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  • richardmitnick 3:21 pm on January 22, 2022 Permalink | Reply
    Tags: "Sprawling Coral Reef Resembling Roses Is Discovered Off Tahiti", , Biology, , Extending for about three kilometers (1.86 miles) the reef is remarkably well preserved and is among the largest ever found at its depth., Mesophotic reefs form their floral shape to gain more surface area and receive more light., , , The reef occupies an area of the ocean known as the mesophotic zone.   

    From The New York Times : “Sprawling Coral Reef Resembling Roses Is Discovered Off Tahiti” 

    From The New York Times

    Jan. 20, 2022
    Neil Vigdor

    The coral reef was discovered in November.Credit: Alexis Rosenfeld/Associated Press.

    An underwater mapping project recently took an unexpected twist off the coast of Tahiti, where deep sea explorers said this week that they had discovered a sprawling coral reef resembling a bed of roses that appeared to be largely unscathed by climate change.

    Extending for about three kilometers (1.86 miles), the reef is remarkably well preserved and is among the largest ever found at its depth, according to those involved in the mapping project sponsored by UNESCO, the U.N. Educational, Scientific and Cultural Organization.

    Some even described the condition of the reef, hidden at depths between 30 meters (about 100 feet) and 100 meters in the crystalline waters of the South Pacific, as “pristine.”

    Alexis Rosenfeld, an underwater photographer from Marseille, France, said on Thursday that the reef lived up to what he had envisioned when he first explored it shortly after its discovery in November.

    “This, my dream, is exactly the same as the reality,” Mr. Rosenfeld said of the reef, which is about two kilometers off the shore.

    Mr. Rosenfeld, 52, photographed the reef as part of a deep sea exploration project called 1 Ocean, partnering with UNESCO and researchers from CRIOBE, a prominent French laboratory specializing in the study of coral reef ecosystems, and The National Centre for Scientific Research [Centre national de la recherche scientifique [CNRS](FR).

    The reef occupies an area of the ocean known as the mesophotic zone — from the Greek words for middle and light — where the algae that coral depends on for survival can still grow but where light penetration is significantly diminished, scientists said.

    Unlike coral reefs found at shallower depths, which are often shaped like branches and are more susceptible to being damaged by rising ocean temperatures, scientists said, mesophotic reefs form their floral shape to gain more surface area and receive more light. To capture images in low-light conditions, Mr. Rosenfeld said he used a Sony Alpha 1, a mirrorless full-frame camera.

    Julian Barbière, the head of the Marine Policy and Regional Coordination Section for the Intergovernmental Oceanographic Commission at UNESCO, said on Thursday that he was blown away by the expanse of rose petals captured in the photos.

    “You can see them as far as the eye can see,” he said. “When they came back and showed the pictures, we were really amazed by the quality of the ecosystem there.”

    Mr. Barbière noted that climate change posed a significant threat to coral reefs, especially those at shallower depths, like the ones damaged in recent years in the South Pacific in what is known as bleaching. As part of that process, coral loses its color and its skeleton is exposed.

    “That can destroy or really impact the coral reef,” he said.

    Reaching the coral reef presented a particular challenge to scientists and photographers because of its depth, those involved in the project said. It required them to use special breathing equipment and a mixture of gases that contained helium, they said.

    John Jackson, a film director with 1 Ocean who is involved with the project, compared the reef’s shape to lacework. In an interview on Thursday, he said that significant work remained when it came to underwater exploration, pointing out that only about 20 percent of the world’s seabeds had been mapped.

    “We know every detail of Mars, every detail of the moon and certain planets,” Mr. Jackson said.

    Richard Norris, a professor of paleobiology at The Scripps Institution of Oceanography (US) at The University of California-San Diego (US), who was not involved with the project, said on Thursday that the discovery was gratifying.

    “Tahiti is nice because it’s far from sediment sources on land where the water could end up being cloudy and making it harder for the algae to grow in these deep water reefs,” Professor Norris said.

    He likened the relationship between coral and algae to that of the human body and yeast, saying that it was critical to maintain a delicate balance.

    “If they get stressed by, for example, unusually warm temperatures, then it turns a symbiotic relationship with the algae to one that is antagonistic, where the algae damage the coral and the coral gets rid of them,” Professor Norris said.

    Once the reef and the marine species that call it home are better understood, those involved in the project said that they would seek to adopt conservation measures to protect the ecosystem.

    “Without exploration,” Mr. Rosenfeld said, “you can’t have science.”

    See the full article here .


    Please help promote STEM in your local schools.

    Stem Education Coalition

  • richardmitnick 9:17 pm on January 20, 2022 Permalink | Reply
    Tags: "Disassembling Evolution’s Engine", , , Biologists discovered as spadefoot tadpoles grow their diet determines their appearance., Biology, , How the environment and form of a parent impacts the behavior and appearance of its offspring., In biology how are novel traits formed; how do phenotypes come to be; what that means for evolution., , , When a research project centered on evolution within spadefoot toads fell through Emily Harmon shifted her focus to microscopic swimmers called rotifers.   

    From Endeavors at The University of North Carolina (US) – Chapel Hill: “Disassembling Evolution’s Engine” 

    From Endeavors at The University of North Carolina (US) – Chapel Hill

    January 13th, 2022
    Megan Suggs

    When a research project centered on evolution within spadefoot toads fell through Emily Harmon shifted her focus to microscopic swimmers called rotifers. The biology PhD student is studying an animal’s ability to adapt in one generation, which could inform conservation efforts in the face of climate change.

    Emily Harmon, a PhD student in the Department of Biology, draws a plankton net from the water while collecting microscopic organisms called rotifers under the fishing dock at Jordan Lake in Chapel Hill. Photo by Andrew Russell.

    When we think of evolution, we imagine Charles Darwin’s Galápagos finches, their beaks lengthening or becoming more powerful over thousands of generations to decrease competition by specializing in one food source. Variation, improved survival, and heredity drive the slow process.

    Today, animals from corals to birds don’t have centuries to adapt to quickly shifting environments. One of the keys to surviving climate change may be an influence most evolutionary biologists have written off until recently.

    Animals changing form or behavior in response to environmental changes within their lifetime is called plasticity — a process Emily Harmon personally experienced while conducting research during the COVID-19 pandemic.

    As a UNC-Chapel Hill biology PhD student, Harmon studies how the environment and form of a parent impacts the behavior and appearance of its offspring. For example, an aphid on a crowded plant has offspring with wings so they can fly to a new plant.

    “These parental effects were once treated as a nuisance or something you needed to control in your experiment,” Harmon says. “In the 1990s, we realized this also plays a role in important things in biology, like how novel traits are formed, how phenotypes come to be, and what that means for evolution.”

    Finding the gas pump

    In 2019, Harmon began her research at the American Museum of Natural History’s Southwestern Research Station in the Chiricahua Mountains near the Mexican border. She collected spadefoot toads, which live where desert and mountains meet in southwestern United States. The landscape is a mix of orange, arid rocks and green oak, juniper, and pine forests.

    About 40 years ago, biologists discovered as spadefoot tadpoles grow, their diet determines their appearance. Those that eat detritus and plants grow into what are considered average omnivorous tadpoles. Those that eat small aquatic creatures, like shrimp, look different.

    “They become these big beefy carnivores,” Harmon says. “They have big jaw muscles. They have pointy mouth parts, and they’re much more likely to eat each other.”

    Ten years ago, biologists observed the mother’s traits also impacted whether tadpoles were destined for the large mouths, often used to eat its siblings. The bigger the mother, the more likely she was to have cannibalistic offspring. When Harmon started her PhD, she wanted to learn where the environment’s influence stopped and where the parent’s influence began. She also wanted to find out how a tadpole became “beefy” if it wasn’t determined by its genes and diet alone.

    “We were essentially focusing in on the egg as the factor through which some sort of information other than just genetic information was being passed down to the offspring,” Harmon says.

    Hypotheses ranged from protein variation to symbiotic bacteria entering the egg and shaping the offspring.

    Spadefoot toads are an ideal organism for studying parental effects because they do not raise their young. Otherwise, quality parenting would be one more variable to consider during the experiment. Harmon planned to travel to spadefoot toad populations in Arizona and New Mexico in 2020 to see what the mothers, eggs, and tadpoles looked like in nature.

    Then COVID-19 hit, and the research station closed. While Harmon could have collected toads, she couldn’t have conducted any experiments, so she turned her eye to a different species.

    Exploring the accelerator

    Harmon has since travelled to several lakes and ponds near Chapel Hill to collect microscopic creatures called rotifers. Like tadpoles, they’re omnivores — eating detritus, algae, and smaller aquatic animals. A certain type of rotifer called the Asplanchna, though, generationally changes form depending on what the parent eats.

    Considered one of the smallest organisms on Earth, rotifers can only be seen with a microscope. Photo courtesy of Wikimedia Commons.

    In the world of microscopic aquatic creatures, the key to survival is being too big to fit in the mouth of the next largest animal. If a rotifer consumes a lot of vitamin E from green algae, its offspring will be bigger, and appendages grow from their body, making them wider. If this second generation consumes enough vitamin E, its offspring will be five to 10 times the size of the original female. Like the spadefoot toad tadpoles, the third generation is carnivorous and often cannibalistic.

    Harmon is collecting Asplanchna from various sites to compare how responsive different lineages are to vitamin E. With this comparison, she hopes to demonstrate how transgenerational plasticity impacts species’ survival in the face of environmental change. This concept is the buying time hypothesis. If animals in a population can quickly adjust to an environmental shift to survive for more generations, it buys the species time to adapt and evolve into a form that better suits its new environment.

    Researchers have observed this in birds. Species that have more plasticity have persisted despite stressful conditions.

    Harmon is creating the first empirical test for the buying time hypothesis. Rotifers are a great subject because they have a fast generation time, it’s easy to maintain multiple lineages, and researchers can create the new environment for them to react to in a small jar.

    Right now, in collaboration with a rotifer researcher in Texas, Harmon is working to create Asplanchna colonies with ancestors from different ponds. Each colony will have plenty of vitamin E. She will document how much carnivorous offspring each colony produces to determine its plasticity. She’ll then introduce the colonies to an environmental change to see if those with more plasticity are better at survival.

    Rotifers can be found all over the world, which makes them easy for Harmon to find and collect across Chapel Hill’s numerous lakes and ponds. Photo by Andrew Russell.

    Harmon’s research could help determine if transgenerational plasticity can help a species persist for multiple generations and eventually evolve. If that’s the case, conservation strategies could shift. Often, conservationists try to introduce new genetic material to a species to increase variation to drive adaptation. For some species, it might be in their best interest to try to trigger plasticity instead.

    “It might even be possible to pre-expose species to stressful environments so that they can develop a plastic response that could be passed down across generations,” Harmon says.

