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  • richardmitnick 9:07 am on August 25, 2021 Permalink | Reply
    Tags: "Evolutionary ‘arms race’ may help keep cell division honest", , Biology, Eggs and sperm are special cells for many reasons-unlike other human cells which have two copies of 23 chromosomes these sex cells or gametes have only one., In a new study Penn biologists show how proteins have evolved to suppress cheating chromosomes and keep the odds close to even., , Scientists looked to heterochromatin-tightly-packed DNA which is also known to recruit proteins to the centromere., Scientists uncover a force at work to balance the scales during meiosis-the cell-division process that gives rise to gametes., The findings illuminate the evolutionary battlefield present in our own bodies., The selfish centromeres were able to bias transmission by recruiting certain proteins that destabilized attachment to the spindle.   

    From Penn Today : “Evolutionary ‘arms race’ may help keep cell division honest” 

    From Penn Today

    at

    U Penn bloc

    University of Pennsylvania

    August 24, 2021
    Katherine Unger Baillie

    Research from the lab of Michael Lampson in the School of Arts & Sciences suggests that certain proteins may have evolved to reduce the likelihood of chromosomes ‘cheating’ to bias their chance of winding up in an egg during the cell-division process meiosis.

    1
    Normally, we think each copy of our 23 chromosomes has a 50-50 shot of getting in our reproductive cells—eggs and sperm—but that’s not the case. In a new study Penn biologists show how proteins have evolved to suppress cheating chromosomes and keep the odds close to even. Image: Jun Ma.

    Eggs and sperm are special cells for many reasons, but one of the characteristics that sets them apart is that, unlike other human cells which have two copies of 23 chromosomes, one from the mother and one from the father, these sex cells or gametes, have only one.

    Previous research, led by Michael Lampson of Penn’s School of Arts & Sciences, has shown that these chromosomes don’t get passed on to gametes by chance; certain factors can tip the scales, making it more likely that one of the two copies will be passed to the next generation.

    In a new paper, Lampson and colleagues uncover a force at work to balance the scales during meiosis-the cell-division process that gives rise to gametes, bringing the odds closer to 50-50 that a particular chromosome will get into a viable egg.

    The work, published in the journal Cell, finds that, while a mechanism exists to give certain chromosomes the upper hand during meiosis, a separate, parallel pathway acts to suppress that advantage. Proteins that act in the two pathways appear to be in an evolutionary arms race, the researchers say, potentially to avoid the possibility of biased chromosome inheritance leading to mistakes and abnormalities in eggs, such as aneuploidy, or having an abnormal number of chromosomes, which can result in birth defects.

    “If we think of these chromosomes that are getting in the egg as being selfish, selfish implies that they’re maximizing their own transmission at some cost to the organism overall,” says Lampson. “If there is a cost, then there might be other genes under pressure to suppress the selfish ones or suppress that cost.”

    The current work aimed to look for that suppressive pathway, building on a 2017 paper in Science in which Lampson and members of his lab laid out the mechanism by which an asymmetry arises in the meiotic spindle, a structure composed of microtubules that pulls chromosomes to opposite sides of a cell prior to division. This asymmetry led to biases in chromosome transmission. They found that “selfish” centromeres, the part of the chromosome that attaches to the spindle, were more likely than “unselfish” centromeres to be able to detach and reattach to the side of the cell that was destined to become a viable egg rather than the polar body, which is typically degraded.

    Then, in a 2019 paper in Cell, the researchers laid out more details of the process. They found that the selfish centromeres were able to bias transmission by recruiting certain proteins that destabilized attachment to the spindle, again increasing the chance of ending up in the egg rather than the polar body. These proteins played a role in enabling the centromeres’ detachment from the spindle.

    “We had gained this understanding of how selfishness works,” Lampson says, so in the new paper, “we wanted to understand how suppression works.”

    Earlier research had shown that some of the proteins acting on the centromere were evolving rapidly in various animal species. Lampson and colleagues hypothesized that this rapid evolution could be evidence of an “arms race” between selfish and suppressive factors, akin to what is seen in the immune system, which can quickly evolve to respond to changing threats from pathogens.

    “It was surprising to find a whole bunch of rapidly evolving proteins functioning at the centromere because you would probably expect those to be highly conserved because they’re so important in cell division,” Lampson says. “But it’s a signature of the arms race, just like we see in the immune system: If selfish centromeres are going to cheat, there are likely proteins evolving to tamp down that suppression.”

    The researchers already knew that effector proteins that bias chromosome transmission were recruited to the centromere by a route known as the kinetochore pathway. To find a suppressive pathway, they looked to heterochromatin-tightly-packed DNA which is also known to recruit proteins to the centromere. To test whether the heterochromatin pathway might be balancing out the biasing effect of the kinetochore pathway, the researchers selectively modified an enzyme that acted in each pathway.

    When they modified the protein CENP-C, disrupting the kinetochore pathway, they observed the bias between selfish and unselfish centromere decline, with chromosomes lining up more symmetrically in the cell prior to the completion of meiosis. In contrast, when they deleted the protein CENP-B, which is involved in recruiting proteins in the heterochromatin pathway, the asymmetry in the chromosomes became more pronounced, with selfish centromeres permitted to bias chromosome transmission to the egg.

    “There seem to be these subtle changes at work,” Lampson says, “because both of these pathways are essential. You can’t kill the kinetochore pathway because it’s fundamental for cell division, but at the same time you want to reduce the opportunity for centromeres to be selfish. So evolution seems to be acting to respond to these simultaneous pressures.”

    The findings illuminate the evolutionary battlefield present in our own bodies, Lampson says. “I think it’s really interesting that there are these selfish components of our own genomes that have essential roles. These very, very fundamental aspects of our cell biology actually reflect competing pressures.”

    He and colleagues hope to continue to explore in follow-up work whether the potential costs of selfish factors can result in impactful mistakes in gamete production or other problems in meiosis. “Females don’t make very many eggs,” Lampson says, “so you would think each one would be precious, and we don’t want to make any mistakes. But mistakes sometimes occur; sometimes too many chromosomes get in. So, are mistakes somehow related to these selfish factors?”

    See the full article here .

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    Please help promote STEM in your local schools.

    Stem Education Coalition

    U Penn campus

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

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

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

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

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

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

    History

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

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

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

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

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

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

    Research, innovations and discoveries

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

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

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

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

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

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

    ENIAC UPenn

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

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

    International partnerships

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

     
  • richardmitnick 3:29 pm on August 19, 2021 Permalink | Reply
    Tags: "Blue-green algae key to unlocking secrets of ancient past", , Around 2500 million years ago young Earth was unrecognisable. No ozone layer existed and there was no oxygen to breathe in the atmosphere., , Biology, , Cyanobacteria are the only bacteria capable of oxygenic photosynthesis-the process also used by plants to convert carbon dioxide into oxygen using sunlight., Cyanobacteria began using antioxidants called superoxide dismutase enzymes (SODs) to manage reactive oxygen., Cyanobacteria worked out early in their evolution how to protect themselves against the side effects of oxygen., , , The planet was dominated by microbes.,   

    From University of Bristol (UK) : “Blue-green algae key to unlocking secrets of ancient past” 

    From University of Bristol (UK)

    17 August 2021

    Oxygen-producing bacteria emerged a thousand millions years before the great oxygenation event approximately 2400 million years ago, scientists have found.

