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  • richardmitnick 12:51 pm on October 19, 2018 Permalink | Reply
    Tags: , , Biology, , ,   

    From Science Magazine: “Chemists find a recipe that may have jump-started life on Earth’ 

    AAAS
    From Science Magazine

    1
    New research spells out the simple chemical steps that may have launched the RNA World. Mark Garlick/Science Source

    Oct. 18, 2018
    Robert F. Service

    In the molecular dance that gave birth to life on Earth, RNA appears to be a central player. But the origins of the molecule, which can store genetic information as DNA does and speed chemical reactions as proteins do, remain a mystery. Now, a team of researchers has shown for the first time that a set of simple starting materials, which were likely present on early Earth, can produce all four of RNA’s chemical building blocks.

    Those building blocks—cytosine, uracil, adenine, and guanine—have previously been re-created in the lab from other starting materials. In 2009, chemists led by John Sutherland at the University of Cambridge in the United Kingdom devised a set of five compounds likely present on early Earth that could give rise to cytosine and uracil, collectively known as pyrimidines. Then, 2 years ago, researchers led by Thomas Carell, a chemist at Ludwig Maximilian University in Munich, Germany, reported that his team had an equally easy way to form adenine and guanine [Nature], the building blocks known as purines. But the two sets of chemical reactions were different. No one knew how the conditions for making both pairs of building blocks could have occurred in the same place at the same time.

    Now, Carell says he may have the answer. On Tuesday, at the Origins of Life Workshop here, he reported that he and his colleagues have come up with a simple set of reactions that could have given rise to all four RNA bases.

    Carell’s story starts with only six molecular building blocks—oxygen, nitrogen, methane, ammonia, water, and hydrogen cyanide, all of which would have been present on early Earth. Other research groups had shown that these molecules could react to form somewhat more complex compounds than the ones Carell used.

    To make the pyrimidines, Carell started with compounds called cyanoacetylene and hydroxylamine, which react to form compounds called amino-isoxazoles. These, in turn, react with another simple molecule, urea, to form compounds that then react with a sugar called ribose to make one last set of intermediate compounds.

    Finally, in the presence of sulfur-containing compounds called thiols and trace amounts of iron or nickel salts, these intermediates transform into the pyrimidines cytosine and uracil. As a bonus, this last reaction is triggered when the metals in the salts harbor extra positive charges, which is precisely what occurs in the final step in a similar molecular cascade that produces the purines, adenine and guanine. Even better, the step that leads to all four nucleotides works in one pot, Carell says, offering for the first time a plausible explanation of how all of RNA’s building blocks could have arisen side by side.

    “It looks pretty good to me,” says Steven Benner, a chemist with the Foundation for Applied Molecular Evolution in Alachua, Florida. The process provides a simple way to produce all four bases under conditions consistent with those believed present on early Earth, he says.

    The process doesn’t solve all of RNA’s mysteries. For example, another chemical step still needs to “activate” each of RNA’s four building blocks to link them into the long chains that form genetic material and carry out chemical reactions. But making RNA under conditions like those present on early Earth now appears within reach.

    See the full article here .


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    • stewarthoughblog 11:31 pm on October 19, 2018 Permalink | Reply

      Some interesting science here, but mostly wildly speculative naturalism. The “molecular dance” is a myth, like Darwin’s “warm little ponds,” Oparin-Haldane primordial soup or Miller-Urey test tube goo. There are no naturalistic processes capable of any appreciable assembly of abiotic chemicals at any level that approach the basic, elemental level of assembly required for the origin of life.

      RNA, in particular, is an intermediate molecule that is easily mutated, easily contaminated, highly reactive, composed of homochiral AGCU that does not develop naturalistically and does not function at any level that produces metabolic processes or reproduce.

      The intelligently designed, highly orchestrated lab experiments are biogeochemically irrelevant to primordial Earth conditions and do no demonstrate any significant achievement relative to the origin of life.

      Like

  • richardmitnick 5:13 pm on October 5, 2018 Permalink | Reply
    Tags: , Biology, , Rutgers Researchers Discover Possible Cause for Alzheimer's and Traumatic Brain Injury,   

    From Rutgers University: “Rutgers Researchers Discover Possible Cause for Alzheimer’s and Traumatic Brain Injury” 

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    From Rutgers University

    September 26, 2018

    Jennifer Forbes Mullenhard
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    Caitlin Coyle
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    The new mechanism may have also led to the discovery of an effective treatment.

    1
    Federico Sesti, a professor of neuroscience and cell biology at Rutgers Robert Wood Johnson Medical School discovered possible cause for Alzheimer’s which may have also led to the discovery of an effective treatment.
    Photo: Kim Sokoloff

    Rutgers researchers have discovered a new mechanism that may contribute to Alzheimer’s disease and traumatic brain injury. They now hope to launch a clinical trial to test the treatment in humans.

    What causes Alzheimer’s is unknown, but a popular theory suggests a protein known as amyloid-beta slowly builds up a plaque in the brains of people with Alzheimer’s. But in a recent study in the journal Cell Death & Disease, Federico Sesti, a professor of neuroscience and cell biology at Rutgers Robert Wood Johnson Medical School, looked at a new mechanism, which involves a non-amyloid-beta protein, a potassium channel referred to as KCNB1.

    Under conditions of stress in a brain affected by Alzheimer’s, KCNB1 builds up and becomes toxic to neurons and then promotes the production of amyloid-beta. The build-up of KCNB1 channels is caused by a chemical process commonly known as oxidation.

    “Indeed, scientists have known for a long time that during aging or in neurodegenerative disease cells produce free radicals,” said Sesti. “Free radicals are toxic molecules that can cause a reaction that results in lost electrons in important cellular components, including the channels.”

