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  • richardmitnick 10:35 am on May 25, 2016 Permalink | Reply
    Tags: Applied Research & Technology, , , , Nerve damage found in prediabetics   

    From Hopkins via The Baltimore Sun: “Nerve damage found in prediabetics” Why to Avoid Dunkin’ Donuts 

    Johns Hopkins
    Johns Hopkins University


    Andrea K. McDaniels

    Michael Jackson suffers from significant nerve damage stemming from prediabetes. (Lloyd Fox / Baltimore Sun)

    The pain shot across the tops of Michael Jackson’s feet as if someone was pounding him with a sledgehammer, sometimes becoming so unbearable he couldn’t sleep.

    The aerospace engineer blamed it on arthritis until his primary care physician ruled that out. Tests for Lupus and Lou Gherig’s disease also came back negative. Finally, a doctor cut a small sample of skin from one of Jackson’s feet and counted the nerve fibers under a microscope.

    Jackson suffered from significant nerve damage stemming from prediabetes — a condition in which people have high blood glucose levels but not enough to be classified as diabetes.

    Doctors have known for a while that those with prediabetes can experience mild weakness, numbness and pain from nerve damage, but a new Johns Hopkins study suggests that so-called neuropathy is much more significant than once thought. Like Jackson, patients can experience excruciating pain more typically associated with full-blown diabetes. About 50 percent of people with diabetes have neuropathy, according to the National Institute of Neurological Disorders and Stroke.

    The numbness associated with neuropathy can contribute to some diabetics’ eventual need for amputation. Diabetics tend to have poor blood circulation, which can lead to infection and ulcers. A patient may not notice an injury or infection due to lack of feeling, leading to amputation.

    The Johns Hopkins researchers say their findings provide evidence that patients should be screened for prediabetes and neuropathy much earlier than once thought. The medical community also needs to do a better job at treating and diagnosing those with prediabetes, the researchers concluded. An estimated one in three Americans — 86 million people — have prediabetes, according to the U.S. Centers for Disease Control, and may be at particular risk to the unknown consequences of the disease.

    “It means that even mild blood sugar elevations are important and it’s important for us to be aggressive in how we treat that,” said Dr. Michael Polydefkis, the study’s senior author and a professor of neurology at the Johns Hopkins University School of Medicine and director of the Cutaneous Nerve Lab.

    The Hopkins study is different from those done in the past because it showed deterioration over the entire length of sensory nerve fibers and not just at the ends, which suggests the damage is not localized.

    The patients with prediabetes, studied over a period of three years, continued to have worsening damage to their small nerve fibers throughout the study just as patients with full-blown diabetes did. Skin samples taken from the ankle, thigh and knee showed a 10 percent loss in the density of nerve cells by the end of the study.

    “I expected that people with diabetes would do worse, but I didn’t really expect people with prediabetes to experience a similar rate of degradation of their small nerve fibers,” Polydefkis said.

    The results come as medical providers already are trying to better diagnose prediabetes.

    For the last few years, the American Medical Association has worked to increase public awareness about prediabetes and get more phyisicians to screen at-risk patients. Working with the U.S. Centers for Disease Control, the association is offering doctors more information about prevention programs for their patients.

    The medical association also is participating in a public service campaign to raise awareness of prediabetes as a serious health problem. The campaign encourages people to find out if they have prediabetes and to take steps to reverse their condition to avoid developing full diabetes.

    If caught early, prediabetes can be treated with lifestyle changes, such as weight loss, exercise and diet modification to bring blood sugar levels down. Some doctors also believe the medicine used to treat diabetes could be used for prediabetes as well.

    Untreated prediabetes could progress to diabetes and lead to lifelong health problems, including cardiovascular disease and skin problems. Diabetes can destroy the blood vessels of the retina leading to blindness and damage the kidneys, which the body uses to filter out waste, leading some patients to need dialysis treatment to survive. Research shows that 15 percent to 30 percent of overweight people with prediabetes will develop type 2 diabetes within five years unless they make lifestyle changes.

    “We know that people who take preventive measures early on can slow the rate of decline,” said Dr. Ruth S. Horowitz, chief of the division of endocrinology and metabolism at Greater Baltimore Medical Center.

    There are some limits to the study. The sample size was small with 62 people, including 16 who were prediabetic and 52 with tingling and pain in their hands and feet.

    Still, the Hopkins research could help convince insurance companies to eventually cover the treatment of prediabetes, some doctors said. Insurance companies don’t always cover nutritional education and supplies for glucose testing until a patient has full-blown diabetes.

    “This study reinforces the need for us to address prediabetes as an even more serious problem,” said Stephen N. Davis, chair of the department of medicine at the University of Maryland School of Medicine. “It really does show there are consequences with prediabetes.”

    Jackson continues to cope with the consequences of his neuropathy. His nerve damage has gotten worse over time. He has lost much of the feeling in his feet and once dropped a cinder block on his foot without knowing until he looked down. His balance is off and he sometimes finds himself falling over in the shower. He is trying to manage the condition with medications and eating better.

    “As a kid I ate a lot of candy,” he said. “I was drowning myself with sugar as a kid, but back in the day nobody said much about sugar. I have tried to cut back now and it has helped.”

    See the full article here .

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    Johns Hopkins Campus

    The Johns Hopkins University opened in 1876, with the inauguration of its first president, Daniel Coit Gilman. “What are we aiming at?” Gilman asked in his installation address. “The encouragement of research … and the advancement of individual scholars, who by their excellence will advance the sciences they pursue, and the society where they dwell.”

    The mission laid out by Gilman remains the university’s mission today, summed up in a simple but powerful restatement of Gilman’s own words: “Knowledge for the world.”

    What Gilman created was a research university, dedicated to advancing both students’ knowledge and the state of human knowledge through research and scholarship. Gilman believed that teaching and research are interdependent, that success in one depends on success in the other. A modern university, he believed, must do both well. The realization of Gilman’s philosophy at Johns Hopkins, and at other institutions that later attracted Johns Hopkins-trained scholars, revolutionized higher education in America, leading to the research university system as it exists today.

