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  • richardmitnick 5:44 pm on January 12, 2022 Permalink | Reply
    Tags: "Chemists use DNA to build the world’s tiniest antenna", , , , , , DNA-based fluorescent nanoantenna, , Protein Studies,   

    From The University of Montréal [Université de Montréal] (CA) : “Chemists use DNA to build the world’s tiniest antenna” 

    From The University of Montréal [Université de Montréal] (CA)

    01/10/2022
    Salle De Presse

    1
    Developed at Université de Montréal, the easy-to-use device promises to help scientists better understand natural and human-designed nanotechnologies – and identify new drugs.

    Researchers at Université de Montréal have created a nanoantenna to monitor the motions of proteins.

    Reported this week in Nature Methods, the device is a new method to monitor the structural change of proteins over time – and may go a long way to helping scientists better understand natural and human-designed nanotechnologies.

    “The results are so exciting that we are currently working on setting up a start-up company to commercialize and make this nanoantenna available to most researchers and the pharmaceutical industry,” said UdeM chemistry professor Alexis Vallée-Bélisle, the study’s senior author.

    Works like a two-way radio

    Over 40 years ago, researchers invented the first DNA synthesizer to create molecules that encode genetic information. “In recent years, chemists have realized that DNA can also be employed to build a variety of nanostructures and nanomachines,” said Vallée-Belisle, who also holds the Canada Research Chair in Bioengineering and Bionanotechnology.

    “Inspired by the ‘Lego-like’ properties of DNA, with building blocks that are typically 20,000 times smaller than a human hair, we have created a DNA-based fluorescent nanoantenna, that can help characterize the function of proteins,” he said.

    “Like a two-way radio that can both receive and transmit radio waves, the fluorescent nanoantenna receives light in one colour, or wavelength, and depending on the protein movement it senses, then transmits light back in another colour, which we can detect.”

    One of the main innovations of these nanoantennae is that the receiver part of the antenna is also employed to sense the molecular surface of the protein studied via molecular interaction.

    One of the main advantages of using DNA to engineer these nanoantennas is that DNA chemistry is relatively simple and programmable,” said Scott Harroun, an UdeM doctoral student in chemistry and the study’s first author.

    “The DNA-based nanoantennas can be synthesized with different lengths and flexibilities to optimize their function,””he said. “One can easily attach a fluorescent molecule to the DNA, and then attach this fluorescent nanoantenna to a biological nanomachine, such as an enzyme.

    “By carefully tuning the nanoantenna design, we have created five nanometer-long antenna that produces a distinct signal when the protein is performing its biological function.”

    Fluorescent nanoantennas open many exciting avenues in biochemistry and nanotechnology, the scientists believe.

    “For example, we were able to detect, in real time and for the first time, the function of the enzyme alkaline phosphatase with a variety of biological molecules and drugs,” said Harroun. “This enzyme has been implicated in many diseases, including various cancers and intestinal inflammation.”

    Added Dominic Lauzon, a co-author of the study doing his PhD in chemistry at UdeM: “In addition to helping us understand how natural nanomachines function or malfunction, consequently leading to disease, this new method can also help chemists identify promising new drugs as well as guide nanoengineers to develop improved nanomachines.”

    One main advance enabled by these nanoantennas is also their ease-of-use, the scientists said.

    “Perhaps what we are most excited by is the realization that many labs around the world, equipped with a conventional spectrofluorometer, could readily employ these nanoantennas to study their favourite protein, such as to identify new drugs or to develop new nanotechnologies,” said Vallée-Bélisle.

    See the full article here.

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    The Université de Montréal is a French-language public research university in Montreal, Quebec, Canada. The university’s main campus is located on the northern slope of Mount Royal in the neighbourhoods of Outremont and Côte-des-Neiges. The institution comprises thirteen faculties, more than sixty departments and two affiliated schools: the Polytechnique Montréal (School of Engineering; formerly the École Polytechnique de Montréal) and HEC Montréal (School of Business). It offers more than 650 undergraduate programmes and graduate programmes, including 71 doctoral programmes.

    The university was founded as a satellite campus of the Université Laval in 1878. It became an independent institution after it was issued a papal charter in 1919 and a provincial charter in 1920. Université de Montréal moved from Montreal’s Quartier Latin to its present location at Mount Royal in 1942. It was made a secular institution with the passing of another provincial charter in 1967.

    The school is co-educational, and has 34,335 undergraduate and 11,925 post-graduate students (excluding affiliated schools). Alumni and former students reside across Canada and around the world, with notable alumni serving as government officials, academics, and business leaders.

    Research

    Université de Montréal is a member of the U15, a group that represents 15 Canadian research universities. The university includes 465 research units and departments. In 2018, Research Infosource ranked the university third in their list of top 50 research universities; with a sponsored research income (external sources of funding) of $536.238 million in 2017. In the same year, the university’s faculty averaged a sponsored research income of $271,000, while its graduates averaged a sponsored research income of $33,900.

    Université de Montréal research performance has been noted in several bibliometric university rankings, which uses citation analysis to evaluate the impact a university has on academic publications. In 2019, The Performance Ranking of Scientific Papers for World Universities ranked the university 104th in the world, and fifth in Canada. The University Ranking by Academic Performance 2018–19 rankings placed the university 99th in the world, and fifth in Canada.

    Since 2017, Université de Montréal has partnered with the McGill University (CA) on Mila (research institute), a community of professors, students, industrial partners and startups working in AI, with over 500 researchers making the institute the world’s largest academic research center in deep learning. The institute was originally founded in 1993 by Professor Yoshua Bengio.

     
  • richardmitnick 12:03 pm on January 2, 2022 Permalink | Reply
    Tags: "At the Dawn of Life Heat May Have Driven Cell Division", , , , , During cell division structural proteins and enzymes coordinate the duplication of DNA., For a protocell to grow before it divides it would have to increase not only the volume inside the cell but also the surface area of the surrounding membrane., Getting these processes right is crucial because errors can lead to daughter cells that are abnormal or unviable., Protein Studies, Protocells must have had some kind of heritable information they could pass down to daughter cells., The asymmetry in lipid membranes could play a role in primitive life., The energy produced by the primitive cellular metabolism would heat up the lipids on the inside of the membrane more quickly than those on the outside., The work is purely theoretical.,   

    From WIRED : “At the Dawn of Life Heat May Have Driven Cell Division” 

    From WIRED

    01.02.2022
    Carrie Arnold

    A mathematical model shows how a thermodynamic mechanism could have made protocells split in two.

    1
    https://newsupdate.uk/


    Membrane-bound vesicles that were the forerunners of living cells may have divided under the influence of internally generated heat, according to a recent study.Video: Getty Images.

    An elegant ballet of proteins enables modern cells to replicate themselves. During cell division structural proteins and enzymes coordinate the duplication of DNA, the division of a cell’s cytoplasmic contents, and the cinching of the membrane that cleaves the cell. Getting these processes right is crucial because errors can lead to daughter cells that are abnormal or unviable.

    Billions of years ago, the same challenge must have faced the first self-organizing membranous bundles of chemicals arising spontaneously from inanimate materials. But these protocells almost certainly had to replicate without relying on large proteins. How they did it is a key question for astrobiologists and biochemists studying the origins of life.

    “If you delete all enzymes in the cell, nothing happens. They’re just inert sacks,” said Anna Wang, an astrobiologist at The University of New South Wales Sydney (AU). “They’re really stable, and that’s kind of the point.”

    However, in a recent paper in Biophysical Journal, Romain Attal, a physicist at the The City of Science and Industry [Cité des Sciences et de l’Industrie](FR), and the cancer biologist Laurent Schwartz of the Paris Public Hospitals developed a series of mathematical equations that model how heat alone could have been enough to drive one important part of the replication process: the fission of one protocell into two.

    Attal thinks that the chemical and physical processes active in early life were probably quite simple, and that thermodynamics alone could therefore have played a significant role in how life began. He said that the kinds of basic equations he has been working on could spell out some of the rules that governed how life first emerged.

    “Temperature gradients are important to life,” Attal said. “If you understand a subject, you need to be able to write down its principles.”

    Flipping for Fission

    For primitive cells to divide themselves without complex protein machinery, the process would have needed a physical or chemical driver. “It’s really about stripping a cell down to its basic functions and thinking, ‘What are the basic physical and chemical principles, and how can we mimic that without proteins?’” Wang said.

    Figuring out these processes becomes more challenging when you consider that scientists still can’t agree on a definition of life in general, and of protocells specifically.

    What scientists do agree on is that protocells must have had some kind of heritable information they could pass down to daughter cells, a metabolism that carried out chemical reactions, and a lipid membrane isolating the metabolism and heritable information from the randomness in the rest of Earth’s primordial soup. Whereas the outside chemical world was inherently random, the partitioning provided by the lipid membrane could create an area of lower entropy.

    For a protocell to grow before it divides it would have to increase not only the volume inside the cell but also the surface area of the surrounding membrane. To create two smaller daughter cells with the same total volume as the parent cell would require additional lipids for their membranes, because their surface area would be larger relative to their volume. The chemical reactions needed to fuel the synthesis of these lipids would give off energy in the form of heat.

    As Attal discussed these ideas with Schwartz, he began to wonder whether this energy was enough to drive early cell division. A search of the research literature revealed a study finding that mitochondria (the cell’s energy center, which began as a symbiotic bacterium billions of years ago) have a slightly higher temperature than the surrounding cell. Attal wanted to know whether that energy difference could be generated in protocells, and whether it was adequate to drive fission.

    He began sketching out a series of equations to model what might be happening. He started with a series of assumptions, such as that the protocell would be rod-shaped and that it had a double-layered membrane allowing nutrients to diffuse in and wastes to diffuse out.

    “It’s a very, very rough model,” he said. “I was surprised that it could be reduced to a single differential equation.”

