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  • richardmitnick 1:57 pm on February 2, 2023 Permalink | Reply
    Tags: "Critical zone": the term scientists use to refer to the area of Earth's land surface responsible for sustaining life., "Microbes are 'active engineers' in Earth's rock-to-life cycle", A strong relationship between the rate at which the rock was weathering to form soil and the activities of the microbiome in the subsurface, An open-air living laboratory that spans parts of Arizona and New Mexico breaks down rock and minerals over timea nd feeds into Earth's intricate life-support system., , , Biology, Chemical and mineral weathering drives the evolution of everything from the soil microbiome to the carbon cycle., , , , Minerals and microorganisms and organics interact with each other constantly to provide all terrestrial life with nutrients energy and suitable living environments.", National Science Foundation Critical Zone Observatory program,   

    From The University of Arizona: “Microbes are ‘active engineers’ in Earth’s rock-to-life cycle” 

    From The University of Arizona

    2.1.23
    Jake Kerr and Rosemary Brandt | College of Agriculture and Life Sciences

    An open-air, living laboratory that spans parts of Arizona and New Mexico is helping researchers better understand how mineral weathering – the breaking down or dissolving of rocks and minerals over time – feeds into Earth’s intricate life-support system.

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    An eddy covariance tower helps researchers measure forest-atmosphere exchanges of gas and water in the Santa Catalina Mountains in Arizona. Courtesy of The University of Arizona Department of Environmental Science.

    The name “critical zone” may give off 1980s action thriller vibes, but it’s the term scientists use to refer to the area of Earth’s land surface responsible for sustaining life. A relatively small portion of the planetary structure, it spans from the bedrock below groundwater all the way up to the lower atmosphere.

    “Think of it as Earth’s skin,” said Jon Chorover, head of the Department of Environmental Science in the University of Arizona College of Agriculture and Life Sciences. “It’s sometimes termed the zone where rock meets life.”

    Most people – even geologists – don’t typically think about rock as the foundation of life or the way life may alter rock, but that cuts to the heart of critical zone science, Chorover said.

    A relatively new framework for approaching Earth sciences, the critical zone aligns researchers across disciplines to better understand how the delicate web of physical, chemical and biological processes come together to form Earth’s life-support system.

    As a biogeochemist, the whole-system approach is a way of thinking that comes naturally to Chorover, who has spent much of his career working to unravel the ways in which chemical and mineral weathering drives the evolution of everything from the soil microbiome to the carbon cycle.

    Together with Qian Fang, a postdoctoral researcher from Peking University in Beijing, Chorover recently published the results [Nature Communications (below)] of nearly 10 years of data collected at the Santa Catalina-Jemez River Basin Critical Zone Observatory – which spans a gradient of elevation and climates on rock basins in northern New Mexico and Southern Arizona.
    Fig. 1: A conceptual model showing the relationship of weathering congruency to the priming effect.
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    Mineral breakdown at high and low weathering congruencies results in different proportions of dissolved vs. solid-phase products (Table 1). High weathering congruency yields more dissolved cations and fewer solids relative to low congruency. Low congruency generates more short-range-order minerals that can bond with and protect organic matter (including dissolved organic matter-DOM) through formation of mineral-organic associations, which are inaccessible to microorganisms and, thus, influence the priming effect. The more limited production of solid phases at high congruency limits bonding and precipitation of dissolved organic matter, thus facilitating the priming of soil organic matter.

    Their findings, according to Chorover, provide a “smoking gun” link between the activities of carbon-consuming microbes and the transformation of rock to life-sustaining soil in the critical zone.

    An open-air, living laboratory

    In the past, measuring something like mineral weathering often wasn’t that exciting — imagine researchers breaking off chunks of rock and watching it dissolve in beakers back at the lab. But viewing that process in a natural ecological system is a different story.

    At the Santa Catalina-Jemez River Basin Critical Zone Observatory, towers that measure the exchange of water between the forest and atmosphere, soil probes that read the transfer of energy and gases, and a host of other in-environment instrumentation offer scientists a firsthand view of the complex systems within the critical zone.

    The site is part of a larger National Science Foundation Critical Zone Observatory program, which unlike traditional brick-and-mortar observatories provides a network of regional ecological environments rigged with scientific instrumentation across the United States.

    Temperature, moisture and gas sensors at the site collect measurements every 15 minutes, and after compiling and correlating the data, “What we found was a strong relationship between the rate at which the rock was weathering to form soil and the activities of the microbiome in the subsurface,” said Chorover, a principal investigator at the Catalina-Jemez observatory.

    Breaking down the rock-to-life cycle

    “Minerals, microorganisms and organics are among the most important components in Earth’s surface,” Fang said. “They interact with each other constantly to provide all terrestrial life with nutrients, energy and suitable living environments.”

    These minerals in the critical zone are continuously attacked by microorganisms, organic acids and water, Fang explained. As the minerals break down, microbes in the soil consume the new organic matter and transform it into material that feeds plants and other microorganisms, while releasing carbon dioxide.

    Previous studies suggest that microbial decomposition of soil organic matter can be fueled when more “fresh” organics – such as plant matter – are introduced to the soil system. This process is called the “priming effect” by soil scientists. However, the relationship between mineral weathering and microbial priming remains unclear.

    “Our study shows, for the first time, how these essential soil processes are coupled, and these two processes continuously influence soil formation, CO2 emission and global climate,” Fang said. “The linkages may even be associated with long-term elemental cycling and rapid turnover of soil carbon and nutrients on Earth.”

    While it is easy to perceive the success of plants and microorganisms as lucky environmental circumstance, Chorover said this study proves even the smallest parts of the critical zone have a substantial role to play.

    “It shows that life is not simply a passive passenger on the trajectory of critical zone evolution, but actually an active engineer in determining the direction and path of how the Earth’s skin evolves,” Chorover said.

    Nature Communications

    See the full article here .

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


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

    Stem Education Coalition

    As of 2019, The University of Arizona enrolled 45,918 students in 19 separate colleges/schools, including The University of Arizona College of Medicine in Tucson and Phoenix and the James E. Rogers College of Law, and is affiliated with two academic medical centers (Banner – University Medical Center Tucson and Banner – University Medical Center Phoenix). The University of Arizona is one of three universities governed by the Arizona Board of Regents. The university is part of the Association of American Universities and is the only member from Arizona, and also part of the Universities Research Association . The university is classified among “R1: Doctoral Universities – Very High Research Activity”.

    Known as the Arizona Wildcats (often shortened to “Cats”), The University of Arizona’s intercollegiate athletic teams are members of the Pac-12 Conference of the NCAA. The University of Arizona athletes have won national titles in several sports, most notably men’s basketball, baseball, and softball. The official colors of the university and its athletic teams are cardinal red and navy blue.

    After the passage of the Morrill Land-Grant Act of 1862, the push for a university in Arizona grew. The Arizona Territory’s “Thieving Thirteenth” Legislature approved The University of Arizona in 1885 and selected the city of Tucson to receive the appropriation to build the university. Tucson hoped to receive the appropriation for the territory’s mental hospital, which carried a $100,000 allocation instead of the $25,000 allotted to the territory’s only university. (Arizona State University was also chartered in 1885, but it was created as Arizona’s normal school, and not a university). Flooding on the Salt River delayed Tucson’s legislators, and by the time they reached Prescott, back-room deals allocating the most desirable territorial institutions had been made. Tucson was largely disappointed with receiving what was viewed as an inferior prize.

    With no parties willing to provide land for the new institution, the citizens of Tucson prepared to return the money to the Territorial Legislature until two gamblers and a saloon keeper decided to donate the land to build the school. Construction of Old Main, the first building on campus, began on October 27, 1887, and classes met for the first time in 1891 with 32 students in Old Main, which is still in use today. Because there were no high schools in Arizona Territory, the university maintained separate preparatory classes for the first 23 years of operation.

    Research

    The University of Arizona is classified among “R1: Doctoral Universities – Very high research activity”. UArizona is the fourth most awarded public university by National Aeronautics and Space Administration for research. The University of Arizona was awarded over $325 million for its Lunar and Planetary Laboratory (LPL) to lead NASA’s 2007–08 mission to Mars to explore the Martian Arctic, and $800 million for its OSIRIS-REx mission, the first in U.S. history to sample an asteroid.

    National Aeronautics Space Agency OSIRIS-REx Spacecraft.

    The LPL’s work in the Cassini spacecraft orbit around Saturn is larger than any other university globally.

    National Aeronautics and Space Administration/European Space Agency [La Agencia Espacial Europea][Agence spatiale européenne][Europäische Weltraumorganization](EU)/ASI Italian Space Agency [Agenzia Spaziale Italiana](IT) Cassini Spacecraft.

    The University of Arizona laboratory designed and operated the atmospheric radiation investigations and imaging on the probe. The University of Arizona operates the HiRISE camera, a part of the Mars Reconnaissance Orbiter.

    U Arizona NASA Mars Reconnaisance HiRISE Camera.

    NASA Mars Reconnaissance Orbiter.

    While using the HiRISE camera in 2011, University of Arizona alumnus Lujendra Ojha and his team discovered proof of liquid water on the surface of Mars—a discovery confirmed by NASA in 2015. The University of Arizona receives more NASA grants annually than the next nine top NASA/JPL-Caltech-funded universities combined. As of March 2016, The University of Arizona’s Lunar and Planetary Laboratory is actively involved in ten spacecraft missions: Cassini VIMS; Grail; the HiRISE camera orbiting Mars; the Juno mission orbiting Jupiter; Lunar Reconnaissance Orbiter (LRO); Maven, which will explore Mars’ upper atmosphere and interactions with the sun; Solar Probe Plus, a historic mission into the Sun’s atmosphere for the first time; Rosetta’s VIRTIS; WISE; and OSIRIS-REx, the first U.S. sample-return mission to a near-earth asteroid, which launched on September 8, 2016.

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    NASA – GRAIL Flying in Formation (Artist’s Concept). Credit: NASA.
    National Aeronautics Space Agency Juno at Jupiter.

    NASA/Lunar Reconnaissance Orbiter.

    NASA/Mars MAVEN

    NASA Parker Solar Probe Plus named to honor Pioneering Physicist Eugene Parker. The Johns Hopkins University Applied Physics Lab.
    National Aeronautics and Space Administration Wise /NEOWISE Telescope.

    The University of Arizona students have been selected as Truman, Rhodes, Goldwater, and Fulbright Scholars. According to The Chronicle of Higher Education, UArizona is among the top 25 producers of Fulbright awards in the U.S.

    The University of Arizona is a member of the Association of Universities for Research in Astronomy , a consortium of institutions pursuing research in astronomy. The association operates observatories and telescopes, notably Kitt Peak National Observatory just outside Tucson.

    National Science Foundation NOIRLab National Optical Astronomy Observatory Kitt Peak National Observatory on Kitt Peak of the Quinlan Mountains in the Arizona-Sonoran Desert on the Tohono O’odham Nation, 88 kilometers (55 mi) west-southwest of Tucson, Arizona, Altitude 2,096 m (6,877 ft), annotated.

    Led by Roger Angel, researchers in the Steward Observatory Mirror Lab at The University of Arizona are working in concert to build the world’s most advanced telescope. Known as the Giant Magellan Telescope (CL), it will produce images 10 times sharper than those from the Earth-orbiting Hubble Telescope.

    GMT Giant Magellan Telescope(CL) 21 meters, to be at the Carnegie Institution for Science’s NOIRLab NOAO Las Campanas Observatory(CL), some 115 km (71 mi) north-northeast of La Serena, Chile, over 2,500 m (8,200 ft) high.

    GMT will ultimately cost $1 billion. Researchers from at least nine institutions are working to secure the funding for the project. The telescope will include seven 18-ton mirrors capable of providing clear images of volcanoes and riverbeds on Mars and mountains on the moon at a rate 40 times faster than the world’s current large telescopes. The mirrors of the Giant Magellan Telescope will be built at The University of Arizona and transported to a permanent mountaintop site in the Chilean Andes where the telescope will be constructed.

    Reaching Mars in March 2006, the Mars Reconnaissance Orbiter contained the HiRISE camera, with Principal Investigator Alfred McEwen as the lead on the project. This National Aeronautics and Space Agency mission to Mars carrying the UArizona-designed camera is capturing the highest-resolution images of the planet ever seen. The journey of the orbiter was 300 million miles. In August 2007, The University of Arizona, under the charge of Scientist Peter Smith, led the Phoenix Mars Mission, the first mission completely controlled by a university. Reaching the planet’s surface in May 2008, the mission’s purpose was to improve knowledge of the Martian Arctic. The Arizona Radio Observatory , a part of The University of Arizona Department of Astronomy Steward Observatory , operates the Submillimeter Telescope on Mount Graham.

    University of Arizona Radio Observatory at NOAO Kitt Peak National Observatory, AZ USA, U Arizona Department of Astronomy and Steward Observatory at altitude 2,096 m (6,877 ft).

    The National Science Foundation funded the iPlant Collaborative in 2008 with a $50 million grant. In 2013, iPlant Collaborative received a $50 million renewal grant. Rebranded in late 2015 as “CyVerse”, the collaborative cloud-based data management platform is moving beyond life sciences to provide cloud-computing access across all scientific disciplines.

    In June 2011, the university announced it would assume full ownership of the Biosphere 2 scientific research facility in Oracle, Arizona, north of Tucson, effective July 1. Biosphere 2 was constructed by private developers (funded mainly by Texas businessman and philanthropist Ed Bass) with its first closed system experiment commencing in 1991. The university had been the official management partner of the facility for research purposes since 2007.