    So far, that’s worked for Harmon, who – like most of us – has found the pandemic frustrating but good for adaptation. She enjoys her new project on rotifers and sees a lot of potential.

    “When it was clear the work with spadefoot toads would be infeasible, I was able to step back, figure out what questions I was really interested in, and pick a study system best suited for that work,” she says. “If this works out, I’ll have not just contributed to the spadefoot system, but started to carve out my own area in the field.”

    See the full article here .


    Please help promote STEM in your local schools.

    Stem Education Coalition

    UNC bloc

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

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

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

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

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

  • richardmitnick 5:20 pm on January 20, 2022 Permalink | Reply
    Tags: "A huge project is underway to sequence the genome of every complex species on Earth", , Biology, , ,   

    From The Conversation: “A huge project is underway to sequence the genome of every complex species on Earth” 

    From The Conversation

    January 18, 2022
    Jenny Graves
    Distinguished Professor of Genetics and Vice Chancellor’s Fellow,
    La Trobe University (AU)

    Chromosomes consist of long double-helical arrays of the four base pairs whose sequence specifies genes. DNA molecules are capped at the end by telomeres. Shutterstock.

    The Earth Biogenome Project, a global consortium that aims to sequence the genomes of all complex life on earth (some 1.8 million described species) in ten years, is ramping up.

    The project’s origins, aims and progress are detailed in two multi-authored papers published [PNAS] today. Once complete, it will forever change the way biological research is done.

    Specifically, researchers will no longer be limited to a few “model species” and will be able to mine the DNA sequence database of any organism that shows interesting characteristics. This new information will help us understand how complex life evolved, how it functions, and how biodiversity can be protected.

    The project was first proposed [PNAS] in 2016, and I was privileged to speak at its launch in London in 2018. It is currently in the process of moving from its startup phase to full-scale production.

    The aim of phase one is to sequence one genome from every taxonomic family on earth, some 9,400 of them. By the end of 2022, one-third of these species should be done. Phase two will see the sequencing of a representative from all 180,000 genera, and phase three will mark the completion of all the species.

    The importance of weird species

    The grand aim of the Earth Biogenome Project is to sequence the genomes of all 1.8 million described species of complex life on Earth. This includes all plants, animals, fungi, and single-celled organisms with true nuclei (that is, all “eukaryotes”).

    While model organisms like mice, rock cress, fruit flies and nematodes have been tremendously important in our understanding of gene functions, it’s a huge advantage to be able to study other species that may work a bit differently.

    Many important biological principles came from studying obscure organisms. For instance, genes were famously discovered by Gregor Mendel in peas, and the rules that govern them were discovered in red bread mould.

    DNA was discovered first in salmon sperm, and our knowledge of some systems that keep it secure came from research on tardigrades. Chromosomes were first seen in mealworms and sex chromosomes in a beetle (sex chromosome action and evolution has also been explored in fish and platypus). And telomeres, which cap the ends of chromosomes, were discovered in pond scum.

    Answering biological questions and protecting biodiversity

    Comparing closely and distantly related species provides tremendous power to discover what genes do and how they are regulated. For instance, in another PNAS paper, coincidentally also published today, my University of Canberra (AU) colleagues and I discovered Australian dragon lizards regulate sex by the chromosome neighbourhood of a sex gene, rather than the DNA sequence itself.

    Scientists also use species comparisons to trace genes and regulatory systems back to their evolutionary origins, which can reveal astonishing conservation of gene function across nearly a billion years. For instance, the same genes are involved in retinal development in humans and in fruit fly photoreceptors. And the BRCA1 gene that is mutated in breast cancer is responsible for repairing DNA breaks in plants and animals.

    The genome of animals is also far more conserved than has been supposed. For instance, several colleagues and I recently demonstrated [The International Journal of Developmental Biology] that animal chromosomes are 684 million years old.

    It will be exciting, too, to explore the “dark matter” of the genome, and reveal how DNA sequences that don’t encode proteins can still play a role in genome function and evolution.

    Another important aim of the Earth Biogenome Project is conservation genomics. This field uses DNA sequencing to identify threatened species, which includes about 28% of the world’s complex organisms – helping us monitor their genetic health and advise on management.

    No longer an impossible task

    Until recently, sequencing large genomes took years and many millions of dollars. But there have been tremendous technical advances that now make it possible to sequence and assemble large genomes for a few thousand dollars. The entire Earth Biogenome Project will cost less in today’s dollars than the human genome project, which was worth about US$3 billion in total.

    In the past, researchers would have to identify the order of the four bases chemically on millions of tiny DNA fragments, then paste the entire sequence together again. Today they can register different bases based on their physical properties, or by binding each of the four bases to a different dye. New sequencing methods [The National Human Genome Research Institute (NHGRI) (US)] can scan long molecules of DNA that are tethered in tiny tubes, or squeezed through tiny holes in a membrane.

    Why sequence everything?

    But why not save time and money by sequencing just key representative species?

    Well, the whole point of the Earth Biogenome Project is to exploit the variation between species to make comparisons, and also to capture remarkable innovations in outliers.

    There is also the fear of missing out. For instance, if we sequence only 69,999 of the 70,000 species of nematode, we might miss the one that could divulge the secrets of how nematodes can cause diseases in animals and plants.

    There are currently 44 affiliated institutions in 22 countries working on the Earth Biogenome Project. There are also 49 affiliated projects, including enormous projects such as The California Conservation Genomics Project (US), The Bird 10,000 Genomes Project (CN) and The Darwin Tree of Life Project (UK), as well as many projects on particular groups such as bats and butterflies.

    See the full article here .


    Please help promote STEM in your local schools.

    Stem Education Coalition

    The Conversation launched as a pilot project in October 2014. It is an independent source of news and views from the academic and research community, delivered direct to the public.
    Our team of professional editors work with university and research institute experts to unlock their knowledge for use by the wider public.
    Access to independent, high quality, authenticated, explanatory journalism underpins a functioning democracy. Our aim is to promote better understanding of current affairs and complex issues. And hopefully allow for a better quality of public discourse and conversation.

  • richardmitnick 10:22 am on January 20, 2022 Permalink | Reply
    Tags: "New Study Sheds Light on Origins of Life on Earth", , , , Biology, Evolution of protein structures entails understanding how new folds arose from previously existing ones., , , , The ability to shuffle electrons was paramount to life., The best elements for electron transfer are metals., The metal-binding cores of existing proteins are indeed similar even though the proteins themselves may not be., The researchers explored how primitive life may have originated on our planet from simple non-living materials., The researchers studied proteins that bind metals., They compared all existing protein structures that bind metals to establish any common features.   

    From Rutgers University (US): “New Study Sheds Light on Origins of Life on Earth” 

    Rutgers smaller
    Our Great Seal.

    From Rutgers University (US)

    January 14, 2022
    John Cramer

    A Rutgers-led team has discovered the structures of proteins that may be responsible for the origins of life in the primordial soup of ancient Earth.Credit: Shutterstock.

    Addressing one of the most profoundly unanswered questions in biology, a Rutgers-led team has discovered the structures of proteins that may be responsible for the origins of life in the primordial soup of ancient Earth.

    The study appears in the journal Science Advances.

    The researchers explored how primitive life may have originated on our planet from simple non-living materials. They asked what properties define life as we know it and concluded that anything alive would have needed to collect and use energy, from sources such as the Sun or hydrothermal vents.

    In molecular terms, this would mean that the ability to shuffle electrons was paramount to life. Since the best elements for electron transfer are metals (think standard electrical wires) and most biological activities are carried out by proteins, the researchers decided to explore the combination of the two — that is, proteins that bind metals.

    They compared all existing protein structures that bind metals to establish any common features, based on the premise that these shared features were present in ancestral proteins and were diversified and passed down to create the range of proteins we see today.

    Evolution of protein structures entails understanding how new folds arose from previously existing ones, so the researchers designed a computational method that found the vast majority of currently existing metal-binding proteins are somewhat similar regardless of the type of metal they bind to, the organism they come from or the functionality assigned to the protein as a whole.

    “We saw that the metal-binding cores of existing proteins are indeed similar even though the proteins themselves may not be,” said the study’s lead author Yana Bromberg, a professor in the Department of Biochemistry and Microbiology at Rutgers University-New Brunswick. “We also saw that these metal-binding cores are often made up of repeated substructures, kind of like LEGO blocks. Curiously, these blocks were also found in other regions of the proteins, not just metal-binding cores, and in many other proteins that were not considered in our study. Our observation suggests that rearrangements of these little building blocks may have had a single or a small number of common ancestors and given rise to the whole range of proteins and their functions that are currently available — that is, to life as we know it.”

    “We have very little information about how life arose on this planet, and our work contributes a previously unavailable explanation,” said Bromberg, whose research focuses on deciphering the DNA blueprints of life’s molecular machinery. “This explanation could also potentially contribute to our search for life on other planets and planetary bodies. Our finding of the specific structural building blocks is also possibly relevant for synthetic biology efforts, where scientists aim to construct specifically active proteins anew.”

    The study, funded by The National Aeronautics and Space Agency(US), also included researchers from The University of Buenos Aires [Universidad de Buenos Aires] (AR).

    See the full article here .


    Please help promote STEM in your local schools.

    Stem Education Coalition


    Rutgers, The State University of New Jersey (US), is a leading national research university and the state’s preeminent, comprehensive public institution of higher education. Rutgers is dedicated to teaching that meets the highest standards of excellence; to conducting research that breaks new ground; and to providing services, solutions, and clinical care that help individuals and the local, national, and global communities where they live.

    Founded in 1766, Rutgers teaches across the full educational spectrum: preschool to precollege; undergraduate to graduate; postdoctoral fellowships to residencies; and continuing education for professional and personal advancement.

    Rutgers University (US) is a public land-grant research university based in New Brunswick, New Jersey. Chartered in 1766, Rutgers was originally called Queen’s College, and today it is the eighth-oldest college in the United States, the second-oldest in New Jersey (after Princeton University (US)), and one of the nine U.S. colonial colleges that were chartered before the American War of Independence. In 1825, Queen’s College was renamed Rutgers College in honor of Colonel Henry Rutgers, whose substantial gift to the school had stabilized its finances during a period of uncertainty. For most of its existence, Rutgers was a private liberal arts college but it has evolved into a coeducational public research university after being designated The State University of New Jersey by the New Jersey Legislature via laws enacted in 1945 and 1956.

    Rutgers today has three distinct campuses, located in New Brunswick (including grounds in adjacent Piscataway), Newark, and Camden. The university has additional facilities elsewhere in the state, including oceanographic research facilities at the New Jersey shore. Rutgers is also a land-grant university, a sea-grant university, and the largest university in the state. Instruction is offered by 9,000 faculty members in 175 academic departments to over 45,000 undergraduate students and more than 20,000 graduate and professional students. The university is accredited by the Middle States Association of Colleges and Schools and is a member of the Big Ten Academic Alliance, the Association of American Universities (US) and the Universities Research Association (US). Over the years, Rutgers has been considered a Public Ivy.


