Tagged: OpenZika project at World Community Grid Toggle Comment Threads | Keyboard Shortcuts

  • richardmitnick 1:48 pm on April 10, 2017 Permalink | Reply
    Tags: , , OpenZika project at World Community Grid,   

    From OpenZika at WCG: “OpenZika Researchers Continue Calculations and Prepare for Next Stage” 

    New WCG Logo

    WCGLarge

    World Community Grid (WCG)

    By: The OpenZika research team
    21 Mar 2017

    Summary
    The OpenZika researchers are continuing to screen millions of chemical compounds as they look for potential treatments for the Zika virus. In this update, they report on the status of their calculations and their continuing work to spread the word about the project.

    Zika depiction. Image copyright John Liebler, www.ArtoftheCell.com

    Project Background

    While the Zika virus may not be getting the continuous press coverage that it received in 2015 and 2016, it is still a threat to the health of people across the globe. New infections continue to be reported in both South America and North America, and medical workers are just beginning to assess the effects of the virus on young children whose mothers were infected while pregnant.

    The search for effective treatments is crucial to stemming the tide of the virus. In addition to the OpenZika project, several other labs are doing cell-based screens with drugs already approved by the US Food and Drug Administration (FDA) agency, but few to none of the “hit” compounds that have been identified thus far are both potent enough against Zika virus and also safe for pregnant women.

    Also, there are a number of efforts underway to develop a vaccine against the Zika virus. However, vaccines do not help people who already have the infection. It will be several years before they are proven effective and safe, and before enough doses can be mass produced and distributed. And even after approved vaccines are available and distributed to the public, not all people will be vaccinated. Consequently, in the meantime and in the future, cures for Zika infections are needed.

    ZIKV NS3 helicase bound to RNA with the predicted binding modes of five approved drugs (from our second set of candidates) selected by virtual screening. These candidates are shown as surfaces with different shades of green. The identification of these candidates and the video were made by Dr. Alexander L. Perryman [see below].

    We began the analysis phase of the project by focusing on the results against the apo NS3 helicase crystal structure (apo means that the protein was not bound to anything else, such as a cofactor, inhibitor, or nucleic acid) to select our first set of candidates, which are currently being assayed by our collaborator at University of California San Diego, Dr. Jair L. Siqueira-Neto, using cell-based assays. The NS3 helicase is a component of the Zika virus that is required for it to replicate itself.

    In the second set of screening results that we recently examined, we used the new crystal structure of NS3 helicase bound to RNA as the target (see the images / animation above). Similar to the first set of candidates, we docked approximately 7,600 compounds in a composite library composed of the US Food and Drug Administration-approved drugs, the drugs approved in the European Union, and the US National Institutes of Health clinical collection library against the new RNA-bound structure of the helicase. Below are the results of this second screening:

    232 compounds passed the larger collection of different energetic and interaction-based docking filters, and their predicted binding modes were inspected and measured in detail.
    Of the compounds that were inspected in detail, 19 unique compounds passed this visual inspection stage of their docked modes.
    From the compounds that passed the visual inspection, 9 passed subsequent medicinal chemistry-based inspection and will be ordered soon.

    Status of the calculations

    In total, we have submitted 2.56 billion docking jobs, which involved the virtual screening of 6 million compounds versus 427 different target sites. We have already received approximately 1.9 billion of these results on our server. (There is some lag time between when the calculations are performed on your volunteered machines and when we get the results, since all of the results per “package” of approximately 10,000 different docking jobs need to be returned to World Community Grid, re-organized, and then compressed before sending them to our server.)

    Except for a few stragglers, we have received all of the results for our experiments that involve docking 6 million compounds versus the proteins NS1, NS3 helicase (both the RNA binding site and the ATP site), and NS5 (both the RNA polymerase and the methyltransferase domains). We are currently receiving the results from our most recent experiments against the NS2B / NS3 protease.

    A new stage of the project

    We just finished preparing and testing the docking input files that will be used for the second stage of this project. Instead of docking 6 million compounds, we will soon be able to start screening 30.2 million compounds against these targets. This new, massive library was originally obtained in a different type of format from the ZINC15 server. It represents almost all of “commercially available chemical space” (that is, almost all of the “small molecule” drug-like and hit-like compounds that can be purchased from reputable chemical vendors).

    The ZINC15 server provided these files as “multi-molecule mol2” files (that is, many different compounds were contained in each “mol2” formatted file). These files had to be re-formatted (we used the Raccoon program from Dr. Stefano Forli, who is part of the FightAIDS@Home team) by splitting them into individual mol2 files (1 compound per file) and then converting them into the “pdbqt” docking input format.

    We then ran a quick quality control test to make sure that the software used for the project, called AutoDock Vina, could properly use each pdbqt file as an input. Many compounds had to be rejected, because they had types of atoms that cause Vina to crash (such as silicon or boron), and we obviously don’t want to waste the computer time that you donate by submitting calculations that will crash.

    By splitting, reformatting, and testing hundreds of thousands of compounds per day, day after day, after approximately six months this massive new library of compounds is ready to be used in our OpenZika calculations. Without the tremendous resources that World Community Grid volunteers provide for this project, we would not even dream of trying to dock over 30 million compounds against many different targets from the Zika virus. Thank you all very much!!!

    For more information about these experiments, please visit our website.

    Our PLoS Neglected Tropical Diseases paper, OpenZika: An IBM World Community Grid Project to Accelerate Zika Virus Drug Discovery, was published on October 20, and it has already been viewed over 4,000 times. Anyone can access and read this paper for free. Another research paper Illustrating and homology modeling the proteins of the Zika virus has been accepted by F1000Research and viewed > 3800 times.