    U Arizona mirror lab-Where else in the world can you find an astronomical observatory mirror lab under a football stadium?

    University of Arizona’s Biosphere 2, located in the Sonoran desert. An entire ecosystem under a glass dome? Visit our campus, just once, and you’ll quickly understand why The University of Arizona is a university unlike any other.

    University of Arizona Landscape Evolution Observatory at Biosphere 2.

     
  • richardmitnick 1:20 pm on February 1, 2023 Permalink | Reply
    Tags: "Biorefinery uses microbial fuel cell to upcycle resistant plant waste", "MEC": microbial electrolysis cell, , Biology, , , Organic waste turns into antioxidant flavonoids for nutrition and medicine., The Robert R. McCormick School of Engineering   

    From The Robert R. McCormick School of Engineering At Northwestern University : “Biorefinery uses microbial fuel cell to upcycle resistant plant waste” 

    From From The Robert R. McCormick School of Engineering

    At

    Northwestern U bloc

    Northwestern University

    1.30.23
    Amanda Morris

    Organic waste turns into antioxidant flavonoids for nutrition and medicine.

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    Paper mills (like the one shown here) are one of the biggest generators of waste lignin, a fibrous material that gives plants their structure.

    When nature designed lignin — the fibrous, woody material that gives plants their rigid structure — it didn’t cut any corners. Incredibly slow to break down, lignin is so sturdy and long lasting that it is resistant to bacteria and rot.

    So, what happens to all the lignin waste from farmlands, breweries and paper mills? Most of it is burned or buried, generating pollution and wasting a potential renewable resource.

    Now, Northwestern University researchers have developed a sustainable, inexpensive two-step process that can upcycle organic carbon waste — including lignin. By processing waste through a microbe-driven biorefinery, the researchers turned lignin into carbon sources that could be used in high-value, plant-derived pharmaceuticals and antioxidant nutraceuticals as well as carbon-based nanoparticles for drug or chemical delivery.

    The study was featured on the cover of the January issue of the journal ACS Sustainable Chemistry and Engineering.

    “Lignin should have tremendous value, but it’s intrinsically regarded as waste,” said Northwestern’s Kimberly Gray, who led the research. “Lignin makes up 20-30% of biomass but 40% of the energy, which is a lot, but it’s difficult to tap this energy source. Nature made lignin so recalcitrant to processing that people haven’t figured out how to use it. Researchers have been trying to solve this problem for decades. Using an oil refinery as a template, we developed a biorefinery that takes in waste streams and produces high-value products.”

    Gray is the Roxelyn and Richard Pepper Family Chair in Civil and Environmental Engineering and professor of civil and environmental engineering in Northwestern’s McCormick School of Engineering.

    Nature’s building material

    One of the most abundant organic polymers in the world, lignin is present in all vascular plants. Found between cell walls, lignin gives strong, sturdy plants — like trees —structural support. Without lignin, wood and bark would be too weak to support trees. And wooden houses and furniture would simply collapse.

    But most industries that use plants — such as the paper manufacturing and brewing industries — strip out lignin, leaving behind cellulose, a type of sugar. Instead of making use of nature’s ultra-resistant material, industrial teams burn lignin as a cheap fuel.

    “Humans want to get rid of lignin to reach the sugars,” Gray said. “They ferment cellulose to make alcohol or process it to make pulp. Then what do they do with the lignin? They burn it as a low-quality fuel. It’s a waste.”

    Bacteria-powered fuel cell

    To develop a biorefinery for breaking down carbon waste, including lignin, the researchers first engineered a microbial electrolysis cell (MEC). Similar to a fuel cell, the MEC exchanges energy between an anode and a cathode. But instead of a metal-based anode, Northwestern’s bio-anode comprises exoelectrogens — a type of bacteria that naturally generate electrical energy by eating organic matter.

    “The microbes act as the catalyst,” said study co-author George Wells, associate professor of civil and environmental engineering at McCormick. “Instead of using chemical catalysts, which are often very expensive and require high temperatures, we’re using biology as the catalyst.”

    The beauty of the MEC is that it can process any type of organic waste — human, agricultural or industrial. The MEC cycles waste-filled water through the bacteria, which eat up the carbon. Here, they degrade the organic carbon into carbon dioxide and then naturally respire electrons. During this process, extracted electrons flow from the bio-anode to the cathode (made of a carbon cloth), where they reduce oxygen to generate water. The process consumes protons, driving up the water’s pH to turn it into a caustic solution. From there, the caustic solution could be used for any number of applications, including wastewater treatment.

    “Another benefit of this process is that it effectively treats wastewater to remove detrimental organic carbon,” Wells said. “So, a key product is clean water.”

    But the researchers took the caustic substance and turned their attention back to the lignin. Lignin compounds are durable because they contain complex chains of aromatic carbon, which have a special bonding pattern that forms a ring of six carbon atoms. Each aromatic ring comprises alternating double and single bonds, which are incredibly difficult to break apart.

    Busting ‘unbreakable’ bonds

    When the researchers exposed lignin to the bio-based caustic chemical, however, lignin’s polymers broke apart in a way that preserved the aromatic rings. About 17% of the processed lignin turned into rings of carbon called flavonoids, an antioxidant-rich phytonutrient often found in supplements. Commonly used in medicinal chemistry, these rings could be used as plant-derived, sustainable precursors to inexpensive pharmaceuticals and supplements.

    “It breaks apart the polymer bonds but selectively leaves the ring,” Gray said. “If you can preserve that ring, then you can make high-value materials. Chemists have developed catalysts that break apart the whole compound, and then they have to rebuild the ring. But we were able to break it selectively to preserve the valuable structures.”

    The rest of the processed lignin (about 80%) became carbon-based nanoparticles, which could be used to encompass substances for targeted drug delivery in humans or targeted nutrient delivery in plants. The nanoparticles also could offer a sustainable, plant-derived alternative for sunscreens and cosmetics.

    “It’s exciting to identify and explore a route for sustainable resource recovery from multiple waste streams,” Wells said. “We have massive wastewater and lignin streams that are expensive to treat on their own. We’re trying to reimagine those as sources of value.”

    Recovering resources without hazardous chemicals

    Although researchers could have used a commercially available caustic substance to process lignin, their MEC-based approach has many advantages. First, the green bio-based chemical just works better. Second, it’s safer, less expensive, can be used in ambient conditions and can generate chemicals at the point of need.

    “There are many caustic substances, such as sodium hydroxide, which is commonly used in many industrial processes and wastewater treatment,” Wells said. “But that involves shipping and storing large amounts of toxic chemicals. Not only is that expensive, it also is hazardous for public health. It’s much safer and more sustainable to generate chemicals on site from waste products. We avoid having to ship or store large quantities of hazardous chemicals and are not reliant on supply chains or trucks arriving on time. It gives us flexibility and adaptability to generate chemicals right on site when they are needed.”

    The study was supported by the Finite Earth Initiative of the McCormick School of Engineering at Northwestern University.

    ACS Sustainable Chemistry and Engineering

    See the full article here .

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

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

    Please help promote STEM in your local schools.

    Stem Education Coalition

    Northwestern South Campus
    South Campus

    Northwestern is recognized nationally and internationally for its educational programs.

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

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

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

    Established in 1909, the From Robert R.McCormick School of Engineering is one of twelve constituent schools at Northwestern University. Most engineering classes are held in the Technological Institute (1942), which students commonly refer to as “Tech.” In October 2005, another building affiliated with the School, the Ford Motor Company Engineering Design Center, opened.

    The trustees of Northwestern University founded a College of Technology in June 1873, but in his report for 1876-77, President Oliver Marcy announced that the new college had failed for lack of financial resources to develop the faculty and facilities.

    In 1891, President Henry Wade Rogers called for the founding of a new Engineering School, stating that universities in general were “not performing the work necessary to prepare men for the various activities of modern life, so different from the life their fathers lived half a century ago.” This was realized in 1909, when the new College of Engineering was opened in Swift Hall. Operationally, the Engineering School until the mid-1920s was a department of the College of Liberal Arts. The major emphasis was on a broad general education with a particular stress on mathematics and science. In 1937, the Engineering School ran into difficulties with the American Engineers’ Council for Professional Development, which denied the School accreditation. In response, a four-year curriculum satisfying the ECPD was put into place.

    In 1939, Walter Patton Murphy (1873–1942), a wealthy inventor of railroad equipment, donated $6.735 million to the School of Engineering.[1] Murphy meant for the Institute to offer a “cooperative” education, whereby academic courses and practical application in industrial settings were closely integrated. In 1942, Northwestern received an additional bequest of $28 million from Murphy’s estate to provide for an engineering school “second to none.” A cooperative education program was designed in the late 1930s by Charles F. Kettering, former research head of General Motors, and Herman Schneider, dean of the engineering school at the University of Cincinnati. The program required undergraduates to work outside the classroom in technical positions for several terms over the course of their college years.

     
  • richardmitnick 11:44 am on January 30, 2023 Permalink | Reply
    Tags: , , “Connectomics”: The study to understanding how individual neurons are connected to one another to form functional networks., Biology, , , Many of us have seen microscopic images of neurons in the brain — each neuron appearing as a glowing cell in a vast sea of blackness., , , The image is misleading: Neurons don’t exist in isolation. In the human brain some 86 billion neurons form 100 trillion connections to each other-numbers too large for the brain to fathom., , To understand what a single neuron is doing ideally you study it within the context of the rest of the neural network.   

    From The Medical School At Harvard University: “A New Field of Neuroscience Aims to Map Connections in the Brain” 

    harvard-medical-school-bloc

    From The Medical School

    At

    Harvard University

    News & Research

    1.19.23
    CATHERINE CARUSO

    Scientists working in “connectomics” are creating comprehensive maps of how neurons connect to one another.

    Many of us have seen microscopic images of neurons in the brain — each neuron appearing as a glowing cell in a vast sea of blackness. This image is misleading: Neurons don’t exist in isolation. In the human brain some 86 billion neurons form 100 trillion connections to each other — numbers that, ironically, are far too large for the human brain to fathom.

    Wei-Chung Allen Lee, Harvard Medical School associate professor of neurology at Boston Children’s Hospital, is working in a new field of neuroscience called connectomics, which aims to comprehensively map connections between neurons in the brain.

    “The brain is structured so that each neuron is connected to thousands of other neurons, and so to understand what a single neuron is doing ideally you study it within the context of the rest of the neural network,” Lee explained.

    Lee recently spoke to Harvard Medicine News about the promise of connectomics. He also described his own research, which combines connectomics with information on neural activity to explore neural circuits that underlie behavior.

    Harvard Medicine News: To start with a basic question, what is connectomics?

    Lee: We define connectomics as understanding how individual neurons are connected to one another to form functional networks. The goal is to create connectomes, or detailed structural maps of connectivity where we can see every neuron and every connection. What’s unique is the comprehensiveness of connectivity: In a perfect connectome, we’d know how every neuron was connected to every other neuron.

    We believe that the connectivity of neurons is fundamental to how they function, since they must receive information from each other in order to use this information. Having comprehensive data about connectivity allows us to look at higher-order interactions between populations of neurons that are important for brain function and behavior. It is challenging to study higher-order interactions without connectomics.

    Some have argued that you are your connectome. When you fall asleep at night, your brain activity dramatically changes, interrupting your thoughts and feelings — but when you wake up, you resume your thoughts and feelings without any break in your sense of self. This is likely because your brain connectivity has remained largely intact through the night. In essence, the structure of how our neurons are wired is our “self,” and connectomics is the key to understanding this structure.

    HMNews: What are you studying within the context of connectomics?

    Lee: My lab is interested in understanding how computations arise in the brain, or the general principles by which neural circuits organize themselves into functional networks. To do this, we aim to comprehensively map how individual neurons are connected to one another in complex networks. At the same time, we want to understand how those neurons are active within the functioning circuit. We do this in the context of behavior, ranging from making decisions to executing actions.

    We are trying to couple connectomics with recordings of neural activity to do what we call functional connectomics. Essentially, we take the map of where every neuron is and how it is connected to every other neuron, and we layer on information about the activity of those neurons in a living animal. We also use genetic engineering approaches to label specific cell types, which is additional information that we can layer on top of connectivity.

    HMNews: What tools do scientists use to map connectomes?

    Lee: We are developing and applying high-throughput microscopy, computational approaches, and machine learning to generate connectomes and translate these detailed maps of neural connectivity into biological and computational insights. One key component of our approach is serial transmission electron microscopy, or EM, which has unsurpassed spatial resolution, signal-to-noise ratio, and speed relative to other serial EM methods. This technique allows us to identify excitatory and inhibitory neurons, as well as the synapses, or small gaps where neurons connect to each other. We can also examine connectivity patterns of neurons, and study the organization of synaptic connections.

    Historically, high-resolution EM has been slow and tedious, but we’ve engineered a high-speed EM platform that allows us to capture the whole nervous system of an adult fruit fly in a few months, generating 5 to 10 terabytes of data a day. We have also developed computational infrastructure and tools that enable us to handle and visualize the large amounts of data that we are generating. For example, we use artificial deep neural networks to extract information about cells and their connectivity from these massive datasets.

    HMNews: What models do you use in your research?