    Attal realized that the energy produced by the primitive cellular metabolism would heat up the lipids on the inside of the membrane more quickly than those on the outside. Thermodynamics would then force the energetic inner lipids to “flip” to the outside, causing the outer membrane layer to expand at the expense of the inner layer. One easy solution to this imbalance would be for the cell to pinch together into two daughter cells. This pinching would occur at the middle of the parent cell, where it was hottest and the lipid movements were most pronounced.

    Too Small to Get Hot?

    The work is purely theoretical, but Attal said it can be tested experimentally by creating similar vesicles in the lab and measuring whether the temperature inside is different from the temperature outside.

    Wang says the work is important as a reminder that the asymmetry in lipid membranes could play a role in primitive life. However, both she and the biophysicist Paul Higgs of McMaster University (CA) are skeptical of some of the assumptions Attal made. They both pointed out that because cells and protocells are small, only minimal heat could be generated, and they questioned whether that temperature difference would be large enough to drive fission before the heat diffused across the membrane.

    Wang also has doubts about the proposed movement of the lipids between the inner and outer membrane. In modern membranes, lipids don’t flip-flop readily between the inside and the outside because their molecules have complex structures. That may not be the case for the simpler lipids that early life is thought to have used. When scientists create vesicles from these compounds in the lab, “they move around like crazy. You can’t stop it from happening,” she said.

    Higgs questioned Attal’s assumption that the cells would be rods. That shape requires specific proteins to stiffen the membrane, which protocells almost certainly lacked. As a result, they would be spherical, not rod-shaped.

    “I don’t see how you can maintain a rod shape without a hard wall,” he said.

    Neither of these issues means that heat didn’t play a role in early cell division, only that Attal’s mathematical model may not be the most accurate, Wang says. Still, Claudia Bonfio, a biochemist at the University of Strasbourg in France, says that the paper adds to the literature on early life because “it’s a nice starting point for experiments. We too often forget that reactions consume and produce heat, which could have an effect on things like fission.”

    See the full article here .

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  • richardmitnick 11:20 am on December 26, 2021 Permalink | Reply
    Tags: "Mirror-image peptides form ‘rippled sheet’ structure predicted in 1953", , , , , Pleated beta sheet, Protein Studies, Proteins consist of long chains of amino acids folded into complex three-dimensional shapes that enable them to carry out a huge variety of functions in all living things., The amino acids that make up proteins can have either a “left-handed” (L) or “right-handed” (D) orientation in the arrangement of their atoms-mirror images., ,   

    From The University of California-Santa Cruz (US) : “Mirror-image peptides form ‘rippled sheet’ structure predicted in 1953” 

    From The University of California-Santa Cruz (US)

    December 17, 2021
    Tim Stephens
    stephens@ucsc.edu

    A UCSC team obtained an x-ray ‘snapshot’ of a novel protein structure with potential applications in biomedicine and materials science.

    1
    This illustration shows the “left-handed” and “right-handed” triphenylalanine peptides which bond together to form a rippled beta sheet. Illustration by Jevgenij Raskatov.

    2
    The dimeric rippled sheets assembled into a layered crystal structure with a herringbone pattern. Image credit: Kuhn et al., Chemical Science 2021.

    By mixing a small peptide with equal amounts of its mirror image, a team of scientists at UC Santa Cruz has created an unusual protein structure known as a “rippled beta sheet” and obtained images of it using x-ray crystallography. They reported their findings in a paper published December 8 in Chemical Science.

    The rippled sheet is a distinctive variation on the pleated beta sheet, which is a well-known structural motif found in thousands of proteins, including important disease-related proteins. Linus Pauling and Robert Corey described the rippled beta sheet in 1953, two years after introducing the concept of the pleated beta sheet.

    While the pleated beta sheet (often called simply the beta sheet) quickly became a textbook example of a common protein structure, the rippled sheet has languished in obscurity as a rarely studied and largely theoretical structure. Previous studies have found experimental evidence of rippled sheet formation, but none using x-ray crystallography, which is the gold standard for determining protein structures.

    “Now, for the first time, we have the crystal structure of a rippled sheet, which is like a snapshot of it, and the structure closely matches the predictions of Pauling and Corey,” said Jevgenij Raskatov, associate professor of chemistry and biochemistry at UC Santa Cruz and corresponding author of the paper.

    “The rippled sheet paradigm may have significance for both materials research and biomedical applications, and having the crystal structure is important for the rational design of rippled sheet materials,” Raskatov noted.

    Proteins consist of long chains of amino acids folded into complex three-dimensional shapes that enable them to carry out a huge variety of functions in all living things. A pleated beta sheet is composed of linear strands (called beta strands) bonded together side by side to form a 2-dimensional sheet-like structure. A rippled beta sheet is similar except that alternate strands are mirror images of each other.

    The amino acids that make up proteins can have either a “left-handed” (L) or “right-handed” (D) orientation in the arrangement of their atoms—the same in all respects but mirror images, like left and right hands. All natural proteins are made with left-handed amino acids, but synthetic proteins can be made with either L or D amino acids.

    In the new study, the researchers used mirror-image forms of triphenylalanine, a short peptide consisting of three phenylalanine amino acids. When mixed in equal amounts, the mirror-image peptides joined in pairs, which then packed together into herringbone layer structures.

    “They pack together to form a crystal, so we could use x-ray crystallography to see that rippled sheet structure,” said coauthor Timothy Johnstone, assistant professor of chemistry and biochemistry. “It’s a highly enabling discovery that opens up new avenues for exploration, because it gives us a new building block, or a new way to put building blocks together, for creating novel polypeptide structures with desirable properties.”

    Having determined the crystal structure, the researchers then searched the Protein Data Bank, an online archive of structural data, for other proteins involving mirror-image peptides. They found three additional crystal structures containing rippled sheets that had not been recognized when the structures were originally analyzed.

    The co-first authors of the paper are Ariel Kuhn, a Ph.D. student in Raskatov’s lab, and Beatriz Ehlke, a Ph.D. student in the lab of coauthor Scott Oliver, professor of chemistry and biochemistry.

    “It was a great collaborative effort between the three labs, as well as demonstrating the incredible capabilities of our new single crystal XRD instrument for x-ray crystallography,” Kuhn said.

    This work was supported by The National Institutes of Health (US) and The National Science Foundation (US).

    See the full article here .


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    UC Santa Cruz (US) Lick Observatory Since 1888 Mt Hamilton, in San Jose, California, Altitude 1,283 m (4,209 ft)

    UC Observatories Lick Automated Planet Finder fully robotic 2.4-meter optical telescope at Lick Observatory, situated on the summit of Mount Hamilton, east of San Jose, California, USA.

    The UCO Lick C. Donald Shane telescope is a 120-inch (3.0-meter) reflecting telescope located at the Lick Observatory, Mt Hamilton, in San Jose, California, Altitude 1,283 m (4,209 ft).
    UC Santa Cruz (US) campus.

    The University of California-Santa Cruz (US) , opened in 1965 and grew, one college at a time, to its current (2008-09) enrollment of more than 16,000 students. Undergraduates pursue more than 60 majors supervised by divisional deans of humanities, physical & biological sciences, social sciences, and arts. Graduate students work toward graduate certificates, master’s degrees, or doctoral degrees in more than 30 academic fields under the supervision of the divisional and graduate deans. The dean of the Jack Baskin School of Engineering oversees the campus’s undergraduate and graduate engineering programs.

    UCSC is the home base for the Lick Observatory.

    UCO Lick Observatory’s 36-inch Great Refractor telescope housed in the South (large) Dome of main building.

    Search for extraterrestrial intelligence expands at Lick Observatory
    New instrument scans the sky for pulses of infrared light
    March 23, 2015
    By Hilary Lebow


    Astronomers are expanding the search for extraterrestrial intelligence into a new realm with detectors tuned to infrared light at UC’s Lick Observatory. A new instrument, called NIROSETI, will soon scour the sky for messages from other worlds.

    “Infrared light would be an excellent means of interstellar communication,” said Shelley Wright, an assistant professor of physics at UC San Diego (US) who led the development of the new instrument while at the U Toronto Dunlap Institute for Astronomy and Astrophysics (CA).

    Shelley Wright of UC San Diego with (US) NIROSETI, developed at U Toronto Dunlap Institute for Astronomy and Astrophysics (CA) at the 1-meter Nickel Telescope at Lick Observatory at UC Santa Cruz

    Wright worked on an earlier SETI project at Lick Observatory as a UC Santa Cruz undergraduate, when she built an optical instrument designed by University of California-Berkeley (US) researchers. The infrared project takes advantage of new technology not available for that first optical search.

    Infrared light would be a good way for extraterrestrials to get our attention here on Earth, since pulses from a powerful infrared laser could outshine a star, if only for a billionth of a second. Interstellar gas and dust is almost transparent to near infrared, so these signals can be seen from great distances. It also takes less energy to send information using infrared signals than with visible light.

    Frank Drake, professor emeritus of astronomy and astrophysics at UC Santa Cruz and director emeritus of the SETI Institute, said there are several additional advantages to a search in the infrared realm.

    Frank Drake with his Drake Equation. Credit Frank Drake.

    “The signals are so strong that we only need a small telescope to receive them. Smaller telescopes can offer more observational time, and that is good because we need to search many stars for a chance of success,” said Drake.

    The only downside is that extraterrestrials would need to be transmitting their signals in our direction, Drake said, though he sees this as a positive side to that limitation. “If we get a signal from someone who’s aiming for us, it could mean there’s altruism in the universe. I like that idea. If they want to be friendly, that’s who we will find.”

    Scientists have searched the skies for radio signals for more than 50 years and expanded their search into the optical realm more than a decade ago. The idea of searching in the infrared is not a new one, but instruments capable of capturing pulses of infrared light only recently became available.

    “We had to wait,” Wright said. “I spent eight years waiting and watching as new technology emerged.”

    Now that technology has caught up, the search will extend to stars thousands of light years away, rather than just hundreds. NIROSETI, or Near-Infrared Optical Search for Extraterrestrial Intelligence, could also uncover new information about the physical universe.