  • richardmitnick 10:13 am on May 25, 2016 Permalink | Reply
    Tags: Applied Research & Technology, , , Rebecca Doerge Appointed Dean of Mellon College of Science,   

    From CMU: “Rebecca Doerge Appointed Dean of Mellon College of Science” Women in Science 

    Carnegie Mellon University logo
    Carnegie Mellon University


    Rebecca Doerge, the Trent and Judith Anderson Distinguished Professor of Statistics at Purdue University, has been appointed as the next dean of the Mellon College of Science at Carnegie Mellon University, effective Aug. 1.

    Doerge also will hold joint faculty appointments in the Department of Biological Sciences in the Mellon College of Science and the Department of Statistics in the Dietrich College of Humanities and Social Sciences.

    Doerge, who joined Purdue in 1995, holds a joint appointment in Purdue’s College of Agriculture and College of Science. Her research focuses on statistical bioinformatics, which brings together multiple scientific disciplines to investigate and disseminate biologically interesting information, and further understand the ultimate function of DNA and epigenomic associations.

    “Rebecca brings more than 25 years of experience as a scholar, educator and leader to CMU,” CMU Provost Farnam Jahanian said. “Collaboration across disciplinary borders is a hallmark of her own scholarship and her academic leadership, and she has demonstrated a deep appreciation for supporting basic research. Those qualities make Rebecca an ideal leader for the Mellon College of Science and a champion for science throughout Carnegie Mellon at this important moment. Science is in our DNA as a university, and touches on the work that all of us do, across colleges and centers.”

    As head of Purdue’s Department of Statistics from 2010-2015, Doerge oversaw the unit’s growth into one of the largest departments of statistics in the country. She led efforts that doubled both the number of undergraduate students and the number of tenured female faculty, while also increasing the department’s number of online and hybrid course offerings.

    “Carnegie Mellon’s focus on educating the whole student across disciplinary boundaries is essential for addressing both societal and global challenges,” Doerge said. “I am deeply honored to be a member of the university’s leadership team and look forward to working with the Mellon College of Science faculty, staff and students to advance discovery, collaboration and innovation.”

    Doerge is an elected fellow of the American Statistical Association and the American Association for the Advancement of Science. She is a member of the board of trustees for the National Institute of Statistical Sciences and the Mathematical Biosciences Institute.

    A recipient of multiple awards at Purdue, Doerge has authored more than 120 scientific articles, published two books and worked with 23 doctoral degree candidates to the successful completion of their studies.

    Doerge earned bachelor’s and master’s degrees in mathematics from the University of Utah and a doctoral degree in statistics from North Carolina State University. She spent two years as a postdoctoral scholar at Cornell University.

    Doerge will succeed Dean Fred Gilman, who will be stepping down after serving in the position since 2007.

    See the full article here .

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    Carnegie Mellon University (CMU) is a global research university with more than 12,000 students, 95,000 alumni, and 5,000 faculty and staff.
    CMU has been a birthplace of innovation since its founding in 1900.
    Today, we are a global leader bringing groundbreaking ideas to market and creating successful startup businesses.
    Our award-winning faculty members are renowned for working closely with students to solve major scientific, technological and societal challenges. We put a strong emphasis on creating things—from art to robots. Our students are recruited by some of the world’s most innovative companies.
    We have campuses in Pittsburgh, Qatar and Silicon Valley, and degree-granting programs around the world, including Africa, Asia, Australia, Europe and Latin America.

  • richardmitnick 9:00 pm on May 24, 2016 Permalink | Reply
    Tags: 'Kidney on a chip', Applied Research & Technology, ,   

    From U Michigan: ” ‘Kidney on a chip’ could lead to safer drug dosing” 

    U Michigan bloc

    University of Michigan

    Gabe Cherry, Michigan Engineering

    No image caption, no image credit

    University of Michigan researchers have used a “kidney on a chip” device to mimic the flow of medication through human kidneys and measure its effect on kidney cells. The new technique could lead to more precise dosing of drugs, including some potentially toxic medicines often delivered in intensive care units.

    Precise dosing in intensive care units is critical, as up to two-thirds of patients in the ICU experience serious kidney injury. Medications contribute to this injury in more than 20 percent of cases, largely because many intensive care drugs are potentially dangerous to the kidneys.

    Determining a safe dosage, however, can be surprisingly difficult. Today, doctors and drug developers rely mainly on animal testing to measure the toxicity of drugs and determine safe doses. But animals process medications more quickly than humans, making it difficult to interpret test results and sometimes leading researchers to underestimate toxicity.

    No image caption, no image credit

    The new technique offers a more accurate way to test medications, closely replicating the environment inside a human kidney. It uses a microfluidic chip device to deliver a precise flow of medication across cultured kidney cells. This is believed to be the first time such a device has been used to study how a medication behaves in the body over time, called its “pharmacokinetic profile.”

    “When you administer a drug, its concentration goes up quickly and it’s gradually filtered out as it flows through the kidneys,” said University of Michigan Biomedical Engineering professor Shuichi Takayama, an author on the paper. “A kidney on a chip enables us to simulate that filtering process, providing a much more accurate way to study how medications behave in the body.”

    Takayama said the use of an artificial device provides the opportunity to run test after test in a controlled environment. It also enables researchers to alter the flow through the device to simulate varying levels of kidney function.

    “Even the same dose of the same drug can have very different effects on the kidneys and other organs, depending on how it’s administered,” said Sejoong Kim, an associate professor at Korea’s Seoul national University Budang Hospital, former U-M researcher and author on the paper. “This device provides a uniform, inexpensive way to capture data that more accurately reflects actual human patients.”

    In the study, the team tested their approach by comparing two different dosing regimens for gentamicin, an antibiotic that’s commonly used in intensive care units. They used a microfluidic device that sandwiches a thin, permeable polyester membrane and a layer of cultured kidney cells between top and bottom compartments.