    A group from Brazil, coordinated by Prof. Glaucius Oliva, has contacted us because of our PLoS Neglected Tropical Diseases paper to discuss a new collaboration to test the selected candidate compounds directly on enzymatic assays with the NS5 protein of Zika virus. They have solved two high-resolution crystal structures of ZIKV NS5, which have been recently released on the PDB (Protein Data Bank) (PDB ID: 5TIT and 5U04).

    Our paper entitled “Molecular Dynamics simulations of Zika Virus NS3 helicase: Insights into RNA binding site activity” was just accepted for publication in a special issue on Flaviviruses for the journal Biochemical and Biophysical Research Communications. This study of the NS3 helicase system helped us learn more about this promising target for blocking Zika replication. The results will help guide how we analyze the virtual screens that we already performed against NS3 helicase, and the molecular dynamics simulations generated new conformations of this protein that we will use as input targets in new virtual screens that we perform as part of OpenZika.

    Additional News

    We have applied and been accepted to present OpenZika: Opening the Discovery of New Antiviral candidates against Zika Virus and Insights into Dynamic behavior of NS3 Helicase to the 46th World Chemistry Congress. The conference will be held in Sao Paulo, Brazil, on July 7-14.

    Dr. Sean Ekins has hired a postdoc and a master level scientist who will get involved with the OpenZika project. We have also started to collate literature inhibitors from Zika papers.

    Also, Drs. Sean Ekins and Carolina Andrade have offered to buy some of the candidate compounds that we identified in the virtual screens from OpenZika, so that they can be assayed in the next round of tests.


    Dr. Alex Perryman models an OpenZika shirt. Profits from the sale of OpenZika merchandise go to purchasing compounds for lab testing. (Photo by Keith Bratcher, courtesy of Rutgers University)

    Alexander L. Perryman, Ph.D., is a senior researcher (Research Teaching Specialist III) in the lab, with extensive training in 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 & Neuroscience. Alex started performing research in Professor Cleo Samudzi’s X-ray crystallography lab as a freshman in the undergraduate Biochemistry program at the University of Missouri-Columbia (“Mizzou” or MU). He then became a Beckman Scholar in Professor Thomas P. Quinn’s protein structure & radiopharmaceuticals lab at MU. He received his Ph.D. in Biomedical Sciences from the University of California, San Diego (UCSD) School of Medicine (Pharmacology Department) as a Howards Hughes Medical Institute fellow in H.H.M.I. Principal Investigator J. Andrew McCammon’s lab. As a graduate student, Alex used Molecular Dynamics simulations to (a) predict a mechanism of multi-drug-resistance for “super bug” mutants of HIV protease, (b) to predict the existence of allosteric binding sites on the surface of HIV protease and then (c) to test the utility of exploiting that allosteric relationship. These predictions are now supported by an ever-growing body of experimental evidence. He also helped create the “Relaxed Complex Scheme,” which was one of the first methods to incorporate the flexibility of the target protein into docking studies of potential drug-like compounds. He conducted post-doctoral research at the California Institute of Technology (“Caltech”) as an Amgen fellow in the Division of Biology. He then became 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 runs on IBM’s World Community Grid). He also designed, led, and ran the day-to-day operations for the largest computational drug discovery project ever performed against malaria, the GO Fight Against Malaria project, also on IBM’s World Community Grid. GO FAM involved screening 5.6 million compounds against 22 different classes of drug targets (including targets from Mycobacterium tuberculosis, as well). GO Fight Against Malaria was the first academic project to ever perform over 1 billion different docking jobs. His experience is highlighted by over 24 publications and one US patent.

    In the Freundlich lab, Alex has broadened his experience by becoming an expert at developing and applying machine learning models and other ligand-based techniques to advance Mtb research, as well as projects against the ESKAPE pathogens. He has also created several machine learning models to help address key shortcomings in chemical tool discovery and drug development (such as metabolic stability, cytotoxicity, and solubility). For a change, Dr. Perryman has also been getting his hands wet–purifying proteins and performing enzyme inhibition assays, to help test his new computational predictions against Mtb targets.

    See the full article here.

    Ways to access the blog:
    https://sciencesprings.wordpress.com
    http://facebook.com/sciencesprings

    Please help promote STEM in your local schools.
    STEM Icon

    Stem Education Coalition

    World Community Grid (WCG) brings people together from across the globe to create the largest non-profit computing grid benefiting humanity. It does this by pooling surplus computer processing power. We believe that innovation combined with visionary scientific research and large-scale volunteerism can help make the planet smarter. Our success depends on like-minded individuals – like you.”
    WCG projects run on BOINC software from UC Berkeley.
    BOINCLarge

    BOINC is a leader in the field(s) of Distributed Computing, Grid Computing and Citizen Cyberscience.BOINC is more properly the Berkeley Open Infrastructure for Network Computing.

    BOINC WallPaper

    CAN ONE PERSON MAKE A DIFFERENCE? YOU BET!!

    MyBOINC

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

    Please visit the project pages-

    FightAIDS@home Phase II

    FAAH Phase II
    OpenZika

    Rutgers Open Zika

    Help Stop TB
    WCG Help Stop TB
    Outsmart Ebola together

    Outsmart Ebola Together

    Mapping Cancer Markers
    mappingcancermarkers2

    Uncovering Genome Mysteries
    Uncovering Genome Mysteries

    Say No to Schistosoma

    GO Fight Against Malaria

    Drug Search for Leishmaniasis

    Computing for Clean Water

    The Clean Energy Project

    Discovering Dengue Drugs – Together

    Help Cure Muscular Dystrophy

    Help Fight Childhood Cancer

    Help Conquer Cancer

    Human Proteome Folding

    FightAIDS@Home

    faah-1-new-screen-saver

    faah-1-new

    World Community Grid is a social initiative of IBM Corporation
    IBM Corporation
    ibm

    IBM – Smarter Planet
    sp

     
  • richardmitnick 10:39 am on December 16, 2016 Permalink | Reply
    Tags: , , OpenZika project at World Community Grid, ,   

    From UCLA: “Zika-linked birth defects more extensive than previously thought, UCLA-led research finds” 

    UCLA bloc

    UCLA

    December 15, 2016
    Enrique Rivero

    New UCLA-led research finds that Zika-linked abnormalities that occur in human fetuses are more extensive — and severe — than previously thought, with 46 percent of 125 pregnancies among Zika-infected women resulting in birth defects in newborns or ending in fetal death.

