for familial income and parental education, so-called achievement tests known as the SAT II had 10 times more predictive ability of college aptitude than the SAT I.

    All University of California campuses except Hastings College of the Law are governed by the Regents of the University of California as required by the Constitution of the State of California. Eighteen regents are appointed by the governor for 12-year terms. One member is a student appointed for a one-year term. There are also seven ex officio members—the governor, lieutenant governor, speaker of the State Assembly, State Superintendent of Public Instruction, president and vice president of the alumni associations of University of California, and the University of California president. The Academic Senate, made up of faculty members, is empowered by the regents to set academic policies. In addition, the system-wide faculty chair and vice-chair sit on the Board of Regents as non-voting members.

    Originally, the president was the chief executive of the first campus, Berkeley. In turn, other University of California locations (with the exception of Hastings College of the Law) were treated as off-site departments of the Berkeley campus, and were headed by provosts who were subordinate to the president. In March 1951, the regents reorganized the university’s governing structure. Starting with the 1952–53 academic year, day-to-day “chief executive officer” functions for the Berkeley and Los Angeles campuses were transferred to chancellors who were vested with a high degree of autonomy, and reported as equals to University of California’s president. As noted above, the regents promoted five additional University of California locations to campuses and allowed them to have chancellors of their own in a series of decisions from 1958 to 1964, and the three campuses added since then have also been run by chancellors. In turn, all chancellors (again, with the exception of Hastings) report as equals to the University of California President. Today, the University of California Office of the President (UCOP) and the Office of the Secretary and Chief of Staff to the Regents of the University of California share an office building in downtown Oakland that serves as the University of California system’s headquarters.

    Kerr’s vision for University of California governance was “one university with pluralistic decision-making.” In other words, the internal delegation of operational authority to chancellors at the campus level and allowing nine other campuses to become separate centers of academic life independent of Berkeley did not change the fact that all campuses remain part of one legal entity. As a 1968 University of California centennial coffee table book explained: “Yet for all its campuses, colleges, schools, institutes, and research stations, it remains one University, under one Board of Regents and one president—the University of California.” University of California continues to take a “united approach” as one university in matters in which it inures to University of California’s advantage to do so, such as when negotiating with the legislature and governor in Sacramento. University of California continues to manage certain matters at the system wide level in order to maintain common standards across all campuses, such as student admissions, appointment and promotion of faculty, and approval of academic programs.

    The State of California currently (2021–2022) spends $3.467 billion on the University of California system, out of total University of California operating revenues of $41.6 billion. The “University of California Budget for Current Operations” lists the medical centers as the largest revenue source, contributing 39% of the budget, the federal government 11%, Core Funds (State General Funds, University of California General Funds, student tuition) 21%, private support (gifts, grants, endowments) 7% ,and Sales and Services at 21%. In 1980, the state funded 86.8% of the University of California budget. While state funding has somewhat recovered, as of 2019 state support still lags behind even recent historic levels (e.g. 2001) when adjusted for inflation.

    According to the California Public Policy Institute, California spends 12% of its General Fund on higher education, but that percentage is divided between the University of California, California State University and California Community Colleges. Over the past forty years, state funding of higher education has dropped from 18% to 12%, resulting in a drop in University of California’s per student funding from $23,000 in 2016 to a current $8,000 per year per student.

    In May 2004, University of California President Robert C. Dynes and CSU Chancellor Charles B. Reed struck a private deal, called the “Higher Education Compact”, with Governor Schwarzenegger. They agreed to slash spending by about a billion dollars (about a third of the university’s core budget for academic operations) in exchange for a funding formula lasting until 2011. The agreement calls for modest annual increases in state funds (but not enough to replace the loss in state funds Dynes and Schwarzenegger agreed to), private fundraising to help pay for basic programs, and large student fee hikes, especially for graduate and professional students. A detailed analysis of the Compact by the Academic Senate “Futures Report” indicated, despite the large fee increases, the university core budget did not recover to 2000 levels. Undergraduate student fees have risen 90% from 2003 to 2007. In 2011, for the first time in Univerchity of California’s history, student fees exceeded contributions from the State of California.

    The First District Court of Appeal in San Francisco ruled in 2007 that the University of California owed nearly $40 million in refunds to about 40,000 students who were promised that their tuition fees would remain steady, but were hit with increases when the state ran short of money in 2003.

    In September 2019, the University of California announced it will divest its $83 billion in endowment and pension funds from the fossil fuel industry, citing ‘financial risk’.

    At present, the University of California system officially describes itself as a “ten campus” system consisting of the campuses listed below.

    Berkeley
    Davis
    Irvine
    Los Angeles
    Merced
    Riverside
    San Diego
    San Francisco
    Santa Barbara
    Santa Cruz

    These campuses are under the direct control of the Regents and President. Only these ten campuses are listed on the official University of California letterhead.

    Although it shares the name and public status of the University of California system, the Hastings College of the Law is not controlled by the Regents or President; it has a separate board of directors and must seek funding directly from the Legislature. However, under the California Education Code, Hastings degrees are awarded in the name of the Regents and bear the signature of the University of California president. Furthermore, Education Code section 92201 states that Hastings “is affiliated with the University of California, and is the law department thereof”.

     
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