    No image caption, no image credit

    They then pumped a gentamicin solution into the top compartment, where it gradually filtered through the cells and the membrane, simulating the flow of medication through a human kidney. One test started with a high concentration that quickly tapered off, mimicking a once-daily drug dose. The other test simulated a slow infusion of the drug, using a lower concentration that stayed constant. Takayama’s team then measured damage to the kidney cells inside the device.

    They found that a once-daily dose of the medication is significantly less harmful than a continuous infusion—even though both cases ultimately delivered the same dose of medication. The results of the test could help doctors better optimize dosing regimens for gentamicin in the future. Perhaps most importantly, they showed that a kidney on a chip device can be used to study the flow of medication through human organs.

    “We were able to get results that better relate to human physiology, at least in terms of dosing effects, than what’s currently possible to obtain from common animal tests,” Takayama said. “The goal for the future is to improve these devices to the point where we’re able to see exactly how a medication affects the body from moment to moment, in real time.”

    Takayama said the techniques used in the study should be generalizable to a wide variety of other organs and medications, enabling researchers to gather detailed information on how medications affect the heart, liver and other organs. In addition to helping researchers fine-tune drug dosing regimens, he believes the technique could also help drug makers test drugs more efficiently, bringing new medications to market faster.

    Within a few years, Takayama envisions the creation of integrated devices that can quickly test multiple medication regimens and deliver a wide variety of information on how they affect human organs. PHASIQ, an Ann Arbor-based spinoff company founded by Takayama is commercializing the biomarker readout aspect of this type of technology in conjunction with the University of Michigan Office of Technology Transfer, where Takayama serves as a Faculty Innovation Ambassador.

    Access mp4 video here .
    University of Michigan researchers used a “kidney on a chip” to mimic the flow of medication through human kidneys. This enabled them to study the dosing regimen for a common intensive care drug. No video credit

    The paper, published in the journal Biofabrication, is titled Pharmacokinetic profile that reduces nephrotoxicity of gentamicin in a perfused kidney-on-a-chip. Funding and assistance for the project was provided by the National Institutes of Health (grant number GM096040), the University of Michigan Center for Integrative Research in Critical Care (MCIRCC), the University of Michigan Biointerfaces Institute, the National Research Foundation of Korea and the Korean Association of Internal Medicine Research Grant 2015.

    See the full article here .

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    U MIchigan Campus

    The University of Michigan (U-M, UM, UMich, or U of M), frequently referred to simply as Michigan, is a public research university located in Ann Arbor, Michigan, United States. Originally, founded in 1817 in Detroit as the Catholepistemiad, or University of Michigania, 20 years before the Michigan Territory officially became a state, the University of Michigan is the state’s oldest university. The university moved to Ann Arbor in 1837 onto 40 acres (16 ha) of what is now known as Central Campus. Since its establishment in Ann Arbor, the university campus has expanded to include more than 584 major buildings with a combined area of more than 34 million gross square feet (781 acres or 3.16 km²), and has two satellite campuses located in Flint and Dearborn. The University was one of the founding members of the Association of American Universities.

    Considered one of the foremost research universities in the United States,[7] the university has very high research activity and its comprehensive graduate program offers doctoral degrees in the humanities, social sciences, and STEM fields (Science, Technology, Engineering and Mathematics) as well as professional degrees in business, medicine, law, pharmacy, nursing, social work and dentistry. Michigan’s body of living alumni (as of 2012) comprises more than 500,000. Besides academic life, Michigan’s athletic teams compete in Division I of the NCAA and are collectively known as the Wolverines. They are members of the Big Ten Conference.

  • richardmitnick 8:44 pm on May 24, 2016 Permalink | Reply
    Tags: Applied Research & Technology, , New Stanford-developed tool allows easier study of blood cancers,   

    From Stanford: “New Stanford-developed tool allows easier study of blood cancers” 

    Stanford University Name
    Stanford University

    May 24, 2016
    Christopher Vaughan

    In the history of science and medicine, the breakthrough discoveries get a lot of deserved attention, but often overlooked are the invention of the tools that made those discoveries possible. Galileo discovered moons around other planets, but it was the invention of the telescope that made his observation possible. Leeuwenhoek discovered microbes only after he created a simple but powerful microscope.

    Researchers in the laboratory of Stanford’s Ravi Majeti, MD, PhD, have just created one such tool — a method of implanting cells to create a human bone-like structure in mice. This allows investigators to study a whole host of blood cancers and other diseases that they had trouble studying before. Majeti and colleagues published* the work this week in the journal Nature Medicine.

    “Transplanting human leukemia cells into mice has been an important way of studying the disease,” postdoctoral fellow Andreas Reinisch, MD, PhD, first author of the paper, recently explained. “This method has given us important insights into how cancer develops and has been the way that all new anti-leukemia drugs have been tested and developed.” Mice engrafted with human leukemia cells are even sometimes used to test possible drug treatments for patients currently undergoing treatment for the blood cancer, he added.

    The problem, said Reinisch, is that even in the best cases, researchers can get human leukemia to take up residence and multiply in mice only half the time. For many types of blood cancers, engraftment doesn’t happen at all. It’s like Galileo’s telescope could only be pointed at a small spot of sky visible through a hole in his roof.

    Majeti, Reinisch, and their co-workers have metaphorically blown the roof off by transplanting special bone marrow-derived cells called stromal cells in mice. These human stromal cells multiply and divide to create a miniature, bone-like structure, complete with a bony outer shell and an internal, marrow-like compartment. This structure allows implanted human blood cells to live and grow in their natural environment — human bone.

    “I’m really excited about this technique because we now have a way to look closely at all kinds of leukemia, as well as many other profilerative disorders of blood cells,” Majeti said. “It also opens up the study of other, non-blood diseases such as metastatic breast cancer, which often spreads to bone in humans but simply won’t spread in existing mouse models.”

    Science paper:
    A humanized bone marrow ossicle xenotransplantation model enables improved engraftment of healthy and leukemic human hematopoietic cells

    See the full article here .