    The blue green algae, which is responsible for seeping oxygen into the Earth’s atmosphere, changing the planet forever, diversified from its relatives to cope with the rise of the gas.

    To understand how oxygen shaped early life, scientists at the University of Bristol have been investigating when cyanobacteria evolved and when they began using antioxidants called superoxide dismutase enzymes (SODs) to manage reactive oxygen.

    They devised a ‘molecular clock’ using geochemical records, cyanobacteria fossils and genetic information to create a timeline of events.

    Around 2500 million years ago young Earth was unrecognisable. No ozone layer existed and there was no oxygen to breathe in the atmosphere. Instead, the planet was dominated by microbes. Cyanobacteria are the only bacteria capable of oxygenic photosynthesis-the process also used by plants to convert carbon dioxide into oxygen using sunlight. Today, cyanobacteria are widespread throughout the ocean, but then they were mostly restricted to freshwater and land.

    Oxygen is highly reactive and toxic. Cyanobacteria uses SODs to protect against e these effects which all have different evolutionary origins – and use different trace metals.

    Group leader author of the paper Dr Patricia Sanchez-Baracaldo of Bristol’s School of Geographical Sciences said: “We studied the evolutionary history of four of these antioxidant enzymes: NiSOD, CuZnSOD and Fe- and Mn-utilising SODs. Such SODs are found in everything from animals to plants and bacteria, where they manage ROS by converting superoxide free radicals into hydrogen peroxide.

    PhD student, Joanne Boden said: “We discovered that cyanobacteria had acquired their SOD genes from other bacteria on several occasions throughout history. As a result, different strains used different antioxidant enzymes depending on their circumstances. For example, cyanobacteria which live planktonic lifestyles, floating in the ocean, often use NiSOD. Whereas most cyanobacteria, regardless of their habitat, use Mn- or Fe-SODs.

    “The evolutionary trajectory of a different SOD, using copper and zinc cofactors instead of nickel matched those of older, more ancestral cyanobacteria which diversified at least 2,700 million years ago. This suggests that oxygen-producing bacteria were equipped with mechanisms of managing ROS before the global atmosphere was flooded with oxygen.”

    This genomic record, which has been published in Nature Communications, contains vital information about ancient habitats and proves the existence of life on land and in the ocean at that time.

    Dr Sanchez-Baracaldo said: “Cyanobacteria worked out early in their evolution how to protect themselves against the side effects of oxygen.

    “Our analyses of metalloenzymes dealing with reactive oxygen species (ROS) show that marine geochemical records alone may not predict patterns of metal usage by living organisms found in other environments such as freshwater and terrestrial habitats.”

    The team now plan to investigate when other antioxidants evolved.

    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 Bristol (UK) is one of the most popular and successful universities in the UK and was ranked within the top 50 universities in the world in the QS World University Rankings 2018.

    The University of Bristol (UK) is at the cutting edge of global research. We have made innovations in areas ranging from cot death prevention to nanotechnology.

    The University has had a reputation for innovation since its founding in 1876. Our research tackles some of the world’s most pressing issues in areas as diverse as infection and immunity, human rights, climate change, and cryptography and information security.

    The University currently has 40 Fellows of the Royal Society and 15 of the British Academy – a remarkable achievement for a relatively small institution.

    We aim to bring together the best minds in individual fields, and encourage researchers from different disciplines and institutions to work together to find lasting solutions to society’s pressing problems.

    We are involved in numerous international research collaborations and integrate practical experience in our curriculum, so that students work on real-life projects in partnership with business, government and community sectors.

     
  • richardmitnick 10:10 am on August 19, 2021 Permalink | Reply
    Tags: "New Technique Surveys Microbial Spatial Gene Expression Patterns", , Biology, , , , par-seqFISH: parallel and sequential fluorescence in situ hybridization   

    From California Institute of Technology (US) : “New Technique Surveys Microbial Spatial Gene Expression Patterns” 

    Caltech Logo

    From California Institute of Technology (US)

    August 16, 2021
    Lori Dajose
    (626) 395‑1217
    ldajose@caltech.edu

    1
    Left: A black-and-white image of a biofilm. Right: A closeup of a portion of this biofilm with individual cells circled and colors corresponding to the expression of particular genes. Credit: Courtesy of the Newman laboratory.

    What do you do at different times in the day? What do you eat? How do you interact with your neighbors? These are some of the questions that biologists would love to ask communities of microbes, from those that live in extreme environments deep in the ocean to those that cause chronic infections in humans. Now, a new technique developed at Caltech can answer these questions by surveying gene expression across a population of millions of bacterial cells while still preserving the cells’ positions relative to one another.

    The technique can be used to understand the wide variety of microbial communities on our planet, including the microbes that live within our gut and influence our health as well as those that colonize the roots of plants and contribute to soil health, to name a few.

    The technique was developed at Caltech by Daniel Dar, a former postdoctoral scholar in the laboratory of Dianne Newman, Gordon M. Binder/Amgen Professor of Biology and Geobiology and executive officer for biology and biological engineering, and by Dr. Nina Dar, a former senior research technician in the laboratory of Long Cai, professor of biology and biological engineering. Daniel Dar is now an assistant professor at the Weizmann Institute of Science (IL). A paper describing the research appears on August 12 in the journal Science.

    We cannot ask a bacterium what it is doing or how it is feeling, but we can look at the genes it is expressing. Gene expression is the basis of any behaviors or actions a microbe can take. For example, if there is a lack of food in a bacterium’s environment, the microbe can turn on a set of genes that will help it to conserve energy and dial back less necessary genes, such as those that are involved in reproduction. Though two bacteria in the same species can have the same genetic information, genes can be turned on and off in different situations, resulting in different behaviors at the individual bacterium level.

    “Traditional methods for measuring gene expression tend to minimize an entire population, in all of its complexity and three-dimensional organization, into a single number,” says Daniel Dar. “Imagine taking a tray of fruits with unique colors, flavors, and scents and having to blend them all together into a single smoothie. All identity is lost. The meaning of this technological limitation for microbiological research, both in medicine and environmental sciences, is that biological signatures that manifest at the microscale—the scale at which microorganisms make their living—remain mostly invisible. This was a major motivation for us along this collaborative study: building on the revolutionary technology first developed in the Cai lab to expose the complexity of microbial populations in a fundamentally new way.”

    The new technique, dubbed par-seqFISH (for parallel and sequential fluorescence in situ hybridization), can track these differences in gene expression with high precision. In this study, par-seqFISH was used to examine gene expression in populations of Pseudomonas aeruginosa, a pathogen that often causes infections (such as those found in the lungs of people with cystic fibrosis or within chronic skin wounds) and is studied extensively in the Newman laboratory. par-seqFISH can be used on virtually any species of bacteria whose genomes have been sequenced and on communities of microbes composed of different species.

    par-seqFISH is precise to the sub-micrometer level and is able to show differences in gene expression even within individual cells. For example, the team found that certain genes can be expressed more at the poles of a cell rather than near the center. The technique preserves the spatial organization of bacteria, or their positions relative to one another. Because of its level of precision, it revealed significant diversity in the gene expression and resulting activity of individual members of a population of the same species of bacteria.

    The method’s ability to image at this level of detail makes it a powerful technique for cellular biology research.

