WorldWideScience

Sample records for bringing molecular tools

  1. Bringing molecules back into molecular evolution.

    Directory of Open Access Journals (Sweden)

    Claus O Wilke

    Full Text Available Much molecular-evolution research is concerned with sequence analysis. Yet these sequences represent real, three-dimensional molecules with complex structure and function. Here I highlight a growing trend in the field to incorporate molecular structure and function into computational molecular-evolution work. I consider three focus areas: reconstruction and analysis of past evolutionary events, such as phylogenetic inference or methods to infer selection pressures; development of toy models and simulations to identify fundamental principles of molecular evolution; and atom-level, highly realistic computational modeling of molecular structure and function aimed at making predictions about possible future evolutionary events.

  2. Molecular tools for chemical biotechnology.

    Science.gov (United States)

    Galanie, Stephanie; Siddiqui, Michael S; Smolke, Christina D

    2013-12-01

    Biotechnological production of high value chemical products increasingly involves engineering in vivo multi-enzyme pathways and host metabolism. Recent approaches to these engineering objectives have made use of molecular tools to advance de novo pathway identification, tunable enzyme expression, and rapid pathway construction. Molecular tools also enable optimization of single enzymes and entire genomes through diversity generation and screening, whole cell analytics, and synthetic metabolic control networks. In this review, we focus on advanced molecular tools and their applications to engineered pathways in host organisms, highlighting the degree to which each tool is generalizable. Copyright © 2013 Elsevier Ltd. All rights reserved.

  3. Bring Your Own Device (BYOD) Programs in the Classroom: Teacher Use, Equity, and Learning Tools

    Science.gov (United States)

    Fincher, Derrel

    2016-01-01

    This study explores teacher perceptions of Bring Your Own Device (BYOD) programs in the classroom, with a focus on teacher use, student equity of access, and student ability to use their devices as learning tools. While one-to-one laptop programs (students assigned identical school-owned laptop or tablet) has an extensive body of literature behind…

  4. Molecular Modeling: A Powerful Tool for Drug Design and Molecular ...

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 9; Issue 5. Molecular Modeling: A Powerful Tool for Drug Design and Molecular Docking. Rama Rao Nadendla. General Article Volume 9 Issue 5 May 2004 pp 51-60. Fulltext. Click here to view fulltext PDF. Permanent link:

  5. Is the Process of Special Measures an Effective Tool for Bringing about Authentic School Improvement?

    Science.gov (United States)

    Willis, Lynne

    2010-01-01

    Managing change in education is a complex process, but to do so under the pressure of a punishment-based measurement system (Fullan, 2008) makes sustainable and meaningful change increasingly difficult. Systems which produce high stakes accountability measures, which bring with it sanctions that create a greater sense of distrust, demoralization…

  6. Can agile software tools bring the benefits of a task board to globally distributed teams?

    NARCIS (Netherlands)

    Katsma, Christiaan; Amrit, Chintan Amrit; van Hillegersberg, Jos; Sikkel, Nicolaas; Oshri, Ilan; Kotlarsky, Julia; Willcocks, Leslie P.

    Software-based tooling has become an essential part of globally disitrbuted software development. In this study we focus on the usage of such tools and task boards in particular. We investigate the deployment of these tools through a field research in 4 different companies that feature agile and

  7. Patents: a tool to bring innovation from the lab bench to the marketplace.

    Science.gov (United States)

    Li, Z Ying; Meyer, Wolfram

    2014-01-01

    Intellectual property (IP) is creations of the mind. Protecting IP through patents is an important venue for a researcher to reap rewards from his scientific endeavors. It is part of a competitive strategy for bringing one's invention to the marketplace. Using the US and European patent systems as examples, we provide here an overview of how patents protect innovation, with a focus on biotechnology. We explain what a patent is, what a patent owner can do with a patent, and how patents are granted. The article ends with some recent examples of noteworthy patents in the field of yeast research.

  8. Applying molecular genetic tools to tiger conservation.

    Science.gov (United States)

    Luo, Shu-Jin; Johnson, Warren E; O'Brien, Stephen J

    2010-12-01

    The utility of molecular genetic approaches in conservation of endangered taxa is now commonly recognized. Over the past decade, conservation genetic analyses based on mitochondrial DNA sequencing and microsatellite genotyping have provided powerful tools to resolve taxonomy uncertainty of tiger subspecies, to define conservation units, to reconstruct phylogeography and demographic history, to examine the genetic ancestry of extinct subspecies, to assess population genetic status non-invasively, and to verify genetic background of captive tigers worldwide. The genetic status of tiger subspecies and populations and implications for developing strategies for the survival of this charismatic species both in situ and ex situ are discussed. © 2010 ISZS, Blackwell Publishing and IOZ/CAS.

  9. Bringing it All Together: NODC's Geoportal Server as an Integration Tool for Interoperable Data Services

    Science.gov (United States)

    Casey, K. S.; Li, Y.

    2011-12-01

    The US National Oceanographic Data Center (NODC) has implemented numerous interoperable data technologies in recent years to enhance the discovery, understanding, and use of the vast quantities of data in the NODC archives. These services include OPeNDAP's Hyrax server, Unidata's THREDDS Data Server (TDS), NOAA's Live Access Server (LAS), and most recently the ESRI ArcGIS Server. Combined, these technologies enable NODC to provide access to its data holdings and products through most of the commonly-used standardized web services like the Data Access Protocol (DAP) and the Open Geospatial Consortium suite of services such as the Web Mapping Service (WMS) and Web Coverage Service (WCS). Despite the strong demand for and use of these services, the acronym-rich environment of services can also result in confusion for producers of data to the NODC archives, for consumers of data from the NODC archives, and for the data stewards at the archives as well. The situation is further complicated by the fact that NODC also maintains some ad hoc services like WODselect, and that not all services can be applied to all of the tens of thousands of collections in the NODC archive; where once every data set was available only through FTP and HTTP servers, now many are also available from the LAS, TDS, Hyrax, and ArcGIS Server. To bring order and clarity to this potentially confusing collection of services, NODC deployed the Geoportal Server into its Archive Management System as an integrating technology that brings together its various data access, visualization, and discovery services as well as its overall metadata management workflows. While providing an enhanced web-based interface for more integrated human-to-machine discovery and access, the deployment also enables NODC for the first time to support a robust set of machine-to-machine discovery services such as the Catalog Service for the Web (CS/W), OpenSearch, and Search and Retrieval via URL (SRU) . This approach allows NODC

  10. Improved molecular tools for sugar cane biotechnology.

    Science.gov (United States)

    Kinkema, Mark; Geijskes, Jason; Delucca, Paulo; Palupe, Anthony; Shand, Kylie; Coleman, Heather D; Brinin, Anthony; Williams, Brett; Sainz, Manuel; Dale, James L

    2014-03-01

    Sugar cane is a major source of food and fuel worldwide. Biotechnology has the potential to improve economically-important traits in sugar cane as well as diversify sugar cane beyond traditional applications such as sucrose production. High levels of transgene expression are key to the success of improving crops through biotechnology. Here we describe new molecular tools that both expand and improve gene expression capabilities in sugar cane. We have identified promoters that can be used to drive high levels of gene expression in the leaf and stem of transgenic sugar cane. One of these promoters, derived from the Cestrum yellow leaf curling virus, drives levels of constitutive transgene expression that are significantly higher than those achieved by the historical benchmark maize polyubiquitin-1 (Zm-Ubi1) promoter. A second promoter, the maize phosphonenolpyruvate carboxylate promoter, was found to be a strong, leaf-preferred promoter that enables levels of expression comparable to Zm-Ubi1 in this organ. Transgene expression was increased approximately 50-fold by gene modification, which included optimising the codon usage of the coding sequence to better suit sugar cane. We also describe a novel dual transcriptional enhancer that increased gene expression from different promoters, boosting expression from Zm-Ubi1 over eightfold. These molecular tools will be extremely valuable for the improvement of sugar cane through biotechnology.

  11. Higher plant transformation: principles and molecular tools.

    Science.gov (United States)

    Anami, Sylvester; Njuguna, Elizabeth; Coussens, Griet; Aesaert, Stijn; Van Lijsebettens, Mieke

    2013-01-01

    In higher plants, genetic transformation, which is part of the toolbox for the study of living organisms, had been reported only 30 years ago, boosting basic plant biology research, generating superior crops, and leading to the new discipline of plant biotechnology. Here, we review its principles and the corresponding molecular tools. In vitro regeneration, through somatic embryogenesis or organogenesis, is discussed because they are prerequisites for the subsequent Agrobacterium tumefaciens-mediated transferred (T)-DNA or direct DNA transfer methods to produce transgenic plants. Important molecular components of the T-DNA are examined, such as selectable marker genes that allow the selection of transformed cells in tissue cultures and are used to follow the gene of interest in the next generations, and reporter genes that have been developed to visualize promoter activities, protein localizations, and protein-protein interactions. Genes of interest are assembled with promoters and termination signals in Escherichia coli by means of GATEWAY-derived binary vectors that represent the current versatile cloning tools. Finally, future promising developments in transgene technology are considered.

  12. Can We Practically Bring Physics-based Modeling Into Operational Analytics Tools?

    Energy Technology Data Exchange (ETDEWEB)

    Granderson, Jessica [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Bonvini, Marco [Whisker Labs, Oakland, CA (United States); Piette, Mary Ann [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Page, Janie [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Lin, Guanjing [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Hu, R. Lilly [Univ. of California, Berkeley, CA (United States)

    2017-08-11

    We present that analytics software is increasingly used to improve and maintain operational efficiency in commercial buildings. Energy managers, owners, and operators are using a diversity of commercial offerings often referred to as Energy Information Systems, Fault Detection and Diagnostic (FDD) systems, or more broadly Energy Management and Information Systems, to cost-effectively enable savings on the order of ten to twenty percent. Most of these systems use data from meters and sensors, with rule-based and/or data-driven models to characterize system and building behavior. In contrast, physics-based modeling uses first-principles and engineering models (e.g., efficiency curves) to characterize system and building behavior. Historically, these physics-based approaches have been used in the design phase of the building life cycle or in retrofit analyses. Researchers have begun exploring the benefits of integrating physics-based models with operational data analytics tools, bridging the gap between design and operations. In this paper, we detail the development and operator use of a software tool that uses hybrid data-driven and physics-based approaches to cooling plant FDD and optimization. Specifically, we describe the system architecture, models, and FDD and optimization algorithms; advantages and disadvantages with respect to purely data-driven approaches; and practical implications for scaling and replicating these techniques. Finally, we conclude with an evaluation of the future potential for such tools and future research opportunities.

  13. The 13RC -- Bringing Together the Most Advanced Radiative Transfer Tools for Cloudy Atmospheres

    Energy Technology Data Exchange (ETDEWEB)

    Cahalan, Robert F.; Oreopoulos, L.; Marshak, A.; Evans, K. F.; Davis, Anthony B; Pincus, Robert M.; Yetzer, K. H.; Mayer, B.; Davies, Roger; Ackerman, Thomas P.; Barker, H. W.; Clothiaux, Eugene E.; Ellingson, Robert G.; Garay, Michael J.; Kassianov, Evgueni I.; Kinne, Stefan; Macke, Andreas; O' Hirok, William; Partain, Philip T.; Prigarin, Sergei M.; Rublev, Alexei N.; Stephens, Graeme L.; Szczap, Frederic; Takara, Ezra E.; Varnai, Tamas; Wen, Guoyong; Zhuravleva, Tatiana B.

    2005-09-01

    The interaction of clouds with solar and terrestrial radiation is one of the most important topics of climate research. In recent years it has been recognized that only full three-dimensional (3D) treatment of this interaction can provide answers to many climate and remote sensing problems, leading to worldwide development of numerous 3D radiative transfer (RT) codes. The international "Intercomparison of 3-Dimensional Radiation Codes," or I3RC, described in this paper, sprung from the natural need to compare the performance of these 3D RT codes used in a variety of current scientific work in the atmospheric sciences. I3RC supports intercomparison and development of both exact and approximate 3D methods in its effort to (1) understand and document the errors/limits of 3D algorithms and their sources; (2) provide "baseline" cases for future code development for 3D radiation; (3) promote sharing and production of 3D radiative tools; (4) derive guidelines for 3D radiative tool selection; and (5) improve atmospheric science education in 3D RT. Results from the two completed phases of I3RC have been presented in two workshops and are expected to guide improvements in both remote sensing and radiative energy budget calculations in cloudy atmospheres.

  14. [What do virtual reality tools bring to child and adolescent psychiatry?

    Science.gov (United States)

    Bioulac, S; de Sevin, E; Sagaspe, P; Claret, A; Philip, P; Micoulaud-Franchi, J A; Bouvard, M P

    2017-09-01

    Virtual reality is a relatively new technology that enables individuals to immerse themselves in a virtual world. It offers several advantages including a more realistic, lifelike environment that may allow subjects to "forget" they are being assessed, allow a better participation and an increased generalization of learning. Moreover, the virtual reality system can provide multimodal stimuli, such as visual and auditory stimuli, and can also be used to evaluate the patient's multimodal integration and to aid rehabilitation of cognitive abilities. The use of virtual reality to treat various psychiatric disorders in adults (phobic anxiety disorders, post-traumatic stress disorder, eating disorders, addictions…) and its efficacy is supported by numerous studies. Similar research for children and adolescents is lagging behind. This may be particularly beneficial to children who often show great interest and considerable success on computer, console or videogame tasks. This article will expose the main studies that have used virtual reality with children and adolescents suffering from psychiatric disorders. The use of virtual reality to treat anxiety disorders in adults is gaining popularity and its efficacy is supported by various studies. Most of the studies attest to the significant efficacy of the virtual reality exposure therapy (or in virtuo exposure). In children, studies have covered arachnophobia social anxiety and school refusal phobia. Despite the limited number of studies, results are very encouraging for treatment in anxiety disorders. Several studies have reported the clinical use of virtual reality technology for children and adolescents with autistic spectrum disorders (ASD). Extensive research has proven the efficiency of technologies as support tools for therapy. Researches are found to be focused on communication and on learning and social imitation skills. Virtual reality is also well accepted by subjects with ASD. The virtual environment offers

  15. USDA Regional Climate Hubs - Partnering to bring information and tools to managers of working lands

    Science.gov (United States)

    Johnson, R.

    2014-12-01

    In February 2014, USDA announced the location of seven Regional Hubs for Risk Adaptation and Mitigation to Climate Change (Climate Hubs) and three "Sub Hubs". The mission of these Climate Hubs is to develop and deliver science-based region-specific information and technologies to agricultural and natural resource managers that enable climate-smart decision-making and to direct land managers to USDA programs that can assist them in implementing those decisions. This mission is similar to that of Cooperative Extension and the Agricultural Experiment Stations (both of which benefit from USDA funding); therefore it is crucial that we partner with Land Grant Universities in order to achieve this mission. As USDA stands up these Climate Hubs we are working closely with USDA agencies, Land Grant Universities, other federal climate science programs, and other partners to determine how best to provide usable information and tools to farmers, ranchers and forest land managers to enable them to make climate-smart decisions.

  16. Diversity-dependence brings molecular phylogenies closer to agreement with the fossil record

    NARCIS (Netherlands)

    Etienne, Rampal S.; Haegeman, Bart; Stadler, Tanja; Aze, Tracy; Pearson, Paul N.; Purvis, Andy; Phillimore, Albert B.

    2012-01-01

    The branching times of molecular phylogenies allow us to infer speciation and extinction dynamics even when fossils are absent. Troublingly, phylogenetic approaches usually return estimates of zero extinction, conflicting with fossil evidence. Phylogenies and fossils do agree, however, that there

  17. Developing molecular tools for Chlamydomonas reinhardtii

    Science.gov (United States)

    Noor-Mohammadi, Samaneh

    Microalgae have garnered increasing interest over the years for their ability to produce compounds ranging from biofuels to neutraceuticals. A main focus of researchers has been to use microalgae as a natural bioreactor for the production of valuable and complex compounds. Recombinant protein expression in the chloroplasts of green algae has recently become more routine; however, the heterologous expression of multiple proteins or complete biosynthetic pathways remains a significant challenge. To take full advantage of these organisms' natural abilities, sophisticated molecular tools are needed to be able to introduce and functionally express multiple gene biosynthetic pathways in its genome. To achieve the above objective, we have sought to establish a method to construct, integrate and express multigene operons in the chloroplast and nuclear genome of the model microalgae Chlamydomonas reinhardtii. Here we show that a modified DNA Assembler approach can be used to rapidly assemble multiple-gene biosynthetic pathways in yeast and then integrate these assembled pathways at a site-specific location in the chloroplast, or by random integration in the nuclear genome of C. reinhardtii. As a proof of concept, this method was used to successfully integrate and functionally express up to three reporter proteins (AphA6, AadA, and GFP) in the chloroplast of C. reinhardtii and up to three reporter proteins (Ble, AphVIII, and GFP) in its nuclear genome. An analysis of the relative gene expression of the engineered strains showed significant differences in the mRNA expression levels of the reporter genes and thus highlights the importance of proper promoter/untranslated-region selection when constructing a target pathway. In addition, this work focuses on expressing the cofactor regeneration enzyme phosphite dehydrogenase (PTDH) in the chloroplast and nuclear genomes of C. reinhardtii. The PTDH enzyme converts phosphite into phosphate and NAD(P)+ into NAD(P)H. The reduced

  18. Application of molecular genetic tools for forest pathology

    Science.gov (United States)

    Mee-Sook Kim; John Hanna; Amy Ross-Davis; Ned Klopfenstein

    2012-01-01

    In recent years, advances in molecular genetics have provided powerful tools to address critical issues in forest pathology to help promote resilient forests. Although molecular genetic tools are initially applied to understand individual components of forest pathosystems, forest pathosystems involve dynamic interactions among biotic and abiotic components of the...

  19. Assessing Plant Genetic Diversity by Molecular Tools

    OpenAIRE

    Linda Mondini; Arshiya Noorani; Pagnotta, Mario A.

    2009-01-01

    This paper is an overview of the diverse, predominantly molecular techniques, used in assessing plant genetic diversity. In recent years, there has been a significant increase in the application of molecular genetic methods for assessing the conservation and use of plant genetic resources. Molecular techniques have been applied in the analysis of specific genes, as well as to increase understanding of gene action, generate genetic maps and assist in the development of gene transfer technologi...

  20. Molecular diagnostic tools targeting different taxonomic levels of ...

    African Journals Online (AJOL)

    Molecular diagnostic tools targeting different taxonomic levels of Xanthomonads aid in disease management. J Adriko, ER Mbega, RB Mabagala, CN Mortensen, EG Wulff, WK Tushemereirwe, J Kubiriba, OS Lund ...

  1. Assessing Plant Genetic Diversity by Molecular Tools

    Directory of Open Access Journals (Sweden)

    Linda Mondini

    2009-08-01

    Full Text Available This paper is an overview of the diverse, predominantly molecular techniques, used in assessing plant genetic diversity. In recent years, there has been a significant increase in the application of molecular genetic methods for assessing the conservation and use of plant genetic resources. Molecular techniques have been applied in the analysis of specific genes, as well as to increase understanding of gene action, generate genetic maps and assist in the development of gene transfer technologies. Molecular techniques have also had critical roles in studies of phylogeny and species evolution, and have been applied to increase our understanding of the distribution and extent of genetic variation within and between species. These techniques are well established and their advantages as well as limitations have been realized and described in this work. Recently, a new class of advanced techniques has emerged, primarily derived from a combination of earlier, more basic techniques. Advanced marker techniques tend to amalgamate advantageous features of several basic techniques, in order to increase the sensitivity and resolution to detect genetic discontinuity and distinctiveness. Some of the advanced marker techniques utilize newer classes of DNA elements, such as retrotransposons, mitochondrial and chloroplast based microsatellites, thereby revealing genetic variation through increased genome coverage. Techniques such as RAPD and AFLP are also being applied to cDNA-based templates to study patterns of gene expression and uncover the genetic basis of biological responses. The most important and recent advances made in molecular marker techniques are discussed in this review, along with their applications, advantages and limitations applied to plant sciences.

  2. Molecular Modeling: A Powerful Tool for Drug Design and Molecular ...

    Indian Academy of Sciences (India)

    gating, interpreting, explaining and discovering new phenom- ena. Like experimental chemistry, it is a skill-demanding sci- ence and must be learnt by doing and not just reading. Molecular modeling is easy to perform with currently available software, but the difficulty lies in getting the right model and proper interpretation.

  3. Advanced molecular tools for the identification of lactic acid bacteria

    NARCIS (Netherlands)

    Amor, Ben K.; Vaughan, E.E.; Vos, de W.M.

    2007-01-01

    Recent years have seen an explosion in the development and application of molecular tools for identifying microbes and analyzing their activity. These tools are increasingly applied to strains of lactic acid bacteria (LAB), including those used in fermentation and as well as those marketed as

  4. A Coupling Tool for Parallel Molecular Dynamics-Continuum Simulations

    KAUST Repository

    Neumann, Philipp

    2012-06-01

    We present a tool for coupling Molecular Dynamics and continuum solvers. It is written in C++ and is meant to support the developers of hybrid molecular - continuum simulations in terms of both realisation of the respective coupling algorithm as well as parallel execution of the hybrid simulation. We describe the implementational concept of the tool and its parallel extensions. We particularly focus on the parallel execution of particle insertions into dense molecular systems and propose a respective parallel algorithm. Our implementations are validated for serial and parallel setups in two and three dimensions. © 2012 IEEE.

  5. Aptamers as Valuable Molecular Tools in Neurosciences.

    Science.gov (United States)

    Wolter, Olga; Mayer, Günter

    2017-03-08

    Aptamers are short nucleic acids that interact with a variety of targets with high affinity and specificity. They have been shown to inhibit biological functions of cognate target proteins, and they are identifiable by an in vitro selection process, also termed SELEX (Systematic Evolution of Ligands by EXponential enrichment). Being nucleic acids, aptamers can be synthesized chemically or enzymatically. The latter renders RNA aptamers compatible with the cell's own transcription machinery and, thus, expressable inside cells. The synthesis of aptamers by chemical approaches opens up the possibility of producing aptamers on a large scale and enables a straightforward access to introduce modifications in a site-specific manner (e.g., fluorophores or photo-labile groups). These characteristics make aptamers broadly applicable (e.g., as an analytical, diagnostic, or separation tool). In this TechSight, we provide a brief overview on aptamer technology and the potential of aptamers as valuable research tools in neurosciences. Copyright © 2017 the authors 0270-6474/17/372517-07$15.00/0.

  6. VCMM: a visual tool for continuum molecular modeling.

    Science.gov (United States)

    Bai, Shiyang; Lu, Benzhuo

    2014-05-01

    This paper describes the design and function of a visualization tool, VCMM, for visualizing and analyzing data, and interfacing solvers for generic continuum molecular modeling. In particular, an emphasis of the program is to treat the data set based on unstructured mesh as used in finite/boundary element simulations, which largely enhances the capabilities of current visualization tools in this area that only support structured mesh. VCMM is segmented into molecular, meshing and numerical modules. The capabilities of molecular module include molecular visualization and force field assignment. Meshing module contains mesh generation, analysis and visualization tools. Numerical module currently provides a few finite/boundary element solvers of continuum molecular modeling, and contains several common visualization tools for the numerical result such as line and plane interpolations, surface probing, volume rendering and stream rendering. Three modules can exchange data with each other and carry out a complete process of modeling. Interfaces are also designed in order to facilitate usage of other mesh generation tools and numerical solvers. We develop a technique to accelerate data retrieval and have combined many graphical techniques in visualization. VCMM is highly extensible, and users can obtain more powerful functions by introducing relevant plug-ins. VCMM can also be useful in other fields such as computational quantum chemistry, image processing, and material science. Copyright © 2014 Elsevier Inc. All rights reserved.

  7. DockingShop: A Tool for Interactive Molecular Docking

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Ting-Cheng; Max, Nelson L.; Ding, Jinhui; Bethel, E. Wes; Crivelli, Silvia N.

    2005-04-24

    Given two independently determined molecular structures, the molecular docking problem predicts the bound association, or best fit between them, while allowing for conformational changes of the individual molecules during construction of a molecular complex. Docking Shop is an integrated environment that permits interactive molecular docking by navigating a ligand or protein to an estimated binding site of a receptor with real-time graphical feedback of scoring factors as visual guides. Our program can be used to create initial configurations for a protein docking prediction process. Its output--the structure of aprotein-ligand or protein-protein complex--may serve as an input for aprotein docking algorithm, or an optimization process. This tool provides molecular graphics interfaces for structure modeling, interactive manipulation, navigation, optimization, and dynamic visualization to aid users steer the prediction process using their biological knowledge.

  8. How to Train a Cell-Cutting-Edge Molecular Tools.

    Science.gov (United States)

    Czapiński, Jakub; Kiełbus, Michał; Kałafut, Joanna; Kos, Michał; Stepulak, Andrzej; Rivero-Müller, Adolfo

    2017-01-01

    In biological systems, the formation of molecular complexes is the currency for all cellular processes. Traditionally, functional experimentation was targeted to single molecular players in order to understand its effects in a cell or animal phenotype. In the last few years, we have been experiencing rapid progress in the development of ground-breaking molecular biology tools that affect the metabolic, structural, morphological, and (epi)genetic instructions of cells by chemical, optical (optogenetic) and mechanical inputs. Such precise dissection of cellular processes is not only essential for a better understanding of biological systems, but will also allow us to better diagnose and fix common dysfunctions. Here, we present several of these emerging and innovative techniques by providing the reader with elegant examples on how these tools have been implemented in cells, and, in some cases, organisms, to unravel molecular processes in minute detail. We also discuss their advantages and disadvantages with particular focus on their translation to multicellular organisms for in vivo spatiotemporal regulation. We envision that further developments of these tools will not only help solve the processes of life, but will give rise to novel clinical and industrial applications.

  9. How to Train a Cell - Cutting-Edge Molecular Tools

    Science.gov (United States)

    Czapiński, Jakub; Kiełbus, Michał; Kałafut, Joanna; Kos, Michał; Stepulak, Andrzej; Rivero-Müller, Adolfo

    2017-03-01

    In biological systems, the formation of molecular complexes is the currency for all cellular processes. Traditionally, functional experimentation was targeted to single molecular players in order to understand its effects in a cell or animal phenotype. In the last few years, we have been experiencing rapid progress in the development of ground-breaking molecular biology tools that affect the metabolic, structural, morphological, and (epi)genetic instructions of cells by chemical, optical (optogenetic) and mechanical inputs. Such precise dissection of cellular processes is not only essential for a better understanding of biological systems, but will also allow us to better diagnose and fix common dysfunctions. Here, we present several of these emerging and innovative techniques by providing the reader with elegant examples on how these tools have been implemented in cells, and, in some cases, organisms, to unravel molecular processes in minute detail. We also discuss their advantages and disadvantages with particular focus on their translation to multicellular organisms for in vivo spatiotemporal regulation. We envision that further developments of these tools will not only help solve the processes of life, but will give rise to novel clinical and industrial applications.

  10. MIMO: an efficient tool for molecular interaction maps overlap

    Science.gov (United States)

    2013-01-01

    Background Molecular pathways represent an ensemble of interactions occurring among molecules within the cell and between cells. The identification of similarities between molecular pathways across organisms and functions has a critical role in understanding complex biological processes. For the inference of such novel information, the comparison of molecular pathways requires to account for imperfect matches (flexibility) and to efficiently handle complex network topologies. To date, these characteristics are only partially available in tools designed to compare molecular interaction maps. Results Our approach MIMO (Molecular Interaction Maps Overlap) addresses the first problem by allowing the introduction of gaps and mismatches between query and template pathways and permits -when necessary- supervised queries incorporating a priori biological information. It then addresses the second issue by relying directly on the rich graph topology described in the Systems Biology Markup Language (SBML) standard, and uses multidigraphs to efficiently handle multiple queries on biological graph databases. The algorithm has been here successfully used to highlight the contact point between various human pathways in the Reactome database. Conclusions MIMO offers a flexible and efficient graph-matching tool for comparing complex biological pathways. PMID:23672344

  11. Leveling the playing field: Bringing development of biomarkers and molecular diagnostics up to the standards for drug development

    NARCIS (Netherlands)

    G. Poste (George); I. Carbone; D.B. Parkinson (David); J. Verweij (Jaap); S.M. Hewitt (Stephen); J.M. Jessup (J. Milburn)

    2012-01-01

    textabstractMolecular diagnostics are becoming increasingly important in clinical research to stratify or identify molecularly profiled patient cohorts for targeted therapies, to modify the dose of a therapeutic, and to assess early response to therapy or monitor patients. Molecular diagnostics can

  12. A Kepler Workflow Tool for Reproducible AMBER GPU Molecular Dynamics.

    Science.gov (United States)

    Purawat, Shweta; Ieong, Pek U; Malmstrom, Robert D; Chan, Garrett J; Yeung, Alan K; Walker, Ross C; Altintas, Ilkay; Amaro, Rommie E

    2017-06-20

    With the drive toward high throughput molecular dynamics (MD) simulations involving ever-greater numbers of simulation replicates run for longer, biologically relevant timescales (microseconds), the need for improved computational methods that facilitate fully automated MD workflows gains more importance. Here we report the development of an automated workflow tool to perform AMBER GPU MD simulations. Our workflow tool capitalizes on the capabilities of the Kepler platform to deliver a flexible, intuitive, and user-friendly environment and the AMBER GPU code for a robust and high-performance simulation engine. Additionally, the workflow tool reduces user input time by automating repetitive processes and facilitates access to GPU clusters, whose high-performance processing power makes simulations of large numerical scale possible. The presented workflow tool facilitates the management and deployment of large sets of MD simulations on heterogeneous computing resources. The workflow tool also performs systematic analysis on the simulation outputs and enhances simulation reproducibility, execution scalability, and MD method development including benchmarking and validation. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  13. AC-ELECTROKINETICS BASED TOOLS IN NANOENGINEERING AND MOLECULAR ELECTRONICS

    Directory of Open Access Journals (Sweden)

    R. Durán

    2005-08-01

    Full Text Available Slllcon-based mlcroeledronics has been following the integration prognosls of MOORE's Law durlng the past decades and posslbly will do so for another decade or two. Physlcal, technological and also flnancialllmlts In the foreseeable future will slow down the contlnued expansiOn of this branch of mlcroeledronlcs and instead wlll force a new technological approach based on molecular-scale eledronics (MOLETRONICS. New tools are needed to allow molecular devlce manufaduring and nanoscale engineering with hlgh precision and produdivlty. One group of methods with the potentlal for use In such a manufaduring process Is based on a.c. eledrokinetlcs effeds, which are descrlbed and discussed in this paper.

  14. Modeling, methodologies and tools for molecular and nano-scale communications modeling, methodologies and tools

    CERN Document Server

    Nakano, Tadashi; Moore, Michael

    2017-01-01

    (Preliminary) The book presents the state of art in the emerging field of molecular and nanoscale communication. It gives special attention to fundamental models, and advanced methodologies and tools used in the field. It covers a wide range of applications, e.g. nanomedicine, nanorobot communication, bioremediation and environmental managements. It addresses advanced graduate students, academics and professionals working at the forefront in their fields and at the interfaces between different areas of research, such as engineering, computer science, biology and nanotechnology.

  15. Molecular tools for the construction of peptide-based materials.

    Science.gov (United States)

    Ramakers, B E I; van Hest, J C M; Löwik, D W P M

    2014-04-21

    Proteins and peptides are fundamental components of living systems where they play crucial roles at both functional and structural level. The versatile biological properties of these molecules make them interesting building blocks for the construction of bio-active and biocompatible materials. A variety of molecular tools can be used to fashion the peptides necessary for the assembly of these materials. In this tutorial review we shall describe five of the main techniques, namely solid phase peptide synthesis, native chemical ligation, Staudinger ligation, NCA polymerisation, and genetic engineering, that have been used to great effect for the construction of a host of peptide-based materials.

  16. Polymerase chain reaction: A molecular diagnostic tool in periodontology.

    Science.gov (United States)

    Maheaswari, Rajendran; Kshirsagar, Jaishree Tukaram; Lavanya, Nallasivam

    2016-01-01

    This review discusses the principles of polymerase chain reaction (PCR) and its application as a diagnostic tool in periodontology. The relevant MEDLINE and PubMed indexed journals were searched manually and electronically by typing PCR, applications of PCR, PCR in periodontics, polymorphism studies in periodontitis, and molecular techniques in periodontology. The searches were limited to articles in English language and the articles describing PCR process and its relation to periodontology were collected and used to prepare a concise review. PCR has now become a standard diagnostic and research tool in periodontology. Various studies reveal that its sensitivity and specificity allow it as a rapid, efficient method of detecting, identifying, and quantifying organism. Different immune and inflammatory markers can be identified at the mRNA expression level, and also the determination of genetic polymorphisms, thus providing the deeper insight into the mechanisms underlying the periodontal disease.

  17. Polymerase chain reaction: A molecular diagnostic tool in periodontology

    Directory of Open Access Journals (Sweden)

    Rajendran Maheaswari

    2016-01-01

    Full Text Available This review discusses the principles of polymerase chain reaction (PCR and its application as a diagnostic tool in periodontology. The relevant MEDLINE and PubMed indexed journals were searched manually and electronically by typing PCR, applications of PCR, PCR in periodontics, polymorphism studies in periodontitis, and molecular techniques in periodontology. The searches were limited to articles in English language and the articles describing PCR process and its relation to periodontology were collected and used to prepare a concise review. PCR has now become a standard diagnostic and research tool in periodontology. Various studies reveal that its sensitivity and specificity allow it as a rapid, efficient method of detecting, identifying, and quantifying organism. Different immune and inflammatory markers can be identified at the mRNA expression level, and also the determination of genetic polymorphisms, thus providing the deeper insight into the mechanisms underlying the periodontal disease.

  18. [Tools of molecular biology, what can be expected from them?].

    Science.gov (United States)

    Delpech, M

    1993-01-01

    The techniques of molecular biology represent a new tool for research and diagnosis. They have been used routinely since the middle 80s. The first applications were mainly in hereditary diseases. These techniques investigated an information and not direct biological activity and so new strategies had to be developed. Two techniques have played key roles. They are Southern's method which enables the detection of specific sequences among DNA fragments in any individual within a few days, and the method of in vitro selective amplification (PCR) which is the equivalent of cloning a sequence of several hundred pairs of bases in any individual in less than 3 hours. In hereditary diseases, molecular biological techniques enable diagnosis of the genetic abnormality responsible for the condition, even when the defect is not known. To this end, two strategies are available. The first, and the most satisfactory, is the direct strategy of characterising the genetic defect itself. This is possible when the mutation is a major alteration of the DNA molecule such as a deletion, an insertion or a recombination or when the mutation is isolated and known. In other cases, an indirect approach may be used which consists of determining whether the subject has received normal or defective chromosomes from his or her parents. The identification of good or bad chromosomes is based on the study of DNA markers: polymorphism. The indirect strategy can only be used under certain conditions: presence of an index case, informativity of polymorphisms, complete family study.(ABSTRACT TRUNCATED AT 250 WORDS)

  19. Development and application of camelid molecular cytogenetic tools.

    Science.gov (United States)

    Avila, Felipe; Das, Pranab J; Kutzler, Michelle; Owens, Elaine; Perelman, Polina; Rubes, Jiri; Hornak, Miroslav; Johnson, Warren E; Raudsepp, Terje

    2014-01-01

    Cytogenetic chromosome maps offer molecular tools for genome analysis and clinical cytogenetics and are of particular importance for species with difficult karyotypes, such as camelids (2n = 74). Building on the available human-camel zoo-fluorescence in situ hybridization (FISH) data, we developed the first cytogenetic map for the alpaca (Lama pacos, LPA) genome by isolating and identifying 151 alpaca bacterial artificial chromosome (BAC) clones corresponding to 44 specific genes. The genes were mapped by FISH to 31 alpaca autosomes and the sex chromosomes; 11 chromosomes had 2 markers, which were ordered by dual-color FISH. The STS gene mapped to Xpter/Ypter, demarcating the pseudoautosomal region, whereas no markers were assigned to chromosomes 14, 21, 22, 28, and 36. The chromosome-specific markers were applied in clinical cytogenetics to identify LPA20, the major histocompatibility complex (MHC)-carrying chromosome, as a part of an autosomal translocation in a sterile male llama (Lama glama, LGL; 2n = 73,XY). FISH with LPAX BACs and LPA36 paints, as well as comparative genomic hybridization, were also used to investigate the origin of the minute chromosome, an abnormally small LPA36 in infertile female alpacas. This collection of cytogenetically mapped markers represents a new tool for camelid clinical cytogenetics and has applications for the improvement of the alpaca genome map and sequence assembly. © The American Genetic Association. 2012. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  20. Molecular tools for gene manipulation in filamentous fungi.