    The study, published in the New England Journal of Medicine, suggests that damage during fetal development from the mosquito-borne virus can occur throughout pregnancy and that other birth defects are more common than microcephaly, when babies are born with very small heads. Further, these defects may only be detected weeks or months after the baby is born, said Dr. Karin Nielsen, the study’s senior author and a professor of clinical pediatrics in the division of pediatric infectious diseases at the David Geffen School of Medicine at UCLA and Mattel Children’s Hospital.

    1
    Dr. Karin Nielsen. UCLA

    “This means that microcephaly is not the most common congenital defect from the Zika virus,” Nielsen said. The absence of that condition does not mean the baby will be free of birth defects, she added, because “there are problems that are not apparent at birth” and such difficulties may not be evident until the age of six months.

    “These are sobering results,” Nielsen said.

    The results are a follow-up to a smaller Brazilian study published in March that used molecular testing to find an association between Zika infection in pregnant women and a series of serious outcomes that included fetal deaths (miscarriages and stillbirths), abnormal fetal growth and damage to the central nervous system. This is the largest study to date of Zika-affected pregnancies in which the women were followed from the time they were infected to the end of their pregnancies. All the women were enrolled before any abnormalities in their pregnancies had been identified.

    The new study was based on a larger sample size of 345 women in Rio de Janeiro, Brazil, who were enrolled from September 2015 through May 2016. Of those women, 182, or 53 percent, tested positive for Zika in the blood, urine or both. In addition, 42 percent of the women who did not have Zika were found to be infected with chikungunya, another mosquito-borne virus; 3 percent of Zika-positive women also had chikungunya.

    From there, the researchers evaluated 125 women infected with Zika and 61 who were not infected with the virus who had given birth by July 2016. The previous study was based mainly on prenatal ultrasound findings; by contrast, the current research evaluated infants from Zika-affected pregnancies through physical examination and brain imaging. Among the findings:

    There were nine fetal deaths among women with Zika infection during pregnancy, five of those in the first trimester.
    Fetal deaths or abnormalities in the infants were present in 46 percent of Zika-positive women, contrasted with 11.5 percent of Zika-negative women.
    Forty-two percent of infants born to the Zika-infected mothers were found to have microcephaly, brain lesions or brain calcifications seen in imaging studies, lesions in the retina, deafness, feeding difficulties and other complications.

    The risks occurred at all stages of pregnancy: 55 percent of pregnancies were affected in the first trimester, 51 percent in the second trimester and 29 percent in the third trimester.

    The researchers noted that they examined the babies during their early infancy, when “more subtle neurologic manifestations of disease are not identified.” So follow-up examinations could turn up evidence of more neurologic diseases that couldn’t be detected earlier in the babies’ lives.

    “Our data show that the risk of severe adverse pregnancy and infant outcomes after maternal Zika infection was substantial,” the authors wrote.

    Supporting the study were the Departamento de Ciência e Tecnologia do Ministério da Saúde do Brasil; Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES/ 88887.116627/2016-01,) and the National Institute of Allergy and Infectious Diseases/National Institutes of Health grant AI AI28697.

    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.

    Rutgers smaller

    boincstatsimage-new

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    UC LA Campus

    For nearly 100 years, UCLA has been a pioneer, persevering through impossibility, turning the futile into the attainable.

    We doubt the critics, reject the status quo and see opportunity in dissatisfaction. Our campus, faculty and students are driven by optimism. It is not naïve; it is essential. And it has fueled every accomplishment, allowing us to redefine what’s possible, time after time.

    This can-do perspective has brought us 12 Nobel Prizes, 12 Rhodes Scholarships, more NCAA titles than any university and more Olympic medals than most nations. Our faculty and alumni helped create the Internet and pioneered reverse osmosis. And more than 100 companies have been created based on technology developed at UCLA.

     
  • richardmitnick 11:07 am on December 11, 2016 Permalink | Reply
    Tags: Colombia Reports Major Rise in Birth Defect Amid Zika Crisis, , OpenZika project at World Community Grid,   

    From NYT: “Colombia Reports Major Rise in Birth Defect Amid Zika Crisis” 

    New York Times

    The New York Times

    DEC. 10, 2016
    DONALD G. McNEIL Jr.

    Colombia, which suffered a Zika epidemic that peaked in February, has reported four times as many cases of babies born with microcephaly this year as it did in 2015, providing more proof that the Zika virus causes brain damage in infants.

    Because births of microcephalic infants peaked five months after the epidemic did, at about nine times the numbers of the previous July, scientists feel sure that the greatest risk is to babies whose mothers were infected during their first trimesters or early in their second.

    The numbers were reported in a study released Friday by the Centers for Disease Control and Prevention and conducted jointly by scientists from the C.D.C. and Colombia’s national health institute.

    With 105,000 suspected Zika cases, Colombia has had the second-largest Zika epidemic after Brazil. Brazil has had proportionally many more cases of microcephaly, and the reason has remained a mystery, although its population is four times larger than Colombia’s and it experienced a much longer, more intense epidemic in 2014 and 2015, especially in the northeast.