    “We saw patterns where certain genes were being expressed spatiotemporally—in space and in time—in ways that we would have never been able to predict, which suggested new ideas about how the population functions as a whole,” says Newman. “The heterogeneity of bacterial populations and communities at spatial scales on the order of a few micrometers is incredibly important and underappreciated. The profound thing that this technique hammers home is that context matters. Every cell is experiencing a slightly different microenvironment; for example, how much oxygen is around a given cell indicates what kind of metabolism that cell will engage in. Appreciating the full extent of such heterogeneities is necessary if we are to be able to manipulate these communities, such as being able to treat chronic bacterial infections. Understanding what all the members of the population are doing will help guide more effective therapeutic strategies.”

    seqFISH, the precursor technique to par-seqFISH, was pioneered in the Cai laboratory.

    “Every time we look at a biological system with both spatial context and genomics information, we find interesting new biology,” says Cai. “Microbial communities, with their rich diversity, show us again how beautiful and complex biology is when looked through the lens of spatial genomics.”

    Newman, who is the lead and faculty supervisor for the Ecology and Biosphere Engineering initiative at Caltech’s Resnick Sustainability Institute (RSI), envisions that the technology will be available to researchers across Caltech to utilize through RSI, assisting studies of microbes in diverse environments, from the soil around plant roots (called the rhizosphere) to deep-sea sediments.

    See the full article here .


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

    Stem Education Coalition

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

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

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

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

    Research

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

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

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

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

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

     
  • richardmitnick 9:35 am on August 19, 2021 Permalink | Reply
    Tags: "Stanford scientist recalls falling in love with microbes" Geomicrobiologist Paula Welander, , Biology, Earth system science, ,   

    From Stanford University (US) : “Stanford scientist recalls falling in love with microbes” Geomicrobiologist Paula Welander 

    Stanford University Name

    From Stanford University (US)

    August 18, 2021
    Josie Garthwaite

    On an autumn day in 1997, Paula Welander watched an invasion in a Petri dish. Millions of rod-shaped Escherichia coli cells squiggled through jelly-like agar smeared on the plate, while predatory bacteria pursued and attacked the rapidly dividing cells.

    2
    Paula Welander. Credit: Steve Castillo.


    Stanford’s Welander Lab discusses microbes, astrobiology, and searching for life on other planets.

    The high-speed transformation of the bacterial hordes under her microscope drew Welander, who is now an associate professor of Earth system science in Stanford’s School of Earth, Energy & Environmental Sciences (Stanford Earth), into a new world.

    “I just fell in love with microbes. I could put a drop in a culture tube and in a few hours have a complete population of these organisms,” she said. “And I had access to their genes and their proteins. Here was a system that would allow me in its simplicity to answer very complex questions. I could use microbes as a system to study life.”

    Welander is petite and quick to laugh. Listening to her describe her work in her sunny office on the Stanford campus, in a time before the coronavirus, microbes can begin to seem like both creative, scrappy beings and impressive machines. “Microbes have found different ways over billions of years of evolution to use their environment so they can just grow. We would never think to breathe arsenic; they breathe arsenic, or they’ll breathe iron and form rust as a byproduct. The only thing we can make is water and carbon dioxide.”

    Welander caught that first glimpse of the diversity of microbial life and the power of what she would later come to know as bench science as an undergraduate student at Occidental College-Los Angeles, California.

    The campus lies less than 30 miles from Welander’s childhood home, but her work in labs there helped her find a path that had been all but invisible in her upbringing. Her parents, who immigrated to Los Angeles from Mexico as teenagers in the early 1970s, had encouraged her to pursue medicine or law. “The idea of an academic career wasn’t something they had been exposed to,” Welander said.

    When a college professor and mentor encouraged Welander to pursue a career in bench science, Welander recalled, “I was like, wait, what does that even mean to be a scientist?” What it meant for Welander was starting out after graduation as a technician in a lab, where she studied the immune systems of mice dealing with herpes infections that go dormant and then suddenly reactivate.

    Working with mice made Welander realize something: She missed microbes.

    “Statistically, the number of mice we were looking at was just so low,” Welander said. “With microbes, for statistical significance, I could kill a million of them and then start a new culture the next day.”

    For Welander, who has begun most days since high school with an early morning run, the daily repetition demanded by laboratory research had hooked her from the start. “I fell in love with the ability to take a protocol and get a result, and if it doesn’t work, then you redo or rethink the experiment.”

    In grad school, at the The University of Illinois at Urbana-Champaign (US), Welander worked in a lab studying the only microbes that generate methane. The experience expanded her thinking from questions about how microbes affect human health and disease to how microbes exist with the Earth. “I realized that the reason the planet looks the way it does today is because of the life that’s on it,” she said. “The ecosystem would fall apart without microbes. That was true 100 million years ago, two billion years ago, even four and a half billion years ago when life was first starting to evolve.”

    After grad school, Welander worked as a postdoc with both a geologist and a geobiologist, and she began learning how to frame questions in a way that fed her curiosity about basic molecular biology while also enabling geologists to better interpret ecological records. She often found herself building intellectual and cultural bridges – familiar territory for a child of immigrants.

    “As a kid of immigrants, you’re bridging two worlds, because you’re at home and you’re speaking Spanish and you have these cultural norms, and then you’re shipped off to school where you’re then speaking English and you have these ambitions and goals and things that maybe don’t correlate well with what the goals are at home. You’re negotiating those two worlds,” Welander said. “I had to explain things to my parents and I had to explain things to my teachers and peers. It might have been why I was comfortable then making the leap from microbiology to studying molecular fossils.”

    Welander says that over time, she has grown more comfortable grappling with big questions about the early days of Earth and complex life. “I like systems that I can use to ask a very specific question and answer it in very fine detail, and then step back later to see if it has any implications for a bigger question,” she said.

    By examining fatty molecules made by marine bacteria, for example, Welander and colleagues have been able to show [PNAS] that a biomarker once thought to be produced only by flowering plants might also have been created by ancient bacteria – long before flowering plants evolved. And by deleting and mutating proteins in a type of microbe that thrives in extreme environments like Yellowstone’s highly acidic hot springs, she helped to prove a decades-old hypothesis about how the organism protects itself while simultaneously shedding light on its evolutionary origins.

    It’s the thrill of discovery at the smallest scales that still drives Welander’s work.

    “I’m uncovering biology that people have thought should happen but had no idea how it’s happening. A question will sit there for 40 years,” she said. “Then we find an answer by discovering new proteins, or a new fossil, or a new molecule made by some ancient organism. With microbes, you can always find new biology. We have just begun to scratch the surface of what’s there.”

    See the full article here .