    Science.gov (United States)

    Wang, Shunxian; Chen, Haiqin; Tang, Xin; Zhang, Hao; Chen, Wei; Chen, Yong Q

    2017-11-01

    Functional genomics of filamentous fungi has gradually uncovered gene information for constructing 'cell factories' and controlling pathogens. Available gene manipulation methods of filamentous fungi include random integration methods, gene targeting technology, gene editing with artificial nucleases and RNA technology. This review describes random gene integration constructed by restriction enzyme-mediated integration (REMI); Agrobacterium-mediated transformation (AMT); transposon-arrayed gene knockout (TAGKO); gene targeting technology, mainly about homologous recombination; and modern gene editing strategies containing transcription activator-like effector nucleases (TALENs) and a clustered regularly interspaced short palindromic repeat/associated protein system (CRISPR/Cas) developed in filamentous fungi and RNA technology including RNA interference (RNAi) and ribozymes. This review describes historical and modern gene manipulation methods in filamentous fungi and presents the molecular tools available to researchers investigating filamentous fungi. The biggest difference of this review from the previous ones is the addition of successful application and details of the promising gene editing tool CRISPR/Cas9 system in filamentous fungi.

  1. Development and Application of Camelid Molecular Cytogenetic Tools

    Science.gov (United States)

    Avila, Felipe; Das, Pranab J.; Kutzler, Michelle; Owens, Elaine; Perelman, Polina; Rubes, Jiri; Hornak, Miroslav; Johnson, Warren E.

    2014-01-01

    Cytogenetic chromosome maps offer molecular tools for genome analysis and clinical cytogenetics and are of particular importance for species with difficult karyotypes, such as camelids (2n = 74). Building on the available human–camel zoo-fluorescence in situ hybridization (FISH) data, we developed the first cytogenetic map for the alpaca (Lama pacos, LPA) genome by isolating and identifying 151 alpaca bacterial artificial chromosome (BAC) clones corresponding to 44 specific genes. The genes were mapped by FISH to 31 alpaca autosomes and the sex chromosomes; 11 chromosomes had 2 markers, which were ordered by dual-color FISH. The STS gene mapped to Xpter/Ypter, demarcating the pseudoautosomal region, whereas no markers were assigned to chromosomes 14, 21, 22, 28, and 36. The chromosome-specific markers were applied in clinical cytogenetics to identify LPA20, the major histocompatibility complex (MHC)-carrying chromosome, as a part of an autosomal translocation in a sterile male llama (Lama glama, LGL; 2n = 73,XY). FISH with LPAX BACs and LPA36 paints, as well as comparative genomic hybridization, were also used to investigate the origin of the minute chromosome, an abnormally small LPA36 in infertile female alpacas. This collection of cytogenetically mapped markers represents a new tool for camelid clinical cytogenetics and has applications for the improvement of the alpaca genome map and sequence assembly. PMID:23109720

  2. Improving molecular tools for global surveillance of measles virus.

    Science.gov (United States)

    Bankamp, Bettina; Byrd-Leotis, Lauren A; Lopareva, Elena N; Woo, Gibson K S; Liu, Chunyu; Jee, Youngmee; Ahmed, Hinda; Lim, Wilina W; Ramamurty, Nalini; Mulders, Mick N; Featherstone, David; Bellini, William J; Rota, Paul A

    2013-09-01

    The genetic characterization of wild-type measles viruses plays an important role in the description of viral transmission pathways and the verification of measles elimination. The 450 nucleotides that encode the carboxyl-terminus of the nucleoprotein (N-450) are routinely sequenced for genotype analysis. The objectives of this study were to develop improved primers and controls for RT-PCR reactions used for genotyping of measles samples and to develop a method to provide a convenient, safe, and inexpensive means to distribute measles RNA for RT-PCR assays and practice panels. A newly designed, genetically defined synthetic RNA and RNA isolated from cells infected with currently circulating genotypes were used to compare the sensitivity of primer pairs in RT-PCR and nested PCR. FTA® cards loaded with lysates of measles infected cells were tested for their ability to preserve viral RNA and destroy virus infectivity. A new primer pair, MeV216/MeV214, was able to amplify N-450 from viruses representing 10 currently circulating genotypes and a genotype A vaccine strain and demonstrated 100-fold increased sensitivity compared to the previously used primer set. A nested PCR assay further increased the sensitivity of detection from patient samples. A synthetic positive control RNA was developed that produced PCR products that are distinguishable by size from PCR products amplified from clinical samples. FTA® cards completely inactivated measles virus and stabilized RNA for at least six months. These improved molecular tools will advance molecular characterization of circulating measles viruses globally and provide enhanced quality control measures. Published by Elsevier B.V.

  3. Molecular Tools for the Detection of Nitrogen Cycling Archaea

    Directory of Open Access Journals (Sweden)

    Antje Rusch

    2013-01-01

    Full Text Available Archaea are widespread in extreme and temperate environments, and cultured representatives cover a broad spectrum of metabolic capacities, which sets them up for potentially major roles in the biogeochemistry of their ecosystems. The detection, characterization, and quantification of archaeal functions in mixed communities require Archaea-specific primers or probes for the corresponding metabolic genes. Five pairs of degenerate primers were designed to target archaeal genes encoding key enzymes of nitrogen cycling: nitrite reductases NirA and NirB, nitrous oxide reductase (NosZ, nitrogenase reductase (NifH, and nitrate reductases NapA/NarG. Sensitivity towards their archaeal target gene, phylogenetic specificity, and gene specificity were evaluated in silico and in vitro. Owing to their moderate sensitivity/coverage, the novel nirB-targeted primers are suitable for pure culture studies only. The nirA-targeted primers showed sufficient sensitivity and phylogenetic specificity, but poor gene specificity. The primers designed for amplification of archaeal nosZ performed well in all 3 criteria; their discrimination against bacterial homologs appears to be weakened when Archaea are strongly outnumbered by bacteria in a mixed community. The novel nifH-targeted primers showed high sensitivity and gene specificity, but failed to discriminate against bacterial homologs. Despite limitations, 4 of the new primer pairs are suitable tools in several molecular methods applied in archaeal ecology.

  4. Earth Exploration Toolbook Workshops: Web-Conferencing and Teleconferencing Professional Development Bringing Earth Science Data Analysis and Visualization Tools to K-12 Teachers and Students

    Science.gov (United States)

    McAuliffe, C.; Ledley, T.

    2008-12-01

    our participants reported that they have not tried to locate a teaching resource in DLESE and forty-eight percent report that they have not to locate a teaching resource in NSDL. As part of an EET Data Analysis workshop, teachers actively visit both digital libraries. Virtual workshops using Web conferencing and teleconferencing are an effective and convenient way to deliver professional development that brings teachers from all over the nation together to learn new technology. Teachers report that the step-by-step facilitation along with the ability to ask questions and interact with their peers are some of the most useful aspects of the workshop. In this presentation, we will share successes and challenges of teachers as they implement these Earth science data analysis and visualization tools in their classrooms.

  5. Molecular tools for the identification of Tuber melanosporum in agroindustry.

    Science.gov (United States)

    Séjalon-Delmas, N; Roux, C; Martins, M; Kulifaj, M; Bécard, G; Dargent, R

    2000-06-01

    Tuber melanosporum Vitt., Tuber magnatum Pico, and Tuber uncinatum Chat. can be differentiated by their morphological characters. Fraud problems have arisen recently with the importation to Europe of truffles from China. T. melanosporum is morphologically very close, but distinct from the Chinese species [Tuber indicum (Cooke and Massee) and T. himalayense BC (Zhang and Winter)]. We have optimized molecular tools to unequivocally identify T. melanosporum. DNA extraction from ascocarps of black truffles is not straightforward. Problems to obtain pure DNA are due to high contents of phenolic compounds, melanine, and various polymers (proteins, polysaccharides, etc). These compounds coprecipitate with the DNA during extraction and strongly inhibit the PCR reaction. We have developed an efficient and reliable protocol for DNA extraction from truffle ascocarps. It was used successfully for DNA extraction from mycorrhizal root tips as well as from canned preparations of T. melanosporum. Several approaches to identify T. melanosporum by PCR were developed. Two specific primers for T. melanosporum were designed after comparison of the ITS region of this species with those of three Chinese fungi. They proved to be efficient to specifically detect the presence of T. melanosporum by PCR. The mycorrhizal status of trees inoculated with T. melanosporum but unable to produce truffles was confirmed in a single-step PCR reaction. A multiplex PCR approach was also developed with three sets of primers (including a specific one for Chinese truffles) to detect, in one PCR reaction, the presence of any other Tuber species mixed with T. melanosporum ascocarps. This optimized protocol, in association with the specific primers we designed, is applicable to quality control in the truffle industry from the production stages to final commercial products.

  6. Molecular beacon – tool for real time studying gene activity in stem cells

    DEFF Research Database (Denmark)

    Ilieva, Mirolyuba; Dufva, Martin

    and cancerogenesis. Molecular beacon technology is based on fluorescence resonance energy transfer (FRET) and the complementary pairing principles. These fluorescent molecular probes are highly specific and sensitive and are one important tool in in vitro diagnostics. Here molecular beacons are used to follow...

  7. Polymerase chain reaction: A molecular diagnostic tool in periodontology

    National Research Council Canada - National Science Library

    Maheaswari, Rajendran; Kshirsagar, Jaishree Tukaram; Lavanya, Nallasivam

    2016-01-01

    ..., and molecular techniques in periodontology. The searches were limited to articles in English language and the articles describing PCR process and its relation to periodontology were collected and used to prepare a concise review...

  8. Bringing reality into the classroom

    NARCIS (Netherlands)

    Heck, A.

    2009-01-01

    Technology offers ample opportunities to bring reality into the classroom. Students and teachers nowadays have many tools to work in an authentic way with real data in mathematics and science education. However, much research and development are still needed to create a consistent learning

  9. Spherical molecularly imprinted polymer particles : A promising tool for molecular recognition in capillary electrokinetic separations

    NARCIS (Netherlands)

    de Boer, T; Mol, R; de Zeeuw, RA; de Jong, GJ; Sherrington, DC; Cormack, PAG; Ensing, K

    Spherical molecularly imprinted polymer particles obtained via precipitation polymerization, were introduced as a pseudostationary phase in capillary electrophoresis (CE) to study molecular recognition. Analyses were performed via a partial filling technique using (+)-ephedrine-imprinted

  10. Biomimetic molecular design tools that learn, evolve, and adapt.

    Science.gov (United States)

    Winkler, David A

    2017-01-01

    A dominant hallmark of living systems is their ability to adapt to changes in the environment by learning and evolving. Nature does this so superbly that intensive research efforts are now attempting to mimic biological processes. Initially this biomimicry involved developing synthetic methods to generate complex bioactive natural products. Recent work is attempting to understand how molecular machines operate so their principles can be copied, and learning how to employ biomimetic evolution and learning methods to solve complex problems in science, medicine and engineering. Automation, robotics, artificial intelligence, and evolutionary algorithms are now converging to generate what might broadly be called in silico-based adaptive evolution of materials. These methods are being applied to organic chemistry to systematize reactions, create synthesis robots to carry out unit operations, and to devise closed loop flow self-optimizing chemical synthesis systems. Most scientific innovations and technologies pass through the well-known "S curve", with slow beginning, an almost exponential growth in capability, and a stable applications period. Adaptive, evolving, machine learning-based molecular design and optimization methods are approaching the period of very rapid growth and their impact is already being described as potentially disruptive. This paper describes new developments in biomimetic adaptive, evolving, learning computational molecular design methods and their potential impacts in chemistry, engineering, and medicine.

  11. Biomimetic molecular design tools that learn, evolve, and adapt

    Directory of Open Access Journals (Sweden)

    David A Winkler

    2017-06-01

    Full Text Available A dominant hallmark of living systems is their ability to adapt to changes in the environment by learning and evolving. Nature does this so superbly that intensive research efforts are now attempting to mimic biological processes. Initially this biomimicry involved developing synthetic methods to generate complex bioactive natural products. Recent work is attempting to understand how molecular machines operate so their principles can be copied, and learning how to employ biomimetic evolution and learning methods to solve complex problems in science, medicine and engineering. Automation, robotics, artificial intelligence, and evolutionary algorithms are now converging to generate what might broadly be called in silico-based adaptive evolution of materials. These methods are being applied to organic chemistry to systematize reactions, create synthesis robots to carry out unit operations, and to devise closed loop flow self-optimizing chemical synthesis systems. Most scientific innovations and technologies pass through the well-known “S curve”, with slow beginning, an almost exponential growth in capability, and a stable applications period. Adaptive, evolving, machine learning-based molecular design and optimization methods are approaching the period of very rapid growth and their impact is already being described as potentially disruptive. This paper describes new developments in biomimetic adaptive, evolving, learning computational molecular design methods and their potential impacts in chemistry, engineering, and medicine.

  12. Biomimetic molecular design tools that learn, evolve, and adapt

    Science.gov (United States)

    2017-01-01

    A dominant hallmark of living systems is their ability to adapt to changes in the environment by learning and evolving. Nature does this so superbly that intensive research efforts are now attempting to mimic biological processes. Initially this biomimicry involved developing synthetic methods to generate complex bioactive natural products. Recent work is attempting to understand how molecular machines operate so their principles can be copied, and learning how to employ biomimetic evolution and learning methods to solve complex problems in science, medicine and engineering. Automation, robotics, artificial intelligence, and evolutionary algorithms are now converging to generate what might broadly be called in silico-based adaptive evolution of materials. These methods are being applied to organic chemistry to systematize reactions, create synthesis robots to carry out unit operations, and to devise closed loop flow self-optimizing chemical synthesis systems. Most scientific innovations and technologies pass through the well-known “S curve”, with slow beginning, an almost exponential growth in capability, and a stable applications period. Adaptive, evolving, machine learning-based molecular design and optimization methods are approaching the period of very rapid growth and their impact is already being described as potentially disruptive. This paper describes new developments in biomimetic adaptive, evolving, learning computational molecular design methods and their potential impacts in chemistry, engineering, and medicine. PMID:28694872

  13. Molecular Laser Spectroscopy as a Tool for Gas Analysis Applications

    Directory of Open Access Journals (Sweden)

    Javis Anyangwe Nwaboh

    2011-01-01

    Full Text Available We have used the traceable infrared laser spectrometric amount fraction measurement (TILSAM method to perform absolute concentration measurements of molecular species using three laser spectroscopic techniques. We report results performed by tunable diode laser absorption spectroscopy (TDLAS, quantum cascade laser absorption spectroscopy (QCLAS, and cavity ring down spectroscopy (CRDS, all based on the TILSAM methodology. The measured results of the different spectroscopic techniques are in agreement with respective gravimetric values, showing that the TILSAM method is feasible with all different techniques. We emphasize the data quality objectives given by traceability issues and uncertainty analyses.

  14. Molecular Beacons: Powerful Tools for Imaging RNA in Living Cells

    Directory of Open Access Journals (Sweden)

    Ricardo Monroy-Contreras

    2011-01-01

    Full Text Available Recent advances in RNA functional studies highlights the pivotal role of these molecules in cell physiology. Diverse methods have been implemented to measure the expression levels of various RNA species, using either purified RNA or fixed cells. Despite the fact that fixed cells offer the possibility to observe the spatial distribution of RNA, assays with capability to real-time monitoring RNA transport into living cells are needed to further understand the role of RNA dynamics in cellular functions. Molecular beacons (MBs are stem-loop hairpin-structured oligonucleotides equipped with a fluorescence quencher at one end and a fluorescent dye (also called reporter or fluorophore at the opposite end. This structure permits that MB in the absence of their target complementary sequence do not fluoresce. Upon binding to targets, MBs emit fluorescence, due to the spatial separation of the quencher and the reporter. Molecular beacons are promising probes for the development of RNA imaging techniques; nevertheless much work remains to be done in order to obtain a robust technology for imaging various RNA molecules together in real time and in living cells. The present work concentrates on the different requirements needed to use successfully MB for cellular studies, summarizing recent advances in this area.

  15. DNA barcoding: A molecular tool to identify Antarctic marine larvae

    Science.gov (United States)

    Webb, Karen E.; Barnes, David K. A.; Clark, Melody S.; Bowden, David A.

    2006-04-01

    To begin to understand overall patterns and processes influencing marine populations, communities and ecosystems, it is important to determine the timing, duration, mode and dispersal of larvae. However, few studies of the spatial and temporal variation in abundance of larvae have been undertaken at any locality, other than for a few commercially important species. In Antarctic seas the abundance and species-richness of marine larvae are key to a number of concepts (such as the validity of Thorson's rule and ecological versus evolutionary success of brooders compared to spawning species). Traditionally, marine larval identification (using microscopy), even to order level, is a time-consuming, labour-intensive and inexact process. Ontogenic changes during larval life make identification difficult and require high levels of expertise, and identification is generally confirmed only by laboratory spawning experiments. New molecular genetic methods enable faster direct identification of marine larvae to a higher resolution. Our preliminary results show that it is possible to identify larvae of Antarctic species using DNA barcoding techniques, but that the resolution is currently limited by the availability of comparative adult sequences in the DNA sequence databases.

  16. Gel Scramble: An E-Tool for Teaching Molecular Neuroscience.

    Science.gov (United States)

    Grisham, William; Keller, Lani; Schottler, Natalie

    2015-01-01

    In this completely digital teaching module, students interpret the results of two separate procedures: a restriction endonuclease digestion, and a polymerase chain reaction (PCR). The first consists of matching restriction endonuclease digest protocols with images obtained from stained agarose gels. Students are given the sequence of six plasmid cDNAs, characteristics of the plasmid vector, and the endonuclease digest protocols, which specify the enzyme(s) used. Students calculate the expected lengths of digestion products using this information and free tools available on the web. Students learn how to read gels and then match their predicted fragment lengths to the digital images obtained from the gel electrophoresis of the cDNA digest. In the PCR experiment, students are given six cDNA sequences and six sets of primers. By querying NCBI BLAST, students can match the PCR fragments to the lengths of the predicted in silico PCR products. The ruse posed to students is that the gels were inadvertently mislabeled during processing. Although students know the experimental details, they do not know which gel goes with a given restriction endonuclease digest or PCR-they must deduce the answers. Because the gel images are from actual students' experiments, the data sometimes result from mishandling/mislabeling or faulty protocol execution. The most challenging part of the exercise is to explain these errors. This latter aspect requires students to use critical thinking skills to explain aberrant outcomes. This entire exercise is available in a digital format and downloadable for free at http://mdcune.psych.ucla.edu/modules/gel.

  17. AMMOS: Automated Molecular Mechanics Optimization tool for in silico Screening

    Science.gov (United States)

    Pencheva, Tania; Lagorce, David; Pajeva, Ilza; Villoutreix, Bruno O; Miteva, Maria A

    2008-01-01

    Background Virtual or in silico ligand screening combined with other computational methods is one of the most promising methods to search for new lead compounds, thereby greatly assisting the drug discovery process. Despite considerable progresses made in virtual screening methodologies, available computer programs do not easily address problems such as: structural optimization of compounds in a screening library, receptor flexibility/induced-fit, and accurate prediction of protein-ligand interactions. It has been shown that structural optimization of chemical compounds and that post-docking optimization in multi-step structure-based virtual screening approaches help to further improve the overall efficiency of the methods. To address some of these points, we developed the program AMMOS for refining both, the 3D structures of the small molecules present in chemical libraries and the predicted receptor-ligand complexes through allowing partial to full atom flexibility through molecular mechanics optimization. Results The program AMMOS carries out an automatic procedure that allows for the structural refinement of compound collections and energy minimization of protein-ligand complexes using the open source program AMMP. The performance of our package was evaluated by comparing the structures of small chemical entities minimized by AMMOS with those minimized with the Tripos and MMFF94s force fields. Next, AMMOS was used for full flexible minimization of protein-ligands complexes obtained from a mutli-step virtual screening. Enrichment studies of the selected pre-docked complexes containing 60% of the initially added inhibitors were carried out with or without final AMMOS minimization on two protein targets having different binding pocket properties. AMMOS was able to improve the enrichment after the pre-docking stage with 40 to 60% of the initially added active compounds found in the top 3% to 5% of the entire compound collection. Conclusion The open source AMMOS

  18. SNPs ANALYSIS AS A TOOL IN MOLECULAR GENETICS DIAGNOSTICS

    Directory of Open Access Journals (Sweden)

    Dewi Rusnita

    2015-05-01

    arrays is its ability in detecting low level mosaicism which was unidentified by conventional cytogenetic examination. Nowadays, SNP arrays are included in IVF process to obtain a healthy baby. It can be done by detecting the absence or the presence of disease-causing single gene in an embryo before it implanted to the womb. SNP analysis with SNP array has many advantages over other SNP analysis methods and is therefore expected can be widely used in the future in the field of molecular diagnostic.

  19. Feasibility of the "Bring Your Own Device" Model in Clinical Research: Results from a Randomized Controlled Pilot Study of a Mobile Patient Engagement Tool.

    Science.gov (United States)

    Pugliese, Laura; Woodriff, Molly; Crowley, Olga; Lam, Vivian; Sohn, Jeremy; Bradley, Scott

    2016-03-16

    Rising rates of smartphone ownership highlight opportunities for improved mobile application usage in clinical trials. While current methods call for device provisioning, the "bring your own device" (BYOD) model permits participants to use personal phones allowing for improved patient engagement and lowered operational costs. However, more evidence is needed to demonstrate the BYOD model's feasibility in research settings. To assess if CentrosHealth, a mobile application designed to support trial compliance, produces different outcomes in medication adherence and application engagement when distributed through study-provisioned devices compared to the BYOD model. 87 participants were randomly selected to use the mobile application or no intervention for a 28-day pilot study at a 2:1 randomization ratio (2 intervention: 1 control) and asked to consume a twice-daily probiotic supplement. The application users were further randomized into two groups: receiving the application on a personal "BYOD" or study-provided smartphone. In-depth interviews were performed in a randomly-selected subset of the intervention group (five BYOD and five study-provided smartphone users). The BYOD subgroup showed significantly greater engagement than study-provided phone users, as shown by higher application use frequency and duration over the study period. The BYOD subgroup also demonstrated a significant effect of engagement on medication adherence for number of application sessions (unstandardized regression coefficient beta=0.0006, p=0.02) and time spent therein (beta=0.00001, p=0.03). Study-provided phone users showed higher initial adherence rates, but greater decline (5.7%) than BYOD users (0.9%) over the study period. In-depth interviews revealed that participants preferred the BYOD model over using study-provided devices. Results indicate that the BYOD model is feasible in health research settings and improves participant experience, calling for further BYOD model validity

  20. Feasibility of the “Bring Your Own Device” Model in Clinical Research: Results from a Randomized Controlled Pilot Study of a Mobile Patient Engagement Tool

    Science.gov (United States)

    Pugliese, Laura; Woodriff, Molly; Crowley, Olga; Sohn, Jeremy; Bradley, Scott

    2016-01-01

    Background Rising rates of smartphone ownership highlight opportunities for improved mobile application usage in clinical trials. While current methods call for device provisioning, the "bring your own device” (BYOD) model permits participants to use personal phones allowing for improved patient engagement and lowered operational costs. However, more evidence is needed to demonstrate the BYOD model’s feasibility in research settings. Objective To assess if CentrosHealth, a mobile application designed to support trial compliance, produces different outcomes in medication adherence and application engagement when distributed through study-provisioned devices compared to the BYOD model. Methods 87 participants were randomly selected to use the mobile application or no intervention for a 28-day pilot study at a 2:1 randomization ratio (2 intervention: 1 control) and asked to consume a twice-daily probiotic supplement. The application users were further randomized into two groups: receiving the application on a personal "BYOD” or study-provided smartphone. In-depth interviews were performed in a randomly-selected subset of the intervention group (five BYOD and five study-provided smartphone users). Results The BYOD subgroup showed significantly greater engagement than study-provided phone users, as shown by higher application use frequency and duration over the study period. The BYOD subgroup also demonstrated a significant effect of engagement on medication adherence for number of application sessions (unstandardized regression coefficient beta=0.0006, p=0.02) and time spent therein (beta=0.00001, p=0.03). Study-provided phone users showed higher initial adherence rates, but greater decline (5.7%) than BYOD users (0.9%) over the study period. In-depth interviews revealed that participants preferred the BYOD model over using study-provided devices.  Conclusions Results indicate that the BYOD model is feasible in health research settings and improves participant

  1. Tools to Analyze Morphology and Spatially Mapped Molecular Data | Informatics Technology for Cancer Research (ITCR)

    Science.gov (United States)

    This project is to develop, deploy, and disseminate a suite of open source tools and integrated informatics platform that will facilitate multi-scale, correlative analyses of high resolution whole slide tissue image data, spatially mapped genetics and molecular data for cancer research. This platform will play an essential role in supporting studies of tumor initiation, development, heterogeneity, invasion, and metastasis.

  2. Practice variability in management of acute respiratory distress syndrome: bringing evidence and clinician education to the bedside using a web-based teaching tool.

    Science.gov (United States)

    Belda, Thomas E; Gajic, Ognjen; Rabatin, Jeffrey T; Harrison, Barry A

    2004-09-01

    Clinical practice often lags behind publication of evidence-based research and national consensus guidelines. To assess practice variability in the clinical management of acute respiratory distress syndrome (ARDS) and test an evidence-based, online clinician-education tool designed to improve intensive-care clinicians' understanding of current evidence about ARDS management. We surveyed 117 intensive care clinicians (16 critical care physician specialists, 28 resident physicians, 50 critical care nurses, and 23 respiratory therapists) with an online questionnaire in our tertiary academic institution. Fifty of the original respondents (12 residents, 26 critical care nurses, and 12 respiratory therapists) also responded to a repeat survey that included context-sensitive hypertext links to a summary of critically appraised primary articles regarding ARDS management, to determine if the responses changed after the clinicians had read the evidence-based summary information. Critical care physician specialists were most likely to choose the low-tidal-volume (low-VT) ventilation strategy and protocol-based ventilator weaning and were least likely to choose neuromuscular blockade or parenteral nutrition (p 48 h, during the 6 months before and after the survey, from which we identified 45 ARDS patients. Following the clinician-education intervention, ARDS patients were less likely to receive potentially injurious high-VT ventilation (mean day-3 VT 10.3 +/- 2.3 mL/kg before vs 8.9 +/- 1.7 mL/kg after, p = 0.02). Web-based teaching tools are useful to educate intensive-care practitioners and to promote evidence-based practice. Copyright 2004 Daedalus Enterprises

  3. Molecular Imaging: A Useful Tool for the Development of Natural Killer Cell-Based Immunotherapies.

    Science.gov (United States)

    Gangadaran, Prakash; Ahn, Byeong-Cheol

    2017-01-01

    Molecular imaging is a relatively new discipline that allows visualization, characterization, and measurement of the biological processes in living subjects, including humans, at a cellular and molecular level. The interaction between cancer cells and natural killer (NK) cells is complex and incompletely understood. Despite our limited knowledge, progress in the search for immune cell therapies against cancer could be significantly improved by dynamic and non-invasive visualization and tracking of immune cells and by visualization of the response of cancer cells to therapies in preclinical and clinical studies. Molecular imaging is an essential tool for these studies, and a multimodal molecular imaging approach can be applied to monitor immune cells in vivo, for instance, to visualize therapeutic effects. In this review, we discuss the usefulness of NK cells in cancer therapies and the preclinical and clinical usefulness of molecular imaging in NK cell-based therapies. Furthermore, we discuss different molecular imaging modalities for use with NK cell-based therapies, and their preclinical and clinical applications in animal and human subjects. Molecular imaging has contributed to the development of NK cell-based therapies against cancers in animal models and to the refinement of current cell-based cancer immunotherapies. Developing sensitive and reproducible non-invasive molecular imaging technologies for in vivo NK cell monitoring and for real-time assessment of therapeutic effects will accelerate the development of NK cell therapies.

  4. Molecular Imaging: A Useful Tool for the Development of Natural Killer Cell-Based Immunotherapies

    Directory of Open Access Journals (Sweden)

    Prakash Gangadaran

    2017-09-01

    Full Text Available Molecular imaging is a relatively new discipline that allows visualization, characterization, and measurement of the biological processes in living subjects, including humans, at a cellular and molecular level. The interaction between cancer cells and natural killer (NK cells is complex and incompletely understood. Despite our limited knowledge, progress in the search for immune cell therapies against cancer could be significantly improved by dynamic and non-invasive visualization and tracking of immune cells and by visualization of the response of cancer cells to therapies in preclinical and clinical studies. Molecular imaging is an essential tool for these studies, and a multimodal molecular imaging approach can be applied to monitor immune cells in vivo, for instance, to visualize therapeutic effects. In this review, we discuss the usefulness of NK cells in cancer therapies and the preclinical and clinical usefulness of molecular imaging in NK cell-based therapies. Furthermore, we discuss different molecular imaging modalities for use with NK cell-based therapies, and their preclinical and clinical applications in animal and human subjects. Molecular imaging has contributed to the development of NK cell-based therapies against cancers in animal models and to the refinement of current cell-based cancer immunotherapies. Developing sensitive and reproducible non-invasive molecular imaging technologies for in vivo NK cell monitoring and for real-time assessment of therapeutic effects will accelerate the development of NK cell therapies.

  5. Bringing together hydrologic models and Earth Observation data with water users through the WebGIS tool SPIDER in the context of the SIRIUS project

    Science.gov (United States)

    Garrido, Jesús; Osann, Anna; Calera, Alfonso; Moreno-Rivera, Juan Manuel; Momblanch, Andrea; Andreu, Joaquin; Solera, Abel; Fernández, Miguel

    2013-04-01

    Scientific expertise on irrigated agriculture or hydrological modelling has achieved advance models with tested results. However, real connexions between this knowledge and its applications, and water end-users (either water managers on the field, or water policy makers) need a meeting point. According with the main aim of Global Monitoring for Environment and Security (GMES) in order to provide global, timely and easily accessible information in applications like land and water management, the EU-project SIRIUS (Sustainable Irrigation water management and River-basin governance: Implementing User-driven Services, www.sirius-gmes.es), is linking hydrologic models and Earth Observation data with water users, through the webGIS tool SPIDER (System of Participatory Information, Decision support and Expert knowledge for River basin water management). The models employed are AQUATOOL (http://www.upv.es/aquatool/) and HidroMORE+® (http://www.hidromore.es/). AQUATOOL is a Decision Support System (DSS) for the management of the water resources in a river basin which integrates in a comprehensive way all relevant water elements and its interactions, in order to provide different scenarios that incorporate water offers and demands. On the other hand, HidroMORE+® computes spatially distributed water balance components remote sensing driven, in large areas at high spatial and temporal resolution. Mainly applied to irrigation practices, HidroMORE+® is aimed to monitories the crop evolutions and water demands. Either AQUATOOL products such scenario reports, or HidroMORE+® products such time series of the water balance components can be integrated in SPIDER, which has been designed to display all these types of products. However, a general feature of models is that they often provide too many parameters, which makes it very difficult for non-experts to understand. Then, it is needed to select among the output variables those that provide maximum useful information, according

  6. GliomaPredict: a clinically useful tool for assigning glioma patients to specific molecular subtypes

    Directory of Open Access Journals (Sweden)

    Fine Howard A

    2010-07-01

    Full Text Available Abstract Background Advances in generating genome-wide gene expression data have accelerated the development of molecular-based tumor classification systems. Tools that allow the translation of such molecular classification schemas from research into clinical applications are still missing in the emerging era of personalized medicine. Results We developed GliomaPredict as a computational tool that allows the fast and reliable classification of glioma patients into one of six previously published stratified subtypes based on sets of extensively validated classifiers derived from hundreds of glioma transcriptomic profiles. Our tool utilizes a principle component analysis (PCA-based approach to generate a visual representation of the analyses, quantifies the confidence of the underlying subtype assessment and presents results as a printable PDF file. GliomaPredict tool is implemented as a plugin application for the widely-used GenePattern framework. Conclusions GliomaPredict provides a user-friendly, clinically applicable novel platform for instantly assigning gene expression-based subtype in patients with gliomas thereby aiding in clinical trial design and therapeutic decision-making. Implemented as a user-friendly diagnostic tool, we expect that in time GliomaPredict, and tools like it, will become routinely used in translational/clinical research and in the clinical care of patients with gliomas.

  7. Molecular tools for functional genomics in filamentous fungi: recent advances and new strategies.

    Science.gov (United States)

    Jiang, Dewei; Zhu, Wei; Wang, Yunchuan; Sun, Chang; Zhang, Ke-Qin; Yang, Jinkui

    2013-12-01

    Advances in genetic transformation techniques have made important contributions to molecular genetics. Various molecular tools and strategies have been developed for functional genomic analysis of filamentous fungi since the first DNA transformation was successfully achieved in Neurospora crassa in 1973. Increasing amounts of genomic data regarding filamentous fungi are continuously reported and large-scale functional studies have become common in a wide range of fungal species. In this review, various molecular tools used in filamentous fungi are compared and discussed, including methods for genetic transformation (e.g., protoplast transformation, electroporation, and microinjection), the construction of random mutant libraries (e.g., restriction enzyme mediated integration, transposon arrayed gene knockout, and Agrobacterium tumefaciens mediated transformation), and the analysis of gene function (e.g., RNA interference and transcription activator-like effector nucleases). We also focused on practical strategies that could enhance the efficiency of genetic manipulation in filamentous fungi, such as choosing a proper screening system and marker genes, assembling target-cassettes or vectors effectively, and transforming into strains that are deficient in the nonhomologous end joining pathway. In summary, we present an up-to-date review on the different molecular tools and latest strategies that have been successfully used in functional genomics in filamentous fungi. © 2013 Elsevier Inc. All rights reserved.

  8. Systems Biology-Driven Hypotheses Tested In Vivo: The Need to Advancing Molecular Imaging Tools.

    Science.gov (United States)

    Verma, Garima; Palombo, Alessandro; Grigioni, Mauro; La Monaca, Morena; D'Avenio, Giuseppe

    2018-01-01

    Processing and interpretation of biological images may provide invaluable insights on complex, living systems because images capture the overall dynamics as a "whole." Therefore, "extraction" of key, quantitative morphological parameters could be, at least in principle, helpful in building a reliable systems biology approach in understanding living objects. Molecular imaging tools for system biology models have attained widespread usage in modern experimental laboratories. Here, we provide an overview on advances in the computational technology and different instrumentations focused on molecular image processing and analysis. Quantitative data analysis through various open source software and algorithmic protocols will provide a novel approach for modeling the experimental research program. Besides this, we also highlight the predictable future trends regarding methods for automatically analyzing biological data. Such tools will be very useful to understand the detailed biological and mathematical expressions under in-silico system biology processes with modeling properties.