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

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  • richardmitnick 4:19 pm on May 24, 2016 Permalink | Reply
    Tags: Applied Research & Technology, , Maria Zuber, ,   

    From MIT: “Maria Zuber elected as chair of the National Science Board” Women in Science 

    MIT News
    MIT News
    MIT Widget

    May 24, 2016
    The following is adapted from a National Science Foundation press release.

    For the first time in the history of the National Science Foundation (NSF), women now hold three key leadership positions — director of the NSF, and chair and vice-chair of its governing body, the National Science Board (NSB). During its May meeting, the NSB elected Maria Zuber, vice president for research at MIT, as its board chair, and Diane Souvaine, vice provost for research at Tufts University, as its vice chair. Zuber and Souvaine replace Dan Arvizu and Kelvin Droegemeier, who stepped down from the Board after twelve years of service, the last four as chair and vice chair.

    Maria Zuber

    Zuber’s research bridges planetary geophysics and the technology of space-based laser and radio systems, and she has published over 200 papers. She has held leadership roles associated with scientific experiments or instrumentation on nine NASA missions and remains involved with six of these missions. The E.A. Griswold Professor of Geophysics at MIT, Zuber is a member of the National Academy of Sciences and the American Philosophical Society, and is a fellow of the American Academy of Arts and Sciences, the American Association for the Advancement of Science, the Geological Society of America, and the American Geophysical Union. In 2002, Discover magazine named her one of the 50 most important women in science. Zuber served on the Presidential Commission on the Implementation of United States Space Exploration Policy in 2004.

    Jointly, the 24-member NSB and the NSF director pursue the goals and function of the Foundation. The NSB establishes the policies of NSF within the framework of applicable national policies set forth by the president and Congress. The board also identifies issues that are critical to NSF’s future, approves the agency’s strategic budget directions and the annual budget submission to the Office of Management and Budget, and new major programs and awards. The NSB serves as an independent body of advisors to both the president and Congress on policy matters related to science and engineering and education in science and engineering. In addition to publishing major reports, the NSB publishes policy papers and statements on issues of importance to U.S. science and engineering.

    NSF director and NSB member ex officio France Córdova said, “I am delighted to say, on behalf of NSF, that we are thrilled with Dr. Zuber’s election as chair of the National Science Board. As a superb scientist and recognized university leader, she has the skills needed to help guide the agency’s policies and programs. I look forward to working with her as NSF launches new big ideas in science and engineering.”

    Zuber is in her fourth year on the NSB and has served on its Committee on Strategy and Budget.

    “It is a privilege to lead the National Science Board and to promote NSF’s bold vision for research and education in science and engineering,” said Zuber. “The outcomes of discovery science inspire the next generation and yield the knowledge that drives innovation and national competitiveness, and contribute to our quality of life. NSB is committed to working with Director Córdova and her talented staff to assure that the very best ideas based on merit review are supported and that exciting, emerging opportunities — many at the intersection of disciplines — are pursued.”

    Souvaine is in her second term on the NSB and has served as chair of its Committee on Strategy and Budget, chair of its Committee on Programs and Plans, and a member of its Committee on Audit and Oversight. In addition, she co-chaired the NSB’s Task Force on Mid-Scale Research and served three years on the Executive Committee.

    A theoretical computer scientist, Souvaine’s research in computational geometry has commercial applications in materials engineering, microchip design, robotics, and computer graphics. She was elected a fellow of the Association for Computing Machinery for her research and for her service on behalf of the computing community. A founding member, Souvaine served for over two years with the NSF Science and Technology Center on Discrete Mathematics and Theoretical Computer Science, that originally spanned Princeton University, Rutgers University, Bell Labs, and Bell Communications Research. She also works to enhance precollege mathematics and foundations of computing education and to advance opportunities for women and minorities in mathematics, science, and engineering.

    “I am truly honored and humbled by this vote of confidence from such esteemed colleagues. I do not take this responsibility lightly,” said Souvaine. “The board is proud of NSF’s accomplishments over its 66 years, from the discovery of gravitational waves at LIGO to our biennial Science and Engineering Indicators report on the state of our nation’s science and engineering enterprise. I look forward to working with Congress, the administration, the science and education communities, and NSF staff to continue the agency’s legacy in advancing the progress of science.”

    The president appoints NSB members, selected for their eminence in research, education, or public service and records of distinguished service, and who represent a variety of science and engineering disciplines and geographic areas. Board members serve six-year terms, and the president may reappoint members for a second term. NSF’s director is an ex officio 25th member of the board.

    See the full article here .

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    The mission of MIT is to advance knowledge and educate students in science, technology, and other areas of scholarship that will best serve the nation and the world in the twenty-first century. We seek to develop in each member of the MIT community the ability and passion to work wisely, creatively, and effectively for the betterment of humankind.

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  • richardmitnick 4:56 pm on May 23, 2016 Permalink | Reply
    Tags: Applied Research & Technology, ,   

    From U Texas at Austin: “Making Virus Sensors Cheap and Simple: New Method Detects Single Viruses” 

    U Texas Austin bloc

    University of Texas at Austin

    23 May 2016
    Marc G Airhart

    Scientists at The University of Texas at Austin have developed a new method to rapidly detect a single virus in urine, as reported* this week in the journal Proceedings of the National Academy of Sciences.

    Researchers at The University of Texas at Austin demonstrated the ability to detect single viruses in a solution containing murine cytomegalovirus (MCMV). The single virus in this image is a human cytomegalovirus, a cousin of MCMV. It was obtained by chilling a sample down with liquid nitrogen and exposing it to high-energy electrons. Image courtesy of Jean-Yves Sgro, U. of Wisconsin-Madison (EMD-5696 data Dai, XH et al., 2013)

    Although the technique presently works on just one virus, scientists say it could be adapted to detect a range of viruses that plague humans including Ebola, Zika and HIV.

    “The ultimate goal is to build a cheap, easy-to-use device to take into the field and measure the presence of a virus like Ebola in people on the spot,” says Jeffrey Dick, a chemistry graduate student and co-lead author of the study. “While we are still pretty far from this, this work is a leap in the right direction.”