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

    Stem Education Coalition

    Stanford University campus
    Stanford University (US)

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

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

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

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

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

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

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

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

    Land

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

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

    Non-central campus

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

    On the founding grant:

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

    Off the founding grant:

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

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

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

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

    Administration and organization

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

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

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

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

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

    Endowment and donations

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

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

    Research centers and institutes

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

    Discoveries and innovation

    Natural sciences

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

    Computer and applied sciences

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

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

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

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

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

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

    Businesses and entrepreneurship

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

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

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

    Some companies closely associated with Stanford and their connections include:

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

    Student body

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

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

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

    Athletics

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

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

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

    Traditions

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

    Award laureates and scholars

    Stanford’s current community of scholars includes:

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

    Stanford University Seal

     
  • richardmitnick 12:03 pm on August 17, 2021 Permalink | Reply
    Tags: "SFI researchers publish new theory of life’s multiple origins", , , Biology, , , Santa Fe Institute (US)   

    From Santa Fe Institute (US): “SFI researchers publish new theory of life’s multiple origins” 

    From Santa Fe Institute (US)

    August 16, 2021
    Santa Fe Institute
    Office of Communications
    news@santafe.edu
    505-946-2798

    1
    What if life is better understood on the analogy of the eye, a convergent organ that evolved from independent origins? (Image: CG Alex/Shutterstock)

    The history of life on Earth has often been likened to a four-billion-year-old torch relay. One flame, lit at the beginning of the chain, continues to pass on life in the same form all the way down. But what if life is better understood on the analogy of the eye, a convergent organ that evolved from independent origins? What if life evolved not just once, but multiple times independently?

    In a new paper, published in the Journal of Molecular Evolution, Santa Fe Institute researchers Chris Kempes and David Krakauer argue that in order to recognize life’s full range of forms, we must develop a new theoretical frame.

    In their three-layered frame, Kempes and Krakauer call for researchers to consider, first, the full space of materials in which life could be possible; second, the constraints that limit the universe of possible life; and, third, the optimization processes that drive adaptation. In general, the framework considers life as adaptive information and adopts the analogy of computation to capture the processes central to life.

    Several significant possibilities emerge when we consider life within the new framework. First, life originates multiple times — some apparent adaptations are actually “a new form of life, not just an adaptation,” explains Krakauer — and it takes a far broader range of forms than conventional definitions allow.

    Culture, computation, and forests are all forms of life in this frame. As Kempes explains, “human culture lives on the material of minds, much like multicellular organisms live on the material of single-celled organisms.”

    When researchers focus on the life traits of single organisms, they often neglect the extent to which organisms’ lives depend upon entire ecosystems as their fundamental material, and also ignore the ways that a life system may be more or less living. Within the Kempes-Krakauer framework, by contrast, another implication appears: life becomes a continuum rather than a binary phenomenon. In this vein, the authors point to a variety of recent efforts that quantitatively place life on a spectrum.

    By taking a broader view of life’s principles, Kempes and Krakauer hope to generate more fertile theories for studying life. With clearer principles for finding life forms, and a new range of possible life forms that emerges from new principles, we’ll not only clarify what life is, explains Krakauer, we’ll also be better equipped “to build devices to find life,” to create it in labs, and to recognize to what degree the life we see is living.

    See the full article here.

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

    Please help promote STEM in your local schools.

    Stem Education Coalition

    The Santa Fe Institute (SFI) (US) is an independent, nonprofit theoretical research institute located in Santa Fe (New Mexico, United States) and dedicated to the multidisciplinary study of the fundamental principles of complex adaptive systems, including physical, computational, biological, and social systems. The Institute is ranked 25th among the world’s Top Science and Technology Think Tanks and 25th among the world’s Best Transdisciplinary Research Think Tanks according to the 2018 edition of the Global Go To Think Tank Index Reports, published annually by the University of Pennsylvania (US).

    The Institute consists of a small number of resident faculty and postdoctoral researchers, a large group of external faculty whose primary appointments are at other institutions, and a number of visiting scholars. The Institute is advised by a group of eminent scholars, including several Nobel Prize-winning scientists. Although theoretical scientific research is the Institute’s primary focus, it also runs several popular summer schools on complex systems, along with other educational and outreach programs aimed at students ranging from middle school up through graduate school.

    The Institute’s annual funding comes from a combination of private donors, grant-making foundations, government science agencies, and companies affiliated with its business network.

    The Santa Fe Institute was founded in 1984 by scientists George Cowan; David Pines; Stirling Colgate; Murray Gell-Mann; Nick Metropolis; Herb Anderson; Peter A. Carruthers; and Richard Slansky. All but Pines and Gell-Mann were scientists with DOE’s Los Alamos National Laboratory (US). Originally called the “Rio Grande Institute”, the scientists sought a forum to conduct theoretical research outside the traditional disciplinary boundaries of academic departments and government agency science budgets.

    SFI’s original mission was to disseminate the notion of a new interdisciplinary research area called complexity theory or simply complex systems. This new effort was intended to provide an alternative to the increasing specialization the founders observed in science by focusing on synthesis across disciplines. As the idea of interdisciplinary science increased in popularity, a number of independent institutes and departments emerged whose focus emphasized similar goals.

    The Santa Fe Institute was created to be a visiting institution, with no permanent or tenured positions, a small group of resident faculty and postdoctoral researchers, a large visitors program, and a larger group of external faculty affiliated with the Institute but located at other institutions. The motivation of this structure was to encourage active turnover in ideas and people, allowing the research to remain on the cutting edge of interdisciplinary science. Today, the Santa Fe Institute continues to follow this organizational model.

    The Institute is composed of several distinct groups. The resident faculty are researchers whose primary appointment is at the Institute. Along with the Omidyar Fellows, a group of postdoctoral scholars in residence, the resident faculty makes up the majority of the researchers physically present at the Institute. The external faculty is a group of roughly 100 affiliated researchers whose primary appointments are at other institutions, typically universities. These individuals form a large and distributed community of scholars who frequently visit the Institute and contribute to its overall research program. The Institute’s Business Network is a group of private companies and government agencies interested in complex systems research. Members of the business network often send representatives to Institute meetings or to serve as research fellows in residence at the Institute. The Institute’s Science Board is a large group of eminent scholars who advise the Institute on important strategic matters. This group includes a number of Nobel Prize winners.

    The Institute is headed by a president, and a Vice President for Science. It is governed by a Board of Trustees.

    Research

    Research at the Institute focuses on systems commonly described as complex adaptive systems or simply complex systems. Recent research has included studies of evolutionary computation; metabolic and ecological scaling laws; the fundamental properties of cities; the evolutionary diversification of viral strains; the interactions and conflicts of primate social groups; the history of languages; the structure and dynamics of species interactions including food webs; the dynamics of financial markets; and the emergence of hierarchy and cooperation in the human species; and biological and technological innovation.

    Historically researchers affiliated with the Institute played roles to varying degrees in the development and use of methods for studying complex systems; including agent-based modeling; network theory; computational immunology; the physics of financial markets; genetic algorithms; the physics of computation; and machine learning.

    The Institute also studies foundational topics in the physics and mathematics of complex systems using tools from related disciplines such as information theory; combinatorics; computational complexity theory; and condensed matter physics. Recent research in this area has included studies of phase transitions in NP-hard problems.

    Some of the Institute’s accomplishments include:

    Complexity research which led to efforts to create artificial life modeling real organisms and ecosystems in the 1980s and 1990s.
    Foundational contributions to the field of chaos theory.
    Foundational contributions to the field of genetic algorithms.
    Foundational contributions to the complexity economics school of thought.
    Foundational contributions to the field of econophysics.
    Foundational contributions to the field of complex networks.
    Foundational contributions to the field of systems biology.
    The “Evolution of Human Languages” project, an attempt to trace all human language to a common ancestor (Proto-Human language).

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

    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 .

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

    Please help promote STEM in your local schools.