  9. Molecular profiling--a tool for addressing emerging gaps in the comparative risk assessment of GMOs.

    Science.gov (United States)

    Heinemann, Jack A; Kurenbach, Brigitta; Quist, David

    2011-10-01

    Assessing the risks of genetically modified organisms (GMOs) is required by both international agreement and domestic legislation. Many view the use of the "omics" tools for profiling classes of molecules as useful in risk assessment, but no consensus has formed on the need or value of these techniques for assessing the risks of all GMOs. In this and many other cases, experts support case-by-case use of molecular profiling techniques for risk assessment. We review the latest research on the applicability and usefulness of molecular profiling techniques for GMO risk assessment. As more and more kinds of GMOs and traits are developed, broader use of molecular profiling in a risk assessment may be required to supplement the comparative approach to risk assessment. The literature-based discussions on the use of profiling appear to have settled on two findings: 1. profiling techniques are reliable and relevant, at least no less so than other techniques used in risk assessment; and 2. although not required routinely, regulators should be aware of when they are needed. The dismissal of routine molecular profiling may be confusing to regulators who then lack guidance on when molecular profiling might be worthwhile. Molecular profiling is an important way to increase confidence in risk assessments if the profiles are properly designed to address relevant risks and are applied at the correct stage of the assessment. Copyright © 2011 Elsevier Ltd. All rights reserved.

  10. Australian endemic pest tephritids: genetic, molecular and microbial tools for improved Sterile Insect Technique

    OpenAIRE

    Raphael, Kathryn A; Shearman, Deborah CA; Gilchrist, A Stuart; Sved, John A; Morrow, Jennifer L; Sherwin, William B; Riegler, Markus; Frommer, Marianne

    2014-01-01

    Among Australian endemic tephritid fruit flies, the sibling species Bactrocera tryoni and Bactrocera neohumeralis have been serious horticultural pests since the introduction of horticulture in the nineteenth century. More recently, Bactrocera jarvisi has also been declared a pest in northern Australia. After several decades of genetic research there is now a range of classical and molecular genetic tools that can be used to develop improved Sterile Insect Technique (SIT) strains for control ...

  11. Prospective Molecular Characterization of Burn Wound Colonization: Novel Tools and Analysis

    Science.gov (United States)

    2012-10-01

    and validated culture-independent molecular tools for quantifying and identifying wound fungi . We also initiated a prospective study to elucidate the...Quantitative polymerase chain reaction (qPCR); Fungi ; Bacteria 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT 18. NUMBER OF PAGES 19a...1) Isolate and purify total DNA, RNA, and Protein from each sample 2) Analyze the microbial community composition by sequencing analysis a. 16S

  12. Ligation-based molecular tools for lab-on-a-chip devices.

    Science.gov (United States)

    Melin, Jonas; Jarvius, Jonas; Larsson, Chatarina; Söderberg, Ola; Landegren, Ulf; Nilsson, Mats

    2008-06-01

    Molecular diagnostics can offer early detection of disease, improved diagnostic accuracy, and qualified follow-up. Moreover, the use of microfluidic devices can in principle render these analyses quickly and user-friendly, placing them within the reach of the general practitioner and maybe even in households. However, the progress launching such devices has been limited so far. We propose that an important limiting factor has been the difficulty of establishing molecular assays suitable for microfabricated formats. The assays should be capable of monitoring a wide range of molecules, including genomic DNA, RNA and proteins with secondary modifications and interaction partners, and they must exhibit excellent sensitivity and specificity. We discuss these problems and describe a series of molecular tools that may present new opportunities for lab-on-a-chip devices at the point-of-care.

  13. Molecular epidemiology tools in the management of healthcare-associated infections: towards the definition of recommendations.

    Science.gov (United States)

    Boccia, Stefania; Pasquarella, Cesira; Colotto, Marco; Barchitta, Martina; Quattrocchi, Annalisa; Agodi, Antonella

    2015-01-01

    Healthcare-Associated Infections (HAIs) are an important cause of morbidity and mortality worldwide and have a significant economic impact for health systems. Molecular epidemiology tools have a central role in HAI prevention programs. In order to give an overview of their specific advantages and disadvantages we reported current and new molecular typing methods for HAI outbreak detection and epidemiological surveillance. The current review was drafted as a short version of a longer document written by the Public Health Genomics (GSP) working group, and the Italian Study Group of Hospital Hygiene (GISIO), entitled Molecular epidemiology of Healthcare Associated Infections: recommendations from the Italian Society of Hygiene, Preventive Medicine and Public Health (SItI). This text considers various aspects related to HAIs: the role of genotyping and bioinformatics, the organizational levels of laboratories, as well as ethical and economic aspects. The use of molecular epidemiology represents a key tool in the management of HAIs, to be used as a complement to conventional control measures. The present contribution aims to increase knowledge on the proper use of such methods, given the major challenge HAI represents for National Health systems.

  14. Synthetic biology and molecular genetics in non-conventional yeasts: Current tools and future advances.

    Science.gov (United States)

    Wagner, James M; Alper, Hal S

    2016-04-01

    Coupling the tools of synthetic biology with traditional molecular genetic techniques can enable the rapid prototyping and optimization of yeast strains. While the era of yeast synthetic biology began in the well-characterized model organism Saccharomyces cerevisiae, it is swiftly expanding to include non-conventional yeast production systems such as Hansenula polymorpha, Kluyveromyces lactis, Pichia pastoris, and Yarrowia lipolytica. These yeasts already have roles in the manufacture of vaccines, therapeutic proteins, food additives, and biorenewable chemicals, but recent synthetic biology advances have the potential to greatly expand and diversify their impact on biotechnology. In this review, we summarize the development of synthetic biological tools (including promoters and terminators) and enabling molecular genetics approaches that have been applied in these four promising alternative biomanufacturing platforms. An emphasis is placed on synthetic parts and genome editing tools. Finally, we discuss examples of synthetic tools developed in other organisms that can be adapted or optimized for these hosts in the near future. Copyright © 2015 Elsevier Inc. All rights reserved.

  15. Bringing down the trash

    Science.gov (United States)

    Ornes, Stephen

    2012-06-01

    The density of junk orbiting the Earth is at or near a critical value beyond which this man-made debris will self-perpetuate, forming many smaller pieces that are even more of a problem. Stephen Ornes reports on the latest ideas about how to bring down the trash.

  16. Bringing Scientists to Life

    Science.gov (United States)

    Casey, Peter

    2010-01-01

    In this article, the author describes how he brings scientists to life when he visits schools. Having retired from teaching Drama and Theatre Studies in Liverpool for more than thirty years, the author set up his one-man Theatre-in-Education company, Blindseer Productions, and now takes his portrayals of Darwin, Galileo and Einstein to schools…

  17. Is high pressure liquid chromatography an effective screening tool for characterization of molecular defects in hemoglobinopathies?

    Science.gov (United States)

    Moorchung, Nikhil; Phillip, Joseph; Sarkar, Ravi Shankar; Prasad, Rupesh; Dutta, Vibha

    2013-01-01

    Hemoglobinopathies constitute entities that are generated by either abnormal hemoglobin or thalassemias. high pressure liquid chromatography (HPLC) is one of the best methods for screening and detection of various hemoglobinopathies but it has intrinsic interpretive problems. The study was designed to evaluate the different mutations seen in cases of hemoglobinopathies and compare the same with screening tests. 68 patients of hemoglobinopathies were screened by HPLC. Mutation studies in the beta globin gene was performed using the polymerase chain reaction (PCR)-based allele-specific Amplification Refractory Mutation System (ARMS). Molecular analysis for the sickle cell mutation was done by standard methods. The IVS 1/5 mutation was the commonest mutation seen and it was seen in 26 (38.23%) of the cases. This was followed by the IVS 1/1, codon 41/42, codon 8/9, del 22 mutation, codon 15 mutation and the -619 bp deletion. No mutation was seen in eight cases. There was a 100% concordance between the sickle cell trait as diagnosed by HPLC and genetic testing. Our study underlies the importance of molecular testing in all cases of hemoglobinopathies. Although HPLC is a useful screening tool, molecular testing is very useful in accurately diagnosing the mutations. Molecular testing is especially applicable in cases with an abnormal hemoglobin (HbD, HbE and HbS) because there may be a concomitant inheritance of a beta thalassemia mutation. Molecular testing is the gold standard when it comes to the diagnosis of hemoglobinopathies.

  18. FlaME: Flash Molecular Editor - a 2D structure input tool for the web

    Directory of Open Access Journals (Sweden)

    Dallakian Pavel

    2011-02-01

    Full Text Available Abstract Background So far, there have been no Flash-based web tools available for chemical structure input. The authors herein present a feasibility study, aiming at the development of a compact and easy-to-use 2D structure editor, using Adobe's Flash technology and its programming language, ActionScript. As a reference model application from the Java world, we selected the Java Molecular Editor (JME. In this feasibility study, we made an attempt to realize a subset of JME's functionality in the Flash Molecular Editor (FlaME utility. These basic capabilities are: structure input, editing and depiction of single molecules, data import and export in molfile format. Implementation The result of molecular diagram sketching in FlaME is accessible in V2000 molfile format. By integrating the molecular editor into a web page, its communication with the HTML elements on this page is established using the two JavaScript functions, getMol( and setMol(. In addition, structures can be copied to the system clipboard. Conclusion A first attempt was made to create a compact single-file application for 2D molecular structure input/editing on the web, based on Flash technology. With the application examples presented in this article, it could be demonstrated that the Flash methods are principally well-suited to provide the requisite communication between the Flash object (application and the HTML elements on a web page, using JavaScript functions.

  19. New tools for the study of chromosome segregation and aneuploidy at the molecular level

    Energy Technology Data Exchange (ETDEWEB)

    Charlieu, J.P.; Marcais, B.; Laurent, A.M.; Roizes, G. [Institut de Biologie, Montpellier (France)

    1993-12-31

    The molecular mechanisms which allow the correct distribution of chromosomes during cell division are not yet well known. The centromere, because of its possible involvement in the attachment of sister chromatids and its participation in the formation of the kinetochore, may play an important role in these mechanisms. Trisomy 21 (down syndrome, DS) provides a good model for studying aneuploidy resulting from the dysfunction of the chromosome distribution process. A possible means of analyzing the mechanisms leading to non-disjunction (NDJ) could be to determine the origin of the supernumerary chromosome 21 and to attempt to find some structural or physical characteristics of the potentially responsible centromere. This could be performed by using molecular tools which allow each of the two parental chromosomes 21 to be distinguished. Possible markers suitable for this purpose are DNA fragments that exhibit length polymorphisms. We present here some examples of such molecular tools, and discuss ways to use them in order to study the parental origin and the meiotic stage of nondisjunction, and we propose an hypothesis suggesting a possible cause of nondisjunction in human chromosomes.

  20. Recent advances in developing molecular tools for targeted genome engineering of mammalian cells.

    Science.gov (United States)

    Lim, Kwang-il

    2015-01-01

    Various biological molecules naturally existing in diversified species including fungi, bacteria, and bacteriophage have functionalities for DNA binding and processing. The biological molecules have been recently actively engineered for use in customized genome editing of mammalian cells as the molecule-encoding DNA sequence information and the underlying mechanisms how the molecules work are unveiled. Excitingly, multiple novel methods based on the newly constructed artificial molecular tools have enabled modifications of specific endogenous genetic elements in the genome context at efficiencies that are much higher than that of the conventional homologous recombination based methods. This minireview introduces the most recently spotlighted molecular genome engineering tools with their key features and ongoing modifications for better performance. Such ongoing efforts have mainly focused on the removal of the inherent DNA sequence recognition rigidity from the original molecular platforms, the addition of newly tailored targeting functions into the engineered molecules, and the enhancement of their targeting specificity. Effective targeted genome engineering of mammalian cells will enable not only sophisticated genetic studies in the context of the genome, but also widely-applicable universal therapeutics based on the pinpointing and correction of the disease-causing genetic elements within the genome in the near future.

  1. Bringing "indigenous" ownership back

    DEFF Research Database (Denmark)

    Kragelund, Peter

    2012-01-01

    understanding of how processes of exclusion interact with domestic politics in Zambia. It argues that the Citizens Economic Empowerment Commission, a new institution to bring ownership back to Zambians, builds on a long tradition of nationalist policies in Zambia, while its actual work is strictly related...... to the critique of the growing foreign dominance over the economy, and in particular of the upsurge in Chinese investments....

  2. Mathematical models in biology bringing mathematics to life

    CERN Document Server

    Ferraro, Maria; Guarracino, Mario

    2015-01-01

    This book presents an exciting collection of contributions based on the workshop “Bringing Maths to Life” held October 27-29, 2014 in Naples, Italy.  The state-of-the art research in biology and the statistical and analytical challenges facing huge masses of data collection are treated in this Work. Specific topics explored in depth surround the sessions and special invited sessions of the workshop and include genetic variability via differential expression, molecular dynamics and modeling, complex biological systems viewed from quantitative models, and microscopy images processing, to name several. In depth discussions of the mathematical analysis required to extract insights from complex bodies of biological datasets, to aid development in the field novel algorithms, methods and software tools for genetic variability, molecular dynamics, and complex biological systems are presented in this book. Researchers and graduate students in biology, life science, and mathematics/statistics will find the content...

  3. Molecular modeling as a predictive tool for the development of solid dispersions.

    Science.gov (United States)

    Maniruzzaman, Mohammed; Pang, Jiayun; Morgan, David J; Douroumis, Dennis

    2015-04-06

    In this study molecular modeling is introduced as a novel approach for the development of pharmaceutical solid dispersions. A computational model based on quantum mechanical (QM) calculations was used to predict the miscibility of various drugs in various polymers by predicting the binding strength between the drug and dimeric form of the polymer. The drug/polymer miscibility was also estimated by using traditional approaches such as Van Krevelen/Hoftyzer and Bagley solubility parameters or Flory-Huggins interaction parameter in comparison to the molecular modeling approach. The molecular modeling studies predicted successfully the drug-polymer binding energies and the preferable site of interaction between the functional groups. The drug-polymer miscibility and the physical state of bulk materials, physical mixtures, and solid dispersions were determined by thermal analysis (DSC/MTDSC) and X-ray diffraction. The produced solid dispersions were analyzed by X-ray photoelectron spectroscopy (XPS), which confirmed not only the exact type of the intermolecular interactions between the drug-polymer functional groups but also the binding strength by estimating the N coefficient values. The findings demonstrate that QM-based molecular modeling is a powerful tool to predict the strength and type of intermolecular interactions in a range of drug/polymeric systems for the development of solid dispersions.

  4. ms 2: A molecular simulation tool for thermodynamic properties, release 3.0

    Science.gov (United States)

    Rutkai, Gábor; Köster, Andreas; Guevara-Carrion, Gabriela; Janzen, Tatjana; Schappals, Michael; Glass, Colin W.; Bernreuther, Martin; Wafai, Amer; Stephan, Simon; Kohns, Maximilian; Reiser, Steffen; Deublein, Stephan; Horsch, Martin; Hasse, Hans; Vrabec, Jadran

    2017-12-01

    A new version release (3.0) of the molecular simulation tool ms 2 (Deublein et al., 2011; Glass et al. 2014) is presented. Version 3.0 of ms 2 features two additional ensembles, i.e. microcanonical (NVE) and isobaric-isoenthalpic (NpH), various Helmholtz energy derivatives in the NVE ensemble, thermodynamic integration as a method for calculating the chemical potential, the osmotic pressure for calculating the activity of solvents, the six Maxwell-Stefan diffusion coefficients of quaternary mixtures, statistics for sampling hydrogen bonds, smooth-particle mesh Ewald summation as well as the ability to carry out molecular dynamics runs for an arbitrary number of state points in a single program execution.

  5. Biopython: freely available Python tools for computational molecular biology and bioinformatics.

    Science.gov (United States)

    Cock, Peter J A; Antao, Tiago; Chang, Jeffrey T; Chapman, Brad A; Cox, Cymon J; Dalke, Andrew; Friedberg, Iddo; Hamelryck, Thomas; Kauff, Frank; Wilczynski, Bartek; de Hoon, Michiel J L

    2009-06-01

    The Biopython project is a mature open source international collaboration of volunteer developers, providing Python libraries for a wide range of bioinformatics problems. Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments, dealing with 3D macro molecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning. Biopython is freely available, with documentation and source code at (www.biopython.org) under the Biopython license.

  6. Molecular and Population Genetics Tools for Animal Resources Conservation: A Brief Overview

    Directory of Open Access Journals (Sweden)

    Claudia Terezia Socol

    2015-05-01

    Full Text Available Advances in animal genome data and in genetic analysis, next to the increasing use of artificial reproductive technology resulted in progress into the animal sciences area, transposing the applied technologies into the omics field. This paper provides a brief overview related to some aspects of the population genetics characterization, as well as on the animal population genetic improvement and on the main molecular tools available for farm animals, highlighting at the same time the perspectives and priorities in terms of the advanced genetic methods, that can be considered for farm animal genetic resources (FAnGR breeding, improvement and conservation programmes in Romania.

  7. Molecular tools and emerging strategies for deep genetic/genomic refactoring of Pseudomonas.

    Science.gov (United States)

    Martínez-García, Esteban; de Lorenzo, Víctor

    2017-10-01

    The interest of the genus Pseudomonas largely relies on the virulence of some of its species for plants and animals (including humans). Yet, pathogenic features of some isolates coexist with others often present in environmental variants that promote plant growth and degrade chemical pollutants. Many of these traits can be traced to the intrinsic properties of the genomic chassis of this genus along with distinct genetic parts and devices. With the tools of Synthetic Biology these can be enhanced and/or repurposed for the sake of biological control, environmental remediation and whole-cell biocatalysis. In this article we take stock of both conceptual and technological developments that have allowed the virtual domestication of Pseudomonas (in particular P. putida) as a major biotechnological workhorse with a range of applications of industrial interest. Adoption of a suite of compositional and measurement standards is advocated for bringing Pseudomonas-based genetic engineering to a superior level of development. Copyright © 2017. Published by Elsevier Ltd.

  8. Bringing Things Together

    DEFF Research Database (Denmark)

    Gundelach, Peter

    2017-01-01

    The first sample surveys in the latter parts of the 19th century were an intellectual social movement. They were motivated by the intention to improve the economic and political conditions of workers. The quantitative survey was considered an ideal because it would present data about the workers...... as facts, i.e. establish a scientific authoritative truth. In a case study from Denmark, the paper shows how the first survey - a study of seamstresses - was carried out by bringing several cognitive and organizational elements together: a network of researchers, a method for sampling, the construction...

  9. Molecular tools for diagnosis of visceral leishmaniasis: systematic review and meta-analysis of diagnostic test accuracy

    NARCIS (Netherlands)

    de Ruiter, C. M.; van der Veer, C.; Leeflang, M. M. G.; Deborggraeve, S.; Lucas, C.; Adams, E. R.

    2014-01-01

    Molecular methods have been proposed as highly sensitive tools for the detection of Leishmania parasites in visceral leishmaniasis (VL) patients. Here, we evaluate the diagnostic accuracy of these tools in a meta-analysis of the published literature. The selection criteria were original studies that

  10. BATMAN-TCM: a Bioinformatics Analysis Tool for Molecular mechANism of Traditional Chinese Medicine

    Science.gov (United States)

    Liu, Zhongyang; Guo, Feifei; Wang, Yong; Li, Chun; Zhang, Xinlei; Li, Honglei; Diao, Lihong; Gu, Jiangyong; Wang, Wei; Li, Dong; He, Fuchu

    2016-02-01

    Traditional Chinese Medicine (TCM), with a history of thousands of years of clinical practice, is gaining more and more attention and application worldwide. And TCM-based new drug development, especially for the treatment of complex diseases is promising. However, owing to the TCM’s diverse ingredients and their complex interaction with human body, it is still quite difficult to uncover its molecular mechanism, which greatly hinders the TCM modernization and internationalization. Here we developed the first online Bioinformatics Analysis Tool for Molecular mechANism of TCM (BATMAN-TCM). Its main functions include 1) TCM ingredients’ target prediction; 2) functional analyses of targets including biological pathway, Gene Ontology functional term and disease enrichment analyses; 3) the visualization of ingredient-target-pathway/disease association network and KEGG biological pathway with highlighted targets; 4) comparison analysis of multiple TCMs. Finally, we applied BATMAN-TCM to Qishen Yiqi dripping Pill (QSYQ) and combined with subsequent experimental validation to reveal the functions of renin-angiotensin system responsible for QSYQ’s cardioprotective effects for the first time. BATMAN-TCM will contribute to the understanding of the “multi-component, multi-target and multi-pathway” combinational therapeutic mechanism of TCM, and provide valuable clues for subsequent experimental validation, accelerating the elucidation of TCM’s molecular mechanism. BATMAN-TCM is available at http://bionet.ncpsb.org/batman-tcm.

  11. FISH and GISH: molecular cytogenetic tools and their applications in ornamental plants.

    Science.gov (United States)

    Younis, Adnan; Ramzan, Fahad; Hwang, Yoon-Jung; Lim, Ki-Byung

    2015-09-01

    The innovations in chromosome engineering have improved the efficiency of interrogation breeding, and the identification and transfer of resistance genes from alien to native species. Recent advances in molecular biology and cytogenetics have brought revolutionary, conceptual developments in mitosis and meiosis research, chromosome structure and manipulation, gene expression and regulation, and gene silencing. Cytogenetic studies offer integrative tools for imaging, genetics, epigenetics, and cytological information that can be employed to enhance chromosome and molecular genomic research in plant taxa. In situ hybridization techniques, such as fluorescence in situ hybridization (FISH) and genomic in situ hybridization (GISH), can identify chromosome morphologies and sequences, amount and distribution of various types of chromatin in chromosomes, and genome organization during the metaphase stage of meiosis. Over the past few decades, various new molecular cytogenetic applications have been developed. The FISH and GISH techniques present an authentic model for analyzing the individual chromosome, chromosomal segments, or the genomes of natural and artificial hybrid plants. These have become the most reliable techniques for studying allopolyploids, because most cultivated plants have been developed through hybridization or polyploidization. Moreover, introgression of the genes and chromatin from the wild types into cultivated species can also be analyzed. Since hybrid derivatives may have variable alien chromosome numbers or chromosome arms, the use of these approaches opens new avenues for accurately identifying genome differences.

  12. Bringing science to business

    Science.gov (United States)

    Lemetti, Paul

    2005-06-01

    Bringing science to business seems rather straight forward. Technology is constantly moving forward and new inventions are being brought into the market place. Science parks and technology parks have sprung out all around the globe competing against each other and trying to keep their own doors open by bringing in new business, thereby creating much needed income to keep their operations moving forward. However, only a small handful ofthese centers around the world can truly be considered successful. It is the relationship between the scientists, start-up business, local universities, local government, and invited bigger business that allows the parks to succeed. The individual scientist wishing to enter into business or just hoping to get his invention into the pool of potential ideas; which might end up in the hands of an entrepreneur or an established company, is not always that simple. Universal success principles must be embraced to ensure success. One must believe in oneself and to strive for excellence. One must be able to see the other persons viewpoint and adapt and change his behavior in order to succeed. One must learn to create trust as well as learn to trust. Furthermore, one must learn to focus on the why of the process and not on the how. A market must be identified and benefits of local area must be sold to potential investor or business partners. A local success has in part to do with local cooperation.

  13. Bringing minds together.

    Science.gov (United States)

    Abele, John

    2011-01-01

    Boston Scientific founder John Abele has been party to his share of groundbreaking innovations over the years. But the revolutionary advances in medical science that these breakthroughs brought about were not the efforts of one firm alone, let alone one inventor. Abele tells two fascinating stories of collaboration--one about Jack Whitehead's upending of hospitals' blood and urine testing procedures and the other about Andreas Gruentzig's success in bringing balloon catheterization into the cardiology mainstream. Both Whitehead and Gruentzig spearheaded the emergence of entirely new fields, bringing together scientist-customers to voluntarily develop standards, training programs, new business models, and even a specialized language to describe their new field. The process of collaboration, Abete says, is fraught with contradictions and subtlety. It takes consummate leadership skills to persuade others to spend countless hours solving important problems in partnership with people they don't necessarily like. Moreover, managing egos so that each person's commitment, energy, and creativity is unleashed in a way that doesn't disadvantage others requires an impresario personality. Finally, true authenticity--something that few people can project--is critical for earning customers' trust and convincing them that their valuable contributions won't be used for anything other than moving the technology forward.

  14. Design and characterization of molecular tools for a Synthetic Biology approach towards developing cyanobacterial biotechnology.

    Science.gov (United States)

    Huang, Hsin-Ho; Camsund, Daniel; Lindblad, Peter; Heidorn, Thorsten

    2010-05-01

    Cyanobacteria are suitable for sustainable, solar-powered biotechnological applications. Synthetic biology connects biology with computational design and an engineering perspective, but requires efficient tools and information about the function of biological parts and systems. To enable the development of cyanobacterial Synthetic Biology, several molecular tools were developed and characterized: (i) a broad-host-range BioBrick shuttle vector, pPMQAK1, was constructed and confirmed to replicate in Escherichia coli and three different cyanobacterial strains. (ii) The fluorescent proteins Cerulean, GFPmut3B and EYFP have been demonstrated to work as reporter proteins in cyanobacteria, in spite of the strong background of photosynthetic pigments. (iii) Several promoters, like P(rnpB) and variants of P(rbcL), and a version of the promoter P(trc) with two operators for enhanced repression, were developed and characterized in Synechocystis sp. strain PCC6803. (iv) It was shown that a system for targeted protein degradation, which is needed to enable dynamic expression studies, is working in Synechocystis sp. strain PCC6803. The pPMQAK1 shuttle vector allows the use of the growing numbers of BioBrick parts in many prokaryotes, and the other tools herein implemented facilitate the development of new parts and systems in cyanobacteria.

  15. Exome sequencing is an efficient tool for variant late-infantile neuronal ceroid lipofuscinosis molecular diagnosis.

    Directory of Open Access Journals (Sweden)

    Liliana Catherine Patiño

    Full Text Available The neuronal ceroid-lipofuscinoses (NCL is a group of neurodegenerative disorders characterized by epilepsy, visual failure, progressive mental and motor deterioration, myoclonus, dementia and reduced life expectancy. Classically, NCL-affected individuals have been classified into six categories, which have been mainly defined regarding the clinical onset of symptoms. However, some patients cannot be easily included in a specific group because of significant variation in the age of onset and disease progression. Molecular genetics has emerged in recent years as a useful tool for enhancing NCL subtype classification. Fourteen NCL genetic forms (CLN1 to CLN14 have been described to date. The variant late-infantile form of the disease has been linked to CLN5, CLN6, CLN7 (MFSD8 and CLN8 mutations. Despite advances in the diagnosis of neurodegenerative disorders mutations in these genes may cause similar phenotypes, which rends difficult accurate candidate gene selection for direct sequencing. Three siblings who were affected by variant late-infantile NCL are reported in the present study. We used whole-exome sequencing, direct sequencing and in silico approaches to identify the molecular basis of the disease. We identified the novel c.1219T>C (p.Trp407Arg and c.1361T>C (p.Met454Thr MFSD8 pathogenic mutations. Our results highlighted next generation sequencing as a novel and powerful methodological approach for the rapid determination of the molecular diagnosis of NCL. They also provide information regarding the phenotypic and molecular spectrum of CLN7 disease.

  16. Techniques to Bring Up Mucus

    Science.gov (United States)

    ... COPD: Lifestyle Management Techniques to Bring Up Mucus Techniques to Bring Up Mucus Make an Appointment Refer ... breathing may become difficult, and infection may occur. Techniques to remove mucus are often done after using ...

  17. Molecular characterization of Thelazia lacrymalis (Nematoda, Spirurida) affecting equids: a tool for vector identification.

    Science.gov (United States)

    Traversa, Donato; Otranto, Domenico; Iorio, Raffaella; Giangaspero, Annunziata

    2005-08-01

    Equine thelaziosis caused by the eyeworm Thelazia lacrymalis is a parasitic disease transmitted by muscid flies. Although equine thelaziosis is known to have worldwide distribution, information on the epidemiology and presence of the intermediate hosts of T. lacrymalis is lacking. In the present work, a PCR-RFLP based assay on the first and/or second internal transcribed spacer (ITS1 and ITS2) of ribosomal DNA was developed for the detection of T. lacrymalis DNA in its putative vector(s). The sensitivity of the technique was also assessed. The restriction patterns obtained readily differentiated T. lacrymalis from four species of Musca (Diptera, Muscidae) (i.e. Musca autumnalis, Musca domestica, Musca larvipara and Musca osiris), which are potential vectors of equine eyeworms. The molecular assay presented herein is a useful tool to identify the intermediate host(s) of T. lacrymalis in natural conditions and to study its/their ecology and epidemiology.

  18. Application of Molecular Tools for Gut Health of Pet Animals: A Review

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    Lipismita Samal

    2011-04-01

    Full Text Available Gut health is an important facet of well being of pet animals; it is in this context, various nutritional and biotechnological approaches have been proposed to manipulate the gut health by specifically targeting the colonic microbiota. Nutritional approaches include supplementation of antioxidants and phytochemicals like flavonoids, isoflavonoids and carotenoids. Biotechnological approaches include supplementation of probiotics, prebiotics, synbiotics in the diet and potential application of molecular tools like fluorescent in situ hybridization, denaturing gradient gel electrophoresis, quantitative dot blot hybridization, and restriction fragment length polymorphism etc. in studying the fecal microbiota composition. Post-genomic and related technologies, i.e. genomics, nutrigenomics, transcriptomics, proteomics, metabolomics and epigenomics in the study of gastrointestinal tract also put forward challenges for nutritionists and microbiologists to elucidate the complex interactions between gut microbiota and host.

  19. Translating molecular medicine into clinical tools: doomed to fail by neglecting basic preanalytical principles

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    Mannello Ferdinando

    2009-10-01

    Full Text Available Abstract This commentary discusses a study on measurements of matrix metalloproteinase 9 (MMP-9 in serum of pseudoxanthoma elasticum patients recently published in Journal of Molecular Medicine. This study can be considered the typical "obstacle" to effective translational medicine as previously documented in JTM journal. Although serum has been frequently proven as inappropriate sample for determining numerous circulating MMPs, among them MMP-9, there are over and over again studies, as in this case, that measure MMP-9 in serum. Comparative measurements in serum and plasma samples demonstrated higher concentrations for MMP-9 in serum due to the additional release from leukocytes and platelets following the coagulation/fibrinolysis process. From this example it can be concluded that translating basic research discoveries into clinical tools needs a more intensive exchange between basic biomedical research and clinical scientists already in an early stage. Otherwise a lost of translation, as discussed in JTM journal, seems to be inevitable.

  20. Exome sequencing of index patients with retinal dystrophies as a tool for molecular diagnosis.

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    Marta Corton

    Full Text Available Retinal dystrophies (RD are a group of hereditary diseases that lead to debilitating visual impairment and are usually transmitted as a Mendelian trait. Pathogenic mutations can occur in any of the 100 or more disease genes identified so far, making molecular diagnosis a rather laborious process. In this work we explored the use of whole exome sequencing (WES as a tool for identification of RD mutations, with the aim of assessing its applicability in a diagnostic context.We ascertained 12 Spanish families with seemingly recessive RD. All of the index patients underwent mutational pre-screening by chip-based sequence hybridization and resulted to be negative for known RD mutations. With the exception of one pedigree, to simulate a standard diagnostic scenario we processed by WES only the DNA from the index patient of each family, followed by in silico data analysis. We successfully identified causative mutations in patients from 10 different families, which were later verified by Sanger sequencing and co-segregation analyses. Specifically, we detected pathogenic DNA variants (∼50% novel mutations in the genes RP1, USH2A, CNGB3, NMNAT1, CHM, and ABCA4, responsible for retinitis pigmentosa, Usher syndrome, achromatopsia, Leber congenital amaurosis, choroideremia, or recessive Stargardt/cone-rod dystrophy cases.Despite the absence of genetic information from other family members that could help excluding nonpathogenic DNA variants, we could detect causative mutations in a variety of genes known to represent a wide spectrum of clinical phenotypes in 83% of the patients analyzed. Considering the constant drop in costs for human exome sequencing and the relative simplicity of the analyses made, this technique could represent a valuable tool for molecular diagnostics or genetic research, even in cases for which no genotypes from family members are available.

  1. Molecular genetic tools to infer the origin of forest plants and wood.

    Science.gov (United States)

    Finkeldey, Reiner; Leinemann, Ludger; Gailing, Oliver

    2010-02-01

    Most forest tree species exhibit high levels of genetic diversity that can be used to trace the origin of living plants or their products such as timber and processed wood. Recent progress to isolate DNA not only from living tissue but also from wood and wood products offers new opportunities to test the declared origin of material such as seedlings for plantation establishment or timber. However, since most forest tree populations are weakly differentiated, the identification of genetic markers to differentiate among spatially isolated populations is often difficult and time consuming. Two important fields of "forensic" applications are described: Molecular tools are applied to test the declared origin of forest reproductive material used for plantation establishment and of internationally traded timber and wood products. These applications are illustrated taking examples from Germany, where mechanisms have been developed to improve the control of the trade with forest seeds and seedlings, and from the trade with wood of the important Southeast Asian tree family Dipterocarpaceae. Prospects and limitations of the use of molecular genetic methods to conclude on the origin of forest plants, wood, and wood products are discussed.

  2. THE EVALUATION OF A TOOL FOR DISSEMINATION OF BIOTECHNOLOGY AND MOLECULAR BIOLOGY CONCEPTS IN FORMAL EDUCATION

    Directory of Open Access Journals (Sweden)

    F.M. Escanhoela

    2007-05-01

    Full Text Available Since 2003, the CBME Scientific Dissemination Coordination hasdeveloped a project related to the production and distribution of a scientificdissemination newspaper, called CBME InFORMAÇÃO, directed to high-schoolstudents and teachers. It is a quarterly publication and shows the concepts andadvances of studies in molecular biology and biotechnology. In order to evaluatethe newspaper, a research was accomplished in 2005. It involved 177 studentsfrom six high schools of São Carlos and region. In addition, opinions of fivescience teachers that worked with the newspaper in their classrooms, as well aseight Biology undergraduates were collected. The teachers received somequestionnaires that had to be answered by them and their students after a specifyactivity with the periodical – basically, the activities consisted of three stages:individual reading of the newspaper; formulation of questions by the teacher and,finally, group discussion on the chosen theme. The research confirmed theimportance of the use of the periodical as a tool in the formation of critical readersof facts related to the biotechnology and molecular biology, what should contributewith the citizenship development in the students. Moreover, it provided a possibilityto reorganize the periodical.