    The study found that in brains affected by Alzheimer’s, the build-up of KCNB1 was much higher compared to normal brains.

    “The discovery of KCNB1’s oxidation/build-up was found through observation of both mouse and human brains, which is significant as most scientific studies do not usually go beyond observing animals,” said Sesti. “Further, KCBB1 channels may not only contribute to Alzheimer’s but also to other conditions of stress as it was found in a recent study that they are formed following brain trauma.”

    In the cases of Alzheimer’s and traumatic brain injury, the build-up of KCNB1 is associated with severe damage of mental function. As a result of this discovery, Sesti successfully tested a drug called Sprycel in mice. The drug is used to treat patients with leukemia.

    “Our study shows that this drug and similar ones could potentially be used to treat Alzheimer’s, a discovery that leads the way to launching a clinical trial to test this drug in humans.”

    See the full article here .


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    Rutgers, The State University of New Jersey, 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.

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  • richardmitnick 1:39 pm on September 30, 2018 Permalink | Reply
    Tags: , , Biology, , Top 10 Design Flaws in the Human Body   

    From Nautilus: “Top 10 Design Flaws in the Human Body” 

    Nautilus

    From Nautilus

    May 14, 2015 [Just now in social media]
    By Chip Rowe Illustrations by Len Small

    From our knees to our eyeballs, our bodies are full of hack solutions [Did G-d do a bad job?].

    1

    The Greeks were obsessed with the mathematically perfect body. But unfortunately for anyone chasing that ideal, we were designed not by Pygmalion, the mythical sculptor who carved a flawless woman, but by MacGyver. Evolution constructed our bodies with the biological equivalent of duct tape and lumber scraps. And the only way to refine the form (short of an asteroid strike or nuclear detonation to wipe clean the slate) is to jerry-rig the current model. “Evolution doesn’t produce perfection,” explains Alan Mann, a physical anthropologist at Princeton University. “It produces function.”

    With that in mind, I surveyed anatomists and biologists to compile a punch list for the human body, just as you’d do before buying a house. Get out your checkbook. This one’s a fixer-upper.

    1. An unsound spine

    Problem: Our spines are a mess. It’s a wonder we can even walk, says Bruce Latimer, director of the Center for Human Origins at Case Western Reserve University, in Cleveland. When our ancestors walked on all fours, their spines arched, like a bow, to withstand the weight of the organs suspended below. But then we stood up. That threw the system out of whack by 90 degrees, and the spine was forced to become a column. Next, to allow for bipedalism, it curved forward at the lower back. And to keep the head in balance—so that we didn’t all walk around as if doing the limbo—the upper spine curved in the opposite direction. This change put tremendous pressure on the lower vertebrae, sticking about 80 percent of adults, according to one estimate, with lower back pain.
    Fix: Go back to the arch. “Think of your dog,” Latimer says. “From the sacrum to the neck, it’s a single bow curve. That’s a great system.” Simple. Strong. Pain-free. There’s only one catch: To keep the weight of our heads from pitching us forward, we’d need to return to all fours.

    2. An inflexible knee

    Problem: As Latimer says, “You take the most complex joint in the body and put it between two huge levers—the femur and the tibia—and you’re looking for trouble.” The upshot is your knee only rotates in two directions: forward and back. “That’s why every major sport, except maybe rugby, makes it illegal to clip, or hit an opponent’s knee from the side.”

    2

    Fix: Replace this hinge with a ball and socket, like in your shoulders and hips. We never developed this type of joint at the knee “because we didn’t need it,” Latimer says. “We didn’t know about football.”

    3. A too-narrow pelvis

    Problem: Childbirth hurts. And to add insult to injury, the width of a woman’s pelvis hasn’t changed for some 200,000 years, keeping our brains from growing larger.
    Fix: Sure, you could stretch out the pelvis, Latimer says, but technologists may already be onto a better solution. “I would bet that in 10,000 years, or even in 1,000 years, no woman in the developed world will deliver naturally. A clinic will combine the sperm and egg, and you’ll come by and pick up the kid.”

    4. Exposed testicles

    Problem: A man’s life-giving organs hang vulnerably outside the body.
    Fix: Moving the testicles indoors would save men the pain of getting hit in the nuts. To accomplish this, first you’d need to tweak the sperm, says Gordon Gallup, an evolutionary psychologist at the State University of New York at Albany. Apparently the testicles (unlike the ovaries) get thrown out in the cold because sperm must be kept at 2.5 to 3 degrees Fahrenheit below the body’s internal temperature. Gallup hypothesizes that these lower temperatures keep sperm relatively inactive until they enter the warm confines of a vagina, at which point they go racing off to fertilize the egg.1 This evolutionary hack prevents sperm from wearing themselves out too early. So change the algorithm, Gallup says. Keep the sperm at body temperature and make the vagina hotter. (And, by the way, there’s no need to draw up new blueprints: Elephants offer a pretty good prototype.)

    5. Crowded teeth

    Problem: Humans typically have three molars on each side of the upper and lower jaws near the back of the mouth. When our brain drastically expanded in size, the jaw grew wider and shorter, leaving no room for the third, farthest back molars. These cusped grinders may have been useful before we learned to cook and process food. But now the “wisdom teeth” mostly just get painfully impacted in the gums.
    Fix: Get rid of them. At one point, they appeared to be on their way out—about 25 percent of people today (most commonly Eskimos) are born without some or all of their third molars. In the meantime, we’ve figured out how to safely extract these teeth with dental tools, which, Mann notes, we probably wouldn’t have invented without the bigger brains. So you could call it a wash.