    Lee: We have mainly worked with mice and fruit flies, which are powerful and well-studied model systems. The field has sophisticated genetic tools that allow us to label different populations of neurons across the central nervous systems of these species. In fruit flies, we can use the technologies we’ve been developing for connectomics to capture the entire brain and nervous system at synapse resolution. In the mouse, we can target relevant neural circuits or subcircuits. We are using these models to study the basic principles of how neural circuits are built and operate — basically how neural networks are connected to each other to perform different computations that underlie behavior.

    We also work in nontraditional model systems such as the mosquito. Mosquito brains are about the same size as fruit fly brains, but the genetics is more challenging. Scientists have used genetics to access the first-order neurons that start carrying information into the mosquito brain, but the rest of the brain is a black box in many respects. We don’t know much about its fundamental neurobiology, including how the mosquito brain integrates different sensory modalities to drive behavior.

    For example, adult female mosquitoes that are trying to reproduce integrate information on human odors, heat, and carbon dioxide. We know that these different sensory cues enter the brain, but we don’t know how they are integrated and converge onto neural circuits that drive mosquitoes’ host-seeking behavior.

    We hope that mapping the whole mosquito brain will provide a new foundation for understanding how sensory integration and action selection works for innate behavior. Additionally, the specific mosquito species we study is a vector for diseases such as malaria, West Nile, Zika, yellow fever, and dengue fever, so there’s a clinical and public health aspect of this that makes it a really important model system.

    HMNews: You recently published a paper in Nature [below] on brain connectivity and pattern association in mice. What was the premise of the study?

    Lee: This was a collaboration with Wade Regehr, professor of neurobiology at HMS. The paper focuses on information processing in the cerebellum, which is a brain region that, among other things, is important for smooth, coordinated movement. One of the things the cerebellum is thought to do is make fine-scale error corrections in movement by comparing patterns from intended and executed actions. For example, if you try to touch your nose and you miss, there is information coming from your motor system that tells your cerebellum what the intended action was, and there is sensory information coming from your finger about what actually happened, including the location of your finger in space. The cerebellum is thought to compute the difference between the intended action and the actual action, and to help correct the error.

    We studied the cerebellar cortex, which is packed full of small neurons called granule cells that make up more than half the neurons in the brain. These granule cells each have, on average, four dendrites, or branching structures that receive information from other neurons. In this case, the dendrites connect to neurons called mossy fibers that bring information into the cerebellum. The granule cells then process this information and communicate it to other neurons called Purkinje cells, with each Purkinje cell integrating information from 100,000 to 200,000 granule cells, and sending this information to other brain regions. These three cell types make up the “feedforward” circuit we wanted to better understand.

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    4
    Rotating 3D images of two neuron types in the mouse cerebellum. Granule cells (blue) receive and process information from mossy fibers and communicate this information to Purkinje cells (green). As the sole output of the cerebellar cortex, Purkinje cells integrate information from hundreds of thousands of granule cells, and send this information to other brain regions. Videos: Lee lab.

    HMNews: What was your key finding in the Nature paper?

    Lee: Previously, scientists and computational models assumed that the dendrites on granule cells randomly connected to different mossy fibers, and this randomness contributed to the complexity and encoding capacity of the information communicated to Purkinje cells. However, using connectomics, we mapped the connections between mossy fibers, granule cells, and Purkinje cells. We found that the dendrites on granule cells don’t connect to mossy fibers in a random way. Instead, they connect to mossy fibers selectively, with more granule cells connecting to the same mossy fibers than expected. This selectivity should decrease the encoding capacity of the information that can be conveyed — but it turns out that for only a very small decrease in capacity, you get more robustness in pattern association. We think this is because there is more redundancy in the connections between granule cells and mossy fibers, and granule cells may be connecting to more-informative mossy fibers.

    This is a finding that leverages connectomics to establish more comprehensive circuit structure by allowing us to look at how large populations of neurons are connected to each other in the same circuit. We need this connectivity information to make detailed and comprehensive models of how information flows through the network. This paper demonstrates how connectomics can be used to provide data to test long-standing theories about information processing and complex neural networks.

    HMNews: What else do you think connectomics can help scientists figure out?

    Lee: Something that I think is going to be really powerful in the near future is what people are calling “comparative connectomics,” or comparing different connectomes. I’m particularly excited about looking at how behavioral differences across individuals correlate with differences in their connectomes. I’m also interested in comparing connectomes for different species to see what principles are conserved in different kinds of brains. In addition to finding conserved principles that can be generalized across species, I want to find differentiating principles that make humans unique. Ultimately, our common humanity may lie in the shared structure of how our brains are wired.

    5
    An image of two granule cells (light and dark blue) connected to three mossy fibers (red, pink, and yellow) in the mouse cerebellum. Researchers discovered that granule cells selectively connect to mossy fibers, with more granule cells connecting to the same mossy fibers than was previously thought. Image: Lee lab.

    HMNews: Why do you think connectomics is such a growing field?

    Lee: Progress has been in part driven by advances in technology, including advances in mechanical engineering that allow us to scale data acquisition, as well as advances in genetic engineering that allow us to label specific cell types. Additionally, the field has been transformed by machine learning, which can be used to analyze these datasets to extract biological insight. The connectomics field is an interesting convergence of neurobiology, engineering, computing power, and artificial intelligence.

    We’ve been developing a lot of different technologies for scaling up data generation and data analysis that I think will be useful in other scientific disciplines. We’re generating some of the biggest image datasets in the world right now, and there are more to come. For example, the NIH has a goal of mapping a whole mouse brain connectome in the next 10 years, which would be about a zettabyte of data, or a trillion gigabytes. Researchers also want to map human and nonhuman primate brains.

    We’ve only scratched the surface of understanding how neurons are connected to one another to form functional networks, but connectomics is arguably transforming neuroscience. I believe we are on the cusp of understanding circuit mechanisms underlying how neurons and networks of neurons compute. We’re on the precipice of understanding the basic building blocks of neural networks, including the rules by which they connect to one another and the rules that underlie the computations they carry out. To me, that is really, really exciting.

    Nature

    See the full article here .

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

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

    Please help promote STEM in your local schools.

    Stem Education Coalition

    harvard-medical-school-campus

    The The Harvard Medical School community is dedicated to excellence and leadership in medicine, education, research and clinical care. To achieve our highest aspirations, and to ensure the success of all members of our community, we value and promote common ideals that center on collaboration and service, diversity, respect, integrity and accountability, lifelong learning, and wellness and balance. To be a citizen of this community means embracing a collegial spirit that fosters inclusion and promotes achievement.

    Harvard University campus

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

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

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

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

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

    Colonial

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

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

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

    19th century

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

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

    20th century

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

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

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

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

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

    21st century

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

     
  • richardmitnick 8:50 am on January 27, 2023 Permalink | Reply
    Tags: "Protein scientists share Frontiers of Knowledge Award", A sophisticated machine-learning technique known as "deep learning", , An anti-coronavirus vaccine created with RoseTTAFold has been clinically tested and distributed in South Korea., , Artificial Intelligence in protein design, Baker co-founded 11 tech firms., Baker directs Rosetta Commons., Baker has authored more than 570 research papers., Baker holds more than 100 patents, , Biology, , , , , Genome Sciences, , , Protein molecules are the workhorses of biology and are involved in almost every cellular activity in all living things., , RoseTTAFold also supports the design of new proteins created to carry out specific functions., RoseTTAFold can accomplish in a just a few seconds what used to take years of laboratory work., RoseTTAFold: A deep learning system that can quickly and accurately decipher the three-dimensional structure of proteins, , , UW Medicine’s David Baker   

    From The School of Medicine At The University of Washington: “Protein scientists share Frontiers of Knowledge Award” 

    From The School of Medicine

    At

    The University of Washington

    1.25.23

    Leila Gray
    UW Medicine
    leilag@uw.edu

    BBVA Foundation honors UW Medicine’s David Baker and British scientists Demis Hassabis and John Jumper for artificial intelligence in protein design.

    UW Medicine biochemist David Baker is among three scientists named to receive The Frontiers of Knowledge Award in Biology and Biomedicine. The BBVA Foundation is honoring Baker and British scientists Demis Hassabis and John Jumper, both at AI company Deep Mind, for leading parallel efforts that are revolutionizing artificial intelligence for protein design.

    Protein molecules are the workhorses of biology and are involved in almost every cellular activity in all living things. The ability to analyze their structure, understand their functions and interactions, and engineer brand new, highly useful proteins not found in nature opens avenues to many medical and other advances.

    Baker, who directs the UW Medicine Institute for Protein Design, oversaw the development of RoseTTAFold.

    1
    Researchers used artificial intelligence to generate hundreds of new protein structures, including this 3D view of human interleukin-12 bound to its receptor. Credit: Ian Haydon.

    2
    Deep learning hallucinating a protein design. Image: Ian Haydon.

    It is a “deep learning” system that can quickly and accurately decipher the three-dimensional structure of proteins. It can accomplish in a just a few seconds what used to take years of laboratory work. This technology also supports the design of new proteins, created to carry out specific functions. This holds promise for the engineering of new therapies against a variety of diseases, including cancer and infectious illness, as well as applications in energy, environmental, nanotech and other fields.

    DeepMind’s CEO Hassabis and chief research scientist Jumper headed the creation of the AlphaFold2 tool, which brought artificial intelligence and deep learning to protein structure prediction and design, and which is powering protein research a variety of medical areas and other bioscientific fields.

    The BBVA Foundation promotes world-class scientific research and cultural creation, and the recognition of talent. It is assisted in evaluating nominees for the Frontiers Award in Biology and Biomedicine by the Spanish National Research Council, the country’s premier public research organization. They were joined by an international jury for this category.

    According to the selection committee, as reported in the BBVA Foundation news announcement on the work being honored by this year’s award, “Both computer methods rely on a sophisticated machine-learning technique known as deep learning to predict the shape of proteins with unprecedented accuracy, similar to that of experimentally determined structures, and with exceptional speed.”

    They added, “This breakthrough is revolutionizing our understanding of how the amino acid sequence of proteins leads to uniquely ordered three-dimensional structures. Scientists are now using these new methods.”

    This is an advance, the announcement noted, with huge potential for the development of new treatments against multiple conditions, from combatting the flu virus or COVID-19, cancer cell growth, or malaria parasites, as a few examples.

    Baker was born in Seattle. He earned his Ph.D. in biochemistry from the University of California-Berkeley. He is currently a Howard Hughes Medical Institute Investigator and the Henrietta and Aubrey Davis Endowed Professor in Biochemistry at the University of Washington School of Medicine, in addition to directing the Institute for Protein Design. He is also an adjunct professor of genome sciences, bioengineering, chemical engineering, computer science and physics at the UW. He has authored more than 570 research papers, holds more than 100 patents, co-founded 11 tech firms, and directs Rosetta Commons, a consortium of labs and researchers working on biomolecular structure predictions and design software. He and his colleagues are also know for their longstanding citizen scientist effort to involve people from a variety of backgrounds and locations in protein design through Rosetta@Home.

    In the BBVA Foundation award announcement, Baker described the revolution in purpose-designed proteins to advance the creation of new drugs and vaccines. He said that the latest RoseTTAFold version even allows for the design of proteins from simple descriptions, similar to the DALL-E system that generates images from text prompts.

    “So, for example, you can tell RoseTTAFold: design a protein which blocks this flu virus protein, or design a protein which will block these cancer cells,” he said in the BBVA Foundation news release. “RoseTTAFold will then make those proteins. We’ve made them in the lab, and we find that they have exactly those functions.”

    An anti-coronavirus vaccine created with RoseTTAFold has been clinically tested and distributed in South Korea. New purpose-designed anti-cancer medicines are being evaluated in human clinical trials. There are plans for a nasal spray that protects against COVID-19 and work underway on an RSV vaccine, a universal flu vaccine, and ideas for a vaccine against a family of viruses related to SARS-CoV-2.

    “We believe that almost all of medicine will be transformed by the protein design revolution,” said Baker. “Most medicines today are made by making small modifications to the proteins which already exist in nature. Now that we can design completely new proteins, we can develop much more improved, more sophisticated medicines that, for example, can treat cancer without the side effects, be made very quickly upon the outbreak of a new pandemic, and in general will be more precise and more robust.”

    RoseTTAFold and AlphaFold2 are freely available to the scientific community. Upgrades have practically equalized the computing times required by each.

    Although these AI tools have not entirely supplanted experimental methods, they are starting to transform both the field of protein design and biological research more generally.

    See the full article here .

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


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

    Please help promote STEM in your local schools.

    Stem Education Coalition

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

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

    The University of Washington is one of the world’s preeminent public universities. Our impact on individuals, on our region, and on the world is profound — whether we are launching young people into a boundless future or confronting the grand challenges of our time through undaunted research and scholarship. Ranked number 10 in the world in Shanghai Jiao Tong University rankings and educating more than 54,000 students annually, our students and faculty work together to turn ideas into impact and in the process transform lives and our world. For more about our impact on the world, every day.

    So what defines us —the students, faculty and community members at the University of Washington? Above all, it’s our belief in possibility and our unshakable optimism. It’s a connection to others, both near and far. It’s a hunger that pushes us to tackle challenges and pursue progress. It’s the conviction that together we can create a world of good. Join us on the journey.