  3. Standardized molecular diagnostic tool for the identification of cryptic species within the Bemisia tabaci complex.

    Science.gov (United States)

    Elfekih, Samia; Tay, Wee Tek; Gordon, Karl; Court, Leon N; De Barro, Paul J

    2018-01-01

    The whitefly Bemisia tabaci complex harbours over 40 cryptic species that have been placed in 11 phylogenetically distinct clades based on the molecular characterization of partial mitochondrial DNA COI (mtCOI) gene region. Four cryptic species are currently within the invasive clade, i.e. MED, MEAM1, MEAM2 and IO. Correct identification of these species is a critical step towards implementing reliable measures for plant biosecurity and border protection; however, no standardized B. tabaci-specific primers are currently available which has caused inconsistencies in the species identification processes. We report three sets of polymerase chain reaction (PCR) primers developed to amplify the mtCOI region which can be used for genotyping MED, MEAM1 and IO species, and tested these primers on 91 MED, 35 MEAM1 and five IO individuals. PCR and sequencing of amplicons identified a total of 21, six and one haplotypes in MED, MEAM1 and IO respectively, of which six haplotypes were new to the B. tabaci database. These primer pairs enabled standardization and robust molecular species identification via mtCOI screening of the targeted invasive cryptic species and will improve quarantine decisions. Use of this diagnostic tool could be extended to other species within the complex. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

  4. Gene silencing by RNA interference in Sarcoptes scabiei: a molecular tool to identify novel therapeutic targets.

    Science.gov (United States)

    Fernando, Deepani D; Marr, Edward J; Zakrzewski, Martha; Reynolds, Simone L; Burgess, Stewart T G; Fischer, Katja

    2017-06-10

    Scabies is one of the most common and widespread parasitic skin infections globally, affecting a large range of mammals including humans, yet the molecular biology of Sarcoptes scabiei is astonishingly understudied. Research has been hampered primarily due to the difficulty of sampling or culturing these obligatory parasitic mites. A further and major impediment to identify and functionally analyse potential therapeutic targets from the recently emerging molecular databases is the lack of appropriate molecular tools. We performed standard BLAST based searches of the existing S. scabiei genome databases using sequences of genes described to be involved in RNA interference in Drosophila and the mite model organism Tetranychus urticae. Experimenting with the S. scabiei mu-class glutathione S-transferase (SsGST-mu1) as a candidate gene we explored the feasibility of gene knockdown in S. scabiei by double-stranded RNA-interference (dsRNAi). We provide here an analysis of the existing S. scabiei draft genomes, confirming the presence of a double stranded RNA (dsRNA) - mediated silencing machinery. We report for the first time experimental gene silencing by RNA interference (RNAi) in S. scabiei. Non-invasive immersion of S. scabiei in dsRNA encoding an S. scabiei glutathione S-transferase mu-class 1 enzyme (SsGST-mu1) resulted in a 35% reduction in the transcription of the target gene compared to controls. A series of experiments identified the optimal conditions allowing systemic experimental RNAi without detrimental side effects on mite viability. This technique can now be used to address the key questions on the fundamental aspects of mite biology and pathogenesis, and to assess the potential therapeutic benefits of silencing S. scabiei target genes.

  5. Snake Venom Peptides and Low Mass Proteins: Molecular Tools and Therapeutic Agents.

    Science.gov (United States)

    Almeida, J R; Resende, L M; Watanabe, R K; Carregari, V C; Huancahuire-Vega, S; da S Caldeira, C A; Coutinho-Neto, A; Soares, A M; Vale, N; de C Gomes, P A; Marangoni, S; de A Calderon, L; Da Silva, S L

    2017-01-01

    Snake venoms are natural sources of biologically active molecules that are able to act selectively and specifically on different cellular targets, modulating physiological functions. Thus, these mixtures, composed mainly of proteins and peptides, provide ample and challenging opportunities and a diversified molecular architecture to design and develop tools and agents of scientific and therapeutic interest. Among these components, peptides and small proteins play diverse roles in numerous physiological processes, exerting a wide range of pharmacological activities, such as antimicrobial, antihypertensive, analgesic, antitumor, analgesic, among others. The pharmaceutical and cosmetic industries have recognized the huge potential of these privileged frameworks and believe them to be a promising alternative to contemporary drugs. A number of natural or synthetic peptides from snake venoms have already found preclinical or clinical applications for the treatment of pain, hypertension, cardiovascular diseases and aging skin. A well-known example is captopril, whose natural peptide precursor was isolated from Bothrops jararaca snake venom, which is a peptide-based drug that inhibits the angiotensin-converting enzyme, producing an anti-hypertensive effect. The present review looks at the main peptides (natriuretic peptides, bradykinin-potentiating peptides and sarafotoxins) and low mass proteins (crotamine, disintegrins and three-Finger toxins) from snake venoms, as well as synthetic peptides inspired by them, describing their biochemical, structural and physiological features, as well as their applications as research tools and therapeutic agents. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  6. Bringing Gravity to Space

    Science.gov (United States)

    Norsk, P.; Shelhamer, M.

    2016-01-01

    This panel will present NASA's plans for ongoing and future research to define the requirements for Artificial Gravity (AG) as a countermeasure against the negative health effects of long-duration weightlessness. AG could mitigate the gravity-sensitive effects of spaceflight across a host of physiological systems. Bringing gravity to space could mitigate the sensorimotor and neuro-vestibular disturbances induced by G-transitions upon reaching a planetary body, and the cardiovascular deconditioning and musculoskeletal weakness induced by weightlessness. Of particular interest for AG during deep-space missions is mitigation of the Visual Impairment Intracranial Pressure (VIIP) syndrome that the majority of astronauts exhibit in space to varying degrees, and which presumably is associated with weightlessness-induced fluid shift from lower to upper body segments. AG could be very effective for reversing the fluid shift and thus help prevent VIIP. The first presentation by Dr. Charles will summarize some of the ground-based and (very little) space-based research that has been conducted on AG by the various space programs. Dr. Paloski will address the use of AG during deep-space exploration-class missions and describe the different AG scenarios such as intra-vehicular, part-of-vehicle, or whole-vehicle centrifugations. Dr. Clement will discuss currently planned NASA research as well as how to coordinate future activities among NASA's international partners. Dr. Barr will describe some possible future plans for using space- and ground-based partial-G analogs to define the relationship between physiological responses and G levels between 0 and 1. Finally, Dr. Stenger will summarize how the human cardiovascular system could benefit from intermittent short-radius centrifugations during long-duration missions.

  7. Molecular Tools for the Detection and the Identification of Hymenoptera Parasitoids in Tortricid Fruit Pests

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    Pierre Franck

    2017-09-01

    Full Text Available Biological control requires specific tools for the accurate detection and identification of natural enemies in order to estimate variations in their abundance and their impact according to changes in environmental conditions or agricultural practices. Here, we developed two molecular methods of detection based on PCR-RFLP with universal primers and on PCR with specific primers to identify commonly occurring larval parasitoids of the tortricid fruit pests and to estimate parasitism in the codling moth. Both methods were designed based on DNA sequences of the COI mitochondrial gene for a range of parasitoids that emerged from Cydia pomonella and Grapholita molesta caterpillars (102 parasitoids; nine species and a range of potential tortricid hosts (40 moths; five species damaging fruits. The PCR-RFLP method (digestion by AluI of a 482 bp COI fragment was very powerful to identify parasitoid adults and their hosts, but failed to detect parasitoid larvae within eggs or within young C. pomonella caterpillars. The PCR method based on specific primers amplified COI fragments of different lengths (131 to 463 bp for Ascogaster quadridentata (Braconidae; Pristomerus vulnerator (Ichneumonidae; Trichomma enecator (Ichneumonidae; and Perilampus tristis (Perilampidae, and demonstrated a higher level of sensibility than the PCR-RFLP method. Molecular estimations of parasitism levels in a natural C. pomonella population with the specific primers did not differ from traditional estimations based on caterpillar rearing (about 60% parasitism in a non-treated apple orchard. These PCR-based techniques provide information about within-host parasitoid assemblage in the codling moth and preliminary results on the larval parasitism of major tortricid fruit pests.

  8. Molecular Tools for the Detection and the Identification of Hymenoptera Parasitoids in Tortricid Fruit Pests.

    Science.gov (United States)

    Franck, Pierre; Maalouly-Matar, Mariline; Olivares, Jérôme

    2017-09-22

    Biological control requires specific tools for the accurate detection and identification of natural enemies in order to estimate variations in their abundance and their impact according to changes in environmental conditions or agricultural practices. Here, we developed two molecular methods of detection based on PCR-RFLP with universal primers and on PCR with specific primers to identify commonly occurring larval parasitoids of the tortricid fruit pests and to estimate parasitism in the codling moth. Both methods were designed based on DNA sequences of the COI mitochondrial gene for a range of parasitoids that emerged from Cydia pomonella and Grapholitamolesta caterpillars (102 parasitoids; nine species) and a range of potential tortricid hosts (40 moths; five species) damaging fruits. The PCR-RFLP method (digestion by AluI of a 482 bp COI fragment) was very powerful to identify parasitoid adults and their hosts, but failed to detect parasitoid larvae within eggs or within young C. pomonella caterpillars. The PCR method based on specific primers amplified COI fragments of different lengths (131 to 463 bp) for Ascogaster quadridentata (Braconidae); Pristomerusvulnerator (Ichneumonidae); Trichomma enecator (Ichneumonidae); and Perilampus tristis (Perilampidae), and demonstrated a higher level of sensibility than the PCR-RFLP method. Molecular estimations of parasitism levels in a natural C. pomonella population with the specific primers did not differ from traditional estimations based on caterpillar rearing (about 60% parasitism in a non-treated apple orchard). These PCR-based techniques provide information about within-host parasitoid assemblage in the codling moth and preliminary results on the larval parasitism of major tortricid fruit pests.

  9. PathogenMIPer: a tool for the design of molecular inversion probes to detect multiple pathogens

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    Akhras Michael

    2006-11-01

    Full Text Available Abstract Background Here we describe PathogenMIPer, a software program for designing molecular inversion probe (MIP oligonucleotides for use in pathogen identification and detection. The software designs unique and specific oligonucleotide probes targeting microbial or other genomes. The tool tailors all probe sequence components (including target-specific sequences, barcode sequences, universal primers and restriction sites and combines these components into ready-to-order probes for use in a MIP assay. The system can harness the genetic variability available in an entire genome in designing specific probes for the detection of multiple co-infections in a single tube using a MIP assay. Results PathogenMIPer can accept sequence data in FASTA file format, and other parameter inputs from the user through a graphical user interface. It can design MIPs not only for pathogens, but for any genome for use in parallel genomic analyses. The software was validated experimentally by applying it to the detection of human papilloma virus (HPV as a model system, which is associated with various human malignancies including cervical and skin cancers. Initial tests of laboratory samples using the MIPs developed by the PathogenMIPer to recognize 24 different types of HPVs gave very promising results, detecting even a small viral load of single as well as multiple infections (Akhras et al, personal communication. Conclusion PathogenMIPer is a software for designing molecular inversion probes for detection of multiple target DNAs in a sample using MIP assays. It enables broader use of MIP technology in the detection through genotyping of pathogens that are complex, difficult-to-amplify, or present in multiple subtypes in a sample.

  10. Molecular identification of livestock breeds: a tool for modern conservation biology.

    Science.gov (United States)

    Yaro, Mohammed; Munyard, Kylie A; Stear, Michael J; Groth, David M

    2017-05-01

    Global livestock genetic diversity includes all of the species, breeds and strains of domestic animals, and their variations. Although a recent census indicated that there were 40 species and over 8000 breeds of domestic animals; for the purpose of conservation biology the diversity between and within breeds rather than species is regarded to be of crucial importance. This domestic animal genetic diversity has developed through three main evolutionary events, from speciation (about 3 million years ago) through domestication (about 12000 years ago) to specialised breeding (starting about 200 years ago). These events and their impacts on global animal genetic resources have been well documented in the literature. The key importance of global domestic animal resources in terms of economic, scientific and cultural heritage has also been addressed. In spite of their importance, there is a growing number of reports on the alarming erosion of domestic animal genetic resources. This erosion of is happening in spite of several global conservation initiatives designed to mitigate it. Herein we discuss these conservation interventions and highlight their strengths and weaknesses. However, pivotal to the success of these conservation initiatives is the reliability of the genetic assignment of individual members to a target breed. Finally, we discuss the prospect of using improved breed identification methodologies to develop a reliable breed-specific molecular identification tool that is easily applicable to populations of livestock breeds in various ecosystems. These identification tools, when developed, will not only facilitate the regular monitoring of threatened or endangered breed populations, but also enhance the development of more efficient and sustainable livestock production systems. © 2016 Cambridge Philosophical Society.

  11. The Annotation, Mapping, Expression and Network (AMEN suite of tools for molecular systems biology

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    Primig Michael

    2008-02-01

    Full Text Available Abstract Background High-throughput genome biological experiments yield large and multifaceted datasets that require flexible and user-friendly analysis tools to facilitate their interpretation by life scientists. Many solutions currently exist, but they are often limited to specific steps in the complex process of data management and analysis and some require extensive informatics skills to be installed and run efficiently. Results We developed the Annotation, Mapping, Expression and Network (AMEN software as a stand-alone, unified suite of tools that enables biological and medical researchers with basic bioinformatics training to manage and explore genome annotation, chromosomal mapping, protein-protein interaction, expression profiling and proteomics data. The current version provides modules for (i uploading and pre-processing data from microarray expression profiling experiments, (ii detecting groups of significantly co-expressed genes, and (iii searching for enrichment of functional annotations within those groups. Moreover, the user interface is designed to simultaneously visualize several types of data such as protein-protein interaction networks in conjunction with expression profiles and cellular co-localization patterns. We have successfully applied the program to interpret expression profiling data from budding yeast, rodents and human. Conclusion AMEN is an innovative solution for molecular systems biological data analysis freely available under the GNU license. The program is available via a website at the Sourceforge portal which includes a user guide with concrete examples, links to external databases and helpful comments to implement additional functionalities. We emphasize that AMEN will continue to be developed and maintained by our laboratory because it has proven to be extremely useful for our genome biological research program.

  12. POLYANA-A tool for the calculation of molecular radial distribution functions based on Molecular Dynamics trajectories

    Science.gov (United States)

    Dimitroulis, Christos; Raptis, Theophanes; Raptis, Vasilios

    2015-12-01

    We present an application for the calculation of radial distribution functions for molecular centres of mass, based on trajectories generated by molecular simulation methods (Molecular Dynamics, Monte Carlo). When designing this application, the emphasis was placed on ease of use as well as ease of further development. In its current version, the program can read trajectories generated by the well-known DL_POLY package, but it can be easily extended to handle other formats. It is also very easy to 'hack' the program so it can compute intermolecular radial distribution functions for groups of interaction sites rather than whole molecules.

  13. Molecular Investigations of Bacteroides as Microbial Source Tracking Tools in Southeast Louisiana Watersheds

    Science.gov (United States)

    Schulz, C. J.; Childers, G. W.; Engel, A. S.

    2006-12-01

    Microbial Source Tracking (MST) is a developing field that is gaining increased attention. MST refers to a host of techniques that discriminates among the origins of fecal material found in natural waters from different sources (e.g. human, livestock, and wildlife) by using microbial indicator species with specificity to only certain host organisms. The development of species-specific molecular markers would allow for better evaluation of public health risks and tracking of nutrient sources impacting a watershed. Although several MST methods have been reported with varying levels of success, few offer general applicability for natural waters due to spatial and temporal constraints associated with these methods. One group of molecular MST markers that show promise for broad environmental applications are molecular 16S rDNA probes for Bacteroides. This method is based on 16S rDNA detection directly from environmental samples without the need for a preliminary cultivation step. In this study we have expanded previous sampling efforts to compile a database of over 1000 partial 16S rRNA Bacteroides genes retrieved from the fecal material of 15 different host species (human, cat, dog, pig, kangaroo). To characterize survival of Bacteroides outside of the host, survival time of the Bacteroides marker was compared to that of E.coli under varying natural environmental conditions (temperature and salinity). Bacteroides displayed a survival curve with shouldering and tailing similar to that of E.coli, but log reduction times differed with treatment. In summary, MST marker stability was identified within host species and the overall Bacteroides community structure correlated to host diet, suggesting that detection of a Bacteroides community could confidently identify fecal contamination point sources. Natural water samples from southeast Louisiana were collected for MST including the Tangipahoa River watershed where the source of fecal contamination has been hotly debated. The

  14. Modelling human behaviour in a bumper car ride using molecular dynamics tools: a student project

    Science.gov (United States)

    Buendía, Jorge J.; Lopez, Hector; Sanchis, Guillem; Pardo, Luis Carlos

    2017-05-01

    Amusement parks are excellent laboratories of physics, not only to check physical laws, but also to investigate if those physical laws might also be applied to human behaviour. A group of Physics Engineering students from Universitat Politècnica de Catalunya has investigated if human behaviour, when driving bumper cars, can be modelled using tools borrowed from the analysis of molecular dynamics simulations, such as the radial and angular distribution functions. After acquiring several clips and obtaining the coordinates of the cars, those magnitudes are computed and analysed. Additionally, an analogous hard disks system is simulated to compare its distribution functions to those obtained from the cars’ coordinates. Despite the clear difference between bumper cars and a hard disk-like particle system, the obtained distribution functions are very similar. This suggests that there is no important effect of the individuals in the collective behaviour of the system in terms of structure. The research, performed by the students, has been undertaken in the frame of a motivational project designed to approach the scientific method for university students named FISIDABO. This project offers both the logistical and technical support to undertake the experiments designed by students at the amusement park of Barcelona TIBIDABO and accompanies them all along the scientific process.

  15. SuiteMSA: visual tools for multiple sequence alignment comparison and molecular sequence simulation

    Directory of Open Access Journals (Sweden)

    Strope Cory L

    2011-05-01

    Full Text Available Abstract Background Multiple sequence alignment (MSA plays a central role in nearly all bioinformatics and molecular evolutionary applications. MSA reconstruction is thus one of the most heavily scrutinized bioinformatics fields. Evaluating the quality of MSA reconstruction is often hindered by the lack of good reference MSAs. The use of sequence evolution simulation can provide such reference MSAs. Furthermore, none of the MSA viewing/editing programs currently available allows the user to make direct comparisons between two or more MSAs. Considering the importance of MSA quality in a wide range of research, it is desirable if MSA assessment can be performed more easily. Results We have developed SuiteMSA, a java-based application that provides unique MSA viewers. Users can directly compare multiple MSAs and evaluate where the MSAs agree (are consistent or disagree (are inconsistent. Several alignment statistics are provided to assist such comparisons. SuiteMSA also includes a graphical phylogeny editor/viewer as well as a graphical user interface for a sequence evolution simulator that can be used to construct reference MSAs. Conclusions SuiteMSA provides researchers easy access to a sequence evolution simulator, reference alignments generated by the simulator, and a series of tools to evaluate the performance of the MSA reconstruction programs. It will help us improve the quality of MSAs, often the most important first steps of bioinformatics and other biological research.

  16. Stability of Culex quinquefasciatus resistance to Bacillus sphaericus evaluated by molecular tools.

    Science.gov (United States)

    Amorim, Liliane Barbosa; de Barros, Rosineide Arruda; Chalegre, Karlos Diogo de Melo; de Oliveira, Cláudia Maria Fontes; Regis, Lêda Narcisa; Silva-Filha, Maria Helena Neves Lobo

    2010-04-01

    Bacillus sphaericus binary toxin action on Culex quinquefasciatus larvae relies on the binding to Cqm1alpha-glucosidases, which act as midgut receptors. Resistance of two laboratory-selected colonies is associated with the allele cqm1(REC) that prevents Cqm1 expression as membrane-bound molecules. This study evaluated stability of resistance after the interruption of selection pressure and introduction of susceptible individuals in these colonies. Bioassays showed that frequency of resistant larvae did not decrease throughout 11 generations, under these conditions, and it was associated to a similar frequency of larvae lacking the Cqm1alpha-glucosidase receptor, detected by in gel enzymatic assays. Direct screening of the cqm1(REC) allele, by specific PCR, showed that its frequency remained stable throughout 11 generations. Parental resistant colony did not display biological costs regarding fecundity, fertility and pupal weight and data from susceptibility assays, enzymatic assays and PCR screening showed that cqm1(REC) was not disfavored in competition with the susceptible allele and persisted in the progenies, in the lack of selection pressure. Characterization of molecular basis of resistance is essential for developing diagnostic tools and data have relevant implication for the establishment of strategies for resistance management. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

  17. Molecular tools for utilization of mitochondrial diversity in faba bean (Vicia faba

    Directory of Open Access Journals (Sweden)

    Aleksić Jelena M.

    2014-01-01

    Full Text Available We performed in silico PCR analyses utilizing complete mitochondrial (mtDNA genome sequences of faba bean (Vicia faba and two related species, Vigna angularis and Vigna radiata, currently available in GenBank, to infer whether 15 published universal primer pairs for amplification of all 14 cis-spliced introns in genes of NADH subunits (nad genes are suitable for V. faba and related species. Then, we tested via PCR reactions whether seven out of 15 primer pairs would generate PCR products suitable for further manipulation in 16 genotypes of V. faba representing all botanical varieties of this species (major, minor, equina and subsp. paucijuga of various levels of improvement (traditional and improved cultivars originating from Europe, Africa, Asia and south America. We provide new PCR primers for amplification of nad1 intron 2/3 in V. faba, and demonstrate intraspecific variability in primary nucleotide sequences at this locus. Based on outcomes of both in silico predictions and PCR amplification, we report a set of PCR primers for amplification of five introns in nad genes that are promising molecular tools for future phylogeographic and other studies in this species for which unambiguous data on wild ancestors, centre of origin and domestication are lacking. [Projekat Ministarstva nauke Republike Srbije, br. 173005

  18. Molecular Tools for the Selective Detection of Nine Diatom Species Biomarkers of Various Water Quality Levels

    Directory of Open Access Journals (Sweden)

    Lucia Cimarelli

    2015-05-01

    Full Text Available Our understanding of the composition of diatom communities and their response to environmental changes is currently limited by laborious taxonomic identification procedures. Advances in molecular technologies are expected to contribute more efficient, robust and sensitive tools for the detection of these ecologically relevant microorganisms. There is a need to explore and test phylogenetic markers as an alternative to the use of rRNA genes, whose limited sequence divergence does not allow the accurate discrimination of diatoms at the species level. In this work, nine diatom species belonging to eight genera, isolated from epylithic environmental samples collected in central Italy, were chosen to implement a panel of diatoms covering the full range of ecological status of freshwaters. The procedure described in this work relies on the PCR amplification of specific regions in two conserved diatom genes, elongation factor 1-a (eEF1-a and silicic acid transporter (SIT, as a first step to narrow down the complexity of the targets, followed by microarray hybridization experiments. Oligonucleotide probes with the potential to discriminate closely related species were designed taking into account the genetic polymorphisms found in target genes. These probes were tested, refined and validated on a small-scale prototype DNA chip. Overall, we obtained 17 highly specific probes targeting eEF1-a and SIT, along with 19 probes having lower discriminatory power recognizing at the same time two or three species. This basic array was validated in a laboratory setting and is ready for tests with crude environmental samples eventually to be scaled-up to include a larger panel of diatoms. Its possible use for the simultaneous detection of diatoms selected from the classes of water quality identified by the European Water Framework Directive is discussed.

  19. Molecular tools for the selective detection of nine diatom species biomarkers of various water quality levels.

    Science.gov (United States)

    Cimarelli, Lucia; Singh, Kumar Saurabh; Mai, Nguyen Thi Nhu; Dhar, Bidhan Chandra; Brandi, Anna; Brandi, Letizia; Spurio, Roberto

    2015-05-22

    Our understanding of the composition of diatom communities and their response to environmental changes is currently limited by laborious taxonomic identification procedures. Advances in molecular technologies are expected to contribute more efficient, robust and sensitive tools for the detection of these ecologically relevant microorganisms. There is a need to explore and test phylogenetic markers as an alternative to the use of rRNA genes, whose limited sequence divergence does not allow the accurate discrimination of diatoms at the species level. In this work, nine diatom species belonging to eight genera, isolated from epylithic environmental samples collected in central Italy, were chosen to implement a panel of diatoms covering the full range of ecological status of freshwaters. The procedure described in this work relies on the PCR amplification of specific regions in two conserved diatom genes, elongation factor 1-a (eEF1-a) and silicic acid transporter (SIT), as a first step to narrow down the complexity of the targets, followed by microarray hybridization experiments. Oligonucleotide probes with the potential to discriminate closely related species were designed taking into account the genetic polymorphisms found in target genes. These probes were tested, refined and validated on a small-scale prototype DNA chip. Overall, we obtained 17 highly specific probes targeting eEF1-a and SIT, along with 19 probes having lower discriminatory power recognizing at the same time two or three species. This basic array was validated in a laboratory setting and is ready for tests with crude environmental samples eventually to be scaled-up to include a larger panel of diatoms. Its possible use for the simultaneous detection of diatoms selected from the classes of water quality identified by the European Water Framework Directive is discussed.

  20. Australian endemic pest tephritids: genetic, molecular and microbial tools for improved Sterile Insect Technique.

    Science.gov (United States)

    Raphael, Kathryn A; Shearman, Deborah C A; Gilchrist, A Stuart; Sved, John A; Morrow, Jennifer L; Sherwin, William B; Riegler, Markus; Frommer, Marianne

    2014-01-01

    Among Australian endemic tephritid fruit flies, the sibling species Bactrocera tryoni and Bactrocera neohumeralis have been serious horticultural pests since the introduction of horticulture in the nineteenth century. More recently, Bactrocera jarvisi has also been declared a pest in northern Australia. After several decades of genetic research there is now a range of classical and molecular genetic tools that can be used to develop improved Sterile Insect Technique (SIT) strains for control of these pests. Four-way crossing strategies have the potential to overcome the problem of inbreeding in mass-reared strains of B. tryoni. The ability to produce hybrids between B. tryoni and the other two species in the laboratory has proved useful for the development of genetically marked strains. The identification of Y-chromosome markers in B. jarvisi means that male and female embryos can be distinguished in any strain that carries a B. jarvisi Y chromosome. This has enabled the study of homologues of the sex-determination genes during development of B jarvisi and B. tryoni, which is necessary for the generation of genetic-sexing strains. Germ-line transformation has been established and a draft genome sequence for B. tryoni released. Transcriptomes from various species, tissues and developmental stages, to aid in identification of manipulation targets for improving SIT, have been assembled and are in the pipeline. Broad analyses of the microbiome have revealed a metagenome that is highly variable within and across species and defined by the environment. More specific analyses detected Wolbachia at low prevalence in the tropics but absent in temperate regions, suggesting a possible role for this endosymbiont in future control strategies.

  1. Molecular dynamics simulation of subnanometric tool-workpiece contact on a force sensor-integrated fast tool servo for ultra-precision microcutting

    Energy Technology Data Exchange (ETDEWEB)

    Cai, Yindi [Department of Nanomechanics, Tohoku University, Sendai 980-8579 (Japan); Chen, Yuan-Liu, E-mail: yuanliuchen@nano.mech.tohoku.ac.jp [Department of Nanomechanics, Tohoku University, Sendai 980-8579 (Japan); Shimizu, Yuki; Ito, So; Gao, Wei [Department of Nanomechanics, Tohoku University, Sendai 980-8579 (Japan); Zhang, Liangchi [School of Mechanical and Manufacturing Engineering, The University of New South Wales, NSW 2052 (Australia)

    2016-04-30

    Highlights: • Subnanometric contact between a diamond tool and a copper workpiece surface is investigated by MD simulation. • A multi-relaxation time technique is proposed to eliminate the influence of the atom vibrations. • The accuracy of the elastic-plastic transition contact depth estimation is improved by observing the residual defects. • The simulation results are beneficial for optimization of the next-generation microcutting instruments. - Abstract: This paper investigates the contact characteristics between a copper workpiece and a diamond tool in a force sensor-integrated fast tool servo (FS-FTS) for single point diamond microcutting and in-process measurement of ultra-precision surface forms of the workpiece. Molecular dynamics (MD) simulations are carried out to identify the subnanometric elastic-plastic transition contact depth, at which the plastic deformation in the workpiece is initiated. This critical depth can be used to optimize the FS-FTS as well as the cutting/measurement process. It is clarified that the vibrations of the copper atoms in the MD model have a great influence on the subnanometric MD simulation results. A multi-relaxation time method is then proposed to reduce the influence of the atom vibrations based on the fact that the dominant vibration component has a certain period determined by the size of the MD model. It is also identified that for a subnanometric contact depth, the position of the tool tip for the contact force to be zero during the retracting operation of the tool does not correspond to the final depth of the permanent contact impression on the workpiece surface. The accuracy for identification of the transition contact depth is then improved by observing the residual defects on the workpiece surface after the tool retracting.

  2. Molecular docking as a popular tool in drug design, an in silico travel

    OpenAIRE

    de Ruyck, Jerome; Brysbaert, Guillaume; Blossey, Ralf; Lensink, Marc F

    2016-01-01

    Jerome de Ruyck, Guillaume Brysbaert, Ralf Blossey, Marc F Lensink University Lille, CNRS UMR8576 UGSF, Lille, FranceAbstract: New molecular modeling approaches, driven by rapidly improving computational platforms, have allowed many success stories for the use of computer-assisted drug design in the discovery of new mechanism- or structure-based drugs. In this overview, we highlight three aspects of the use of molecular docking. First, we discuss the combination of molecular and quantum mecha...

  3. Buried Volume Analysis for Propene Polymerization Catalysis Promoted by Group 4 Metals: a Tool for Molecular Mass Prediction

    KAUST Repository

    Falivene, Laura

    2015-10-02

    A comparison of the steric properties of homogeneous single site catalysts for propene polymerization using the percentage of buried volume (%VBur) as molecular descriptor is reported. The %VBur calculated on the neutral precursors of the active species seems to be a reliable tool to explain several experimental data related to the propene insertion and to the monomer chain transfer. Interestingly, a linear correlation between the buried volume calculated for a large set of neutral precursors and the energetic difference between propagation and termination steps calculated by DFT methods is found for Group 4 metal catalysts. The “master curves” derived for Ti, Zr and Hf confirm not only that the %VBur is an appropriate molecular descriptor for the systems considered but also that it could be used as tool for a large computational screening of new ligands.

  4. Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing.

    Science.gov (United States)

    Sánchez, Rubén; Serra, François; Tárraga, Joaquín; Medina, Ignacio; Carbonell, José; Pulido, Luis; de María, Alejandro; Capella-Gutíerrez, Salvador; Huerta-Cepas, Jaime; Gabaldón, Toni; Dopazo, Joaquín; Dopazo, Hernán

    2011-07-01

    Phylemon 2.0 is a new release of the suite of web tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing. It has been designed as a response to the increasing demand of molecular sequence analyses for experts and non-expert users. Phylemon 2.0 has several unique features that differentiates it from other similar web resources: (i) it offers an integrated environment that enables evolutionary analyses, format conversion, file storage and edition of results; (ii) it suggests further analyses, thereby guiding the users through the web server; and (iii) it allows users to design and save phylogenetic pipelines to be used over multiple genes (phylogenomics). Altogether, Phylemon 2.0 integrates a suite of 30 tools covering sequence alignment reconstruction and trimming; tree reconstruction, visualization and manipulation; and evolutionary hypotheses testing.

  5. Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology

    Directory of Open Access Journals (Sweden)

    Peter J.A. Cock

    2013-09-01

    Full Text Available The Galaxy Project offers the popular web browser-based platform Galaxy for running bioinformatics tools and constructing simple workflows. Here, we present a broad collection of additional Galaxy tools for large scale analysis of gene and protein sequences. The motivating research theme is the identification of specific genes of interest in a range of non-model organisms, and our central example is the identification and prediction of “effector” proteins produced by plant pathogens in order to manipulate their host plant. This functional annotation of a pathogen’s predicted capacity for virulence is a key step in translating sequence data into potential applications in plant pathology.This collection includes novel tools, and widely-used third-party tools such as NCBI BLAST+ wrapped for use within Galaxy. Individual bioinformatics software tools are typically available separately as standalone packages, or in online browser-based form. The Galaxy framework enables the user to combine these and other tools to automate organism scale analyses as workflows, without demanding familiarity with command line tools and scripting. Workflows created using Galaxy can be saved and are reusable, so may be distributed within and between research groups, facilitating the construction of a set of standardised, reusable bioinformatic protocols.The Galaxy tools and workflows described in this manuscript are open source and freely available from the Galaxy Tool Shed (http://usegalaxy.org/toolshed or http://toolshed.g2.bx.psu.edu.

  6. Diet analysis in piscivorous birds: What can the addition of molecular tools offer?

    Science.gov (United States)

    Oehm, Johannes; Thalinger, Bettina; Eisenkölbl, Stephanie; Traugott, Michael

    2017-03-01

    In trophic studies on piscivorous birds, it is vital to know which kind of dietary sample provides the information of interest and how the prey can be identified reliably and efficiently. Often, noninvasively obtained dietary samples such as regurgitated pellets, feces, and regurgitated fish samples are the preferred source of information. Fish prey has usually been identified via morphological analysis of undigested hard parts, but molecular approaches are being increasingly used for this purpose. What remains unknown, however, is which dietary sample type is best suited for molecular diet analysis and how the molecular results compare to those obtained by morphological analysis. Pellets, feces, and regurgitated fish samples of Great Cormorants (Phalacrocorax carbo sinensis) were examined for prey using both morphological hard part analysis and molecular prey identification. The sample types and methods were compared regarding number of species detected (overall and per sample) as well as the prey species composition and its variability among individual samples. Via molecular analysis, significantly higher numbers of prey species were detected in pellets, feces, and fish samples. Of the three sample types, pellets contained the most comprehensive trophic information and could be obtained with the lowest sampling effort. Contrastingly, dietary information obtained from feces was least informative and most variable. For all sample types, the molecular approach outperformed morphological hard part identification regarding the detectable prey spectrum and prey species composition. We recommend the use of pellets in combination with molecular prey identification to study the diet of piscivorous birds.

  7. Bring Your Own Device or Bring Your Own Distraction

    Science.gov (United States)

    Laxman, Kumar; Holt, Craig

    2017-01-01

    The purpose of this exploratory case study was to investigate the utilisation of Bring Your Own Device (BYOD) technologies in the classroom to determine if students and teachers perceive that the use of a digital device increased a learner's access to learning opportunities within the classroom, and, if the use of digital devices increased their…

  8. Molecular markers in breast cancer: new tools in imaging and prognosis

    OpenAIRE

    Vermeulen, J.F.

    2012-01-01

    Breast cancer is the most frequently diagnosed cancer in women. Although breast cancer is mainly diagnosed by mammography, other imaging modalities (e.g. MRI, PET) are increasingly used. The most recent developments in the field of molecular imaging comprise the application of near-infrared fluorescent labeled (NIRF) tracers for detection of breast cancer. Thus far, only a few molecular imaging tracers have been taken to the clinic of which most are suitable for PET. My thesis describes the e...

  9. Developing Molecular Genetic Tools to Facilitate Economic Production in Green Algae

    Science.gov (United States)

    2012-09-10

    species they are not readily available for algae that are being identified as potential biofuel production strains. Our work was focused on developing...the genetic tools required to enable green algae to become efficient biofuel production strains. Being able to efficiently apply genetic...genomes require distinct sets of transforma Algae , Biofuels , Algal Genetic Tools, Marine Algae U U U UU 5 Stephen P. Mayfield 858-822-7743 Reset AFOSR

  10. Bringing Secrecy into the Open

    DEFF Research Database (Denmark)

    Costas, Jana; Grey, Christopher

    2014-01-01

    This paper brings into focus the concept of organizational secrecy, defined as the ongoing formal and informal social processes of intentional concealment of information from actors by actors in organizations. It is argued that existing literature on the topic is fragmented and predominantly...

  11. Computational genes: a tool for molecular diagnosis and therapy of aberrant mutational phenotype

    Directory of Open Access Journals (Sweden)

    Ignatova Zoya

    2007-09-01

    Full Text Available Abstract Background A finite state machine manipulating information-carrying DNA strands can be used to perform autonomous molecular-scale computations at the cellular level. Results We propose a new finite state machine able to detect and correct aberrant molecular phenotype given by mutated genetic transcripts. The aberrant mutations trigger a cascade reaction: specific molecular markers as input are released and induce a spontaneous self-assembly of a wild type protein or peptide, while the mutational disease phenotype is silenced. We experimentally demostrated in in vitro translation system that a viable protein can be autonomously assembled. Conclusion Our work demostrates the basic principles of computational genes and particularly, their potential to detect mutations, and as a response thereafter administer an output that suppresses the aberrant disease phenotype and/or restores the lost physiological function.