    6. Meandering arteries

    Problem: Blood flows into each of your arms and legs via one main artery, which enters the limb on the front side of the body, by the biceps or hip flexors. To supply blood to tissues at a limb’s back side, such as the triceps and hamstrings, the artery branches out, taking circuitous routes around bones and bundling itself with nerves. This roundabout plumbing can make for some rather annoying glitches. At the elbow, for instance, an artery branch meets up with the ulnar nerve, which animates your little finger, just under the skin. That’s why your arm goes numb when the lower tip of your upper arm bone, called the humerus or “funny bone,” takes a sharp blow.
    The Fix: Feed a second artery into the back side of each arm and leg, by the shoulder blades or buttock, says Rui Diogo, an assistant professor of anatomy at Howard University, in Washington, DC, who studies the evolution of primate muscles. This extra pipe would provide a more direct route from the shoulder to the back of the hand, preventing vessels and nerves from wandering too close to the skin.

    7. A backward retina

    Problem: The photoreceptor cells in the retina of the eye are like microphones facing backward, writes Nathan Lents, an associate professor of molecular biology at the City University of New York. This design forces light to travel the length of each cell, as well as through blood and tissue, to reach the equivalent of a receiver on the cell’s backside. The setup may encourage the retina to detach from its supporting tissue—a leading cause of blindness. It also creates a blind spot where cell fibers, akin to microphone cables, converge at the optic nerve—making the brain refill the hole.
    Fix: Poach the obvious solution from the octopus or the squid: Just flip the retina.

    3

    8. A misrouted nerve

    Problem: The recurrent laryngeal nerve (RLN) plays a vital role in our ability to speak and swallow. It feeds instructions from the brain to the muscles of the voice box, or larynx, below the vocal cords. Theoretically, the trip should be a quick one. But during fetal development, the RLN gets entwined in a tiny lump of tissue in the neck, which descends to become blood vessels near the heart. That drop causes the nerve to loop around the aorta before traveling back up the larynx. Having this nerve in your chest makes it vulnerable during surgery—or a fist fight.
    Fix: “This one’s easy,” says Rebecca Z. German, a professor of anatomy and neurobiology at Northeast Ohio Medical University, in Rootstown. While a baby is in utero, develop the RCN after sending that irksome neck lump of vessel tissue to the chest. That way, the nerve won’t get dragged down with it.

    9. A misplaced voice box

    Problem: The trachea (windpipe) and esophagus (food pipe) open into the same space, the pharynx, which extends from the nose and mouth to the larynx (voice box). To keep food out of the trachea, a leaf-shaped flap called the epiglottis reflexively covers the opening to the larynx whenever you swallow. But sometimes, the epiglottis isn’t fast enough. If you’re talking and laughing while eating, food may slip down and get lodged in your airway, causing you to choke.
    Fix: Take a cue from whales, whose larynx is located in their blowholes. If we moved the larynx into our nose, says German, we could have two independent tubes. Sure, we’d lose the ability to talk. But we could still communicate in song, as whales do, through vibrations in our nostrils.

    10. A klugey brain

    Problem: The human brain evolved in stages. As new additions were being built, older parts had to remain online to keep us up and running, explains psychologist Gary Marcus in his book Kluge: The Haphazard Evolution of the Mind.2 And that live-in construction project led to slapdash workarounds. It’s as if the brain were a dysfunctional workplace, where young employees (the forebrain) handled newfangled technologies like language while the old guard (the midbrain and hindbrain) oversaw the institutional memory—and the fuse box in the basement. A few outcomes: depression, madness, unreliable memories, and confirmation bias.
    Fix: We’re screwed.

    6

    References

    1. Gallup, G.G., Finn, M.M., & Sammis, B. On the origin of descended scrotal testicles: The activation hypothesis. Evolutionary Psychology 7, 517-526 (2009).

    2. Marcus, G. Kluge: The Haphazard Evolution of the Human Mind Houghton Mifflin, Boston, MA (2008).

    See the full article here .

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    Welcome to Nautilus. We are delighted you joined us. We are here to tell you about science and its endless connections to our lives. Each month we choose a single topic. And each Thursday we publish a new chapter on that topic online. Each issue combines the sciences, culture and philosophy into a single story told by the world’s leading thinkers and writers. We follow the story wherever it leads us. Read our essays, investigative reports, and blogs. Fiction, too. Take in our games, videos, and graphic stories. Stop in for a minute, or an hour. Nautilus lets science spill over its usual borders. We are science, connected.

     
  • richardmitnick 4:51 pm on September 28, 2018 Permalink | Reply
    Tags: , Biology, , , , ,   

    From World Community Grid (WCG): “A Graduation, a Paper, and a Continuing Search for the ‘Help Stop TB’ Researchers” 

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    From World Community Grid (WCG)

    By: Dr. Anna Croft
    University of Nottingham, UK
    28 Sep 2018

    Summary
    In this update, principal investigator Dr. Anna Croft shares two recent milestones for the Help Stop TB research team, and discusses their continuing search for additional researchers.

    The Help Stop TB (HSTB) project uses the massive computing power of World Community Grid to examine part of the coating of Mycobacterium tuberculosis, the bacterium that causes tuberculosis. We hope that by learning more about the mycolic acids that are part of this coating, we can contribute to the search for better treatments for tuberculosis, which is one of the world’s deadliest diseases.

    Graduation Ceremony for Dr. Athina Meletiou

    In recent news for the HSTB project, Dr. Athina Meletiou has now officially graduated. It was a lovely day, finished off with some Pimms and Lemonade in the British tradition.

    1
    Athina (center) with supervisors Christof (left) and Anna (right)

    2
    Athina and her scientific “body-guard,” Christof

    Search for New Team Members Continues

    We are still looking for suitably qualified chemists, biochemists, mathematicians, engineers and computer scientists to join our team, especially to develop the new analytical approaches (including machine-learning approaches) to understand the substantial data generated by the World Community Grid volunteers.

    We will be talking to students from our BBSRC-funded doctoral training scheme in the next few days and encouraging them to join the project. Click here for more details.

    Paper Published

    Dr. Wilma Groenwald, one of the founding researchers for the HSTB project, recently published a paper describing some of the precursor work to the project. The paper, which discusses the folding behavior of mycolic acids, is now freely available on ChemRXiv Revealing Solvent-Dependent Folding Behavior of Mycolic Acids from Mycobacterium Tuberculosis by Advanced Simulation Analysis.

    We hope to have Athina’s first papers with World Community Grid data available later in the year, and will keep you updated.

    Thank you to all volunteers for your support.

    See the full article here.


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    World Community Grid (WCG) brings people together from across the globe to create the largest non-profit computing grid benefiting humanity. It does this by pooling surplus computer processing power. We believe that innovation combined with visionary scientific research and large-scale volunteerism can help make the planet smarter. Our success depends on like-minded individuals – like you.”
    WCG projects run on BOINC software from UC Berkeley.
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    BOINC is a leader in the field(s) of Distributed Computing, Grid Computing and Citizen Cyberscience.BOINC is more properly the Berkeley Open Infrastructure for Network Computing.

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    CAN ONE PERSON MAKE A DIFFERENCE? YOU BET!!

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    “Download and install secure, free software that captures your computer’s spare power when it is on, but idle. You will then be a World Community Grid volunteer. It’s that simple!” You can download the software at either WCG or BOINC.

    Please visit the project pages-

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    World Community Grid is a social initiative of IBM Corporation
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  • richardmitnick 11:00 am on September 28, 2018 Permalink | Reply
    Tags: Biology, , , GRIK1, How a Molecular Signal Helps Plant Cells Decide When to Make Oil, How a sugar-signaling molecule helps regulate oil production in plant cells, KIN10, Microscale thermophoresis, The work could point to new ways to engineer plants to produce substantial amounts of oil for use as biofuels or in the production of other oil-based products, Trehalose 6-phosphate (T6P)   

    From Brookhaven National Lab: “How a Molecular Signal Helps Plant Cells Decide When to Make Oil” 

    From Brookhaven National Lab

    September 24, 2018
    Karen McNulty Walsh
    kmcnulty@bnl.gov
    (631) 344-8350

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

    Details of mechanism suggest new strategy for engineering plants to make more oil.

    1
    Jantana Keereetaweep, John Shanklin, and Zhiyang Zhai prepare samples for studying the biochemical pathways that regulate oil production in plants.

    A study at the U.S. Department of Energy’s Brookhaven National Laboratory identifies new details of how a sugar-signaling molecule helps regulate oil production in plant cells. As described in a paper appearing in the journal The Plant Cell, the work could point to new ways to engineer plants to produce substantial amounts of oil for use as biofuels or in the production of other oil-based products.

    The study builds on previous research led by Brookhaven Lab biochemist John Shanklin that established clear links between a protein complex that senses sugar levels in plant cells (specifically a subunit called KIN10) and another protein that serves as the “on switch” for oil production (WRINKLED1) [The Plant Cell]. Using this knowledge, Shanklin’s team recently demonstrated that they could use combinations of genetic variants that increase sugar accumulation in plant leaves to drive up oil production. The new work provides a more detailed understanding of the link between sugar signaling and oil production, identifying precisely which molecules regulate the balance and how.

    “If you were a cell, you’d want to know if you should be making new compounds or breaking existing ones down,” said Shanklin. “Making oil is demanding; you want to make it when you have lots of energy—which in cells is measured by the amount of sugar available. By understanding how the availability of sugar drives oil production, we hope to find ways to get plants to boost the priority of making oil.”

    The team’s earlier research revealed some key biochemical details of the sugar-oil balancing act. Specifically, they found that when sugar levels are low, the KIN10 portion of the sugar-sensing complex shuts off oil production by triggering degradation of the oil “on” switch (WRINKLED1). High sugar levels somehow prevented this degradation, leaving the on-switch protein stabilized to crank out oil. But the scientists didn’t understand exactly how.

    For the new paper, first authors Zhiyang Zhai and Jantana Keereetaweep led a detailed investigation to unravel how these molecular players interact to drive up oil production when sugar is abundant.

    The team used an emerging technique, called microscale thermophoresis, which uses fluorescent dyes and heat to precisely measure the strength of molecular interactions.

    “You label the molecules with a fluorescent dye and measure how they move away from a heat source,” Shanklin explained. “Then, if you add another molecule that binds to the labeled molecule, it changes the rate at which the labeled molecule moves away from the heat.”

    “Jan and Zhiyang’s rapid application of this novel technique to this tough research problem was key to solving it,” Shanklin said.

    3
    When a plant is low on sugar (left), a cascade of molecular interactions degrades (DEG) a protein (W) that turns on fatty acid synthesis (FAS). However, when sugar levels are high (right), key steps in this process are blocked, leaving the W protein intact to start fatty acid (oil) production. KEY: K = KIN10, G = GRIK1, P = phosphoryl group, W = WRINKLED1, FAS = fatty acid synthesis, DEG = degradation, T6P = trehalose 6-phosphate. Faded molecules and pathways are less active than those shown in bold colors.

    Among the substances included in the study was a molecule known as trehalose 6-phosphate (T6P), the levels of which rise and fall with those of sugar. The study revealed that T6P interacts directly with the KIN10 component of the sugar-sensing complex. And it showed how that binding interferes with KIN10’s ability to shut off oil biosynthesis.

    “By measuring the interactions among many different molecules, we determined that the sugar-signaling molecule, T6P, binds with KIN10 and interferes with its interaction with a previously unidentified intermediate in this process, known as GRIK1, which is needed for KIN10 to tag WRINKLED1 for destruction. This explains how the signal affects the chain of events and leads to increased oil production,” Shanklin said. “It’s not just sugar but the signaling molecule that rises and falls with sugar that inhibits the oil shut-off mechanism.”