    The University of Washington is a public research university in Seattle, Washington, United States. Founded in 1861, University of Washington is one of the oldest universities on the West Coast; it was established in downtown Seattle approximately a decade after the city’s founding to aid its economic development. Today, the university’s 703-acre main Seattle campus is in the University District above the Montlake Cut, within the urban Puget Sound region of the Pacific Northwest. The university has additional campuses in Tacoma and Bothell. Overall, University of Washington encompasses over 500 buildings and over 20 million gross square footage of space, including one of the largest library systems in the world with more than 26 university libraries, as well as the UW Tower, lecture halls, art centers, museums, laboratories, stadiums, and conference centers. The university offers bachelor’s, master’s, and doctoral degrees through 140 departments in various colleges and schools, sees a total student enrollment of roughly 46,000 annually, and functions on a quarter system.

    University of Washington is a member of the Association of American Universities and is classified among “R1: Doctoral Universities – Very high research activity”. According to the National Science Foundation, UW spent $1.41 billion on research and development in 2018, ranking it 5th in the nation. As the flagship institution of the six public universities in Washington state, it is known for its medical, engineering and scientific research as well as its highly competitive computer science and engineering programs. Additionally, University of Washington continues to benefit from its deep historic ties and major collaborations with numerous technology giants in the region, such as Amazon, Boeing, Nintendo, and particularly Microsoft. Paul G. Allen, Bill Gates and others spent significant time at Washington computer labs for a startup venture before founding Microsoft and other ventures. The University of Washington’s 22 varsity sports teams are also highly competitive, competing as the Huskies in the Pac-12 Conference of the NCAA Division I, representing the United States at the Olympic Games, and other major competitions.

    The university has been affiliated with many notable alumni and faculty, including 21 Nobel Prize laureates and numerous Pulitzer Prize winners, Fulbright Scholars, Rhodes Scholars and Marshall Scholars.

    In 1854, territorial governor Isaac Stevens recommended the establishment of a university in the Washington Territory. Prominent Seattle-area residents, including Methodist preacher Daniel Bagley, saw this as a chance to add to the city’s potential and prestige. Bagley learned of a law that allowed United States territories to sell land to raise money in support of public schools. At the time, Arthur A. Denny, one of the founders of Seattle and a member of the territorial legislature, aimed to increase the city’s importance by moving the territory’s capital from Olympia to Seattle. However, Bagley eventually convinced Denny that the establishment of a university would assist more in the development of Seattle’s economy. Two universities were initially chartered, but later the decision was repealed in favor of a single university in Lewis County provided that locally donated land was available. When no site emerged, Denny successfully petitioned the legislature to reconsider Seattle as a location in 1858.

    In 1861, scouting began for an appropriate 10 acres (4 ha) site in Seattle to serve as a new university campus. Arthur and Mary Denny donated eight acres, while fellow pioneers Edward Lander, and Charlie and Mary Terry, donated two acres on Denny’s Knoll in downtown Seattle. More specifically, this tract was bounded by 4th Avenue to the west, 6th Avenue to the east, Union Street to the north, and Seneca Streets to the south.

    John Pike, for whom Pike Street is named, was the university’s architect and builder. It was opened on November 4, 1861, as the Territorial University of Washington. The legislature passed articles incorporating the University, and establishing its Board of Regents in 1862. The school initially struggled, closing three times: in 1863 for low enrollment, and again in 1867 and 1876 due to funds shortage. University of Washington awarded its first graduate Clara Antoinette McCarty Wilt in 1876, with a bachelor’s degree in science.

    19th century relocation

    By the time Washington state entered the Union in 1889, both Seattle and the University had grown substantially. University of Washington’s total undergraduate enrollment increased from 30 to nearly 300 students, and the campus’s relative isolation in downtown Seattle faced encroaching development. A special legislative committee, headed by University of Washington graduate Edmond Meany, was created to find a new campus to better serve the growing student population and faculty. The committee eventually selected a site on the northeast of downtown Seattle called Union Bay, which was the land of the Duwamish, and the legislature appropriated funds for its purchase and construction. In 1895, the University relocated to the new campus by moving into the newly built Denny Hall. The University Regents tried and failed to sell the old campus, eventually settling with leasing the area. This would later become one of the University’s most valuable pieces of real estate in modern-day Seattle, generating millions in annual revenue with what is now called the Metropolitan Tract. The original Territorial University building was torn down in 1908, and its former site now houses the Fairmont Olympic Hotel.

    The sole-surviving remnants of Washington’s first building are four 24-foot (7.3 m), white, hand-fluted cedar, Ionic columns. They were salvaged by Edmond S. Meany, one of the University’s first graduates and former head of its history department. Meany and his colleague, Dean Herbert T. Condon, dubbed the columns as “Loyalty,” “Industry,” “Faith”, and “Efficiency”, or “LIFE.” The columns now stand in the Sylvan Grove Theater.

    20th century expansion

    Organizers of the 1909 Alaska-Yukon-Pacific Exposition eyed the still largely undeveloped campus as a prime setting for their world’s fair. They came to an agreement with Washington’s Board of Regents that allowed them to use the campus grounds for the exposition, surrounding today’s Drumheller Fountain facing towards Mount Rainier. In exchange, organizers agreed Washington would take over the campus and its development after the fair’s conclusion. This arrangement led to a detailed site plan and several new buildings, prepared in part by John Charles Olmsted. The plan was later incorporated into the overall University of Washington campus master plan, permanently affecting the campus layout.

    Both World Wars brought the military to campus, with certain facilities temporarily lent to the federal government. In spite of this, subsequent post-war periods were times of dramatic growth for the University. The period between the wars saw a significant expansion of the upper campus. Construction of the Liberal Arts Quadrangle, known to students as “The Quad,” began in 1916 and continued to 1939. The University’s architectural centerpiece, Suzzallo Library, was built in 1926 and expanded in 1935.

    After World War II, further growth came with the G.I. Bill. Among the most important developments of this period was the opening of the School of Medicine in 1946, which is now consistently ranked as the top medical school in the United States. It would eventually lead to the University of Washington Medical Center, ranked by U.S. News and World Report as one of the top ten hospitals in the nation.

    In 1942, all persons of Japanese ancestry in the Seattle area were forced into inland internment camps as part of Executive Order 9066 following the attack on Pearl Harbor. During this difficult time, university president Lee Paul Sieg took an active and sympathetic leadership role in advocating for and facilitating the transfer of Japanese American students to universities and colleges away from the Pacific Coast to help them avoid the mass incarceration. Nevertheless, many Japanese American students and “soon-to-be” graduates were unable to transfer successfully in the short time window or receive diplomas before being incarcerated. It was only many years later that they would be recognized for their accomplishments during the University of Washington’s Long Journey Home ceremonial event that was held in May 2008.

    From 1958 to 1973, the University of Washington saw a tremendous growth in student enrollment, its faculties and operating budget, and also its prestige under the leadership of Charles Odegaard. University of Washington student enrollment had more than doubled to 34,000 as the baby boom generation came of age. However, this era was also marked by high levels of student activism, as was the case at many American universities. Much of the unrest focused around civil rights and opposition to the Vietnam War. In response to anti-Vietnam War protests by the late 1960s, the University Safety and Security Division became the University of Washington Police Department.

    Odegaard instituted a vision of building a “community of scholars”, convincing the Washington State legislatures to increase investment in the University. Washington senators, such as Henry M. Jackson and Warren G. Magnuson, also used their political clout to gather research funds for the University of Washington. The results included an increase in the operating budget from $37 million in 1958 to over $400 million in 1973, solidifying University of Washington as a top recipient of federal research funds in the United States. The establishment of technology giants such as Microsoft, Boeing and Amazon in the local area also proved to be highly influential in the University of Washington’s fortunes, not only improving graduate prospects but also helping to attract millions of dollars in university and research funding through its distinguished faculty and extensive alumni network.

    21st century

    In 1990, the University of Washington opened its additional campuses in Bothell and Tacoma. Although originally intended for students who have already completed two years of higher education, both schools have since become four-year universities with the authority to grant degrees. The first freshman classes at these campuses started in fall 2006. Today both Bothell and Tacoma also offer a selection of master’s degree programs.

    In 2012, the University began exploring plans and governmental approval to expand the main Seattle campus, including significant increases in student housing, teaching facilities for the growing student body and faculty, as well as expanded public transit options. The University of Washington light rail station was completed in March 2015, connecting Seattle’s Capitol Hill neighborhood to the University of Washington Husky Stadium within five minutes of rail travel time. It offers a previously unavailable option of transportation into and out of the campus, designed specifically to reduce dependence on private vehicles, bicycles and local King County buses.

    University of Washington has been listed as a “Public Ivy” in Greene’s Guides since 2001, and is an elected member of the American Association of Universities. Among the faculty by 2012, there have been 151 members of American Association for the Advancement of Science, 68 members of the National Academy of Sciences, 67 members of the American Academy of Arts and Sciences, 53 members of the National Academy of Medicine, 29 winners of the Presidential Early Career Award for Scientists and Engineers, 21 members of the National Academy of Engineering, 15 Howard Hughes Medical Institute Investigators, 15 MacArthur Fellows, 9 winners of the Gairdner Foundation International Award, 5 winners of the National Medal of Science, 7 Nobel Prize laureates, 5 winners of Albert Lasker Award for Clinical Medical Research, 4 members of the American Philosophical Society, 2 winners of the National Book Award, 2 winners of the National Medal of Arts, 2 Pulitzer Prize winners, 1 winner of the Fields Medal, and 1 member of the National Academy of Public Administration. Among UW students by 2012, there were 136 Fulbright Scholars, 35 Rhodes Scholars, 7 Marshall Scholars and 4 Gates Cambridge Scholars. UW is recognized as a top producer of Fulbright Scholars, ranking 2nd in the US in 2017.

    The Academic Ranking of World Universities has consistently ranked University of Washington as one of the top 20 universities worldwide every year since its first release. In 2019, University of Washington ranked 14th worldwide out of 500 by the ARWU, 26th worldwide out of 981 in the Times Higher Education World University Rankings, and 28th worldwide out of 101 in the Times World Reputation Rankings. Meanwhile, QS World University Rankings ranked it 68th worldwide, out of over 900.

    U.S. News & World Report ranked University of Washington 8th out of nearly 1,500 universities worldwide for 2021, with University of Washington’s undergraduate program tied for 58th among 389 national universities in the U.S. and tied for 19th among 209 public universities.

    In 2019, it ranked 10th among the universities around the world by SCImago Institutions Rankings. In 2017, the Leiden Ranking, which focuses on science and the impact of scientific publications among the world’s 500 major universities, ranked University of Washington 12th globally and 5th in the U.S.

    In 2019, Kiplinger Magazine’s review of “top college values” named University of Washington 5th for in-state students and 10th for out-of-state students among U.S. public colleges, and 84th overall out of 500 schools. In the Washington Monthly National University Rankings University of Washington was ranked 15th domestically in 2018, based on its contribution to the public good as measured by social mobility, research, and promoting public service.

     
  • richardmitnick 12:34 pm on January 21, 2023 Permalink | Reply
    Tags: "Desperately Seeking Salamanders", , Biology, , , , , Two undergraduates search for salamanders in western North Carolina — and find so much more.   

    From “Endeavors” At The University of North Carolina-Chapel Hill: “Desperately Seeking Salamanders” 

    From “Endeavors”

    At

    The University of North Carolina-Chapel Hill

    1.18.23
    Andrew Russell

    Two undergraduates search for salamanders in western North Carolina — and find so much more.


    Desperately Seeking Salamanders.

    About an hour after the sun sets over the ridgeline of the Blue Ridge Mountains, Kristina Hefferle and Leah Morrissey hike to a nearby creek in total darkness under a tangle of rhododendron, dog hobble, and towering pine trees. The elusive needle they’re seeking in this botanical haystack is the male Blue Ridge two-lined salamander — a bright orange 6- to 10-centimeter-long amphibian about the thickness of a pencil, known to hang out around the streams and lakes of the southern Appalachian Mountains.

    1
    Photo by Todd Pierson.

    2
    The shaded region represents the range of the Blue Ridge Two-Lined Salamander in North Carolina.

    Stumbling through mountainous terrain in the dark for hours on end, turning over rocks and leaves in muddy creek beds, and looking for an animal the size and color of a baby carrot makes having a reliable research partner crucial.

    “There’s honestly nothing better than having a partner that can do everything that you can’t, and vice versa, especially if you have to go out in the middle of the woods in the dark,” Hefferle, a UNC-Chapel Hill junior, says. “I cannot, for the life of me, spot a salamander — but Leah can. And she might miss it when she tries to catch it, but I’m there to back her up if she needs it.”

    UNC Institute for the Environment offers a program for undergraduates at the Highlands Biological Station that allows them to live and work on projects centered around the diverse wildlife of the Appalachian Mountains.

    It’s the kind of teamwork that develops after a semester of close collaboration at the UNC Institute for the Environment’s Highlands Field Site — a program for a small cohort of UNC-Chapel Hill undergraduates to live and conduct research at the Highlands Biological Station in western North Carolina. Each student takes on a research project and learns to tackle field and lab work, analyze data, use statistical research software, conduct a literature search, and create a research report.

    3
    UNC Institute for the Environment offers a program for undergraduates at the Highlands Biological Station that allows them to live and work on projects centered around the diverse wildlife of the Appalachian Mountains.

    At first, Hefferle felt anxious about the program’s semester-long commitment.

    “I think when I first signed up for this program, I was really nervous about leaving Chapel Hill,” she says. “I was afraid that all my friends would be there, and I would just be out here in the wilderness. But it was effortless to adjust. We have a lot of fun here outside of our classwork, but even in class, it’s tough not to become friends with the 15 people you live, work, and eat with.”