  12. Molecular docking as a popular tool in drug design, an in silico travel.

    Science.gov (United States)

    de Ruyck, Jerome; Brysbaert, Guillaume; Blossey, Ralf; Lensink, Marc F

    2016-01-01

    New molecular modeling approaches, driven by rapidly improving computational platforms, have allowed many success stories for the use of computer-assisted drug design in the discovery of new mechanism-or structure-based drugs. In this overview, we highlight three aspects of the use of molecular docking. First, we discuss the combination of molecular and quantum mechanics to investigate an unusual enzymatic mechanism of a flavoprotein. Second, we present recent advances in anti-infectious agents' synthesis driven by structural insights. At the end, we focus on larger biological complexes made by protein-protein interactions and discuss their relevance in drug design. This review provides information on how these large systems, even in the presence of the solvent, can be investigated with the outlook of drug discovery.

  13. Molecular Modeling and Simulation Tools in the Development of Peptide-Based Biosensors for Mycotoxin Detection: Example of Ochratoxin

    Directory of Open Access Journals (Sweden)

    Aby A. Thyparambil

    2017-12-01

    Full Text Available Mycotoxin contamination of food and feed is now ubiquitous. Exposures to mycotoxin via contact or ingestion can potentially induce adverse health outcomes. Affordable mycotoxin-monitoring systems are highly desired but are limited by (a the reliance on technically challenging and costly molecular recognition by immuno-capture technologies; and (b the lack of predictive tools for directing the optimization of alternative molecular recognition modalities. Our group has been exploring the development of ochratoxin detection and monitoring systems using the peptide NFO4 as the molecular recognition receptor in fluorescence, electrochemical and multimodal biosensors. Using ochratoxin as the model mycotoxin, we share our perspective on addressing the technical challenges involved in biosensor fabrication, namely: (a peptide receptor design; and (b performance evaluation. Subsequently, the scope and utility of molecular modeling and simulation (MMS approaches to address the above challenges are described. Informed and enabled by phage display, the subsequent application of MMS approaches can rationally guide subsequent biomolecular engineering of peptide receptors, including bioconjugation and bioimmobilization approaches to be used in the fabrication of peptide biosensors. MMS approaches thus have the potential to reduce biosensor development cost, extend product life cycle, and facilitate multi-analyte detection of mycotoxins, each of which positively contributes to the overall affordability of mycotoxin biosensor monitoring systems.

  14. Review on the Molecular Tools for the Understanding of the Epidemiology of Animal Trypanosomosis in West Africa

    Directory of Open Access Journals (Sweden)

    Duvallet G

    1999-01-01

    Full Text Available The epidemiology of animal trypanosomosis around Bobo-Dioulasso (Burkina Faso, West Africa benefited a lot in the last years from the progress of molecular tools. The two most used molecular techniques were the polymerase chain reaction for the diagnosis of the disease in cattle and the characterization of the trypanosomes in the host and the vector on one hand, and the microsatellite DNA polymorphism in tsetse flies to study the intraspecific genetic variability of the vector on the other hand. The results obtained in the Sideradougou area during a recent two year survey with these techniques, associated with many other georeferenced informations concerning vector and cattle distribution, natural environment, landuse, ground occupation, livestock management, were combined in a Geographical Information System. This new approach of a complex pathogenic system led to a better evaluation of the risk of trypanosome transmission.

  15. Beyond a pedagogical tool: 30 years of Molecular biology of the cell.

    Science.gov (United States)

    Serpente, Norberto

    2013-02-01

    In 1983, a bulky and profusely illustrated textbook on molecular and cell biology began to inhabit the shelves of university libraries worldwide. The effect of capturing the eyes and souls of biologists was immediate as the book provided them with a new and invigorating outlook on what cells are and what they do.

  16. Using Molecular Visualization to Explore Protein Structure and Function and Enhance Student Facility with Computational Tools

    Science.gov (United States)

    Terrell, Cassidy R.; Listenberger, Laura L.

    2017-01-01

    Recognizing that undergraduate students can benefit from analysis of 3D protein structure and function, we have developed a multiweek, inquiry-based molecular visualization project for Biochemistry I students. This project uses a virtual model of cyclooxygenase-1 (COX-1) to guide students through multiple levels of protein structure analysis. The…

  17. Molecular markers in breast cancer: new tools in imaging and prognosis

    NARCIS (Netherlands)

    Vermeulen, J.F.|info:eu-repo/dai/nl/338877169

    2012-01-01

    Breast cancer is the most frequently diagnosed cancer in women. Although breast cancer is mainly diagnosed by mammography, other imaging modalities (e.g. MRI, PET) are increasingly used. The most recent developments in the field of molecular imaging comprise the application of near-infrared

  18. CAChe Molecular Modeling: A Visualization Tool Early in the Undergraduate Chemistry Curriculum.

    Science.gov (United States)

    Crouch, R. David; And Others

    1996-01-01

    Describes a "Synthesis and Reactivity" curriculum that focuses on the correlation of laboratory experiments with lecture topics and the extension of laboratory exercises beyond the usual four-hour period. Highlights experiments developed and an out-of-class computational chemistry exercise using CAChe, a versatile molecular modeling…

  19. Molecular Docking of Enzyme Inhibitors: A Computational Tool for Structure-Based Drug Design

    Science.gov (United States)

    Rudnitskaya, Aleksandra; Torok, Bela; Torok, Marianna

    2010-01-01

    Molecular docking is a frequently used method in structure-based rational drug design. It is used for evaluating the complex formation of small ligands with large biomolecules, predicting the strength of the bonding forces and finding the best geometrical arrangements. The major goal of this advanced undergraduate biochemistry laboratory exercise…

  20. The Need for Novel Informatics Tools for Integrating and Planning Research in Molecular and Cellular Cognition

    Science.gov (United States)

    Silva, Alcino J.; Müller, Klaus-Robert

    2015-01-01

    The sheer volume and complexity of publications in the biological sciences are straining traditional approaches to research planning. Nowhere is this problem more serious than in molecular and cellular cognition, since in this neuroscience field, researchers routinely use approaches and information from a variety of areas in neuroscience and other…

  1. Taming a wild beast: Developing molecular tools and new methods to understand the biology of Zymoseptoria tritici.

    Science.gov (United States)

    Talbot, Nicholas J

    2015-06-01

    Septoria blotch of wheat is one of the world's most serious plant diseases, which is difficult to control due to the absence of durable host resistance and the increasing frequency of fungicide-resistance. The ascomycete fungus that causes the disease, Zymoseptoria tritici, has been very challenging to study. This special issue of Fungal Genetics and Biology showcases an integrated approach to method development and the innovation of new molecular tools to study the biology of Z. tritici. When considered together, these new methods will have a rapid and dramatic effect on our ability to combat this significant disease. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

  2. Experimental mixture design as a tool for the synthesis of antimicrobial selective molecularly imprinted monodisperse microbeads.

    Science.gov (United States)

    Benito-Peña, Elena; Navarro-Villoslada, Fernando; Carrasco, Sergio; Jockusch, Steffen; Ottaviani, M Francesca; Moreno-Bondi, Maria C

    2015-05-27

    The effect of the cross-linker on the shape and size of molecular imprinted polymer (MIP) beads prepared by precipitation polymerization has been evaluated using a chemometric approach. Molecularly imprinted microspheres for the selective recognition of fluoroquinolone antimicrobials were prepared in a one-step precipitation polymerization procedure using enrofloxacin (ENR) as the template molecule, methacrylic acid as functional monomer, 2-hydroxyethyl methacrylate as hydrophilic comonomer, and acetonitrile as the porogen. The type and amount of cross-linker, namely ethylene glycol dimethacrylate, divinylbenzene or trimethylolpropane trimethacrylate, to obtain monodispersed MIP spherical beads in the micrometer range was optimized using a simplex lattice design. Particle size and morphology were assessed by scanning electron microscopy, dynamic light scattering, and nitrogen adsorption measurements. Electron paramagnetic resonance spectroscopy in conjunction with a nitroxide as spin probe revealed information about the microviscosity and polarity of the binding sites in imprinted and nonimprinted polymer beads.

  3. Characterization of microbial communities in pest colonized books by molecular biology tools

    Directory of Open Access Journals (Sweden)

    Franco Palla

    2011-08-01

    Full Text Available This work presents the identification of bacteria and fungi colonies in insect infesting books, by cultural-independent methodologies based on molecular biology techniques. Microbial genomic DNA extraction, in vitro amplification of specific target sequences by polymerase chain reactions (PCR, sequencing and sequence analysis were performed. These procedures minimized the samples amount, optimized the diagnostic studies on bacteria and fungi colonization and allowed the identification of many species also in complex microbial consortia. The molecular techniques for sure accomplish and integrate the microbiological standard methods (in vitro culture and morphological analyses (OM, SEM, CLSM, in order to understand the role of microorganisms in bio-deterioration of cultural assets. This monitoring is also indispensable to shed light on the risk for visitors and/or professionals to contract potential illnesses within indoor environments.

  4. Molecular Paleoparasitological Hybridization Approach as Effective Tool for Diagnosing Human Intestinal Parasites from Scarce Archaeological Remains

    Science.gov (United States)

    Jaeger, Lauren Hubert; Iñiguez, Alena Mayo

    2014-01-01

    Paleoparasitology is the science that uses parasitological techniques for diagnosing parasitic diseases in the past. Advances in molecular biology brought new insights into this field allowing the study of archaeological material. However, due to technical limitations a proper diagnosis and confirmation of the presence of parasites is not always possible, especially in scarce and degraded archaeological remains. In this study, we developed a Molecular Paleoparasitological Hybridization (MPH) approach using ancient DNA (aDNA) hybridization to confirm and complement paleoparasitological diagnosis. Eight molecular targets from four helminth parasites were included: Ascaris sp., Trichuris trichiura, Enterobius vermicularis, and Strongyloides stercoralis. The MPH analysis using 18th century human remains from Praça XV cemetery (CPXV), Rio de Janeiro, Brazil, revealed for the first time the presence E. vermicularis aDNA (50%) in archaeological sites of Brazil. Besides, the results confirmed T. trichiura and Ascaris sp. infections. The prevalence of infection by Ascaris sp. and E. vermicularis increased considerably when MPH was applied. However, a lower aDNA detection of T. trichiura (40%) was observed when compared to the diagnosis by paleoparasitological analysis (70%). Therefore, based on these data, we suggest a combination of Paleoparasitological and MPH approaches to verify the real panorama of intestinal parasite infection in human archeological samples. PMID:25162694

  5. Molecular and histological tools to diagnose an imported case of American cutaneous leishmaniasis in Cuba.

    Science.gov (United States)

    Montalvo, Ana M; De Armas, Yaxsier; Fraga, Jorge; Blanco, Orestes; Menéndez, Reinaldo; Montoto, Vicente; Capó de Paz, Virginia

    2015-10-01

    Leishmaniasis represents a polymorphous group of diseases caused by around 20 different species of Leishmania parasite. Increases in the number of cases of leishmaniasis reported as a consequence of the growth in travel and migration are of concern to epidemiologists and are diagnostically challenging in non-endemic areas. Molecular and histological analyses of a paraffin-embedded skin biopsy were used in parallel to detect Leishmania parasites in a Cuban woman with suspicious lesions arriving in Cuba from Venezuela. Primers based on the 18S fragment of ribosomal ribonucleic acid (rRNA) and heat shock protein 70 genes (hsp70) were used for molecular detection. Histological studies detected the presence of the parasite. A small fragment of Leishmania DNA was amplified by polymerase chain reaction (PCR) targeting the 18S fragment using, for the first time, nucleic acid obtained from paraffin-embedded tissue as a template. Amplification of a larger fragment from the hsp70 gene did not occur. The detection of Leishmania DNA from paraffin-embedded tissue by means of 18S-targeted PCR is a feasible approach to diagnosis. In combination with classical methods such as histology, the molecular detection of the parasite was demonstrated to be useful in confirming Leishmania infection in a traveler. © 2015 The International Society of Dermatology.

  6. Molecular docking as a popular tool in drug design, an in silico travel

    Directory of Open Access Journals (Sweden)

    de Ruyck J

    2016-06-01

    Full Text Available Jerome de Ruyck, Guillaume Brysbaert, Ralf Blossey, Marc F Lensink University Lille, CNRS UMR8576 UGSF, Lille, FranceAbstract: New molecular modeling approaches, driven by rapidly improving computational platforms, have allowed many success stories for the use of computer-assisted drug design in the discovery of new mechanism- or structure-based drugs. In this overview, we highlight three aspects of the use of molecular docking. First, we discuss the combination of molecular and quantum mechanics to investigate an unusual enzymatic mechanism of a flavoprotein. Second, we present recent advances in anti-infectious agents' synthesis driven by structural insights. At the end, we focus on larger biological complexes made by protein–protein interactions and discuss their relevance in drug design. This review provides information on how these large systems, even in the presence of the solvent, can be investigated with the outlook of drug discovery.Keywords: structure-based drug design, protein–protein docking, quaternary structure prediction, residue interaction networks, RINs, water position

  7. Utilizing a combination of molecular and spatial tools to assess the effect of a public health intervention.

    Science.gov (United States)

    Muellner, P; Marshall, J C; Spencer, S E F; Noble, A D; Shadbolt, T; Collins-Emerson, J M; Midwinter, A C; Carter, P E; Pirie, R; Wilson, D J; Campbell, D M; Stevenson, M A; French, N P

    2011-12-01

    Until recently New Zealand had one of the highest rates of human campylobacteriosis reported by industrialized countries. Since the introduction of a range of control measures in the poultry production chain a reduction in human cases of around 50% has been observed nationwide. To inform risk managers a combination of spatial, temporal and molecular tools - including minimum spanning trees, risk surfaces, rarefaction analysis and dynamic source attribution modelling - was used in this study to formally evaluate the reduction in disease risk that occurred after the implementation of control measures in the poultry industry. Utilizing data from a sentinel surveillance site in the Manawatu region of New Zealand, our analyses demonstrated a reduction in disease risk attributable to a reduction in the number of poultry-associated campylobacteriosis cases. Before the implementation of interventions poultry-associated cases were more prevalent in urban than rural areas, whereas for ruminant-associated cases the reverse was evident. In addition to the overall reduction in prevalence, this study also showed a stronger intervention effect in urban areas where poultry sources were more dominant. Overall a combination of molecular and spatial tools has provided evidence that the interventions aimed at reducing Campylobacter contamination of poultry were successful in reducing poultry-associated disease and this will inform the development of future control strategies. Copyright © 2011 Elsevier B.V. All rights reserved.

  8. Development of molecular and cellular tools to decipher the type I IFN pathway of the common vampire bat.

    Science.gov (United States)

    Sarkis, Sarkis; Lise, Marie-Claude; Darcissac, Edith; Dabo, Stéphanie; Falk, Marcel; Chaulet, Laura; Neuveut, Christine; Meurs, Eliane F; Lavergne, Anne; Lacoste, Vincent

    2017-11-06

    Though the common vampire bat, Desmodus rotundus, is known as the main rabies virus reservoir in Latin America, no tools are available to investigate its antiviral innate immune system. To characterize the IFN-I pathway, we established an immortalized cell line from a D. rotundus fetal lung named FLuDero. Then we molecularly characterized some of the Toll-like receptors (TLR3, 7, 8 and 9), the three RIG-I-like receptor members, as well as IFNα1 and IFNβ. Challenging the FLuDero cell line with poly (I:C) resulted in an up-regulation of both IFNα1 and IFNβ and the induction of expression of the different pattern recognition receptors characterized. These findings provide evidence of the intact dsRNA recognition machinery and the IFN-I signaling pathway in our cellular model. Herein, we generated a sum of insightful specific molecular and cellular tools that will serve as a useful model to study virus-host interactions of the common vampire bat. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  9. Contemporary molecular tools in microbial ecology and their application to advancing biotechnology

    KAUST Repository

    Rashid, Mamoon

    2015-09-25

    Novel methods in microbial ecology are revolutionizing our understanding of the structure and function of microbes in the environment, but concomitant advances in applications of these tools to biotechnology are mostly lagging behind. After more than a century of efforts to improve microbial culturing techniques, about 70–80% of microbial diversity – recently called the “microbial dark matter” – remains uncultured. In early attempts to identify and sample these so far uncultured taxonomic lineages, methods that amplify and sequence ribosomal RNA genes were extensively used. Recent developments in cell separation techniques, DNA amplification, and high-throughput DNA sequencing platforms have now made the discovery of genes/genomes of uncultured microorganisms from different environments possible through the use of metagenomic techniques and single-cell genomics. When used synergistically, these metagenomic and single-cell techniques create a powerful tool to study microbial diversity. These genomics techniques have already been successfully exploited to identify sources for i) novel enzymes or natural products for biotechnology applications, ii) novel genes from extremophiles, and iii) whole genomes or operons from uncultured microbes. More can be done to utilize these tools more efficiently in biotechnology.

  10. Contemporary molecular tools in microbial ecology and their application to advancing biotechnology.

    Science.gov (United States)

    Rashid, Mamoon; Stingl, Ulrich

    2015-12-01

    Novel methods in microbial ecology are revolutionizing our understanding of the structure and function of microbes in the environment, but concomitant advances in applications of these tools to biotechnology are mostly lagging behind. After more than a century of efforts to improve microbial culturing techniques, about 70-80% of microbial diversity - recently called the "microbial dark matter" - remains uncultured. In early attempts to identify and sample these so far uncultured taxonomic lineages, methods that amplify and sequence ribosomal RNA genes were extensively used. Recent developments in cell separation techniques, DNA amplification, and high-throughput DNA sequencing platforms have now made the discovery of genes/genomes of uncultured microorganisms from different environments possible through the use of metagenomic techniques and single-cell genomics. When used synergistically, these metagenomic and single-cell techniques create a powerful tool to study microbial diversity. These genomics techniques have already been successfully exploited to identify sources for i) novel enzymes or natural products for biotechnology applications, ii) novel genes from extremophiles, and iii) whole genomes or operons from uncultured microbes. More can be done to utilize these tools more efficiently in biotechnology. Copyright © 2015 Elsevier Inc. All rights reserved.

  11. Fuzzy logic selection as a new reliable tool to identify molecular grade signatures in breast cancer--the INNODIAG study.

    Science.gov (United States)

    Kempowsky-Hamon, Tatiana; Valle, Carine; Lacroix-Triki, Magali; Hedjazi, Lyamine; Trouilh, Lidwine; Lamarre, Sophie; Labourdette, Delphine; Roger, Laurence; Mhamdi, Loubna; Dalenc, Florence; Filleron, Thomas; Favre, Gilles; François, Jean-Marie; Le Lann, Marie-Véronique; Anton-Leberre, Véronique

    2015-02-07

    Personalized medicine has become a priority in breast cancer patient management. In addition to the routinely used clinicopathological characteristics, clinicians will have to face an increasing amount of data derived from tumor molecular profiling. The aims of this study were to develop a new gene selection method based on a fuzzy logic selection and classification algorithm, and to validate the gene signatures obtained on breast cancer patient cohorts. We analyzed data from four published gene expression datasets for breast carcinomas. We identified the best discriminating genes by comparing molecular expression profiles between histologic grade 1 and 3 tumors for each of the training datasets. The most pertinent probes were selected and used to define fuzzy molecular grade 1-like (good prognosis) and fuzzy molecular grade 3-like (poor prognosis) profiles. To evaluate the prognostic performance of the fuzzy grade signatures in breast cancer tumors, a Kaplan-Meier analysis was conducted to compare the relapse-free survival deduced from histologic grade and fuzzy molecular grade classification. We applied the fuzzy logic selection on breast cancer databases and obtained four new gene signatures. Analysis in the training public sets showed good performance of these gene signatures for grade (sensitivity from 90% to 95%, specificity 67% to 93%). To validate these gene signatures, we designed probes on custom microarrays and tested them on 150 invasive breast carcinomas. Good performance was obtained with an error rate of less than 10%. For one gene signature, among 74 histologic grade 3 and 18 grade 1 tumors, 88 cases (96%) were correctly assigned. Interestingly histologic grade 2 tumors (n = 58) were split in these two molecular grade categories. We confirmed the use of fuzzy logic selection as a new tool to identify gene signatures with good reliability and increased classification power. This method based on artificial intelligence algorithms was successfully

  12. The virtual cell animation collection: tools for teaching molecular and cellular biology.

    Directory of Open Access Journals (Sweden)

    Katie M Reindl

    2015-04-01

    Full Text Available A cell is a minifactory in which structures and molecules are assembled, rearranged, disassembled, packaged, sorted, and transported. Because cellular structures and molecules are invisible to the human eye, students often have difficulty conceptualizing the dynamic nature of cells that function at multiple scales across time and space. To represent these dynamic cellular processes, the Virtual Cell Productions team at North Dakota State University develops freely available multimedia materials to support molecular and cellular biology learning inside and outside the high school and university classroom.

  13. The virtual cell animation collection: tools for teaching molecular and cellular biology.

    Science.gov (United States)

    Reindl, Katie M; White, Alan R; Johnson, Christina; Vender, Bradley; Slator, Brian M; McClean, Phillip

    2015-04-01

    A cell is a minifactory in which structures and molecules are assembled, rearranged, disassembled, packaged, sorted, and transported. Because cellular structures and molecules are invisible to the human eye, students often have difficulty conceptualizing the dynamic nature of cells that function at multiple scales across time and space. To represent these dynamic cellular processes, the Virtual Cell Productions team at North Dakota State University develops freely available multimedia materials to support molecular and cellular biology learning inside and outside the high school and university classroom.

  14. Using Augmented Reality to Bring interactivity to Metabolism Teaching

    Directory of Open Access Journals (Sweden)

    Galembeck E.

    2014-08-01

    Full Text Available INTRODUCTION: A glycolysis paper puzzle designed to introduce students to theprinciples of metabolic pathways have being used for several years, and it seems to helpstudents to learn the topic. We noticed that both the number of instructors and the timethey spend with the students, plays a major role in the success of the activity. Aninsufficient number of instructors do not permit adequate contact with all the students,which frustrate and discourage them. OBJECTIVES: In order to bring this activity to largeraudiences with a few instructors, we added a technological tool called augmented reality tothe paper puzzle. MATERIALS AND METHODS: The app was developed using Unity, and3D molecules obtained from Protein Data Bank. RESULTS AND DISCUSSION: Using thisapp the students were able to check their achievements as they progress through theactivity. The augmented reality also allowed the addition of more information to the cardslike answers to frequently asked questions and information via flashcards. The virtualflashcards displayed on the tablet screens show information such as the molecular 3Dstructure, and clues for assembling the puzzle. CONCLUSIONS: The above-mentionedtechnological improvement has enabled its use in larger classrooms with fewer instructorssince the students are able to have access to clues and discuss with the peers. Thus, thepaper puzzle is still the way students interact with each other, but the technological supportgives them more autonomy to solve the proposed exercises.

  15. The high resolution melting analysis (HRM) as a molecular tool for monitoring parasites of the wildlife.

    Science.gov (United States)

    Héritier, Laurent; Verneau, Olivier; Breuil, Gregory; Meistertzheim, Anne-Leila

    2017-04-01

    In an interconnected world, the international pet trade on wild animals is becoming increasingly important. As a consequence, non-native parasite species are introduced, which affect the health of wildlife and contribute to the loss of biodiversity. Because the investigation of parasite diversity within vulnerable host species implies the molecular identification of large samples of parasite eggs, the sequencing of DNA barcodes is time-consuming and costly. Thereby, the objectives of our study were to apply the high resolution melting (HRM) approach for species determination from pools of parasite eggs. Molecular assays were validated on flatworm parasites (polystomes) infecting the Mediterranean pond turtle Mauremys leprosa and the invasive red-eared slider Trachemys scripta elegans in French natural environments. HRM analysis results indicated that double or multiple parasitic infections could be detected from wild animal populations. They also showed that the cycle of parasite eggs production was not regular over time and may depend on several factors, among which the ecological niche and the target species. Thereby, monitoring parasites from wild endangered animals implies periodic parasitological surveys to avoid false negative diagnostics, based solely on eggs production.

  16. Molecularly Imprinted Polymer of Colocynthin, An Effective Tool for Quality Control of Citrullus colocynthis Extracts.

    Science.gov (United States)

    Farid, Ramezani; Mahnaz, Khanavi; Ardekani Mohammad Reza, Shams; Börje, Sellergren; Mahdieh, Eftekhari; Hossein, Rastegar; Maryam, Shekarchi

    2017-01-01

    Different parts of Colocynth, Citrullus colocynthis (L.) Schrad., are used in traditional phytotherapy and homeopathy. In our new approach, a molecularly imprinted polymer was synthesized to absorb colocynthin, the major plant marker, and its capability was evaluated using HPLC-UV. A new method was considered to achieve optimal conditions. FT-infrared, N2 adsorption porosimetry, fluorescent and scanning electron microscopy and thermo gravimetric profile of the polymers were studied. The imprinted polymer was applied as molecularly imprinted solid phase extraction sorbent to enrich colocynthin from colocynth oil extract, a traditional medicine dosage form. The imprinted polymer showed high capacity and affinity toward colocynthin. Physical assessments demonstrated no major differences between imprinted and nonimprinted polymers. The imprinted polymer was able to absorb colocynthin more efficiently than non-imprinted and control simple solvent extraction from the real sample. In conclusion, this polymer is capable of being applied as a promising adsorbent for analysis of colocynth traditional medicine products. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  17. Breaching Biological Barriers: Protein Translocation Domains as Tools for Molecular Imaging and Therapy

    Directory of Open Access Journals (Sweden)

    Benjamin L. Franc

    2003-10-01

    Full Text Available The lipid bilayer of a cell presents a significant barrier for the delivery of many molecular imaging reagents into cells at target sites in the body. Protein translocation domains (PTDs are peptides that breach this barrier. Conjugation of PTDs to imaging agents can be utilized to facilitate the delivery of these agents through the cell wall, and in some cases, into the cell nucleus, and have potential for in vitro and in vivo applications. PTD imaging conjugates have included small molecules, peptides, proteins, DNA, metal chelates, and magnetic nanoparticles. The full potential of the use of PTDs in novel in vivo molecular probes is currently under investigation. Cells have been labeled in culture using magnetic nanoparticles derivatized with a PTD and monitored in vivo to assess trafficking patterns relative to cells expressing a target antigen. In vivo imaging of PTD-mediated gene transfer to cells of the skin has been demonstrated in living animals. Here we review several natural and synthetic PTDs that have evolved in the quest for easier translocation across biological barriers and the application of these peptide domains to in vivo delivery of imaging agents.

  18. Development, optimization, and integration of molecular fitting tools and models in UCSF Chimera.

    OpenAIRE

    Solar Rodríguez, Pablo

    2017-01-01

    This project lies within the field of structural biology and will be focused on computational tools development to integrate 3D information of proteins and nucleic acids from different experimental sources such as cryo-electron microscopy (EM) or X-ray crystallography. El TFM se encuadra en el campo de la bioinformática estructural y se centra en el desarrollo de herramientas computacionales para interpretar información 3D de proteínas y ácidos nucleicos proveniente de distintas fuentes ex...

  19. Discerning molecular interactions: A comprehensive review on biomolecular interaction databases and network analysis tools.

    Science.gov (United States)

    Miryala, Sravan Kumar; Anbarasu, Anand; Ramaiah, Sudha

    2017-11-09

    Computational analysis of biomolecular interaction networks is now gaining a lot of importance to understand the functions of novel genes/proteins. Gene interaction (GI) network analysis and protein-protein interaction (PPI) network analysis play a major role in predicting the functionality of interacting genes or proteins and gives an insight into the functional relationships and evolutionary conservation of interactions among the genes. An interaction network is a graphical representation of gene/protein interactome, where each gene/protein is a node, and interaction between gene/protein is an edge. In this review, we discuss the popular open source databases that serve as data repositories to search and collect protein/gene interaction data, and also tools available for the generation of interaction network, visualization and network analysis. Also, various network analysis approaches like topological approach and clustering approach to study the network properties and functional enrichment server which illustrates the functions and pathway of the genes and proteins has been discussed. Hence the distinctive attribute mentioned in this review is not only to provide an overview of tools and web servers for gene and protein-protein interaction (PPI) network analysis but also to extract useful and meaningful information from the interaction networks. Copyright © 2017. Published by Elsevier B.V.

  20. Toward in silico prediction of glass-forming ability from molecular structure alone: a screening tool in early drug development.

    Science.gov (United States)

    Mahlin, Denny; Ponnambalam, Sopana; Höckerfelt, Mina Heidarian; Bergström, Christel A S

    2011-04-04

    We present a novel computational tool which predicts the glass-forming ability of drug compounds solely from their molecular structure. Compounds which show solid-state limited aqueous solubility were selected, and their glass-forming ability was determined upon spray-drying, melt-quenching and mechanical activation. The solids produced were analyzed by differential scanning calorimetry (DSC) and powder X-ray diffraction. Compounds becoming at least partially amorphous on processing were classified as glass-formers, whereas those remaining crystalline regardless of the process method were classified as non-glass-forming compounds. A predictive model of the glass-forming ability, designed to separate between these two classes, was developed through the use of partial least-squares projection to latent structure discriminant analysis (PLS-DA) and calculated molecular descriptors. In total, ten of the 16 compounds were determined experimentally to be good glass-formers and the PLS-DA model correctly sorted 15 of the compounds using four molecular descriptors only. An external test set was predicted with an accuracy of 75%, and, hence, the PLS-DA model developed was shown to be applicable for the identification of compounds that have the potential to be designed as amorphous formulations. The model suggests that larger molecules with a low number of benzene rings, low level of molecular symmetry, branched carbon skeletons and electronegative atoms have the ability to form a glass. To conclude, we have developed a predictive, transparent and interpretable computational model for the identification of drug molecules capable of being glass-formers. The model allows an assessment of amorphization as a formulation strategy in the early drug development process, and can be applied before compound synthesis.

  1. Bring Your Own Device: Parental Guidance (PG) Suggested

    Science.gov (United States)

    Kiger, Derick; Herro, Dani

    2015-01-01

    Educators are incorporating students' mobile devices into the schooling experience via Bring Your Own Device (BYOD) initiatives. This is advantageous for many reasons, most notably, improving access to Internet resources and digital tools in support of teaching and learning. Obtaining parental support is key to BYOD success. Therefore, this study…

  2. Bringing Foreign Language Learning into the 21st century | Thomas ...

    African Journals Online (AJOL)

    Bringing Foreign Language Learning into the 21st Century. The different challenges facing foreign language lecturers are considered as well as the different methods used to teach a foreign language. Technology and multimedia are proposed not only as tools and supports but also as a possible solution. With the change ...

  3. Parasite zoonoses and climate change: molecular tools for tracking shifting boundaries.

    Science.gov (United States)

    Polley, Lydden; Thompson, R C Andrew

    2009-06-01

    For human, domestic animal and wildlife health, key effects of directional climate change include the risk of the altered occurrence of infectious diseases. Many parasite zoonoses have high potential for vulnerability to the new climate, in part because their free-living life-cycle stages and ectothermic hosts are directly exposed to climatic conditions. For these zoonoses, climate change can shift boundaries for ecosystem components and processes integral to parasite transmission and persistence, and these shifts can impact host health. Vulnerable boundaries include those for spatial distributions, host-parasite assemblages, demographic rates, life-cycle phenologies, associations within ecosystems, virulence, and patterns of infection and disease. This review describes these boundary shifts and how molecular techniques can be applied to defining the new boundaries.

  4. Detection of molecular biomarkers as a diagnostic tool in the planning and progression of orthodontic treatment

    Directory of Open Access Journals (Sweden)

    Aditi Gaur

    2017-01-01

    Full Text Available Orthodontic treatment focuses on providing patient care at the appropriate timing to utilize the growth potential for best results. It involves growth modification of the craniofacial region along with alveolar bone remodeling during tooth movement. The dynamic process of bone metabolism involves the release of biochemical mediators in the circulation. These molecules are indicative of the bone remodeling activity of osteoblastic deposition and osteoclastic resorption. Such biomarkers when detectable in the systemic circulation highlight the skeletal maturity of orthodontic patients and when detected locally as, in gingival crevicular fluid (GCF and saliva, indicate the progression of orthodontically induced alveolar bone remodeling. Assessment of molecular biomarkers of bone remodeling in the body fluids would aid the clinicians in planning orthodontic treatment at the ideal timing and evaluating the advent of the treatment.

  5. Phenotypic Prenatal Diagnosis of Chronic Granulomatous Disease: A Useful Tool in The Absence Of Molecular Diagnosis.

    Science.gov (United States)

    Kulkarni, M; Gupta, M; Madkaikar, M

    2017-12-01

    Chronic granulomatous disease (CGD) is an inherited immunodeficiency disorder affecting the microbicidal function of the phagocytes. It is characterized by susceptibility to recurrent infections leading to significant morbidity and mortality. Antibacterial and antifungal prophylaxis, though, has significantly reduced the rate and severity of the infections; the breakthrough infections still remain a challenge. Currently, allogenic haematopoietic stem cell transplantation is the only curative option which is very expensive and unavailable for many due to lack of suitable donor. Thus, prenatal diagnosis (PND) forms an important component of management in the affected families. PND is challenging in families approaching late in pregnancy with an uncharacterized molecular defect. In such cases, PND can be performed by analysis of NADPH activity of fetal blood (FB) neutrophils at 18-20 weeks of gestation. Cord blood samples at 18 weeks of gestation from healthy control were used to establish normal ranges for NBT and DHR. PND was offered for six pregnancies (NBT: n = 3, DHR: n = 6) with index cases of CGD confirmed by abnormal NBT and DHR analysis. NBT and DHR tests were found to be negative for all the six cases, confirming the same on samples post-delivery. NBT and DHR tests offer a rapid and sensitive PND of CGD in the absence of facilities for molecular diagnosis. It was observed that addition of CD15 along with CD45 led to an accurate DHR analysis. It is recommended to perform the diagnosis with adequate precautions only at centres with considerable experience and expertise in the diagnosis of CGD. © 2017 The Foundation for the Scandinavian Journal of Immunology.

  6. A new molecular diagnostic tool for surveying and monitoring Triops cancriformis populations

    Directory of Open Access Journals (Sweden)

    Graham S. Sellers

    2017-05-01

    Full Text Available The tadpole shrimp, Triops cancriformis, is a freshwater crustacean listed as endangered in the UK and Europe living in ephemeral pools. Populations are threatened by habitat destruction due to land development for agriculture and increased urbanisation. Despite this, there is a lack of efficient methods for discovering and monitoring populations. Established macroinvertebrate monitoring methods, such as net sampling, are unsuitable given the organism’s life history, that include long lived diapausing eggs, benthic habits and ephemerally active populations. Conventional hatching methods, such as sediment incubation, are both time consuming and potentially confounded by bet-hedging hatching strategies of diapausing eggs. Here we develop a new molecular diagnostic method to detect viable egg banks of T. cancriformis, and compare its performance to two conventional monitoring methods involving diapausing egg hatching. We apply this method to a collection of pond sediments from the Wildfowl & Wetlands Trust Caerlaverock National Nature Reserve, which holds one of the two remaining British populations of T. cancriformis. DNA barcoding of isolated eggs, using newly designed species-specific primers for a large region of mtDNA, was used to estimate egg viability. These estimates were compared to those obtained by the conventional methods of sediment and isolation hatching. Our method outperformed the conventional methods, revealing six ponds holding viable T. cancriformis diapausing egg banks in Caerlaverock. Additionally, designed species-specific primers for a short region of mtDNA identified degraded, inviable eggs and were used to ascertain the levels of recent mortality within an egg bank. Together with efficient sugar flotation techniques to extract eggs from sediment samples, our molecular method proved to be a faster and more powerful alternative for assessing the viability and condition of T. cancriformis diapausing egg banks.