    Rutgers is home to the Rutgers University Center for Cognitive Science, also known as RUCCS. This research center hosts researchers in psychology, linguistics, computer science, philosophy, electrical engineering, and anthropology.

    It was at Rutgers that Selman Waksman (1888–1973) discovered several antibiotics, including actinomycin, clavacin, streptothricin, grisein, neomycin, fradicin, candicidin, candidin, and others. Waksman, along with graduate student Albert Schatz (1920–2005), discovered streptomycin—a versatile antibiotic that was to be the first applied to cure tuberculosis. For this discovery, Waksman received the Nobel Prize for Medicine in 1952.

    Rutgers developed water-soluble sustained release polymers, tetraploids, robotic hands, artificial bovine insemination, and the ceramic tiles for the heat shield on the Space Shuttle. In health related field, Rutgers has the Environmental & Occupational Health Science Institute (EOHSI).

    Rutgers is also home to the RCSB Protein Data bank, “…an information portal to Biological Macromolecular Structures’ cohosted with the San Diego Supercomputer Center (US). This database is the authoritative research tool for bioinformaticists using protein primary, secondary and tertiary structures worldwide….”

    Rutgers is home to the Rutgers Cooperative Research & Extension office, which is run by the Agricultural and Experiment Station with the support of local government. The institution provides research & education to the local farming and agro industrial community in 19 of the 21 counties of the state and educational outreach programs offered through the New Jersey Agricultural Experiment Station Office of Continuing Professional Education.

    Rutgers University Cell and DNA Repository (RUCDR) is the largest university based repository in the world and has received awards worth more than $57.8 million from the National Institutes of Health (US). One will fund genetic studies of mental disorders and the other will support investigations into the causes of digestive, liver and kidney diseases, and diabetes. RUCDR activities will enable gene discovery leading to diagnoses, treatments and, eventually, cures for these diseases. RUCDR assists researchers throughout the world by providing the highest quality biomaterials, technical consultation, and logistical support.

    Rutgers–Camden is home to the nation’s PhD granting Department of Childhood Studies. This department, in conjunction with the Center for Children and Childhood Studies, also on the Camden campus, conducts interdisciplinary research which combines methodologies and research practices of sociology, psychology, literature, anthropology and other disciplines into the study of childhoods internationally.

    Rutgers is home to several National Science Foundation (US) IGERT fellowships that support interdisciplinary scientific research at the graduate-level. Highly selective fellowships are available in the following areas: Perceptual Science, Stem Cell Science and Engineering, Nanotechnology for Clean Energy, Renewable and Sustainable Fuels Solutions, and Nanopharmaceutical Engineering.

    Rutgers also maintains the Office of Research Alliances that focuses on working with companies to increase engagement with the university’s faculty members, staff and extensive resources on the four campuses.

    As a ’67 graduate of University College, second in my class, I am proud to be a member of

    Alpha Sigma Lamda, National Honor Society of non-tradional students.

  • richardmitnick 5:22 pm on January 19, 2022 Permalink | Reply
    Tags: "Crystallography for the Misfit Crystals", , , Biology, , , Francis Crick-who famously co-discovered the shape of DNA- said: “If you want to understand function study structure.” This remains a tenet of biology; chemistry and materials science., , Linac Coherent Light Source [LCLS] at DOE's SLAC National Accelerator Laboratory (US)., , Molecular Foundry at Berkeley Lab, National Energy Research Scientific Computing Center [NERSC] at Berkeley Lab, Serial femtosecond X-ray crystallography process, smSFX uses an X-ray free electron laser (XFEL)., smSFX: small-molecule serial femtosecond X-ray crystallography, SPring-8 Angstrom Compact free electron LAser (SACLA) at Riken [理研](JP)., X-ray crystallography is most straightforward when the material can be grown into a large single crystal., X-ray crystallography: a technique that maps the density of electrons in a molecule based on how beams of X-ray radiation diffract through the spaces between atoms in the sample.   

    From DOE’s Lawrence Berkeley National Laboratory (US): “Crystallography for the Misfit Crystals” 

    From DOE’s Lawrence Berkeley National Laboratory (US)

    January 19, 2022
    Aliyah Kovner

    An illustration of the serial femtosecond X-ray crystallography process, showing a jet of liquid solvent combined with the sample particles being blasted with the laser beam to capture diffraction data. This action is completed in just a few femtoseconds – that is quadrillionths of a second, or a few millionths of one billionth of a second. Credit: Ella Maru Studio.

    Francis Crick-who famously co-discovered the shape of DNA-once said: “If you want to understand function study structure.” Many decades later, this remains a tenet of biology, chemistry, and materials science.

    A key breakthrough in the quest for DNA’s structure came from X-ray crystallography, a technique that maps the density of electrons in a molecule based on how beams of X-ray radiation diffract through the spaces between atoms in the sample. The diffraction patterns generated by crystallography can then be used to deduce the overall molecular structure. Thanks to a steady stream of advances over the decades, X-ray crystallography is now exponentially more powerful than it was in Crick’s time, and can even reveal the placement of individual atoms.

    Yet the process is not easy. As the name implies, it requires crystals – specifically, purified samples of the molecule of interest, coaxed into a crystal form. And not all molecules form picture-ready crystals.

    “X-ray crystallography is most straightforward when the material can be grown into a large single crystal,” said Nicholas Sauter, a computer senior scientist at Lawrence Berkeley National Laboratory (Berkeley Lab), in the Molecular Biophysics and Integrated Bioimaging (MBIB) division. “However, most substances instead form powders composed of small granules, whose X-ray diffraction patterns are harder to disentangle.”

    Sauter is co-leading a team working to provide a better way for scientists to study the structures of the many materials that don’t form tidy single crystals, such as solar absorbers and metal-organic frameworks: two diverse material groups with huge potential for combating climate change and producing renewable energy.

    Their new technique, called small-molecule serial femtosecond X-ray crystallography, or smSFX, supercharges traditional crystallography with the addition of custom-built image processing algorithms and an X-ray free electron laser (XFEL). The XFEL, built from a fusion of particle accelerator and laser-based physics, can point X-ray beams that are much more powerful, focused, and speedy than other X-ray sources for crystallography. The entire process, from X-ray pulse to diffraction image, is completed in a few quadrillionths of a second.

    “It’s diffraction before destruction,” said Daniel Paley, an MBIB project scientist and author on the team’s new paper, published today in Nature. “The idea is that the crystal is going to explode instantly when it’s hit by this beam of photons, but with a femtosecond pulse, you collect all the diffraction data before the damage occurs. It’s really cool.”

    Part of the XFEL where the sample is injected into the path of the X-ray beam. This XFEL facility, called the SPring-8 Angstrom Compact free electron LAser (SACLA) is in Japan. The team traveled there and performed their experiments in 2019. Credit: Nate Hohman/The University of Connecticut(US))

    SACLA Free-Electron – Laser Riken [理研](JP) Japan.

    Paley and co-leader Aaron Brewster, a research scientist in MBIB, developed the algorithms needed to convert XFEL data into high-quality diffraction patterns that can be analyzed to reveal the unit cell – the basic unit of a crystal that is repeated over and over in three dimensions – of each tiny crystalline grain within the sample.

    When you have a true powder, Paley explained, it’s like having a million crystals that are all jumbled together, full of imperfections, and scrambled in every possible orientation. Rather than diffracting the whole jumble together and getting a muddied readout of electron densities (which is what happens with existing powder diffraction techniques), smSFX is so precise that it can diffract individual granules, one at a time. “This gives it a special sharpening effect,” he said. “So that is actually the kind of secret sauce of this whole method. Normally you shoot all million at once, but now you shoot 10,000 all in sequence.”

    The cherry on top is that smSFX is performed without freezing the sample or exposing it to a vacuum – another benefit for the delicate materials studied by materials scientists. “No fancy vacuum chamber required,” said Sauter.

    (Left) The team, pictured in 2019, preparing for an XFEL session with their mascot. (Right) An image of the sample injection apparatus, full of a sample of mithrene, a metallic-organic material that glows blue when exposed to UV light. Credit: Nate Hohman/University of Connecticut.

    In the new study, the team demonstrated proof-of-principle for smSFX, then went one step further. They reported the previously unknown structures of two metal-organic materials known as chacogenolates. Nathan Hohman, a chemical physicist at University of Connecticut and the project’s third co-leader, studies chacogenolates for their semiconducting and light-interaction properties, which could make them ideal for next-generation transistors, photovoltaics (solar cells and panels), energy storage devices, and sensors.

    “Every single one of these is a special snowflake – growing them is really difficult,” said Hohman. With smSFX, he and graduate student Elyse Schriber were able to successfully diffract powder chacogenolates and examine the structures to learn why some of the silver-based materials glow bright blue under UV light, a phenomenon that the scientists affectionately compare to Frodo’s sword in The Lord of the Rings.

    “There is a huge array of fascinating physical and even chemical dynamics that occur at ultrafast timescales, and our experiment could help to connect the dots between a material’s structure and its function,” said Schriber, a Berkeley Lab affiliate and researcher in Hohman’s lab. “After further improvements are made to streamline the smSFX process, we can imagine programs to offer this technique to other researchers. These types of programs are integral for increasing access to light source facilities, especially for smaller universities and colleges.”

    An illustrated collage composed of all the diffraction data gathered at the SACLA. Credit: Nate Hohman/University of Connecticut.

    This work involved the use of the SACLA free-electron laser in Japan [above], the Linac Coherent Light Source at DOE’s SLAC National Accelerator Laboratory (US), and the National Energy Research Scientific Computing Center [below] and Molecular Foundry [below], two U.S. Department of Energy Office of Science user facilities located at Berkeley Lab.


    See the full article here.


    Please help promote STEM in your local schools.

    Stem Education Coalition

    LBNL campus

    LBNL Molecular Foundry

    Bringing Science Solutions to the World

    In the world of science, Lawrence Berkeley National Laboratory (Berkeley Lab) (US) is synonymous with “excellence.” Thirteen Nobel prizes are associated with Berkeley Lab. Seventy Lab scientists are members of the The National Academy of Sciences (US), one of the highest honors for a scientist in the United States. Thirteen of our scientists have won the National Medal of Science, our nation’s highest award for lifetime achievement in fields of scientific research. Eighteen of our engineers have been elected to the The National Academy of Engineering (US), and three of our scientists have been elected into the Institute of Medicine. In addition, Berkeley Lab has trained thousands of university science and engineering students who are advancing technological innovations across the nation and around the world.