    Morrissey, a UNC-Chapel Hill sophomore, shares Hefferle’s sentiments.

    4
    Leah Morrissey looks for the elusive male Blue Ridge two-lined salamander under a footbridge in the botanical garden of the Highlands Biological Station.

    “I barely had any college experience, let alone fieldwork experience,” she admits. “I did a creek week in eighth grade. We splashed around in the creek, not like anything really scientific.”

    During the application process, Morrissey voiced her misgivings to Rada Petric, director of the Highlands Field Site.

    “She said, ‘It’s okay, we’ll meet you where you are.’ And I think it’s definitely lived up to that,” Morrissey says.

    On Morrissey and Hefferle’s first night in the field, they got lost in the botanical garden, emerging from the forest at a neighboring nature center. They were joined by Yatin Kalki, a master’s student also working on the project. He pointed out salamanders, helping the two undergrads get accustomed to looking for them.

    “At some point, he just said, ‘Okay, now you guys point them out,’” Morrissey recounts. “And it was a good several minutes of us just walking in silence because we couldn’t find any. So that first night was stressful, but we eventually got a lot better.”

    Better together

    Aside from the initial steep learning curve of the first night, both have grown to love fieldwork — and they’ve gotten good at it. This semester, they gathered data on 105 salamanders, three times the number of last year’s survey. Both credit their success to their partnership.

    “I don’t know if it was just pure luck or because we have similar interests, but I think it really came together well,” Hefferle acknowledges. “Having someone who could really fulfill all the skills that you need, and you fulfill theirs, it’s really just so harmonious. I’m surprised that it worked out so well.”

    5
    The male Blue Ridge two-lined salamander makes its home in and around the streams and lakes of the southern Appalachian Mountains.

    Three days a week, Morrissey and Hefferle would head into the botanical gardens, focusing their search on the undergrowth near creek beds. When they’d eventually spot a male two-lined salamander, they’d guide it into a wet plastic bag. Salamanders breathe through their skin, and the moisture in a bag ensures their safety, as Morrissey and Hefferle gathered data.

    “It’s been really cool seeing our progress from not even being able to see a single salamander to going into the creek and finding them in challenging places — and wrangling them and wrestling around in the water but still getting them,” Morrissey says.

    First, they’d measure the length and photograph the spots on their backs. Later, they’d upload these into a database that uses AI to compare photos of the spots, allowing other researchers to identify and track individuals over time. They’d also take a small sample of the specimen’s tail for a polymerase chain reaction (PCR) test to establish a genetic snapshot of the animal. Finally, they’d determine the reproductive tactic used.

    Male Blue Ridge two-lined salamanders pursue reproduction in two ways: Searching males are more terrestrial and spend rainy nights on the forest floor among vegetation while guarding males are more physically dominant and mainly found in the streams. Searching males are typically leaner. They have fleshy protrusions from their nostrils called cirri and maxillary teeth and glands that aid in the release of pheromones. Guarding males don’t have any of that, but they do have a prominent jaw they use to fight off other salamanders when searching for a nesting spot.

    The project compares the genetic makeup of males, their reproductive behavior, and how they may change over a lifetime.

    6
    Kristina Hefferle looks for the male Blue Ridge two-lined salamander in the botanical garden of the Highlands Biological Station.

    “The genetic component of this project and getting an opportunity to do PCR has been so alluring to me. It’s been so exciting to do,” Hefferle says. “When I first started taking biology in middle school, that thing that really drew me in was the genetic component.”

    Morrissey, on the other hand, responded to the fieldwork. Growing up in Asheville, she would play outdoors in the forest near her house as a child, even spotting salamanders regularly in a nearby creek. But over the years, she spent less and less time in nature. Then, during the first week at the Highlands Field Site, her cohort took a hiking trip to the Great Smoky Mountains — and she realized what she’d been missing.

    “And then later, getting out on the trail, looking for salamanders, just really sparked that childlike curiosity about nature,” Morrissey says. “This program has convinced me to switch my major to science in the hopes of more fieldwork either during school or in a future career.”

    See the full article here .

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

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

    Please help promote STEM in your local schools.

    Stem Education Coalition

    UNC campus
    The University of North Carolina at Chapel Hill is a public research university in Chapel Hill, North Carolina. The flagship of the University of North Carolina system, it is considered to be a Public Ivy, or a public institution which offers an academic experience similar to that of an Ivy League university. After being chartered in 1789, the university first began enrolling students in 1795, making it one of the oldest public universities in the United States. Among the claimants, the University of North Carolina at Chapel Hill is the only one to have held classes and graduated students as a public university in the eighteenth century.

    The first public institution of higher education in North Carolina, the school opened its doors to students on February 12, 1795. North Carolina became coeducational under the leadership of President Kemp Plummer Battle in 1877 and began the process of desegregation under Chancellor Robert Burton House when African-American graduate students were admitted in 1951. In 1952, North Carolina opened its own hospital, UNC Health Care, for research and treatment, and has since specialized in cancer care through UNC’s Lineberger Comprehensive Cancer Center which is one of only 51 national NCI designated comprehensive centers.

    The university offers degrees in over 70 courses of study and is administratively divided into 13 separate professional schools and a primary unit, the College of Arts & Sciences. Five of the schools have been named: the UNC Kenan–Flagler Business School, the UNC Hussman School of Journalism and Media, the UNC Gillings School of Global Public Health, the UNC Eshelman School of Pharmacy, and the UNC Adams School of Dentistry. All undergraduates receive a liberal arts education and have the option to pursue a major within the professional schools of the university or within the College of Arts and Sciences from the time they obtain junior status. It is classified among “R1: Doctoral Universities – Very high research activity”, and is a member of the Association of American Universities . According to the National Science Foundation, UNC spent $1.14 billion on research and development in 2018, ranking it 12th in the nation.

    UNC’s faculty and alumni include 9 Nobel Prize laureates, 23 Pulitzer Prize winners, and 51 Rhodes Scholars. Additional notable alumni include a U.S. President, a U.S. Vice President, 38 Governors of U.S. States, 98 members of the United States Congress, and nine Cabinet members as well as CEOs of Fortune 500 companies, Olympians and professional athletes.

    The campus covers 729 acres (3 km^2) of Chapel Hill’s downtown area, encompassing the Morehead Planetarium and the many stores and shops located on Franklin Street. Students can participate in over 550 officially recognized student organizations. The student-run newspaper The Daily Tar Heel has won national awards for collegiate media, while the student radio station WXYC provided the world’s first internet radio broadcast. UNC Chapel Hill is one of the charter members of the Atlantic Coast Conference, which was founded on June 14, 1953. Competing athletically as the Tar Heels, UNC has achieved great success in sports, most notably in men’s basketball, women’s soccer, and women’s field hockey.

     
  • richardmitnick 2:58 pm on January 20, 2023 Permalink | Reply
    Tags: , "Connectomics": aims to comprehensively map connections between neurons in the brain., , Biology, , Combining "connectomics" with information on neural activity to explore neural circuits that underlie behavior., , Neurons don’t exist in isolation. In the human brain some 86 billion neurons form 100 trillion connections to each other — numbers that ironically are far too large for the human brain to fathom., ,   

    From The Medical School At Harvard University: “A New Field of Neuroscience Aims to Map Connections in the Brain” 

    harvard-medical-school-bloc

    From The Medical School

    At

    Harvard University

    News & Research

    1.19.23
    CATHERINE CARUSO

    Scientists working in “connectomics” are creating comprehensive maps of how neurons connect to one another.

    1
    An image of two granule cells (light and dark blue) connected to three mossy fibers (red, pink, and yellow) in the mouse cerebellum. Researchers discovered that granule cells selectively connect to mossy fibers, with more granule cells connecting to the same mossy fibers than was previously thought. Image: Lee lab.

    Wei-Chung Allen Lee is working in a new field of neuroscience called connectomics that aims to comprehensively map connections between neurons. Video: Catherine Caruso, Stephanie Dutchen, and Tyler Sloan. Credit: HMS.

    Many of us have seen microscopic images of neurons in the brain — each neuron appearing as a glowing cell in a vast sea of blackness. This image is misleading: Neurons don’t exist in isolation. In the human brain some 86 billion neurons form 100 trillion connections to each other — numbers that ironically are far too large for the human brain to fathom.

    Wei-Chung Allen Lee, Harvard Medical School associate professor of neurology at Boston Children’s Hospital, is working in a new field of neuroscience called “connectomics”, which aims to comprehensively map connections between neurons in the brain.

    “The brain is structured so that each neuron is connected to thousands of other neurons, and so to understand what a single neuron is doing, ideally you study it within the context of the rest of the neural network,” Lee explained.

    Lee recently spoke to Harvard Medicine News about the promise of connectomics. He also described his own research, which combines connectomics with information on neural activity to explore neural circuits that underlie behavior.

    Harvard Medicine News: To start with a basic question, what is connectomics?

    Lee: We define connectomics as understanding how individual neurons are connected to one another to form functional networks. The goal is to create connectomes, or detailed structural maps of connectivity where we can see every neuron and every connection. What’s unique is the comprehensiveness of connectivity: In a perfect connectome, we’d know how every neuron was connected to every other neuron.

    We believe that the connectivity of neurons is fundamental to how they function, since they must receive information from each other in order to use this information. Having comprehensive data about connectivity allows us to look at higher-order interactions between populations of neurons that are important for brain function and behavior. It is challenging to study higher-order interactions without connectomics.

    Some have argued that you are your connectome. When you fall asleep at night, your brain activity dramatically changes, interrupting your thoughts and feelings — but when you wake up, you resume your thoughts and feelings without any break in your sense of self. This is likely because your brain connectivity has remained largely intact through the night. In essence, the structure of how our neurons are wired is our “self,” and connectomics is the key to understanding this structure.

    HMNews: What are you studying within the context of connectomics?

    Lee: My lab is interested in understanding how computations arise in the brain, or the general principles by which neural circuits organize themselves into functional networks. To do this, we aim to comprehensively map how individual neurons are connected to one another in complex networks. At the same time, we want to understand how those neurons are active within the functioning circuit. We do this in the context of behavior, ranging from making decisions to executing actions.

    We are trying to couple connectomics with recordings of neural activity to do what we call functional connectomics. Essentially, we take the map of where every neuron is and how it is connected to every other neuron, and we layer on information about the activity of those neurons in a living animal. We also use genetic engineering approaches to label specific cell types, which is additional information that we can layer on top of connectivity.

    HMNews: What tools do scientists use to map connectomes?

    Lee: We are developing and applying high-throughput microscopy, computational approaches, and machine learning to generate connectomes and translate these detailed maps of neural connectivity into biological and computational insights. One key component of our approach is serial transmission electron microscopy, or EM, which has unsurpassed spatial resolution, signal-to-noise ratio, and speed relative to other serial EM methods. This technique allows us to identify excitatory and inhibitory neurons, as well as the synapses, or small gaps where neurons connect to each other. We can also examine connectivity patterns of neurons, and study the organization of synaptic connections.

    Historically, high-resolution EM has been slow and tedious, but we’ve engineered a high-speed EM platform that allows us to capture the whole nervous system of an adult fruit fly in a few months, generating 5 to 10 terabytes of data a day. We have also developed computational infrastructure and tools that enable us to handle and visualize the large amounts of data that we are generating. For example, we use artificial deep neural networks to extract information about cells and their connectivity from these massive datasets.

    HMNews: What models do you use in your research?

    Lee: We have mainly worked with mice and fruit flies, which are powerful and well-studied model systems. The field has sophisticated genetic tools that allow us to label different populations of neurons across the central nervous systems of these species. In fruit flies, we can use the technologies we’ve been developing for connectomics to capture the entire brain and nervous system at synapse resolution. In the mouse, we can target relevant neural circuits or subcircuits. We are using these models to study the basic principles of how neural circuits are built and operate — basically how neural networks are connected to each other to perform different computations that underlie behavior.

    We also work in nontraditional model systems such as the mosquito. Mosquito brains are about the same size as fruit fly brains, but the genetics is more challenging. Scientists have used genetics to access the first-order neurons that start carrying information into the mosquito brain, but the rest of the brain is a black box in many respects. We don’t know much about its fundamental neurobiology, including how the mosquito brain integrates different sensory modalities to drive behavior.

    For example, adult female mosquitoes that are trying to reproduce integrate information on human odors, heat, and carbon dioxide. We know that these different sensory cues enter the brain, but we don’t know how they are integrated and converge onto neural circuits that drive mosquitoes’ host-seeking behavior.

    We hope that mapping the whole mosquito brain will provide a new foundation for understanding how sensory integration and action selection works for innate behavior. Additionally, the specific mosquito species we study is a vector for diseases such as malaria, West Nile, Zika, yellow fever, and dengue fever, so there’s a clinical and public health aspect of this that makes it a really important model system.

    HMNews: You recently published a paper in Nature [below] on brain connectivity and pattern association in mice. What was the premise of the study?

    Lee: This was a collaboration with Wade Regehr, professor of neurobiology at HMS. The paper focuses on information processing in the cerebellum, which is a brain region that, among other things, is important for smooth, coordinated movement. One of the things the cerebellum is thought to do is make fine-scale error corrections in movement by comparing patterns from intended and executed actions. For example, if you try to touch your nose and you miss, there is information coming from your motor system that tells your cerebellum what the intended action was, and there is sensory information coming from your finger about what actually happened, including the location of your finger in space. The cerebellum is thought to compute the difference between the intended action and the actual action, and to help correct the error.