  7. Biochemical and molecular tools reveal two diverse Xanthomonas groups in bananas

    DEFF Research Database (Denmark)

    Adriko, John; Aritua, V.; Mortensen, Carmen Nieves

    2016-01-01

    of tools provides the most accurate identity and characterization of these plant associated bacteria. The interactions between the pathogenic and non-pathogenic xanthomonads in bananas may pave way to understanding effect of microbial interactions on BXW disease development and offer clues to biocontrol...... pathogenic and non-pathogenic xanthomonads. In this study, gram-negative and yellow-pigmented mucoid bacteria were isolated from BXW symptomatic and symptomless bananas collected from different parts of Uganda. Biolog, Xcm-specific (GspDm), Xanthomonas vasicola species-specific (NZ085) and Xanthomonas genus......-specific (X1623) primers in PCR, and sequencing of ITS region were used to identify and characterize the isolates. Biolog tests revealed several isolates as xanthomonads. The GspDm and NZ085 primers accurately identified three isolates from diseased bananas as Xcm and these were pathogenic when re...

  8. BYOD: Bring your own disaster

    CERN Multimedia

    Computer Security Team

    2013-01-01

    Have you ever heard of “BYOD”? No, it is not a pop band. Try again. It is short for “Bring Your Own Device” (the French use “AVEC” -  “Apporter Votre Equipement personnel de Communication”) and describes an option long since offered at CERN: the possibility to bring along your personal laptop, smartphone or PDA, use it on CERN premises and connect it to the CERN office network. But hold on. As practical as it is, there is also a dark side.   The primary advantage, of course, is having a digital work environment tuned to your needs and preferences. It allows you to continue working at home. Similarly, you always have your music, address books and bookmarks with you. However, as valuable as this is, it is also a responsibility. Laptop theft is happening - outside CERN but also on site. In France, 30% of stolen laptops were stolen out of cars or homes, and 10% during travel. At CERN, on average one ...

  9. How to get more out of molecular fingerprints: practical tools for microbial ecology.

    Science.gov (United States)

    Marzorati, Massimo; Wittebolle, Lieven; Boon, Nico; Daffonchio, Daniele; Verstraete, Willy

    2008-06-01

    Community-level molecular techniques are widely used in comparative microbial ecology to assess the diversity of microbial communities and their response to changing environments. These include among others denaturing and temperature gradient gel electrophoresis (DGGE/TGGE), single-strand conformation polymorphism (SSCP), length heterogeneity-PCR (LH-PCR), terminal-restriction fragment length polymorphism (tRFLP) and 16S rRNA gene clone libraries. The amount of data derived from these techniques available in literature is continuously increasing and the lack of a universal way to interpret the raw fingerprint itself makes it difficult to compare between different results. Taking the DGGE technique as an example, we propose a setting-independent theoretical interpretation of the DGGE pattern, based on a straightforward processing on three levels of analysis: (i) the range-weighted richness (Rr) reflecting the carrying capacity of the system, (ii) the dynamics (Dy) reflecting the specific rate of species coming to significance, and (iii) functional organization (Fo), defined through a relation between the structure of a microbial community and its functionality. These Rr, Dy and Fo values, each representing a score to describe a microbial community, can be plotted in a 3D graph. The latter represents a visual ecological interpretation of the initial raw fingerprinting pattern.

  10. DNA Barcoding as a Molecular Tool to Track Down Mislabeling and Food Piracy

    Directory of Open Access Journals (Sweden)

    Gianni Barcaccia

    2015-12-01

    Full Text Available DNA barcoding is a molecular technology that allows the identification of any biological species by amplifying, sequencing and querying the information from genic and/or intergenic standardized target regions belonging to the extranuclear genomes. Although these sequences represent a small fraction of the total DNA of a cell, both chloroplast and mitochondrial barcodes chosen for identifying plant and animal species, respectively, have shown sufficient nucleotide diversity to assess the taxonomic identity of the vast majority of organisms used in agriculture. Consequently, cpDNA and mtDNA barcoding protocols are being used more and more in the food industry and food supply chains for food labeling, not only to support food safety but also to uncover food piracy in freshly commercialized and technologically processed products. Since the extranuclear genomes are present in many copies within each cell, this technology is being more easily exploited to recover information even in degraded samples or transformed materials deriving from crop varieties and livestock species. The strong standardization that characterizes protocols used worldwide for DNA barcoding makes this technology particularly suitable for routine analyses required by agencies to safeguard food safety and quality. Here we conduct a critical review of the potentials of DNA barcoding for food labeling along with the main findings in the area of food piracy, with particular reference to agrifood and livestock foodstuffs.

  11. Molecular and biochemical taxonomic tools for the identification and classification of plant-pathogenic Penicillium species

    Directory of Open Access Journals (Sweden)

    Mohamed A. Mahmoud

    2016-11-01

    Full Text Available Five species of Penicillium (Penicillium chrysogenum, P. funiculosum, P. griseofulvum, P. implicatum and P. oxalicum are implicated in seed-borne diseases. Here, we report the discovery of molecular markers based on the internal transcribed spacer regions of fungal ribosomal DNA (rDNA, which are described as primary DNA barcode markers of fungi, for rapid diagnosis and early detection of Penicillium spp. The present markers are expected to be useful for the prevention of seedling and systemic plant diseases associated with Penicillium spp. Our findings, which provide valuable insights into the taxonomy of Penicillium spp., should contribute to improve safety of agricultural produce, thereby protecting both humans and animals from harmful food contaminants such as mycotoxins. In addition, we examined the cellular fatty acid composition of five species of Penicillium. The species studied were found to possess similar fatty acid composition; however, they differed in terms of relative concentration. The principal fatty acids were oleic acid (C18:1 and linoleic acid (C18:2, comprising 80% or more of the total fatty acid composition of these species. These fatty acid profiles may be useful for characterization and identification of fungi. Data derived from the present study highlight the importance of using polyphasic methods for accurate species-level identification of Penicillium.

  12. Intense electron beams from GaAs photocathodes as a tool for molecular and atomic physics

    Energy Technology Data Exchange (ETDEWEB)

    Krantz, Claude

    2009-10-28

    We present cesium-coated GaAs photocathodes as reliable sources of intense, quasi-monoenergetic electron beams in atomic and molecular physics experiments. In long-time operation of the Electron Target of the ion storage ring TSR in Heidelberg, cold electron beams could be realised at steadily improving intensity and reliability. Minimisation of processes degrading the quantum efficiency allowed to increase the extractable current to more than 1mA at usable cathode lifetimes of 24 h or more. The benefits of the cold electron beam with respect to its application to electron cooling and electron-ion recombination experiments are discussed. Benchmark experiments demonstrate the superior cooling force and energy resolution of the photoelectron beam compared to its thermionic counterparts. The long period of operation allowed to study the long-time behaviour of the GaAs samples during multiple usage cycles at the Electron Target and repeated in-vacuum surface cleaning by atomic hydrogen exposure. An electron emission spectroscopy setup has been implemented at the photocathode preparation chamber of the Electron Target. Among others, this new facility opened the way to a novel application of GaAs (Cs) photocathodes as robust, ultraviolet-driven electron emitters. Based on this principle, a prototype of an electron gun, designed for implementation at the HITRAP setup at GSI, has been built and taken into operation successfully. (orig.)

  13. Molecular tools and bumble bees: revealing hidden details of ecology and evolution in a model system.

    Science.gov (United States)

    Woodard, S Hollis; Lozier, Jeffrey D; Goulson, David; Williams, Paul H; Strange, James P; Jha, Shalene

    2015-06-01

    Bumble bees are a longstanding model system for studies on behaviour, ecology and evolution, due to their well-studied social lifestyle, invaluable role as wild and managed pollinators, and ubiquity and diversity across temperate ecosystems. Yet despite their importance, many aspects of bumble bee biology have remained enigmatic until the rise of the genetic and, more recently, genomic eras. Here, we review and synthesize new insights into the ecology, evolution and behaviour of bumble bees that have been gained using modern genetic and genomic techniques. Special emphasis is placed on four areas of bumble bee biology: the evolution of eusociality in this group, population-level processes, large-scale evolutionary relationships and patterns, and immunity and resistance to pesticides. We close with a prospective on the future of bumble bee genomics research, as this rapidly advancing field has the potential to further revolutionize our understanding of bumble bees, particularly in regard to adaptation and resilience. Worldwide, many bumble bee populations are in decline. As such, throughout the review, connections are drawn between new molecular insights into bumble bees and our understanding of the causal factors involved in their decline. Ongoing and potential applications to bumble bee management and conservation are also included to demonstrate how genetics- and genomics-enabled research aids in the preservation of this threatened group. © 2015 John Wiley & Sons Ltd.

  14. Molecular inversion probe: a new tool for highly specific detection of plant pathogens.

    Directory of Open Access Journals (Sweden)

    Han Yih Lau

    Full Text Available Highly specific detection methods, capable of reliably identifying plant pathogens are crucial in plant disease management strategies to reduce losses in agriculture by preventing the spread of diseases. We describe a novel molecular inversion probe (MIP assay that can be potentially developed into a robust multiplex platform to detect and identify plant pathogens. A MIP has been designed for the plant pathogenic fungus Fusarium oxysporum f.sp. conglutinans and the proof of concept for the efficiency of this technology is provided. We demonstrate that this methodology can detect as little as 2.5 ng of pathogen DNA and is highly specific, being able to accurately differentiate Fusarium oxysporum f.sp. conglutinans from other fungal pathogens such as Botrytis cinerea and even pathogens of the same species such as Fusarium oxysporum f.sp. lycopersici. The MIP assay was able to detect the presence of the pathogen in infected Arabidopsis thaliana plants as soon as the tissues contained minimal amounts of pathogen. MIP methods are intrinsically highly multiplexable and future development of specific MIPs could lead to the establishment of a diagnostic method that could potentially screen infected plants for hundreds of pathogens in a single assay.

  15. Molecular inversion probe: a new tool for highly specific detection of plant pathogens.

    Science.gov (United States)

    Lau, Han Yih; Palanisamy, Ramkumar; Trau, Matt; Botella, Jose R

    2014-01-01

    Highly specific detection methods, capable of reliably identifying plant pathogens are crucial in plant disease management strategies to reduce losses in agriculture by preventing the spread of diseases. We describe a novel molecular inversion probe (MIP) assay that can be potentially developed into a robust multiplex platform to detect and identify plant pathogens. A MIP has been designed for the plant pathogenic fungus Fusarium oxysporum f.sp. conglutinans and the proof of concept for the efficiency of this technology is provided. We demonstrate that this methodology can detect as little as 2.5 ng of pathogen DNA and is highly specific, being able to accurately differentiate Fusarium oxysporum f.sp. conglutinans from other fungal pathogens such as Botrytis cinerea and even pathogens of the same species such as Fusarium oxysporum f.sp. lycopersici. The MIP assay was able to detect the presence of the pathogen in infected Arabidopsis thaliana plants as soon as the tissues contained minimal amounts of pathogen. MIP methods are intrinsically highly multiplexable and future development of specific MIPs could lead to the establishment of a diagnostic method that could potentially screen infected plants for hundreds of pathogens in a single assay.

  16. An interaction network predicted from public data as a discovery tool: application to the Hsp90 molecular chaperone machine.

    Directory of Open Access Journals (Sweden)

    Pablo C Echeverría

    Full Text Available Understanding the functions of proteins requires information about their protein-protein interactions (PPI. The collective effort of the scientific community generates far more data on any given protein than individual experimental approaches. The latter are often too limited to reveal an interactome comprehensively. We developed a workflow for parallel mining of all major PPI databases, containing data from several model organisms, and to integrate data from the literature for a protein of interest. We applied this novel approach to build the PPI network of the human Hsp90 molecular chaperone machine (Hsp90Int for which previous efforts have yielded limited and poorly overlapping sets of interactors. We demonstrate the power of the Hsp90Int database as a discovery tool by validating the prediction that the Hsp90 co-chaperone Aha1 is involved in nucleocytoplasmic transport. Thus, we both describe how to build a custom database and introduce a powerful new resource for the scientific community.

  17. Transition metal-catalyzed C-H bond functionalization in multicomponent reactions: a tool toward molecular diversity.

    Science.gov (United States)

    Wan, Jie-Ping; Gan, Lu; Liu, Yunyun

    2017-11-07

    Transition metal-catalyzed C-H bond functionalization has numerous applications in organic synthesis as a powerful type of bond transformation. In particular, the combination of C-H functionalization with other types of chemical transformations in the manner of multicomponent reactions is an even more beneficial tool in the synthesis of small organic molecules because such reactions provide a platform for the rapid generation of high molecular diversity and complexity by making use of the advantages of both latent C-H bond transformation and the multicomponent reaction. Herein, we provide a review highlighting the research advances in the multicomponent reactions built upon transition metal-catalyzed C-H bond functionalization. The content spans from the reactions featuring the functionalization of C(sp(3))-H, C(sp(2))-H and C(sp)-H bonds over the last decade.

  18. Biodiversity Patterns on an Inshore to Offshore Gradient Using Metabarcoding and Barcoding Molecular Tools

    KAUST Repository

    Villalobos Vazquez de la Parra, Rodrigo

    2015-12-01

    It has been estimated that coral reefs shelter 830 000 species. Well-studied biodiversity patterns provide tools for better representation of species in marine protected areas. A cross-shelf gradient in biodiversity exists for fishes, corals, and macroalgae. Here, an inshore to offshore gradient in biodiversity on the Saudi Arabian coast of the Red Sea was sampled using Autonomous Reef Monitoring Structures (ARMS) with barcoding and metabarcoding techniques. It was hypothesized that differences in community structure would be driven by an increase in habitat area. The difference was attributed to the greater accumulation of sediments close to shore that increases the area habitable for sediment dwelling organisms and favors macroalgal cover. Macroalgae are inhabited by a greater number of species than live coral. Only 10% of the sequences of the barcoded fraction and <1% of the metabarcoded fraction had a BLAST hit on the NCBI database with a previously identified species sequence. In addition, the rarefaction curves for all fractions did not plateau. The ARMS community composition changed from inshore to offshore and was significantly correlated with the percentage of algal and bryozoan plate cover. The differences in community composition were related to changes in habitat but not to sediments retrieved from the ARMS.

  19. Genetic engineering: a promising tool to engender physiological, biochemical and molecular stress resilience in green microalgae

    Directory of Open Access Journals (Sweden)

    Freddy eGuiheneuf

    2016-03-01

    Full Text Available As we march into the 21st century, the prevailing scenario of depleting energy resources, global warming and ever increasing issues of human health and food security will quadruple. In this context, genetic and metabolic engineering of green microalgae complete the quest towards a continuum of environmentally clean fuel and food production. Evolutionarily related, but unlike land plants, microalgae need nominal land or water, and are best described as unicellular autotrophs using light energy to fix atmospheric CO2 into algal biomass, mitigating fossil CO2 pollution in the process. Remarkably, a feature innate to most microalgae is synthesis and accumulation of lipids (60–65% of dry weight, carbohydrates and secondary metabolites like pigments and vitamins, especially when grown under abiotic stress conditions. Particularly fruitful, such an application of abiotic stress factors like nitrogen starvation , salinity, heat shock etc. can be used in a biorefinery concept for production of multiple valuable products. The focus of this mini-review underlies metabolic reorientation practices and tolerance mechanisms as applied to green microalgae under specific stress stimuli for a sustainable pollution-free future. Moreover, we entail current progress on genetic engineering as a promising tool to grasp adaptive processes for improving strains with potential biotechnological interests.

  20. Genetic Engineering: A Promising Tool to Engender Physiological, Biochemical, and Molecular Stress Resilience in Green Microalgae

    Science.gov (United States)

    Guihéneuf, Freddy; Khan, Asif; Tran, Lam-Son P.

    2016-01-01

    As we march into the 21st century, the prevailing scenario of depleting energy resources, global warming and ever increasing issues of human health and food security will quadruple. In this context, genetic and metabolic engineering of green microalgae complete the quest toward a continuum of environmentally clean fuel and food production. Evolutionarily related, but unlike land plants, microalgae need nominal land or water, and are best described as unicellular autotrophs using light energy to fix atmospheric carbon dioxide (CO2) into algal biomass, mitigating fossil CO2 pollution in the process. Remarkably, a feature innate to most microalgae is synthesis and accumulation of lipids (60–65% of dry weight), carbohydrates and secondary metabolites like pigments and vitamins, especially when grown under abiotic stress conditions. Particularly fruitful, such an application of abiotic stress factors such as nitrogen starvation, salinity, heat shock, etc., can be used in a biorefinery concept for production of multiple valuable products. The focus of this mini-review underlies metabolic reorientation practices and tolerance mechanisms as applied to green microalgae under specific stress stimuli for a sustainable pollution-free future. Moreover, we entail current progress on genetic engineering as a promising tool to grasp adaptive processes for improving strains with potential biotechnological interests. PMID:27066043

  1. Multimode sensors as new tools for molecular recognition of testosterone, dihydrotestosterone and estradiol in children's saliva.

    Science.gov (United States)

    Gugoasa, Livia Alexandra; Stefan-van Staden, Raluca-Ioana; Calenic, Bogdan; Legler, Juliette

    2015-01-01

    Increased levels of testosterone (T2 ), dihydrotestosterone (DHT) and estradiol (E2 ) in children may be responsible for their early/delayed puberty and obesity conditions. Therefore, multimode sensors based on carbon matrices, such as graphite, graphene, fullerene C60 and multiwall carbon nanotubes modified with maltodextrin, were designed to assess reliably T2 , DHT and E2 in children saliva. The modes used for the assay of hormones were stochastic mode (for qualitative and quantitative determination of hormones) and differential pulse voltammetry mode (for quantitative determination of hormones). The advantage of this type of sensors, for hormone analysis, is their possibility to reach low concentration levels- are placed for children saliva under the detection limit of standard methods (e.g. ELISA used for the determination of these hormones in saliva). This made the multimode sensors an excellent tool for clinical analysis and especially for determination of substances of clinical importance in saliva samples. The proposed method is fast and simple, and no sampling of saliva is required. Copyright © 2014 John Wiley & Sons, Ltd.

  2. Molecular dynamics simulation: a tool for exploration and discovery using simple models

    Science.gov (United States)

    Rapaport, D. C.

    2014-12-01

    Emergent phenomena share the fascinating property of not being obvious consequences of the design of the system in which they appear. This characteristic is no less relevant when attempting to simulate such phenomena, given that the outcome is not always a foregone conclusion. The present survey focuses on several simple model systems that exhibit surprisingly rich emergent behavior, all studied by molecular dynamics (MD) simulation. The examples are taken from the disparate fields of fluid dynamics, granular matter and supramolecular self-assembly. In studies of fluids modeled at the detailed microscopic level using discrete particles, the simulations demonstrate that complex hydrodynamic phenomena in rotating and convecting fluids—the Taylor-Couette and Rayleigh-Bénard instabilities—can not only be observed within the limited length and time scales accessible to MD, but even allow quantitative agreement to be achieved. Simulation of highly counter-intuitive segregation phenomena in granular mixtures, again using MD methods, but now augmented by forces producing damping and friction, leads to results that resemble experimentally observed axial and radial segregation in the case of a rotating cylinder and to a novel form of horizontal segregation in a vertically vibrated layer. Finally, when modeling self-assembly processes analogous to the formation of the polyhedral shells that package spherical viruses, simulation of suitably shaped particles reveals the ability to produce complete, error-free assembly and leads to the important general observation that reversible growth steps contribute to the high yield. While there are limitations to the MD approach, both computational and conceptual, the results offer a tantalizing hint of the kinds of phenomena that can be explored and what might be discovered when sufficient resources are brought to bear on a problem.

  3. Assessment of the Simulated Molecular Composition with the GECKO-A Modeling Tool Using Chamber Observations for α-Pinene.

    Science.gov (United States)

    Aumont, B.; Camredon, M.; Isaacman-VanWertz, G. A.; Karam, C.; Valorso, R.; Madronich, S.; Kroll, J. H.

    2016-12-01

    Gas phase oxidation of VOC is a gradual process leading to the formation of multifunctional organic compounds, i.e., typically species with higher oxidation state, high water solubility and low volatility. These species contribute to the formation of secondary organic aerosols (SOA) viamultiphase processes involving a myriad of organic species that evolve through thousands of reactions and gas/particle mass exchanges. Explicit chemical mechanisms reflect the understanding of these multigenerational oxidation steps. These mechanisms rely directly on elementary reactions to describe the chemical evolution and track the identity of organic carbon through various phases down to ultimate oxidation products. The development, assessment and improvement of such explicit schemes is a key issue, as major uncertainties remain on the chemical pathways involved during atmospheric oxidation of organic matter. An array of mass spectrometric techniques (CIMS, PTRMS, AMS) was recently used to track the composition of organic species during α-pinene oxidation in the MIT environmental chamber, providing an experimental database to evaluate and improve explicit mechanisms. In this study, the GECKO-A tool (Generator for Explicit Chemistry and Kinetics of Organics in the Atmosphere) is used to generate fully explicit oxidation schemes for α-pinene multiphase oxidation simulating the MIT experiment. The ability of the GECKO-A chemical scheme to explain the organic molecular composition in the gas and the condensed phases is explored. First results of this model/observation comparison at the molecular level will be presented.

  4. CapsID: a web-based tool for developing parsimonious sets of CAPS molecular markers for genotyping

    Directory of Open Access Journals (Sweden)

    Provart Nicholas J

    2006-05-01

    Full Text Available Abstract Background Genotyping may be carried out by a number of different methods including direct sequencing and polymorphism analysis. For a number of reasons, PCR-based polymorphism analysis may be desirable, owing to the fact that only small amounts of genetic material are required, and that the costs are low. One popular and cheap method for detecting polymorphisms is by using cleaved amplified polymorphic sequence, or CAPS, molecular markers. These are also known as PCR-RFLP markers. Results We have developed a program, called CapsID, that identifies snip-SNPs (single nucleotide polymorphisms that alter restriction endonuclease cut sites within a set or sets of reference sequences, designs PCR primers around these, and then suggests the most parsimonious combination of markers for genotyping any individual who is not a member of the reference set. The output page includes biologist-friendly features, such as images of virtual gels to assist in genotyping efforts. CapsID is freely available at http://bbc.botany.utoronto.ca/capsid. Conclusion CapsID is a tool that can rapidly provide minimal sets of CAPS markers for molecular identification purposes for any biologist working in genetics, community genetics, plant and animal breeding, forensics and other fields.

  5. MOVING FROM HISTOPATHOLOGY TO MOLECULAR TOOLS IN THE DIAGNOSIS OF MOLLUSKS DISEASES OF CONCERN UNDER EU LEGISLATION

    Directory of Open Access Journals (Sweden)

    Raquel Aranguren

    2016-11-01

    Full Text Available One of the main factors limiting molluscs production is the presence of pathogens and diseases. Disease agent transfer via transfers of live molluscs has been a major cause of disease outbreaks and epizootics. Because of that, the European Union has adopted several decisions and directives, the last in 2006 (2006/88/EC to control movements of marine organisms over the European countries. Once the disease is established in a determined area its eradication is a complicated task because life cycle of pathogens are not completely known and only a good and early diagnosis of the disease could be the most appropriate way to deal with it. Besides, molluscs do not have an adaptive immune response and vaccination strategies are not possibleMolluscs listed diseases under EU legislation are mainly protozoan parasites, that’s why histological techniques are recognized for their diagnosis. However, molecular techniques are being increasingly used primarily as confirmatory techniques of the presence of the pathogens but also in disease monitoring programs. Research perspectives are mainly focussed in the optimization, of the already described techniques to gain in sensitivity and sensibility and in the development of new molecular biology techniques (quantitative real time PCRs, that are faster and easier to apply and that allow a positive diagnosis even in early stages of infection. However, molecular tools detect DNA sequences of the pathogen which does not imply that pathogen is viable in the cell host and the infection is established. Consequently, it needs to be validated against other techniques, such as histology or in situ hybridization, so that its reliability can be determined.

  6. Biochemical and molecular tools reveal two diverse Xanthomonas groups in bananas.

    Science.gov (United States)

    Adriko, J; Aritua, V; Mortensen, C N; Tushemereirwe, W K; Mulondo, A L; Kubiriba, J; Lund, O S

    2016-02-01

    Xanthomonas campestris pv. musacearum (Xcm) causing the banana Xanthomonas wilt (BXW) disease has been the main xanthomonad associated with bananas in East and Central Africa based on phenotypic and biochemical characteristics. However, biochemical methods cannot effectively distinguish between pathogenic and non-pathogenic xanthomonads. In this study, gram-negative and yellow-pigmented mucoid bacteria were isolated from BXW symptomatic and symptomless bananas collected from different parts of Uganda. Biolog, Xcm-specific (GspDm), Xanthomonas vasicola species-specific (NZ085) and Xanthomonas genus-specific (X1623) primers in PCR, and sequencing of ITS region were used to identify and characterize the isolates. Biolog tests revealed several isolates as xanthomonads. The GspDm and NZ085 primers accurately identified three isolates from diseased bananas as Xcm and these were pathogenic when re-inoculated into bananas. DNA from more isolates than those amplified by GspDm and NZ085 primers were amplified by the X1623 primers implying they are xanthomonads, these were however non-pathogenic on bananas. In the 16-23 ITS sequence based phylogeny, the pathogenic bacteria clustered together with the Xcm reference strain, while the non-pathogenic xanthomonads isolated from both BXW symptomatic and symptomless bananas clustered with group I xanthomonads. The findings reveal dynamic Xanthomonas populations in bananas, which can easily be misrepresented by only using phenotyping and biochemical tests. A combination of tools provides the most accurate identity and characterization of these plant associated bacteria. The interactions between the pathogenic and non-pathogenic xanthomonads in bananas may pave way to understanding effect of microbial interactions on BXW disease development and offer clues to biocontrol of Xcm. Copyright © 2016. Published by Elsevier GmbH.

  7. Use of Molecular Diagnostic Tools for the Identification of Species Responsible for Snakebite in Nepal: A Pilot Study.

    Directory of Open Access Journals (Sweden)

    Sanjib Kumar Sharma

    2016-04-01

    Full Text Available Snakebite is an important medical emergency in rural Nepal. Correct identification of the biting species is crucial for clinicians to choose appropriate treatment and anticipate complications. This is particularly important for neurotoxic envenoming which, depending on the snake species involved, may not respond to available antivenoms. Adequate species identification tools are lacking. This study used a combination of morphological and molecular approaches (PCR-aided DNA sequencing from swabs of bite sites to determine the contribution of venomous and non-venomous species to the snakebite burden in southern Nepal. Out of 749 patients admitted with a history of snakebite to one of three study centres, the biting species could be identified in 194 (25.9%. Out of these, 87 had been bitten by a venomous snake, most commonly the Indian spectacled cobra (Naja naja; n = 42 and the common krait (Bungarus caeruleus; n = 22. When both morphological identification and PCR/sequencing results were available, a 100% agreement was noted. The probability of a positive PCR result was significantly lower among patients who had used inadequate "first aid" measures (e.g. tourniquets or local application of remedies. This study is the first to report the use of forensic genetics methods for snake species identification in a prospective clinical study. If high diagnostic accuracy is confirmed in larger cohorts, this method will be a very useful reference diagnostic tool for epidemiological investigations and clinical studies.

  8. IBiSA_Tools: A Computational Toolkit for Ion-Binding State Analysis in Molecular Dynamics Trajectories of Ion Channels.

    Science.gov (United States)

    Kasahara, Kota; Kinoshita, Kengo

    2016-01-01

    Ion conduction mechanisms of ion channels are a long-standing conundrum. Although the molecular dynamics (MD) method has been extensively used to simulate ion conduction dynamics at the atomic level, analysis and interpretation of MD results are not straightforward due to complexity of the dynamics. In our previous reports, we proposed an analytical method called ion-binding state analysis to scrutinize and summarize ion conduction mechanisms by taking advantage of a variety of analytical protocols, e.g., the complex network analysis, sequence alignment, and hierarchical clustering. This approach effectively revealed the ion conduction mechanisms and their dependence on the conditions, i.e., ion concentration and membrane voltage. Here, we present an easy-to-use computational toolkit for ion-binding state analysis, called IBiSA_tools. This toolkit consists of a C++ program and a series of Python and R scripts. From the trajectory file of MD simulations and a structure file, users can generate several images and statistics of ion conduction processes. A complex network named ion-binding state graph is generated in a standard graph format (graph modeling language; GML), which can be visualized by standard network analyzers such as Cytoscape. As a tutorial, a trajectory of a 50 ns MD simulation of the Kv1.2 channel is also distributed with the toolkit. Users can trace the entire process of ion-binding state analysis step by step. The novel method for analysis of ion conduction mechanisms of ion channels can be easily used by means of IBiSA_tools. This software is distributed under an open source license at the following URL: http://www.ritsumei.ac.jp/~ktkshr/ibisa_tools/.

  9. IBiSA_Tools: A Computational Toolkit for Ion-Binding State Analysis in Molecular Dynamics Trajectories of Ion Channels.

    Directory of Open Access Journals (Sweden)

    Kota Kasahara

    Full Text Available Ion conduction mechanisms of ion channels are a long-standing conundrum. Although the molecular dynamics (MD method has been extensively used to simulate ion conduction dynamics at the atomic level, analysis and interpretation of MD results are not straightforward due to complexity of the dynamics. In our previous reports, we proposed an analytical method called ion-binding state analysis to scrutinize and summarize ion conduction mechanisms by taking advantage of a variety of analytical protocols, e.g., the complex network analysis, sequence alignment, and hierarchical clustering. This approach effectively revealed the ion conduction mechanisms and their dependence on the conditions, i.e., ion concentration and membrane voltage. Here, we present an easy-to-use computational toolkit for ion-binding state analysis, called IBiSA_tools. This toolkit consists of a C++ program and a series of Python and R scripts. From the trajectory file of MD simulations and a structure file, users can generate several images and statistics of ion conduction processes. A complex network named ion-binding state graph is generated in a standard graph format (graph modeling language; GML, which can be visualized by standard network analyzers such as Cytoscape. As a tutorial, a trajectory of a 50 ns MD simulation of the Kv1.2 channel is also distributed with the toolkit. Users can trace the entire process of ion-binding state analysis step by step. The novel method for analysis of ion conduction mechanisms of ion channels can be easily used by means of IBiSA_tools. This software is distributed under an open source license at the following URL: http://www.ritsumei.ac.jp/~ktkshr/ibisa_tools/.

  10. The Chemistry and Flow Dynamics of Molecular Biological Tools Used to Confirm In Situ Bioremediation of Benzene, TBA, and MTBE

    Science.gov (United States)

    North, K. P.; Mackay, D. M.; Scow, K. M.

    2010-12-01

    In situ bioremediation has typically been confirmed by collecting sediment and groundwater samples to directly demonstrate a degradation process in a laboratory microcosm. However, recent advances in molecular biological tools present options for demonstrating degradation processes with field-based tools that are less time-consuming. We have been investigating the capability of some of these molecular biological tools to evaluate in situ biodegradation of tert-butyl alcohol (TBA), methyl tert-butyl ether (MTBE), and benzene at two field sites in California. At both sites, we have deployed Bio-Traps® (“traps”), made of Bio-Sep® beads in slotted PVC pipe, which provide ideal environments for microbial colonization. Stable Isotope Probing can be accomplished by sorbing the13C-labeled organic contaminant of concern onto Bio-Sep® beads (“baiting”); incorporation of 13C into the biomass collected by the trap would indicate that the microbial community was capable of degrading the labeled compound. In addition, we examined the chemistry and flow dynamics of these traps and present those results here. We performed a field experiment and a lab experiment to, in part, define the rate that different baits leached off various traps. At a TBA- and MTBE-contaminated site at Vandenberg AFB, Lompoc, CA, the TBA-dominant plume was effectively treated by recirculation/oxygenation of groundwater, decreasing TBA and MTBE concentrations to detection limits along predicted flowpaths created by two pairs of recirculation wells. We used the generated aerobic treatment zone to deploy traps baited with 13C-labeled MTBE or TBA in a novel, ex situ experimental setup. The groundwater flow extracted from the aerobic treatment zone was split through several chambers, each containing a trap and monitoring of influent and effluent. The chamber effluent was measured throughout a six-week deployment and analyzed for both TBA and MTBE; the majority of mass leached from the baited traps did

  11. Lipids and Molecular Tools as Biomarkers in Monitoring Air Sparging Bioremediation Processes

    Science.gov (United States)

    Heipieper, Hermann J.; Fischer, Janett

    2010-05-01

    The fluctuation of membrane lipids offers a promising tool as biomarkers for the analysis of microbial population changes as well as for the physiological status of micro-organisms. The investigation of changes in lipid composition is of common use for the assessment of physiological conditions in pure cultures. However, as lipid composition does not show drastic diversity among living organisms the use of lipids as biomarkers in mixed cultures and environmental samples has certain limitations. Therefore, special marker phospholipid fatty acids as well as modern statistical analysis of the results are necessary to receive certain information about the qualitative and quantitative changes of e.g. a soil microflora due to a contamination with organic compounds and its bioremediation. The use of lipids as biomarker in monitoring bioremediation are shown at the Hradčany site, a former Russian air force base in the Czech Republic that operated until 1990. In this time in an area of 32 ha soil and groundwater were contaminated with kerosene and BTEX compounds in an amount of 7,150 tons. This highly contaminated site is treated with the so-called air sparging method to clean-up the contamination by aerobic biodegradation. The results of PLFA analysis demonstrated a community shift to a gram-negative bacterial biomass with time. The results, including a principal component analysis (PCA) of the obtained fatty acid profiles, showed that the air sparging leads to substantial differences in microbial communities depending on the contamination levels and length of treatment, respectively. Obviously, the length of air sparging treatment controlling the BTEX concentration in soils causes temporal changes of bacterial community and adaptations of its respective members. This work was supported by the project BIOTOOL (Contract No. 003998) of the European Commission within its Sixth Framework Programme. Kabelitz N., Machackova J., Imfeld G., Brennerova M., Pieper D.H., Heipieper H

  12. La modelización molecular como herramienta para el diseño de nuevos polímeros conductores Molecular modeling tools to design new conducting polymers

    Directory of Open Access Journals (Sweden)

    Jordi Casanovas

    2005-11-01

    Full Text Available Se presenta la capacidad de las técnicas de modelización molecular basadas en métodos de la química cuántica para predecir la estructura molecular y electrónica de polímeros conductores. Concretamente, se discute la aplicabilidad de estas herramientas computacionales al estudio de diferentes aspectos del politiofeno y sus derivados: geometría molecular y planaridad, cambios estructurales producidos por el dopado, propiedades electrónicas y desarrollo de nuevos materiales conductores.The ability of molecular modeling techniques based on quantum chemical methods to predict the molecular and electronic structure of organic conducting polymers is examined. More specifically, we report on the applicability of these computational tools to study different aspects of polythiophene and its derivatives: molecular geometry and planarity, the structural changes induced by the doping process, the electronic properties and the design of new conducting materials.

  13. Bringing mask repair to the next level

    Science.gov (United States)

    Edinger, K.; Wolff, K.; Steigerwald, H.; Auth, N.; Spies, P.; Oster, J.; Schneider, H.; Budach, M.; Hofmann, T.; Waiblinger, M.

