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  • richardmitnick 6:53 am on August 24, 2016 Permalink | Reply
    Tags: , , OpenZika project at World Community Grid,   

    From OpenZika: Meet the Team 

    Rutgers Open Zika
    OpenZika

    OpenZika is a global research collaboration, led by Dr. Carolina Horta at the Universidade Federal de Goiás, Brazil.

    1
    Carolina Horta Andrade

    Professor, Universidade Federal de Goiás

    OpenZika Principal Investigator
    Dr. Carolina Horta is Adjunct Professor at Faculty of Pharmacy of Universidade Federal de Goiás (UFG), Brazil, and head of LabMol – Laboratory for Molecular Modeling and Drug Design. Her lab focuses on Computer-Aided Drug Design approaches for Neglected Tropical Diseases and Cancer, as well as the development of computational tools to predict pharmacokinetics and toxicity properties of chemical compounds. In 2015, she received the “International Rising Talents” award from L’Oréal – UNESCO for her project on Leishmaniasis Drug Discovery and she is affiliated member of the Brazilian Academy of Sciences (ABC).

    2
    Sean Ekins

    CEO, Collaborations Pharmaceuticals, Inc.

    OpenZika Co-Principal Investigator

    Dr. Sean Ekins graduated from the University of Aberdeen; receiving his M.Sc., Ph.D. and D.Sc in Clinical Pharmacology. He is CEO of Collaborations Pharmaceuticals, Inc., CEO and Co-Founder at Phoenix Nest, CSO at the Hereditary Neuropathy Foundation. He is on the Editorial Board of Pharmaceutical Research and has authored or co-authored ~250 peer reviewed scientific papers and book chapters as well as edited/ co-edited four books. He has received numerous SBIR or STTR grants and consults widely with academia and industry. His main interests are to identify compounds for neglected and rare diseases with academic collaborators and to try and work as openly as possible.

    3
    Alexander L. Perryman

    Research Teaching Specialist, Rutgers University

    OpenZika Co-Principal Investigator

    Dr. Alexander Perryman is a senior researcher in the Freundlich lab, with extensive training in developing and applying computational methods in drug discovery and in the biochemical mechanisms of multi-drug-resistance in infectious diseases. He is a member of the Center for Emerging & Re-emerging Pathogens, in the Department of Pharmacology, Physiology, and Neuroscience, at the Rutgers University, New Jersey Medical School. Previously, he was a Research Associate in Prof. Arthur J. Olson’s lab at The Scripps Research Institute (TSRI), where he ran the day-to-day operations of the FightAIDS@Home project (FAAH, the largest computational drug discovery project devoted to HIV/AIDS, which runs on IBM’s World Community Grid). While in the Olson lab, he also designed, led, and ran the largest computational drug discovery project ever performed against malaria, the GO Fight Against Malaria project (GO FAM), also on IBM’s World Community Grid.

    Rodolpho Braga
    4

    Research Associate, Universidade Federal de Goiás

    OpenZika Technical Coordinator

    Dr. Rodolpho Braga joined Prof. Andrade’s laboratory in 2009. In 2015, he received his Ph.D. in Medicinal Chemistry at Universidade Federal de Goiás (UFG) and is currently a Research Associate. He develops chemoinformatics tools to support the computer-assisted drug design targeting Neglected Tropical Diseases (NTDs) and ADME/Tox properties prediction. He also designs novel chemoinformatic algorithms in R and Python. In 2012 and 2014 he was awarded with CINF Scholarship for Scientific Excellence of the American Chemical Society. In 2015, he was Visiting Professor at the University of Torino, Italy.

    Melina Mottin

    Research Associate, Universidade Federal de Goiás

    Dr. Melina Mottin joined Prof. Andrade’s laboratory in 2016 as a Research Associate. She received her Ph.D in 2015 in Physical Chemistry at University of Campinas (UNICAMP). She is an expert in molecular dynamics simulations of biomolecules and molecular docking. The main goal of her research is to find new molecules able to inhibit Zika and other flavivirus proteins and to investigate the interaction between molecules and proteins, through the integration of several computational strategies.

    Roosevelt Alves da Silva

    Professor, Universidade Federal de Goiás

    Dr. Roosevelt Silva is Adjunct Professor at Regional Jataí, Universidade Federal de Goiás (UFG), Brazil, and head of NCBios – Collaborative Center of Biosystems. His lab focuses on Protein Structure Prediction and Computer-Aided Drug Design approaches for Neglected Tropical Diseases. He develops algorithms for Monte Carlo sampling of protein structures and Molecular Docking. In 2014-2015, he was a Postdoctoral fellow at the Yang Zhang Lab, Dep. of Computational Medicine and Bioinformatics, University of Michigan, USA.

    Collaborators

    Wim Degrave

    Senior Researcher, Laboratory for Functional Genomics and Bioinformatics, Oswaldo Cruz Foundation (Fiocruz)

    Dr. Degrave is a researcher at the Oswaldo Cruz Foundation, in Rio de Janeiro, Brazil. His laboratory is dedicated to the functional study of genomes of microorganisms important in human health, comparative genomics using bioinformatics tools and wet lab research dedicated to the design and evaluation of new drugs, mostly in the field of neglected diseases, study of environmental bacteria, and biotechnology. Dr. Degrave led the Genome Comparison project and is currently co-running the Uncovering Genome Mysteries project on World Community Grid.

    Ana Carolina Ramos Guimarães

    Researcher, Oswaldo Cruz Foundation (Fiocruz)

    Dr. Ramos is a Researcher in Computational and Systems Biology at Fiocruz. She holds a BSc degree (2003) in Biology from the State University of Rio de Janeiro (Brazil). She received her Master’s degree (2006) and PhD (2010) on Cellular and Molecular Biology at the Oswaldo Cruz Institute (Oswaldo Cruz Foundation – Brazil) where she focused on bioinformatics and computational biology. Since 2013, she has been a researcher at Oswaldo Cruz Foundation working on the identification of molecular targets for drug development against parasitic organisms.

    João Herminio

    Researcher, Oswaldo Cruz Foundation (Fiocruz), Ceará Division

    Dr. Herminio is a public health researcher with a degree in Biological Sciences, master’s degree in biophysics and a PhD in cellular and molecular biology. His area of study is focused on computational simulations of biological systems, particularly protein-protein interactions. His research fields are molecular dynamics of proteins and drugs, prediction of protein structures, molecular docking and computational prediction of free energy. His current interest is the development and application of drug design using “de novo” methods and virtual screening.

    Lucio Freitas-Junior

    Independent Researcher

    Dr. Lucio Freitas-Junior has been working in the field of tropical diseases for the past 15 years. From 2005 to 2012 Dr. Freitas-Junior was the director of the Center for Neglected Diseases Drug Discovery (CND3) at Institut Pasteur Korea, where his group worked on assay development, high throughput screening and lead optimization for Leishmaniasis, Chagas disease, Malaria, Dengue and Chikungunya. Since 2013 Dr. Freitas-Junior is back at his home country, Brazil, where he continues to work on translational research and drug discovery for neglected diseases, including recently the development of a zika drug screening assay.

    Jair L. Siqueira-Neto

    Assistant Professor, University of California at San Diego

    Dr. Jair Siqueira-Neto is Director of the Screening Center at University of California at San Diego (UCSD) and Assistant Professor at the Skaggs School of Pharmacy and Pharmaceutical Sciences – UCSD. He has experience in drug discovery and development for tropical neglected disease, having worked at the Institut Pasteur Korea and at the University of California San Francisco (UCSF) prior to becoming faculty at UCSD. He was a pioneer in the development of the first phenotypic screening for Leishmania sp. and Trypanosoma cruzi. His research is focused on the development and implementation of high-throughput and high-content screening assays to identify active compounds against infectious agents. He is also interested in studying parasite-host interaction to understand the basics of disease and new targets for chemotherapy. His goal in this project will be to test the candidate compounds generated by this consortium for anti-viral activity.

    Joel S. Freundlich

    Associate Professor, Rutgers University

    Medicinal Chemistry Consultant

    Dr. Joel Freundlich is an Associate Professor of Pharmacology, Physiology & Neuroscience and of Medicine at Rutgers University–New Jersey Medical School. Prior to his return to academic research in 2006, he spent eight years in the pharmaceutical industry as a medicinal chemist. His undergraduate and master’s degree training were in chemical engineering at Cornell University as a McMullen Dean’s Scholar. He received his doctorate in organic chemistry from the Massachusetts Institute of Technology under the tutelage of 2005 Nobel Prize in Chemistry awardee Richard Schrock.

    IBM World Community Grid Team

    Viktors Berstis, Technical Coordinator of OpenZika & Scientist

    Juan Hindo, Project Manager

    Erika Tuttle, Program Coordinator

    Al Seippel, Developer

    Jonathan Armstrong, Developer

    Keith Uplinger, Lead Developer

    Kevin Reed, Senior Developer

    Sophia Tu, Program Manager

    Caitlin Larkin, Communications

    See the full article here .