    As of Thursday, Brazil had reported 2,211 cases of microcephaly in which Zika infection had been confirmed to the World Health Organization, while Colombia had reported only 60.

    W.H.O. reports of confirmed cases have sometimes lagged weeks behind local reports. The study released by the C.D.C. found 476 cases of microcephaly in Colombia between January and mid-November. Of those, only 147 — about 30 percent — had laboratory evidence of Zika virus infection. But many others were not tested, and the virus is not always detectable months after it damages a fetus, so the true numbers may be higher.

    About 4 percent of the fetuses tested had evidence of other infections that can cause microcephaly, such as toxoplasmosis, herpes, cytomegalovirus or syphilis. Many other fetuses were not tested or their microcephaly had no clear cause.

    Of the total, 432 of the microcephaly cases were in babies born alive, and 44 were in fetuses that were stillborn, miscarried or aborted. One theory — still unproven — is that Colombia had fewer microcephaly cases than expected because many fearful women aborted their pregnancies, legally or illegally. Abortion is much more restricted in Brazil than in Colombia.

    The number of confirmed cases of microcephaly is in line with predictions made by health officials after they declared an end to the Zika epidemic in Colombia in July. Early in the year, based on Brazil’s experience, Dr. Fernando Ruiz, the vice minister for public health, estimated that Colombia would have 700 cases of Zika-related microcephaly this year. In August, he changed that estimate to between 100 and 250.

    Although Colombia is widely believed to have a better disease-surveillance system than Brazil, it still relies on doctors to voluntarily report birth defects. They may have been underreported in 2015, before microcephaly was in the news.

    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.

    Rutgers smaller

    boincstatsimage-new

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

     
  • richardmitnick 12:19 pm on December 5, 2016 Permalink | Reply
    Tags: , , , OpenZika project at World Community Grid,   

    From Harvard Medical School: “Zika’s Entry Points” 

    Harvard University
    Harvard University

    harvard-medical-school-bloc

    Harvard Medical School

    December 1, 2016
    HANNAH ROBBINS
    ERIC BENDER

    Fast-spreading virus can take multiple routes into the growing brain.

    1
    Zika virus (light blue) spreads through a three-dimensional model of a developing brain. Image: Max Salick and Nathaniel Kirkpatrick/Novartis

    Around the world, hundreds of women infected with the Zika virus have given birth to children suffering from microcephaly or other brain defects, as the virus attacks key cells responsible for generating neurons and building the brain as the embryo develops.

    Studies have suggested that Zika enters these cells, called neural progenitor cells or NPCs, by grabbing onto a specific protein called AXL on the cell surface. Now scientists at the Harvard Stem Cell Institute (HSCI) and Novartis have shown that this is not the only route of infection for NPCs.

    The scientists demonstrated that the Zika virus infected NPCs even when the cells did not produce the AXL surface receptor protein that is widely thought to be the main vehicle of entry for the virus.

    “Our finding really recalibrates this field of research, because it tells us we still have to go and find out how Zika is getting into these cells,” said Kevin Eggan, principal faculty member at HSCI, professor of stem cell and regenerative biology at Harvard University’s Faculty of Arts and Sciences and Harvard Medical School, and co-corresponding author on a paper reporting the research in Cell Stem Cell.

    “It’s very important for the research community to learn that targeting the AXL protein alone will not defend against Zika,” agreed Ajamete Kaykas, co-corresponding author and a senior investigator in neuroscience at the Novartis Institutes for Biomedical Research (NIBR).

    Previous studies have shown that blocking expression of the AXL receptor protein does defend against the virus in a number of human cell types. Given that the protein is highly expressed on the surface of NPCs, many labs have been working on the hypothesis that AXL is the entry point for Zika in the developing brain.

    “We were thinking that the knocked-out NPCs devoid of AXL wouldn’t get infected,” said Max Salick, a NIBR postdoctoral researcher and co-first author on the paper. “But we saw these cells getting infected just as much as normal cells.”

    Working in a facility dedicated to infectious disease research, the scientists exposed two-dimensional cell cultures of AXL-knockout human NPCs to the Zika virus. They followed up by exposing three-dimensional mini-brain “organoids” containing such NPCs to the virus. In both cases, cells clearly displayed Zika infection. This finding was supported by an earlier study that knocked out AXL in the brains of mice.

    “We knew that organoids are great models for microcephaly and other conditions that show up very early in development and have a very pronounced effect,” said Kaykas. “For the first few months, the organoids do a really good job in recapitulating normal brain development.”

    Historically, human NPCs have been difficult to study in the lab because it would be impossible to obtain samples without damaging brain tissue. With the advancements in induced pluripotent stem cell (iPS cell) technology, a cell reprogramming process that allows researchers to coax any cell in the body back into a stem cell-like state, researchers can now generate these previously inaccessible human tissues in a petri dish.

    The team was able to produce human iPS cells and then, using gene-editing technology, modify the cells to knock out AXL expression, said Michael Wells, a Harvard postdoctoral researcher in the Eggan Lab and co-first author. The scientists pushed the iPS cells to become NPCs, building the two-dimensional and three-dimensional models that were infected with Zika.

    The Harvard and NIBR collaborators started working with the virus in mid-April 2016, only six months before they published their findings. This unusual speed of research reflects the urgency of Zika’s global challenge, as the virus has spread to more than 70 countries and territories.

    “At the genesis of the project, my wife was pregnant,” Eggan remarked. “One can’t read the newspapers without being concerned.”

    The collaboration grew out of interactions at the Broad Institute of Harvard and MIT’s Stanley Center for Psychiatric Research, where Eggan directs the stem cell program. His lab already had developed cell culture systems for studying NPCs in motor neuron and psychiatric diseases. The team at Novartis had created brain organoids for research on tuberous sclerosis complex and other genetic neural disorders.