    2014-10-01

    Mask repair is an essential step in the mask manufacturing process as the extension of 193nm technology and the insertion of EUV are drivers for mask complexity and cost. The ability to repair all types of defects on all mask blank materials is crucial for the economic success of a mask shop operation. In the future mask repair is facing several challenges. The mask minimum features sizes are shrinking and require a higher resolution repair tool. At the same time mask blanks with different new mask materials are introduced to optimize optical performance and long term durability. For EUV masks new classes of defects like multilayer and phase defects are entering the stage. In order to achieve a high yield, mask repair has to cover etch and deposition capabilities and must not damage the mask. These challenges require sophisticated technologies to bring mask repair to the next level. For high end masks ion-beam based and e-based repair technologies are the obvious choice when it comes to the repair of small features. Both technologies have their pro and cons. The scope of this paper is to review and compare the performance of ion-beam based mask repair to e-beam based mask repair. We will analyze the limits of both technologies theoretically and experimentally and show mask repair related performance data. Based on this data, we will give an outlook to future mask repair tools.

  14. CAChe Molecular Modeling: A Visualization Tool Early in the Undergraduate Chemistry Curriculum

    Science.gov (United States)

    Crouch, R. David; Holden, Michael S.; Samet, Cindy

    1996-10-01

    In Dickinson's chemistry curriculum, "Synthesis & Reactivity" replaces the traditional organic chemistry sequence and begins in the second semester of the freshman year. A key aspect of our sequence is the correlation of laboratory experiments with lecture topics and the extension of laboratory exercises beyond the usual 4-hour period. With this goal in mind, a number of "Synthesis & Reactivity" experiments have been developed that include an out-of-class computational chemistry exercise using CAChe (1), a versatile molecular modeling software package. Because the first semester of "Synthesis & Reactivity" has a large number of freshmen, emphasis is placed on developing an insight for where nucleophiles and electrophiles might attack a molecule. The Visualizer+ routine in CAChe generates striking graphical images of these sites and the reaction of NBS/H2O with 3-sulfolene (2) presents an excellent opportunity to introduce CAChe into an experiment. Before the laboratory, students are introduced to CAChe to determine how NBS might interact with a nucleophile such as an alkene. Students then return to the laboratory to perform the bromohydrin synthesis but are asked to consider what the regiochemistry would be were the alkene not symmetric. Specifically, students are instructed to visit the computer laboratory during the week and perform calculations on the bromonium ion formed from 2-methylpropene to determine where a nucleophilic H2O molecule might attack. The MOPAC routine in CAChe provides data that are converted to a graphical depiction of the frontier density of the intermediate, indicating potential reactive sites based on electron distribution of orbitals near the HOMO and LUMO. When these data are manipulated by Visualizer+, the obvious conclusion is that the nucleophilic water molecule should attack the more highly substituted carbon of the bromonium ion (Fig. 1) and generate one regioisomer. Figure 1. Relative nucleophilic susceptibilities ofr the

  15. ESIF: Bring Us Your Challenges

    Energy Technology Data Exchange (ETDEWEB)

    2016-08-01

    This brochure highlights the Energy Systems Integration Facility (ESIF) -- the United States' premier lab focused on energy systems research, development, and demonstration (RD&D). Topics covered include an overview of Energy Systems Integration, research focus areas, RD&D tools unique to the ESIF, and information on how to partner with NREL at the ESIF.

  16. A molecular method for the delivery of small molecules and proteins across the cell wall of algae using molecular transporters

    OpenAIRE

    Hyman, Joel M.; Geihe, Erika I.; Trantow, Brian M.; Parvin, Bahram; Wender, Paul A.

    2012-01-01

    Interest in algae has significantly accelerated with the increasing recognition of their potentially unique role in medical, materials, energy, bioremediation, and synthetic biological research. However, the introduction of tools to study, control, or expand the inner-workings of algae has lagged behind. Here we describe a general molecular method based on guanidinium-rich molecular transporters (GR-MoTrs) for bringing small and large cargos into algal cells. Significantly, this method is sho...

  17. MDcons: Intermolecular contact maps as a tool to analyze the interface of protein complexes from molecular dynamics trajectories

    KAUST Repository

    Abdel-Azeim, Safwat

    2014-05-06

    Background: Molecular Dynamics ( MD) simulations of protein complexes suffer from the lack of specific tools in the analysis step. Analyses of MD trajectories of protein complexes indeed generally rely on classical measures, such as the RMSD, RMSF and gyration radius, conceived and developed for single macromolecules. As a matter of fact, instead, researchers engaged in simulating the dynamics of a protein complex are mainly interested in characterizing the conservation/variation of its biological interface. Results: On these bases, herein we propose a novel approach to the analysis of MD trajectories or other conformational ensembles of protein complexes, MDcons, which uses the conservation of inter-residue contacts at the interface as a measure of the similarity between different snapshots. A "consensus contact map" is also provided, where the conservation of the different contacts is drawn in a grey scale. Finally, the interface area of the complex is monitored during the simulations. To show its utility, we used this novel approach to study two protein-protein complexes with interfaces of comparable size and both dominated by hydrophilic interactions, but having binding affinities at the extremes of the experimental range. MDcons is demonstrated to be extremely useful to analyse the MD trajectories of the investigated complexes, adding important insight into the dynamic behavior of their biological interface. Conclusions: MDcons specifically allows the user to highlight and characterize the dynamics of the interface in protein complexes and can thus be used as a complementary tool for the analysis of MD simulations of both experimental and predicted structures of protein complexes.

  18. Molecular Tools for Monitoring the Ecological Sustainability of a Stone Bio-Consolidation Treatment at the Royal Chapel, Granada.

    Directory of Open Access Journals (Sweden)

    Fadwa Jroundi

    Full Text Available Biomineralization processes have recently been applied in situ to protect and consolidate decayed ornamental stone of the Royal Chapel in Granada (Spain. While this promising method has demonstrated its efficacy regarding strengthening of the stone, little is known about its ecological sustainability.Here, we report molecular monitoring of the stone-autochthonous microbiota before and at 5, 12 and 30 months after the bio-consolidation treatment (medium/long-term monitoring, employing the well-known molecular strategy of DGGE analyses. Before the bio-consolidation treatment, the bacterial diversity showed the exclusive dominance of Actinobacteria (100%, which decreased in the community (44.2% after 5 months, and Gamma-proteobacteria (30.24% and Chloroflexi (25.56% appeared. After 12 months, Gamma-proteobacteria vanished from the community and Cyanobacteria (22.1% appeared and remained dominant after thirty months, when the microbiota consisted of Actinobacteria (42.2% and Cyanobacteria (57.8% only. Fungal diversity showed that the Ascomycota phylum was dominant before treatment (100%, while, after five months, Basidiomycota (6.38% appeared on the stone, and vanished again after twelve months. Thirty months after the treatment, the fungal population started to stabilize and Ascomycota dominated on the stone (83.33% once again. Members of green algae (Chlorophyta, Viridiplantae appeared on the stone at 5, 12 and 30 months after the treatment and accounted for 4.25%, 84.77% and 16.77%, respectively.The results clearly show that, although a temporary shift in the bacterial and fungal diversity was observed during the first five months, most probably promoted by the application of the bio-consolidation treatment, the microbiota tends to regain its initial stability in a few months. Thus, the treatment does not seem to have any negative side effects on the stone-autochthonous microbiota over that time. The molecular strategy employed here is suggested

  19. Barcoding amoebae: comparison of SSU, ITS and COI genes as tools for molecular identification of naked lobose amoebae.

    Science.gov (United States)

    Nassonova, Elena; Smirnov, Alexey; Fahrni, Jose; Pawlowski, Jan

    2010-01-01

    Morphological identification of naked lobose amoebae has always been a problem, hence the development of reliable molecular tools for species distinction is a priority for amoebae systematics. Previous studies based on SSU rDNA sequences provided a backbone for the phylogeny of Amoebozoa but were of little help for the species distinctions in this group. On one hand, the SSU rDNA sequences were rather conserved between closely related species; on the other hand, the intra-strain polymorphism of the SSU gene obscured species identification. In the present study, a 3' fragment of the SSU, a complete ITS1-5.8S-ITS2 block and a 5' fragment of COI gene were cloned and sequenced for six Vannella morphospecies, of which V. simplex was represented by six different isolates. SSU rDNA and ITS were found to be inappropriate for species differentiation, while distinctive and homogenous COI sequences were obtained for each well-defined morphospecies. Moreover, a number of distinct COI genotypes have been identified among V. simplex isolates. This suggests that COI may be a good candidate for DNA barcoding of amoebae, but further studies are necessary to confirm the accurateness of the COI gene as a barcode in other gymnamoebae, and to understand the taxonomic meaning of COI variations. Copyright 2009 Elsevier GmbH. All rights reserved.

  20. Integration of molecular biology tools for identifying promoters and genes abundantly expressed in flowers of Oncidium Gower Ramsey

    Directory of Open Access Journals (Sweden)

    Tung Shu-Yun

    2011-04-01

    Full Text Available Abstract Background Orchids comprise one of the largest families of flowering plants and generate commercially important flowers. However, model plants, such as Arabidopsis thaliana do not contain all plant genes, and agronomic and horticulturally important genera and species must be individually studied. Results Several molecular biology tools were used to isolate flower-specific gene promoters from Oncidium 'Gower Ramsey' (Onc. GR. A cDNA library of reproductive tissues was used to construct a microarray in order to compare gene expression in flowers and leaves. Five genes were highly expressed in flower tissues, and the subcellular locations of the corresponding proteins were identified using lip transient transformation with fluorescent protein-fusion constructs. BAC clones of the 5 genes, together with 7 previously published flower- and reproductive growth-specific genes in Onc. GR, were identified for cloning of their promoter regions. Interestingly, 3 of the 5 novel flower-abundant genes were putative trypsin inhibitor (TI genes (OnTI1, OnTI2 and OnTI3, which were tandemly duplicated in the same BAC clone. Their promoters were identified using transient GUS reporter gene transformation and stable A. thaliana transformation analyses. Conclusions By combining cDNA microarray, BAC library, and bombardment assay techniques, we successfully identified flower-directed orchid genes and promoters.

  1. PGAdb-builder: A web service tool for creating pan-genome allele database for molecular fine typing.

    Science.gov (United States)

    Liu, Yen-Yi; Chiou, Chien-Shun; Chen, Chih-Chieh

    2016-11-08

    With the advance of next generation sequencing techniques, whole genome sequencing (WGS) is expected to become the optimal method for molecular subtyping of bacterial isolates. To use WGS as a general subtyping method for disease outbreak investigation and surveillance, the layout of WGS-based typing must be comparable among laboratories. Whole genome multilocus sequence typing (wgMLST) is an approach that achieves this requirement. To apply wgMLST as a standard subtyping approach, a pan-genome allele database (PGAdb) for the population of a bacterial organism must first be established. We present a free web service tool, PGAdb-builder (http://wgmlstdb.imst.nsysu.edu.tw), for the construction of bacterial PGAdb. The effectiveness of PGAdb-builder was tested by constructing a pan-genome allele database for Salmonella enterica serovar Typhimurium, with the database being applied to create a wgMLST tree for a panel of epidemiologically well-characterized S. Typhimurium isolates. The performance of the wgMLST-based approach was as high as that of the SNP-based approach in Leekitcharoenphon's study used for discerning among epidemiologically related and non-related isolates.

  2. Management strategies of Bring Your Own Device

    Directory of Open Access Journals (Sweden)

    Li Peixuan

    2017-01-01

    Full Text Available The rapid development of mobile Internet and mobile terminals promote business office system from PC to mobile terminals gradually. Thus Bring Your Own Device (BYOD has become one of the important development trends of enterprise office mode. We analyse the driving factors of implementing Bring Your Own Device, then point out some problems in the process of implementing Bring Your Own Device. Further, we propose the corresponding management strategies of Bring Your Own Device in order to provide references for enterprises to meet the need of mobile office.

  3. Lymphatic Filariasis Elimination in American Samoa: Evaluation of Molecular Xenomonitoring as a Surveillance Tool in the Endgame.

    Directory of Open Access Journals (Sweden)

    Colleen L Lau

    2016-11-01

    Full Text Available The Global Programme to Eliminate Lymphatic Filariasis has made significant progress toward interrupting transmission of lymphatic filariasis (LF through mass drug administration (MDA. Operational challenges in defining endpoints of elimination programs include the need to determine appropriate post-MDA surveillance strategies. As humans are the only reservoirs of LF parasites, one such strategy is molecular xenomonitoring (MX, the detection of filarial DNA in mosquitoes using molecular methods (PCR, to provide an indirect indicator of infected persons nearby. MX could potentially be used to evaluate program success, provide support for decisions to stop MDA, and conduct post-MDA surveillance. American Samoa has successfully completed MDA and passed WHO recommended Transmission Assessment Surveys in 2011 and 2015, but recent studies using spatial analysis of antigen (Ag and antibody (Ab prevalence in adults (aged ≥18 years and entomological surveys showed evidence of possible ongoing transmission. This study evaluated MX as a surveillance tool in American Samoa by linking village-level results of published human and mosquito studies. Of 32 villages, seropositive persons for Og4C3 Ag were identified in 11 (34.4%, for Wb123 Ab in 18 (56.3% and for Bm14 Ab in 27 (84.4% of villages. Village-level seroprevalence ranged from 0-33%, 0-67% and 0-100% for Og4C3 Ag, Wb123 Ab and Bm14 Ab respectively. PCR-positive Aedes polynesiensis mosquitoes were found in 15 (47% villages, and their presence was significantly associated with seropositive persons for Og4C3 Ag (67% vs 6%, p<0.001 and Wb123 Ab (87% vs 29%, p = 0.001, but not Bm14 Ab. In villages with persons seropositive for Og4C3 Ag and Wb123 Ab, PCR-positive Ae. polynesiensis were found in 90.9% and 72.2% respectively. In villages without seropositive persons for Og4C3 Ag or Wb123 Ab, PCR-positive Ae. polynesiensis were also absent in 94.1% and 70.6% of villages respectively. Our study provides

  4. Lymphatic Filariasis Elimination in American Samoa: Evaluation of Molecular Xenomonitoring as a Surveillance Tool in the Endgame.

    Science.gov (United States)

    Lau, Colleen L; Won, Kimberly Y; Lammie, Patrick J; Graves, Patricia M

    2016-11-01

    The Global Programme to Eliminate Lymphatic Filariasis has made significant progress toward interrupting transmission of lymphatic filariasis (LF) through mass drug administration (MDA). Operational challenges in defining endpoints of elimination programs include the need to determine appropriate post-MDA surveillance strategies. As humans are the only reservoirs of LF parasites, one such strategy is molecular xenomonitoring (MX), the detection of filarial DNA in mosquitoes using molecular methods (PCR), to provide an indirect indicator of infected persons nearby. MX could potentially be used to evaluate program success, provide support for decisions to stop MDA, and conduct post-MDA surveillance. American Samoa has successfully completed MDA and passed WHO recommended Transmission Assessment Surveys in 2011 and 2015, but recent studies using spatial analysis of antigen (Ag) and antibody (Ab) prevalence in adults (aged ≥18 years) and entomological surveys showed evidence of possible ongoing transmission. This study evaluated MX as a surveillance tool in American Samoa by linking village-level results of published human and mosquito studies. Of 32 villages, seropositive persons for Og4C3 Ag were identified in 11 (34.4%), for Wb123 Ab in 18 (56.3%) and for Bm14 Ab in 27 (84.4%) of villages. Village-level seroprevalence ranged from 0-33%, 0-67% and 0-100% for Og4C3 Ag, Wb123 Ab and Bm14 Ab respectively. PCR-positive Aedes polynesiensis mosquitoes were found in 15 (47%) villages, and their presence was significantly associated with seropositive persons for Og4C3 Ag (67% vs 6%, p<0.001) and Wb123 Ab (87% vs 29%, p = 0.001), but not Bm14 Ab. In villages with persons seropositive for Og4C3 Ag and Wb123 Ab, PCR-positive Ae. polynesiensis were found in 90.9% and 72.2% respectively. In villages without seropositive persons for Og4C3 Ag or Wb123 Ab, PCR-positive Ae. polynesiensis were also absent in 94.1% and 70.6% of villages respectively. Our study provides promising

  5. Obesity management: what brings success?

    Science.gov (United States)

    Rössner, Stephan

    2013-01-01

    The upward trend in obesity prevalence across regions and continents is a worldwide concern. Today a majority of the world’s population live in a country where being overweight or obese causes more deaths than being underweight. Only a portion of those qualifying for treatment will get the health care they need. Still, a minor weight loss of 5–10% seems to be sufficient to provide a clinically significant health benefit in terms of risk factors for cardiovascular disease and diabetes. Diet, exercise and behavior modifications remain the current cornerstones of obesity treatment. Weight-loss drugs play a minor role. Drugs which were available and reasonably effective have been withdrawn because of side effects. The fact that the ‘old’ well known, but pretty unexciting tools remain the basic armamentarium causes understandable concern and disappointment among both patients and therapists. Hence, bariatric surgery has increasingly been recognized and developed, as it offers substantial weight loss and prolonged weight control. The present review highlights the conventional tools to counter obesity, lifestyle modification, pharmacotherapy and bariatric surgery, including some of the barriers to successful weight loss: (1) unrealistic expectations of success; (2) high attrition rates; (3) cultural norms of self-acceptance in terms of weight and beliefs of fat being healthy; (4) neighborhood attributes such as a lack of well-stocked supermarkets and rather the presence of convenience stores with low-quality foods; and (5) the perception of the neighborhood as less safe and with low walkability. Prevention is the obvious key. Cost-effective societal interventions such as a tax on unhealthy food and beverages, front-of-pack traffic light nutrition labeling and prohibition of advertising of junk food and beverages to children are also discussed. PMID:23320052

  6. Obesity management: what brings success?

    Science.gov (United States)

    Lagerros, Ylva Trolle; Rössner, Stephan

    2013-01-01

    The upward trend in obesity prevalence across regions and continents is a worldwide concern. Today a majority of the world's population live in a country where being overweight or obese causes more deaths than being underweight. Only a portion of those qualifying for treatment will get the health care they need. Still, a minor weight loss of 5-10% seems to be sufficient to provide a clinically significant health benefit in terms of risk factors for cardiovascular disease and diabetes. Diet, exercise and behavior modifications remain the current cornerstones of obesity treatment. Weight-loss drugs play a minor role. Drugs which were available and reasonably effective have been withdrawn because of side effects. The fact that the 'old' well known, but pretty unexciting tools remain the basic armamentarium causes understandable concern and disappointment among both patients and therapists. Hence, bariatric surgery has increasingly been recognized and developed, as it offers substantial weight loss and prolonged weight control. The present review highlights the conventional tools to counter obesity, lifestyle modification, pharmacotherapy and bariatric surgery, including some of the barriers to successful weight loss: (1) unrealistic expectations of success; (2) high attrition rates; (3) cultural norms of self-acceptance in terms of weight and beliefs of fat being healthy; (4) neighborhood attributes such as a lack of well-stocked supermarkets and rather the presence of convenience stores with low-quality foods; and (5) the perception of the neighborhood as less safe and with low walkability. Prevention is the obvious key. Cost-effective societal interventions such as a tax on unhealthy food and beverages, front-of-pack traffic light nutrition labeling and prohibition of advertising of junk food and beverages to children are also discussed.

  7. Next-generation phage display: integrating and comparing available molecular tools to enable cost-effective high-throughput analysis.

    Directory of Open Access Journals (Sweden)

    Emmanuel Dias-Neto

    Full Text Available BACKGROUND: Combinatorial phage display has been used in the last 20 years in the identification of protein-ligands and protein-protein interactions, uncovering relevant molecular recognition events. Rate-limiting steps of combinatorial phage display library selection are (i the counting of transducing units and (ii the sequencing of the encoded displayed ligands. Here, we adapted emerging genomic technologies to minimize such challenges. METHODOLOGY/PRINCIPAL FINDINGS: We gained efficiency by applying in tandem real-time PCR for rapid quantification to enable bacteria-free phage display library screening, and added phage DNA next-generation sequencing for large-scale ligand analysis, reporting a fully integrated set of high-throughput quantitative and analytical tools. The approach is far less labor-intensive and allows rigorous quantification; for medical applications, including selections in patients, it also represents an advance for quantitative distribution analysis and ligand identification of hundreds of thousands of targeted particles from patient-derived biopsy or autopsy in a longer timeframe post library administration. Additional advantages over current methods include increased sensitivity, less variability, enhanced linearity, scalability, and accuracy at much lower cost. Sequences obtained by qPhage plus pyrosequencing were similar to a dataset produced from conventional Sanger-sequenced transducing-units (TU, with no biases due to GC content, codon usage, and amino acid or peptide frequency. These tools allow phage display selection and ligand analysis at >1,000-fold faster rate, and reduce costs approximately 250-fold for generating 10(6 ligand sequences. CONCLUSIONS/SIGNIFICANCE: Our analyses demonstrates that whereas this approach correlates with the traditional colony-counting, it is also capable of a much larger sampling, allowing a faster, less expensive, more accurate and consistent analysis of phage enrichment. Overall

  8. Computational immunology meets bioinformatics: the use of prediction tools for molecular binding in the simulation of the immune system.

    Science.gov (United States)

    Rapin, Nicolas; Lund, Ole; Bernaschi, Massimo; Castiglione, Filippo

    2010-04-16

    We present a new approach to the study of the immune system that combines techniques of systems biology with information provided by data-driven prediction methods. To this end, we have extended an agent-based simulator of the immune response, C-ImmSim, such that it represents pathogens, as well as lymphocytes receptors, by means of their amino acid sequences and makes use of bioinformatics methods for T and B cell epitope prediction. This is a key step for the simulation of the immune response, because it determines immunogenicity. The binding of the epitope, which is the immunogenic part of an invading pathogen, together with activation and cooperation from T helper cells, is required to trigger an immune response in the affected host. To determine a pathogen's epitopes, we use existing prediction methods. In addition, we propose a novel method, which uses Miyazawa and Jernigan protein-protein potential measurements, for assessing molecular binding in the context of immune complexes. We benchmark the resulting model by simulating a classical immunization experiment that reproduces the development of immune memory. We also investigate the role of major histocompatibility complex (MHC) haplotype heterozygosity and homozygosity with respect to the influenza virus and show that there is an advantage to heterozygosity. Finally, we investigate the emergence of one or more dominating clones of lymphocytes in the situation of chronic exposure to the same immunogenic molecule and show that high affinity clones proliferate more than any other. These results show that the simulator produces dynamics that are stable and consistent with basic immunological knowledge. We believe that the combination of genomic information and simulation of the dynamics of the immune system, in one single tool, can offer new perspectives for a better understanding of the immune system.

  9. Bringing voice in policy building.

    Science.gov (United States)

    Lotrecchiano, Gaetano R; Kane, Mary; Zocchi, Mark S; Gosa, Jessica; Lazar, Danielle; Pines, Jesse M

    2017-07-03

    Purpose The purpose of this paper is to describe the use of group concept mapping (GCM) as a tool for developing a conceptual model of an episode of acute, unscheduled care from illness or injury to outcomes such as recovery, death and chronic illness. Design/methodology/approach After generating a literature review drafting an initial conceptual model, GCM software (CS Global MAXTM) is used to organize and identify strengths and directionality between concepts generated through feedback about the model from several stakeholder groups: acute care and non-acute care providers, patients, payers and policymakers. Through online and in-person population-specific focus groups, the GCM approach seeks feedback, assigned relationships and articulated priorities from participants to produce an output map that described overarching concepts and relationships within and across subsamples. Findings A clustered concept map made up of relational data points that produced a taxonomy of feedback was used to update the model for use in soliciting additional feedback from two technical expert panels (TEPs), and finally, a public comment exercise was performed. The results were a stakeholder-informed improved model for an acute care episode, identified factors that influence process and outcomes, and policy recommendations, which were delivered to the Department of Health and Human Services's (DHHS) Assistant Secretary for Preparedness and Response. Practical implications This study provides an example of the value of cross-population multi-stakeholder input to increase voice in shared problem health stakeholder groups. Originality/value This paper provides GCM results and a visual analysis of the relational characteristics both within and across sub-populations involved in the study. It also provides an assessment of observational key factors supporting how different stakeholder voices can be integrated to inform model development and policy recommendations.

  10. Can chromatin conformation technologies bring light into human molecular pathology?

    Science.gov (United States)

    Kubiak, Marta; Lewandowska, Marzena Anna

    2015-01-01

    Regulation of gene expression in eukaryotes involves many complex processes, in which chromatin structure plays an important role. In addition to the epigenetic effects, such as DNA methylation and phosphorylation or histone modifications, gene expression is also controlled by the spatial organization of chromatin. For example, distant regulatory elements (enhancers, insulators) may come into direct physical interaction with target genes or other regulatory elements located in genomic regions of up to several hundred kilobases in size. Such long-range interactions result in the formation of chromatin loops. In the last several years, there has been a rapid increase in our knowledge of the spatial organization of chromatin in the nucleus through the chromosome conformation capture (3C) technology. Here we review and compare the original 3C and 3C-based methods including chromosome conformation capture-on-chip (4C), chromosome conformation capture carbon copy (5C), hi-resolution chromosome confomation capture (HiC). In this article, we discuss different aspects of how the nuclear organization of chromatin is associated with gene expression regulation and how this knowledge is useful in translational medicine and clinical applications. We demonstrate that the knowledge of the chromatin 3D organization may help understand the mechanisms of gene expression regulation of genes involved in the development of human diseases, such as CFTR (responsible for cystic fibrosis) or IGFBP3 (associated with breast cancer pathogenesis). Additionally, 3C-derivative methods have been also useful in the diagnosis of some leukemia subtypes.

  11. Bringing the Unidata IDV to the Cloud

    Science.gov (United States)

    Fisher, W. I.; Oxelson Ganter, J.

    2015-12-01

    Maintaining software compatibility across new computing environments and the associated underlying hardware is a common problem for software engineers and scientific programmers. While traditional software engineering provides a suite of tools and methodologies which may mitigate this issue, they are typically ignored by developers lacking a background in software engineering. Causing further problems, these methodologies are best applied at the start of project; trying to apply them to an existing, mature project can require an immense effort. Visualization software is particularly vulnerable to this problem, given the inherent dependency on particular graphics hardware and software API's. As a result of these issues, there exists a large body of software which is simultaneously critical to the scientists who are dependent upon it, and yet increasingly difficult to maintain.The solution to this problem was partially provided with the advent of Cloud Computing; Application Streaming. This technology allows a program to run entirely on a remote virtual machine while still allowing for interactivity and dynamic visualizations, with little-to-no re-engineering required. When coupled with containerization technology such as Docker, we are able to easily bring the same visualization software to a desktop, a netbook, a smartphone, and the next generation of hardware, whatever it may be.Unidata has been able to harness Application Streaming to provide a tablet-compatible version of our visualization software, the Integrated Data Viewer (IDV). This work will examine the challenges associated with adapting the IDV to an application streaming platform, and include a brief discussion of the underlying technologies involved.

  12. Identification of abiotic and biotic reductive dechlorination in a chlorinated ethene plume after thermal source remediation by means of isotopic and molecular biology tools

    DEFF Research Database (Denmark)

    Badin, Alice; Broholm, Mette Martina; Jacobsen, Carsten S.

    2016-01-01

    was the predominant chlorinated ethene near the source area prior to thermal treatment. After thermal treatment, cDCE became predominant. The biotic contribution to these changes was supported by the presence of Dehalococcoides sp. DNA (Dhc) and Dhc targeted rRNA close to the source area. In contrast, dual C...... with molecular biology tools to evaluate which biogeochemical processes are taking place in an aquifer contaminated with chlorinated ethenes....

  13. A Proposal for Measuring Interactivity that Brings Learning Effectiveness

    Directory of Open Access Journals (Sweden)

    Tosh Yamamoto

    2010-03-01

    Full Text Available It is proposed in this paper that some type of way to measure and visualize interactivity in the multimedia or e-Learning contents is necessary in order to clearly identify interactivity that brings learning effectiveness. Interactivity during learning will arouse students’ intellectual curiosity and motivate them to learn further. Although the interaction in the communication between the teacher and his/her students in a regular classroom is ideal, it is not possible to maintain the equivalence in the multimedia or e-Learning contents. In order to rigorously formalize the field of measuring interactivity as a theory, theoretical constructs such as interactivity, interest, knowledge, and experience are redefined first. Then, the defined “interactivity” is broken down to subcomponents to develop an assessment tool for the interactivity which brings learning effectiveness. In the end, it is proved that the interactivity in learning can be measured.

  14. Healthy Family 2009: Bringing in Baby

    Science.gov (United States)

    ... Navigation Bar Home Current Issue Past Issues Healthy Family 2009 Bringing in Baby Past Issues / Winter 2009 ... Down syndrome and other common genetic disorders, inherited family conditions, such as Duchenne muscular dystrophy, or disorders ...

  15. Exercise Brings Bone Benefits that Last

    Science.gov (United States)

    ... Special Issues Subscribe May 2014 Print this issue Exercise Brings Bone Benefits that Last En español Send ... lose bone. Studies of animals have shown that exercise during periods of rapid growth can lead to ...

  16. Polymer Molecular Architecture As a Tool for Controlling the Rheological Properties of Aqueous Polyacrylamide Solutions for Enhanced Oil Recovery

    NARCIS (Netherlands)

    Wever, Diego A. Z.; Polgar, Lorenzo M.; Stuart, Marc C. A.; Picchioni, Francesco; Broekhuis, Antonius A.

    2013-01-01

    The controlled synthesis of high molecular weight branched polyacrylamide (PAM) has been accomplished by using atomic transfer radical polymerization (ATRP) of acrylamide (AM) in water at room temperature. Halogen-functionalized aliphatic polyketones acted as macroinitiators in the polymerization.

  17. Serological and molecular tools to diagnose visceral leishmaniasis: 2-years' experience of a single center in Northern Italy.

    Directory of Open Access Journals (Sweden)

    Stefania Varani

    Full Text Available The diagnosis of visceral leishmaniasis (VL remains challenging, due to the limited sensitivity of microscopy, the poor performance of serological methods in immunocompromised patients and the lack of standardization of molecular tests. The aim of this study was to implement a combined diagnostic workflow by integrating serological and molecular tests with standardized clinical criteria. Between July 2013 and June 2015, the proposed workflow was applied to specimens obtained from 94 in-patients with clinical suspicion of VL in the Emilia-Romagna region, Northern Italy. Serological tests and molecular techniques were employed. Twenty-one adult patients (22% had a confirmed diagnosis of VL by clinical criteria, serology and/or real-time polymerase chain reaction; 4 of these patients were HIV-positive. Molecular tests exhibited higher sensitivity than serological tests for the diagnosis of VL. In our experience, the rK39 immunochromatographic test was insufficiently sensitive for use as a screening test for the diagnosis of VL caused by L. infantum in Italy. However, as molecular tests are yet not standardized, further studies are required to identify an optimal screening test for Mediterranean VL.

  18. Bring Your Own Technology (BYOT to Education

    Directory of Open Access Journals (Sweden)

    Joseph M. Woodside

    2014-06-01

    Full Text Available In an effort to reduce costs and increase worker satisfaction, many businesses have implemented a concept known as Bring Your Own Device (BYOD or Bring Your Own Technology (BYOT. Similarly, many school districts are beginning to implement BYOT policies and programs to improve educational learning opportunities for students who have a wide variety of technology devices. BYOT allow districts with limited budgets enable usage of technology while improving student engagement. This paper explores the technology devices, and educational implications of policies, device management, security and included components.

  19. Pyrosequencing as a tool for the detection of Phytophthora species: error rate and risk of false Molecular Operational Taxonomic Units

    NARCIS (Netherlands)

    Vettraino, A.M.; Bonants, P.J.M.; Tomassini, A.; Bruni, N.; Vannini, A.

    2012-01-01

    Aims: To evaluate the accuracy of pyrosequencing for the description of Phytophthora communities in terms of taxa identification and risk of assignment for false Molecular Operational Taxonomic Units (MOTUs). Methods and Results: Pyrosequencing of Internal Transcribed Spacer 1 (ITS1) amplicons was

  20. SaVanT: a web-based tool for the sample-level visualization of molecular signatures in gene expression profiles.

    Science.gov (United States)

    Lopez, David; Montoya, Dennis; Ambrose, Michael; Lam, Larry; Briscoe, Leah; Adams, Claire; Modlin, Robert L; Pellegrini, Matteo

    2017-10-25

    Molecular signatures are collections of genes characteristic of a particular cell type, tissue, disease, or perturbation. Signatures can also be used to interpret expression profiles generated from heterogeneous samples. Large collections of gene signatures have been previously developed and catalogued in the MSigDB database. In addition, several consortia and large-scale projects have systematically profiled broad collections of purified primary cells, molecular perturbations of cell types, and tissues from specific diseases, and the specificity and breadth of these datasets can be leveraged to create additional molecular signatures. However, to date there are few tools that allow the visualization of individual signatures across large numbers of expression profiles. Signature visualization of individual samples allows, for example, the identification of patient subcategories a priori on the basis of well-defined molecular signatures. Here, we generate and compile 10,985 signatures (636 newly-generated and 10,349 previously available from MSigDB) and provide a web-based Signature Visualization Tool (SaVanT; http://newpathways.mcdb.ucla.edu/savant ), to visualize these signatures in user-generated expression data. We show that using SaVanT, immune activation signatures can distinguish patients with different types of acute infections (influenza A and bacterial pneumonia). Furthermore, SaVanT is able to identify the prominent signatures within each patient group, and identify the primary cell types underlying different leukemias (acute myeloid and acute lymphoblastic) and skin disorders. The development of SaVanT facilitates large-scale analysis of gene expression profiles on a patient-level basis to identify patient subphenotypes, or potential therapeutic target pathways.

  1. Cancer in silico drug discovery: a systems biology tool for identifying candidate drugs to target specific molecular tumor subtypes.

    Science.gov (United States)

    San Lucas, F Anthony; Fowler, Jerry; Chang, Kyle; Kopetz, Scott; Vilar, Eduardo; Scheet, Paul

    2014-12-01

    Large-scale cancer datasets such as The Cancer Genome Atlas (TCGA) allow researchers to profile tumors based on a wide range of clinical and molecular characteristics. Subsequently, TCGA-derived gene expression profiles can be analyzed with the Connectivity Map (CMap) to find candidate drugs to target tumors with specific clinical phenotypes or molecular characteristics. This represents a powerful computational approach for candidate drug identification, but due to the complexity of TCGA and technology differences between CMap and TCGA experiments, such analyses are challenging to conduct and reproduce. We present Cancer in silico Drug Discovery (CiDD; scheet.org/software), a computational drug discovery platform that addresses these challenges. CiDD integrates data from TCGA, CMap, and Cancer Cell Line Encyclopedia (CCLE) to perform computational drug discovery experiments, generating hypotheses for the following three general problems: (i) determining whether specific clinical phenotypes or molecular characteristics are associated with unique gene expression signatures; (ii) finding candidate drugs to repress these expression signatures; and (iii) identifying cell lines that resemble the tumors being studied for subsequent in vitro experiments. The primary input to CiDD is a clinical or molecular characteristic. The output is a biologically annotated list of candidate drugs and a list of cell lines for in vitro experimentation. We applied CiDD to identify candidate drugs to treat colorectal cancers harboring mutations in BRAF. CiDD identified EGFR and proteasome inhibitors, while proposing five cell lines for in vitro testing. CiDD facilitates phenotype-driven, systematic drug discovery based on clinical and molecular data from TCGA. ©2014 American Association for Cancer Research.

  2. Waleli: Bringing Wireless Opportunities to Life

    NARCIS (Netherlands)

    Kirwan, P.M.; Gutierrez, Jairo

    2009-01-01

    This chapter tells the development story of Waleli, a high-tech company utilizing the latest proven developments in wireless communications to bring innovations to the market. It presents the journey of the firm through the entrepreneurial process, from initial idea right through to value creation.