    Stem Education Coalition

    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 12:11 pm on August 16, 2021 Permalink | Reply
    Tags: "Guest molecules", "Quick way to create molecular cages could revamp search for new materials", A new way to predict the outcome of reactions could lead to faster discovery of new materials including for sensing; catalysis; and drug delivery., , , Biology, By using unsymmetrical building blocks ‘wonky’ cages with interesting cavity shapes can be created., , , Researchers at Imperial are developing ways to assemble cages with lower symmetry allowing more guest-specific cavity shapes by using more complex components in their construction.   

    From Imperial College London (UK) : “Quick way to create molecular cages could revamp search for new materials” 

    From Imperial College London (UK)

    16 August 2021
    Hayley Dunning

    1
    A new way to predict the outcome of reactions could lead to faster discovery of new materials including for sensing; catalysis; and drug delivery. One of the team’s ‘wonky’ cages, binding two guest molecules of the anion tetrafluoroborate (BF4-) inside the cavity.

    Enzymes perform essential chemical and biological processes by taking biomolecules into cavities within their structures and facilitating important reactions. Chemists have attempted to emulate this with ‘molecular cages’ – chemical structures that contain cavities that can bind smaller molecules within, called ‘guests’.

    These molecular cages have the potential to act as artificial enzyme-mimics and have been shown to accelerate important reactions such as the hydrolysis of amide bonds, degradation of toxins and a range of chemical transformations. Improving these reactions could one day drive the development of new technologies in areas such as chemical sensing.

    However, it can be difficult for researchers to design structures that will be useful as well as successfully synthesised in the lab. Now, researchers from the Department of Chemistry at Imperial College London have used a computer-driven approach to predict the results of cage-building reactions with high precision.

    This will help chemists select the ideal building blocks to prepare cages with desirable structures and properties before trying to synthesise them in the lab, minimising unsuccessful experimentation. The study is published today in Angewandte Chemie.

    New building blocks

    Currently, to simplify their synthesis, most cages and their cavities are highly symmetric. However, this limits the design of cages for potential guest molecules. This contrasts with natural enzymes’ ability to be highly selective in which molecules can bind with them.

    Researchers at Imperial are developing ways to assemble cages with lower symmetry allowing more guest-specific cavity shapes by using more complex components in their construction. By using unsymmetrical building blocks ‘wonky’ cages with interesting cavity shapes can be created.

    However, unsymmetrical building blocks are more difficult to create because the outcomes of the ‘self-assembly’ reactions needed to construct them are harder to predict. Failed reactions can result in the formation of an undesirable molecule, or even a mixture of products, rather than the single target structure.

    All this means constructing new cages can be a time-consuming and costly trial-and-error process, with lots of wasted effort.

    The new approach instead analyses computational models of potential cages to make predictions about their self-assembly. The predictions use the energy and geometry of the computationally constructed cages and are good guides for whether a self-assembly process will lead to a single structure. This information can then be used to select target cage molecules to prepare in the lab.

    Study co-author Dr Jamie Lewis, from the Department of Chemistry at Imperial, said: “Previously, we’ve just had to get in the lab and try lots of things until something worked. Now we can run some quick calculations, identify cages with properties that are useful, and be confident that we can synthesise them without any problems.”

    Prediction power

    The team used software called “stk”, previously developed at Imperial, to build the computational models. As well as having large predicting power, the calculations are also very rapid, taking only a few hours on a common desktop PC.

    Lead author of the study Dr Andrew Tarzia, from the Department of Chemistry at Imperial, said: “The efficiency of our approach is the key because it allows us to test on a computer many more building blocks in a week than could be tested in the laboratory and with more diversity too.”

    Based on the computational data, the team selected a number of building blocks to synthesise in the lab. They found that the approach successfully predicted the experimental outcomes of the self-assembly process.

    This allowed them to prepare several new low-symmetry ‘wonky cages’ that had never been synthesised before, and verified the usefulness of the calculations for predicting which molecules would form.

    The team are now continuing to develop and improve this approach to computationally informed, efficient synthesis to access new molecular cages. With the ability to rapidly predict which cages can be readily prepared in the lab, they hope to use this to make novel materials with a wide range of applications in sensing, catalysis, gas storage and drug delivery.

    See the full article here .


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

    Please help promote STEM in your local schools.

    Stem Education Coalition

    Imperial College London (UK) is a science-based university with an international reputation for excellence in teaching and research. Consistently rated amongst the world’s best universities, Imperial is committed to developing the next generation of researchers, scientists and academics through collaboration across disciplines. Located in the heart of London, Imperial is a multidisciplinary space for education, research, translation and commercialisation, harnessing science and innovation to tackle global challenges.

    Imperial College London (legally Imperial College of Science, Technology and Medicine) is a public research university in London. Imperial grew out of Prince Albert’s vision of an area for culture, including the Royal Albert Hall; Imperial Institute; numerous museums and the Royal Colleges that would go on to form the college. In 1907, Imperial College was established by Royal Charter, merging the Royal College of Science; Royal School of Mines; and City and Guilds College. In 1988, the Imperial College School of Medicine was formed by combining with St Mary’s Hospital Medical School. In 2004, Queen Elizabeth II opened the Imperial College Business School.

    The college focuses exclusively on science; technology; medicine; and business. The college’s main campus is located in South Kensington, and it has an innovation campus in White City; a research field station at Silwood Park; and teaching hospitals throughout London. The college was a member of the University of London(UK) from 1908, becoming independent on its centenary in 2007. Imperial has an international community, with more than 59% of students from outside the UK and 140 countries represented on campus. Student, staff, and researcher affiliations include 14 Nobel laureates; 3 Fields Medalists; 2 Breakthrough Prize winners; 1 Turing Award winner; 74 Fellows of the Royal Society; 87 Fellows of the Royal Academy of Engineering; and 85 Fellows of the Academy of Medical Sciences.

    History

    19th century

    The earliest college that led to the formation of Imperial was the Royal College of Chemistry founded in 1845 with the support of Prince Albert and parliament. This was merged in 1853 into what became known as the Royal School of Mines. The medical school has roots in many different schools across London, the oldest of which being Charing Cross Hospital Medical School which can be traced back to 1823 followed by teaching starting at Westminster Hospital in 1834 and St Mary’s Hospital in 1851.

    In 1851 the Great Exhibition was organised as an exhibition of culture and industry by Henry Cole and by Prince Albert- husband of the reigning monarch of the United Kingdom Queen Victoria. An enormously popular and financial success proceeds from the Great Exhibition were designated to develop an area for cultural and scientific advancement in South Kensington. Within the next 6 years the Victoria and Albert Museum and Science Museum had opened joined by new facilities in 1871 for the Royal College of Chemistry and in 1881 for the Royal School of Mines; the opening of the Natural History Museum in 1881; and in 1888 the Imperial Institute.

    In 1881 the Normal School of Science was established in South Kensington under the leadership of Thomas Huxley taking over responsibility for the teaching of the natural sciences and agriculture from the Royal School of Mines. The school was renamed the Royal College of Science by royal consent in 1890. The Central Institution of the City and Guilds of London Institute was opened as a technical education school on Exhibition Road by the Prince of Wales in early 1885.

    20th century

    At the start of the 20th century, there was a concern that Britain was falling behind Germany in scientific and technical education. A departmental committee was set up at the Board of Education in 1904, to look into the future of the Royal College of Science. A report released in 1906 called for the establishment of an institution unifying the Royal College of Science and the Royal School of Mines, as well as – if an agreement could be reached with the City and Guilds of London Institute – their Central Technical College.

    On 8 July 1907 King Edward VII granted a Royal Charter establishing the Imperial College of Science and Technology. This incorporated the Royal School of Mines and the Royal College of Science. It also made provisions for the City and Guilds College to join once conditions regarding its governance were met as well as for Imperial to become a college of the University of London. The college joined the University of London on 22 July 1908 with the City and Guilds College joining in 1910. The main campus of Imperial College was constructed beside the buildings of the Imperial Institute- the new building for the Royal College of Science having opened across from it in 1906 and the foundation stone for the Royal School of Mines building being laid by King Edward VII in July 1909.

    As students at Imperial had to study separately for London degrees in January 1919 students and alumni voted for a petition to make Imperial a university with its own degree awarding powers independent of the University of London. In response the University of London changed its regulations in 1925 so that the courses taught only at Imperial would be examined by the university enabling students to gain a BSc.

    In October 1945 King George VI and Queen Elizabeth visited Imperial to commemorate the centenary of the Royal College of Chemistry which was the oldest of the institutions that united to form Imperial College. “Commemoration Day” named after this visit is held every October as the university’s main graduation ceremony. The college also acquired a biology field station at Silwood Park near Ascot, Berkshire in 1947.

    Following the Second World War, there was again concern that Britain was falling behind in science – this time to the United States. The Percy Report of 1945 and Barlow Committee in 1946 called for a “British MIT”-equivalent backed by influential scientists as politicians of the time including Lord Cherwell; Sir Lawrence Bragg; and Sir Edward Appleton. The University Grants Committee strongly opposed however. So a compromise was reached in 1953 where Imperial would remain within the university but double in size over the next ten years. The expansion led to a number of new buildings being erected. These included the Hill building in 1957 and the Physics building in 1960 and the completion of the East Quadrangle built in four stages between 1959 and 1965. The building work also meant the demolition of the City and Guilds College building in 1962–63 and the Imperial Institute’s building by 1967. Opposition from the Royal Fine Arts Commission and others meant that Queen’s Tower was retained with work carried out between 1966 and 1968 to make it free standing. New laboratories for biochemistry established with the support of a £350,000 grant from the Wolfson Foundation were opened by the Queen in 1965.

    In 1988 Imperial merged with St Mary’s Hospital Medical School under the Imperial College Act 1988. Amendments to the royal charter changed the formal name of the institution to The Imperial College of Science Technology and Medicine and made St Mary’s a constituent college. This was followed by mergers with the National Heart and Lung Institute in 1995 and the Charing Cross and Westminster Medical School; Royal Postgraduate Medical School; and the Institute of Obstetrics and Gynaecology in 1997 with the Imperial College Act 1997 formally establishing the Imperial College School of Medicine.

    21st century

    In 2003, Imperial was granted degree-awarding powers in its own right by the Privy Council. In 2004, the Imperial College Business School and a new main entrance on Exhibition Road were opened by Queen Elizabeth II. The UK Energy Research Centre was also established in 2004 and opened its headquarters at Imperial. On 9 December 2005, Imperial announced that it would commence negotiations to secede from the University of London. Imperial became fully independent of the University of London in July 2007.

    In April 2011 Imperial and King’s College London joined the UK Centre for Medical Research and Innovation as partners with a commitment of £40 million each to the project. The centre was later renamed the Francis Crick Institute and opened on 9 November 2016. It is the largest single biomedical laboratory in Europe. The college began moving into the new White City campus in 2016 with the launching of the Innovation Hub. This was followed by the opening of the Molecular Sciences Research Hub for the Department of Chemistry officially opened by Mayor of London- Sadiq Khan in 2019. The White City campus also includes another biomedical centre funded by a £40 million donation by alumnus Sir Michael Uren.

    Research

    Imperial submitted a total of 1,257 staff across 14 units of assessment to the 2014 Research Excellence Framework (REF) assessment. This found that 91% of Imperial’s research is “world-leading” (46% achieved the highest possible 4* score) or “internationally excellent” (44% achieved 3*) giving an overall GPA of 3.36. In rankings produced by Times Higher Education based upon the REF results Imperial was ranked 2nd overall. Imperial is also widely known to have been a critical contributor of the discovery of penicillin; the invention of fiber optics; and the development of holography. The college promotes research commercialisation partly through its dedicated technology transfer company- Imperial Innovations- which has given rise to a large number of spin-out companies based on academic research. Imperial College has a long-term partnership with the Massachusetts Institute of Technology(US) that dates back from World War II. The United States is the college’s top collaborating foreign country with more than 15,000 articles co-authored by Imperial and U.S.-based authors over the last 10 years.

    In January 2018 the mathematics department of Imperial and the CNRS-The National Center for Scientific Research[Centre national de la recherche scientifique](FR) launched UMI Abraham de Moivre at Imperial- a joint research laboratory of mathematics focused on unsolved problems and bridging British and French scientific communities. The Fields medallists Cédric Villani and Martin Hairer hosted the launch presentation. The CNRS-Imperial partnership started a joint PhD program in mathematics and further expanded in June 2020 to include other departments. In October 2018, Imperial College launched the Imperial Cancer Research UK Center- a research collaboration that aims to find innovative ways to improve the precision of cancer treatments inaugurated by former Vice President of the United States Joe Biden as part of his Biden Cancer Initiative.

    Imperial was one of the ten leading contributors to the National Aeronautics and Space Administration(US) InSight Mars lander which landed on planet Mars in November 2018, with the college logo appearing on the craft. InSight’s Seismic Experiment for Interior Structure, developed at Imperial, measured the first likely marsquake reading in April 2019. In 2019 it was revealed that the Blackett Laboratory would be constructing an instrument for the European Space Agency [Agence spatiale européenne](EU) Solar Orbiter in a mission to study the Sun, which launched in February 2020. The laboratory is also designing part of the DUNE/LBNF Deep Underground Neutrino Experiment(US).

    In early 2020 immunology research at the Faculty of Medicine focused on SARS-CoV-2 under the leadership of Professor Robin Shattock as part of the college’s COVID-19 Response Team including the search of a cheap vaccine which started human trials on 15 June 2020. Professor Neil Ferguson’s 16 March report entitled Impact of non-pharmaceutical interventions (NPIs) to reduce COVID- 19 mortality and healthcare demand was described in a 17 March The New York Times article as the coronavirus “report that jarred the U.S. and the U.K. to action”. Since 18 May 2020 Imperial College’s Dr. Samir Bhatt has been advising the state of New York for its reopening plan. Governor of New York Andrew Cuomo said that “the Imperial College model- as we’ve been following this for weeks- was the best most accurate model.” The hospitals from the Imperial College Healthcare NHS Trust which have been caring for COVID-19 infected patients partnered with Microsoft to use their HoloLens when treating those patients reducing the amount of time spent by staff in high-risk areas by up to 83% as well as saving up to 700 items of PPE per ward, per week.