    “Zika seemed to be a big issue where we could have an impact, and we all shared that interest,” Eggan said. “It’s been great to have this public/private collaboration.”

    The researchers are studying other receptor proteins that may be open to Zika infection in hopes that their basic research eventually will help in the quest to develop vaccines or other drugs that defend against the virus.

    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.

    Rutgers smaller

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    harvard-medical-school-campus

    The Harvard Medical School community is dedicated to excellence and leadership in medicine, education, research and clinical care. To achieve our highest aspirations, and to ensure the success of all members of our community, we value and promote common ideals that center on collaboration and service, diversity, respect, integrity and accountability, lifelong learning, and wellness and balance. To be a citizen of this community means embracing a collegial spirit that fosters inclusion and promotes achievement.

    Harvard University campus

    Harvard is the oldest institution of higher education in the United States, established in 1636 by vote of the Great and General Court of the Massachusetts Bay Colony. It was named after the College’s first benefactor, the young minister John Harvard of Charlestown, who upon his death in 1638 left his library and half his estate to the institution. A statue of John Harvard stands today in front of University Hall in Harvard Yard, and is perhaps the University’s best known landmark.

    Harvard University has 12 degree-granting Schools in addition to the Radcliffe Institute for Advanced Study. The University has grown from nine students with a single master to an enrollment of more than 20,000 degree candidates including undergraduate, graduate, and professional students. There are more than 360,000 living alumni in the U.S. and over 190 other countries.

     
  • richardmitnick 8:55 am on October 3, 2016 Permalink | Reply
    Tags: Amber Gourdine, OpenZika project at World Community Grid, , ,   

    From Rutgers: SWomen in STEM: “Zika and Water Safety Education a Mission for Rutgers Alumna” Amber Gourdine 

    Rutgers University
    Rutgers University

    10.3.16
    Patti Verbanas

    1
    Amber Gourdine, shown with members of the community she served, spent hours each day walking to residences to examine filtration systems, assess residents’ knowledge about water sanitation and educate them about Zika. Photo: Courtesy Amber Gourdine

    Amber Gourdine wasn’t taking any chances.

    Braving the humid, 90-degree days in central Nicaragua, the recent Rutgers graduate donned long sleeves and tucked her pants into her socks to avoid mosquito bites. Then, she embarked on daylong hikes to rural homes to educate residents on water safety and how to protect themselves against the Zika virus, which is on the rise throughout most of the country.

    “I sprayed Permethrin and Off on my clothes and used mosquito nets, but despite my best attempts, I got bitten,” says Gourdine, who spent nine weeks this summer serving in the global health intensive program at AMOS Health and Hope, a nonprofit that works in impoverished Nicaraguan communities to improve citizens’ health through education and development projects. “That’s why education is so important – reducing mosquitos and taking precautions by eliminating standing water and proper hygiene is the best defense.”

    Although the incidence of Zika has fallen in many Central American countries, Nicaragua and Costa Rica are still reporting increases, according to the Pan American Health Organization. In August, Nicaragua confirmed its first microcephaly birth linked to Zika.

    Gourdine was part of a rapid response to the Zika outbreak by the Nicaraguan government, which relies on organizations like AMOS to teach remotely located residents how the virus spreads and ways to prevent mosquito breeding grounds.

    Gourdine, who graduated in May with a bachelor’s of science degrees in public health and in arts and sciences, learned about AMOS during an on-campus information session in New Brunswick, where she was enrolled at Douglass Residential College. “It excited me because it would allow me to put my interest in public health education into action,” she says.

    As part of AMOS’s clean water team, Gourdine’s mission was to educate the rural community on safe water practices and daily hygiene to help stem water-borne diseases. The Zika education is a new component AMOS added this year to the team’s mission.

    Joining three colleagues and a supervisor, she spent hours each day walking from their home base to residences sprinkled throughout the countryside to examine water filtration systems AMOS had installed, assess the residents’ knowledge about water sanitation and educate them about Zika.

    Zika is the latest public health threat in the communities AMOS serves, where less than 20 percent of the families have access to safe drinking water. To date, the organization has installed more than 1,000 water filters and relies on volunteers like Gourdine to make sure the residents know how to use and maintain the systems.

    “It was eye-opening how little people knew about Zika,” says Gourdine, whose Spanish studies allowed her to speak to residents without a translator. “Many knew the name and that the virus was spread by mosquitos, but few knew it could be sexually transmitted. Before I left each home, I put an informational poster on the wall.”

    Gourdine also assisted with teaching residents about water sanitation and trash disposal. “Waste management is a huge issue,” she says. “Since the houses are so spread apart, there is no trash collection. Instead of burning or burying trash, people leave it to decay in the yard, where it becomes a breeding ground for mosquitos.”

    2
    Amber Gourdine shown here demonstrating proper hygiene to community members.

    The AMOS mission was Gourdine’s second visit to the country since graduation. In late May, she joined the Rutgers Global Brigade for a week of building latrines, installing septic tanks and educating residents on healthy habits. Originally, she considered pursuing nursing, but she became intrigued with public health after taking a course sponsored by Rutgers at Academica Latinoamericana de Español in Peru in 2014 as part of her Spanish studies. While there, she researched local women’s public health issues, such as domestic violence and HIV/AIDs, and presented the report to the faculty at the school.

    Upon completing her work in Nicaragua in August, Gourdine returned to her home in Magnolia, New Jersey, where she aspires to work with Americorps as a community health coordinator and eventually apply to graduate school.

    “Public health is fascinating because you have to view a population the same as the patient: Just as a patient knows more about their bodies and themselves than a doctor, a community of people know more about their own issues in ways more than an outsider would,” she says. “I love the mutual exchange of ideas with community members to resolve health issues together.”