    YOU CAN HELP FIND A CURE FOR THE ZIKA VIRUS.

    There is a new project at World Community Grid [WCG] called OpenZika.
    Zika
    Zika depiction. Image copyright John Liebler, http://www.ArtoftheCell.com
    Rutgers Open Zika

    WCG runs on your home computer or tablet on software from Berkeley Open Infrastructure for Network Computing [BOINC]. Many other scientific projects run on BOINC software.Visit WCG or BOINC, download and install the software, then at WCG attach to the OpenZika project. You will be joining tens of thousands of other “crunchers” processing computational data and saving the scientists literally thousands of hours of work at no real cost to you.

    This project is directed by Dr. Alexander Perryman a senior researcher in the Freundlich lab, with extensive training in developing and applying computational methods in drug discovery and in the biochemical mechanisms of multi-drug-resistance in infectious diseases. He is a member of the Center for Emerging & Re-emerging Pathogens, in the Department of Pharmacology, Physiology, and Neuroscience, at the Rutgers University, New Jersey Medical School. Previously, he was a Research Associate in Prof. Arthur J. Olson’s lab at The Scripps Research Institute (TSRI), where he ran the day-to-day operations of the FightAIDS@Home project, the largest computational drug discovery project devoted to HIV/AIDS, which also runs on WCG. While in the Olson lab, he also designed, led, and ran the largest computational drug discovery project ever performed against malaria, the GO Fight Against Malaria project, also on WCG.

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  • richardmitnick 12:01 pm on August 18, 2016 Permalink | Reply
    Tags: , , OpenZika project at World Community Grid, ,   

    From Rockefeller: “Zika infection may affect adult brain cells, suggesting risk may not be limited to pregnant women” 

    Rockefeller U bloc

    Rockefeller University

    August 18, 2016
    No clear writer credit

    1
    Zika in the adult brain: Illumination of the fluorescent biomarker in green revealed that Zika can infect the adult mouse brain in a region full of neural progenitor cells, which play an important role in learning and memory.

    Concerns over the Zika virus have focused on pregnant women due to mounting evidence that it causes brain abnormalities in developing fetuses. However, new research in mice from scientists at The Rockefeller University and La Jolla Institute for Allergy and Immunology suggests that certain adult brain cells may be vulnerable to infection as well. Among these are populations of cells that serve to replace lost or damaged neurons throughout adulthood, and are also thought to be critical to learning and memory.

    “This is the first study looking at the effect of Zika infection on the adult brain,” says Joseph Gleeson, adjunct professor at Rockefeller, head of the Laboratory of Pediatric Brain Disease, and Howard Hughes Medical Institute investigator. “Based on our findings, getting infected with Zika as an adult may not be as innocuous as people think.”

    Although more research is needed to determine if this damage has long-term biological implications or the potential to affect behavior, the findings suggest the possibility that the Zika virus, which has become widespread in Central and South America over the past eight months, may be more harmful than previously believed. The new findings were published in Cell Stem Cell on August 18.

    “Zika can clearly enter the brain of adults and can wreak havoc,” says Sujan Shresta, a professor at the La Jolla Institute of Allergy and Immunology. “But it’s a complex disease—it’s catastrophic for early brain development, yet the majority of adults who are infected with Zika rarely show detectable symptoms. Its effect on the adult brain may be more subtle, and now we know what to look for.”

    Neuronal progenitors

    Early in gestation, before our brains have developed into a complex organ with specialized zones, they are comprised entirely of neural progenitor cells. With the capability to replenish the brain’s neurons throughout its lifetime, these are the stem cells of the brain. In healthy individuals, neural progenitor cells eventually become fully formed neurons, and it is thought that at some point along this progression they become resistant to Zika, explaining why adults appear less susceptible to the disease.

    But current evidence suggests that Zika targets neural progenitor cells, leading to loss of these cells and to reduced brain volume. This closely mirrors what is seen in microcephaly, a developmental condition linked to Zika infection in developing fetuses that results in a smaller-than-normal head and a wide variety of developmental disabilities.

    The mature brain retains niches of these neural progenitor cells that appear to be especially impacted by Zika. These niches—in mice they exist primarily in two regions, the subventricular zone of the anterior forebrain and the subgranular zone of the hippocampus—are vital for learning and memory.

    Gleeson and his colleagues suspected that if Zika can infect fetal neural progenitor cells, it wouldn’t be a far stretch for them to also be able to infect these cells in adults. In a mouse model engineered by Shresta and her team to mimic Zika infection in humans, fluorescent biomarkers illuminated to reveal that adult neural progenitor cells could indeed be hijacked by the virus.

    “Our results are pretty dramatic—in the parts of the brain that lit up, it was like a Christmas tree,” says Gleeson. “It was very clear that the virus wasn’t affecting the whole brain evenly, like people are seeing in the fetus. In the adult, it’s only these two populations that are very specific to the stem cells that are affected by virus. These cells are special, and somehow very susceptible to the infection.”

    Beyond fetal brain infection

    The researchers found that infection correlated with evidence of cell death and reduced generation of new neurons in these regions. Integration of new neurons into learning and memory circuits is crucial for neuroplasticity, which allows the brain to change over time. Deficits in this process are associated with cognitive decline and neuropathological conditions, such as depression and Alzheimer’s disease.

    Gleeson and colleagues recognize that healthy humans may be able to mount an effective immune response and prevent the virus from attacking. However, they suggest that some people, such as those with weakened immune systems, may be vulnerable to the virus in a way that has not yet been recognized.

    “In more subtle cases, the virus could theoretically impact long-term memory or risk of depression,” says Gleeson, “but tools do not exist to test the long-term effects of Zika on adult stem cell populations.”

    In addition to microcephaly, Zika has been linked to Guillain-Barré syndrome, a rare condition in which the immune system attacks parts of the nervous system, leading to muscle weakness or even paralysis. “The connection has been hard to trace since Guillain-Barré usually develops after the infection has cleared,” says Shresta. “We propose that infection of adult neural progenitor cells could be the mechanism behind this.”

    There are still many unanswered questions, including exactly how translatable findings in this mouse model are to humans. Gleeson’s findings in particular raise questions such as: Does the damage inflicted on progenitor cells by the virus have lasting biological consequences, and can this in turn affect learning and memory? Or, do these cells have the capability to recover? Nonetheless, these findings raise the possibility that Zika is not simply a transient infection in adult humans, and that exposure in the adult brain could have long-term effects.

    “The virus seems to be traveling quite a bit as people move around the world,” says Gleeson. “Given this study, I think the public health enterprise should consider monitoring for Zika infections in all groups, not just pregnant women.”

    Joseph Gleeson also holds appointments at the University of California San Diego School of Medicine and Rady Children’s Hospital-San Diego. This research was supported by NIH grants R01NS041537, R01NS048453, R01NS052455, P01HD070494, and P30NS047101; the Simons Foundation Autism Research Initiative (SFARI); the Howard Hughes Medical Institute; California Institute of Regenerative Medicine (to J.G. Gleeson); NIH grant R01 AI116813 (to S. Shresta); and a Druckenmiller Fellowship from New York Stem Cell Foundation (to H. Li).

    See the full article here .

    YOU CAN HELP FIND A CURE FOR THE ZIKA VIRUS.

    There is a new project at World Community Grid [WCG] called OpenZika.
    Zika
    Zika depiction. Image copyright John Liebler, http://www.ArtoftheCell.com
    Rutgers Open Zika

    WCG runs on your home computer or tablet on software from Berkeley Open Infrastructure for Network Computing [BOINC]. Many other scientific projects run on BOINC software.Visit WCG or BOINC, download and install the software, then at WCG attach to the OpenZika project. You will be joining tens of thousands of other “crunchers” processing computational data and saving the scientists literally thousands of hours of work at no real cost to you.

    This project is directed by Dr. Alexander Perryman a senior researcher in the Freundlich lab, with extensive training in developing and applying computational methods in drug discovery and in the biochemical mechanisms of multi-drug-resistance in infectious diseases. He is a member of the Center for Emerging & Re-emerging Pathogens, in the Department of Pharmacology, Physiology, and Neuroscience, at the Rutgers University, New Jersey Medical School. Previously, he was a Research Associate in Prof. Arthur J. Olson’s lab at The Scripps Research Institute (TSRI), where he ran the day-to-day operations of the FightAIDS@Home project, the largest computational drug discovery project devoted to HIV/AIDS, which also runs on WCG. While in the Olson lab, he also designed, led, and ran the largest computational drug discovery project ever performed against malaria, the GO Fight Against Malaria project, also on WCG.