    Berkeley Lab is a member of the national laboratory system supported by the U.S. Department of Energy through its Office of Science. It is managed by the University of California (US) and is charged with conducting unclassified research across a wide range of scientific disciplines. Located on a 202-acre site in the hills above the University of California- Berkeley campus that offers spectacular views of the San Francisco Bay, Berkeley Lab employs approximately 3,232 scientists, engineers and support staff. The Lab’s total costs for FY 2014 were $785 million. A recent study estimates the Laboratory’s overall economic impact through direct, indirect and induced spending on the nine counties that make up the San Francisco Bay Area to be nearly $700 million annually. The Lab was also responsible for creating 5,600 jobs locally and 12,000 nationally. The overall economic impact on the national economy is estimated at $1.6 billion a year. Technologies developed at Berkeley Lab have generated billions of dollars in revenues, and thousands of jobs. Savings as a result of Berkeley Lab developments in lighting and windows, and other energy-efficient technologies, have also been in the billions of dollars.

    Berkeley Lab was founded in 1931 by Ernest Orlando Lawrence, a University of California-Berkeley (US) physicist who won the 1939 Nobel Prize in physics for his invention of the cyclotron, a circular particle accelerator that opened the door to high-energy physics. It was Lawrence’s belief that scientific research is best done through teams of individuals with different fields of expertise, working together. His teamwork concept is a Berkeley Lab legacy that continues today.



    The laboratory was founded on August 26, 1931, by Ernest Lawrence, as the Radiation Laboratory of the University of California, Berkeley, associated with the Physics Department. It centered physics research around his new instrument, the cyclotron, a type of particle accelerator for which he was awarded the Nobel Prize in Physics in 1939.

    LBNL 88 inch cyclotron.

    LBNL 88 inch cyclotron.

    Throughout the 1930s, Lawrence pushed to create larger and larger machines for physics research, courting private philanthropists for funding. He was the first to develop a large team to build big projects to make discoveries in basic research. Eventually these machines grew too large to be held on the university grounds, and in 1940 the lab moved to its current site atop the hill above campus. Part of the team put together during this period includes two other young scientists who went on to establish large laboratories; J. Robert Oppenheimer founded DOE’s Los Alamos Laboratory (US), and Robert Wilson founded Fermi National Accelerator Laboratory(US).


    Leslie Groves visited Lawrence’s Radiation Laboratory in late 1942 as he was organizing the Manhattan Project, meeting J. Robert Oppenheimer for the first time. Oppenheimer was tasked with organizing the nuclear bomb development effort and founded today’s Los Alamos National Laboratory to help keep the work secret. At the RadLab, Lawrence and his colleagues developed the technique of electromagnetic enrichment of uranium using their experience with cyclotrons. The “calutrons” (named after the University) became the basic unit of the massive Y-12 facility in Oak Ridge, Tennessee. Lawrence’s lab helped contribute to what have been judged to be the three most valuable technology developments of the war (the atomic bomb, proximity fuse, and radar). The cyclotron, whose construction was stalled during the war, was finished in November 1946. The Manhattan Project shut down two months later.


    After the war, the Radiation Laboratory became one of the first laboratories to be incorporated into the Atomic Energy Commission (AEC) (now Department of Energy (US). The most highly classified work remained at Los Alamos, but the RadLab remained involved. Edward Teller suggested setting up a second lab similar to Los Alamos to compete with their designs. This led to the creation of an offshoot of the RadLab (now the Lawrence Livermore National Laboratory (US)) in 1952. Some of the RadLab’s work was transferred to the new lab, but some classified research continued at Berkeley Lab until the 1970s, when it became a laboratory dedicated only to unclassified scientific research.

    Shortly after the death of Lawrence in August 1958, the UC Radiation Laboratory (both branches) was renamed the Lawrence Radiation Laboratory. The Berkeley location became the Lawrence Berkeley Laboratory in 1971, although many continued to call it the RadLab. Gradually, another shortened form came into common usage, LBNL. Its formal name was amended to Ernest Orlando Lawrence Berkeley National Laboratory in 1995, when “National” was added to the names of all DOE labs. “Ernest Orlando” was later dropped to shorten the name. Today, the lab is commonly referred to as “Berkeley Lab”.

    The Alvarez Physics Memos are a set of informal working papers of the large group of physicists, engineers, computer programmers, and technicians led by Luis W. Alvarez from the early 1950s until his death in 1988. Over 1700 memos are available on-line, hosted by the Laboratory.

    The lab remains owned by the Department of Energy (US), with management from the University of California (US). Companies such as Intel were funding the lab’s research into computing chips.

    Science mission

    From the 1950s through the present, Berkeley Lab has maintained its status as a major international center for physics research, and has also diversified its research program into almost every realm of scientific investigation. Its mission is to solve the most pressing and profound scientific problems facing humanity, conduct basic research for a secure energy future, understand living systems to improve the environment, health, and energy supply, understand matter and energy in the universe, build and safely operate leading scientific facilities for the nation, and train the next generation of scientists and engineers.

    The Laboratory’s 20 scientific divisions are organized within six areas of research: Computing Sciences; Physical Sciences; Earth and Environmental Sciences; Biosciences; Energy Sciences; and Energy Technologies. Berkeley Lab has six main science thrusts: advancing integrated fundamental energy science; integrative biological and environmental system science; advanced computing for science impact; discovering the fundamental properties of matter and energy; accelerators for the future; and developing energy technology innovations for a sustainable future. It was Lawrence’s belief that scientific research is best done through teams of individuals with different fields of expertise, working together. His teamwork concept is a Berkeley Lab tradition that continues today.

    Berkeley Lab operates five major National User Facilities for the DOE Office of Science (US):

    The Advanced Light Source (ALS) is a synchrotron light source with 41 beam lines providing ultraviolet, soft x-ray, and hard x-ray light to scientific experiments.


    DOE’s Lawrence Berkeley National Laboratory (US) Advanced Light Source .
    The ALS is one of the world’s brightest sources of soft x-rays, which are used to characterize the electronic structure of matter and to reveal microscopic structures with elemental and chemical specificity. About 2,500 scientist-users carry out research at ALS every year. Berkeley Lab is proposing an upgrade of ALS which would increase the coherent flux of soft x-rays by two-three orders of magnitude.

    The DOE Joint Genome Institute (US) supports genomic research in support of the DOE missions in alternative energy, global carbon cycling, and environmental management. The JGI’s partner laboratories are Berkeley Lab, DOE’s Lawrence Livermore National Laboratory (US), DOE’s Oak Ridge National Laboratory (US)(ORNL), DOE’s Pacific Northwest National Laboratory (US) (PNNL), and the HudsonAlpha Institute for Biotechnology (US). The JGI’s central role is the development of a diversity of large-scale experimental and computational capabilities to link sequence to biological insights relevant to energy and environmental research. Approximately 1,200 scientist-users take advantage of JGI’s capabilities for their research every year.

    The LBNL Molecular Foundry (US) [above] is a multidisciplinary nanoscience research facility. Its seven research facilities focus on Imaging and Manipulation of Nanostructures; Nanofabrication; Theory of Nanostructured Materials; Inorganic Nanostructures; Biological Nanostructures; Organic and Macromolecular Synthesis; and Electron Microscopy. Approximately 700 scientist-users make use of these facilities in their research every year.

    The DOE’s NERSC National Energy Research Scientific Computing Center (US) is the scientific computing facility that provides large-scale computing for the DOE’s unclassified research programs. Its current systems provide over 3 billion computational hours annually. NERSC supports 6,000 scientific users from universities, national laboratories, and industry.

    DOE’s NERSC National Energy Research Scientific Computing Center(US) at Lawrence Berkeley National Laboratory.

    Cray Cori II supercomputer at National Energy Research Scientific Computing Center(US) at DOE’s Lawrence Berkeley National Laboratory(US), named after Gerty Cori, the first American woman to win a Nobel Prize in science.

    NERSC Hopper Cray XE6 supercomputer.

    NERSC Cray XC30 Edison supercomputer.

    NERSC GPFS for Life Sciences.

    The Genepool system is a cluster dedicated to the DOE Joint Genome Institute’s computing needs. Denovo is a smaller test system for Genepool that is primarily used by NERSC staff to test new system configurations and software.

    NERSC PDSF computer cluster in 2003.

    PDSF is a networked distributed computing cluster designed primarily to meet the detector simulation and data analysis requirements of physics, astrophysics and nuclear science collaborations.

    Cray Shasta Perlmutter SC18 AMD Epyc Nvidia pre-exascale supercomputer.

    NERSC is a DOE Office of Science User Facility.

    The DOE’s Energy Science Network (US) is a high-speed network infrastructure optimized for very large scientific data flows. ESNet provides connectivity for all major DOE sites and facilities, and the network transports roughly 35 petabytes of traffic each month.

    Berkeley Lab is the lead partner in the DOE’s Joint Bioenergy Institute (US) (JBEI), located in Emeryville, California. Other partners are the DOE’s Sandia National Laboratory (US), the University of California (UC) campuses of Berkeley and Davis, the Carnegie Institution for Science (US), and DOE’s Lawrence Livermore National Laboratory (US) (LLNL). JBEI’s primary scientific mission is to advance the development of the next generation of biofuels – liquid fuels derived from the solar energy stored in plant biomass. JBEI is one of three new U.S. Department of Energy (DOE) Bioenergy Research Centers (BRCs).

    Berkeley Lab has a major role in two DOE Energy Innovation Hubs. The mission of the Joint Center for Artificial Photosynthesis (JCAP) is to find a cost-effective method to produce fuels using only sunlight, water, and carbon dioxide. The lead institution for JCAP is the California Institute of Technology (US) and Berkeley Lab is the second institutional center. The mission of the Joint Center for Energy Storage Research (JCESR) is to create next-generation battery technologies that will transform transportation and the electricity grid. DOE’s Argonne National Laboratory (US) leads JCESR and Berkeley Lab is a major partner.

    The University of California-Berkeley US) is a public land-grant research university in Berkeley, California. Established in 1868 as the state’s first land-grant university, it was the first campus of the University of California (US) system and a founding member of the Association of American Universities (US). Its 14 colleges and schools offer over 350 degree programs and enroll some 31,000 undergraduate and 12,000 graduate students. Berkeley is ranked among the world’s top universities by major educational publications.

    Berkeley hosts many leading research institutes, including the Mathematical Sciences Research Institute and the Space Sciences Laboratory. It founded and maintains close relationships with three national laboratories at DOE’s Lawrence Berkeley National Laboratory(US), DOE’s Lawrence Livermore National Laboratory(US) and DOE’s Los Alamos National Lab(US), and has played a prominent role in many scientific advances, from the Manhattan Project and the discovery of 16 chemical elements to breakthroughs in computer science and genomics. Berkeley is also known for student activism and the Free Speech Movement of the 1960s.