    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.

    Rutgers smaller

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

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

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

     
  • richardmitnick 9:16 am on September 10, 2016 Permalink | Reply
    Tags: , OpenZika project at World Community Grid, ,   

    For WCG From Orlando Sentinel 

    New WCG Logo

    WCGLarge

    World Community Grid (WCG)

    1

    Orlando Sentinel

    9.10.16
    Kate Santich

    If you knew you could fight Zika by downloading an app, would you?

    In the battle against Zika, Danny Leoni of Casselberry has been called a superhero. Night and day, the 26-year-old is running algorithms to find the chemical compounds that could deactivate the virus and offer a cure.

    But don’t look for his name in the Nobel Prize nominations anytime soon. He is simply lending the spare capacity of his computer.

    “I figured, ‘Hey, it’s something actually useful instead of being on Netflix for eight hours at a time,'” he says.

    Leoni is a volunteer for the nonprofit Hands On Orlando, which has recruited nearly 1,000 people whose computers, tablets and phones act as a collective supercomputer for researchers around the globe.

    “The beauty of it is, you don’t have to have any particular skills. You don’t have to have any scientific background. You just have to care,” says Chris Allen, executive director of Hands On Orlando, which matches volunteers to group projects — such as sorting donations at food banks or washing dogs at pet shelters.

    But for eight years, Allen’s nonprofit organization also has enlisted participants for what he dubbed the Super Heroes team.

    Together they run scientific calculations that have led to advances in solar energy, treating childhood cancer and fighting AIDS. All volunteers need to do is download an app that allows their computers and phones to process data.

    The app comes from the World Community Grid — an award-winning philanthropic project of IBM Corporate Citizenship, the tech company’s social responsibility initiative. For anyone worried that getting involved would open their devices to hackers, IBM is quick to point out that it installs the app on its own employees’ computers.

    “As you can imagine, we take security very, very seriously,” says Juan Hindo, the World Community Grid program manager. “So we have all kinds of security measures in place. … It doesn’t touch any of the private data on your device.”

    Since the project’s launch, researchers have used the grid to run massive computer simulations involving billions of variables by breaking up the data into personal computer-sized morsels that can run in the background as long as your device is turned on and connected to the internet.

    The work, researchers report, has led to progress in fighting malaria, tuberculosis, muscular dystrophy, cancer and influenza. It has spurred the development of filtration systems for clean water and rice that has higher crop yields and more protein. And it is helping to map climate change.

    But the Super Heroes’ most recent work has been on OpenZika, a project by an international team of scientists searching for a critically needed anti-viral drug to combat the disease. Currently, there is none.

    Leoni, an aspiring web developer who joined the team a year and a half ago, says that project and another on cancer inspired him to sign up.

    “Several people in my family have had cancer,” he says. “To know I’m contributing to the research definitely makes me feel good. Although I admit — the whole thing still blows my mind a little bit.”

    Though the Super Heroes team ranks No. 224 out of nearly 32,600 teams participating worldwide, both Allen and Hindo acknowledge the potential is still largely untapped. The biggest hurdle, they say, is that most people just don’t understand it.

    “A typical researcher, if they’re lucky, might have access to a supercomputer a few weeks a year — and then they’re sharing with dozens of other researchers on campus,” Hindo says. “And because there’s a very difficult funding climate for scientific researchers, they don’t want to spend a lot of their money on computer time, so they end up scaling down the scope of their research.”

    But by distributing the load through thousands of volunteers worldwide, each researcher can have the equivalent of his or her own small supercomputer for as long as necessary, 24 hours a day, Allen says.

    More than 720,000 people around the world have joined the effort so far.

    In the Hands On office alone, 16 computers are enlisted. Kyle Trager, the community partnerships manager there, also has the app on his phone and his computer at home.

    “You don’t even know it’s running,” he says. “I just plug in my phone to charge overnight, and once it gets to 90 percent, it’ll crunch these calculations.”

    There’s never a slowdown of processing, Allen insists. And if the charity’s power bill went up as a result, it wasn’t noticeable.

    “The benefit of joining our team [handsonorlando.com/superheroes] is that you can call us and we will help you set it up,” he says. “And when scientists find a drug for Zika or a cure for cancer, you can say you helped make it happen.”

    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.

    Rutgers smaller

    Please help promote STEM in your local schools.
    STEM Icon

    Stem Education Coalition

    World Community Grid (WCG) brings people together from across the globe to create the largest non-profit computing grid benefiting humanity. It does this by pooling surplus computer processing power. We believe that innovation combined with visionary scientific research and large-scale volunteerism can help make the planet smarter. Our success depends on like-minded individuals – like you.”

    WCG projects run on BOINC software from UC Berkeley.
    BOINCLarge

    BOINC is a leader in the field(s) of Distributed Computing, Grid Computing and Citizen Cyberscience.BOINC is more properly the Berkeley Open Infrastructure for Network Computing.

    BOINC WallPaper

    CAN ONE PERSON MAKE A DIFFERENCE? YOU BET!!