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    Rockefeller U Campus

    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 9:19 am on August 12, 2016 Permalink | Reply
    Tags: , , , OpenZika project at World Community Grid,   

    From Hopkins: “Four Johns Hopkins research teams win funding to combat Zika virus” 

    Johns Hopkins
    Johns Hopkins University

    8.10.16

    Four teams of researchers from Johns Hopkins University—including three from the Johns Hopkins Bloomberg School of Public Health and another pursuing an idea that originated at a recent Zika hackathon at JHU—will be awarded grants from U.S. Agency for International Development’s Combating Zika and Future Threats Grand Challenge, the agency announced today.

    In what the agency is calling “potentially game-changing solutions to mitigate the spread and impact of the Zika virus,” 21 grants totaling $15 million will be awarded for groundbreaking ideas from around the world to both address the current Zika outbreak and improve the ability to prevent, detect, and respond to future infectious disease outbreaks. In just nine weeks, USAID received nearly 900 submissions from across the globe in response to the Challenge, which will invest up to $30 million.

    A complete list of grant recipients can be found on the USAID website. No other institution received more than two awards from USAID.

    The research of Conor McMeniman, an assistant professor at the Johns Hopkins Malaria Research Institute at the Bloomberg School, will focus on what parts of human scent are attractive to Aedes aegypti, the mosquito that carries the Zika virus, as well as other viruses including dengue, chikungunya, and yellow fever. The goal is to mimic the scent of humans to develop a powerful lure that can be used as bait in mosquito traps in an effort to prevent mosquitoes from spreading diseases.

    “Body odor and breath are made up of about 300 different chemicals, and we want to understand what part of the chemistry of human scent is most attractive to the mosquitoes that carry Zika,” McMeniman says. “The goal is to develop a custom fragrance to bait mosquito traps and improve our ability to fight mosquito-borne illnesses.”

    To accomplish this, McMeniman and his team will use two-photon microscopy to see which of the chemicals of human scent activate the olfactory centers of the mosquito brain. Using mosquitoes that have been genetically engineered to have olfactory centers light up when they are activated, the researchers will literally look inside the brains of these tiny insects to understand how to create the best chemical lure.

    McMeniman says better understanding how the mosquito nervous system detects humans will provide new avenues to control diseases spread by Aedes aegypti and other species, including the mosquitoes that carry malaria, which kills more than 500,000 people worldwide each year, mostly in young children in sub-Saharan Africa.

    The current outbreak of Zika—a virus recently linked to brain-related birth defects in babies born to pregnant mothers who contract it—is most prevalent in Brazil, Colombia, Puerto Rico, and other parts of the Americas. More than 1,800 cases of Zika have been reported in the U.S., though most of those were contracted by people who had traveled outside the U.S. Recently, however, Zika-carrying mosquitoes were found in a small section of Miami, Florida, and health officials say nearly two dozen cases have now been reported in people who were infected domestically.

    Current Zika control strategies are mainly based on the use of insecticides and personal mosquito repellents. But a continuous emergence of mosquito resistance to insecticides and the lack of drugs and vaccines for Zika and other mosquito-transmitted pathogens render the development of novel, cost-effective mosquito control strategies urgent, says George Dimopoulos, a professor at the Malaria Institute.

    Dimopoulos’ team has identified a new bacterium, Chromobacterium Csp_P, which can kill larvae and adults of various species of mosquito that transmit malaria, dengue, Zika, yellow fever, and West Nile virus. The bacterium also blocks the pathogens inside the mosquitoes, preventing infectious transmission in the mosquito gut.

    “This can be a highly potent weapon against current and future mosquito-borne diseases,” Dimopoulos says.

    His team aims to develop Chromobacterium Csp_P into a cost-effective, environmentally-friendly, and logistically simple mosquito control biopesticide. Chromobacteria are abundant soil bacteria and have already been developed for agricultural pest control by live spraying on fields, but not for mosquito control. The end users of Chromobacterium Csp_P –based products could range from mosquito control organizations to individual households.

    The third award will go to the Bloomberg School’s Center for Communication Programs, or CCP. Researchers there note that changing household and community behaviors around the proper and consistent cleaning of standing water will be key to stopping Zika in its tracks. Mosquitoes breed in standing water.

    Susan Krenn, executive director of CCP, says that rapid change of habits, attitudes, and behaviors is a challenging but critical component of disease containment. CCP will work with consulting firm Catalyst Behavioral Sciences to develop the Rapid SBCC Habit Optimization Tool, or R-SHOT, which will combine local data with evidence-based behavior change and habit formation principles to determine the best way to help people in communities impacted by Zika control the mosquito problem themselves.

    “As we saw during the Ebola crisis, changes in habits and behavior can have substantial impact on the spread of disease,” Krenn says. “To be successful, behavior change strategies for Zika will need to be tailored to local contexts and leverage existing behaviors and habits.”

    The final funded project, known as VectorWEB, would improve upon the existing approach to mosquito population surveillance. Currently, ovitraps—designed to kill adult breeding mosquitos—are placed in the field, then later collected, and the number of mosquitoes in each trap is counted manually in a lab.

    A team led by Soumyadipta Acharya, an assistant professor in JHU’s Department of Biomedical Engineering, has proposed a modified trap that would have the ability to provide real-time data to health administrators, community health workers, and others. That data could then be used for outbreak modeling, targeted resource allocation and redirection, and community-driven public health interventions.

    The VectorWEB project is the result of a collaboration between the Center for Bioengineering Innovation and Design, a center within the Department of Biomedical Engineering shared by the Whiting School of Engineering and the School of Medicine, and Jhpiego, a university-affiliated global health nonprofit.

    Several VectorWEB teammates have been working on the project since a spring hackathon sponsored by CBID and Jhpiego to meet the daunting public health challenges presented by the Zika outbreak. The hackathon drew more than 60 participants for a weekend of problem-solving and development of innovative, creative, low-cost design solutions.

    See the full article here .

    YOU CAN HELP FIND A CURE FOR THE ZIKA VIRUS.

    There is a new project at World Community Grid [WCG] called OpenZika.
    Zika
    Zika depiction. Image copyright John Liebler, http://www.ArtoftheCell.com
    Rutgers Open Zika

    WCG runs on your home computer or tablet on software from Berkeley Open Infrastructure for Network Computing [BOINC]. Many other scientific projects run on BOINC software.Visit WCG or BOINC, download and install the software, then at WCG attach to the OpenZika project. You will be joining tens of thousands of other “crunchers” processing computational data and saving the scientists literally thousands of hours of work at no real cost to you.

    This project is directed by Dr. Alexander Perryman a senior researcher in the Freundlich lab, with extensive training in developing and applying computational methods in drug discovery and in the biochemical mechanisms of multi-drug-resistance in infectious diseases. He is a member of the Center for Emerging & Re-emerging Pathogens, in the Department of Pharmacology, Physiology, and Neuroscience, at the Rutgers University, New Jersey Medical School. Previously, he was a Research Associate in Prof. Arthur J. Olson’s lab at The Scripps Research Institute (TSRI), where he ran the day-to-day operations of the FightAIDS@Home project, the largest computational drug discovery project devoted to HIV/AIDS, which also runs on WCG. While in the Olson lab, he also designed, led, and ran the largest computational drug discovery project ever performed against malaria, the GO Fight Against Malaria project, also on WCG.

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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 11:40 am on August 2, 2016 Permalink | Reply
    Tags: , , , , OpenZika project at World Community Grid,   

    From Chicago Tribune via ANL: “This giant X-ray machine helped decode one of the Zika virus’ secrets “ 

    Argonne Lab

    News from Argonne National Laboratory

    1

    Chicago Tribune

    8.2.16
    Ally Marotti

    2
    Other viruses in the same family as Zika, such as dengue, West Nile and yellow fever, also produce the NS1 protein. (Argonne National Laboratory)

    A group of Midwest researchers is one step closer to a Zika vaccine, and they used a giant X-ray machine at the Chicago area’s Argonne National Lab to get there.

    University of Michigan and Purdue University researchers used equipment at Lemont-based Argonne to map the molecular structure of a protein the Zika virus produces.

    That knowledge can lead to more accurate diagnoses of Zika and possibly a vaccine or antiviral drugs, said Janet Smith, professor of biological chemistry in the Life Sciences Institute at Michigan.

    “We don’t have good diagnostic tools to know if a person has been infected with Zika,” said Smith, who led the study. “There are a bunch of antibody tests out there to see if you’ve been exposed to Zika — the problem is they’re not specific enough.”

    Of course no vaccine will come in time for the Olympics, which start next week, Smith said, but these findings are important in the fight against the disease.

    Zika is a growing concern in the U.S., as cases are increasingly reported in countries outside of the tropics. The virus is known to cause devastating birth defects, and the World Health Organization declared an international health emergency over its spread.

    Nearly 1,500 cases have been reported in the U.S., according to the Centers for Disease Control and Prevention, but all were acquired while traveling. However, experts say that will change by the end of the year.

    Although a study out of Yale University found it’s highly unlikely those traveling to Rio de Janeiro for the Olympics will contract the disease, fear has amplified as the games approach.