    “This is the first time Earthlings have looked at the universe at infrared wavelengths with nanosecond time scales,” said Dan Werthimer, UC Berkeley SETI Project Director. “The instrument could discover new astrophysical phenomena, or perhaps answer the question of whether we are alone.”

    NIROSETI will also gather more information than previous optical detectors by recording levels of light over time so that patterns can be analyzed for potential signs of other civilizations.

    “Searching for intelligent life in the universe is both thrilling and somewhat unorthodox,” said Claire Max, director of UC Observatories and professor of astronomy and astrophysics at UC Santa Cruz. “Lick Observatory has already been the site of several previous SETI searches, so this is a very exciting addition to the current research taking place.”

    NIROSETI will scan the skies several times a week on the Nickel 1-meter telescope at Lick Observatory, located on Mt. Hamilton east of San Jose.

     
  • richardmitnick 4:24 pm on October 21, 2021 Permalink | Reply
    Tags: , "Supercomputer simulations reveal how protein crowding in cells impacts interactions", , , Protein Studies, , The scientists developed a highly optimized software program called GENESIS for use with supercomputers in Japan., These simulations could help improve drug development since they shed light on why some drugs work in theory but flop in practice.   

    From RIKEN [理研](JP) via phys.org: “Supercomputer simulations reveal how protein crowding in cells impacts interactions” 

    RIKEN bloc

    From RIKEN [理研](JP)

    via

    phys.org

    October 21, 2021

    1
    Figure 1: Simulations of the interaction of the enzyme c-Src kinase (green) with inhibitor PP1 (magenta, blue and white spheres) in the presence of low (left) and high (right) concentrations of bovine serum albumin (BSA; gray). The simulations reveal that crowding by BSA reduces the ability of PP1 to bind with c-Src kinase. Credit: Laguna Design/Science Photo Library.

    Supercomputer simulations by RIKEN researchers have revealed how drug binding to a protein target changes as the surrounding environment becomes more cluttered with other proteins. These simulations could help improve drug development since they shed light on why some drugs work in theory but flop in practice.

    The initial stages of drug development usually involve simulating the interactions between a molecule and its target protein. Although these simulations can suggest a drug is effective, the interaction can frequently fail to live up to its promise when tested on living cells. Computational biophysicist Yuji Sugita of the RIKEN Center for Biosystems Dynamics Research (BDR) and his colleagues wanted to make simulations more accurate by accounting for cells’ normally crowded environments.

    “Many proteins and macromolecules are present inside cells, making it a crowded environment,” explains Sugita. “In fact, large molecules account for anywhere between a fourth and a half of the volume of a cell’s cytoplasm. We wanted to discover how these crowded environments affect drug binding to target proteins.”

    To do this, they developed a highly optimized software program called GENESIS for use with supercomputers in Japan. They then conducted microsecond-scale simulations of the interaction of an enzyme (c-Src kinase) with an inhibitor (PP1) in the presence of different concentrations of bovine serum albumin (BSA). Sugita’s collaborator, Michael Feig, a professor at The Michigan State University (US), also performed simulations of the same systems using a molecular-dynamics supercomputer in the United States. The team chose c-Src kinase because the enzyme regulates signal transduction pathways and its dysregulation is associated with many diseases, including cancers.

    The researchers found that crowding by BSA reduced the amount of PP1 able to reach the enzyme by physically blocking its access and also by weakly and non-specifically interacting with it.

    Still, small amounts of PP1 were able to slip through the crowds. But the simulations showed that BSA crowding also covered some binding sites on c-Src kinase and changed the enzyme’s shape, altering the pathways available for it to reach its main binding site.

    The team validated their results by performing laboratory tests using the actual proteins in similar conditions. These experiments conducted by Mikako Shirouzu and her colleagues in RIKEN BDR showed that PP1’s efficacy in inhibiting c-Src kinase decreased with increasing BSA crowding.

    The team now wants to examine how crowding affects other target proteins and drugs. They also intend to use their supercomputers to study protein function inside biological membranes and cell organelles. “These different environments could affect protein functions similarly or differently,” says Sugita. “We just don’t know.”

    Science paper:
    Nature Communications

    See the full article here .

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    RIKEN campus

    RIKEN [理研](JP) is Japan’s largest comprehensive research institution renowned for high-quality research in a diverse range of scientific disciplines. Founded in 1917 as a private research foundation in Tokyo, RIKEN has grown rapidly in size and scope, today encompassing a network of world-class research centers and institutes across Japan. Founded in 1917, it now has about 3,000 scientists on seven campuses across Japan, including the main site at Wakō, Saitama Prefecture, just outside Tokyo. Riken is a Designated National Research and Development Institute, and was formerly an Independent Administrative Institution.

    Riken conducts research in many areas of science including physics; chemistry; biology; genomics; medical science; engineering; high-performance computing and computational science and ranging from basic research to practical applications with 485 partners worldwide. It is almost entirely funded by the Japanese government, and its annual budget is about ¥88 billion (US$790 million).

    Organizational structure:

    The main divisions of Riken are listed here. Purely administrative divisions are omitted.

    Headquarters (mostly in Wako)
    Wako Branch
    Center for Emergent Matter Science (research on new materials for reduced power consumption)
    Center for Sustainable Resource Science (research toward a sustainable society)
    Nishina Center for Accelerator-Based Science (site of the Radioactive Isotope Beam Factory, a heavy-ion accelerator complex)
    Center for Brain Science
    Center for Advanced Photonics (research on photonics including terahertz radiation)
    Research Cluster for Innovation
    Cluster for Pioneering Research (chief scientists)
    Interdisciplinary Theoretical and Mathematical Sciences Program
    Tokyo Branch
    Center for Advanced Intelligence Project (research on artificial intelligence)
    Tsukuba Branch
    BioResource Research Center
    Harima Institute
    Riken SPring-8 Center (site of the SPring-8 synchrotron and the SACLA x-ray free electron laser)

    Riken SPring-8 synchrotron, located in Hyōgo Prefecture, Japan.

    RIKEN/HARIMA (JP) X-ray Free Electron Laser

    Yokohama Branch (site of the Yokohama Nuclear magnetic resonance facility)
    Center for Sustainable Resource Science
    Center for Integrative Medical Sciences (research toward personalized medicine)
    Center for Biosystems Dynamics Research (also based in Kobe and Osaka) [6]
    Program for Drug Discovery and Medical Technology Platform
    Structural Biology Laboratory
    Sugiyama Laboratory
    Kobe Branch
    Center for Biosystems Dynamics Research (developmental biology and nuclear medicine medical imaging techniques)
    Center for Computational Science (R-CCS, home of the K computer and The post-K (Fugaku) computer development plan)

    Riken Fujitsu K supercomputer manufactured by Fujitsu, installed at the Riken Advanced Institute for Computational Science campus in Kobe, Hyōgo Prefecture, Japan.

    Fugaku is a claimed exascale supercomputer (while only at petascale for mainstream benchmark), at the RIKEN Center for Computational Science in Kobe, Japan. It started development in 2014 as the successor to the K computer, and is officially scheduled to start operating in 2021. Fugaku made its debut in 2020, and became the fastest supercomputer in the world in the June 2020 TOP500 list, the first ever supercomputer that achieved 1 exaFLOPS. As of April 2021, Fugaku is currently the fastest supercomputer in the world.

     
  • richardmitnick 11:06 am on August 17, 2021 Permalink | Reply
    Tags: "Computer algorithms are currently revolutionising biology", , , Protein Studies,   

    From Swiss Federal Institute of Technology in Zürich [ETH Zürich] [Eidgenössische Technische Hochschule Zürich] (CH): “Computer algorithms are currently revolutionising biology” 

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

    17.08.2021

    Artificial intelligence can help predict the three-​dimensional structure of proteins. Professor Beat Christen describes how such algorithms should soon help to develop tailored artificial proteins.

    Computer algorithms have been a helpful tool in biomedical research for decades, and their importance has been growing steadily over that time. But what we’re now experiencing is nothing short of a quantum leap; it overshadows all that came before and it will have unforeseen effects. Artificial intelligence (AI) algorithms have made it possible to use nothing but the linear sequence of the building blocks of proteins – amino acids – to deliver extremely accurate predictions of the three-​dimensional structure into which this chain of amino acids will assemble.

    Grasping the importance of this development hinges on knowing that biology on a cellular level is actually always about spatial interactions between molecules – and that it’s the three-​dimensional structure of these molecules that determine those interactions. Once we understand the structures and interactions in play, we understand the biology. And only once we understand the structure of molecules can we engineer medications capable of influencing the function of these molecules.

    1
    Proteins are thread-​like molecules that assemble to form a specific three-​dimensional structure. (Visualisation: Shutterstock)

    Up to now, there have been three experimental methods for determining the three-​dimensional structure of proteins: X-​ray structure analysis, nuclear magnetic resonance and, just in the past few years, cryo-​electron microscopy. The addition now of AI as a fourth precision method is due not just to improvements in AI algorithms and the vast computing power that is available today. For AI to make accurate predictions, it also needs to be trained using a wealth of data of exceptional quality. What makes the abovementioned quantum leap possible is considerable progress and effort in both data science and experimental protein research.

    Competition between private and public research

    Currently occupying most of the spotlight is the AlphaFold AI program developed by DeepMind, a sister company of Google. At present, DeepMind is undoubtedly the most important player in predicting protein structures. But what gets lost in the public discussion is that DeepMind is by no means the only player in this area; in particular the team led by David Baker from the University of Washington (US) is conducting some outstanding research.

    Overall, this competition between private and public research has surely served to inspire and invigorate the field, even if, as one would expect, private players keep many of their insights to themselves to protect their own business interests. But highly competitive research has also led to vast improvements to the AI algorithms that are in the public domain, which the entire scientific community can now use and develop. I expect this trend to continue. AI algorithms will soon provide us with highly precise structures for all known proteins. This will enable us to design precision medications on the computer.

    In the future, it should be possible to start from a three-​dimensional molecular scafold designed on a computer and employ AI to calculate a sequence of amino acids that will precisely assemble into the desired structure with the desired molecular function.