    MyBOINC

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

    Please visit the project pages-

    FightAIDS@home Phase II

    FAAH Phase II
    OpenZika

    Rutgers Open Zika

    Help Stop TB
    WCG Help Stop TB
    Outsmart Ebola together

    Outsmart Ebola Together

    Mapping Cancer Markers
    mappingcancermarkers2

    Uncovering Genome Mysteries
    Uncovering Genome Mysteries

    Say No to Schistosoma

    GO Fight Against Malaria

    Drug Search for Leishmaniasis

    Computing for Clean Water

    The Clean Energy Project

    Discovering Dengue Drugs – Together

    Help Cure Muscular Dystrophy

    Help Fight Childhood Cancer

    Help Conquer Cancer

    Human Proteome Folding

    FightAIDS@Home

    World Community Grid is a social initiative of IBM Corporation
    IBM Corporation
    ibm

    IBM – Smarter Planet
    sp

     
  • richardmitnick 2:55 pm on August 29, 2016 Permalink | Reply
    Tags: , , , OpenZika project at World Community Grid,   

    From JHU: “Scientists screen existing drugs in hopes of fast-tracking Zika treatment” 

    Johns Hopkins
    Johns Hopkins University

    8.29.16
    Rachel Butch

    A specialized drug screen test using lab-grown human cells has revealed two classes of compounds already in the pharmaceutical arsenal that may work against mosquito-borne Zika virus infections, scientists say.

    1
    Zika virus infection in cell death in human forebrain organoids. Image credit: Xuyu Qian, Johns Hopkins University

    In a summary of their work, published today in Nature Medicine, the investigators say they screened 6,000 existing compounds currently in late-stage clinical trials or already approved for human use for other conditions. The screening process identified several compounds that showed the ability to hinder or halt the progress of the Zika virus in lab-grown human neural cells.

    The research collaboration includes teams from the Johns Hopkins University School of Medicine, the National Institutes of Health, and Florida State University.

    “It takes years, if not decades, to develop a new drug,” says Hongjun Song, director of the Stem Cell Biology Program in the Institute of Cell Engineering at Johns Hopkins. “In this sort of global health emergency, we don’t have that kind of time.”

    Adds Guo-li Ming, professor of neurology at JHU’s School of Medicine: “Instead of using new drugs, we chose to screen existing drugs. In this way, we hope to create a therapy much more quickly.”

    The current outbreak of Zika, which began in South America last year, is known to be responsible for an increase in cases of microcephaly—a severe birth defect in which afflicted infants are born with underdeveloped brains. In the continental United States, there have been a total of 2,260 reported cases of Zika. Though most cases are associated with travel, 43 cases of local transmission have been reported in Florida, in the Miami area. In addition, Puerto Rico has reported 7,855 locally transmitted cases, spurring the Obama administration to declare a public health emergency in the territory on Aug. 12.

    The Zika virus is commonly transmitted from mosquito bites or from an infected person to an uninfected person through sexual contact. Despite the potential effects of infection, only one in four infected people will present symptoms if Zika infection, allowing the virus to spread rapidly in areas with local transmission. Because of this, the CDC recommends all pregnant women with ongoing risk of Zika infection, including residence or frequent travel to areas with active Zika virus transmission, receive screening throughout their pregnancy.

    Many research groups are fast tracking the development of vaccines, treatments, and mosquito-control measures to combat further spread of the virus.

    The new findings are an extension of previous work by the same research team, which found that Zika mainly targets specialized stem cells that give rise to neurons in the brain’s outer layer, the cortex. The researchers observed Zika’s effects in two- and three-dimensional cell cultures called “mini-brains,” which share structures with the human brain and allow researchers to study the effects of Zika in a more accurate model for human infection.

    In the current study, the research team exposed similar cell cultures to the Zika virus and the drugs one at a time, measuring for indicators of cell death, including caspase-3 activity, a chemical marker of cell death, and ATP, a molecule whose presence is indicative of cell vitality.

    Typically, after Zika infection, the damage done to neural cells is “dramatic and irreversible,” says Hengli Tang, professor of biological sciences at Florida State University. However, some of the compounds tested allowed the cells to survive longer and, in some cases, fully recover from infections.

    Further analysis of the surviving cells, Ming says, showed that the promising drugs could be divided into two classes: neuroprotective drugs, which prevent the activation of mechanisms that cause cell death; and antiviral drugs, which slow or stop viral infection or replication.

    Overall, Song says, three drugs showed robust enough results to warrant further study:

    PHA-690509, an investigational compound with antiviral properties
    emricasan, now in clinical trials to reduce liver damage from hepatitis C virus and shown to have neuroprotective effects
    niclosamide, a drug already used in humans and livestock to combat parasitic infections, which worked as an antiviral agent in these experiments

    Song cautioned that the three drugs “are very effective against Zika in the dish, but we don’t know if they can work in humans in the same way.” For example, he says, although niclosamide can safely treat parasites in the human gastrointestinal tract, scientists have not yet determined if the drug can even penetrate the central nervous system of adults or a fetus inside a carrier’s womb to treat the brain cells targeted by Zika.

    Nor, he says, do they know if the drugs would address the wide range of effects of Zika infection, which include microcephaly in fetuses and temporary paralysis from Guillain-Barre syndrome in adults.

    “To address these questions, additional studies need to be done in animal models as well as humans to demonstrate their ability to treat Zika infection,” Ming says. “So we could still be years away from finding a treatment that works.”

    The researchers say their next steps include testing the efficacy of these drugs in animal models to see if they have the ability to combat Zika in vivo.

    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.

    Rutgers smaller

    WCGLarge
    WCG Logo New

    BOINCLarge
    BOINC WallPaper

    Please help promote STEM in your local schools.
    STEM Icon

    Stem Education Coalition

    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 10:15 am on August 26, 2016 Permalink | Reply
    Tags: , , Johns Hopkins Wilmer Zika Center, OpenZika project at World Community Grid,   

    From JHU: “Johns Hopkins launches first-known multidisciplinary Zika virus center in the world” 

    Johns Hopkins
    Johns Hopkins University

    8.24.16
    Kim Polyniak

    Center team will provide comprehensive care to patients with mosquito-borne virus, conduct research

    As the number of patients with Zika virus grows worldwide, Johns Hopkins Medicine today announced the opening of the new Johns Hopkins Wilmer Zika Center dedicated primarily to caring for patients with the mosquito-borne and sexually transmitted virus.