    The protein Smith and her team looked at is called NS1. Other viruses in the same family as Zika, such as dengue, West Nile and yellow fever, also produce the protein. When a person gets infected, the virus induces their body to make the protein.

    “It helps the virus to make more copies of itself, infect (the body’s) cells and hide from the immune system in ways that are really not very well understood at all,” Smith said.

    Since Zika is a problem in places where dengue fever is prevalent, inaccurate diagnoses sometimes prevent people from knowing which disease they were exposed to. These new findings will hopefully change that, Smith said.

    The researchers used Argonne’s Advanced Photon Source to conduct the study. The facility is used to conduct X-ray research, and is so large that its diameter measures just a little less than the height of the Willis Tower, said Stephen Streiffer, director of the facility.

    “APS is used to produce hard X-rays — the same type you’d get in the dentist’s office,” Streiffer said. “The difference is that the APS produces X-rays which are about a billion times more intense.”

    Smith and her team made a stable NS1 protein from Zika and put it into a crystal, which scatters the X-ray beam. Smith’s team uses a detector to measure the scattering, and can then figure out the structure of the molecule inside.

    The researchers had already been studying structures of the proteins from West Nile and dengue, so that sped up the process, Smith said. Richard Kuhn, professor and head of Purdue’s Department of Biological Sciences, co-authored the study, which was published Monday in the journal Nature Structural & Molecular Biology.

    The protein they looked at was from the first strain of Zika identified in Uganda in 1947, Smith said. Knowing its structure can help scientists understand how the virus has mutated since it spread to Brazil.

    “Has it gotten worse when it evolved on its way to Brazil, or has it been this bad all along?” Smith said. “Viruses are amazing at sneaking around mutating … It’s like cancer. They produce fast and make a bunch of mistakes, but just one needs to take off.

    See the full article here .

    YOU CAN HELP FIND A CURE FOR THE ZIKA VIRUS.

    There is a new project at World Community Grid [WCG] called OpenZika.
    Zika
    Image of the Zika virus, Image copyright John Liebler, http://www.ArtoftheCell.com
    Rutgers Open Zika

    WCG runs on your home computer or tablet on software from Berkeley Open Infrastructure for Network Computing [BOINC]. Many other scientific projects run on BOINC software.Visit WCG or BOINC, download and install the software, then at WCG attach to the OpenZika project. You will be joining tens of thousands of other “crunchers” processing computational data and saving the scientists literally thousands of hours of work at no real cost to you.

    This project is directed by Dr. Alexander Perryman a senior researcher in the Freundlich lab, with extensive training in developing and applying computational methods in drug discovery and in the biochemical mechanisms of multi-drug-resistance in infectious diseases. He is a member of the Center for Emerging & Re-emerging Pathogens, in the Department of Pharmacology, Physiology, and Neuroscience, at the Rutgers University, New Jersey Medical School. Previously, he was a Research Associate in Prof. Arthur J. Olson’s lab at The Scripps Research Institute (TSRI), where he ran the day-to-day operations of the FightAIDS@Home project, the largest computational drug discovery project devoted to HIV/AIDS, which also runs on WCG. While in the Olson lab, he also designed, led, and ran the largest computational drug discovery project ever performed against malaria, the GO Fight Against Malaria project, also on WCG.

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    Argonne National Laboratory seeks solutions to pressing national problems in science and technology. The nation’s first national laboratory, Argonne conducts leading-edge basic and applied scientific research in virtually every scientific discipline. Argonne researchers work closely with researchers from hundreds of companies, universities, and federal, state and municipal agencies to help them solve their specific problems, advance America’s scientific leadership and prepare the nation for a better future. With employees from more than 60 nations, Argonne is managed by UChicago Argonne, LLC for the U.S. Department of Energy’s Office of Science. For more visit http://www.anl.gov.

    The Advanced Photon Source at Argonne National Laboratory is one of five national synchrotron radiation light sources supported by the U.S. Department of Energy’s Office of Science to carry out applied and basic research to understand, predict, and ultimately control matter and energy at the electronic, atomic, and molecular levels, provide the foundations for new energy technologies, and support DOE missions in energy, environment, and national security. To learn more about the Office of Science X-ray user facilities, visit http://science.energy.gov/user-facilities/basic-energy-sciences/.

    Argonne is managed by UChicago Argonne, LLC for the U.S. Department of Energy’s Office of Science

    Argonne Lab Campus

     
  • richardmitnick 6:41 am on July 31, 2016 Permalink | Reply
    Tags: , , , OpenZika project at World Community Grid,   

    From NYT: “Zika Cases in Puerto Rico Are Skyrocketing” 

    New York Times

    The New York Times

    JULY 30, 2016
    DONALD G. McNEIL Jr.
    Omaya Sosa Pascual contributed reporting.

    1
    Since Danelle, 36, was infected with the Zika virus in late April, danger signs have appeared in her fetus. At 23 weeks, she grappled with the decision of whether to abort. Credit Ángel Franco/The New York Times

    The Zika epidemic that has spread from Brazil to the rest of Latin America is now raging in Puerto Rico — and the island’s response is in chaos.

    The war against the Aedes aegypti mosquito carrying the virus is sputtering out in failure. Infections are skyrocketing: Many residents fail to protect themselves against bites because they believe the threat is exaggerated.

    Federal and local health officials are feuding, and the governor’s special adviser on Zika has quit in disgust.

    There are only about 5,500 confirmed infections on the island, including of 672 pregnant women. But experts at the Centers for Disease Control and Prevention say they believe that is a radical undercount.

    Just four cases of infection were confirmed last week in Florida. But in Puerto Rico, officials believe thousands of residents — including up to 50 pregnant women — are infected each day.

    2
    The sonogram of a patient of Dr. Alberto De la Vega whose fetus shows clumps of dead cells. “Her fetus does not have microcephaly now,” he said, “but this is what leads to it.” Credit Ángel Franco/The New York Times

    Most never get tested. Tests on donated blood, the most reliable barometer of the epidemic’s spread, show that almost 2 percent of the donors were infected in the last 10 days.

    “That’s a stunning number and reflects an explosion of cases,” Dr. Thomas R. Frieden, the director of the C.D.C., said in an interview.

    The proportion of pregnant women testing positive for the virus has risen sevenfold since January, the agency said on Friday. Officials warned that hundreds of infants could be born with microcephaly in the coming year.

    But a wave of microcephaly like Brazil’s may yet be averted for two reasons. The pregnancy rate is falling so precipitously that this year, for the first time in history, Puerto Rico will have fewer births than deaths.

    Obstetricians, too, are quietly urging their infected pregnant patients to have regular ultrasounds and to consider abortion if brain damage turns up.

    And damage is turning up.

    In an office at the University of Puerto Rico Hospital, the gentle curves of the graph on Dr. Alberto De la Vega’s computer screen trace a horror story. They are the head circumferences of dozens of fetuses whose mothers have been infected with the Zika virus for at least a month — and almost 75 percent are below the mean; normally, only half should be.

    Only one was clearly microcephalic, with the extreme shrinkage and brain damage that is the worst consequence of the infection, and that curve abruptly ends: The mother chose abortion.

    “What worries me is not 100 kids with microcephaly,” said Dr. De la Vega, chief of ultrasound diagnosis at the university. “What worries me is a lot of kids affected in some way we cannot determine yet.”

    “We may be facing a generation with learning and behavioral disabilities,” he said.

    On the scan of a patient who had fled his office fighting back tears, he pointed out three large white spots — clumps of dead cells.

    “Her fetus does not have microcephaly now,” he said, “but this is what leads to it.”

    A ‘Very Dire’ Situation

    Cases of Zika infection are expected to keep rising through October, and by year’s end, a quarter of the island’s population of 3.5 million will have been exposed, a “very dire” situation, said Dr. Lyle R. Petersen, the C.D.C.’s chief of vector-borne diseases and director of its fight against Zika.

    In a normal year, that would mean about 8,000 infected pregnancies, but the birthrate is dropping rapidly, said Jose A. Lopez, the health department’s demographer. In past years, births normally outnumbered deaths by about 400 per month, but since January, that ratio has reversed itself, and there have been, on average, 135 more deaths than births.

    The drop is partly a result of rising divorce rates and couples emigrating as the economy deteriorates, but also of “mothers delaying giving birth because of the campaign against Zika,” Mr. Lopez said.

    3
    Standing water in a cemetery in Puerto Rico. Removing such water from cemeteries was part of the government’s plan, but rains in many areas have hampered efforts. Credit Ángel Franco/The New York Times

    Federal health officials have accused Congress of stoking the epidemic here by failing to appropriate $1.9 billion requested by the administration to fight the Zika virus. But the story on the ground is far more complex.

    In February, the governor’s office and the health department announced ambitious battle plans. Millions of old tires where mosquitoes breed would be collected. Cemeteries would be drained of standing water.