    We studied the cerebellar cortex, which is packed full of small neurons called granule cells that make up more than half the neurons in the brain. These granule cells each have, on average, four dendrites, or branching structures that receive information from other neurons. In this case, the dendrites connect to neurons called mossy fibers that bring information into the cerebellum. The granule cells then process this information and communicate it to other neurons called Purkinje cells, with each Purkinje cell integrating information from 100,000 to 200,000 granule cells, and sending this information to other brain regions. These three cell types make up the “feedforward” circuit we wanted to better understand.

    HMNews: What was your key finding in the Nature paper?

    Lee: Previously, scientists and computational models assumed that the dendrites on granule cells randomly connected to different mossy fibers, and this randomness contributed to the complexity and encoding capacity of the information communicated to Purkinje cells. However, using connectomics, we mapped the connections between mossy fibers, granule cells, and Purkinje cells. We found that the dendrites on granule cells don’t connect to mossy fibers in a random way. Instead, they connect to mossy fibers selectively, with more granule cells connecting to the same mossy fibers than expected. This selectivity should decrease the encoding capacity of the information that can be conveyed — but it turns out that for only a very small decrease in capacity, you get more robustness in pattern association. We think this is because there is more redundancy in the connections between granule cells and mossy fibers, and granule cells may be connecting to more-informative mossy fibers.

    This is a finding that leverages connectomics to establish more comprehensive circuit structure by allowing us to look at how large populations of neurons are connected to each other in the same circuit. We need this connectivity information to make detailed and comprehensive models of how information flows through the network. This paper demonstrates how connectomics can be used to provide data to test long-standing theories about information processing and complex neural networks.

    HMNews: What else do you think connectomics can help scientists figure out?

    Lee: Something that I think is going to be really powerful in the near future is what people are calling “comparative connectomics,” or comparing different connectomes. I’m particularly excited about looking at how behavioral differences across individuals correlate with differences in their connectomes. I’m also interested in comparing connectomes for different species to see what principles are conserved in different kinds of brains. In addition to finding conserved principles that can be generalized across species, I want to find differentiating principles that make humans unique. Ultimately, our common humanity may lie in the shared structure of how our brains are wired.

    HMNews: Why do you think connectomics is such a growing field?

    Lee: Progress has been in part driven by advances in technology, including advances in mechanical engineering that allow us to scale data acquisition, as well as advances in genetic engineering that allow us to label specific cell types. Additionally, the field has been transformed by machine learning, which can be used to analyze these datasets to extract biological insight. The connectomics field is an interesting convergence of neurobiology, engineering, computing power, and artificial intelligence.

    We’ve been developing a lot of different technologies for scaling up data generation and data analysis that I think will be useful in other scientific disciplines. We’re generating some of the biggest image datasets in the world right now, and there are more to come. For example, the NIH has a goal of mapping a whole mouse brain connectome in the next 10 years, which would be about a zettabyte of data, or a trillion gigabytes. Researchers also want to map human and nonhuman primate brains.

    We’ve only scratched the surface of understanding how neurons are connected to one another to form functional networks, but connectomics is arguably transforming neuroscience. I believe we are on the cusp of understanding circuit mechanisms underlying how neurons and networks of neurons compute. We’re on the precipice of understanding the basic building blocks of neural networks, including the rules by which they connect to one another and the rules that underlie the computations they carry out. To me, that is really, really exciting.

    Additional authors on the paper include Tri Nguyen, Jeffrey Rhoades, Xintong (Cindy) Yuan, Logan Thomas, Ilaria Ricchi, and David Hildebrand of HMS; and Jan Funke and Arlo Sheridan of the Howard Hughes Medical Institute.

    Nature

    See the full article here .

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

    Please help promote STEM in your local schools.

    Stem Education Coalition

    harvard-medical-school-campus

    The The Harvard Medical School community is dedicated to excellence and leadership in medicine, education, research and clinical care. To achieve our highest aspirations, and to ensure the success of all members of our community, we value and promote common ideals that center on collaboration and service, diversity, respect, integrity and accountability, lifelong learning, and wellness and balance. To be a citizen of this community means embracing a collegial spirit that fosters inclusion and promotes achievement.

    Harvard University campus

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

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

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

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

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

    Colonial

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

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

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

    19th century

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

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

    20th century

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

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

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

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

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

    21st century

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

     
  • richardmitnick 4:40 pm on January 19, 2023 Permalink | Reply
    Tags: "Special drone collects environmental DNA from trees", , Biology, , , , , WSL [Eidgenössische Forschungsanstalt für Wald - Schnee und Landschaft][Institut fédéral de recherches sur la forêt - la neige et le paysage] (CH)   

    From The Swiss Federal Institute of Technology in Zürich [ETH Zürich] [Eidgenössische Technische Hochschule Zürich] (CH): “Special drone collects environmental DNA from trees” 

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

    1.19.23
    Peter Rüegg

    1
    Photograph: Gottardo Pestalozzi / WSL.

    Researchers at ETH Zürich and WSL Swiss Federal Institute for Forest Snow and Landscape Research [Eidgenössische Forschungsanstalt für Wald – Schnee und Landschaft][Institut fédéral de recherches sur la forêt – la neige et le paysage] (CH) have developed a flying device that can land on tree branches to take samples. This opens up a new dimension for scientists previously reserved for biodiversity researchers.

    Ecologists are increasingly using traces of genetic material left behind by living organisms left behind in the environment, called environmental DNA (eDNA), to catalogue and monitor biodiversity. Based on these DNA traces, researchers can determine which species are present in a certain area.

    Obtaining samples from water or soil is easy, but other habitats – such as the forest canopy – are difficult for researchers to access. As a result, many species remain untracked in poorly explored areas.

    Researchers at ETH Zürich and the Swiss Federal Institute for Forest, Snow and Landscape Research Wald – Schnee und Landschaft, and the company SPYGEN have partnered to develop a special drone that can autonomously collect samples on tree branches.


    Special drone collects environmental DNA from trees. (Video: ETH Zürich)

    How the drone collects material

    The drone is equipped with adhesive strips. When the aircraft lands on a branch, material from the branch sticks to these strips. Researchers can then extract DNA in the lab, analyze it and assign it to genetic matches of the various organisms using database comparisons.

    But not all branches are the same: they vary in terms of their thickness and elasticity. Branches also bend and rebound when a drone lands on them. Programming the aircraft in such a way that it can still approach a branch autonomously and remain stable on it long enough to take samples was a major challenge for the roboticists.

    “Landing on branches requires complex control,” explains Stefano Mintchev, Professor of Environmental Robotics at ETH Zürich and WSL. Initially, the drone does not know how flexible a branch is, so the researchers fitted it with a force sensing cage. This allows the drone to measure this factor at the scene and incorporate it into its flight manoeuvre.

    3
    Scheme: DNA is extracted from the collected branch material, amplified, sequenced and the sequences found are compared with databases. This allows the species to be identified. (Graphic: Stefano Mintchev / ETH Zürich)

    Preparing rainforest operations at Zoo Zürich

    Researchers have tested their new device on seven tree species. In the samples, they found DNA from 21 distinct groups of organisms, or taxa, including birds, mammals and insects. “This is encouraging, because it shows that the collection technique works,“ says Mintchev, who co-​authored the study that has just appeared in the journal Science Robotics [below].

    The researchers now want to improve their drone further to get it ready for a competition in which the aim is to detect as many different species as possible across 100 hectares of rainforest in Singapore in 24 hours.

    To test the drone’s efficiency under conditions similar to those it will experience at the competition, Mintchev and his team are currently working at the Zoo Zurich’s Masoala Rainforest. „Here we have the advantage of knowing which species are present, which will help us to better assess how thorough we are in capturing all eDNA traces with this technique or if we’re missing something,“ Mintchev says.

    For this event, however, the collection device must become more efficient and mobilize faster. In the tests in Switzerland, the drone collected material from seven trees in three days; in Singapore, it must be able to fly to and collect samples from ten times as many trees in just one day.

    Collecting samples in a natural rainforest, however, presents the researchers with even tougher challenges. Frequent rain washes eDNA off surfaces, while wind and clouds impede drone operation. „We are therefore very curious to see whether our sampling method will also prove itself under extreme conditions in the tropics,” Mintchev says.

    Science Robotics
    See the science paper for instructive material with images and video.

    See the full article here .

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

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

    Please help promote STEM in your local schools.

    Stem Education Coalition

    ETH Zurich campus

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

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

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

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

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

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

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

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

    Reputation and ranking

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

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

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

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

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

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

     
  • richardmitnick 4:34 pm on January 18, 2023 Permalink | Reply
    Tags: "The Oracle of Leaves", A large gene pool gives plants more leeway to react to negative environmental factors such as pests or droughts., , , Biology, , , , Computer models help them pinpoint concordance between spectral and field data and provide input on how to read the spectral information that they have obtained., , , Leaves reflect infrared rays at the edge of the visible light spectrum., Monitoring plant life using satellites airplanes and drones, Pigments like green chlorophyll absorb specific wavelengths of the spectrum of light waves., Scientists are in the process of finding out which aspects of plant biodiversity can be measured with remote sensing., Scientists developed a spectral diversity index that shows diversity both within and between plant communities (alpha and beta diversity respectively)., , , The characteristics of plants, The combination of laser scanning and spectroscopy is considered highly promising as these data allow researchers to calculate the biomass and the amount of stored carbon., The folded leaf of an oak tree-faded yellow-dotted with dark spots., The spectrum is like a fingerprint unique to each plant., , Using a spectrometer scientists measure the light reflected by leaves which gives them insight into the chemical and structural properties of plants.   

    From The University of Zürich (Universität Zürich) (CH): “The Oracle of Leaves” 

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

    1.18.23
    Text by Stéphanie Hegelbach
    English translation by Gena Olson

    1
    Biodiversity from above: View of the forest “Lägern” mountain range near the city of Zurich. (Picture used with permission)

    Two UZH researchers are harnessing the light reflections from leaves to learn more about biodiversity and the characteristics of plants. Analyzing spectral data is revolutionizing not only the way in which we research ecosystems but also allows us to protect them more effectively.

    The folded leaf of an oak tree, faded yellow, dotted with dark spots. We pick up on the information contained in leaves almost subconsciously when strolling through the forest. But the researchers at UZH’s Remote Sensing Laboratories are taking this ability to the next level.

    Using a spectrometer, they measure the light reflected by leaves, which gives them insight into the chemical and structural properties of plants – even from outer space. “The spectrum is like a fingerprint unique to each plant,” explains Meredith Schuman, professor of spatial genetics in the Department of Geography.

    Monitoring plant life using satellites, airplanes and drones is known as remote sensing, and it could become an important tool to counteract the biodiversity crisis. Remote sensing makes it possible to monitor the health and species composition of ecosystems, almost in real time. This could help governments identify areas that require protection at an early stage and provide direct feedback on conservation measures.

    Calibration using field measurements

    “We’re in the process of finding out which aspects of plant biodiversity can be measured with remote sensing,” explains Anna Schweiger, a researcher at the UZH Remote Sensing Lab. Schweiger and Schuman need reference data from the field to ensure that they are interpreting the spectral data correctly. Computer models help them pinpoint concordance between spectral and field data and provide input on how to read the spectral information that they have obtained. “Pigments like green chlorophyll are the easiest to identify, since they absorb specific wavelengths,” explains Schuman.

    Spectrometry isn’t just confined to visible light, however: it also includes additional parts of the electromagnetic spectrum such as infrared light. Leaves reflect infrared rays at the edge of the visible light spectrum, the near-infrared spectrum, particularly strongly. “We call this transitional area the ‘red edge’,” says Schuman. “This reflection pattern provides insight into chlorophyll content and the waxy layer on the surface of the leaves.”

    Her group is working on using spectral data to obtain information about the genetic profiles of plants, which would allow researchers to study genetic differences within species and to draw conclusions about genetic diversity. A long-term study of beech trees in the Lägern mountain range led by doctoral student Ewa Czyz showed that spectral data points involving water content, phenols, pigments and wax composition are suitable indicators for obtaining information about the genetic structure of flora.

    One of the team’s goals is to improve their understanding of these relationships. Genetic variation within a species is particularly important for biodiversity, since a large gene pool gives plants more leeway to react to negative environmental factors such as pests or droughts. “If we lose genetic diversity and species diversity, ecosystems lose their ability to absorb external shocks,” explains Schweiger.

    Researchers in Schuman’s unit – chiefly the 4D Forests group led by Felix Morsdorf – combine spectroscopy with laser scanning, which involves measuring a laser beam reflected back by the soil or plants and recording the topography and height of the vegetation. “The 3D models that we calculate from this provide insight into the macrostructure – the structure of the plants visible to the eye – as well as how this influences spectral data,” says Schuman. The combination of laser scanning and spectroscopy is considered highly promising, as these data allows researchers to calculate the biomass and the amount of stored carbon, for example.

    Diverse plant communities

    The two researchers aren’t just looking for direct connections between spectra and plant characteristics; they are also comparing the spectra with one another. “Plants with similar characteristics and related species display similar spectra,” explains Schweiger.

    She has developed a spectral diversity index that shows diversity both within and between plant communities (alpha and beta diversity, respectively). The resolution of the spectral data is critical in terms of assessing diversity of this kind. “We need extremely high resolution in order to identify individual plants, which is required for estimating the alpha diversity. This means that there should only be one plant per pixel,” says Schweiger.