    To put this knowledge into action to increase oil production, the scientists will need even more details. So, the next step will be to get a close-up look at the interaction of T6P with its target protein, KIN10, at Brookhaven’s National Synchrotron Light Source II (NSLS-II). This DOE Office of Science user facility produces extremely bright x-rays, which the team will use to reveal exactly how the interacting molecules fit together.

    “With NSLS-II at Brookhaven Lab, we are in the perfect place to bring this research to the next stage,” Shanklin said. “There are unique tools available at the Light Source that will allow us to add atomic-level details to the interactions that we discovered.”

    BNL NSLS-II

    And those details could point to ways to change the sequence of KIN10, T6P’s target protein, to mimic the effects of the interaction and modify the cell’s regulatory circuitry to prioritize the production of oil.

    This work was funded by the DOE Office of Science. John Lunn and Regina Feil from the Max Planck Institute of Molecular Plant Physiology in Potsdam-Golm, Germany, collaborated on this study.

    See the full article here .


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    One of ten national laboratories overseen and primarily funded by the Office of Science of the U.S. Department of Energy (DOE), Brookhaven National Laboratory conducts research in the physical, biomedical, and environmental sciences, as well as in energy technologies and national security. Brookhaven Lab also builds and operates major scientific facilities available to university, industry and government researchers. The Laboratory’s almost 3,000 scientists, engineers, and support staff are joined each year by more than 5,000 visiting researchers from around the world. Brookhaven is operated and managed for DOE’s Office of Science by Brookhaven Science Associates, a limited-liability company founded by Stony Brook University, the largest academic user of Laboratory facilities, and Battelle, a nonprofit, applied science and technology organization.
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  • richardmitnick 9:41 am on September 27, 2018 Permalink | Reply
    Tags: 3D virtual cadaver, , , Biology, Digital Cadavers Offer a High-Tech Lesson in Anatomy,   

    From Rutgers University: “Digital Cadavers Offer a High-Tech Lesson in Anatomy” 

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    Our Great Seal.

    From Rutgers University

    September 26, 2018
    Beverly McCarron

    1
    Rebekah J. Thomas, center, an assistant professor at the School of Health Professions, demonstrates how to operate the school’s new virtual dissection table.
    Photo: Nick Romanenko/Rutgers University

    Rutgers University physician assistant students hovered over a virtual dissection table displaying the life-size image of a cadaver –the body of a 38-year-old man who had donated his body for medical research.

    The minutely detailed, 3D virtual cadaver had been recreated in vivid color based on actual body scans and loaded into the 6-foot long, touch-screen table.

    Swiping the screen, students peeled back layers of the cadaver, revealing pink organs and muscles, blue veins and, finally, the skeleton. To find the appendix, first-year student Lindsey DuBoff tapped on a scalpel icon, and then sliced away muscle and tissue with her finger, exposing the small organ.

    Seemingly out of science fiction (it has been used by the fictional doctors on Grey’s Anatomy), the virtual dissection table brings the future of gross anatomy and clinical science education to Rutgers’ School of Health Professions, one of eight schools and clinical and education resources that comprise the university’s academic health center. Rutgers is New Jersey’s first university to use this technology.

    “This table helps our students visualize and better understand anatomy and lays the foundation for stronger skills in clinical medicine,” said Matthew McQuillan, director of the physician assistant program, which confers a Master of Science degree.

    “Many go into surgery and subspecialties and having them understand spatial relationships is critical to becoming good clinicians. Anyone doing a physical exam has to be able to visualize the body structure. The virtual dissection table helps lay a foundation to build better skills in clinical medicine.

    Rebekah Thomas, an assistant professor in the program who brought the idea of the virtual cadaver to Rutgers, anticipates that it will complement – not replace – the school’s real cadavers.

    Removing a kidney from a real cadaver gives students a tactile sense of the body. Students holding the organ will feel its weight and size in a way they can’t on a screen.

    But a virtual kidney enables them to study the histology of an organ right down to its microscopic tissue and cells. Students can zoom in and out and see blood vessels and nerves.

    In addition, once an organ is removed, a flesh-and-bone cadaver is no longer pristine. After a year of training its students with a cadaver, the university must obtain a new donor. Virtual cadavers, on the other hand, can be digitally refreshed without limit.

    The computerized table gives students the flexibility to work on a variety of patient donors with different clinical and pathological conditions, body types, ethnicities and causes of death, Students also have access to a library of more than 1,000 images involving living clinical cases, which include conditions, such as an ectopic pregnancy and conjoined twins – with all patients giving prior consent to the digital use of their data, according to Anatomage, the California-based company that developed the table.

    “I’ve done cadaver dissections before,” said PA student Victoria Latella. “But I feel like this is a tool we never knew we needed.”

    See the full article here .


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

    Please help promote STEM in your local schools.

    Stem Education Coalition

    rutgers-campus

    Rutgers, The State University of New Jersey, 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.

    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 7:39 am on September 27, 2018 Permalink | Reply
    Tags: , , Biology, BioXFEL- short for Biology with X-ray Free Electron Lasers, HWI-Hauptman-Woodward Medical Research Institute, HWI-High-Throughput Crystallization Center, UB-University at Buffalo SUNY, , , X-ray Laser technology   

    From University at Buffalo: UB, HWI and partners awarded $22.5 million to capture biology at the atomic level using X-ray lasers” 

    U Buffalo bloc.

    From University at Buffalo

    September 26, 2018
    Ellen Goldbaum
    News Content Manager
    Medicine
    Tel: 716-645-4605
    goldbaum@buffalo.edu

    BioXFEL is revolutionizing bioimaging through collaborations with academia and industry, including Google Brain.