     
  • richardmitnick 10:58 am on August 13, 2021 Permalink | Reply
    Tags: "University of Washington and Microsoft researchers develop 'nanopore-tal' enabling cells to talk to computers", A commercially available nanopore array — in this case the Oxford Nanopore Technologies MinION device., A new class of reporter proteins that can be directly read by a commercially available nanopore sensing device., , Biology, , , Genetically encoded reporter proteins have been a mainstay of biotechnology research., Scientists are currently working to scale up the number of "NTERs" to hundreds; thousands; maybe even millions more., The new system-dubbed “Nanopore-addressable protein Tags Engineered as Reporters” also known as NanoporeTERs or NTERs for short., This is a fundamentally new interface between cells and computers., University of Washington Paul G. Allen College of Electrical and Computer of Engineering (US)   

    From University of Washington Paul G. Allen College of Electrical and Computer of Engineering (US) : “University of Washington and Microsoft researchers develop ‘nanopore-tal’ enabling cells to talk to computers” 

    From University of Washington Paul G. Allen College of Electrical and Computer of Engineering (US)

    August 12, 2021

    1
    MISL researcher Nicolas Cardozo pipes cell cultures containing NanoporeTERs onto a portable MinION nanopore sensing device for processing as professor Jeff Nivala looks on. Credit: Dennis Wise/University of Washington.

    Genetically encoded reporter proteins have been a mainstay of biotechnology research, allowing scientists to track gene expression, understand intracellular processes and debug engineered genetic circuits. But conventional reporting schemes that rely on fluorescence and other optical approaches come with practical limitations that could cast a shadow over the field’s future progress. Now, thanks to a team of researchers at the University of Washington and Microsoft, scientists are about to see reporter proteins in a whole new light.

    In a paper published today in the journal Nature Biotechnology, members of the Molecular Information Systems Laboratory housed at the UW’s Paul G. Allen School of Computer Science & Engineering introduce a new class of reporter proteins that can be directly read by a commercially available nanopore sensing device. The new system ― dubbed “Nanopore-addressable protein Tags Engineered as Reporters” also known as NanoporeTERs or NTERs for short ― can perform multiplexed detection of protein expression levels from bacterial and human cell cultures far beyond the capacity of existing techniques.

    You could say the new system offers a “nanopore-tal” into what is happening inside these complex biological systems where, up until this point, scientists have largely been operating in the dark.

    “NanoporeTERs offer a new and richer lexicon for engineered cells to express themselves and shed new light on the factors they are designed to track. They can tell us a lot more about what is happening in their environment all at once,” said co-lead author Nicolas Cardozo, a graduate student in the UW’s molecular engineering Ph.D. program. “We’re essentially making it possible for these cells to ‘talk’ to computers about what’s happening in their surroundings at a new level of detail, scale and efficiency that will enable deeper analysis than what we could do before.”

    2
    Raw nanopore signals streaming from the MinION device, which contains an array of hundreds of nanopore sensors; each color represents data from an individual nanopore. The team uses machine learning to interpret these signals as NanoporeTERs barcodes. Credit: Dennis Wise/University of Washington.

    Conventional methods that employ optical reporter proteins, such as green fluorescent protein (GFP), are limited in the number of distinct genetic outputs that they can track simultaneously due to their overlapping spectral properties. For example, it’s difficult to distinguish between more than three different fluorescent protein colors, limiting multiplexed reporting to a maximum of three outputs. In contrast, NTERs were designed to carry distinct protein “barcodes” composed of strings of amino acids that, when used in combination, enable a degree of multiplexing approaching an order of magnitude more. These synthetic proteins are secreted outside of the cell into the surrounding environment, where they are collected and directly analyzed using a commercially available nanopore array — in this case the Oxford Nanopore Technologies MinION device. To make nanopore analysis possible, the NTER proteins were engineered with charged “tails” that get pulled into the tiny nanopore sensors by an electric field. Machine learning is then used to classify their electrical signals in order to determine the output levels of each NTER barcode.

    “This is a fundamentally new interface between cells and computers,” explained Allen School research professor and corresponding author Jeff Nivala. “One analogy I like to make is that fluorescent protein reporters are like lighthouses, and NanoporeTERs are like messages in a bottle. Lighthouses are really useful for communicating a physical location, as you can literally see where the signal is coming from, but it’s hard to pack more information into that kind of signal. A message in a bottle, on the other hand, can pack a lot of information into a very small vessel, and you can send many of them off to another location to be read. You might lose sight of the precise physical location where the messages were sent, but for many applications that’s not going to be an issue.”

    In developing this new, more expressive vessel, Nivala and his colleagues eschewed time-consuming sample preparation or the need for other specialized laboratory equipment to minimize both latency and cost. The NTERs scheme is also highly extensible. As a proof of concept, the team developed a library of more than 20 distinct tags; according to co-lead author Karen Zhang, the potential is significantly greater.

    3
    Co-authors of the Nature Biotechnology paper (left to right): Karen Zhang, Nicolas Cardozo, Kathryn Doroschak and Jeff Nivala. Not pictured: Aerilynn Nguyen, Zoheb Siddiqui, Nicholas Bogard, Karin Strauss and Luis Ceze. Credit: Tara Brown Photography.

    “We are currently working to scale up the number of NTERs to hundreds; thousands; maybe even millions more,” Zhang, who graduated this year from the UW with bachelor’s degrees in biochemistry and microbiology, explained. “The more we have, the more things we can track. We’re particularly excited about the potential in single-cell proteomics, but this could also be a game-changer in terms of our ability to do multiplexed biosensing to diagnose disease and even target therapeutics to specific areas inside the body. And debugging complicated genetic circuit designs would become a whole lot easier and much less time consuming if we could measure the performance of all the components in parallel instead of by trial and error.”

    MISL researchers have made novel use of the ONT MinION device before. Allen School alumna Kathryn Doroschak (Ph.D., ‘21), one of the lead co-authors of this paper, was also involved in an earlier project in which she and her teammates developed a molecular tagging system to replace conventional inventory control methods. That system relied on barcodes comprising synthetic strands of DNA that could be decoded on demand using the portable ONT reader. This time, she and her colleagues went a step further in demonstrating how versatile such devices can be.

    “This is the first paper to show how a commercial nanopore sensor device can be repurposed for applications other than the DNA and RNA sequencing for which they were originally designed,” explained Doroschak. “This is exciting as a precursor for nanopore technology becoming more accessible and ubiquitous in the future. You can already plug a nanopore device into your cell phone; I could envision someday having a choice of ‘molecular apps’ that will be relatively inexpensive and widely available outside of traditional genomics.”

    Additional co-authors of the paper include research assistants Aerilynn Nguyen and Zoheb Siddiqui, former postdoc Nicholas Bogard, Allen School affiliate professor Karin Strauss, senior principal research manager at Microsoft; and Allen School professor Luis Ceze.

    See the full article here .


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

    Please help promote STEM in your local schools.

    Stem Education Coalition

    About the University of Washington Paul G. Allen College of Electrical and Computer Engineering (US)

    Mission, Facts, and Stats

    Our mission is to develop outstanding engineers and ideas that change the world.

    Faculty:
    275 faculty (25.2% women)
    Achievements:

    128 NSF Young Investigator/Early Career Awards since 1984
    32 Sloan Foundation Research Awards
    2 MacArthur Foundation Fellows (2007 and 2011)

    A national leader in educating engineers, each year the College turns out new discoveries, inventions and top-flight graduates, all contributing to the strength of our economy and the vitality of our community.