    Satellite-based image spectrometers – similar to what NASA and the ESA are currently developing – make records of the Earth’s surface in 30 x 30-meter chunks. “What’s easy to compare with these large pixels that capture a lot of individual specimens are the differences in species composition between plant communities: in other words, the beta diversity,” explains Schweiger.

    From leaf to soil

    The idea is that in the future, leaves should even be able to provide information about soil quality, since plants are a main contributor to soil characteristics. “Dead vegetation, for example, influences soil processes and microbial activities,” says Schweiger. She worked on a study that used remote sensing data to investigate which properties of plants impact the enzyme activity, microorganism diversity, organic carbon content and nitrogen content of soil.

    The results of the study indicate that the relationships between vegetation and soil processes vary depending on the ecosystem. “First we need to understand how productive and species-rich a particular ecosystem is compared to other ecosystems before we can start making statements about the properties of the soil,” adds Schweiger. It is this complexity that makes it a challenge to analyze remote sensing data – in addition to the vast quantities of information that remote sensing generates. The data points depend on when they were recorded and the environmental conditions at that moment – spectrums that change within a matter of seconds.

    Schuman would even like to extend remote sensing to certain chemical compounds that are emitted by cells and organisms to communicate with one another. Insects can detect molecules from food plants several kilometers away and use these scents to navigate toward their source of sustenance. “For our technology, it’s still difficult to record this kind of information remotely,” says Schuman. A geneticist by training, Schuman is particularly intrigued by the idea of using remote sensing to record molecules of this kind, since they have a direct tie to genes. “Genes contain the assembly instructions for proteins, which in turn put these chemical compounds together,” she explains.

    The only one of its kind

    Schuman and Schweiger found their way to their current research field in part thanks to conversations with UZH president and remote sensing expert Michael Schaepman. For decades now, the University of Zurich has been on the bleeding edge of developing remote sensing technology, and the university recognized the significance of remote sensing for biodiversity early on. UZH has been commissioned by NASA and the ESA to conduct test flights with AVIRIS-NG, the latest device in imaging spectrometry. “This measuring instrument is the only one of its kind in the world,” says Schweiger.

    It wasn’t always the case that the two researchers’ work forced them to gaze upon the heavens. They both spent a lot of time evaluating small patches of land in the field, particularly early on in their careers in ecology. “I always wondered if my findings also held true for nearby habitats,” says Schweiger. Remote sensing methods allow for field measurements to be extrapolated to larger areas and for larger areas to be monitored more easily. Remote sensing was also the missing piece for Schuman. “This method poses new questions and has changed the way we research ecosystems,” she says. It remains to be seen what mysteries leaves will reveal about the Earth’s ecosystems in the future.
    ________________________________________________________
    Keyword spectroscopy

    Depending on how they are structured, materials reflect electromagnetic waves of certain wavelengths. Spectroscopy is an analytical method that measures this interplay between electromagnetic waves and materials. This also involves hitting the object with certain desired wavelengths and using a spectroscope to break apart and analyze the waves that are reflected and absorbed – like a prism does to visible light. The distribution of intensity that results – the spectrum – is recorded in lines or bands with the help of a spectrometer. A rainbow is an example of a spectrum. Spectroscopy is an important method of analysis in physics, chemistry and astronomy. It is also used in industrial applications, for instance to detect impurities in food and medicine.

    See the full article here .

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

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

    Please help promote STEM in your local schools.

    Stem Education Coalition

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

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

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

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

    Sharing Knowledge

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

    1. Identity of the University of Zürich

    Scholarship

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

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

    Academic freedom and responsibility

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

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

    Universitas

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

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

    2. The University of Zurich’s goals and responsibilities

    Basic principles

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

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

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

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

    Research

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

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

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

     
  • richardmitnick 10:09 am on January 18, 2023 Permalink | Reply
    Tags: "Starting a Microbial Revolution", , , Biology, , , , , Microbiomes, Welcome to the Microbial Revolution   

    From Duke University: “Starting a Microbial Revolution” 


    From Duke University

    1.18.23

    Welcome to the Microbial Revolution

    1
    Credit: Duke.

    Say the word “microbe” and many people reflexively reach for a bottle of disinfectant. But where most see an adversary to be destroyed posthaste, Claudia Gunsch has always seen potential. She believes that microbiomes — the communities of microorganisms thriving all around us — can be engineered to serve both environmental and human health.  

    “A lot of the work that I’ve done has focused on bioremediation,” said Gunsch, a professor of civil and environmental engineering at Duke University and the director of a new $26million, NSF–funded multi–institution center that focuses on engineering the microbiomes of indoor spaces. “That means I’ve been trying to figure out how we can engineer microbial communities to degrade pollutants and explore the connections between environmental contaminants and human health.”

    That specialty led Gunsch to sites across North Carolina where creosote, a distilled tar used to preserve wooden telephone poles until the late 1990s, had leached into the surrounding soil, river sediment and groundwater over many decades. Gunsch’s lab was trying to determine whether fungal microbiomes existed at the sites despite toxic conditions, and whether they could be stimulated to actually break down the pollution.

    In a separate project closer to home, she collaborated with Duke professor of environmental science and CEE Heather Stapleton on a study investigating the gut microbiomes of children in the Durham area. The results were surprising to Gunsch, despite her expertise.

    It was a pivotal moment in her research. Gunsch began to think broadly about what additional areas of strength would be needed to fully understand and engineer the microbiomes in all the places where humans live, work and play. Building on a long-established training program with biology professor Joseph Graves at North Carolina Agricultural and Technical State University, Gunsch invited a host of collaborators from institutions within the state to tackle the challenge. Joining her in the new Engineering Research Center for Precision Microbiome Engineering, or PreMiEr for short, are:

    Jill Stewart, the Philip C. Singer Distinguished Professor of Environmental Sciences and Engineering at the UNC-Chapel Hill Gillings School of Global Public Health 
    Joseph Graves Jr, professor of biological sciences at NC A&T 
    Jennifer Kuzma, the Goodnight-NCGSK Foundation Distinguished Professor in the School of Public and International Affairs and co-director of the Genetic Engineering and Society Center at NC State
    Anthony Fodor, professor of bioinformatics at UNC Charlotte.  

    “The research center includes a core area for investigating the societal and ethical implications of microbiome engineering to innovate responsibly,” said Gunsch. “The truly interdisciplinary nature of the center is going to make real societal impact.”

    Gunsch imagines that the new center will eventually enable diagnostic tools that can quickly identify the members of the microbial communities that surround us, revolutionizing approaches in agriculture, environmental health, human health and beyond. “Imagine a day when a doctor could walk into a hospital room and, with a really quick diagnostic test, be able to detect the presence of a pathogen before it affects an immunocompromised patient,” said Gunsch. The tools that the center aims to develop over the next several years, said Gunsch, may shift the imaginary into reality.


    PreMiEr ERC – Precision Microbiome Engineering Research Center

    See the full article here .

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

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

    Please help promote STEM in your local schools.

    Stem Education Coalition

    Younger than most other prestigious U.S. research universities, Duke University consistently ranks among the very best. Duke’s graduate and professional schools — in business, divinity, engineering, the environment, law, medicine, nursing and public policy — are among the leaders in their fields. Duke’s home campus is situated on nearly 9,000 acres in Durham, N.C, a city of more than 200,000 people. Duke also is active internationally through the Duke-NUS Graduate Medical School in Singapore, Duke Kunshan University in China and numerous research and education programs across the globe. More than 75 percent of Duke students pursue service-learning opportunities in Durham and around the world through DukeEngage and other programs that advance the university’s mission of “knowledge in service to society.”

    Duke University is a private research university in Durham, North Carolina. Founded by Methodists and Quakers in the present-day town of Trinity in 1838, the school moved to Durham in 1892. In 1924, tobacco and electric power industrialist James Buchanan Duke established The Duke Endowment and the institution changed its name to honor his deceased father, Washington Duke.

    The campus spans over 8,600 acres (3,500 hectares) on three contiguous sub-campuses in Durham, and a marine lab in Beaufort. The West Campus—designed largely by architect Julian Abele, an African American architect who graduated first in his class at the University of Pennsylvania School of Design—incorporates Gothic architecture with the 210-foot (64-meter) Duke Chapel at the campus’ center and highest point of elevation, is adjacent to the Medical Center. East Campus, 1.5 miles (2.4 kilometers) away, home to all first-years, contains Georgian-style architecture. The university administers two concurrent schools in Asia, Duke-NUS Medical School in Singapore (established in 2005) and Duke Kunshan University in Kunshan, China (established in 2013).

    Duke is ranked among the top universities in the United States. The undergraduate admissions are among the most selective in the country, with an overall acceptance rate of 5.7% for the class of 2025. Duke spends more than $1 billion per year on research, making it one of the ten largest research universities in the United States. More than a dozen faculty regularly appear on annual lists of the world’s most-cited researchers. As of 2019, 15 Nobel laureates and 3 Turing Award winners have been affiliated with the university. Duke alumni also include 50 Rhodes Scholars, 25 Churchill Scholars, 13 Schwarzman Scholars, and 8 Mitchell Scholars. The university has produced the third highest number of Churchill Scholars of any university (behind Princeton University and Harvard University) and the fifth-highest number of Rhodes, Marshall, Truman, Goldwater, and Udall Scholars of any American university between 1986 and 2015. Duke is the alma mater of one president of the United States (Richard Nixon) and 14 living billionaires.

    Duke is the second-largest private employer in North Carolina, with more than 39,000 employees. The university has been ranked as an excellent employer by several publications.

    Research

    Duke’s research expenditures in the 2018 fiscal year were $1.168 billion, the tenth largest in the U.S. In fiscal year 2019 Duke received $571 million in funding from the National Institutes of Health. Duke is classified among “R1: Doctoral Universities – Very high research activity”.

    Throughout the school’s history, Duke researchers have made breakthroughs, including the biomedical engineering department’s development of the world’s first real-time, three-dimensional ultrasound diagnostic system and the first engineered blood vessels and stents. In 2015, Paul Modrich shared the Nobel Prize in Chemistry. In 2012, Robert Lefkowitz along with Brian Kobilka, who is also a former affiliate, shared the Nobel Prize in chemistry for their work on cell surface receptors. Duke has pioneered studies involving nonlinear dynamics, chaos, and complex systems in physics.

    In May 2006 Duke researchers mapped the final human chromosome, which made world news as it marked the completion of the Human Genome Project. Reports of Duke researchers’ involvement in new AIDS vaccine research surfaced in June 2006. The biology department combines two historically strong programs in botany and zoology, while one of the divinity school’s leading theologians is Stanley Hauerwas, whom Time named “America’s Best Theologian” in 2001. The graduate program in literature boasts several internationally renowned figures, including Fredric Jameson, Michael Hardt, and Rey Chow, while philosophers Robert Brandon and Lakatos Award-winner Alexander Rosenberg contribute to Duke’s ranking as the nation’s best program in philosophy of biology, according to the Philosophical Gourmet Report.

     
  • richardmitnick 9:31 am on January 16, 2023 Permalink | Reply
    Tags: "LAIs": long-acting injectables, "University of Toronto scientists use AI to fast-track drug formulation development", , Biology, , , , Machine-learning algorithms can be used to predict experimental drug release from long-acting injectables (LAI) and can also help guide the design of new LAIs., , Reducing ‘trial and error’ for new drug development, , Theoretical and Quantum Chemistry   

    From The University of Toronto (CA): “University of Toronto scientists use AI to fast-track drug formulation development” 

    From The University of Toronto (CA)

    1.11.23
    Kate Richards | Leslie Dan Faculty of Pharmacy

    1
    Researchers Christine Allen and Alán Aspuru-Guzik used machine learning to predict experimental drug release from long-acting injectables (photo by Steve Southon)

    In a bid to reduce the time and cost associated with developing promising new medicines, University of Toronto scientists have successfully tested the use of artificial intelligence to guide the design of long-acting injectable drug formulations.

    The study, published this week in Nature Communication [below], was led by Professor Christine Allen in the Leslie Dan Faculty of Pharmacy and Alán Aspuru-Guzik in the departments of chemistry and computer science in the Faculty of Arts & Science.

    Fig. 1: Schematic demonstrating traditional and data-driven formulation development approaches for long-acting injectables (LAIs).
    2
    [a] Selected routes of administration for FDA-approved LAI formulations. [b] Typical trial-and-error loop commonly employed during the development of LAIs termed “traditional LAI formulation development”. [c] Workflow employed in this study to train and analyze machine learning (ML) models to accelerate the design of new LAI systems, termed “Data-driven LAI formulation development”.

    Their multidisciplinary research shows that machine-learning algorithms can be used to predict experimental drug release from long-acting injectables (LAI) and can also help guide the design of new LAIs.

    “This study takes a critical step towards data-driven drug formulation development with an emphasis on long-acting injectables,” said Allen, who is a member of U of T’s Acceleration Consortium, a global initiative that uses artificial intelligence and automation to accelerate the discovery of materials and molecules needed for a sustainable future.

    “We’ve seen how machine learning has enabled incredible leap-step advances in the discovery of new molecules that have the potential to become medicines. We are now working to apply the same techniques to help us design better drug formulations and, ultimately, better medicines.”

    Considered one of the most promising therapeutic strategies for the treatment of chronic diseases, long-acting injectables are a class of advanced drug delivery systems that are designed to release their cargo over extended periods of time to achieve a prolonged therapeutic effect. This approach can help patients better adhere to their medication regimen, reduce side effects and increase efficacy when injected close to the site of action in the body.