    Once this sequence of amino acids has been determined, my area of research comes into play. My work deals with the development of artificial genes and genomes, and it also employs computer algorithms. Based on sequences of amino acids, we calculate how protein information can be encoded into sequences of genetic building blocks – in other words into DNA. And we do it in a way that provides a simple means of synthesising these genes for practical applications.

    Reversing the information flow

    This means we are on the verge of being able to calculate an artificial gene for any given three-​dimensional protein structure designed on a computer, and then synthesise that gene. In biotechnology, this paves the way for manufacturing artificial proteins in microorganisms – including new pharmaceutical agents, vaccines or enzymes for use in industry.

    Ever since the earliest lifeforms emerged several billion years ago, to this day biological information has always been stored in the form of DNA. Inside biological cells, this information is transcribed– first into RNA molecules, and then translated into proteins. Until now, there has been no mechanism for reversing the flow of information such that protein information is translated back into DNA information. AI will soon change all that. For biologists such as myself, this is an incredibly spectacular development, one that will have a profound impact on biotechnology and medicine.

    See the full article here .

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    ETH Zurich campus
    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 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 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(US), Stanford University(US) and University of Cambridge(UK). In 2015, ETH Zürich also ranked 6th in the world in Natural Sciences, and in 2016 ranked 1st in the world for Earth & Marine Sciences for the second consecutive year.

    In 2016, Times Higher Education World University Rankings ranked ETH Zürich 9th overall in the world and 8th in the world in the field of Engineering & Technology, just behind the Massachusetts Institute of Technology(US), Stanford University(US), California Institute of Technology(US), Princeton University(US), University of Cambridge(UK), Imperial College London(UK) and 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 ExcellenceRanking 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 2:36 pm on July 24, 2021 Permalink | Reply
    Tags: "DeepMind and EMBL release the most complete database of predicted 3D structures of human proteins", , , , European Molecular Biology Laboratory, Protein Studies   

    From European Molecular Biology Laboratory : “DeepMind and EMBL release the most complete database of predicted 3D structures of human proteins” 

    EMBL European Molecular Biology Laboratory bloc

    From European Molecular Biology Laboratory

    22 Jul 2021

    1
    Protein structures representing the data obtained via AlphaFold. Source image: AlphaFold. Design credit: Karen Arnott/EMBL-EBI.

    DeepMind today announced its partnership with the European Molecular Biology Laboratory (EMBL), Europe’s flagship laboratory for the life sciences, to make the most complete and accurate database yet of predicted protein structure models for the human proteome. This will cover all ~20,000 proteins expressed by the human genome, and the data will be freely and openly available to the scientific community. The database and artificial intelligence system provide structural biologists with powerful new tools for examining a protein’s three-dimensional structure, and offer a treasure trove of data that could unlock future advances and herald a new era for AI-enabled biology.

    AlphaFold’s recognition in December 2020 by the organisers of the Critical Assessment of protein Structure Prediction (CASP) benchmark as a solution to the 50-year-old grand challenge of protein structure prediction was a stunning breakthrough for the field. The AlphaFold Protein Structure Database builds on this innovation and the discoveries of generations of scientists, from the early pioneers of protein imaging and crystallography, to the thousands of prediction specialists and structural biologists who’ve spent years experimenting with proteins since. The database dramatically expands the accumulated knowledge of protein structures, more than doubling the number of high-accuracy human protein structures available to researchers. Advancing the understanding of these building blocks of life, which underpin every biological process in every living thing, will help enable researchers across a huge variety of fields to accelerate their work.

    Last week, the methodology behind the latest highly innovative version of AlphaFold, the sophisticated AI system announced last December that powers these structure predictions, and its open source code were published in Nature. Today’s announcement coincides with a second Nature paper that provides the fullest picture of proteins that make up the human proteome, and the release of 20 additional organisms that are important for biological research.

    “Our goal at DeepMind has always been to build AI and then use it as a tool to help accelerate the pace of scientific discovery itself, thereby advancing our understanding of the world around us,” said DeepMind Founder and CEO Demis Hassabis, PhD. “We used AlphaFold to generate the most complete and accurate picture of the human proteome. We believe this represents the most significant contribution AI has made to advancing scientific knowledge to date, and is a great illustration of the sorts of benefits AI can bring to society.”

    AlphaFold is already helping scientists to accelerate discovery

    The ability to predict a protein’s shape computationally from its amino acid sequence – rather than determining it experimentally through years of painstaking, laborious and often costly techniques – is already helping scientists to achieve in months what previously took years.

    “The AlphaFold database is a perfect example of the virtuous circle of open science,” said EMBL Director General Edith Heard. “AlphaFold was trained using data from public resources built by the scientific community so it makes sense for its predictions to be public. Sharing AlphaFold predictions openly and freely will empower researchers everywhere to gain new insights and drive discovery. I believe that AlphaFold is truly a revolution for the life sciences, just as genomics was several decades ago and I am very proud that EMBL has been able to help DeepMind in enabling open access to this remarkable resource.”

    AlphaFold is already being used by partners such as the Drugs for Neglected Diseases Initiative (DNDi), which has advanced their research into life-saving cures for diseases that disproportionately affect the poorer parts of the world, and the Centre for Enzyme Innovation (CEI) is using AlphaFold to help engineer faster enzymes for recycling some of our most polluting single-use plastics. For those scientists who rely on experimental protein structure determination, AlphaFold’s predictions have helped accelerate their research. For example, a team at the University of Colorado Boulder is finding promise in using AlphaFold predictions to study antibiotic resistance, while a group at the University of California-San Francisco (US) has used them to increase their understanding of SARS-CoV-2 biology.

    The AlphaFold Protein Structure Database

    The AlphaFold Protein Structure Database builds on many contributions from the international scientific community, as well as AlphaFold’s sophisticated algorithmic innovations and EMBL-EBI’s decades of experience in sharing the world’s biological data. DeepMind and EMBL’s European Bioinformatics Institute (EMBL-EBI) are providing access to AlphaFold’s predictions so that others can use the system as a tool to enable and accelerate research and open up completely new avenues of scientific discovery.

    “This will be one of the most important datasets since the mapping of the Human Genome,” said EMBL Deputy Director General, and EMBL-EBI Director Ewan Birney. “Making AlphaFold predictions accessible to the international scientific community opens up so many new research avenues, from neglected diseases to new enzymes for biotechnology and everything in between. This is a great new scientific tool, which complements existing technologies, and will allow us to push the boundaries of our understanding of the world.”

    In addition to the human proteome, the database launches with ~350,000 structures including 20 biologically-significant organisms such as E.coli, fruit fly, mouse, zebrafish, malaria parasite and tuberculosis bacteria. Research into these organisms has been the subject of countless research papers and numerous major breakthroughs. These structures will enable researchers across a huge variety of fields – from neuroscience to medicine – to accelerate their work.

    The future of AlphaFold

    The database and system will be periodically updated as we continue to invest in future improvements to AlphaFold, and over the coming months we plan to vastly expand the coverage to almost every sequenced protein known to science – over 100 million structures covering most of the UniProt reference database.

    To learn more, please see the Nature papers describing our full method and the human proteome, and read the Authors’ Notes. See the open-source code to AlphaFold if you want to view the workings of the system, and Colab notebook to run individual sequences. To explore the structures, visit EMBL-EBI’s searchable database that is open and free to all.

    See the full article here .

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    EMBL European Molecular Biology Laboratory campus

    European Molecular Biology Laboratory (EU) is Europe’s flagship laboratory for the life sciences, with more than 80 independent groups covering the spectrum of molecular biology. EMBL is international, innovative and interdisciplinary – its 1800 employees, from many nations, operate across five sites: the main laboratory in Heidelberg, and outstations in Grenoble; Hamburg; Hinxton, near Cambridge (the European Bioinformatics Institute (EU)), and Monterotondo, near Rome. Founded in 1974, EMBL is an inter-governmental organisation funded by public research monies from its member states. The cornerstones of EMBL’s mission are: to perform basic research in molecular biology; to train scientists, students and visitors at all levels; to offer vital services to scientists in the member states; to develop new instruments and methods in the life sciences and actively engage in technology transfer activities, and to integrate European life science research. Around 200 students are enrolled in EMBL’s International PhD programme. Additionally, the Laboratory offers a platform for dialogue with the general public through various science communication activities such as lecture series, visitor programmes and the dissemination of scientific achievements.

     
  • richardmitnick 1:46 pm on July 4, 2021 Permalink | Reply
    Tags: "New insights into the assembly of photosynthetic membranes", , Protein Studies, The team used cryo-electron microscopy to determine the three-dimensional structure of VIPP1 at high resolution., Using a related technique known as cryo-electron tomography the scientists were also able to image VIPP1 membranes in their natural state in algal cells., VIPP1: "vesicle-inducing protein in plastids"   

    From Ludwig Maximilian University of Munich [Ludwig-Maximilians-Universität München] (DE) : “New insights into the assembly of photosynthetic membranes” 

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

    13
    VIPP1 play a central role in the assembly of thylakoid membranes, which are indispensable for plant growth. | © Ben Engel/Helmholtz Centre Munich [Helmholtz Zentrum München] (DE)

    Plants, algae and cyanobacteria convert carbon dioxide and water into biomass and oxygen with the aid of photosynthesis. This process forms the basis of most forms of life on Earth. Global warming is exposing photosynthetic organisms to increasing levels of stress. This reduces growth rates, and in the longer term presents a threat to food supplies for human populations. An international project, in which LMU biologist Jörg Nickelsen and his research group played a significant role, has now determined the three-dimensional structure of a protein involved in the formation and maintenance of the membranes in which photosynthesis takes place. The insights provided by the study will facilitate biotechnological efforts to boost the ability of plants to cope with environmental stresses.