    Berkeley alumni and faculty count among their ranks 110 Nobel laureates (34 alumni), 25 Turing Award winners (11 alumni), 14 Fields Medalists, 28 Wolf Prize winners, 103 MacArthur “Genius Grant” recipients, 30 Pulitzer Prize winners, and 19 Academy Award winners. The university has produced seven heads of state or government; five chief justices, including Chief Justice of the United States Earl Warren; 21 cabinet-level officials; 11 governors; and 25 living billionaires. It is also a leading producer of Fulbright Scholars, MacArthur Fellows, and Marshall Scholars. Berkeley alumni, widely recognized for their entrepreneurship, have founded many notable companies.

    Berkeley’s athletic teams compete in Division I of the NCAA, primarily in the Pac-12 Conference, and are collectively known as the California Golden Bears. The university’s teams have won 107 national championships, and its students and alumni have won 207 Olympic medals.

    Made possible by President Lincoln’s signing of the Morrill Act in 1862, the University of California was founded in 1868 as the state’s first land-grant university by inheriting certain assets and objectives of the private College of California and the public Agricultural, Mining, and Mechanical Arts College. Although this process is often incorrectly mistaken for a merger, the Organic Act created a “completely new institution” and did not actually merge the two precursor entities into the new university. The Organic Act states that the “University shall have for its design, to provide instruction and thorough and complete education in all departments of science, literature and art, industrial and professional pursuits, and general education, and also special courses of instruction in preparation for the professions”.

    Ten faculty members and 40 students made up the fledgling university when it opened in Oakland in 1869. Frederick H. Billings, a trustee of the College of California, suggested that a new campus site north of Oakland be named in honor of Anglo-Irish philosopher George Berkeley. The university began admitting women the following year. In 1870, Henry Durant, founder of the College of California, became its first president. With the completion of North and South Halls in 1873, the university relocated to its Berkeley location with 167 male and 22 female students.

    Beginning in 1891, Phoebe Apperson Hearst made several large gifts to Berkeley, funding a number of programs and new buildings and sponsoring, in 1898, an international competition in Antwerp, Belgium, where French architect Émile Bénard submitted the winning design for a campus master plan.

    20th century

    In 1905, the University Farm was established near Sacramento, ultimately becoming the University of California-Davis. In 1919, Los Angeles State Normal School became the southern branch of the University, which ultimately became the University of California-Los Angeles. By 1920s, the number of campus buildings had grown substantially and included twenty structures designed by architect John Galen Howard.

    In 1917, one of the nation’s first ROTC programs was established at Berkeley and its School of Military Aeronautics began training pilots, including Gen. Jimmy Doolittle. Berkeley ROTC alumni include former Secretary of Defense Robert McNamara and Army Chief of Staff Frederick C. Weyand as well as 16 other generals. In 1926, future fleet admiral Chester W. Nimitz established the first Naval ROTC unit at Berkeley.

    In the 1930s, Ernest Lawrence helped establish the Radiation Laboratory (now DOE’s Lawrence Berkeley National Laboratory (US)) and invented the cyclotron, which won him the Nobel physics prize in 1939. Using the cyclotron, Berkeley professors and Berkeley Lab researchers went on to discover 16 chemical elements—more than any other university in the world. In particular, during World War II and following Glenn Seaborg’s then-secret discovery of plutonium, Ernest Orlando Lawrence’s Radiation Laboratory began to contract with the U.S. Army to develop the atomic bomb. Physics professor J. Robert Oppenheimer was named scientific head of the Manhattan Project in 1942. Along with the Lawrence Berkeley National Laboratory, Berkeley founded and was then a partner in managing two other labs, Los Alamos National Laboratory (1943) and Lawrence Livermore National Laboratory (1952).

    By 1942, the American Council on Education ranked Berkeley second only to Harvard University (US) in the number of distinguished departments.

    In 1952, the University of California reorganized itself into a system of semi-autonomous campuses, with each campus given its own chancellor, and Clark Kerr became Berkeley’s first Chancellor, while Sproul remained in place as the President of the University of California.

    Berkeley gained a worldwide reputation for political activism in the 1960s. In 1964, the Free Speech Movement organized student resistance to the university’s restrictions on political activities on campus—most conspicuously, student activities related to the Civil Rights Movement. The arrest in Sproul Plaza of Jack Weinberg, a recent Berkeley alumnus and chair of Campus CORE, in October 1964, prompted a series of student-led acts of formal remonstrance and civil disobedience that ultimately gave rise to the Free Speech Movement, which movement would prevail and serve as precedent for student opposition to America’s involvement in the Vietnam War.

    In 1982, the Mathematical Sciences Research Institute (MSRI) was established on campus with support from the National Science Foundation and at the request of three Berkeley mathematicians — Shiing-Shen Chern, Calvin Moore and Isadore M. Singer. The institute is now widely regarded as a leading center for collaborative mathematical research, drawing thousands of visiting researchers from around the world each year.

    21st century

    In the current century, Berkeley has become less politically active and more focused on entrepreneurship and fundraising, especially for STEM disciplines.

    Modern Berkeley students are less politically radical, with a greater percentage of moderates and conservatives than in the 1960s and 70s. Democrats outnumber Republicans on the faculty by a ratio of 9:1. On the whole, Democrats outnumber Republicans on American university campuses by a ratio of 10:1.

    In 2007, the Energy Biosciences Institute was established with funding from BP and Stanley Hall, a research facility and headquarters for the California Institute for Quantitative Biosciences, opened. The next few years saw the dedication of the Center for Biomedical and Health Sciences, funded by a lead gift from billionaire Li Ka-shing; the opening of Sutardja Dai Hall, home of the Center for Information Technology Research in the Interest of Society; and the unveiling of Blum Hall, housing the Blum Center for Developing Economies. Supported by a grant from alumnus James Simons, the Simons Institute for the Theory of Computing was established in 2012. In 2014, Berkeley and its sister campus, Univerity of California-San Fransisco (US), established the Innovative Genomics Institute, and, in 2020, an anonymous donor pledged $252 million to help fund a new center for computing and data science.

    Since 2000, Berkeley alumni and faculty have received 40 Nobel Prizes, behind only Harvard and Massachusetts Institute of Technology (US) among US universities; five Turing Awards, behind only MIT and Stanford; and five Fields Medals, second only to Princeton University (US). According to PitchBook, Berkeley ranks second, just behind Stanford University, in producing VC-backed entrepreneurs.

    UC Berkeley Seal

  • richardmitnick 12:10 pm on January 18, 2022 Permalink | Reply
    Tags: "Protein controlled by both light and temperature can inform cell signal pathways", , , Biology, , Compared to previous probes this research was based on a single protein called BcLOV4., , , The field of optogenetics relies on such proteins to better understand and manipulate these processes., , The scientists serendipitously discovered that BcLOV4 could sense not only light but also temperature., This research will open new horizons for both basic science and translational research.   

    From Penn Today and The Penn School of Engineering and Applied Science (US): “Protein controlled by both light and temperature can inform cell signal pathways” 

    From Penn Today


    The Penn School of Engineering and Applied Science (US)


    U Penn bloc

    University of Pennsylvania

    January 14, 2022
    Melissa Pappas

    Most organisms have proteins that react to light. Even creatures that don’t have eyes or other visual organs use these proteins to regulate many cellular processes, such as transcription, translation, cell growth and cell survival.

    The brighter edges of the cells in the middle and upper right panels show the optogenetic proteins collecting at the membrane after light exposure. At higher temperatures, however, the proteins become rapidly inactivated and thus do not stay at the membrane, resulting in the duller edges seen in the bottom right panel. Image: Penn Engineering Today.

    The field of optogenetics relies on such proteins to better understand and manipulate these processes. Using lasers and genetically engineered versions of these naturally occurring proteins, known as probes, researchers can precisely activate and deactivate a variety of cellular pathways, just like flipping a switch.

    Now, Penn Engineering researchers have described a new type of optogenetic protein that can be controlled not only by light, but also by temperature, allowing for a higher degree of control in the manipulation of cellular pathways. The research will open new horizons for both basic science and translational research.

    Lukasz Bugaj, assistant professor in bioengineering, Bomyi Lim, assistant professor in chemical and biomolecular engineering, Brian Chow, associate professor in bioengineering, and graduate students William Benman in Bugaj’s lab, Hao Deng in Lim’s lab, and Erin Berlew and Ivan Kuznetsov in Chow’s lab, published their study in Nature Chemical Biology. Arndt Siekmann, associate professor of cell and developmental biology at the Perelman School of Medicine, and Caitlyn Parker, a research technician in his lab, also contributed to this research.

    “Compared to previous probes ours were based on a single protein called BcLOV4, which was recently described by Brian Chow’s lab,” says Bugaj. “As a single protein, BcLOV4 can stimulate signals in a manner that required multiple proteins in previous approaches, thus making it simpler and easier to use.”

    The authors successfully showed that BcLOV4-based probes could stimulate the Ras and PI3K pathways in mammalian cells, as well as in zebrafish and fruit flies, two common model organisms.

    “However, in the course of our experiments, we serendipitously discovered that BcLOV4 could sense not only light, but also temperature,” says Bugaj. “As far as we know, this type of dual light and temperature sensitivity is a completely new feature for photosensory proteins.”

    See the full article here .


    Please help promote STEM in your local schools.

    Stem Education Coalition

    The University of Pennsylvania School of Engineering and Applied Science, is an undergraduate and graduate school of the University of Pennsylvania. The School offers programs that emphasize hands-on study of engineering fundamentals (with an offering of approximately 300 courses) while encouraging students to leverage the educational offerings of the broader University. Engineering students can also take advantage of research opportunities through interactions with Penn’s School of Medicine, School of Arts and Sciences and the Wharton School.

    Penn Engineering offers bachelors, masters and Ph.D. degree programs in contemporary fields of engineering study. The nationally ranked bioengineering department offers the School’s most popular undergraduate degree program. The Jerome Fisher Program in Management and Technology, offered in partnership with the Wharton School, allows students to simultaneously earn a Bachelor of Science degree in Economics as well as a Bachelor of Science degree in Engineering. SEAS also offers several masters programs, which include: Executive Master’s in Technology Management, Master of Biotechnology, Master of Computer and Information Technology, Master of Computer and Information Science and a Master of Science in Engineering in Telecommunications and Networking.


    The study of engineering at the University of Pennsylvania can be traced back to 1850 when the University trustees adopted a resolution providing for a professorship of “Chemistry as Applied to the Arts”. In 1852, the study of engineering was further formalized with the establishment of the School of Mines, Arts and Manufactures. The first Professor of Civil and Mining Engineering was appointed in 1852. The first graduate of the school received his Bachelor of Science degree in 1854. Since that time, the school has grown to six departments. In 1973, the school was renamed as the School of Engineering and Applied Science.

    The early growth of the school benefited from the generosity of two Philadelphians: John Henry Towne and Alfred Fitler Moore. Towne, a mechanical engineer and railroad developer, bequeathed the school a gift of $500,000 upon his death in 1875. The main administration building for the school still bears his name. Moore was a successful entrepreneur who made his fortune manufacturing telegraph cable. A 1923 gift from Moore established the Moore School of Electrical Engineering, which is the birthplace of the first electronic general-purpose Turing-complete digital computer, ENIAC, in 1946.

    During the latter half of the 20th century the school continued to break new ground. In 1958, Barbara G. Mandell became the first woman to enroll as an undergraduate in the School of Engineering. In 1965, the university acquired two sites that were formerly used as U.S. Army Nike Missile Base (PH 82L and PH 82R) and created the Valley Forge Research Center. In 1976, the Management and Technology Program was created. In 1990, a Bachelor of Applied Science in Biomedical Science and Bachelor of Applied Science in Environmental Science were first offered, followed by a master’s degree in Biotechnology in 1997.

    The school continues to expand with the addition of the Melvin and Claire Levine Hall for computer science in 2003, Skirkanich Hall for bioengineering in 2006, and the Krishna P. Singh Center for Nanotechnology in 2013.


    Penn’s School of Engineering and Applied Science is organized into six departments:

    Chemical and Biomolecular Engineering
    Computer and Information Science
    Electrical and Systems Engineering
    Materials Science and Engineering
    Mechanical Engineering and Applied Mechanics

    The school’s Department of Bioengineering, originally named Biomedical Electronic Engineering, consistently garners a top-ten ranking at both the undergraduate and graduate level from U.S. News & World Report. The department also houses the George H. Stephenson Foundation Educational Laboratory & Bio-MakerSpace (aka Biomakerspace) for training undergraduate through PhD students. It is Philadelphia’s and Penn’s only Bio-MakerSpace and it is open to the Penn community, encouraging a free flow of ideas, creativity, and entrepreneurship between Bioengineering students and students throughout the university.

    Founded in 1893, the Department of Chemical and Biomolecular Engineering is “America’s oldest continuously operating degree-granting program in chemical engineering.”

    The Department of Electrical and Systems Engineering is recognized for its research in electroscience, systems science and network systems and telecommunications.

    Originally established in 1946 as the School of Metallurgical Engineering, the Materials Science and Engineering Department “includes cutting edge programs in nanoscience and nanotechnology, biomaterials, ceramics, polymers, and metals.”

    The Department of Mechanical Engineering and Applied Mechanics draws its roots from the Department of Mechanical and Electrical Engineering, which was established in 1876.

    Each department houses one or more degree programs. The Chemical and Biomolecular Engineering, Materials Science and Engineering, and Mechanical Engineering and Applied Mechanics departments each house a single degree program.

    Bioengineering houses two programs (both a Bachelor of Science in Engineering degree as well as a Bachelor of Applied Science degree). Electrical and Systems Engineering offers four Bachelor of Science in Engineering programs: Electrical Engineering, Systems Engineering, Computer Engineering, and the Networked & Social Systems Engineering, the latter two of which are co-housed with Computer and Information Science (CIS). The CIS department, like Bioengineering, offers Computer and Information Science programs under both bachelor programs. CIS also houses Digital Media Design, a program jointly operated with PennDesign.


    Penn’s School of Engineering and Applied Science is a research institution. SEAS research strives to advance science and engineering and to achieve a positive impact on society. Faculty at Penn’s School of Engineering and Applied Science have created several centers for advanced study including.

    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.


    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 9:30 am on January 18, 2022 Permalink | Reply
    Tags: "Earth on trajectory to Sixth Mass Extinction say biologists", , Biology, , ,   

    From The University of Hawai’i-Manoa (US): “Earth on trajectory to Sixth Mass Extinction say biologists” 

    From The University of Hawai’i-Manoa (US)

    January 14, 2022
    Marcie Grabowski

    Shells from recently extinct land snails from French Polynesia. Photo credit: O.Gargominy, A.Sartori.

    Mass biodiversity extinction events caused by extreme natural phenomena have marked the history of life on Earth five times. Today, many experts warn that a Sixth Mass Extinction crisis is underway, this time entirely caused by human activities.

    A comprehensive assessment of evidence of this ongoing extinction event was published in Biological Reviews by biologists from the University of Hawaiʻi at Mānoa and The National Museum of Natural History [Muséum National d’Histoire Naturelle] (MNHN)(FR).

    “Drastically increased rates of species extinctions and declining abundances of many animal and plant populations are well documented, yet some deny that these phenomena amount to mass extinction,” said Robert Cowie, lead author of the study and research professor at the UH Mānoa Pacific Biosciences Research Center in the School of Ocean and Earth Science and Technology. “This denial is based on a highly biased assessment of the crisis which focuses on mammals and birds and ignores invertebrates, which of course constitute the great majority of biodiversity.”

    By extrapolating from estimates obtained for land snails and slugs, Cowie and co-authors estimated that since the year 1500, Earth could already have lost between 7.5% and 13% of the two million known species—a staggering 150,000 to 260,000 species.

    “Including invertebrates was key to confirming that we are indeed witnessing the onset of the Sixth Mass Extinction in Earth’s history,” said Cowie.

    Extinction hits island species disproportionately

    Native Hawaiian snail habitat on Puʻu Kukui, Maui. Photo credit: Robert Cowie.

    The situation is not the same everywhere, however. Although marine species face significant threats, there is no evidence that the crisis is affecting the oceans to the same extent as the land. On land, island species, such as those of the Hawaiian Islands, are much more affected than continental species. And the rate of extinction of plants seems lower than that of terrestrial animals.

    Denial of Sixth Mass Extinction

    Unfortunately, along with science denial taking a foothold in modern society on a range of issues, the new study points out that some people also deny that the sixth extinction has begun. Additionally, others accept it as a new and natural evolutionary trajectory, as humans are just another species playing their natural role in Earth’s history. Some even consider that biodiversity should be manipulated solely for the benefit of humanity—but benefit defined by whom?

    “Humans are the only species capable of manipulating the biosphere on a large scale,” Cowie emphasized. “We are not just another species evolving in the face of external influences. In contrast, we are the only species that has conscious choice regarding our future and that of Earth’s biodiversity.”

    To fight the crisis, various conservation initiatives have been successful for certain charismatic animals. But these initiatives cannot target all species, and they cannot reverse the overall trend of species extinction. The authors believe it is essential to continue such efforts, to continue to cultivate a wonder for nature, and crucially to document biodiversity before it disappears.

    “Despite the rhetoric about the gravity of the crisis, and although remedial solutions exist and are brought to the attention of decision-makers, it is clear that political will is lacking,” said Cowie. “Denying the crisis, accepting it without reacting, or even encouraging it constitutes an abrogation of humanity’s common responsibility and paves the way for Earth to continue on its sad trajectory towards the Sixth Mass Extinction.”

    This research is an example of UH Mānoa’s goal of Excellence in Research: Advancing the Research and Creative Work Enterprise (PDF), one of four goals identified in the 2015–25 Strategic Plan (PDF), updated in December 2020.

    See the full article here .


    Please help promote STEM in your local schools.

    Stem Education Coalition

    System Overview

    The The University of Hawai‘I (US) includes 10 campuses and dozens of educational, training and research centers across the Hawaiian Islands. As the public system of higher education in Hawai‘i, UH offers opportunities as unique and diverse as our Island home.

    The 10 UH campuses and educational centers on six Hawaiian Islands provide unique opportunities for both learning and recreation.

    UH is the State’s leading engine for economic growth and diversification, stimulating the local economy with jobs, research and skilled workers.

    The University of Hawaiʻi system, formally the University of Hawaiʻi (US) is a public college and university system that confers associate, bachelor’s, master’s, and doctoral degrees through three university campuses, seven community college campuses, an employment training center, three university centers, four education centers and various other research facilities distributed across six islands throughout the state of Hawaii in the United States. All schools of the University of Hawaiʻi system are accredited by the Western Association of Schools and Colleges. The U.H. system’s main administrative offices are located on the property of the University of Hawaiʻi at Mānoa in Honolulu CDP.

    The University of Hawaiʻi-Mānoa is the flagship institution of the University of Hawaiʻi system. It was founded as a land-grant college under the terms of the Morrill Acts of 1862 and 1890. Programs include Hawaiian/Pacific Studies, Astronomy, East Asian Languages and Literature, Asian Studies, Comparative Philosophy, Marine Science, Second Language Studies, along with Botany, Engineering, Ethnomusicology, Geophysics, Law, Business, Linguistics, Mathematics, and Medicine. The second-largest institution is the University of Hawaiʻi at Hilo on the “Big Island” of Hawaiʻi, with over 3,000 students. The University of Hawaiʻi-West Oʻahu in Kapolei primarily serves students who reside in Honolulu’s western and central suburban communities. The University of Hawaiʻi Community College system comprises four community colleges island campuses on O’ahu and one each on Maui, Kauaʻi, and Hawaiʻi. The schools were created to improve accessibility of courses to more Hawaiʻi residents and provide an affordable means of easing the transition from secondary school/high school to college for many students. University of Hawaiʻi education centers are located in more remote areas of the State and its several islands, supporting rural communities via distance education.

    Research facilities

    Center for Philippine Studies
    Cancer Research Center of Hawaiʻi
    East-West Center
    Haleakalā Observatory
    Hawaiʻi Natural Energy Institute
    Institute for Astronomy
    Institute of Geophysics and Planetology
    Institute of Marine Biology
    Lyon Arboretum
    Mauna Kea Observatory
    W. M. Keck Observatory
    Waikīkī Aquarium

    U Hawaii 2.2 meter telescope, Mauna Kea, Hawai’I (US)
    University of Hawaii 2.2 meter telescope.

    The W. M. Keck Observatory operates the largest, most scientifically productive telescopes on Earth.

    W.M. Keck Observatory two ten meter telescopes operated by California Institute of Technology(US) and the University of California(US) Maunakea Hawaii USA, altitude 4,207 m (13,802 ft). Credit: Caltech.

    The two, 10-meter optical/infrared telescopes near the summit of Maunakea on the island of Hawai’i feature a suite of advanced instruments including imagers, multi-object spectrographs, high-resolution spectrographs, integral-field spectrographs and world-leading laser guide star adaptive optics systems.

    Pann-STARS 1 Telescope, U Hawaii, situated at Haleakala Observatories near the summit of Haleakala in Hawaii, USA, altitude 3,052 m (10,013 ft).

  • richardmitnick 9:53 am on January 15, 2022 Permalink | Reply
    Tags: "E. coli", "New Spheres of Knowledge on the Origin of Life", , Biology, , , The primordial environment on Earth is thought to have consisted of vesicles-or compartments-of fatty acids., The shape of a cell affects its physical and chemical properties.,   

    From The University of Tsukuba [筑波大学](JP): “New Spheres of Knowledge on the Origin of Life” 

    From The University of Tsukuba [筑波大学](JP)

    Jan 11, 2022

    Associate Professor YING BEIWEN
    Faculty of Life and Environmental Sciences
    University of Tsukuba

    Image by Maximillian cabinet/Shutterstock.

    Cell shapes imaged by SEM. A Single-cell images of the Ori in both glucose and OAVs. B The six lineages evolved in either glucose or OAVs (C) are shown on two size scales. Scale bars are indicated. The upper and bottom panels in (C) indicate the lineages evolved in OAVs newly grown in OAVs and glucose, respectively. Credit: DOI: 10.1038/s42003-021-02954-w

    Researchers from the University of Tsukuba, in collaboration with The East China Normal University(CN), show that E. coli cells become spherical when grown in conditions mimicking a primordial environment.

    The shape of a cell affects its physical and chemical properties. Different cell types have developed different shapes to enable effective functioning. But what shape were the very first cells, as life began to evolve?

    Primitive cells are thought to have been spherical, but experimental evidence supporting this belief remains elusive. Now, however, researchers from the University of Tsukuba, in collaboration with East China Normal University, have shown that E. coli bacteria grown in a primordial-like environment become spherical.

    The primordial environment on Earth is thought to have consisted of vesicles-or compartments-of fatty acids. Oleic acid is the most common fatty acid in nature and can be metabolized by E. coli. The team therefore mimicked primordial conditions by growing six different lineages of cells in an environment where the only available nutrient was oleic-acid vesicles (OAVs), rather than the more usual glucose sugar.

    E. coli’s usual rod shape allows rapid growth and nutrient uptake. However, their shape can change in response to their environment, turning into a filament when starved of nutrients. “Our team grew these bacteria in an OAV environment and found that as the cells better adapted to the new conditions, they grew more quickly, became spherical, and decreased in both size and area-to-volume ratio compared with the original parent cells (Ori cells),” says senior author Professor Bei-Wen Ying. “Even when we relocated these evolved cells (Evo cells) to a glucose environment, they maintained their new spherical shape.”

    The six different lineages of Evo cells all evolved to adapt to the OAV conditions without common mutations. Notably, two distinct strategies were observed: some cells developed mutations that directly targeted the cell wall so that the cell structure became spherical, while others accumulated mutations in other biological processes.

    Three of the six lineages developed various mutations in the common crp gene. The protein product of crp acts as a regulator of transcription, the process by which the genetic information in the DNA is turned into a molecule known as RNA. “This implies that transcriptional regulation by crp may be crucial for E. coli to use carbon sources effectively,” explains Professor Bei-Wen Ying.

    This work is the first to show typically rod-shaped cells shifting to a spherical shape in a primordial-like environment, supporting the theory that when life began to evolve, the earliest primitive cells were spherical.

    Science paper:
    Communications Biology

    The research was supported by the National Key R&D Program of China, Synthetic Biology Research (2019YFA0904500), and the MOE International Joint Laboratory of Trustworthy Software at ECNU and was partially supported by JSPS KAKENHI, Grant-in-Aid for Scientific Research (B) grant number 19H03215 (to BWY).

    See the full article here.


    Please help promote STEM in your local schools.

    Stem Education Coalition

    The University of Tsukuba [筑波大学](JP) located in Tsukuba, Ibaraki, is one of top 9 Designated National University and selected as a Top Type university of Top Global University Project by the Japanese government.

    The university’s academic strength is in STEMM fields (Science, Technology, Engineering, Mathematics, Medicine), physical education, and related interdisciplinary fields. It is by taking located in Tsukuba Science City which has more than 300 research institutions. The university has had three Nobel laureates (two in Physics and one in Chemistry, see also “History”), and about 70 athletes, their students and alumni, have participated in the Olympic Games.

    It has established interdisciplinary Ph.D. programs in Human Biology and Empowerment Informatics, and the International Institute for Integrative Sleep Medicine, which were created through the Ministry of Education, Culture, Sports, Science and Technology’s competitive funding projects.

    Its Graduate School of Life and Environmental Sciences is represented on the national Coordinating Committee for Earthquake Prediction.

    Research performance

    Tsukuba is one of the leading research institutions in Japan. According to Thomson Reuters, Tsukuba is the 10th best research institutions among all the universities and non-educational research institutions in Japan.

    Weekly Diamond [ja] reported that Tsukuba has the 27th highest research standard in Japan in research fundings per researchers in COE Program. In the same article, it’s ranked 11th in the quality of education by GP (in Japanese) funds per student.

    It has a good research standard in Economics, as Research Papers in Economics ranked Tsukuba as the eighth best Economics research university in January 2011.

    Undergraduate schools and colleges

    School of Humanities and Culture, with separate colleges for the humanities, for comparative culture and for Japanese language and culture.
    School of Social and International Studies, including colleges for social sciences and for international studies.
    School of Human Sciences, with separate colleges for education, for psychology and for disability sciences.
    School of Life and Environmental Sciences, incorporating colleges for biological sciences, for agro-biological resources and for geoscience.
    School of Science and Engineering, with colleges for mathematics, physics, chemistry, engineering sciences and engineering systems, as well as for policy and planning sciences.
    School of Informatics, incorporating separate colleges for information sciences; for media arts, science and technology; and for knowledge and library sciences.
    School of Medicine and Medical Sciences, including schools of medicine, nursing nd medical sciences.
    School of Health and Physical Education.
    School of Art and Design.

    Graduate schools and programs

    Master’s Program in Education
    School Leadership and Professional Development
    Secondary Education
    Graduate School of Humanities and Social Sciences
    Doctoral Program in Philosophy
    Doctoral Program in History and Anthropology
    Doctoral Program in Literature and Linguistics
    Master’s Program in Modern Languages and Cultures
    Doctoral Program in Modern Languages and Cultures
    Master’s Program in International Public Policy
    Doctoral Program in International Public Policy
    Master’s Program in Economics
    Doctoral Program in Economics
    Master’s Program in Law
    Doctoral Program in Law
    Master’s Program in International Area Studies
    Doctoral Program in International and Advanced Japanese Studies
    Graduate School of Business Sciences (programs for working individuals)
    Master’s Program in Systems Management
    Master’s Program in Advanced Studies of Business Law
    Doctoral Program in Systems Management and Business Law
    Law School Program
    MBA Program in International Business
    Graduate School of Pure and Applied Sciences
    Master’s Program in Mathematics
    Doctoral Program in Mathematics
    Master’s Program in Physics
    Doctoral Program in Physics
    Master’s Program in Chemistry
    Doctoral Program in Chemistry
    Doctoral Program in Nano-Science and Nano-Technology
    Master’s Program in Applied Physics
    Doctoral Program in Applied Physics
    Master’s Program in Materials Science
    Doctoral Program in Materials Science
    Doctoral Program in Materials Sciences and Technology
    Graduate School of Systems and Information Engineering
    Master’s Program in Policy and Planning Sciences
    Master’s Program in Service Engineering
    Doctoral Program in Policy and Planning Sciences
    Master’s Program in Risk Engineering
    Doctoral Program in Risk Engineering
    Master’s Program in Computer Science
    Doctoral Program in Computer Science
    Master’s Program in Intelligent Interaction Technologies
    Doctoral Program in Intelligent Interaction Technologies
    Master’s Program in Engineering Mechanics and Energy
    Doctoral Program in Engineering Mechanics and Energy
    Master’s Program in Social Systems Engineering
    Master’s Program in Business Administration and Public Policy
    Doctoral Program in Social Systems and Management
    Graduate School of Life and Environmental Sciences
    Doctoral Program in Integrative Environment and Biomass Sciences
    Master’s Program in Geosciences
    Doctoral Program in Geoenvironmental Sciences
    Doctoral Program in Earth Evolution Sciences
    Master’s Program in Biological Sciences
    Doctoral Program in Biological Sciences
    Master’s Program in Agro-bioresources Science and Technology
    Doctoral Program in Appropriate Technology and Sciences for Sustainable Development
    Doctoral Program in Biosphere Resource Science and Technology
    Doctoral Program in Life Sciences and Bioengineering
    Doctoral Program in Bioindustrial Sciences
    Master’s Program in Environmental Sciences
    Doctoral Program in Sustainable Environmental Studies
    Doctoral Program in Advanced Agricultural Technology and Sciences
    Graduate School of Comprehensive Human Sciences
    Master’s Program in Medical Sciences (Tokyo Campus (evening programs for working adults))
    Master’s Program in Sports and Health Promotion
    Master’s Program in Education Sciences
    Doctoral Program in Education
    Doctoral Program in School Education
    Master’s Program in Psychology
    Doctoral Program in Psychology
    Master’s Program in Disability Sciences
    Doctoral Program in Disability Sciences
    Master’s Program in Lifespan Development (Tokyo Campus (evening programs for working adults))
    Doctoral Program in Lifespan Developmental Sciences (Tokyo Campus (evening programs for working adults))
    Master’s Program in Kansei, Behavioral and Brain Sciences
    Doctoral Program in Kansei, Behavioral and Brain Sciences
    Master’s Program in Nursing Sciences
    Doctoral Program in Nursing Sciences
    Master’s Program in Health and Sport Sciences
    Doctoral Program in Physical Education, Health and Sport Sciences
    Master’s Program in Art and Design
    Doctoral Program in Art and Design
    Master’s Program in World Heritage Studies
    Doctoral Program in World Cultural Heritage Studies
    Doctoral Program in Human Care Science
    Doctoral Program in Sports Medicine
    Doctoral Program in Coaching Science
    Doctoral Program in Biomedical Sciences
    Doctoral Program in Clinical Sciences
    Graduate School of Library, Information and Media Studies
    Master’s Program in Library, Information and Media Studies
    Doctoral Program in Library, Information and Media Studies
    School of Integrative and Global Majors (SIGMA)
    Ph.D. Program in Human Biology
    Ph.D. Program in Empowerment Informatics
    Master’s Program in Life Science Innovation
    Doctoral Program in Life Science Innovation

    Research centers

    Center for Computational Sciences
    Shimoda Marine Research Center
    Gene Research Center
    Plasma Research Center
    University’s inter-department education research institutes (Research)
    Life Science Center of Tsukuba Advanced Research Alliance (Life Science Center of TARA)
    International Institute for Integrative Sleep Medicine (WPI-IIIS)
    Agricultural and Forestry Research Center
    Terrestrial Environment Research Center
    Laboratory Animal Resource Center
    Sugadaira Montane Research Center
    Research Center for University Studies
    Proton Medical Research Center
    Tsukuba Industrial Liaison and Cooperative Research Center
    Center for Research on International Cooperation in Educational Development
    Research Center for Knowledge Communities
    Tsukuba Research Center for Interdisciplinary Materials Science
    Special Needs Education Research Center
    The Alliance for Research on North Africa
    Academic Computing and Communications Center
    Research Facility Center for Science and Technology
    Radioisotope Center
    Tsukuba Critical Path Research and Education Integrated Leading Center
    Center for Cybernics Research
    University’s inter-department education research institutes (student support)
    Foreign Language Center
    Sport and Physical Education Center
    International Student Center
    Admission Center
    University Health Center

  • richardmitnick 9:24 pm on January 12, 2022 Permalink | Reply
    Tags: "Arabidopsis thaliana"-the “lab rat among plants” because of its relatively small genome of around 120 million base pairs., "Study Challenges Evolutionary Theory That DNA Mutations Are Random", -DNA mutations are not random as previously thought, -Findings change our understanding of evolution, -May help researchers breed better crops and fight cancer, , Biology, , Findings Could Lead to Advances in Plant Breeding and Human Genetics, Humans-by comparison-have roughly 3 billion base pairs., Mutation is very non-random and it’s non-random in a way that benefits the plant., Mutations occur when DNA is damaged and left unrepaired creating a new variation., Scientists always thought of mutation as basically random across the genome., The areas that are the most biologically important are the ones being protected from mutation., The MPG Institute for Developmental Biology (DE), The plant has evolved to protect its genes from mutation to ensure survival., The scientists discovered an over-representation of essential genes such as those involved in cell growth and gene expression., The scientists found specific patches of the genome with low mutation rates., The scientists found that the way DNA was wrapped around different types of proteins was a good predictor of whether a gene would mutate or not., , Within the mutations-more than 1 million-a nonrandom pattern was revealed.   

    From The University of California-Davis (US) : “Study Challenges Evolutionary Theory That DNA Mutations Are Random” 

    UC Davis bloc

    From The University of California-Davis (US)

    January 12, 2022

    Media Contacts:

    Grey Monroe
    Plant Sciences
    Cell 530-304-9329

    Amy Quinton
    UC Davis News and Media Relations
    Cell 530-601-8077

    Emily C. Dooley
    College of Agricultural and Environmental Sciences,
    Cell 530-650-6807

    Findings Could Lead to Advances in Plant Breeding and Human Genetics

    Studying the genome of thale cress, a small flowering weed, led to a new understanding about DNA mutations. (Pádraic Flood)

    -DNA mutations are not random as previously thought
    -Findings change our understanding of evolution
    -May help researchers breed better crops and fight cancer

    A simple roadside weed may hold the key to understanding and predicting DNA mutation, according to new research from The University of California-Davis(US), and The MPG Institute for Developmental Biology [Max-Planck-Institut für Entwicklungsbiologie](DE).

    The findings, published today in the journal Nature radically change our understanding of evolution and could one day help researchers breed better crops or even help humans fight cancer.

    Mutations occur when DNA is damaged and left unrepaired creating a new variation. The scientists wanted to know if mutation was purely random or something deeper. What they found was unexpected.

    “We always thought of mutation as basically random across the genome,” said Grey Monroe, an assistant professor in the UC Davis Department of Plant Sciences who is lead author on the paper. “It turns out that mutation is very non-random and it’s non-random in a way that benefits the plant. It’s a totally new way of thinking about mutation.”

    Researchers spent three years sequencing the DNA of hundreds of Arabidopsis thaliana, or thale cress, a small, flowering weed considered the “lab rat among plants” because of its relatively small genome comprising around 120 million base pairs. Humans-by comparison-have roughly 3 billion base pairs.

    “It’s a model organism for genetics,” Monroe said.

    Lab-grown plants yield many variations

    Work began at the Max Planck Institute where researchers grew specimens in a protected lab environment, which allowed plants with defects that may not have survived in nature be able to survive in a controlled space.

    Sequencing of those hundreds of Arabidopsis thaliana plants revealed more than 1 million mutations. Within those mutations a nonrandom pattern was revealed, counter to what was expected.

    “At first glance, what we found seemed to contradict established theory that initial mutations are entirely random and that only natural selection determines which mutations are observed in organisms,” said Detlef Weigel, scientific director at the Max Planck Institute and senior author on the study.

    Instead of randomness they found patches of the genome with low mutation rates. In those patches, they were surprised to discover an over-representation of essential genes, such as those involved in cell growth and gene expression.

    “These are the really important regions of the genome,” Monroe said. “The areas that are the most biologically important are the ones being protected from mutation.”

    The areas are also sensitive to the harmful effects of new mutations. “DNA damage repair seems therefore to be particularly effective in these regions,” Weigel added.

    Plant evolved to protect itself

    The scientists found that the way DNA was wrapped around different types of proteins was a good predictor of whether a gene would mutate or not. “It means we can predict which genes are more likely to mutate than others and it gives us a good idea of what’s going on,” Weigel said.

    The findings add a surprising twist to Charles Darwin’s Theory of Evolution by Natural Selection because it reveals that the plant has evolved to protect its genes from mutation to ensure survival.

    “The plant has evolved a way to protect its most important places from mutation,” Weigel said. “This is exciting because we could even use these discoveries to think about how to protect human genes from mutation.”

    Future uses

    Knowing why some regions of the genome mutate more than others could help breeders who rely on genetic variation to develop better crops. Scientists could also use the information to better predict or develop new treatments for diseases like cancer that are caused by mutation.

    “Our discoveries yield a more complete account of the forces driving patterns of natural variation; they should inspire new avenues of theoretical and practical research on the role of mutation in evolution,” the paper concludes.

    Co-authors from UC Davis include Daniel Kliebenstein, Mariele Lensink, Marie Klein, from the Department of Plant Sciences. Researchers from The Carnegie Institution for Science (US), Stanford University (US), The Westfield State University (US), The University of Montpellier [Université de Montpellier](FR), Uppsala University[Uppsala universitet](SE), The College of Charleston(US), and The South Dakota State University(US) contributed to the research.

    See the full article here .


    Please help promote STEM in your local schools.

    Stem Education Coalition

    UC Davis Campus

    The University of California-Davis (US) is a public land-grant research university near Davis, California. Named a Public Ivy, it is the northernmost of the ten campuses of The University of California (US) system. The institution was first founded as an agricultural branch of the system in 1905 and became the seventh campus of the University of California in 1959.

    The university is classified among “R1: Doctoral Universities – Very high research activity”. The University of California-Davis faculty includes 23 members of The National Academy of Sciences, 30 members of The American Academy of Arts and Sciences (US), 17 members of the American Law Institute, 14 members of the Institute of Medicine, and 14 members of the National Academy of Engineering. Among other honors that university faculty, alumni, and researchers have won are two Nobel Prizes, a Presidential Medal of Freedom, three Pulitzer Prizes, three MacArthur Fellowships, and a National Medal of Science.

    Founded as a primarily agricultural campus, the university has expanded over the past century to include graduate and professional programs in medicine (which includes the University of California-Davis Medical Center), law, veterinary medicine, education, nursing, and business management, in addition to 90 research programs offered by University of California-Davis Graduate Studies. The University of California-Davis School of Veterinary Medicine is the largest veterinary school in the United States and has been ranked first in the world for five consecutive years (2015–19). University of California-Davis also offers certificates and courses, including online classes, for adults and non-traditional learners through its Division of Continuing and Professional Education.

    The UC Davis Aggies athletic teams compete in NCAA Division I, primarily as members of the Big West Conference with additional sports in the Big Sky Conference (football only) and the Mountain Pacific Sports Federation.

    Seventh UC campus

    In 1959, the campus was designated by the Regents of the University of California as the seventh general campus in the University of California system.

    University of California-Davis’s Graduate Division was established in 1961, followed by the creation of the College of Engineering in 1962. The law school opened for classes in fall 1966, and the School of Medicine began instruction in fall 1968. In a period of increasing activism, a Native American studies program was started in 1969, one of the first at a major university; it was later developed into a full department within the university.

    Graduate Studies

    The University of California-Davis Graduate Programs of Study consist of over 90 post-graduate programs, offering masters and doctoral degrees and post-doctoral courses. The programs educate over 4,000 students from around the world.

    UC Davis has the following graduate and professional schools, the most in the entire University of California system:

    UC Davis Graduate Studies
    Graduate School of Management
    School of Education
    School of Law
    School of Medicine
    School of Veterinary Medicine
    Betty Irene Moore School of Nursing


    University of California-Davis is one of 62 members in The Association of American Universities (US), an organization of leading research universities devoted to maintaining a strong system of academic research and education.

    Research centers and laboratories

    The campus supports a number of research centers and laboratories including:

    Advanced Highway Maintenance Construction Technology Research Laboratory
    BGI at UC Davis Joint Genome Center (in planning process)
    Bodega Marine Reserve
    C-STEM Center
    CalEPR Center
    California Animal Health and Food Safety Laboratory System
    California International Law Center
    California National Primate Research Center
    California Raptor Center
    Center for Health and the Environment
    Center for Mind and Brain
    Center for Poverty Research
    Center for Regional Change
    Center for the Study of Human Rights in the Americas
    Center for Visual Sciences
    Contained Research Facility
    Crocker Nuclear Laboratory
    Davis Millimeter Wave Research Center (A joint effort of Agilent Technologies Inc. and UC Davis) (in planning process)
    Information Center for the Environment
    John Muir Institute of the Environment (the largest research unit at UC Davis, spanning all Colleges and Professional Schools)
    McLaughlin Natural Reserve
    MIND Institute
    Plug-in Hybrid Electric Vehicle Research Center
    Quail Ridge Reserve
    Stebbins Cold Canyon Reserve
    Tahoe Environmental Research Center (TERC) (a collaborative effort with Sierra Nevada University)
    UC Center Sacramento
    UC Davis Nuclear Magnetic Resonance Facility
    University of California Pavement Research Center
    University of California Solar Energy Center (UC Solar)
    Energy Efficiency Center (the very first university run energy efficiency center in the Nation).
    Western Institute for Food Safety and Security

    The Crocker Nuclear Laboratory on campus has had a nuclear accelerator since 1966. The laboratory is used by scientists and engineers from private industry, universities and government to research topics including nuclear physics, applied solid state physics, radiation effects, air quality, planetary geology and cosmogenics. University of California-Davis is the only University of California campus, besides The University of California-Berkeley (US), that has a nuclear laboratory.

    Agilent Technologies will also work with the university in establishing a Davis Millimeter Wave Research Center to conduct research into millimeter wave and THz systems.

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

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

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

    Salle De Presse

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

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

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

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

    Works like a two-way radio

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

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

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

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

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

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

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

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

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

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

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

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

    See the full article here.


    Please help promote STEM in your local schools.

    Stem Education Coalition

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

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

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


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

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

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

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