    A research consortium led by the University at Buffalo has been awarded $22.5 million from the National Science Foundation (NSF) to continue its groundbreaking work developing advanced imaging techniques for critical biological processes that are difficult, if not impossible, to see with conventional methods.

    1
    No image credit

    BioXFEL, an NSF Science and Technology Center and UB’s first such center, was created in November 2013 with an initial, $25 million award to UB, Hauptman-Woodward Medical Research Institute (HWI) and partner institutions.

    “The successful renewal of UB’s first NSF Science and Technology Center award confirms Western New York’s leadership in the areas of X-ray crystallography and structural biology, historically based in the Hauptman-Woodward Medical Research Institute and related departments at UB, including, most recently, the Department of Materials Design and Innovation,” said Venu Govindaraju, PhD, vice president for research and economic development at UB.

    “BioXFEL center scientists have made revolutionary advances in just a few years, using X-ray lasers to probe phenomena previously hidden from view,” he said. “They have discovered about 350 new molecular structures, expanding the knowledge base by describing these structures in more than 500 publications. With these incredibly powerful new tools, they are helping us better understand some of society’s most intractable health and science problems.”

    In addition to UB and HWI, BioXFEL partners include Arizona State University, the University of Wisconsin-Milwaukee, Stanford University, Cornell University, Rice University, the University of California, San Francisco and Miami University in Ohio.

    The goal of the research is to harness the power of X-ray lasers to transform a broad range of scientific fields, focused on structural biology and drug development and extending to potential innovations in environmental technologies and the development of new materials.

    Intensely bright, incredibly short pulses

    Called BioXFEL, short for Biology with X-ray Free Electron Lasers, the consortium of UB, HWI and their partners, is dedicated to using X-ray free electron lasers, which produce incredibly intense X-rays in extremely short pulses.

    “X-ray lasers provide two huge advantages over conventional methods,” explained Edward Snell, PhD, BioXFEL director, president and CEO of HWI and professor in the Department of Materials Design and Innovation in the School of Engineering and Applied Sciences at UB. “They are intensely bright beams that allow us to see much smaller things, like nanocrystals. And their pulses are incredibly short, which allows us to see critical processes, like how drugs bind, at rates as fast as a billionth of a billionth of a second.”

    BioXFEL is developing the next-generation of X-ray-based structural biology research, a field in which Buffalo has a long and rich history. In 1985, the Nobel Prize was awarded to the late Herbert Hauptman and Jerome Karle for their work developing the groundbreaking direct methods technique, a robust means of obtaining the shape and form of pharmaceuticals and their targets that is still used today, Snell explained.

    From photograph to movie

    In the few years that BioXFEL has existed, Snell explained, its researchers have significantly expanded the detail with which biological and other processes can be imaged. “Initially, the molecular images we made were based on distinct snapshots of molecules at certain timepoints,” he said. “Now we’re going from the photograph to the movie, we’re able to see the continuous process. With this renewal, we will be able to understand the complete dynamics of biological mechanisms.”

    HWI’s role in BioXFEL stems from its high-throughput crystallization center that over the past two decades has generated 180 million images from crystallization experiments. Many of these crystals were too small to be analyzed by conventional techniques, but may be deciphered using the power of X-ray lasers.

    The same images have attracted a collaboration with Google Brain, in this case promoting the use of artificial intelligence to expedite new discoveries in protein crystallization. “Buried within all those images are clues about how to go about finding the useful data in them more easily, but there is a lot of noise and we’ve got to work out a way to tease out the clues by somehow automating the process,” he said.

    “It’s well-known that we have this archive of images at HWI generated by our High-Throughput Crystallization Center, so crystallization centers and major pharmaceutical companies worldwide have been eager to collaborate with us,” Snell said.

    Particles in solution

    UB scientist Thomas Grant, PhD, based at HWI, has used X-ray free laser techniques to develop a new way to look at molecular structures in solution, critical for understanding how proteins function in the human body. Other BioXFEL advances include:

    · Developing a method that dramatically reduces the amount of sample needed for analysis.

    · Viewing the motions of molecules during reactions called time-resolved imaging dynamics, which allowed researchers to see how antibiotic resistance develops in tuberculosis and how a virus infects its host.

    · Using X-ray lasers to probe molecular motion studies for new technologies and materials.

    · Eight supported faculty at Arizona State University, where a compact campus XFEL is under construction, who use worldwide XFEL facilities to obtain movies of molecular machines at work in photosynthesis, viruses and drugs, while developing experimental techniques and new algorithms.

    · Four supported faculty at the University of Wisconsin-Milwaukee, leading to the first movies of biological processes underlying vision, antibiotic resistance, and the extrusion of the genome from a virus.

    · New technology developed at Cornell University that has enabled the first millisecond scale mix and inject experiments: watching proteins as they work with near atomic resolution.

    The scientific work of BioXFEL takes place through collaborations between all of the partner institutions. The initial X-ray laser experiments can only be done at the Linac Coherent Light Source at BioXFEL partner Stanford University, where a mile-long facility produces a beam one-tenth of the thickness of a human hair. A handful of these facilities are opening worldwide and BioXFEL is leading research at all of them.

    SLAC/LCLS

    BioXFEL has also implemented a diverse and vigorous set of training programs to help prepare young scientists for careers in XFEL science, including summer intern programs, graduate student support, and postdoctoral career development activities.

    BioXFEL is headquartered at 700 Ellicott St. on the Buffalo Niagara Medical Campus in the building that houses both HWI and members of the UB Department of Materials Design and Innovation.

    The NSF Science and Technology Centers: Integrative Partnerships program supports innovative, potentially transformative research and education projects that require large-scale, long-term awards. The centers foster cutting-edge research, education of the next generations of scientists and broad distribution of the knowledge and technology produced.