    The initial steps in photosynthesis take place within the ‘thylakoid’ membranes, which harbor pigment-protein complexes that absorb energy from sunlight. It has been known for decades that, in virtually all photosynthetic organisms, a protein called VIPP1 (which stands for ‘vesicle-inducing protein in plastids’) is indispensable for the assembly of thylakoids. “However, how VIPP1 actually performs this essential function has remained enigmatic up to now,” says Steffen Heinz, a postdoc in Nickelsen’s group and joint first author of the new publication. Thanks to the new study, which was led by the Helmholtz Zentrum München, researchers now know a great deal more.

    Assembly of photosynthetic membranes

    The team used cryo-electron microscopy to determine the three-dimensional structure of VIPP1 at high resolution. Analysis of this structure, in combination with functional investigation of the protein’s mode of action, demonstrated how small numbers of VIPP1 molecules form short strands, which are interwoven to form a basket-like structure. This then serves as a scaffold for the assembly of the thylakoid membrane, and determines its curvature. Using a related technique known as cryo-electron tomography the scientists were also able to image VIPP1 membranes in their natural state in algal cells. By introducing site-specific mutations into VIPP1, they showed that the interaction of VIPP1 with thylakoid membranes is vital for the maintenance of their structural integrity under high levels of light stress. This finding demonstrates that the protein not only mediates the assembly of thylakoids, but also plays a role in enabling them to adapt to environmental fluctuations.

    The results provide the basis for a better understanding of the mechanisms that underlie the formation and stabilization of thylakoids. They will also open up new opportunities to enhance the ability of green plants to withstand extreme environmental stresses.

    Science paper:
    Cell

    See the full article here.

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

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

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

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

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

    Faculties

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

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

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

    Research centres

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

    Some of the research centres which have been established include:

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

     
  • richardmitnick 10:41 am on June 25, 2021 Permalink | Reply
    Tags: "Putting Functional Proteins in Their Place", , , , Protein Studies, Scientists have organized proteins—nature’s most versatile building blocks—in desired 2-D and 3-D ordered arrays while maintaining their structural stability and biological activity.   

    From DOE’s Brookhaven National Laboratory (US) : “Putting Functional Proteins in Their Place” 

    From DOE’s Brookhaven National Laboratory (US)

    June 25, 2021
    Ariana Manglaviti
    amanglaviti@bnl.gov
    (631) 344-2347

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

    Using DNA-based assembly, scientists developed a method for creating designed and biologically active 2-D and 3-D protein arrays, which show promise for applications in structural biology, biomaterials, nanomedicine, and biocatalysis.

    1
    (Left to right) Honghu Zhang, Shih-Ting (Christine) Wang, and Oleg Gang at the Center for Functional Nanomaterials Electron Microscopy Facility, where they imaged designed protein arrays.

    Scientists have organized proteins—nature’s most versatile building blocks—in desired 2-D and 3-D ordered arrays while maintaining their structural stability and biological activity. They built these designer functional protein arrays by using DNA as a programmable construction material. The team—representing the U.S. Department of Energy’s (DOE) Brookhaven National Laboratory, Columbia University (US), DOE’s Lawrence Berkeley National Laboratory (US), and City University of New York (CUNY) (US)—described their approach in the June 17 issue of Nature Communications.

    “For decades, scientists have dreamed about rationally assembling proteins into specific organizations with preserved protein function,” said corresponding author Oleg Gang, leader of the Center for Functional Nanomaterials (CFN) [below] Soft and Bio Nanomaterials Group at Brookhaven Lab and a professor of chemical engineering and of applied physics and materials science at Columbia Engineering. “Our DNA-based platform has enormous potential not only for structural biology but also for various bioengineering, biomedical, and bionanomaterial applications.”

    The primary motivation of this work was to establish a rational way to organize proteins into designed 2-D and 3-D architectures while preserving their function. The importance of organizing proteins is well known in the field of protein crystallography. For this technique, proteins are taken from their native solution-based environments and condensed to form an orderly arrangement of atoms (crystalline structure), which can then be structurally characterized. However, because of their flexibility and aggregation properties, many proteins are difficult to crystallize, requiring trial and error. The structure and function of proteins may change during the crystallization process, and they may become nonfunctional when crystallized by traditional methods. This new approach opens many possibilities for creating engineered biomaterials, beyond the goals of structural biology.

    “The ability to make biologically active protein lattices is relevant to many applications, including tissue engineering, multi-enzyme systems for biochemical reactions, large-scale profiling of proteins for precision medicine, and synthetic biology,” added first author Shih-Ting (Christine) Wang, a postdoc in the CFN Soft and Bio Nanomaterials Group.

    Though DNA is best known for its role in storing our genetic information, the very same base-pairing processes used for this storage can be leveraged to construct desired nanostructures. A single strand of DNA is made of subunits, or nucleotides, of which there are four kinds (known by the letters A, C, T, and G). Each nucleotide has a complementary nucleotide it attracts and binds to (A with T and C with G) when two DNA strands are near each other. Using this concept in the technique of DNA origami, scientists mix multiple short strands of synthetic DNA with a single long strand of DNA. The short strands bind to and “fold” the long strand into a particular shape based on the sequence of bases, which scientists can specify.

    In this case, the scientists created octahedral-shaped DNA origami. Inside these cage-like frameworks, they placed DNA strands with a particular “color,” or coding sequence, at targeted locations (center and off center). To the surface of proteins—specifically, ferritin, which stores and releases iron, and apoferritin, its iron-free counterpart—they attached complementary DNA strands. By mixing the DNA cages and conjugated proteins and heating up the mixture to promote the reaction, the proteins went to the internal designated locations. They also created empty cages, without any protein inside.

    To connect these nanoscale building blocks, or protein “voxels” (DNA cages with encapsulated proteins), in desired 2-D and 3-D arrays, second author and Columbia PhD student Brian Minevich designed different colors for the external bonds of the voxels. With this color scheme, the voxels would recognize each other in programmable, controllable ways leading to the formation of specifically prescribed types of protein lattices. To demonstrate the versatility of the platform, the team constructed single- and double-layered 2D arrays, as well as 3D arrays.

    “By arranging the colors in a particular way, we can program the formation of different lattices,” explained Gang. “We have full control to design and build the protein lattice architectures we want.”

    2
    An illustration showing the approach for assembling biologically functional proteins into ordered 2-D and 3-D arrays through programmable octahedral-shaped DNA frameworks. These frameworks can host and control the placement of the proteins internally—for example, at the center (1) or off-center (2)—and be encoded with specific sequences externally (color coding scheme) to create desired 2-D and 3-D lattices. For example, red only connects to red, blue to blue, and so on. The team demonstrated the preserved biological activity of ferritin lattices by adding a compound (ascorbate) that induced the release of iron irons forming the ferritin core.

    To confirm that the proteins had been encapsulated inside the cages and the lattices had been constructed as designed, the team turned to various electron- and x-ray-based imaging and scattering techniques. These techniques included electron microscopy (EM) imaging at the CFN; small-angle x-ray scattering at the National Synchrotron Light Source II (NSLS-II) [below] Complex Materials Scattering (CMS) and Life Science X-ray Scattering (LiX) beamlines at Brookhaven; and cryogenic-EM imaging at the Molecular Foundry (MF) of Lawrence Berkeley and the CUNY Advanced Science Research Center. The CFN, NSLS-II, and MF are all DOE Office of Science User Facilities; CFN and MF are two of five DOE Nanoscale Science Research Centers.

    3
    CUNY Advanced Science Research Center. Credit: CUNY.

    “The science was enabled by advanced synthesis and characterization capabilities at three user facilities within the national lab system and one university-based facility,” said Gang. “Without these facilities and the expertise of scientists from each of them, this study wouldn’t have been possible.”

    4
    To visualize the assembled arrays in 3-D, the team applied nanoscale tomography based on the images obtained by cryo-electron microscopy. The top figure is a selected lattice area and the bottom a representative view. The color bars indicate different heights of the lattice (in angstroms).

    Following these assembly studies, they investigated the biological activity of ferritin. By adding a reducing reagent to the ferritin lattice, they induced the release of iron ions from the center of the ferritin proteins.

    “By monitoring the evolution of SAXS patterns during iron release, we could quantify how much iron was released and how quickly it was released, as well as confirm that the integrity of the lattice was maintained during this protein operation,” said Minevich. “According to our TEM studies, the proteins remained inside the frames.”

    “We showed that the proteins can perform the same function as they do in a biological environment while keeping the spatial organization we created,” explained Wang.

    Next, the team will apply their DNA-based platform to other types of proteins, with the goal of building more complex, operational protein systems.

    “This research represents an important step in bringing together different components from real biological machinery and organizing them into desired 2-D and 3-D architectures to create engineered and bioactive materials,” said Gang. “It’s exciting because we see the rational path for fabricating desired functional bio-nano systems never-before produced by nature.”

    This work was supported by the DOE Office of Science, a Laboratory Directed Research and Development Program grant, and the National Science Foundation (US). The LiX beamline is part of the Life Science Biomedical Technology Research resource, cofunded by the National Institute of General Medical Sciences and the DOE Office of Biological and Environmental Research, with additional support from the National Institutes of Health. Brookhaven’s Biology Department supplied the proteins.

    See the full article here .


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    One of ten national laboratories overseen and primarily funded by the DOE(US) Office of Science, DOE’s Brookhaven National Laboratory (US) conducts research in the physical, biomedical, and environmental sciences, as well as in energy technologies and national security. Brookhaven Lab also builds and operates major scientific facilities available to university, industry and government researchers. The Laboratory’s almost 3,000 scientists, engineers, and support staff are joined each year by more than 5,000 visiting researchers from around the world. Brookhaven is operated and managed for DOE’s Office of Science by Brookhaven Science Associates, a limited-liability company founded by Stony Brook University(US), the largest academic user of Laboratory facilities, and Battelle(US), a nonprofit, applied science and technology organization.

    Research at BNL specializes in nuclear and high energy physics, energy science and technology, environmental and bioscience, nanoscience and national security. The 5,300 acre campus contains several large research facilities, including the Relativistic Heavy Ion Collider [below] and National Synchrotron Light Source II [below]. Seven Nobel prizes have been awarded for work conducted at Brookhaven lab.