    Septic tanks and water meters would get screens, as would all schools attended by girls old enough to get pregnant. Teams would visit pregnant women’s houses to spray larvicide and screen windows.

    Some of that was done, sometimes effectively. Humacao, a town on the southeast coast with pharmaceutical and electric plants that provide a steady tax base, moved faster than most municipalities, said José L. Báez, its chief of emergency management.

    Workers collected 200,000 tires, packing them into two abandoned factories. At the local historic cemetery, teams filled empty urns with sand. Spray trucks worked steadily.

    But it was never enough. Discarded tires kept popping up on roadsides. Mosquitoes bred in garbage cans. Teams could not legally enter abandoned properties or even fill depressions in privately owned graves. The town’s permethrin insecticides turned out to be ineffective, and daily rains washed away previous efforts.

    4
    Old tires, picked up from tire shops, were stored in an abandoned factory in San Juan, P.R. In February, the governor’s office and the health department announced plans to collect old tires to aid mosquito control. Credit Ángel Franco/The New York Times

    No cutting-edge plans like releasing genetically modified mosquitoes are ready for deployment yet. The C.D.C. lab here has developed a bucket trap that drastically cuts mosquito populations, but millions of them would be needed to cover the island.

    So, as a last resort, the C.D.C. on July 6 endorsed aerial spraying to eliminate mosquitoes with an insecticide called naled.

    It was a gamble. Naled failed to stop a 1987 dengue outbreak here “and there is no guarantee it will work this time,” Dr. Petersen said. “But it’s the only thing that will alter the course of this epidemic.”

    Modern spray nozzles and GPS-guided planes were more accurate, he argued, and superfine mists with small amounts of naled would drift into houses where mosquitoes hid in closets. Counties in Florida and Louisiana had recently knocked down populations of the yellow-fever mosquito by up to 99 percent with naled, he and others noted.

    But naled is toxic to bees, birds and fish. The insecticide is not used in flea collars because it might be picked up by children stroking pets. It is banned in the European Union.

    Skepticism All Around

    Puerto Rico rebelled. Protest marches drew hundreds wearing gas masks and carrying bee puppets. Top radio personalities, already angry over Congress imposing a control board to run the territory’s finances, accused federal officials of “colonialism” and reminded listeners that the military tested Agent Orange on Puerto Rico’s jungles before deploying it in Vietnam.

    Medical groups joined the opposition, including the largest, the Puerto Rican College of Physicians and Surgeons. Dr. Iván González Cancel, a surgeon famous for performing the island’s first heart transplant, denounced the plan, saying: “I don’t believe in conspiracy theories, but I think this is an experiment with the C.D.C. using Puerto Rico as a laboratory.”

    On July 21, a local TV station revealed that the C.D.C. had quietly imported naled. The next day, Gov. Alejandro García Padilla accused the agency of “blackmail” and emphatically killed the idea. The agency apologized, saying it was only trying to be prepared. But it was too late.

    That same week, Dr. Johnny Rullán, a former health secretary advising Governor Padilla on the epidemic, gave up his post, saying the whole atmosphere had become too vicious. Since January, he had held town meetings explaining the mosquito control plans to skeptical audiences. “I felt like a scratched record saying the same things over and over,” he said. When he endorsed aerial spraying, he was falsely accused of plotting to make millions by basing planes at a remote airport he was accused of owning. (It is owned by someone with a similar name.)

    He ultimately decided the spraying would be a public relations disaster. “Any microcephaly cases that occur now will be blamed on the spray, not the virus,” he said.

    He resigned and left for a vacation in Spain. “In October,” he said, “I’ll write something saying, ‘I told you.’ ”

    Skepticism of the danger remains high. Local papers still refer to the “theory” that the Zika virus causes microcephaly, although the World Health Organization considers it a fact.

    Seventy-two apparently healthy babies have been born to infected mothers while only one stillborn fetus has shown evidence of microcephaly, so no disturbing pictures of tiny-headed babies, like those in Brazil, have appeared. Although officials have explained that most of the 72 mothers were infected late in pregnancy, the sense that the danger is remote persists.

    Alba Sanchez, 25, and nearing the end of her fourth pregnancy, attended a hospital Zika-prevention workshop wearing the skimpiest of maternity dresses. Asked if she used repellent, she wrinkled her nose.

    “Never!” she said loudly. “It’s stinky. And I don’t know anyone who’s had Zika.”

    Asked how she protected herself, she mimed slaps to her bare arms and legs. “I smack every one I see.”

    Her husband, Jandy Vasquez, 22, a mountainous man towering over her, rolled his eyes and smiled ruefully. “I’d spray a whole can on her every day,” he said. “But she does what she wants.”

    Indeed, the fight against birth defects is taking place largely in face-to-face meetings between doctors and patients like Ms. Sanchez.

    Agonizing Decisions

    Many obstetricians said they were urging women to put off pregnancy. And through the CDC Foundation, pharmaceutical companies like Bayer, Allergan and Merck have donated or discounted more than 100,000 sets of IUD’s, implants, vaginal rings and other contraceptives.

    “I tell my patients: ‘If you can avoid pregnancy for one year, please do,’ ” said Dr. Carmen D. Zorrilla, founder of the University of Puerto Rico’s Maternal-Infant Studies Center, the territory’s leading maternal H.I.V. unit, which now holds workshops in Zika-related care.

    The doctors also remind patients whose fetuses show signs of brain damage that abortion is available in major hospitals and, for the uninsured, through Profamilias, a reproductive-rights group.

    Some religious women will say, “‘But this is God’s gift,’ ” Dr. Zorrilla said. “But at the same time, they’re afraid to have a baby they know will need assistance 24/7 for life.”

    How many women are terminating pregnancies is unknown. Although the health department tabulates legal abortions, current figures are unavailable, a department spokeswoman said.

    “Anecdotally, they’re on the increase,” Dr. Rullán said. “One doctor told me he did 15 in a period where he normally would have done one or two.”

    Making that choice is excruciating. Danelle, a patient of Dr. De la Vega’s who agreed to be interviewed on the condition that only her middle name be used, wept as she described her predicament.

    Her fetus is 23 weeks along. On sonograms, Danelle, 36, can see a face, even hair: To her, the outlines resemble a small, sleeping child, nestled against the placenta as if it were a pillow.

    Danger signs have appeared since Danelle was infected with the virus in late April. The fetus’s growth abruptly slowed and is now well below normal. An enlarged brain artery indicates that too little nutrition is crossing the placenta.

    Because she herself is a doctor, Danelle knows what that means: Severe mental deficits are possible. Her husband, a train dispatcher who held her hand as she spoke, “is the more positive one of us — and he’s also in denial,” she said.

    “But I’m the G.I. one,” she added, using a local term for hewing strictly to the book.

    She was having ultrasounds every 14 days and must decide very soon whether to abort.

    “The window is closing,” she said, wiping her eyes. “I don’t sleep at night. I don’t want to do this, but I don’t want her to come into this world and then suffer.

    “And when I’m not here, who’s going to take care of her?”

    See the full article here .

    YOU CAN HELP FIND A CURE FOR THE ZIKA VIRUS.

    There is a new project at World Community Grid [WCG] called OpenZika.
    Zika
    Image of the Zika virus, Image copyright John Liebler, www.ArtoftheCell.com

    Rutgers Open Zika

    WCG runs on your home computer or tablet on software from Berkeley Open Infrastructure for Network Computing [BOINC]. Many other scientific projects run on BOINC software.Visit WCG or BOINC, download and install the software, then at WCG attach to the OpenZika project. You will be joining tens of thousands of other “crunchers” processing computational data and saving the scientists literally thousands of hours of work at no real cost to you.

    This project is directed by Dr. Alexander Perryman a senior researcher in the Freundlich lab, with extensive training in developing and applying computational methods in drug discovery and in the biochemical mechanisms of multi-drug-resistance in infectious diseases. He is a member of the Center for Emerging & Re-emerging Pathogens, in the Department of Pharmacology, Physiology, and Neuroscience, at the Rutgers University, New Jersey Medical School. Previously, he was a Research Associate in Prof. Arthur J. Olson’s lab at The Scripps Research Institute (TSRI), where he ran the day-to-day operations of the FightAIDS@Home project, the largest computational drug discovery project devoted to HIV/AIDS, which also runs on WCG. While in the Olson lab, he also designed, led, and ran the largest computational drug discovery project ever performed against malaria, the GO Fight Against Malaria project, also on WCG.

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  • richardmitnick 7:05 am on July 29, 2016 Permalink | Reply
    Tags: , , , OpenZika project at World Community Grid,   

    From Chicago Tribune via ANL: “This giant X-ray machine helped decode one of the Zika virus’ secrets” 

    ANL APS
    News from Argonne National Laboratory
    Advanced Photon Source at ANL

    1

    http://www.chicagotribune.com

    7.26.16
    Ally Marotti

    A group of Midwest researchers is one step closer to a Zika vaccine, and they used a giant X-ray machine at the Chicago area’s Argonne National Lab to get there.

    University of Michigan and Purdue University researchers used equipment at Lemont-based Argonne to map the molecular structure of a protein the Zika virus produces.

    That knowledge can lead to more accurate diagnoses of Zika and possibly a vaccine or antiviral drugs, said Janet Smith, professor of biological chemistry in the Life Sciences Institute at Michigan.

    “We don’t have good diagnostic tools to know if a person has been infected with Zika,” said Smith, who led the study. “There are a bunch of antibody tests out there to see if you’ve been exposed to Zika — the problem is they’re not specific enough.”

    Of course no vaccine will come in time for the Olympics, which start next week, Smith said, but these findings are important in the fight against the disease.

    Zika is a growing concern in the U.S., as cases are increasingly reported in countries outside of the tropics. The virus is known to cause devastating birth defects, and the World Health Organization declared an international health emergency over its spread.

    Nearly 1,500 cases have been reported in the U.S., according to the Centers for Disease Control and Prevention, but all were acquired while traveling. However, experts say that will change by the end of the year.

    Although a study out of Yale University found it’s highly unlikely those traveling to Rio de Janeiro for the Olympics will contract the disease, fear has amplified as the games approach.

    The protein Smith and her team looked at is called NS1. Other viruses in the same family as Zika, such as dengue, West Nile and yellow fever, also produce the protein. When a person gets infected, the virus induces their body to make the protein.

    “It helps the virus to make more copies of itself, infect (the body’s) cells and hide from the immune system in ways that are really not very well understood at all,” Smith said.

    Since Zika is a problem in places where dengue fever is prevalent, inaccurate diagnoses sometimes prevent people from knowing which disease they were exposed to. These new findings will hopefully change that, Smith said.

    The researchers used Argonne’s Advanced Photon Source to conduct the study. The facility is used to conduct X-ray research, and is so large that its diameter measures just a little less than the height of the Willis Tower, said Stephen Streiffer, director of the facility.

    “APS is used to produce hard X-rays — the same type you’d get in the dentist’s office,” Streiffer said. “The difference is that the APS produces X-rays which are about a billion times more intense.”

    Smith and her team made a stable NS1 protein from Zika and put it into a crystal, which scatters the X-ray beam. Smith’s team uses a detector to measure the scattering, and can then figure out the structure of the molecule inside.

    The researchers had already been studying structures of the proteins from West Nile and dengue, so that sped up the process, Smith said. Richard Kuhn, professor and head of Purdue’s Department of Biological Sciences, co-authored the study, which was published Monday in the journal “Nature Structural & Molecular Biology.”

    The protein they looked at was from the first strain of Zika identified in Uganda in 1947, Smith said. Knowing its structure can help scientists understand how the virus has mutated since it spread to Brazil.

    “Has it gotten worse when it evolved on its way to Brazil, or has it been this bad all along?” Smith said. “Viruses are amazing at sneaking around mutating … It’s like cancer. They produce fast and make a bunch of mistakes, but just one needs to take off.”

    See the full article here .

    YOU CAN HELP FIND A CURE FOR THE ZIKA VIRUS.

    There is a new project at World Community Grid [WCG] called OpenZika.
    Zika
    Image of the Zika virus

    Rutgers Open Zika

    WCG runs on your home computer or tablet on software from Berkeley Open Infrastructure for Network Computing [BOINC]. Many other scientific projects run on BOINC software.Visit WCG or BOINC, download and install the software, then at WCG attach to the OpenZika project. You will be joining tens of thousands of other “crunchers” processing computational data and saving the scientists literally thousands of hours of work at no real cost to you.

    This project is directed by Dr. Alexander Perryman a senior researcher in the Freundlich lab, with extensive training in developing and applying computational methods in drug discovery and in the biochemical mechanisms of multi-drug-resistance in infectious diseases. He is a member of the Center for Emerging & Re-emerging Pathogens, in the Department of Pharmacology, Physiology, and Neuroscience, at the Rutgers University, New Jersey Medical School. Previously, he was a Research Associate in Prof. Arthur J. Olson’s lab at The Scripps Research Institute (TSRI), where he ran the day-to-day operations of the FightAIDS@Home project, the largest computational drug discovery project devoted to HIV/AIDS, which also runs on WCG. While in the Olson lab, he also designed, led, and ran the largest computational drug discovery project ever performed against malaria, the GO Fight Against Malaria project, also on WCG.

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    Argonne National Laboratory seeks solutions to pressing national problems in science and technology. The nation’s first national laboratory, Argonne conducts leading-edge basic and applied scientific research in virtually every scientific discipline. Argonne researchers work closely with researchers from hundreds of companies, universities, and federal, state and municipal agencies to help them solve their specific problems, advance America’s scientific leadership and prepare the nation for a better future. With employees from more than 60 nations, Argonne is managed by UChicago Argonne, LLC for the U.S. Department of Energy’s Office of Science. For more visit http://www.anl.gov.

    The Advanced Photon Source at Argonne National Laboratory is one of five national synchrotron radiation light sources supported by the U.S. Department of Energy’s Office of Science to carry out applied and basic research to understand, predict, and ultimately control matter and energy at the electronic, atomic, and molecular levels, provide the foundations for new energy technologies, and support DOE missions in energy, environment, and national security. To learn more about the Office of Science X-ray user facilities, visit http://science.energy.gov/user-facilities/basic-energy-sciences/.

    Argonne is managed by UChicago Argonne, LLC for the U.S. Department of Energy’s Office of Science

    Argonne Lab Campus

     
  • richardmitnick 5:08 pm on July 25, 2016 Permalink | Reply
    Tags: , , OpenZika project at World Community Grid,   

    From Nature: “Brazil asks whether Zika acts alone to cause birth defects” 

    Nature Mag
    Nature

    25 July 2016
    Declan Butler

    1
    A health worker sprays insecticide to combat the mosquito that spreads Zika virus, in Paraíba state, Brazil.

    Researchers at Brazil’s ministry of health have launched a study to explore why the country has a peculiar distribution of Zika-linked microcephaly cases — babies born with abnormally small heads.

    Zika virus has spread throughout Brazil, but extremely high rates of microcephaly have been reported only in the country’s northeast. Although evidence suggests that Zika can cause microcephaly, the clustering pattern hints that other environmental, socio-economic or biological factors could be at play.

    “We suspect that something more than Zika virus is causing the high intensity and severity of cases,” says Fatima Marinho, director of information and health analysis at the ministry. If that turns out to be true, it could change researchers’ assessment of the risk that Zika poses to pregnant women and their children.

    The idea has long been on Brazilian researchers’ radar. “This is being discussed in almost every scientific meeting,” says Lavinia Schüler-Faccini, a researcher at the Federal University of Rio Grande do Sul. But the new inquiry marks the first time that scientists at the health ministry have taken up the hypothesis.

    The ministry has asked Oliver Brady, an epidemiologist at the London School of Hygiene & Tropical Medicine, and Simon Hay, director of geospatial science at the Institute for Health Metrics and Evaluation in Seattle, Washington, to assist the collaboration, along with researchers in Brazil. “The aim is to understand why we are only observing elevated rates in the northeast,” says Brady, who flew into Brasília this month to begin work.

    “I think they may be on to something,” says Linda Birnbaum, director of the US National Institute of Environmental Health Sciences (NIEHS). Zika was discovered in 1947 and hadn’t been implicated in birth defects until now; and current strains of the virus don’t show any significant mutations that might have increased its virulence. “So why now?” she asks.

    Surprising clusters

    The northeast was where the first reported surge in microcephaly cases in Brazil began a year ago. Health officials had expected that they would later see the same high rates in other parts of the country. “We were expecting an explosion of birth defects,” says Marinho.

    But as of 20 July, almost 90% of the 1,709 confirmed cases of congenital microcephaly or birth defects of the central nervous system that have been reported in Brazil since last November are in a relatively small area: in the coastal hinterland of the northeastern tip. The affected area is about the size of the United Kingdom, whereas Brazil is almost as large as the United States.

    What’s particularly surprising, says Marinho, is that just three cases have been confirmed in Brazil’s second-most populous state, Minas Gerais, which borders the most-affected part of the northeast region. Poor data on the scale and timing of Zika outbreaks across Brazil make it difficult to tell whether large increases in microcephaly elsewhere may simply have been delayed — but ministry scientists now think that the northeast represents a marked outlier, she says.

    Other factors at play?

    There are many hypotheses about what might be going on. Marinho says that her team’s data, submitted for publication, hint that socio-economic factors might be involved. The majority of women who have had babies with microcephaly have, for example, been young, single, black, poor and tend to live in small cities or on the outskirts of big ones, she says.

    Another idea is that co-infections of Zika and other viruses, such as dengue and chikungunya, might be interacting to cause the high intensity of birth defects in the area.

    A third possibility was put forward in a paper published last month [1], in which researchers from Brazilian labs noted a correlation between low vaccination rates for yellow fever and the microcephaly clusters. Because yellow fever and Zika are in the same virus family — they are both flaviviruses — the scientists speculated that the vaccine might provide some protection against Zika. “It is a plausible hypothesis,” says Duane Gubler, who studies mosquito-borne diseases at Duke–NUS Medical School in Singapore. Marinho, however, is sceptical — arguing that there are many areas with low yellow fever vaccination rates that haven’t had many confirmed microcephaly cases.

    The Brazilian doctor who was the first to report a firm link between Zika and microcephaly — Adriana Melo at IPESQ, a research institute in Campina Grande — is also among those who have suggested that other factors could be involved. In a preprint posted on the bioRxiv server on 15 July [2], Melo and her colleagues at the Federal University of Rio de Janeiro reported that they had found bovine viral diarrhoea virus (BVDV) proteins in the brains of three fetuses with microcephaly from Paraíba state. The brains tested positive for Zika RNA, but the researchers found no Zika proteins.

    BVDV causes serious birth defects in cattle but is not known to infect people. Melo’s team suggest that Zika infection might reduce physiological barriers, making it easier for BVDV to cause infections. But they haven’t ruled out the possibility, raised by other researchers, that their findings might be due to contamination (BVDV is a common contaminant of fetal bovine serum and other bovine-derived lab reagents).

    Patchy data

    The Brazilian health ministry’s study will test for BVDV among other hypotheses, says Brady. Researchers will re-analyse raw data on microcephaly cases, and will model connections with possible co-factors such as socio-economic status, water contamination, and mosquito-borne diseases. Most of this information will come from health ministry databases, but the team will also study experimental data, such as how people’s immune response may change after past infection with other viruses such as dengue.

    But researchers say that the information they have may not be enough to pin down whether factors in addition to Zika are involved. Much of the microcephaly raw data comes from routine hospital reports, which are often incomplete. And lab tests to confirm Zika infection are rarely carried out.

    Ultimately, researchers and public-health officials might have to wait for higher-quality data from research programmes such as the Zika in Infants and Pregnancy Study, which launched last month in Puerto Rico and aims to monitor as many as 10,000 pregnant women. The US National Institutes of Health (including Birnbaum’s NIEHS) and the Oswaldo Cruz Foundation in Brazil are doing the work, which will also include testing whether nutritional, socio-economic and environmental factors have a role. The study will expand to Brazil, Colombia and other Zika-affected areas.

    Until more is known about Zika and the causes of increased microcephaly rates in Brazil’s northeast, public-health actions and advice must err on the side of precaution, says Ian Lipkin, a virologist and outbreak specialist at Columbia University in New York.

    Nature doi:10.1038/nature.2016.20309

    References:
    1. De Goes Cavalcanti, L. P. et al. J. Infect. Dev. Countries 10, 563–566 (2016).

    2. Nogueira, F. C. S., Velasquez, E., Melo, A. S. O. & Domont, G. B. Preprint at bioRxiv
    http://dx.doi.org/10.1101/062596 (2016)

    See the full article here .

    YOU CAN HELP FIND A CURE FOR THE ZIKA VIRUS.

    There is a new project at World Community Grid [WCG] called OpenZika.
    Zika
    Image of the Zika virus

    Rutgers Open Zika

    WCG runs on your home computer or tablet on software from Berkeley Open Infrastructure for Network Computing [BOINC]. Many other scientific projects run on BOINC software.Visit WCG or BOINC, download and install the software, then at WCG attach to the OpenZika project. You will be joining tens of thousands of other “crunchers” processing computational data and saving the scientists literally thousands of hours of work at no real cost to you.

    This project is directed by Dr. Alexander Perryman a senior researcher in the Freundlich lab, with extensive training in developing and applying computational methods in drug discovery and in the biochemical mechanisms of multi-drug-resistance in infectious diseases. He is a member of the Center for Emerging & Re-emerging Pathogens, in the Department of Pharmacology, Physiology, and Neuroscience, at the Rutgers University, New Jersey Medical School. Previously, he was a Research Associate in Prof. Arthur J. Olson’s lab at The Scripps Research Institute (TSRI), where he ran the day-to-day operations of the FightAIDS@Home project, the largest computational drug discovery project devoted to HIV/AIDS, which also runs on WCG. While in the Olson lab, he also designed, led, and ran the largest computational drug discovery project ever performed against malaria, the GO Fight Against Malaria project, also on WCG.

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  • richardmitnick 4:30 pm on July 18, 2016 Permalink | Reply
    Tags: , , OpenZika project at World Community Grid,   

    From NYT: “New Utah Zika Case Baffles Health Officials” 

    New York Times

    The New York Times

    JULY 18, 2016
    SABRINA TAVERNISE

    1
    The mosquito that typically transmits Zika — the Aedes aegypti — does not usually range into northern Utah, but maps of the mosquito’s range can be unreliable and experts say it is theoretically possible that it has made it there. Credit Felipe Dana/Associated Press

    The Zika virus continues to surprise. On Monday, the Utah Department of Health reported that a new case had been diagnosed that did not appear to have been contracted through the two known sources of transmission: a mosquito bite or sexual contact.

    The patient, who has since fully recovered, was a “family contact” who helped care for an older man who had become infected with the virus after traveling abroad.

    The Zika virus is spread mostly by mosquitoes and has caused more than 1,500 cases of birth defects in newborns in Latin America, where it has spread rapidly, and even in the United States, mostly in pregnant women who traveled to countries where it is circulating. In the United States and its territories, there are several hundred pregnant women that have been infected with the Zika virus, with the largest concentration in Puerto Rico.

    The new case is something of a medical mystery: Zika is known to be transmitted by the Aedes aegypti mosquito and through sex, but neither seemed to be a plausible explanation for what happened in Utah.

    “We have found no evidence that mosquitoes here in Utah are transmitting the Zika virus,” said Dr. Angela Dunn, deputy state epidemiologist at the Utah Department of Health.

    Dr. Erin Staples of the Centers for Disease Control and Prevention, which has a team on the ground in Utah, said the case was “unique. We’re learning something new about Zika every day.”

    The elderly man died in Salt Lake County in the northern part of the state in June. The man had Zika and his symptoms included a rash and fever, but he also had other ailments and it was unclear whether the virus contributed to his death.

    Local health workers had been trapping mosquitoes since last year, including most recently around the house of the man who died, but had found no Aedes aegypti. Joseph Conlon, technical adviser to the American Mosquito Control Association, said neither Aedes aegypti, nor a cousin — Aedes albopictus — are found in Salt Lake County.

    If it was not by a mosquito, how else might it have been transmitted?

    “This raises some interesting questions,” said Dr. William Schaffner, an infectious disease specialist in Tennessee. “Was there a needle stick or injury? Or if not, possible contact with other bodily fluid like urine or saliva?”

    Zika has surprised scientists with its ability to be transmitted by sex — both from men to women, and, in a recent discovery in New York City, from women to men. But it is not known to be transmitted in any other way — without the help of a mosquito — so the Utah case is remarkable.

    The mosquito that transmits Zika — the Aedes aegypti — does not typically range into northern Utah, but maps of the mosquito’s range are unreliable and experts say it is theoretically possible that the bug exists there.

    The Centers for Disease Control and Prevention said it has a team on the ground in Utah. Those experts will help determine whether the virus was transmitted by mosquito.

    See the full article here .

    YOU CAN HELP FIND A CURE FOR THE ZIKA VIRUS.

    There is a new project at World Community Grid [WCG] called OpenZika.
    Zika
    Image of the Zika virus

    Rutgers Open Zika

    WCG runs on your home computer or tablet on software from Berkeley Open Infrastructure for Network Computing [BOINC]. Many other scientific projects run on BOINC software.Visit WCG or BOINC, download and install the software, then at WCG attach to the OpenZika project. You will be joining tens of thousands of other “crunchers” processing computational data and saving the scientists literally thousands of hours of work at no real cost to you.

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  • richardmitnick 3:41 pm on June 26, 2016 Permalink | Reply
    Tags: , OpenZika project at World Community Grid, ,   

    From SA: “List of Possible Zika Birth Defects Grows Longer” 

    Scientific American

    Scientific American

    June 24, 2016
    Dina Fine Maron

    The full scope of Zika-related birth defects may extend far beyond abnormally small heads and brain damage. Research to be presented next week at a teratology conference in San Antonio, Texas, suggests that serious joint problems, seizures, vision impairment, trouble feeding and persistent crying can be added to the list of risks from Zika exposure in the womb.

    The new findings confirm doctors’ concerns that even when Zika-exposed babies are born without microcephaly and appear largely normal at birth they can go on to have health issues including seizures and developmental delays that only become apparent in the weeks and months after birth. The new work also reinforces recent findings that suggest the type of outcomes the babies experience also varies by what trimester their mothers were in when they were exposed to Zika—with few cases of microcephaly when mothers were exposed during the third trimester.

    The research underscores the steep learning curve that scientists and officials face with this virus, which is transmitted through mosquito bites and sexual contact. Earlier studies chronicling apparent Zika-related damage had also hinted that doctors had much to learn about viral-driven birth defects. In March researchers published findings in the New England Journal of Medicine suggesting that 29 percent of pregnant women who tested positive for Zika had fetuses with abnormalities already apparent via ultrasound. The finding was particularly alarming because doctors knew many more central nervous system issues would likely only be recognizable months or even years after the child’s birth.

    Today it remains unclear exactly how many babies born to women infected with Zika during pregnancy will develop birth defects. But the new findings from Brazil do give a better sense of the breadth of obstacles Zika-affected families may face within the first year of their newborns’ lives.

    Brazilian researchers followed 83 infants born since August 2015 to mothers believed to have been infected with Zika. The study included families from eight states, mostly in Brazil’s northeast, where birth defects have soared. Because solid testing for Zika was not yet in place last fall, however, only 10 of the 83 mothers were confirmed as Zika-exposed through laboratory testing—a major caveat that applies to most current Zika-outcome studies. That reality leaves open the possibility that the birth defects could be due to other environmental or genetic factors. Still, about 70 percent of the mothers in this study remember experiencing a rash—a known Zika symptom—during their pregnancies, and the researchers eliminated other leading causes of the birth defects including certain toxic exposures and viral infections from cytomegalovirus.

    The Brazilian team found that about 10 percent of the 83 babies had knee or elbow joint limitations so severe that the infants cannot fully extend their arms or legs. Another 43 percent of the babies had less-pronounced joint problems that impeded finger or toe motion, or the babies had other limb abnormalities like clubfeet. And half of the babies had seizures and abnormal eye exams.

    This study reflects the situation of a relatively small study group—and only included babies with abnormalities. But it does provide some insights, including that birth defects may vary depending on what trimester the mother became infected with the virus. “These findings are in line with our findings about babies exposed to Zika in utero,” says Karin Nielsen-Saines, a pediatric infectious diseases specialist and senior author of the March NEJM research. Still, she cautioned that because this new study only includes babies with abnormalities it does not give a good snapshot of how common birth defects might really be among the Zika-exposed. “You might be missing children who are normal so you may skew your data toward abnormalities,” she says.

    Zika has ushered in a number of unwelcome surprises. It is the first insect-borne disease with a proven link to serious birth defects (vision problems have been linked to West Nile Virus but not yet causally verified). Yet infection with several other viruses during pregnancy—in particular toxoplasmosis, rubella or cytomegalovirus—can also lead to microcephaly, vision problems or hearing loss that may not be immediately apparent at birth, so viral-driven birth defects are not unprecedented. CVM and toxoplasmosis can also, rarely, lead to joint issues, says Dee Quinn, director of the Arizona branch of the nonprofit MotherToBaby and a senior genetic counselor on staff at the Colleges of Medicine and Pharmacy at the University of Arizona.

    The new Brazil findings on Zika also echo certain patterns related to those other viral infections. Notably, mothers infected with Zika late in their pregnancies tended to have babies with relatively less-serious side effects: The children more often had developmental delays including trouble sitting up, as well as seizures instead of microcephaly and significant brain calcifications, says Lavinia Schuler-Faccini, the president of the Brazilian Society of Medical Genetics and the scientist presenting the findings next week. Still, that does not mean fetuses exposed during the third trimester are better off. Nielsen-Saines says that in her published work and in ongoing analysis she is seeing that such late exposure is more likely to lead to stillbirths.

    Pinning down more concrete answers about how common birth defects may be among pregnant women remains an arduous task, and scientists still do not know if other factors including genetics, exposure to other viruses or how women contracted the virus—via sex or mosquito bite—may play a role. Further complicating efforts to get a handle on the issue: according to the World Health Organization, more pregnant women infected with Zika are now aborting their fetuses.

    See the full article here .

    YOU CAN HELP FIND A CURE FOR THE ZIKA VIRUS.

    There is a new project at World Community Grid [WCG] called OpenZika.
    Zika
    Image of the Zika virus

    Rutgers Open Zika

    WCG runs on your home computer or tablet on software from Berkeley Open Infrastructure for Network Computing [BOINC]. Many other scientific projects run on BOINC software.Visit WCG or BOINC, download and install the software, then at WCG attach to the OpenZika project. You will be joining tens of thousands of other “crunchers” processing computational data and saving the scientists literally thousands of hours of work at no real cost to you.

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    BOINCLarge
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    Please help promote STEM in your local schools.

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    Scientific American, the oldest continuously published magazine in the U.S., has been bringing its readers unique insights about developments in science and technology for more than 160 years.

     
  • richardmitnick 8:22 am on June 24, 2016 Permalink | Reply
    Tags: , , OpenZika project at World Community Grid,   

    From AAAS: “Zika infection may be worse in people already exposed to a common virus” 

    AAAS

    AAAS

    Jun. 23, 2016
    Gretchen Vogel

    1
    Larvae of the Aedes aegypti mosquito. Adults of the species can spread both dengue and Zika viruses. Conrad Guatemala/Flickr

    A previous encounter with a disease that is rampant across Latin America could leave people more vulnerable to the Zika virus. Antibodies to dengue virus, a relative of Zika, can interfere with the immune system’s response to Zika and boost the virus’s ability to replicate, according to work in two independent labs. That may help explain why the complications of Zika virus infections have been more severe in South and Central America than in previous epidemics elsewhere.

    In some regions of Brazil, as many as 90% of people carry antibodies to dengue. Dengue viruses—there are four types—have an unusual relationship with the immune system. Antibodies that develop after an infection with one type don’t protect against infection with another type. Instead, the antibodies can actually help the second virus invade certain immune-system cells, where the virus readily replicates, making the infection worse. The phenomenon is called antibody-dependent enhancement (ADE), and it helps explain why more severe cases of dengue—including a very dangerous condition called dengue hemorrhagic fever—tend to happen when a patient catches a second type of dengue.

    Scientists have wondered whether Zika virus, which is close enough to dengue to cloud the results of diagnostic tests that look for antibodies, might also be close enough to cause ADE. That could help explain why Zika, which has long been thought to cause only mild disease, has suddenly been blamed for causing much more severe symptoms in Brazil and elsewhere, including birth defects in babies infected in the womb and a temporary paralysis called Guillain-Barré syndrome.

    The first support for that theory came from a paper posted on the preprint server bioRxiv in April. Sharon Isern and Scott Michael of Florida Gulf Coast University in Fort Myers and their colleagues reported that both lab-grown antibodies to dengue and blood serum from dengue patients (which contains antibodies) dramatically boosted the replication of Zika virus in cells in the lab.

    Today, in a paper published online in Nature Immunology, an independent group at Imperial College London reports similar results, showing that a number of different antibodies to dengue virus react to Zika, but not strongly enough to neutralize the virus. Instead, when blood plasma from patients who had recovered from dengue was added to cell cultures infected with Zika, it increased the amount of virus in the cultures by as much as 100-fold.

    The data are persuasive, says Ernesto Marques, a public health expert at the University of Pittsburgh in Pennsylvania. But clinical and epidemiology studies need to confirm that the effect plays a role in patients. There are cases of congenital Zika syndrome in babies and mothers that do not have antidengue antibodies, he notes, so although antidengue antibodies may increase the risk of a mother passing the virus to her fetus, the antibodies are not essential to cause birth defects. Studies that look for antibodies to dengue in Zika patients are complicated by the similarity of the viruses, notes Gavin Screaton, an immunologist at Imperial College London and an author on the Nature Immunology paper. “We desperately need” blood tests that can easily distinguish whether a patient has antibodies to dengue, Zika, or both, he says.

    Even if the findings are confirmed, there’s not much people who were previously infected with dengue can do to protect themselves except reduce the risk of mosquito bites, for instance by using repellent. But such precautions are already recommended for everyone in Zika-affected countries.

    See the full article here .

    YOU CAN HELP FIND A CURE FOR THE ZIKA VIRUS.

    There is a new project at World Community Grid [WCG] called OpenZika.
    Zika
    Image of the Zika virus

    Rutgers Open Zika

    WCG runs on your home computer or tablet on software from Berkeley Open Infrastructure for Network Computing [BOINC]. Many other scientific projects run on BOINC software.Visit WCG or BOINC, download and install the software, then at WCG attach to the OpenZika project. You will be joining tens of thousands of other “crunchers” processing computational data and saving the scientists literally thousands of hours of work at no real cost to you.

    WCGLarge
    WCG Logo New

    BOINCLarge
    BOINC WallPaper

    The American Association for the Advancement of Science is an international non-profit organization dedicated to advancing science for the benefit of all people.

    Please help promote STEM in your local schools.
    STEM Icon
    Stem Education Coalition

     
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