    See the full article here .

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

    Please help promote STEM in your local schools.

    Stem Education Coalition

    U Buffalo Campus

    UB is a premier, research-intensive public university and a member of the Association of American Universities. As the largest, most comprehensive institution in the 64-campus State University of New York system, our research, creative activity and people positively impact the world.

     
  • richardmitnick 4:01 pm on September 20, 2018 Permalink | Reply
    Tags: , , Biology, , His first award in 1954 was in chemistry. His second eight years later was the Peace Prize, Linus Pauling: The man who won two Nobel Prizes   

    From COSMOS Magazine: “Linus Pauling: The man who won two Nobel Prizes” 

    Cosmos Magazine bloc

    From COSMOS Magazine

    20 September 2018

    1
    Credit: Jeffrey Phillips

    Technically speaking, Linus Carl Pauling failed high school, even though he was ferociously smart.

    By the age of 15 – this would have been in 1916 – he had earned enough high school credits to win admission to Oregon State University. However, because he had not completed two mandatory American history courses the school refused to give him a diploma.

    He was finally presented with the all-important piece of paper 45 years later, by which point it was arguably a redundant gesture. After all, by then Pauling had won two Nobel Prizes, and was generally regarded as one of the most important scientists of all time.

    Pauling – born in the US city of Portland, Oregon, in 1901 – is one of only four people to be awarded two Nobels, and one of only two to achieve the feat in completely different fields.*

    His first award, in 1954, was in chemistry. His second, eight years later, was the Peace Prize, recognising an energetic commitment to nuclear disarmament that began in 1946 when he joined an organisation called the Emergency Committee of Atomic Scientists, alongside Albert Einstein, Bertrand Russell and a small group of other prominent researchers.

    As a chemist, Pauling’s work was truly foundational in fields as distant as organic chemistry and molecular biology. For instance, his research served as the basis of later investigations by Francis Crick, Rosalind Franklin and James Watson that resulted in the discovery of the structure of DNA.

    He is regularly included in lists of the all-time great scientists, but if it wasn’t for a chance experience during his childhood his life may have taken an entirely different shape.

    Following the birth of his sister, Pauline, Linus Pauling’s parents uprooted the family and, after a couple of intermediate stops, relocated to the Oregon town of Condon. By then a second sister, Lucile, had joined the family.

    His father, Herman, was a travelling salesman and later drugstore owner, who died from a perforated ulcer when Linus was just nine, leaving his mother, Lucy, to raise the family.

    One day, when he was about 10, he visited a friend, who happened to be playing with small chemistry kit. Pauling was immediately entranced, and from that moment dreamed of nothing but becoming a chemist. (The friend, Lloyd Jeffress, went on to become a professor of experimental psychology at the University of Texas.)

    Spurred into action, and while still at school, Pauling and another mate set up a laboratory in a basement and offered to run quality tests on butterfat for local dairy farmers. It was not a successful venture.

    In order to put himself through university, Linus took a variety of jobs, including working as a grocery retailer, a machinist and a photographic developer. On campus, he quickly distinguished himself, and was offered teaching positions before even earning his first degree. After leaving Oregon State he went to Caltech and received his PhD in physical chemistry and mathematical physics.

    By the time he died in 1994, Pauling had published more than 1,200 books and papers. Despite his success, and his willingness to campaign hard for the causes in which he believed, he was not without his critics.

    The difference between genius and eccentricity is sometimes difficult to distinguish and in his later years, following a bout of kidney disease, he became increasingly obsessed with the role of vitamins in treating illness.

    It is almost entirely because of his advocacy that today vitamin C is firmly associated with good health. Sometimes that advocacy crossed the boundary between science and obsession. Throughout the second half of his life he continued to suggest that high doses of vitamin C could cure cancer, despite many studies finding no evidence to support the contention.

    Despite this, however, today he is remembered primarily as a brilliant researcher who made very real and substantial contributions to areas as diverse as quantum mechanics and medicine. His memory is honoured across the US and beyond. Oregon has a public holiday bearing his name, which also adorns several streets in various states, a research centre at Oxford University in the UK – and an asteroid that orbits the sun every 926 days.

    *Marie Curie was the other one, in case you were wondering.

    See the full article here .


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

    Stem Education Coalition

     
  • richardmitnick 9:36 am on September 17, 2018 Permalink | Reply
    Tags: , , Biology, , Rutgers Opens State-of-the-Art Chemistry and Chemical Biology Building,   

    From Rutgers University: “Rutgers Opens State-of-the-Art Chemistry and Chemical Biology Building” 

    Rutgers smaller
    Our Great Seal.

    From Rutgers University

    September 13, 2018
    Neal Buccino
    neal.buccino@rutgers.edu

    1
    Peter March, executive dean of the School of Arts and Sciences, speaks at the ribbon cutting ceremony for the new 144,000-square-foot Chemistry and Chemical Biology building.
    Photo: Nick Romanenko

    2
    New Chemistry and Chemical Biology Building. Flad Architects

    The new home for the Department of Chemistry and Chemical Biology at Rutgers University–New Brunswick, which provides expanded teaching, laboratory and support space, is open for classes and research.

    Rutgers University President Robert Barchi and Rutgers–New Brunswick Interim Chancellor Christopher Molloy on Friday unveiled the building that launches a new era in research and education.

    The four-story, 144,000-square-foot facility will help accelerate innovative work in biophysical chemistry related to human health, drug design and synthesis, alternative energy, biomaterials, nanotechnology and other fields. The $115 million project was funded largely by New Jersey’s 2012 Building Our Future Bond Act.

    “We’re grateful to the people of the state for their investment in the bond act, and we’ve created a facility they can be proud of,” President Barchi said. “It is both visually appealing in its architecture and equipped with state-of-the-art laboratories that will enable our scientists and students to make important new discoveries.”

    Interim Chancellor Molloy said, “Rutgers’ chemistry and chemical biology research is discovering new ways to improve lives, from clean energy solutions, to potential new treatments for cancer and HIV, to high-speed computing. We’re preparing students for success in fields from pharmaceuticals to flavors, from petroleum to semiconductors. This new building will allow us to do even more.”

    “The Department of Chemistry and Chemical Biology educates thousands of undergraduates and graduate students, and produces research that benefits health, energy, and the environment,” said School of Arts and Sciences Executive Dean Peter March. “Now the department has a fitting 21st century home.”

    “Designed with an eye toward collaboration, combining instructional spaces with flexible research spaces, and inviting common areas, the building will enhance already excellent teaching and research,” said Arts and Sciences Vice Dean of Research and Graduate Studies and Distinguished Professor of Chemistry Jean Baum. “The new possibilities will attract graduate students and new faculty and bolster our partnership with industry.”

    3
    Graduate student Tariq Bhatti leads visitors on a tour in the new Chemistry and Chemical Biology building. Photo: Nick Romanenko.

    More than 6,000 Rutgers students take chemistry courses each semester, and they will benefit from the new classrooms and labs. The building allows the university to expand upon its tradition of collaborative research with leading academic labs, federal agencies and private companies in New Jersey and around the world. The building includes a microscopy suite and optical spectroscopy, nuclear magnetic resonance spectroscopy and X-ray crystallography laboratories. The facility’s modular design and versatile infrastructure allow reconfiguration of labs and classrooms to respond as teaching methods and technology evolve and the needs of students and faculty change. Common areas are designed to promote collaborations.

    Adjacent to the Wright-Reiman Chemistry complex on the Busch campus, the new building’s front courtyard features The PhD Molecule, a 27-foot-tall sculpture by Larry Kirkland, which includes a stainless steel depiction of a caffeine molecule on a black granite base representing a blackboard with etched chemistry symbols.

    In addition to conforming to New Jersey energy mandates and guidelines, Rutgers seeks to achieve a Leadership in Energy and Environmental Design (LEED) Gold certification for the building by reducing its energy usage. Green features include windows that maximize natural light and manage heat gain, advanced air handling and exhaust systems, construction materials made from a significant percentage of recycled content and native vegetation to encourage biodiversity and reduce the need for irrigation.

    See the full article here .


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

    Please help promote STEM in your local schools.

    Stem Education Coalition

    rutgers-campus

    Rutgers, The State University of New Jersey, 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.

    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 9:55 am on September 16, 2018 Permalink | Reply
    Tags: A new level of “self-awareness” to Earth’s self-regulation which is at the heart of the original Gaia theory, , , Biology, , Creating transformative solutions to the global changes that humans are now causing is a key focus of the University of Exeter’s new Global Systems Institute, , GAIA 2.0, , , Selection by survival alone, Self-regulating system, Stability comes from “sequential selection”   

    From Astrobiology Magazine: ” Famous theory of the living Earth upgraded to ‘Gaia 2.0’ “ 

    Astrobiology Magazine

    From Astrobiology Magazine

    and

    4

    Sep 15, 2018
    No writer credit

    1
    The original Gaia Theory was developed in the late 1960’s by James Lovelock, a British scientist and inventor. Credit: NASA

    1
    James Lovelock. The original uploader was Bruno Comby at English Wikipedia.

    A time-honoured theory into why conditions on Earth have remained stable enough for life to evolve over billions of years has been given a new, innovative twist.

    For around half a century, the ‘Gaia’ hypothesis has provided a unique way of understanding how life has persisted on Earth.

    It champions the idea that living organisms and their inorganic surroundings evolved together as a single, self-regulating system that has kept the planet habitable for life – despite threats such as a brightening Sun, volcanoes and meteorite strikes.

    However, Professor Tim Lenton from the University of Exeter and famed French sociologist of science Professor Bruno Latour are now arguing that humans have the potential to ‘upgrade’ this planetary operating system to create “Gaia 2.0”.

    They believe that the evolution of both humans and their technology could add a new level of “self-awareness” to Earth’s self-regulation, which is at the heart of the original Gaia theory.

    As humans become more aware of the global consequences of their actions, including climate change, a new kind of deliberate self-regulation becomes possible where we limit our impacts on the planet.

    Professors Lenton and Latour suggest that this “conscience choice” to self-regulate introduces a “fundamental new state of Gaia” – which could help us achieve greater global sustainability in the future.

    However, such self-aware self-regulation relies on our ability to continually monitor and model the state of the planet and our effects upon it.

    Professor Lenton, Director of Exeter’s new Global Systems Institute, said: “If we are to create a better world for the growing human population this century then we need to regulate our impacts on our life support-system, and deliberately create a more circular economy that relies – like the biosphere – on the recycling of materials powered by sustainable energy.”

    The original Gaia Theory was developed in the late 1960’s by James Lovelock, a British scientist and inventor. It suggested that both the organic and inorganic components of Earth evolved together as one single, self-regulating system which can control global temperature and atmospheric composition to maintain its own habitability.

    The new perspective article is published in leading journal Science on September 14, 2018.

    It follows recent research, led by Professor Lenton, which offered a fresh solution to how the Gaia hypothesis works in real terms: Stability comes from “sequential selection” in which situations where life destabilises the environment tend to be short-lived and result in further change until a stable situation emerges, which then tends to persist.

    Once this happens, the system has more time to acquire further properties that help to stabilise and maintain it – a process known as “selection by survival alone”.

    Creating transformative solutions to the global changes that humans are now causing is a key focus of the University of Exeter’s new Global Systems Institute.

    See the full article here .


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

    Stem Education Coalition

     
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