    BNL is staffed by approximately 2,750 scientists, engineers, technicians, and support personnel, and hosts 4,000 guest investigators every year. The laboratory has its own police station, fire department, and ZIP code (11973). In total, the lab spans a 5,265-acre (21 km^2) area that is mostly coterminous with the hamlet of Upton, New York. BNL is served by a rail spur operated as-needed by the New York and Atlantic Railway. Co-located with the laboratory is the Upton, New York, forecast office of the National Weather Service.

    Major programs

    Although originally conceived as a nuclear research facility, Brookhaven Lab’s mission has greatly expanded. Its foci are now:

    Nuclear and high-energy physics
    Physics and chemistry of materials
    Environmental and climate research
    Nanomaterials
    Energy research
    Nonproliferation
    Structural biology
    Accelerator physics

    Operation

    Brookhaven National Lab was originally owned by the Atomic Energy Commission(US) and is now owned by that agency’s successor, the United States Department of Energy (DOE). DOE subcontracts the research and operation to universities and research organizations. It is currently operated by Brookhaven Science Associates LLC, which is an equal partnership of Stony Brook University(US) and Battelle Memorial Institute(US). From 1947 to 1998, it was operated by Associated Universities, Inc. (AUI) (US), but AUI lost its contract in the wake of two incidents: a 1994 fire at the facility’s high-beam flux reactor that exposed several workers to radiation and reports in 1997 of a tritium leak into the groundwater of the Long Island Central Pine Barrens on which the facility sits.

    Foundations

    Following World War II, the US Atomic Energy Commission was created to support government-sponsored peacetime research on atomic energy. The effort to build a nuclear reactor in the American northeast was fostered largely by physicists Isidor Isaac Rabi and Norman Foster Ramsey Jr., who during the war witnessed many of their colleagues at Columbia University leave for new remote research sites following the departure of the Manhattan Project from its campus. Their effort to house this reactor near New York City was rivalled by a similar effort at the Massachusetts Institute of Technology (US) to have a facility near Boston, Massachusettes(US). Involvement was quickly solicited from representatives of northeastern universities to the south and west of New York City such that this city would be at their geographic center. In March 1946 a nonprofit corporation was established that consisted of representatives from nine major research universities — Columbia University(US), Cornell University(US), Harvard University(US), Johns Hopkins University(US), Massachusetts Institute of Technology(US), Princeton University(US), University of Pennsylvania(US), University of Rochester(US), and Yale University(US).

    Out of 17 considered sites in the Boston-Washington corridor, Camp Upton on Long Island was eventually chosen as the most suitable in consideration of space, transportation, and availability. The camp had been a training center from the US Army during both World War I and World War II. After the latter war, Camp Upton was deemed no longer necessary and became available for reuse. A plan was conceived to convert the military camp into a research facility.

    On March 21, 1947, the Camp Upton site was officially transferred from the U.S. War Department to the new U.S. Atomic Energy Commission (AEC), predecessor to the U.S. Department of Energy (DOE).

    Research and facilities

    Reactor history

    In 1947 construction began on the first nuclear reactor at Brookhaven, the Brookhaven Graphite Research Reactor. This reactor, which opened in 1950, was the first reactor to be constructed in the United States after World War II. The High Flux Beam Reactor operated from 1965 to 1999. In 1959 Brookhaven built the first US reactor specifically tailored to medical research, the Brookhaven Medical Research Reactor, which operated until 2000.

    Accelerator history

    In 1952 Brookhaven began using its first particle accelerator, the Cosmotron. At the time the Cosmotron was the world’s highest energy accelerator, being the first to impart more than 1 GeV of energy to a particle.


    The Cosmotron was retired in 1966, after it was superseded in 1960 by the new Alternating Gradient Synchrotron (AGS).

    The AGS was used in research that resulted in 3 Nobel prizes, including the discovery of the muon neutrino, the charm quark, and CP violation.

    In 1970 in BNL started the ISABELLE project to develop and build two proton intersecting storage rings.

    The groundbreaking for the project was in October 1978. In 1981, with the tunnel for the accelerator already excavated, problems with the superconducting magnets needed for the ISABELLE accelerator brought the project to a halt, and the project was eventually cancelled in 1983.

    The National Synchrotron Light Source (US) operated from 1982 to 2014 and was involved with two Nobel Prize-winning discoveries. It has since been replaced by the National Synchrotron Light Source II (US) [below].

    After ISABELLE’S cancellation, physicist at BNL proposed that the excavated tunnel and parts of the magnet assembly be used in another accelerator. In 1984 the first proposal for the accelerator now known as the Relativistic Heavy Ion Collider (RHIC)[below] was put forward. The construction got funded in 1991 and RHIC has been operational since 2000. One of the world’s only two operating heavy-ion colliders, RHIC is as of 2010 the second-highest-energy collider after the Large Hadron Collider(CH). RHIC is housed in a tunnel 2.4 miles (3.9 km) long and is visible from space.

    On January 9, 2020, It was announced by Paul Dabbar, undersecretary of the US Department of Energy Office of Science, that the BNL eRHIC design has been selected over the conceptual design put forward by DOE’s Thomas Jefferson National Accelerator Facility [Jlab] (US) as the future Electron–ion collider (EIC) in the United States.

    In addition to the site selection, it was announced that the BNL EIC had acquired CD-0 (mission need) from the Department of Energy. BNL’s eRHIC design proposes upgrading the existing Relativistic Heavy Ion Collider, which collides beams light to heavy ions including polarized protons, with a polarized electron facility, to be housed in the same tunnel.

    Other discoveries

    In 1958, Brookhaven scientists created one of the world’s first video games, Tennis for Two. In 1968 Brookhaven scientists patented Maglev, a transportation technology that utilizes magnetic levitation.

    Major facilities

    Relativistic Heavy Ion Collider (RHIC), which was designed to research quark–gluon plasma and the sources of proton spin. Until 2009 it was the world’s most powerful heavy ion collider. It is the only collider of spin-polarized protons.
    Center for Functional Nanomaterials (CFN), used for the study of nanoscale materials.
    BNL National Synchrotron Light Source II(US), Brookhaven’s newest user facility, opened in 2015 to replace the National Synchrotron Light Source (NSLS), which had operated for 30 years.[19] NSLS was involved in the work that won the 2003 and 2009 Nobel Prize in Chemistry.
    Alternating Gradient Synchrotron, a particle accelerator that was used in three of the lab’s Nobel prizes.
    Accelerator Test Facility, generates, accelerates and monitors particle beams.
    Tandem Van de Graaff, once the world’s largest electrostatic accelerator.
    Computational Science resources, including access to a massively parallel Blue Gene series supercomputer that is among the fastest in the world for scientific research, run jointly by Brookhaven National Laboratory and Stony Brook University.
    Interdisciplinary Science Building, with unique laboratories for studying high-temperature superconductors and other materials important for addressing energy challenges.
    NASA Space Radiation Laboratory, where scientists use beams of ions to simulate cosmic rays and assess the risks of space radiation to human space travelers and equipment.

    Off-site contributions

    It is a contributing partner to ATLAS experiment, one of the four detectors located at the Large Hadron Collider (LHC).


    It is currently operating at CERN near Geneva, Switzerland.

    Brookhaven was also responsible for the design of the SNS accumulator ring in partnership with Spallation Neutron Source at DOE’s Oak Ridge National Laboratory (US), Tennessee.

    Brookhaven plays a role in a range of neutrino research projects around the world, including the Daya Bay Neutrino Experiment (CN) nuclear power plant, approximately 52 kilometers northeast of Hong Kong and 45 kilometers east of Shenzhen, China.


     
  • richardmitnick 4:18 pm on June 16, 2021 Permalink | Reply
    Tags: "UChicago scientists experiment with materials that can 'remember' ", , , Material memory is called "hysteresis"., Protein strands-called actin filaments-act as bones within a cell., Protein Studies,   

    From University of Chicago (US): Women in STEM-Danielle Scheff; Margaret Gardel “UChicago scientists experiment with materials that can ‘remember’ “ 

    U Chicago bloc

    From University of Chicago (US)

    Jun 15, 2021
    Briana Carroll

    New research identifies properties that allow proteins to strengthen under pressure.

    1
    A research team at the University of Chicago is exploring how cells remember and respond to environmental pressure. In a simulated actin network, actin filaments start out randomly oriented (left) but align after pressure is applied (right). Image courtesy Scheff et al.

    A new rubber band stretches, but then snaps back into its original shape and size. Stretched again, it does the same. But what if the rubber band was made of a material that remembered how it had been stretched? Just as our bones strengthen in response to impact, medical implants or prosthetics composed of such a material could adjust to environmental pressures such as those encountered in strenuous exercise.

    A research team at the University of Chicago is now exploring the properties of a material found in cells which allows cells to remember and respond to environmental pressure. In a paper published on May 14, 2021 in Soft Matter, they teased out secrets for how it works—and how it could someday form the basis for making useful materials.

    Protein strands-called actin filaments-act as bones within a cell. A separate family of proteins called cross-linkers hold these bones together into a cellular skeleton. The study found that an optimal concentration of cross-linkers, which bind and unbind to permit the actin to rearrange under pressure, allow this skeletal scaffolding to remember and respond to past experience. This material memory is called hysteresis.

    “Our findings show that the properties of actin networks can be changed by how filaments are aligned,” said Danielle Scheff, a graduate student in the Department of Physics who conducted the research in the lab of Margaret Gardel, Horace B. Horton Professor of Physics and Molecular Engineering, the James Franck Institute, and the Institute of Biophysical Dynamics. “The material adapts to stress by becoming stronger.”

    To understand how the composition of this cellular scaffolding determines its hysteresis, Scheff mixed up a buffer containing actin, isolated from rabbit muscle, and cross-linkers, isolated from bacteria. She then applied pressure to the solution, using an instrument called a rheometer. If stretched in one direction, the cross-linkers allowed the actin filaments to rearrange, strengthening against subsequent pressure in the same direction.