    The other co-lead author is Adam Hilterbrand, a microbiology graduate student.

    The new method is highly selective, meaning it is only sensitive to one type of virus, filtering out possible false negatives caused by other viruses or contaminants.

    There are two other commonly used methods for detecting viruses in biological samples, but they have drawbacks. One requires a much higher concentration of viruses, and the other requires samples to be purified to remove contaminants. The new method, however, can be used with urine straight from a person or animal.

    The other co-authors are Lauren Strawsine, a postdoctoral fellow in chemistry; Jason Upton, an assistant professor of molecular biosciences; and Allen Bard, professor of chemistry and director of the Center for Electrochemistry.

    The researchers demonstrated their new technique on a virus that belongs to the same family as the herpes virus, called murine cytomegalovirus (MCMV). To detect individual viruses, the team places an electrode — a wire that conducts electricity, in this case, one that is thinner than a human cell — in a sample of mouse urine. They then add to the urine some special molecules made up of enzymes and antibodies that naturally stick to the virus of interest. When all three stick together and then bump into the electrode, there’s a spike in electric current that can be easily detected.

    The researchers say their new method still needs refinement. For example, the electrodes become less sensitive over time because a host of other naturally occurring compounds stick to them, leaving less surface area for viruses to interact with them. To be practical, the process will also need to be engineered into a compact and rugged device that can operate in a range of real-world environments.

    Support for this research was provided by the National Science Foundation, the Welch Foundation and the Cancer Prevention & Research Institute of Texas.

    *Science paper:
    Enzymatically enhanced collisions on ultramicroelectrodes for specific and rapid detection of individual viruses

    See the full article here .

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    In 1839, the Congress of the Republic of Texas ordered that a site be set aside to meet the state’s higher education needs. After a series of delays over the next several decades, the state legislature reinvigorated the project in 1876, calling for the establishment of a “university of the first class.” Austin was selected as the site for the new university in 1881, and construction began on the original Main Building in November 1882. Less than one year later, on Sept. 15, 1883, The University of Texas at Austin opened with one building, eight professors, one proctor, and 221 students — and a mission to change the world. Today, UT Austin is a world-renowned higher education, research, and public service institution serving more than 51,000 students annually through 18 top-ranked colleges and schools.

  • richardmitnick 4:39 pm on May 23, 2016 Permalink | Reply
    Tags: , Applied Research & Technology,   

    From Rockefeller: “New method gives scientists a better look at how HIV infects and takes over its host cells” 

    Rockefeller U bloc

    Rockefeller University

    May 23, 2016
    No writer credit found

    Cell to cell: When HIV infects a cell, it programs the cell to express the viral protein Env, which the virus uses to spread to neighboring cells. Above, Env (red) produced by one infected cell has recruited other, uninfected cells, causing them to fuse, and their nuclei (blue) to cluster.

    Viruses attack cells and commandeer their machinery in a complex and carefully orchestrated invasion. Scientists have longed probed this process for insights into biology and disease, but essential details still remain out of reach.

    A new approach, developed by a team of researchers led by the Rockefeller University and the Aaron Diamond AIDS Research Center (ADARC), offers an unprecedented view of how a virus infects and appropriates a host cell, step by step. In research published* May 23 in Nature Microbiology, they applied their method to HIV, a virus whose genome is less than 100,000 the size of ours.

    “HIV is truly an expert at living large on a small budget,” says first author Yang Luo, a postdoc at ADARC and a former graduate student at Rockefeller University. “We asked the question, how does such a compact virus manipulate the host cell to gain entry and replicate itself, all while escaping the immune system?”

    Mapping HIV’s ‘interactome’

    The study focused on two viral proteins known to bring about HIV’s infection of human white blood cells. The first one, called envelope or Env, sits on the surface of the virus and, by binding to receptors on the host cell, helps the membrane that encapsulates the virus fuse with the cell’s outer membrane. A second protein, Vif, destroys an enzyme that host cells produce to defend themselves against the virus.

    In an effort to better understand how these two proteins function, the team wanted to map their interactome—meaning all the proteins with which they associate within a host cell. To accomplish this, the researchers needed to devise a way to isolate clusters of interacting proteins from cells during different stages of infection. Such experiments can be done by introducing a genetic sequence into the viral genome—a “tag” that acts like a piece of molecular Velcro, allowing one viral protein to be yanked out along with all the other proteins associated with it.


    It sounds simple, but making it work took a decade.

    “Inserting a tag sequence into small viruses is a challenge to begin with,” says corresponding author Mark Muesing, a principal investigator at ADARC. “If you disrupt their nucleic acid and protein sequences, you can easily compromise the virus’s ability to replicate. And HIV represents a particular challenge because it can quickly revert back to its original sequence.”

    “We developed a technique to find places in the HIV genome where we can insert stable tags without affecting the virus’s capacity to proliferate. In effect, this allowed us to expand cultures of the infected cells along with the tagged viral protein,” he added.

    The host’s contribution

    Next, the researchers infected human cells with viruses carrying the tagged protein sequences, and were able to pull out and identify a large number of host proteins directly during the infectious process. This provided the first evidence that many previously underappreciated host proteins interact with the viral machinery during replication.

    “Imagine you have a factory assembly line where only one component of, say, the stamping machine, actually touches the product,” says co-author Michael Rout, professor and head of Rockefeller’s Laboratory of Cellular and Structural Biology. “Other parts support and power the stamp. Likewise, within an infected cell, we can identify the components of a particular cellular machine, not just the piece that comes in contact with the viral protein.”

    “Every host protein we pull out generates new questions,” adds co-first author Erica Jacobs, a research associate in Brian Chait’s lab. “Does it help the virus invade and coopt the host to replicate itself? Or does it harm it? The answers will not only help us understand the virus, but also shed light on our cells’ ability to defend themselves.”

    One important discovery has already emerged from the lists of proteins. Viruses, including HIV, often attack as so-called virions, which are individual packets of protein and genetic code. But they can also pass directly from an infected to an uninfected cell, a more effective mode of transmission. To do so, the virus appears to use host proteins to construct a platform, a close junctional surface, between cells.

    From the list of proteins that interact with Env, the researchers have identified cellular proteins predicted to contribute to this platform between cells. Because this route of transmission protects the virus in a sequestered environment, away from host defenses, the new findings may aid in the development of future anti-HIV therapies.

    A live infection, step by step

    According to co-author Brian Chait, Camille and Henry Dreyfus Professor and head of the Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, the new approach offers a rare glimpse into the process by which HIV invades and resurrects itself within a cell.

    “Often, studies of this sort are done with viral proteins in the absence of a true viral infection “However, because viral infections are exquisitely orchestrated events, you are likely to miss all kinds of important details if you study the action of these proteins out of their proper context.”

    “Deciphering the intricacies of virus-host protein interactions in space and time during the progression of an infection is remarkably powerful” says co-author Ileana Cristea, an associate professor of molecular biology at Princeton University. “The challenge is to discover which precise interactions are the critical ones.”

    Todd Greco, a co-first author, and an associate research scholar and lecturer in molecular biology in Cristea’s lab, says that “even for host proteins within the same family, their relative stability within HIV-1 protein complexes can be very different. More broadly, by understanding these mechanisms we will better understand the coordinated responses of cells.”

    *Science paper:
    HIV–host interactome revealed directly from infected cells

    See the full article here .

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    The Rockefeller University is a world-renowned center for research and graduate education in the biomedical sciences, chemistry, bioinformatics and physics. The university’s 76 laboratories conduct both clinical and basic research and study a diverse range of biological and biomedical problems with the mission of improving the understanding of life for the benefit of humanity.

    Founded in 1901 by John D. Rockefeller, the Rockefeller Institute for Medical Research was the country’s first institution devoted exclusively to biomedical research. The Rockefeller University Hospital was founded in 1910 as the first hospital devoted exclusively to clinical research. In the 1950s, the institute expanded its mission to include graduate education and began training new generations of scientists to become research leaders around the world. In 1965, it was renamed The Rockefeller University.

  • richardmitnick 3:55 pm on May 23, 2016 Permalink | Reply
    Tags: Applied Research & Technology, , , Water-Energy Nexus New Focus of Berkeley Lab Research   

    From LBL: “Water-Energy Nexus New Focus of Berkeley Lab Research” 

    Berkeley Logo

    Berkeley Lab

    May 23, 2016
    Julie Chao
    (510) 486-6491

    Water banking, desalination, and high-resolution climate models are all part of the new Berkeley Lab Water Resilience Initiative. (California snowpack photo credit: Dan Pisut/ NASA)

    Billions of gallons of water are used each day in the United States for energy production—for hydroelectric power generation, thermoelectric plant cooling, and countless other industrial processes, including oil and gas mining. And huge amounts of energy are required to pump, treat, heat, and deliver water.

    This interdependence of water and energy is the focus of a major new research effort at the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab). With the twin challenges of population growth and climate change adding to the resource pressures, Berkeley Lab’s Water Resilience Initiative aims to use science and technology to optimize coupled water-energy systems and guide investments in such systems.

    “Considering water and energy as separate issues is passé,” said Berkeley Lab scientist Robert Kostecki, one of the three leads of the initiative. “Now the two are becoming critically interdependent. And both the energy and water sectors are expected to experience serious stresses from extreme climate events. However the problem on each side is dealt with, there needs to be an understanding of possible implications on the other side.”

    The Initiative has three main goals: hydroclimate and ecosystem predictions, revolutionary concepts for efficient and sustainable groundwater systems, and science and technology breakthroughs in desalination. The goals can be viewed as analogous to energy distribution, storage, and generation, says Susan Hubbard, Berkeley Lab’s Associate Lab Director for Earth and Environmental Sciences.

    “We consider improved hydroclimate predictions as necessary for understanding future water distribution,” Hubbard said. “We are exploring water banking as a subsurface strategy to store water that is delivered by snowmelt or extreme precipitation. To remain water resilient in other locations and to take advantage of seawater through brackish inland produced waters, Berkeley Lab is performing fundamental investigations to explore new approaches to desalinate water, ideally leading to cost and energy efficient approaches to generate water.”

    Climate: the Source of All Water

    The climate, ultimately, is the source of all water, and in places like California, where the snow pack plays an important role, climate change will have a big impact on how much water there will be and when it will come. The goal of the climate focus of the Initiative, led by Berkeley Lab climate scientist Andrew Jones, is to develop approaches to predict hydroclimate at scales that can be used to guide water-energy strategies.

    “Historically we’ve developed climate models that are global models, developed to answer global science questions,” Jones said. “But there’s an increasing demand for information at much finer spatial scales to support climate adaptation planning.”

    Ten years ago, Berkeley Lab scientists helped develop global climate models with a resolution of 200 kilometers. By 2012, the most advanced models had 25 km resolution. Now a project is underway to develop a regional climate model of the San Francisco Bay Area with resolution of 1 km, or the neighborhood level.

    “We’ll be looking at the risk of extreme heat events and how that interacts with the microclimates of the Bay Area, and additionally, how change in the urban built environment can exacerbate or ameliorate those heat events,” Jones said. “Then we want to understand the implications of those heat events for water and energy demands.”

    The eventual goal is to transfer this model for use in other urban areas to be able to predict extreme precipitation events as well as drought and flood risk.

    Subsurface: Storage, Quality, and Movement of Water Underground

    Another Initiative focus, led by Peter Nico, head of Berkeley Lab’s Geochemistry Department, studies what’s happening underground. “We have a lot of expertise in understanding the subsurface—using various geophysical imaging techniques, measuring chemical changes, using different types of hydrologic and reactive transport models to simulate what’s happening,” he said. “So our expertise matches up very well with groundwater movement and management and groundwater quality.”

    Groundwater issues have become more important with the drought of the last four years. “California has been ‘overdrafting’ water for a long time, especially in the San Joaquin Valley, where we’re pulling more water out than is naturally infiltrating back in,” Nico said. “With the drought the use of groundwater has gone up even more. That’s causing a lot of problems, like land subsidence.”