    Engineering innovation

    PEOPLE Innovation at UW ECE is exemplified by our outstanding faculty and by the exceptional group of students they advise and mentor. Students receive a robust education through a strong technical foundation, group project work and hands-on research opportunities. Our faculty work in dynamic research areas with diverse opportunities for projects and collaborations. Through their research, they address complex global challenges in health, energy, technology and the environment, and receive significant research and education grants.IMPACT We continue to expand our innovation ecosystem by promoting an entrepreneurial mindset in our teaching and through diverse partnerships. The field of electrical and computer engineering is at the forefront of solving emerging societal challenges, empowered by innovative ideas from our community. As our department evolves, we are dedicated to expanding our faculty and student body to meet the growing demand for engineers. We welcomed six new faculty hires in the 2018-2019 academic year. Our meaningful connections and collaborations place the department as a leader in the field.

    Engineers drive the innovation economy and are vital to solving society’s most challenging problems. The College of Engineering is a key part of a world-class research university in a thriving hub of aerospace, biotechnology, global health and information technology innovation. Over 50% of UW startups in FY18 came from the College of Engineering.

    Commitment to diversity and access

    The College of Engineering is committed to developing and supporting a diverse student body and faculty that reflect and elevate the populations we serve. We are a national leader in women in engineering; 25.5% of our faculty are women compared to 17.4% nationally. We offer a robust set of diversity programs for students and faculty.
    Research and commercialization

    The University of Washington is an engine of economic growth, today ranked third in the nation for the number of startups launched each year, with 65 companies having been started in the last five years alone by UW students and faculty, or with technology developed here. The College of Engineering is a key contributor to these innovations, and engineering faculty, students or technology are behind half of all UW startups. In FY19, UW received $1.58 billion in total research awards from federal and nonfederal sources.

    u-washington-campus

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

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

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

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

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

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

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

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

    19th century relocation

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

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

    20th century expansion

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

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

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

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

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

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

    21st century

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

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

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

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

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

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

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

     
  • richardmitnick 12:41 pm on August 12, 2021 Permalink | Reply
    Tags: "Salt marsh resilience compromised by crabs along tidal creek edges", , Biology, Elkhorn Slough is one of the largest estuaries in California., The striped shore crab "Pachygrapsus crassipes",   

    From University of California-Santa Cruz (US) : “Salt marsh resilience compromised by crabs along tidal creek edges” 

    From University of California-Santa Cruz (US)

    August 09, 2021
    Tim Stephens
    stephens@ucsc.edu

    Coastal marshes are vulnerable to erosion caused by rising seas, pounding waves, and tidal flows. In Elkhorn Slough, these vulnerabilities are made worse by superabundant crabs found at their highest densities along the estuary’s tidal creeks, according to a new study published August 8 in Ecosphere.

    2
    The striped shore crab (Pachygrapsus crassipes) is a small crab found all along the West Coast of North America, and it is extremely abundant in Elkhorn Slough. Photo by K. Beheshti.

    The striped shore crab (Pachygrapsus crassipes) is a small crab found all along the West Coast of North America, and it is extremely abundant in Elkhorn Slough. The study demonstrated the dual role of these crabs as both consumers of salt marsh vegetation and as ecosystem engineers.

    “Their burrowing weakens the creekbank edges, so that whole chunks of marsh will sometimes calve off, and by lowering biomass they are reducing the ability of marsh plants to prevent erosion,” said lead author Kathryn Beheshti, who earned her Ph.D. in ecology and evolutionary biology at UC Santa Cruz in 2021 and is currently a California Sea Grant State Fellow at the Ocean Protection Council’s Climate Change Program.

    Beheshti and her coauthors conducted a five-year field experiment to assess the effects of crabs on the vegetation and sediments along eroding creekbank edges. Using fencing and traps made of empty tennis-ball cans to exclude crabs from experimental enclosures, they found that reducing crab abundance led to increased growth of salt marsh vegetation and enhanced sediment density.

    3
    Pickleweed grows noticeably taller and denser in the fenced area from which crabs are excluded.Photo by K. Beheshti.

    The researchers also found that the number of burrows did not change over the study period, even with researchers experimentally removing crabs. The unexpected persistence of the burrows highlights the value of long-term field experiments. The experiment was maintained for five years thanks in large part to the efforts of a team of over 50 UC Santa Cruz undergraduate students and high school interns.

    “Field experiments that span multiple seasons and years are rare,” said coauthor Kerstin Wasson, research coordinator of the Elkhorn Slough National Estuarine Research Reserve and an adjunct professor at UC Santa Cruz. “This work demonstrates the value of long-term studies by showing that burrows, which weaken the stability of tidal creek banks, persist despite the near absence of the crabs that build them.”

    Coauthor Brent Hughes, assistant professor at Sonoma State University (US), noted that the crabs were most abundant in spring and summer, when the pickleweed marshes are at peak production. “This synchrony suggests that the effect of crabs as consumers is more punctuated than their more chronic effect as engineers,” he said.

    Elkhorn Slough is one of the largest estuaries in California, with the largest tract of tidal salt marsh in the state outside of San Francisco Bay. It has been highly altered by human activities, however, and erosion along the edges of the tidal creeks and main channel is steadily eating away at the marsh.

    “It’s a big issue, because when the marsh erodes away along the tidal creeks it’s a permanent loss,” Beheshti said.

    The impacts of crabs on marsh biomass and soil structure near tidal creek banks are likely to make the marsh less resilient to erosion and sea-level rise, presenting a unique challenge to managers. Restoring populations of crab predators, such as herons, racoons, and sea otters, may be one way to mitigate these negative effects.

    “In this system, top-predator recovery is key,” said coauthor Brian Silliman, distinguished professor at Duke University (US).

    This collaborative study brought together marsh ecologists from both the East and West Coasts who have led the field in exploring how animals affect the marshes they inhabit. Over the past few decades, the U.S. East Coast has been the epicenter of studies exploring top-down effects in salt marshes, and this study is one of the few to explore such effects in a West Coast salt marsh.

    “Southeastern U.S. marshes appear to be a harbinger of what’s to come for marshes along the Pacific coast, with sea-level rise amplifying the effects of what would otherwise be considered an innocuous crab,” said coauthor Christine Angelini, associate professor at University of Florida (US).

    The authors called for similar long-term studies to be conducted in other West Coast marsh systems to determine how widespread these crab effects are. “It’d be great for contextualizing our findings,” Beheshti said. “We’d like to know if Elkhorn Slough is the canary in the coal mine, signaling yet another pathway for accelerated marsh edge loss for one of California’s rarest coastal habitats.”

    This work was supported in part by grants from the David H. Smith Conservation Research Fellowship, the Myers Ocean Trust, and Friends of Long Marine Laboratory.

    See the full article here .


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

    Please help promote STEM in your local schools.

    Stem Education Coalition
    The University of 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 in the South (large) Dome of main building.

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

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

    Caltech Logo

    From California Institute of Technology (US)

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

    1
    Shasha Chong. Credit: Caltech.

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

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

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

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

    Describe your work for us.

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

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

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

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

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

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

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

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

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

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

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

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

    What are you looking forward to most in joining Caltech?

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

    What do you like to do with your free time?

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

    See the full article here .


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

    Stem Education Coalition

    Caltech campus

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

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

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

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

    Research

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

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

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

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

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

     
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