    To see how hysteresis depended on the solution’s consistency, she mixed different concentrations of cross-linkers into the buffer.

    Surprisingly, these experiments indicated that hysteresis was most pronounced at an optimal cross-linker concentration; solutions exhibited increased hysteresis as she added more cross-linkers, but past this optimal point, the effect again became less pronounced.

    “I remember being in lab the first time I plotted that relationship and thinking something must be wrong, running down to the rheometer to do more experiments to double-check,” Scheff said.

    To better understand the structural changes, Steven Redford, a graduate student in Biophysical Sciences in the labs of Gardel and Aaron Dinner, Professor of Chemistry, the James Franck Institute, and the Institute for Biophysical Dynamics, created a computational simulation of the protein mixture Scheff produced in the lab. In this computational rendition, Redford wielded a more systematic control over variables than possible in the lab. By varying the stability of bonds between actin and its cross-linkers, Redford showed that unbinding allows actin filaments to rearrange under pressure, aligning with the applied strain, while binding stabilizes the new alignment, providing the tissue a ‘memory’ of this pressure. Together, these simulations demonstrated that impermanent connections between the proteins enable hysteresis.

    “People think of cells as very complicated, with a lot of chemical feedback. But this is a stripped-down system where you can really understand what is possible,” said Gardel.

    The team expects these findings, established in a material isolated from biological systems, to generalize to other materials. For example, using impermanent cross-linkers to bind polymer filaments could allow them to rearrange as actin filaments do, and thus produce synthetic materials capable of hysteresis.

    “If you understand how natural materials adapt, you can carry it over to synthetic materials,” said Dinner.

    See the full article here .

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

    Please help promote STEM in your local schools.

    Stem Education Coalition

    U Chicago Campus

    An intellectual destination

    One of the world’s premier academic and research institutions, the University of Chicago (US) has driven new ways of thinking since our 1890 founding. Today, UChicago is an intellectual destination that draws inspired scholars to our Hyde Park and international campuses, keeping UChicago at the nexus of ideas that challenge and change the world.

    The University of Chicago is an urban research university that has driven new ways of thinking since 1890. Our commitment to free and open inquiry draws inspired scholars to our global campuses, where ideas are born that challenge and change the world.

    We empower individuals to challenge conventional thinking in pursuit of original ideas. Students in the College develop critical, analytic, and writing skills in our rigorous, interdisciplinary core curriculum. Through graduate programs, students test their ideas with UChicago scholars, and become the next generation of leaders in academia, industry, nonprofits, and government.

    UChicago research has led to such breakthroughs as discovering the link between cancer and genetics, establishing revolutionary theories of economics, and developing tools to produce reliably excellent urban schooling. We generate new insights for the benefit of present and future generations with our national and affiliated laboratories: DOE’s Argonne National Laboratory (US), DOE’s Fermi National Accelerator Laboratory (US), and the Marine Biological Laboratory in Woods Hole, Massachusetts.

    The University of Chicago is enriched by the city we call home. In partnership with our neighbors, we invest in Chicago’s mid-South Side across such areas as health, education, economic growth, and the arts. Together with our medical center, we are the largest private employer on the South Side.

    In all we do, we are driven to dig deeper, push further, and ask bigger questions—and to leverage our knowledge to enrich all human life. Our diverse and creative students and alumni drive innovation, lead international conversations, and make masterpieces. Alumni and faculty, lecturers and postdocs go on to become Nobel laureates, CEOs, university presidents, attorneys general, literary giants, and astronauts. The University of Chicago is a private research university in Chicago, Illinois. Founded in 1890, its main campus is located in Chicago’s Hyde Park neighborhood. It enrolled 16,445 students in Fall 2019, including 6,286 undergraduates and 10,159 graduate students. The University of Chicago is ranked among the top universities in the world by major education publications, and it is among the most selective in the United States.

    The university is composed of one undergraduate college and five graduate research divisions, which contain all of the university’s graduate programs and interdisciplinary committees. Chicago has eight professional schools: the Law School, the Booth School of Business, the Pritzker School of Medicine, the School of Social Service Administration, the Harris School of Public Policy, the Divinity School, the Graham School of Continuing Liberal and Professional Studies, and the Pritzker School of Molecular Engineering. The university has additional campuses and centers in London, Paris, Beijing, Delhi, and Hong Kong, as well as in downtown Chicago.

    University of Chicago scholars have played a major role in the development of many academic disciplines, including economics, law, literary criticism, mathematics, religion, sociology, and the behavioralism school of political science, establishing the Chicago schools in various fields. Chicago’s Metallurgical Laboratory produced the world’s first man-made, self-sustaining nuclear reaction in Chicago Pile-1 beneath the viewing stands of the university’s Stagg Field. Advances in chemistry led to the “radiocarbon revolution” in the carbon-14 dating of ancient life and objects. The university research efforts include administration of DOE’s Fermi National Accelerator Laboratory(US) and DOE’s Argonne National Laboratory(US), as well as the U Chicago Marine Biological Laboratory in Woods Hole, Massachusetts (MBL)(US). The university is also home to the University of Chicago Press, the largest university press in the United States. The Barack Obama Presidential Center is expected to be housed at the university and will include both the Obama presidential library and offices of the Obama Foundation.

    The University of Chicago’s students, faculty, and staff have included 100 Nobel laureates as of 2020, giving it the fourth-most affiliated Nobel laureates of any university in the world. The university’s faculty members and alumni also include 10 Fields Medalists, 4 Turing Award winners, 52 MacArthur Fellows, 26 Marshall Scholars, 27 Pulitzer Prize winners, 20 National Humanities Medalists, 29 living billionaire graduates, and have won eight Olympic medals.

    One of the world’s premier academic and research institutions, the University of Chicago has driven new ways of thinking since our 1890 founding. Today, UChicago is an intellectual destination that draws inspired scholars to our Hyde Park and international campuses, keeping UChicago at the nexus of ideas that challenge and change the world.

    The University of Chicago is an urban research university that has driven new ways of thinking since 1890. Our commitment to free and open inquiry draws inspired scholars to our global campuses, where ideas are born that challenge and change the world.

    We empower individuals to challenge conventional thinking in pursuit of original ideas. Students in the College develop critical, analytic, and writing skills in our rigorous, interdisciplinary core curriculum. Through graduate programs, students test their ideas with UChicago scholars, and become the next generation of leaders in academia, industry, nonprofits, and government.

    UChicago research has led to such breakthroughs as discovering the link between cancer and genetics; establishing revolutionary theories of economics; and developing tools to produce reliably excellent urban schooling. We generate new insights for the benefit of present and future generations.

    The University of Chicago is enriched by the city we call home. In partnership with our neighbors, we invest in Chicago’s mid-South Side across such areas as health, education, economic growth, and the arts. Together with our medical center, we are the largest private employer on the South Side.

    In all we do, we are driven to dig deeper, push further, and ask bigger questions—and to leverage our knowledge to enrich all human life. Our diverse and creative students and alumni drive innovation, lead international conversations, and make masterpieces. Alumni and faculty, lecturers and postdocs go on to become Nobel laureates, CEOs, university presidents, attorneys general, literary giants, and astronauts.

     
  • richardmitnick 4:36 pm on March 31, 2021 Permalink | Reply
    Tags: "Mystery of photosynthetic algae evolution finally solved", , , , , , From University of New South Wales (AU), , Protein Studies   

    From University of New South Wales (AU) : “Mystery of photosynthetic algae evolution finally solved” 

    U NSW bloc

    From University of New South Wales (AU)

    30 Mar 2021
    Lachlan Gilbert

    Scientists have identified the protein that was the missing evolutionary link between two ancient algae species – red algae and cryptophytes.

    1
    A computer model of the novel protein structure in the cryptophyte’s antenna that traps sunlight energy. Credit: UNSW.

    An evolutionary mystery that had eluded molecular biologists for decades may never have been solved if it weren’t for the COVID-19 pandemic.

    “Being stuck at home was a blessing in disguise, as there were no experiments that could be done. We just had our computers and lots of time,” says Professor Paul Curmi, a structural biologist and molecular biophysicist with UNSW Sydney.

    Prof. Curmi is referring to research published this month in Nature Communications that details the painstaking unravelling and reconstruction of a key protein in a single-celled, photosynthetic organism called a cryptophyte, a type of algae that evolved over a billion years ago.

    Up until now, how cryptophytes acquired the proteins used to capture and funnel sunlight to be used by the cell had molecular biologists scratching their heads. They already knew that the protein was part of a sort of antenna that the organism used to convert sunlight into energy. They also knew that the cryptophyte had inherited some antenna components from its photosynthetic ancestors – red algae, and before that cyanobacteria, one of the earliest lifeforms on earth that are responsible for stromatolites [Trends in Microbiology].

    An image of Cyanobacteria, Tolypothrix.

    2
    Stromatolites at Shark Bay, Western Australia. Credit: Brendan Burns/ UNSW Sydney.

    But how the protein structures fit together in the cryptophyte’s own, novel antenna structure remained a mystery – until Prof. Curmi, PhD student Harry Rathbone and colleagues from University of Queensland (AU) and University of British Columbia (CA) pored over the electron microscope images of the antenna protein from a progenitor red algal organism made public by Chinese researchers in March 2020 [Nature].

    Unravelling the mystery meant the team could finally tell the story of how this protein had enabled these ancient single-celled organisms to thrive in the most inhospitable conditions – metres under water with very little direct sunlight to convert into energy.

    3
    A cryogenic electron microscopy map of a cryptophyte-like protein found in red algae. The red indicates the elusive protein that was re-used by cryptophytes in their own antenna. Credit: UNSW.

    Prof. Curmi says the major implications of the work are for evolutionary biology.

    “We provide a direct link between two very different antenna systems and open the door for discovering exactly how one system evolved into a different system – where both appear to be very efficient in capturing light,” he says.

    “Photosynthetic algae have many different antenna systems which have the property of being able to capture every available light photon and transferring it to a photosystem protein that converts the light energy to chemical energy.”