    While there is already a lot of activity associated with groundwater management in California, Nico added, “we still can’t confidently store and retrieve clean water in the subsurface when and where we need it. We think there’s a place to contribute a more scientific chemistry- and physics-based understanding to efficient groundwater storage in California.”

    For example, Berkeley Lab scientists have expertise in using geophysical imaging, which allows them to “see” underground without drilling a well. “We have very sophisticated hydrologic and geochemical computer codes we think we can couple with imaging to predict where water will go and how its chemistry may change through storage or retrieval,” he said.

    Berkeley Lab researchers are helping test “water banking” on almond orchards. (Courtesy of Almond Board of California)

    They have a new project with the Almond Board of California to determine the ability to recharge over-drafted groundwater aquifers in the San Joaquin Valley by applying peak flood flows to active orchards, known as “water banking.” The project is part of the Almond Board’s larger Accelerated Innovation Management (AIM) program, which includes an emphasis on creating sustainable water resources. Berkeley Lab scientists will work with existing partners, Sustainable Conservation and UC Davis, who are currently conducting field trials and experiments, and contribute their expertise on the deeper subsurface, below the root zone of the almond trees, to determine what happens to banked water as it moves through the subsurface.

    Another project, led by Berkeley Lab researcher Larry Dale, is developing a model of the energy use and cost of groundwater pumping statewide in order to improve the reliability of California’s electric and water systems, especially in cases of drought and increase in electricity demand. The project has been awarded a $625,000 grant by the California Energy Commission.

    Desalination: Aiming for Pipe Parity

    Reverse osmosis is the state-of-the-art desalination technology and has been around since the 1950s. Unfortunately, there have been few breakthroughs in the field of desalination since then, and it remains prohibitively expensive. “The challenge is to lower the cost of desalination of sea water by a factor of five to achieve ‘pipe parity,’ or cost parity with water from natural sources,” said Kostecki, who is leading the project. “This is a formidable endeavor and it cannot be done with incremental improvements of existing technologies.”

    To reach this goal, Kostecki and other Berkeley Lab researchers are working on several different approaches for more efficient desalination. Some are new twists on existing technologies—such as forward osmosis using heat from geothermal sources, graphene-based membranes, and capacitive deionization—while others are forging entirely new paradigms, such as using the quantum effects in nanoconfined spaces and new nano-engineered materials architectures.

    “The reality is that if one is shooting for a 5X reduction in the cost of desalination of water, then this requires a completely new way of thinking, new science, new technology—this is what we are shooting for,” said Ramamoorthy Ramesh, Associate Lab Director for Energy Technologies.

    Some of these projects are part of the U.S./China Clean Energy Research Center for Water Energy Technologies (CERC-WET), a new $64-million collaboration between China and the United States to tackle water conservation in energy production and use. It is a cross-California collaboration led on the U.S. side by Berkeley Lab researcher Ashok Gadgil and funded primarily by the Department of Energy.

    “Berkeley Lab is ideally suited to take on the water-energy challenge,” said Ramesh. “As a multidisciplinary lab with deep expertise in energy technologies, computational sciences, energy sciences as well as earth and climate sciences, we have the opportunity to develop and integrate fundamental insights through systems-level approaches. Relevant to California, we are focusing on developing scalable water systems that are resilient in an energy-constrained and uncertain water future.”

    See the full article here .

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  • richardmitnick 12:36 pm on May 23, 2016 Permalink | Reply
    Tags: Applied Research & Technology, , ,   

    From SLAC: “Caught on Camera: First Movies of Droplets Getting Blown Up by X-ray Laser” 

    SLAC Lab

    May 23, 2016

    Details Revealed in SLAC Footage Will Give Researchers More Control in X-ray Laser Experiments

    Researchers have made the first microscopic movies of liquids getting vaporized by the world’s brightest X-ray laser at the Department of Energy’s SLAC National Accelerator Laboratory. The new data could lead to better and novel experiments at X-ray lasers, whose extremely bright, fast flashes of light take atomic-level snapshots of some of nature’s speediest processes.

    “Understanding the dynamics of these explosions will allow us to avoid their unwanted effects on samples,” says Claudiu Stan of Stanford PULSE Institute, a joint institute of Stanford University and SLAC. “It could also help us find new ways of using explosions caused by X-rays to trigger changes in samples and study matter under extreme conditions. These studies could help us better understand a wide range of phenomena in X-ray science and other applications.”

    Researchers have recorded the first movies of liquids getting vaporized by SLAC’s Linac Coherent Light Source (LCLS), the world’s brightest X-ray laser. The movies reveal new details that could lead to better and novel experiments at X-ray lasers. (SLAC National Accelerator Laboratory)
    Access mp4 video here .

    Liquids are a common way of bringing samples into the path of the X-ray beam for analysis at SLAC’s Linac Coherent Light Source (LCLS), a DOE Office of Science User Facility, and other X-ray lasers. At full power, ultrabright X-rays can blow up samples within a tiny fraction of a second. Fortunately, in most cases researchers can take the data they need before the damage sets in.

    Access the mp4 video here .

    The new study, published* today in Nature Physics, shows in microscopic detail how the explosive interaction unfolds and provides clues as to how it could affect X-ray laser experiments.

    Stan and his team looked at two ways of injecting liquid into the path of the X-ray laser: as a series of individual drops or as a continuous jet. For each X-ray pulse hitting the liquid, the team took one image, timed from five billionths of a second to one ten-thousandth of a second after the pulse. They strung hundreds of these snapshots together into movies.

    “Thanks to a special imaging system developed for this purpose, we were able to record these movies for the first time,” says co-author Sébastien Boutet from LCLS. “We used an ultrafast optical laser like a strobe light to illuminate the explosion, and made images with a high-resolution microscope that is suitable for use in the vacuum chamber where the X-rays hit the samples.”

    The footage shows how an X-ray pulse rips a drop of liquid apart. This generates a cloud of smaller particles and vapor that expands toward neighboring drops and damages them. These damaged drops then start moving toward the next-nearest drops and merge with them.

    This movie shows how a drop of liquid explodes after being struck by a powerful X-ray pulse from LCLS. The vertical white line at the center shows the position of the X-ray beam. The movie captures the first 9 millionths of a second after the explosion. (SLAC National Accelerator Laboratory)
    Access mp4 video here .

    In the case of jets, the movies show how the X-ray pulse initially punches a hole into the stream of liquid. This gap continues to grow, with the ends of the jet on either side of the gap beginning to form a thin liquid film. The film develops an umbrella-like shape, which eventually folds back and merges with the jet.

    Researchers studied the explosive interaction of X-ray pulses from LCLS with liquid jets, as shown in this movie of the first 9 millionths of a second after the explosion. (SLAC National Accelerator Laboratory)
    Access mp4 video here .

    Based on their data, the researchers were able to develop mathematical models that accurately describe the explosive behavior for a number of factors that researchers vary from one LCLS experiment to another, including pulse energy, drop size and jet diameter.

    They were also able to predict how gap formation in jets could pose a challenge in experiments at the future light sources European XFEL in Germany and LCLS-II, under construction at SLAC. Both are next-generation X-ray lasers that will fire thousands of times faster than current facilities.

    European XFEL Test module
    European XFEL Test module

    SLAC LCLS-II line
    SLAC LCLS-II line

    “The jets in our study took up to several millionths of a second to recover from each explosion, so if X-ray pulses come in faster than that, we may not be able to make use of every single pulse for an experiment,” Stan says. “Fortunately, our data show that we can already tune the most commonly used jets in a way that they recover quickly, and there are ways to make them recover even faster. This will allow us to make use of LCLS-II’s full potential.”

    The movies also show for the first time how an X-ray blast creates shock waves that rapidly travel through the liquid jet. The team is hopeful that these data could benefit novel experiments, in which shock waves from one X-ray pulse trigger changes in a sample that are probed by a subsequent X-ray pulse. This would open up new avenues for studies of changes in matter that occur at time scales shorter than currently accessible.

    Other institutions involved in the study were Max Planck Institute for Medical Research, Germany; Princeton University; and Paul Scherrer Institute, Switzerland. Funding was received from the DOE Office of Science; Max Planck Society; Human Frontiers Science Project; and SLAC’s Laboratory Directed Research & Development program.

    *Science paper:
    Liquid explosions induced by X-ray laser pulses

    See the full article here .

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    SLAC is a multi-program laboratory exploring frontier questions in photon science, astrophysics, particle physics and accelerator research. Located in Menlo Park, California, SLAC is operated by Stanford University for the DOE’s Office of Science.

  • richardmitnick 12:14 pm on May 23, 2016 Permalink | Reply
    Tags: Applied Research & Technology, , , UW Medical Center ready to deploy tiniest pacemaker ever   

    From U Washington: “UW Medical Center ready to deploy tiniest pacemaker ever” 

    U Washington

    University of Washington

    Brian Donohue

    The old and the new: a conventional pacemaker, left, and the Medtronic Micra are displayed by UW Medicine electrophysiologists Jordan Prutkin and Kristen Patton.

    The world’s smallest pacemaker will debut soon at UW Medical Center – one of two Washington state hospitals that will offer the device for the next several months.

    Drs. Jordan Prutkin and Kristen Patton, cardiac electrophysiologists with the UW Medicine Regional Heart Center, received final training this week from representatives of Medtronic, the manufacturer of the device, named Micra.

    About as tall and wide as a AAA battery, the device is threaded up through the femoral vein to the heart, where it is attached to the right ventricle to deliver impuses when a patient’s heartbeat is too slow. The unit’s direct placement takes advantage of another advance: Its battery is inside, so there are no wires connected to a separate power source.

    For decades, pacemakers have comprised a generator, usually implanted under the skin in the patient’s left chest, and leads, which carry impulses from the generator into the heart. The wires are these devices’ main vulnerability, wearing out over time and heightening risk of infections. Removing broken leads years after implant can be problematic because they often have become enmeshed within the tissue of blood vessels.

    “That’s why this miniature technology is so important and transformative – because it really does reduce risks associated with these devices,” Patton said.

    On April 6, the U.S. Food and Drug Administration approved the Micra for patients with slow or irregular heart rhythms. The FDA based its decision on a clinical trial of 719 patients implanted with the device. In the study, 98 percent of patients experienced adequate heart pacing and fewer than 7 percent had complications such as blood clots, heart injury and device dislocation.

    The risk of dislodgement is low, Patton said. “Its tiny hooks deploy straight into the muscle and grab and it is very hard to detach.”

    The Micra will have limited applicability, at least initially, because it paces only one chamber. About 75 percent of conventional pacemakers pace at least two of the heart’s chambers.

    “This is good for people who only need pacing in the ventricle because they have atrial fibrillation in the top chamber, and for people who only need pacing a small percentage of the time,” Prutkin said.

    Illustration of the Micra being deployed into a right ventricle. Medtronic

    Similar to other single-chamber devices on the market, the Micra’s battery is projected to last 10 to 14 years, depending on how much pacing a patient requires.

    At the Micra training, Patton said, she heard something that she hadn’t expected.

    “The two physicians leading the session have a lot of experience with this device, and they said it makes a difference psychologically to patients; it removes the visible bump under the skin of the generator and that persistent reminder that ‘something is wrong with my heart.’

    “We hear from patients all the time, wondering whether they should move less to protect against lead fracture. Patients ask, ‘What if I wear a backpack? Can I still do pushups or play golf?’ This device seems to be a positive step in that way,” Patton said.

    Prutkin sees this device as the beginning of the next generation of pacemakers.

    “Right now this can only go in the ventricle, but in time this will be available for both the atria and ventricles, and multiple devices in one person will be able to talk to one another to regulate a heartbeat. That’s down the road, but that’s where this technology is heading.”

    The device also will be available at Sacred Heart Medical Center in Spokane.

    See the full article here .

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

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