    However, achieving the optimal amount of drug release over the desired period of time requires the development of a wide array of formulation candidates through extensive and time-consuming experiments. This trial-and-error approach has created a significant bottleneck in LAI development compared to more conventional types of drug formulation.

    “AI is transforming the way we do science. It helps accelerate discovery and optimization. This is a perfect example of a ‘before AI’ and an ‘after AI’ moment and shows how drug delivery can be impacted by this multidisciplinary research,” said Aspuru-Guzik, who is director of the Acceleration Consortium and holds the CIFAR Artificial Intelligence Research Chair at the Vector Institute in Toronto and the Canada 150 Research Chair in Theoretical and Quantum Chemistry.

    3
    From left: Zeqing Bao, PhD trainee in pharmaceutical sciences, and Riley Hickman, PhD trainee in chemistry, are co-authors on the study published in Nature Communication (photo by Steve Southon)

    Reducing ‘trial and error’ for new drug development

    To investigate whether machine-learning tools could accurately predict the rate of drug release, the research team trained and evaluated a series of 11 different models, including multiple linear regression (MLR), random forest (RF), light gradient boosting machine (lightGBM) and neural networks (NN). The data set used to train the selected panel of machine learning models was constructed from previously published studies by the authors and other research groups.

    “Once we had the data set, we split it into two subsets: one used for training the models and one for testing,” said Pauric Bannigan, research associate with the Allen research group at the Leslie Dan Faculty of Pharmacy. “We then asked the models to predict the results of the test set and directly compared with previous experimental data. We found that the tree-based models, and specifically lightGBM, delivered the most accurate predictions.”

    As a next step, the team worked to apply these predictions and illustrate how machine learning models might be used to inform the design of new LAIs by using advanced analytical techniques to extract design criteria from the lightGBM model. This allowed the design of a new LAI formulation for a drug currently used to treat ovarian cancer.

    Expectations around the speed with which new drug formulations are developed have heightened drastically since the onset of the COVID-19 pandemic.

    “We’ve seen in the pandemic that there was a need to design a new formulation in weeks, to catch up with evolving variants. Allowing for new formulations to be developed in a short period of time, relative to what has been done in the past using conventional methods, is crucially important so that patients can benefit from new therapies,” Allen said, explaining that the research team is also investigating using machine learning to support the development of novel mRNA and lipid nanoparticle formulations.

    More robust databases needed for future advances

    The results of the current study signal the potential for machine learning to reduce reliance on trial-and-error testing. However, Allen and the research team identify that the lack of available open-source data sets in pharmaceutical sciences represents a significant challenge to future progress.

    “When we began this project, we were surprised by the lack of data reported across numerous studies using polymeric microparticles,” Allen said. “This meant the studies and the work that went into them couldn’t be leveraged to develop the machine learning models we need to propel advances in this space. There is a real need to create robust databases in pharmaceutical sciences that are open access and available for all so that we can work together to advance the field.”

    To that end, Allen and the research team have published their datasets and code on the open-source platform Zenodo.

    “For this study our goal was to lower the barrier of entry to applying machine learning in pharmaceutical sciences,” Bannigan said. “We’ve made our data sets fully available so others can hopefully build on this work. We want this to be the start of something and not the end of the story for machine learning in drug formulation.”

    The study was supported by the Natural Sciences and Engineering Research Council of Canada, the Defense Advance Research Projects Agency and the Vector Institute.

    Science paper:
    Nature Communication

    See the full article here .

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


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

    Please help promote STEM in your local schools.

    Stem Education Coalition

    The The University of Toronto (CA) is a public research university in Toronto, Ontario, Canada, located on the grounds that surround Queen’s Park. It was founded by royal charter in 1827 as King’s College, the oldest university in the province of Ontario.

    Originally controlled by the Church of England, the university assumed its present name in 1850 upon becoming a secular institution.

    As a collegiate university, it comprises eleven colleges each with substantial autonomy on financial and institutional affairs and significant differences in character and history. The university also operates two satellite campuses located in Scarborough and Mississauga.

    University of Toronto has evolved into Canada’s leading institution of learning, discovery and knowledge creation. We are proud to be one of the world’s top research-intensive universities, driven to invent and innovate.

    Our students have the opportunity to learn from and work with preeminent thought leaders through our multidisciplinary network of teaching and research faculty, alumni and partners.

    The ideas, innovations and actions of more than 560,000 graduates continue to have a positive impact on the world.

    Academically, the University of Toronto is noted for movements and curricula in literary criticism and communication theory, known collectively as the Toronto School.

    The university was the birthplace of insulin and stem cell research, and was the site of the first electron microscope in North America; the identification of the first black hole Cygnus X-1; multi-touch technology, and the development of the theory of NP-completeness.

    The university was one of several universities involved in early research of deep learning. It receives the most annual scientific research funding of any Canadian university and is one of two members of the Association of American Universities outside the United States, the other being McGill(CA).

    The Varsity Blues are the athletic teams that represent the university in intercollegiate league matches, with ties to gridiron football, rowing and ice hockey. The earliest recorded instance of gridiron football occurred at University of Toronto’s University College in November 1861.

    The university’s Hart House is an early example of the North American student centre, simultaneously serving cultural, intellectual, and recreational interests within its large Gothic-revival complex.

    The University of Toronto has educated three Governors General of Canada, four Prime Ministers of Canada, three foreign leaders, and fourteen Justices of the Supreme Court. As of March 2019, ten Nobel laureates, five Turing Award winners, 94 Rhodes Scholars, and one Fields Medalist have been affiliated with the university.

    Early history

    The founding of a colonial college had long been the desire of John Graves Simcoe, the first Lieutenant-Governor of Upper Canada and founder of York, the colonial capital. As an University of Oxford (UK)-educated military commander who had fought in the American Revolutionary War, Simcoe believed a college was needed to counter the spread of republicanism from the United States. The Upper Canada Executive Committee recommended in 1798 that a college be established in York.

    On March 15, 1827, a royal charter was formally issued by King George IV, proclaiming “from this time one College, with the style and privileges of a University … for the education of youth in the principles of the Christian Religion, and for their instruction in the various branches of Science and Literature … to continue for ever, to be called King’s College.” The granting of the charter was largely the result of intense lobbying by John Strachan, the influential Anglican Bishop of Toronto who took office as the college’s first president. The original three-storey Greek Revival school building was built on the present site of Queen’s Park.

    Under Strachan’s stewardship, King’s College was a religious institution closely aligned with the Church of England and the British colonial elite, known as the Family Compact. Reformist politicians opposed the clergy’s control over colonial institutions and fought to have the college secularized. In 1849, after a lengthy and heated debate, the newly elected responsible government of the Province of Canada voted to rename King’s College as the University of Toronto and severed the school’s ties with the church. Having anticipated this decision, the enraged Strachan had resigned a year earlier to open Trinity College as a private Anglican seminary. University College was created as the nondenominational teaching branch of the University of Toronto. During the American Civil War the threat of Union blockade on British North America prompted the creation of the University Rifle Corps which saw battle in resisting the Fenian raids on the Niagara border in 1866. The Corps was part of the Reserve Militia lead by Professor Henry Croft.

    Established in 1878, the School of Practical Science was the precursor to the Faculty of Applied Science and Engineering which has been nicknamed Skule since its earliest days. While the Faculty of Medicine opened in 1843 medical teaching was conducted by proprietary schools from 1853 until 1887 when the faculty absorbed the Toronto School of Medicine. Meanwhile the university continued to set examinations and confer medical degrees. The university opened the Faculty of Law in 1887, followed by the Faculty of Dentistry in 1888 when the Royal College of Dental Surgeons became an affiliate. Women were first admitted to the university in 1884.

    A devastating fire in 1890 gutted the interior of University College and destroyed 33,000 volumes from the library but the university restored the building and replenished its library within two years. Over the next two decades a collegiate system took shape as the university arranged federation with several ecclesiastical colleges including Strachan’s Trinity College in 1904. The university operated the Royal Conservatory of Music from 1896 to 1991 and the Royal Ontario Museum from 1912 to 1968; both still retain close ties with the university as independent institutions. The University of Toronto Press was founded in 1901 as Canada’s first academic publishing house. The Faculty of Forestry founded in 1907 with Bernhard Fernow as dean was Canada’s first university faculty devoted to forest science. In 1910, the Faculty of Education opened its laboratory school, the University of Toronto Schools.

    World wars and post-war years

    The First and Second World Wars curtailed some university activities as undergraduate and graduate men eagerly enlisted. Intercollegiate athletic competitions and the Hart House Debates were suspended although exhibition and interfaculty games were still held. The David Dunlap Observatory in Richmond Hill opened in 1935 followed by the University of Toronto Institute for Aerospace Studies in 1949. The university opened satellite campuses in Scarborough in 1964 and in Mississauga in 1967. The university’s former affiliated schools at the Ontario Agricultural College and Glendon Hall became fully independent of the University of Toronto and became part of University of Guelph (CA) in 1964 and York University (CA) in 1965 respectively. Beginning in the 1980s reductions in government funding prompted more rigorous fundraising efforts.

    Since 2000

    In 2000 Kin-Yip Chun was reinstated as a professor of the university after he launched an unsuccessful lawsuit against the university alleging racial discrimination. In 2017 a human rights application was filed against the University by one of its students for allegedly delaying the investigation of sexual assault and being dismissive of their concerns. In 2018 the university cleared one of its professors of allegations of discrimination and antisemitism in an internal investigation after a complaint was filed by one of its students.

    The University of Toronto was the first Canadian university to amass a financial endowment greater than c. $1 billion in 2007. On September 24, 2020 the university announced a $250 million gift to the Faculty of Medicine from businessman and philanthropist James C. Temerty- the largest single philanthropic donation in Canadian history. This broke the previous record for the school set in 2019 when Gerry Schwartz and Heather Reisman jointly donated $100 million for the creation of a 750,000-square foot innovation and artificial intelligence centre.

    Research

    Since 1926 the University of Toronto has been a member of the Association of American Universities a consortium of the leading North American research universities. The university manages by far the largest annual research budget of any university in Canada with sponsored direct-cost expenditures of $878 million in 2010. In 2018 the University of Toronto was named the top research university in Canada by Research Infosource with a sponsored research income (external sources of funding) of $1,147.584 million in 2017. In the same year the university’s faculty averaged a sponsored research income of $428,200 while graduate students averaged a sponsored research income of $63,700. The federal government was the largest source of funding with grants from the Canadian Institutes of Health Research; the Natural Sciences and Engineering Research Council; and the Social Sciences and Humanities Research Council amounting to about one-third of the research budget. About eight percent of research funding came from corporations- mostly in the healthcare industry.

    The first practical electron microscope was built by the physics department in 1938. During World War II the university developed the G-suit- a life-saving garment worn by Allied fighter plane pilots later adopted for use by astronauts.Development of the infrared chemiluminescence technique improved analyses of energy behaviours in chemical reactions. In 1963 the asteroid 2104 Toronto was discovered in the David Dunlap Observatory (CA) in Richmond Hill and is named after the university. In 1972 studies on Cygnus X-1 led to the publication of the first observational evidence proving the existence of black holes. Toronto astronomers have also discovered the Uranian moons of Caliban and Sycorax; the dwarf galaxies of Andromeda I, II and III; and the supernova SN 1987A. A pioneer in computing technology the university designed and built UTEC- one of the world’s first operational computers- and later purchased Ferut- the second commercial computer after UNIVAC I. Multi-touch technology was developed at Toronto with applications ranging from handheld devices to collaboration walls. The AeroVelo Atlas which won the Igor I. Sikorsky Human Powered Helicopter Competition in 2013 was developed by the university’s team of students and graduates and was tested in Vaughan.

    The discovery of insulin at the University of Toronto in 1921 is considered among the most significant events in the history of medicine. The stem cell was discovered at the university in 1963 forming the basis for bone marrow transplantation and all subsequent research on adult and embryonic stem cells. This was the first of many findings at Toronto relating to stem cells including the identification of pancreatic and retinal stem cells. The cancer stem cell was first identified in 1997 by Toronto researchers who have since found stem cell associations in leukemia; brain tumors; and colorectal cancer. Medical inventions developed at Toronto include the glycaemic index; the infant cereal Pablum; the use of protective hypothermia in open heart surgery; and the first artificial cardiac pacemaker. The first successful single-lung transplant was performed at Toronto in 1981 followed by the first nerve transplant in 1988; and the first double-lung transplant in 1989. Researchers identified the maturation promoting factor that regulates cell division and discovered the T-cell receptor which triggers responses of the immune system. The university is credited with isolating the genes that cause Fanconi anemia; cystic fibrosis; and early-onset Alzheimer’s disease among numerous other diseases. Between 1914 and 1972 the university operated the Connaught Medical Research Laboratories- now part of the pharmaceutical corporation Sanofi-Aventis. Among the research conducted at the laboratory was the development of gel electrophoresis.

    The University of Toronto is the primary research presence that supports one of the world’s largest concentrations of biotechnology firms. More than 5,000 principal investigators reside within 2 kilometres (1.2 mi) from the university grounds in Toronto’s Discovery District conducting $1 billion of medical research annually. MaRS Discovery District is a research park that serves commercial enterprises and the university’s technology transfer ventures. In 2008, the university disclosed 159 inventions and had 114 active start-up companies. Its SciNet Consortium operates the most powerful supercomputer in Canada.

     
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