    By working to understand the algal systems, the scientists hope to uncover the fundamental physical principles that underlie the exquisite photon efficiency of these photosynthetic systems. Prof. Curmi says these may one day have application in optical devices including solar energy systems.

    Eating for two

    To better appreciate the significance of the protein discovery, it helps to understand the very strange world of single-celled organisms which take the adage “you are what you eat” to a new level.

    As study lead author, PhD student Harry Rathbone explains, when a single-celled organism swallows another, it can enter a relationship of endosymbiosis, where one organism lives inside the other and the two become inseparable.

    “Often with algae, they’ll go and find some lunch – another alga – and they’ll decide not to digest it. They’ll keep it to do its bidding, essentially,” Mr Rathbone says. “And those new organisms can be swallowed by other organisms in the same way, sort of like a matryoshka doll.”

    In fact, this is likely what happened when about one and a half billion years ago, a cyanobacterium was swallowed by another single-celled organism. The cyanobacteria already had a sophisticated antenna of proteins that trapped every photon of light. But instead of digesting the cyanobacterium, the host organism effectively stripped it for parts – retaining the antenna protein structure that the new organism – the red algae – used for energy.

    And when another organism swallowed a red alga to become the first cryptophyte, it was a similar story. Except this time the antenna was brought to the other side of the membrane of the host organism and completely remoulded into new protein shapes that were equally as efficient at trapping sunlight photons.

    Evolution

    As Prof. Curmi explains, these were the first tiny steps towards the evolution of modern plants and other photosynthetic organisms such as seaweeds.

    “In going from cyanobacteria that are photosynthetic, to everything else on the planet that is photosynthetic, some ancient ancestor gobbled up a cyanobacteria which then became the cell’s chloroplast that converts sunlight into chemical energy.

    “And the deal between the organisms is sort of like, I’ll keep you safe as long as you do photosynthesis and give me energy.”

    One of the collaborators on this project, Dr Beverley Green, Professor Emerita with the University of British Columbia’s Department of Botany says Prof. Curmi was able to make the discovery by approaching the problem from a different angle.

    “Paul’s novel approach was to search for ancestral proteins on the basis of shape rather than similarity in amino acid sequence,” she says.

    “By searching the 3D structures of two red algal multi-protein complexes for segments of protein that folded in the same way as the cryptophyte protein, he was able to find the missing puzzle piece.”

    See the full article here .


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

    Please help promote STEM in your local schools.

    Stem Education Coalition

    UNSW Campus

    Welcome to University of New South Wales (AU), one of Australia’s leading research and teaching universities. At UNSW, we take pride in the broad range and high quality of our teaching programs. Our teaching gains strength and currency from our research activities, strong industry links and our international nature; UNSW has a strong regional and global engagement.

    In developing new ideas and promoting lasting knowledge we are creating an academic environment where outstanding students and scholars from around the world can be inspired to excel in their programs of study and research. Partnerships with both local and global communities allow UNSW to share knowledge, debate and research outcomes. UNSW’s public events include concert performances, open days and public forums on issues such as the environment, healthcare and global politics. We encourage you to explore the UNSW website so you can find out more about what we do.

    Established in 1949, UNSW is a research university, ranked 44th in the world in the 2021 QS World University Rankings and 67th in the world in the 2021 Times Higher Education World University Rankings. UNSW is one of the founding members of the Group of Eight, a coalition of Australian research-intensive universities, and of Universitas 21, a global network of research universities. It has international exchange and research partnerships with over 200 universities around the world.

    The university comprises seven faculties, through which it offers bachelor’s, master’s and doctoral degrees. The main campus is in the Sydney suburb of Kensington, 7 kilometres (4.3 mi) from the Sydney CBD. The creative arts faculty, UNSW Art & Design, is located in Paddington, and subcampuses are located in the Sydney CBD as well as several other suburbs, including Randwick and Coogee. Research stations are located throughout the state of New South Wales.

    The university’s second largest campus, known as UNSW Canberra(AU) at ADFA, is situated in Canberra, in the Australian Capital Territory (ACT). ADFA is the military academy of the Australian Defence Force, and UNSW Camberra is the only national academic institution with a defence focus.

    Foundation

    The origins of the university can be traced to the Sydney Mechanics’ School of Arts established in 1833 and the Sydney Technical College established in 1878. These institutions were established to meet the growing demand for capabilities in new technologies as the New South Wales economy shifted from its pastoral base to industries fueled by the industrial age.

    The idea of founding the university originated from the crisis demands of World War II, during which the nation’s attention was drawn to the critical role that science and technology played in transforming an agricultural society into a modern and industrial one. The post-war Labor government of New South Wales recognised the increasing need to have a university specialized in training high-quality engineers and technology-related professionals in numbers beyond that of the capacity and characteristics of the existing University of Sydney. This led to the proposal to establish the Institute of Technology, submitted by the then-New South Wales Minister for Education Bob Heffron, accepted on 9 July 1946.

    The university, originally named the “New South Wales University of Technology”, gained its statutory status through the enactment of the New South Wales University of Technology Act 1949 (NSW) by the Parliament of New South Wales in Sydney in 1949.

    Early years

    In March 1948, classes commenced with a first intake of 46 students pursuing programs including civil engineering, mechanical engineering, mining engineering, and electrical engineering. At that time, the thesis programs were innovative. Each course embodied a specified and substantial period of practical training in the relevant industry. It was also unprecedented for tertiary institutions at that time to include compulsory instruction in humanities.

    Initially, the university operated from the inner Sydney Technical College city campus in Ultimo as a separate institution from the college. However, in 1951, the Parliament of New South Wales passed the New South Wales University of Technology (Construction) Act 1951 (NSW) to provide funding and allow buildings to be erected at the Kensington site where the university is now located.

    The lower campus area of the Kensington campus was vested in the university in two lots, in December 1952 and June 1954. The upper campus area was vested in the university in November 1959.

    Expansion

    In 1958, the university’s name was changed to the “University of New South Wales” reflecting a transformation from a technology-based institution to a generalist university. In 1960, the faculties of arts and medicine were established, with the faculty of law coming into being in 1971.

    The university’s first director was Arthur Denning (1949–1952), who made important contributions to founding the university. In 1953, he was replaced by Philip Baxter, who continued as vice-chancellor when this position’s title was changed in 1955. Baxter’s dynamic, if authoritarian, management was central to the university’s first 20 years. His visionary, but at times controversial, energies saw the university grow from a handful to 15,000 students by 1968. The new vice-chancellor, Rupert Myers (1969–1981), brought consolidation and an urbane management style to a period of expanding student numbers, demand for change in university style, and challenges of student unrest.

    In 1962 the academic book publishing company University of New South Wales Press was launched. Now an ACNC not-for-profit entity, it has three divisions: NewSouth Publishing (the publishing arm of the company), NewSouth Books (the sales, marketing and distribution part of the company), and the UNSW Bookshop, situated at the Kensington campus.

    The stabilizing techniques of the 1980s managed by the vice-chancellor, Michael Birt (1981–1992), provided a firm base for the energetic corporatism and campus enhancements pursued by the subsequent vice-chancellor, John Niland (1992–2002). The 1990s had the addition of fine arts to the university. The university established colleges in Newcastle (1951) and Wollongong (1961), which eventually became the University of Newcastle and the University of Wollongong in 1965 and 1975, respectively.

    The former St George Institute of Education (part of the short-lived Sydney College of Advanced Education) amalgamated with the university from 1 January 1990, resulting in the formation of a School of Teacher Education at the former SGIE campus at Oatley. A School of Sports and Leisure Studies and a School of Arts and Music Education were also subsequently based at St George. The campus was closed in 1999.

    Recent history

    In 2010 the Lowy Cancer Research Centre, Australia’s first facility to bring together researchers in childhood and adult cancer, costing $127 million, opened.

    In 2003, the university was invited by Singapore’s Economic Development Board to consider opening a campus there. Following a 2004 decision to proceed, the first phase of a planned $200 m campus opened in 2007. Students and staff were sent home and the campus closed after one semester following substantial financial losses.

    In 2008, it collaborated with two other universities in forming The Centre for Social Impact. In 2019, the university moved to a trimester timetable as part of UNSW’s 2025 Strategy. Under the trimester timetable, the study load changed from offering four subjects per 13-week semester, to three subjects per 10-week term. The change to trimesters has been widely criticised by staff and students as a money-making move, with little consideration as to the well-being of students.

    In 2012 UNSW Press celebrated its 50th anniversary and launched the UNSW Bragg Prize for Science Writing. The annual Best Australian Science Writing anthology contains the winning and shortlisted entries among a collection of the year’s best writing from Australian authors, journalists and scientists and is published annually in the NewSouth imprint under a different editorship. The UNSW Press Bragg Student Prize celebrates excellence in science writing by Australian high school students and is supported by the Copyright Agency Cultural Fund and UNSW Science.

    In the 2019 Student Experience Survey, the University of New South Wales recorded the lowest student satisfaction rating out of all Australian universities, with an overall satisfaction rating of 62.9, which was lower than the overall national average of 78.4. UNSW’s low student satisfaction numbers for 2019 was attributed to the university’s switch to a trimester system.

    On 15 July 2020, the university announced 493 job cuts and a 25 percent reduction in management due to the effects of COVID-19 and a $370 million budget shortfall.

    Research centres

    The university has a number of purpose-built research facilities, including:

    UNSW Lowy Cancer Research Centre is Australia’s first facility bringing together researchers in childhood and adult cancers, as well as one of the country’s largest cancer-research facilities, housing up to 400 researchers.
    The Mark Wainwright Analytical Centre is a centre for the faculties of science, medicine, and engineering. It is used to study the structure and composition of biological, chemical, and physical materials.
    UNSW Canberra Cyber is a cyber-security research and teaching centre.
    The Sino-Australian Research Centre for Coastal Management (SARCCM) has a multidisciplinary focus, and works collaboratively with the Ocean University of China [中國海洋大學; pinyin: Zhōngguó; Hǎiyáng Dàxué](CN) in coastal management research.

     
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