    The center is composed of providers and staff from departments and divisions at Johns Hopkins Medicine and the Bloomberg School of Public Health, including epidemiology, infectious diseases, maternal-fetal medicine, ophthalmology, orthopaedics, pediatrics, physiotherapy, psychiatry, and social work. Medical experts from Brazil, a country greatly affected by Zika virus, are also members of the center.

    “Patients will no longer be required to travel to multiple centers for care relating to Zika virus,” says William May, associate professor of ophthalmology at the Johns Hopkins Wilmer Eye Institute. “Physicians and staff members in various departments at Johns Hopkins will be available to provide comprehensive care to patients within one institution.”

    Infections from Zika virus have reached epidemic proportions in parts of the world in the past year, with Brazil being the epicenter of the outbreak. Several non-travel-related cases have recently been reported in Florida, suggesting local transmission there. According to the World Health Organization, Zika may be responsible for thousands of babies being born with microcephaly, a severe birth defect that affects the brain, and for some adults experiencing neurological symptoms.

    The Wilmer Eye Institute led the development of what is believed to be the first such comprehensive and multidisciplinary Zika center. In addition to microcephaly, Zika is also reported to cause eye abnormalities in up to more than half of babies infected with the illness, according to a recent study in Brazil. The Wilmer Eye Institute is able to diagnose and, in many cases, treat eye concerns associated with Zika virus—including cataracts and other vision issues—with specialized technology.

    Adult and pediatric patients worldwide can be referred to the center by outside physicians or through Johns Hopkins departments and divisions, including emergency medicine and maternal-fetal medicine. Patients can also call the Wilmer Eye Institute to schedule an appointment. A case manager will work with patients to develop a care plan and identify specialists with whom the patient should follow up.

    “When a patient, particularly a pregnant woman, contracts Zika virus, it can be a tremendously alarming experience,” says Jeanne Sheffield, director of maternal-fetal medicine for the Johns Hopkins Hospital. “Our team will be able to coordinate our efforts to determine patients’ needs and provide the best care possible.”

    The Zika center team will also be involved in research to learn more about the virus, about which many unknowns still exist.

    “Our No. 1 priority will be focused on our patients,” May says, “but our hope is that our care will also lead to many new developments in the effort to fight this potentially devastating disease.”

    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.

    Rutgers smaller

    WCGLarge
    WCG Logo New

    BOINCLarge
    BOINC WallPaper

    Please help promote STEM in your local schools.
    STEM Icon

    Stem Education Coalition

    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 9:24 am on August 25, 2016 Permalink | Reply
    Tags: Fetal microcephaly, OpenZika project at World Community Grid, Sofosbuvir, ,   

    From Yale: “Yale team discovers how Zika virus causes fetal brain damage” 

    Yale University bloc

    Yale University

    August 24, 2016
    Bill Hathaway
    william.hathaway@yale.edu

    1
    Human neuroepithelial stem cells self-organize into rose-like patterns and express the typical neural stem cell markers nestin (green) and SOX2 (red). They were used to understand how Zika virus infection works and to block its proliferation. No image credit.

    Infection by the Zika virus diverts a key protein necessary for neural cell division in the developing human fetus, thereby causing the birth defect microcephaly, a team of Yale scientists reported Aug. 24 in the journal Cell Reports.

    The findings suggest that Zika virus might be susceptible to existing antiviral drugs that may prevent disruption to the developing nervous system, said the researchers.

    One of the frightening side-effects of Zika virus infection in pregnant women is the risk of fetal microcephaly, in which babies are born with abnormally small brains. The multidisciplinary collaboration of Yale scientists revealed that Zika virus kills stem cells in the brain and disrupts the process of creating brain cells. An analysis shows that the virus diverts a form of the protein TBK1 from its primary job of organizing cell division to the mitochondria, the cell’s power pack, where it helps initiate an immune response. Lacking the protein at the site of cell division, cells die instead of forming new brain cells, resulting in microcephaly. The data suggest this mechanism may also contribute to microcephaly associated with other common congenital viral infections.

    Researchers note that an existing FDA-approved drug, Sofosbuvir, showed promise in preventing Zika virus infection of neural stem cells in laboratory culture and also seems to keep phospho-TBK1 involved in cell division. More study needs to be conducted to prove the efficacy of the drug as a medical therapy for Zika virus, the authors said.

    “There is an urgent need to identify therapeutic approaches to halt Zika infection, especially in pregnant women,” said Marco Onorati, co-first author of the paper and researcher in the lab of senior author Nenad Sestan, professor of neuroscience, comparative medicine, genetics, and psychiatry. “In the interim, we hope these findings can lead to therapies that might minimize the damage caused by this virus.”

    Co-first authors of the paper are Zhen Li, Fuchen Liu, and Andre M.M. Sousa of Yale. Tamas L. Horvath and Brett Lindenbach, also of Yale, are co-senior authors of the work.

    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.

    Rutgers smaller

    WCGLarge
    WCG Logo New

    BOINCLarge
    BOINC WallPaper

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    Yale University Campus

    Yale University comprises three major academic components: Yale College (the undergraduate program), the Graduate School of Arts and Sciences, and the professional schools. In addition, Yale encompasses a wide array of centers and programs, libraries, museums, and administrative support offices. Approximately 11,250 students attend Yale.

     
  • 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.

    Rutgers smaller

    WCGLarge
    WCG Logo New

    BOINCLarge
    BOINC WallPaper

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

     
c
Compose new post
j
Next post/Next comment
k
Previous post/Previous comment
r
Reply
e
Edit
o
Show/Hide comments
t
Go to top
l
Go to login
h
Show/Hide help
shift + esc
Cancel
%d bloggers like this: