Induction and suppression of RNA silencing: insights from plant viral infections��a BARD workshop report

An international workshop on 'Induction and Suppression of RNA Silencing: Insights from Plant Viral Infections' was sponsored by the United States-Israel Binational Agricultural Research and Development Fund (BARD) and organized in Eilat, Israel in March 2010. The focus of this workshop was on molecular mechanisms employed by viruses or their hosts, and their interactions, for the regulation of virus-induced silencing and suppression. Several of the talks also served as potent reminders of scientific hubris and the need to be attentive to earlier results, both for analyses and perspective regarding new findings.     

Molecular movies... coming to a lecture near you

Scientific visualizations are powerful tools for communicating the intricacies of cellular and molecular structures and dynamics. There is a disconnect, however, between the research data sets we seek to represent and the kinds of animation that allow us to visualize and communicate them. Scientists are increasingly turning to 3D animation software borrowed from the entertainment industry to import, animate, and even create simulations of their data.     

Ecological Indicators in Risk Assessment: Workshop Summary

Ecological indicators can be defined as relatively simple measurements that relay scientific information about complex ecosystems. Such indicators are used to characterize risk in ecological risk assessment (ERA) and to mark progress toward resource management goals. In late 1997, scientists from the U.S. Environmental Protection Agency and from the Chemical Manufacturers Association (CMA) held a workshop to explore opportunities for collaborative research and scientific exchange on the development and application of ecological indicators. Several scientific challenges were identified as they relate to problem formulation, exposure and effects assessment, and risk characterization. Chief among these were a better understanding of multiple stressors (both chemical and non-chemical), characterization of reference sites and natural variability, extrapolation of measures to ecologically relevant scales, development of comprehensive, ecosystem-based models that incorporate multiple stressors and receptors, and a consistent system for evaluating ecological indicators.     

Workshops Without Walls: broadening access to science around the world

The National Aeronautics and Space Administration (NASA) Astrobiology Institute (NAI) conducted two "Workshops Without Walls" during 2010 that enabled global scientific exchange--with no travel required. The second of these was on the topic "Molecular Paleontology and Resurrection: Rewinding the Tape of Life." Scientists from diverse disciplines and locations around the world were joined through an integrated suite of collaborative technologies to exchange information on the latest developments in this area of origin of life research. Through social media outlets and popular science blogs, participation in the workshop was broadened to include educators, science writers, and members of the general public. In total, over 560 people from 31 US states and 30 other nations were registered. Among the scientific disciplines represented were geochemistry, biochemistry, molecular biology and evolution, and microbial ecology. We present this workshop as a case study in how interdisciplinary collaborative research may be fostered, with substantial public engagement, without sustaining the deleterious environmental and economic impacts of travel.     

Frontiers in glycomics: bioinformatics and biomarkers in disease. An NIH white paper prepared from discussions by the focus groups at a workshop on the NIH campus, Bethesda MD (September 11-13, 2006)

Key issues relating to glycomics research were discussed after the workshop entitled "Frontiers in Glycomics: Bioinformatics and Biomarkers in Disease" by two focus groups nominated by the organizers. The groups focused on two themes: (i) glycomics as the new frontier for the discovery of biomarkers of disease and (ii) requirements for the development of informatics for glycomics and glycobiology. The mandate of the focus groups was to build consensus on these issues and develop a summary of findings and recommendations for presentation to the NIH and the greater scientific community. A list of scientific priorities was developed, presented, and discussed at the workshops. Additional suggestions were solicited from workshop participants and collected using the workshop mailing list. The results are summarized in this White Paper, authored by the co-chairs of the focus groups.     

West Nile Virus workshop: scientific considerations for tissue donors

This report contains selected excerpts, presented as a summary, from a public workshop sponsored by the American Association of Tissue Banks (AATB) held to discuss West Nile Virus (WNV) and scientific considerations for tissue donors. The daylong workshop was held 9 July 2010 at the Ritz-Carlton Hotel at Tyson's Corner in McLean, Virginia, United States (U.S.). The workshop was designed to determine and discuss scientific information that is known, and what is not known, regarding WNV infection and transmission. The goal is to determine how to fill gaps in knowledge of WNV and tissue donation and transplantation by pursuing relevant scientific studies. This information should ultimately support decisions leading to appropriate tissue donor screening and testing considerations. Discussion topics were related to identifying these gaps and determining possible solutions. Workshop participants included subject-matter experts from the U.S. Food and Drug Administration, the Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Health Canada, the Public Health Agency of Canada, AATB-accredited tissue banks including reproductive tissue banks, accredited eye banks of the Eye Bank Association of America, testing laboratories, and infectious disease and organ transplantation professionals. After all presentations concluded, a panel addressed this question: "What are the scientific considerations for tissue donors and what research could be performed to address those considerations?" The slide presentations from the workshop are available at: http://www.aatb.org/2010-West-Nile-Virus-Workshop-Presentations.     

Dynamic molecules: molecular dynamics for everyone. An internet-based access to molecular dynamic simulations: basic concepts

Molecular dynamics is a rapidly developing field of science and has become an established tool for studying the dynamic behavior of biomolecules. Although several high quality programs for performing molecular dynamic simulations are freely available, only well-trained scientists are currently able to make use of the broad scientific potential that molecular dynamic simulations offer to gain insight into structural questions at an atomic level. The "Dynamic Molecules" approach is the first internet portal that provides an interactive access to set up, perform and analyze molecular dynamic simulations. It is completely based on standard web technologies and uses only publicly available software. The aim is to open molecular dynamics techniques to a broader range of users including undergraduate students, teachers and scientists outside the bioinformatics field. The time-limiting factors are the availability of free capacity on the computing server to run the simulations and the time required to transport the history file through the internet for the animation mode. The interactive access mode of the portal is acceptable for animations of molecules having up to about 500 atoms.Figure Several main menus (see top) are provided to start "New Simulations", to "Display Simulations" and to "Analyze" statistical and geometrical properties of the molecule. Here the "Display Simulation" interface is shown. The Chime plugin is used to visualize molecular 3D structures and motions.     

Visualization of the relationship between Fischer and Haworth projections of monosaccharides by animation on a microcomputer

An animation is described to assist in the visualization of the relationship between the Fischer and Haworth projections of monosaccharides. The animation helps the understanding of two quite different, commonly used representations of the same molecule. The animation runs on a 386-based PC with VGA graphics. The method for realizing such an animation on this hardware is described in detail; C code is provided in the Appendix.     

Cellular commitment to radiation-induced apoptosis

The basic elements of the machinery of programmed cell death (apoptosis) are built into all mammalian cells and are conserved evolutionarily from nematodes to humans. The workshop on Commitment to Radiation-Induced Apoptosis at the 11th International Congress of Radiation Research in Dublin, Ireland reviewed recent information regarding the basic molecular mechanisms which are fundamental to the understanding of the process of apoptosis after treatment with ionizing radiation and some other agents.     

Report on the ILAR International Workshop on the Development of Science-based Guidelines for Laboratory Animal Care

The Institute for Laboratory Animal Research of the National Academies hosted a meeting in November 2003 in Washington, DC, titled "International Workshop on the Development of Science-based Guidelines for Laboratory Animal Care." The purpose of the workshop was to bring together experts from around the world to assess the available scientific knowledge that can have an impact on the current and pending guidelines for laboratory animal care. Platform presentations focused on a variety of issues, from information exchange on mechanisms for the development of regulations across different countries and cultures, to data-based scientific studies on the effects of environmental enrichment on research outcomes. In the discussion sessions, participants were tasked with addressing the current scientific literature on the specific session topics; identifying gaps in the current knowledge in order to encourage future research endeavors; and assessing the effects of current and proposed regulations on facilities, research, and animal welfare. Participants had ample opportunities to share research outcomes and viewpoints in the multiple breakout sessions. Summaries of all breakout sessions were presented in the general session. On the final day of the workshop during the point/counterpoint session, a diverse group of speakers presented their cases for and against harmonization of standards. Although some of the speakers had serious reservations about harmonization, most of the panel members supported some form of harmonization. A positive outcome of the workshop was the opportunity for scientists and veterinarians from many countries to begin a dialogue with a goal of understanding the basis for the differences in regulatory approaches in laboratory animal care and the hope of continuing discussions on ways to work together toward some type of harmonization.     

RNAi‐based GM plants: food for thought for risk assessors

RNA interference (RNAi) is an emerging technology that offers new opportunities for the generation of new traits in genetically modified (GM) plants. Potential risks associated with RNAi‐based GM plants and issues specific to their risk assessment were discussed during an international scientific workshop (June 2014) organized by the European Food Safety Authority (EFSA). Selected key outcomes of the workshop are reported here.     

Workshop on Animal free Detection of Pertussis Toxin in Vaccines--Alternatives to the Histamine Sensitisation Test

The Paul-Ehrlich-Institut (PEI), the Nederlands Vaccin Instituut (NVI) and the European Directorate for the Quality of Medicines & HealthCare (EDQM) organised the international scientific workshop "Animal free Detection of Pertussis Toxin in Vaccines--Alternatives to the Histamine Sensitisation Test" at the PEI in Langen (Germany) on 09-10 June 2011. Twenty-seven experts (regulators, representatives from national control laboratories, vaccine manufacturers and academia) from 7 countries participated in this workshop. The meeting was triggered by the lack of satisfaction with the current safety testing for acellular pertussis vaccines, the "Histamine Sensitisation Test" (HIST) in mice, and the growing attention for the alternatives under development. The workshop objectives were: a) to review the current status of available alternative methods, b) to discuss the sensitivity that an alternative test needs, c) to plan experiments that allow for comparison of the alternative tests. The results of the workshop are summarised in this meeting report.     

Sixth International Workshop on Scleroderma Research, Oxford, UK, 30 July–2 August 2000

We discuss major topics presented at this recent international workshop, illustrating how recent progress in areas as diverse as free radical biochemistry, developmental biology, molecular genetics and vascular biology is facilitating greater understanding of the multisystem connective tissue disease scleroderma. Some of the opportunities for translating this into novel and improved therapy are considered.     

Developing New Methods to Answer Old and New Questions in Neurodegenerative Diseases

The HUPO Brain Proteome Project (HUPO BPP) held its 21^st workshop in Honolulu, Hawaii. During the 23–24 January 2014 the island became the center of the open workshop of the scientific community.     

The human proteome – a scientific opportunity for transforming diagnostics, therapeutics, and healthcare

A National Institutes of Health (NIH) workshop was convened in Bethesda, MD on September 26?C27, 2011, with representative scientific leaders in the field of proteomics and its applications to clinical settings. The main purpose of this workshop was to articulate ways in which the biomedical research community can capitalize on recent technology advances and synergize with ongoing efforts to advance the field of human proteomics. This executive summary and the following full report describe the main discussions and outcomes of the workshop.     

The human proteome - a scientific opportunity for transforming diagnostics, therapeutics, and healthcare

ABSTRACT: A National Institutes of Health (NIH) workshop was convened in Bethesda, MD on September 26-27, 2011, with representative scientific leaders in the field of proteomics and its applications to clinical settings. The main purpose of this workshop was to articulate ways in which the biomedical research community can capitalize on recent technology advances and synergize with ongoing efforts to advance the field of human proteomics. This executive summary and the following full report describe the main discussions and outcomes of the workshop.     

Conference Proceedings: 9th Molecular Modeling Workshop

Preface As editor of this journal and as secretary of the Molecular Graphics and Modelling Society (Deutschsprachige Sektion), I have pleasure in presenting this volume: It contains a wealth of material including all aspects of molecular modeling, ranging from method development and application to multimedia data presentation. With over 200 attendees the workshop attracted more people than ever before. As always, the meeting was devoted mainly to talks by graduate students and postdocs, so that the traditional workshop character was once again evident. Thanks are due to all those who have submitted contributions and the keynote speakers Manfred Sippl (University of Vienna), Hugo Kubinyi (BASF Ludwigshafen) and Gerd Volkers (ETH Zuerich). Special thanks go to Dr. Michael Krug (Merck, Darmstadt) who was in charge of the organization of the scientific program and to Prof. Juergen Brickmann and his group for trouble-free course of the technical part of the program that also offered the chance to get insight into the possibilities of real multimedia application in the field of molecular modeling. The abstracts collected here give a flavour of the meeting. We do hope that this collection of abstracts will encourage attendance of the 10th Molecular Modelling Workshop 1996 in Darmstadt. The Molecular Modelling Workshops are organized under the auspices of the Molecular Graphics and Modelling Society - Deutschsprachige Sektion. Tim Clark, Erlangen 6th July 1995     

ePMV embeds molecular modeling into professional animation software environments

Increasingly complex research has made it more difficult to prepare data for publication, education, and outreach. Many scientists must also wade through black-box code to interface computational algorithms from diverse sources to supplement their bench work. To reduce these barriers we have developed an open-source plug-in, embedded Python Molecular Viewer (ePMV), that runs molecular modeling software directly inside of professional 3D animation applications (hosts) to provide simultaneous access to the capabilities of these newly connected systems. Uniting host and scientific algorithms into a single interface allows users from varied backgrounds to assemble professional quality visuals and to perform computational experiments with relative ease. By enabling easy exchange of algorithms, ePMV can facilitate interdisciplinary research, smooth communication between broadly diverse specialties, and provide a common platform to frame and visualize the increasingly detailed intersection(s) of cellular and molecular biology.