  3. DNA Barcoding Investigations Bring Biology to Life

    Science.gov (United States)

    Musante, Susan

    2010-01-01

    This article describes how DNA barcoding investigations bring biology to life. Biologists recognize the power of DNA barcoding not just to teach biology through connections to the real world but also to immerse students in the exciting process of science. As an investigator in the Program for the Human Environment at Rockefeller University in New…

  4. Bringing History Alive in the Classroom!

    Science.gov (United States)

    McRae, Lee, Ed.

    1996-01-01

    This document consists of the first four issues of a serial publication, "Bringing History Alive in the Classroom!" The volumes focus on: (1) "A Sampling of Renaissance Instruments," which includes: information on Christopher Columbus, Leondardo da Vinci, and William Shakespeare, a timeline from the middle ages through the renaissance, Queen…

  5. Electron-Induced Vibrational Spectroscopy. A New and Unique Tool To Unravel the Molecular Structure of Polymer Surfaces

    NARCIS (Netherlands)

    Pireaux, J.J.; Gregoire, Ch.; Caudano, R.; Rei Vilar, M.; Brinkhuis, R.; Schouten, A.J.

    1991-01-01

    Among the surface-sensitive spectroscopies used to characterize clean and surface-modified polymers, one technique has rather recently emerged as a very promising complementary tool. High-resolution electron energy loss spectroscopy, or electron-induced vibrational spectroscopy, has potentially all

  6. The Centipede Genus Scolopendra in Mainland Southeast Asia: Molecular Phylogenetics, Geometric Morphometrics and External Morphology as Tools for Species Delimitation

    Science.gov (United States)

    Siriwut, Warut; Edgecombe, Gregory D.; Sutcharit, Chirasak; Panha, Somsak

    2015-01-01

    Seven Scolopendra species from the Southeast Asian mainland delimited based on standard external morphological characters represent monophyletic groups in phylogenetic trees inferred from concatenated sequences of three gene fragments (cytochrome c oxidase subunit 1, 16S rRNA and 28S rRNA) using Maximum likelihood and Bayesian inference. Geometric morphometric description of shape variation in the cephalic plate, forcipular coxosternite, and tergite of the ultimate leg-bearing segment provides additional criteria for distinguishing species. Colouration patterns in some Scolopendra species show a high degree of fit to phylogenetic trees at the population level. The most densely sampled species, Scolopendra dehaani Brandt, 1840, has three subclades with allopatric distributions in mainland SE Asia. The molecular phylogeny of S. pinguis Pocock, 1891, indicated ontogenetic colour variation among its populations. The taxonomic validation of S. dawydoffi Kronmüller, 2012, S. japonica Koch, 1878, and S. dehaani Brandt, 1840, each a former subspecies of S. subspinipes Leach, 1814 sensu Lewis, 2010, as full species was supported by molecular information and additional morphological data. Species delimitation in these taxonomically challenging animals is facilitated by an integrative approach that draws on both morphology and molecular phylogeny. PMID:26270342

  7. Magneto-optical Kerr effect spectroscopy--a sensitive tool for investigating the molecular orientation in organic semiconductor films.

    Science.gov (United States)

    Bräuer, Björn; Fronk, Michael; Lehmann, Daniel; Zahn, Dietrich R T; Salvan, Georgeta

    2009-11-12

    The detection and control of the molecular growth mode is a key prerequisite for fabricating opto-electronic devices. In this work we present the magneto-optical Kerr effect (MOKE) spectroscopy to be a highly sensitive method for the detection of the molecular orientation. On the example of metal free phthalocyanine (H(2)Pc) in thin films, it will be shown that also for diamagnetic molecules a strong magneto-optical response can be expected. The growth mode and thus the intensity of the MOKE signal of H2Pc is strongly influenced by a templating effect using ultrathin layers of 3,4,9,10-perylenetetracarboxylic dianhydride (PTCDA). From the MOKE spectra in the energy range from 1.5 to 5.0 eV and the optical constants, the Voigt constant of thin organic films was determined. From the strong in-plane/out-of-plane anisotropy of the optical constants and the value of the Voigt constant the average molecular tilt angle of H2Pc molecules with respect to the substrate plane can be obtained.

  8. The Centipede Genus Scolopendra in Mainland Southeast Asia: Molecular Phylogenetics, Geometric Morphometrics and External Morphology as Tools for Species Delimitation.

    Directory of Open Access Journals (Sweden)

    Warut Siriwut

    Full Text Available Seven Scolopendra species from the Southeast Asian mainland delimited based on standard external morphological characters represent monophyletic groups in phylogenetic trees inferred from concatenated sequences of three gene fragments (cytochrome c oxidase subunit 1, 16S rRNA and 28S rRNA using Maximum likelihood and Bayesian inference. Geometric morphometric description of shape variation in the cephalic plate, forcipular coxosternite, and tergite of the ultimate leg-bearing segment provides additional criteria for distinguishing species. Colouration patterns in some Scolopendra species show a high degree of fit to phylogenetic trees at the population level. The most densely sampled species, Scolopendra dehaani Brandt, 1840, has three subclades with allopatric distributions in mainland SE Asia. The molecular phylogeny of S. pinguis Pocock, 1891, indicated ontogenetic colour variation among its populations. The taxonomic validation of S. dawydoffi Kronmüller, 2012, S. japonica Koch, 1878, and S. dehaani Brandt, 1840, each a former subspecies of S. subspinipes Leach, 1814 sensu Lewis, 2010, as full species was supported by molecular information and additional morphological data. Species delimitation in these taxonomically challenging animals is facilitated by an integrative approach that draws on both morphology and molecular phylogeny.

  9. The Centipede Genus Scolopendra in Mainland Southeast Asia: Molecular Phylogenetics, Geometric Morphometrics and External Morphology as Tools for Species Delimitation.

    Science.gov (United States)

    Siriwut, Warut; Edgecombe, Gregory D; Sutcharit, Chirasak; Panha, Somsak

    2015-01-01

    Seven Scolopendra species from the Southeast Asian mainland delimited based on standard external morphological characters represent monophyletic groups in phylogenetic trees inferred from concatenated sequences of three gene fragments (cytochrome c oxidase subunit 1, 16S rRNA and 28S rRNA) using Maximum likelihood and Bayesian inference. Geometric morphometric description of shape variation in the cephalic plate, forcipular coxosternite, and tergite of the ultimate leg-bearing segment provides additional criteria for distinguishing species. Colouration patterns in some Scolopendra species show a high degree of fit to phylogenetic trees at the population level. The most densely sampled species, Scolopendra dehaani Brandt, 1840, has three subclades with allopatric distributions in mainland SE Asia. The molecular phylogeny of S. pinguis Pocock, 1891, indicated ontogenetic colour variation among its populations. The taxonomic validation of S. dawydoffi Kronmüller, 2012, S. japonica Koch, 1878, and S. dehaani Brandt, 1840, each a former subspecies of S. subspinipes Leach, 1814 sensu Lewis, 2010, as full species was supported by molecular information and additional morphological data. Species delimitation in these taxonomically challenging animals is facilitated by an integrative approach that draws on both morphology and molecular phylogeny.

  10. The use of agrobiodiversity for plant improvement and the intellectual property paradigm: institutional fit and legal tools for mass selection, conventional and molecular plant breeding.

    Science.gov (United States)

    Batur, Fulya; Dedeurwaerdere, Tom

    2014-12-01

    Focused on the impact of stringent intellectual property mechanisms over the uses of plant agricultural biodiversity in crop improvement, the article delves into a systematic analysis of the relationship between institutional paradigms and their technological contexts of application, identified as mass selection, controlled hybridisation, molecular breeding tools and transgenics. While the strong property paradigm has proven effective in the context of major leaps forward in genetic engineering, it faces a systematic breakdown when extended to mass selection, where innovation often displays a collective nature. However, it also creates partial blockages in those innovation schemes rested between on-farm observation and genetic modification, i.e. conventional plant breeding and upstream molecular biology research tools. Neither overly strong intellectual property rights, nor the absence of well delineated protection have proven an optimal fit for these two intermediary socio-technological systems of cumulative incremental innovation. To address these challenges, the authors look at appropriate institutional alternatives which can create effective incentives for in situ agrobiodiversity conservation and the equitable distribution of technologies in plant improvement, using the flexibilities of the TRIPS Agreement, the liability rules set forth in patents or plant variety rights themselves (in the form of farmers', breeders' and research exceptions), and other ad hoc reward regimes.

  11. Characterization of Citrus tristeza virus isolates recovered in Syria and Apulia (southern Italy using different molecular tools

    Directory of Open Access Journals (Sweden)

    Raied ABOU KUBAA

    2013-01-01

    Full Text Available Citrus tristeza virus (CTV is the causal agent of the most important virus disease of citrus. CTV isolates differing in biological and molecular characteristics have been reported worldwide. Recently, CTV was detected in Syria in citrus groves from two Governorates (Lattakia and Tartous and several CTV outbreaks have been reported in Apulia (southern Italy since 2003. To molecularly characterize the CTV populations spreading in Syria and Italy, a number of isolates from each region was selected and examined by different molecular approaches including: Multiple Molecular Markers analysis (MMM, real time RT-(qPCR, single strand conformation polymorphism (SSCP of the major coat protein (CP gene (P25, and sequence analysis of the CP (P25, P18, P20 and RdRp genes. SSCP analysis of CP25 yielded two distinct simple patterns among the Syrian isolates and three different patterns in the Italian isolates. Based on MMM analysis, all Syrian CTV isolates were categorized as VT-like genotype, whereas the Italian isolates reacted only with the markers specific for the T30 genotype. These findings were also confirmed by RT-qPCR and by sequencing analysis of four genomic regions. The Italian isolates had nucleotide identities which varied: from 99.5 to 99.8 for the CP gene; from 97.4% to 98.3% for the P18 gene; from 98.6% to 99.8% for the P20 and from 97.8% to 99.1% for the partial RdRp sequenced. High sequence identity was found for all genomic regions analyzed between the Syrian isolates (from 98.9% to 99.6%. These results show that the CTV populations spreading in Apulia and Syria are associated with different genotypes, indicating different potential impacts on the citrus trees in the field. Since in both areas the introduction of the virus is relatively recent, infected plants resulted to contain a single and common genotype, suggesting that CTV is spreading from the first outbreaks by aphids or local movement of autochthonous infected plant material.

  12. Bringing Breast Cancer Technologies to Market | Poster

    Science.gov (United States)

    CCR research is recognized in novel competition to encourage the commercialization of breast cancer inventions. Editor’s note: This article was originally published in CCR Connections (Volume 8, No. 1). The Breast Cancer Startup Challenge was named one of six finalists in the HHS Innovates Award Competition, and was one of three finalists recognized by HHS Secretary Sylvia Mathews Burwell and Deputy Secretary Bill Corr. For more information on the Challenge, see previous article on the Poster website. Start-up companies are instrumental in bringing the fruits of scientific research to market. Recognizing an opportunity to bring entrepreneurial minds to bear on the diagnosis and treatment of breast cancer, the Avon Foundation for Women partnered with NCI and the Center for Advancing Innovation to launch the Breast Cancer Startup Challenge.

  13. Mumps virus F gene and HN gene sequencing as a molecular tool to study mumps virus transmission.

    Science.gov (United States)

    Gouma, Sigrid; Cremer, Jeroen; Parkkali, Saara; Veldhuijzen, Irene; van Binnendijk, Rob S; Koopmans, Marion P G

    2016-11-01

    Various mumps outbreaks have occurred in the Netherlands since 2004, particularly among persons who had received 2 doses of measles, mumps, and rubella (MMR) vaccination. Genomic typing of pathogens can be used to track outbreaks, but the established genotyping of mumps virus based on the small hydrophobic (SH) gene sequences did not provide sufficient resolution. Therefore, we expanded the sequencing to include fusion (F) gene and haemagglutinin-neuraminidase (HN) gene sequences in addition to the SH gene sequences from 109 mumps virus genotype G strains obtained between 2004 and mid 2015 in the Netherlands. When the molecular information from these 3 genes was combined, we were able to identify separate mumps virus clusters and track mumps virus transmission. The analyses suggested that multiple mumps virus introductions occurred in the Netherlands between 2004 and 2015 resulting in several mumps outbreaks throughout this period, whereas during some local outbreaks the molecular data pointed towards endemic circulation. Combined analysis of epidemiological data and sequence data collected in 2015 showed good support for the phylogenetic clustering. Copyright © 2016 Elsevier B.V. All rights reserved.

  14. Gene Expression Profiling as a Tool to Investigate the Molecular Machinery Activated during Hippocampal Neurodegeneration Induced by Trimethyltin (TMT Administration

    Directory of Open Access Journals (Sweden)

    Maria Concetta Geloso

    2013-08-01

    Full Text Available Trimethyltin (TMT is an organotin compound exhibiting neurotoxicant effects selectively localized in the limbic system and especially marked in the hippocampus, in both experimental animal models and accidentally exposed humans. TMT administration causes selective neuronal death involving either the granular neurons of the dentate gyrus or the pyramidal cells of the Cornu Ammonis, with a different pattern of localization depending on the different species studied or the dosage schedule. TMT is broadly used to realize experimental models of hippocampal neurodegeneration associated with cognitive impairment and temporal lobe epilepsy, though the molecular mechanisms underlying the associated selective neuronal death are still not conclusively clarified. Experimental evidence indicates that TMT-induced neurodegeneration is a complex event involving different pathogenetic mechanisms, probably acting differently in animal and cell models, which include neuroinflammation, intracellular calcium overload, and oxidative stress. Microarray-based, genome-wide expression analysis has been used to investigate the molecular scenario occurring in the TMT-injured brain in different in vivo and in vitro models, producing an overwhelming amount of data. The aim of this review is to discuss and rationalize the state-of-the-art on TMT-associated genome wide expression profiles in order to identify comparable and reproducible data that may allow focusing on significantly involved pathways.

  15. Molecular motors

    Science.gov (United States)

    Allemand, Jean François Desbiolles, Pierre

    2015-10-01

    How do we move? More precisely, what are the molecular mechanisms that can explain that our muscles, made of very small components can move at a osopic scale? To answer these questions we must introduce molecular motors. Those motors are proteins, or small protein assemblies that, in our cells, transform chemical energy into mechanical work. Then, like we could do for a oscopic motor, used in a car or in a fan, we are going to study the basic behavior of these molecular machines, present what are their energy sources, calculate their power, their yield. If molecular motors are crucial for our oscopic movements, we are going to see that they are also essential to cellular transport and that considering the activity of some enzymes as molecular motors bring some interesting new insights on their activity.

  16. Editorial: Biotechnology Journal brings more than biotechnology.

    Science.gov (United States)

    Jungbauer, Alois; Lee, Sang Yup

    2015-09-01

    Biotechnology Journal always brings the state-of-the-art biotechnologies to our readers. Different from other topical issues, this issue of Biotechnology Journal is complied with a series of exiting reviews and research articles from spontaneous submissions, again, addressing society's actual problems and needs. The progress is a real testimony how biotechnology contributes to achievements in healthcare, better utilization of resources, and a bio-based economy. Copyright © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Development of molecular tools to differentiate Indian wild pig (Sus scrofa cristatus meat from exotic and local domestic pig meat

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    Kajal Kumar Jadav

    2013-10-01

    Full Text Available Aim: Identification of wild pig and domestic pig is essential to prevent illegal poaching of wild pig and to implement Wildlife (Protection Act, 1972. PCR-RFLP was used to differentiate Wild pig (Sus scrofa cristatus from Domestic pig (Sus scrofa domestica meat. Materials and Methods: DNA was isolated from meat samples of both the sub species and a fragment of Cytochrome b gene was amplified using universal primers and the PCR products were subjected to restriction digestion. Results: All the known samples of each of the sub-species amplified 474 bp fragment successfully using b1 and b2 primers. To differentiate between wild and domestic pig meat, restriction digestion of the PCR products was carried out to produce characteristic PCR-RFLP patterns for each species. StuI digestion yielded a RFLP pattern which distinguished the closely related sub species. The alignment of sequences of Wild pigs with sequences of local domestic pig, European wild pig and exotic breeds revealed 7 intra-species polymorphic sites within Cytochrome b gene fragment.Conclusion: This study showed that The PCR-RFLP is a simple and very effective tool for differentiating the samples of both the sub species and could prove to be a useful tool in forensic identification of wild pig and domestic pig.

  18. A Brief Review on Diagnosis of Foot-and-Mouth Disease of Livestock: Conventional to Molecular Tools

    Science.gov (United States)

    Longjam, Neeta; Deb, Rajib; Sarmah, A. K.; Tayo, Tilling; Awachat, V. B.; Saxena, V. K.

    2011-01-01

    Foot-and-mouth disease (FMD) is one of the highly contagious diseases of domestic animals. Effective control of this disease needs sensitive, specific, and quick diagnostic tools at each tier of control strategy. In this paper we have outlined various diagnostic approaches from old to new generation in a nutshell. Presently FMD diagnosis is being carried out using techniques such as Virus Isolation (VI), Sandwich-ELISA (S-ELISA), Liquid-Phase Blocking ELISA (LPBE), Multiplex-PCR (m-PCR), and indirect ELISA (DIVA), and real time-PCR can be used for detection of antibody against nonstructural proteins. Nucleotide sequencing for serotyping, microarray as well as recombinant antigen-based detection, biosensor, phage display, and nucleic-acid-based diagnostic are on the way for rapid and specific detection of FMDV. Various pen side tests, namely, lateral flow, RT-LAMP, Immunostrip tests, and so forth. are also developed for detection of the virus in field condition. PMID:21776357

  19. Evaluation of the new advanced 15-loci MIRU-VNTR genotyping tool in Mycobacterium tuberculosis molecular epidemiology studies

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    Bouza Emilio

    2008-02-01

    Full Text Available Abstract Background During the last few years, PCR-based methods have been developed to simplify and reduce the time required for genotyping Mycobacterium tuberculosis (MTB by standard approaches based on IS6110-Restriction Fragment Length Polymorphism (RFLP. Of these, MIRU-12-VNTR (Mycobacterial interspersed repetitive units- variable number of tandem repeats (MIRU-12 has been considered a good alternative. Nevertheless, some limitations and discrepancies with RFLP, which are minimized if the technique is complemented with spoligotyping, have been found. Recently, a new version of MIRU-VNTR targeting 15 loci (MIRU-15 has been proposed to improve the MIRU-12 format. Results We evaluated the new MIRU-15 tool in two different samples. First, we analyzed the same convenience sample that had been used to evaluate MIRU-12 in a previous study, and the new 15-loci version offered higher discriminatory power (Hunter-Gaston discriminatory index [HGDI]: 0.995 vs 0.978; 34.4% of clustered cases vs 57.5% and better correlation (full or high correlation with RFLP for 82% of the clusters vs 47%. Second, we evaluated MIRU-15 on a population-based sample and, once again, good correlation with the RFLP clustering data was observed (for 83% of the RFLP clusters. To understand the meaning of the discrepancies still found between MIRU-15 and RFLP, we analyzed the epidemiological data for the clustered patients. In most cases, splitting of RFLP-clustered patients by MIRU-15 occurred for those without epidemiological links, and RFLP-clustered patients with epidemiological links were also clustered by MIRU-15, suggesting a good epidemiological background for clustering defined by MIRU-15. Conclusion The data obtained by MIRU-15 suggest that the new design is very efficient at assigning clusters confirmed by epidemiological data. If we add this to the speed with which it provides results, MIRU-15 could be considered a suitable tool for real-time genotyping.

  20. Bringing medicinal plants into cultivation: opportunities and challenges for biotechnology.

    Science.gov (United States)

    Canter, Peter H; Thomas, Howard; Ernst, Edzard

    2005-04-01

    Consumption of herbal medicines is widespread and increasing. Harvesting from the wild, the main source of raw material, is causing loss of genetic diversity and habitat destruction. Domestic cultivation is a viable alternative and offers the opportunity to overcome the problems that are inherent in herbal extracts: misidentification, genetic and phenotypic variability, extract variability and instability, toxic components and contaminants. The use of controlled environments can overcome cultivation difficulties and could be a means to manipulate phenotypic variation in bioactive compounds and toxins. Conventional plant-breeding methods can improve both agronomic and medicinal traits, and molecular marker assisted selection will be used increasingly. There has been significant progress in the use of tissue culture and genetic transformation to alter pathways for the biosynthesis of target metabolites. Obstacles to bringing medicinal plants into successful commercial cultivation include the difficulty of predicting which extracts will remain marketable and the likely market preference for what is seen as naturally sourced extracts.

  1. Combining `OMIC tools and other targeted molecular methods to evaluate iron limitation of diatoms in the Northeast Pacific Ocean.

    Science.gov (United States)

    Chappell, D.; Wallace, J.; Jenkins, B. D.; Powell, K.

    2016-02-01

    Diatoms are an abundant and widespread group of phytoplankton capable of exerting a profound influence on global carbon cycling. It is widely accepted that iron (Fe) controls diatom production in many ocean systems and the Fe stress response has been a focus of research for some time. Assessing the Fe status of natural diatom populations has proven challenging, as diatom species in the same genus may be difficult to distinguish using microscopy and the physiological and molecular responses to Fe stress can vary widely within a genus. A targeted high-throughput sequencing method to characterize the diatom community in field samples has been developed. Additionally, comparative transcriptomics of laboratory experiments with ecologically relevant species have been used to elucidate genes whose expression is tightly coupled to specific limitation scenarios. These two methods have been combined with data mining of the growing database of diatom transcriptomes to develop species-specific markers of physiological status in field populations. Data will be presented on the development and use of these methods to analyze samples collected on field expeditions to the Northeast Pacific Ocean sampling across gradients of Fe.

  2. Efficient somatic embryogenesis and molecular marker based analysis as effective tools for conservation of red-listed plant Commiphora wightii

    Directory of Open Access Journals (Sweden)

    ASHOK KUMAR PARMAR

    2014-08-01

    Full Text Available A refined and high efficiency protocol for in vitro regeneration of Commiphora wightii, a red-listed medicinal plant of medicinal importance, has been developed through optimized somatic embryogenesis pathway. Cultures from immature fruits were induced and proliferated on B5 medium supplemented with 2.26 µM 2,4-D. Embryogenic calli were obtained and then maintained for extended periods by alternately subculturing on modified MS medium supplemented with 1.11 µM BAP, 0.57 µM IBA and with 0.5% activated charcoal or without PGR every 3-4 weeks. Cyclic embryogenesis was obtained. Late torpedo and early cotyledonary stages somatic embryos were regularly harvested from PGR-free modified MS medium. It was found that percent moisture available in culture containers play a critical role in maturation and subsequent germination of somatic embryos of C. wighti. Maximum germination of more than 80% was achieved through media recycling. Somatic embryo derived plants (emblings were acclimatized. After 5 months, acclimatized plants were out-planted in experimental field. These morphologically normal plants have been surviving for over 3 years. Molecular polymorphism was clearly evident when these plants were tested using RAPD primers, making the plants suitable for use in its species restoration program.

  3. Pyrosequencing as a tool for the detection of Phytophthora species: error rate and risk of false Molecular Operational Taxonomic Units.

    Science.gov (United States)

    Vettraino, A M; Bonants, P; Tomassini, A; Bruni, N; Vannini, A

    2012-11-01

    To evaluate the accuracy of pyrosequencing for the description of Phytophthora communities in terms of taxa identification and risk of assignment for false Molecular Operational Taxonomic Units (MOTUs). Pyrosequencing of Internal Transcribed Spacer 1 (ITS1) amplicons was used to describe the structure of a DNA mixture comprising eight Phytophthora spp. and Pythium vexans. Pyrosequencing resulted in 16 965 reads, detecting all species in the template DNA mixture. Reducing the ITS1 sequence identity threshold resulted in a decrease in numbers of unmatched reads but a concomitant increase in the numbers of false MOTUs. The total error rate was 0·63% and comprised mainly mismatches (0·25%) Pyrosequencing of ITS1 region is an efficient and accurate technique for the detection and identification of Phytophthora spp. in environmental samples. However, the risk of allocating false MOTUs, even when demonstrated to be low, may require additional validation with alternative detection methods. Phytophthora spp. are considered among the most destructive groups of invasive plant pathogens, affecting thousands of cultivated and wild plants worldwide. Simultaneous early detection of Phytophthora complexes in environmental samples offers an unique opportunity for the interception of known and unknown species along pathways of introduction, along with the identification of these organisms in invaded environments. © 2012 The Authors Letters in Applied Microbiology © 2012 The Society for Applied Microbiology.

  4. Emerging new tools to study and treat muscle pathologies: genetics and molecular mechanisms underlying skeletal muscle development, regeneration, and disease.

    Science.gov (United States)

    Crist, Colin

    2017-01-01

    Skeletal muscle is the most abundant tissue in our body, is responsible for generating the force required for movement, and is also an important thermogenic organ. Skeletal muscle is an enigmatic tissue because while on the one hand, skeletal muscle regeneration after injury is arguably one of the best-studied stem cell-dependent regenerative processes, on the other hand, skeletal muscle is still subject to many degenerative disorders with few therapeutic options in the clinic. It is important to develop new regenerative medicine-based therapies for skeletal muscle. Future therapeutic strategies should take advantage of rapidly developing technologies enabling the differentiation of skeletal muscle from human pluripotent stem cells, along with precise genome editing, which will go hand in hand with a steady and focused approach to understanding underlying mechanisms of skeletal muscle development, regeneration, and disease. In this review, I focus on highlighting the recent advances that particularly have relied on developmental and molecular biology approaches to understanding muscle development and stem cell function. Copyright © 2016 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. Copyright © 2016 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

  5. Cell-free RNA content in urine as a possible molecular diagnostic tool for clear cell renal cell carcinoma.

    Science.gov (United States)

    Zhao, An; Péoc'h, Michel; Cottier, Michèle; Genin, Christian; Mottet, Nicolas; Li, Guorong

    2015-06-01

    There is limited research on cell-free RNA (cf-RNA) in the urine of cancer patients. The present study was performed to detect the cf-RNA in the urine of patients with clear cell renal cell carcinoma (ccRCC). Ninety-five urine samples from ccRCC patients and 50 urine samples from control subjects were analyzed. The cf-RNA integrity index was calculated by using quantitative real-time RT-PCR assays of the small-sized fragment (106 bp) and the big-sized fragment (416 bp) in GAPDH mRNA. The initial analysis showed that cf-RNA was stable and detectable in the urine. The mean cf-RNA integrity index was significantly lower in the urine of ccRCC patients (mean: 0.07, 95%CI: 0.05-0.10) when compared with the urine from control subjects (mean: 0.25, 95%CI: 0.16-0.33) (p big-sized (420 bp) VEGF mRNA fragment was an infrequent event. Our findings suggest that the small-sized cf-RNA in urine was more abundant in cancer patients. The tumor-related gene VEGF mRNA fragment was detectable in the urine of cancer patients. Our finding may provide a new molecular assay for the diagnosis of renal cell carcinoma. © 2014 UICC.

  6. Gorilla gorilla gorilla gut: a potential reservoir of pathogenic bacteria as revealed using culturomics and molecular tools.

    Science.gov (United States)

    Bittar, Fadi; Keita, Mamadou B; Lagier, Jean-Christophe; Peeters, Martine; Delaporte, Eric; Raoult, Didier

    2014-11-24

    Wild apes are considered to be the most serious reservoir and source of zoonoses. However, little data are available about the gut microbiota and pathogenic bacteria in gorillas. For this propose, a total of 48 fecal samples obtained from 21 Gorilla gorilla gorilla individuals (as revealed via microsatellite analysis) were screened for human bacterial pathogens using culturomics and molecular techniques. By applying culturomics to one index gorilla and using specific media supplemented by plants, we tested 12,800 colonies and identified 147 different bacterial species, including 5 new species. Many opportunistic pathogens were isolated, including 8 frequently associated with human diseases; Mycobacterium bolletii, Proteus mirabilis, Acinetobacter baumannii, Klebsiella pneumoniae, Serratia marcescens, Escherichia coli, Staphylococcus aureus and Clostridium botulinum. The genus Treponema accounted for 27.4% of the total reads identified at the genus level via 454 pyrosequencing. Using specific real-time PCR on 48 gorilla fecal samples, in addition to classical human pathogens, we also observed the fastidious bacteria Bartonella spp. Borrelia spp., Coxiella burnetii and Tropheryma whipplei in the gorilla population. We estimated that the prevalence of these pathogens vary between 4.76% and 85.7%. Therefore, gorillas share many bacterial pathogens with humans suggesting that they could be a reservoir for their emergence.

  7. Authentication of animal origin of heparin and low molecular weight heparin including ovine, porcine and bovine species using 1D NMR spectroscopy and chemometric tools.

    Science.gov (United States)

    Monakhova, Yulia B; Diehl, Bernd W K; Fareed, Jawed

    2017-10-27

    High resolution (600MHz) nuclear magnetic resonance (NMR) spectroscopy is used to distinguish heparin and low-molecular weight heparins (LMWHs) produced from porcine, bovine and ovine mucosal tissues as well as their blends. For multivariate analysis several statistical methods such as principal component analysis (PCA), factor discriminant analysis (FDA), partial least squares - discriminant analysis (PLS-DA), linear discriminant analysis (LDA) were utilized for the modeling of NMR data of more than 100 authentic samples. Heparin and LMWH samples from the independent test set (n=15) were 100% correctly classified according to its animal origin. Moreover, by using 1H NMR coupled with chemometrics and several batches of bovine heparins from two producers were differentiated. Thus, NMR spectroscopy combined with chemometrics is an efficient tool for simultaneous identification of animal origin and process based manufacturing difference in heparin products. Copyright © 2017 Elsevier B.V. All rights reserved.

  8. Bringing the power of dynamic languages to hardware control systems

    CERN Document Server

    Caicedo, J M; Neufeld, N

    2009-01-01

    Hardware control systems are normally programmed using high-performance languages like C or C++ and increasingly also Java. All these languages are strongly typed and compiled which brings usually good performance but at the cost of a longer development and testing cycle and the need for more programming expertise. Dynamic languages which were long thought to be too slow and not powerful enough for control purposes are, thanks to modern powerful computers and advanced implementation techniques, fast enough for many of these tasks. We present examples from the LHCb Experiment Control System (ECS), which is based on a commercial SCADA software. We have successfully used Python to integrate hardware devices into the ECS. We present the necessary lightweight middle-ware we have developed, including examples for controlling hardware and software devices. We also discuss the development cycle, tools used and compare the effort to traditional solutions.

  9. The Bring Your Own Technology Initiative: An Examination of Teachers' Adoption

    Science.gov (United States)

    Cardoza, Yanet; Tunks, Jeanne

    2014-01-01

    This case study explored teachers' concerns, use, and actual practices in their adoption of the Bring Your Own Technology (BYOT) initiative. Participants were 12 secondary teachers in a private school setting. The Concerns-Based Adoption Model tools provided data: Stages of Concern Questionnaire (SoCQ), Levels of Use interview, and the Innovation…

  10. Current understanding of PrnP Genetics: A tool for Molecular Assisted Selection in Sheep Populations (A review

    Directory of Open Access Journals (Sweden)

    Viorica Cosier

    2016-04-01

    Full Text Available Scrapie is a neurodegenerative prion disease of sheep, goats and mouflons, belonging to the group of transmissible spongiform encephalopathies (TSEs, which affects humans as well. Even though classical scrapie has been known for over 250 years, the 1985 BSE crisis related to the advent of new forms of the Creutzfeldt-Jakob disease (vCJD in humans imposed the implementation of rapid coercive legal measures of prevention, control and eradication of TSEs. According to the prion hypothesis, the transmissible agent is the pathological isoform (PrPSc of cellular prion protein (PrPC. Specific polymorphisms of the gene that encodes cell prion protein (PrnP in sheep have been associated with resistance / natural susceptibility to the development and progression of the disease. Combinations of alleles at three adjacent codons (136 [A/V], 154 [H/R], 171 [H/Q/R] underpin the classification of 15 possible genotypes in risk classes, applicable in selection schemes where the maximum resistance is conferred by ARR allele, and the minimum by the VRQ allele. Although, after applying these programmes, the genetic structure of sheep populations has changed favourably, genotype association studies showed that no genotype is completely resistant to the infection, including homozygote ARR / ARR. With the discovery of atypical scrapie (Nor98, it became evident that the connection between the genetics of prion protein gene polymorphisms and susceptibility to the disease must be re-evaluated individually for each breed. In scrapie monitoring and control programmes, three diagnostic categories of the disease are observed: classical scrapie, atypical scrapie and BSE scrapie in small ruminant. This review shows the chronology of progress in the fight for the eradication of TSEs in sheep, 30 years after the BSE epidemic outburst, focusing especially on the link between the molecular diagnostic forms and the genetics of the disease.

  11. Glioma FMISO PET/MR Imaging Concurrent with Antiangiogenic Therapy: Molecular Imaging as a Clinical Tool in the Burgeoning Era of Personalized Medicine

    Science.gov (United States)

    Barajas, Ramon F.; Krohn, Kenneth A.; Link, Jeanne M.; Hawkins, Randall A.; Clarke, Jennifer L.; Pampaloni, Miguel H.; Cha, Soonmee

    2016-01-01

    The purpose of this article is to provide a focused overview of the current use of positron emission tomography (PET) molecular imaging in the burgeoning era of personalized medicine in the treatment of patients with glioma. Specifically, we demonstrate the utility of PET imaging as a tool for personalized diagnosis and therapy by highlighting a case series of four patients with recurrent high grade glioma who underwent 18F-fluoromisonidazole (FMISO) PET/MR (magnetic resonance) imaging through the course of antiangiogenic therapy. Three distinct features were observed from this small cohort of patients. First, the presence of pseudoprogression was retrospectively associated with the absence of hypoxia. Second, a subgroup of patients with recurrent high grade glioma undergoing bevacizumab therapy demonstrated disease progression characterized by an enlarging nonenhancing mass with newly developed reduced diffusion, lack of hypoxia, and preserved cerebral blood volume. Finally, a reduction in hypoxic volume was observed concurrent with therapy in all patients with recurrent tumor, and markedly so in two patients that developed a nonenhancing reduced diffusion mass. This case series demonstrates how medical imaging has the potential to influence personalized medicine in several key aspects, especially involving molecular PET imaging for personalized diagnosis, patient specific disease prognosis, and therapeutic monitoring. PMID:28536391

  12. Anti-RAINBOW dye-specific antibodies as universal tools for the visualization of prestained protein molecular weight markers in Western blot analysis.

    Science.gov (United States)

    Schüchner, Stefan; Andorfer, Peter; Mudrak, Ingrid; Ogris, Egon

    2016-08-17

    Western blotting is one of the most widely used techniques in molecular biology and biochemistry. Prestained proteins are used as molecular weight standards in protein electrophoresis. In the chemiluminescent Western blot analysis, however, these colored protein markers are invisible leaving researchers with the unsatisfying situation that the signal for the protein of interest and the signal for the markers are not captured simultaneously and have to be merged in an error-prone step. To allow the simultaneous detection of marker proteins we generated monoclonal antibodies specific for the protein dyes. To elicit a dye rather than protein specific immune response we immunized mice sequentially with dye-carrier protein complexes, in which a new carrier protein was used for each subsequent immunization. Moreover, by sequentially immunizing with dye-carrier protein complexes, in which different but structurally related dyes were used, we could also generate an antibody, termed anti-RAINBOW, that cross-reacted even with structurally related dyes not used in the immunizations. Our novel antibodies represent convenient tools for the simultaneous Western blot detection of commercially available prestained marker proteins in combination with the detection of any specific protein of interest. These antibodies will render obsolete the anachronistic tradition of manually charting marker bands on film.

  13. Leishmania OligoC-TesT as a simple, rapid, and standardized tool for molecular diagnosis of cutaneous leishmaniasis in Peru.

    Science.gov (United States)

    Espinosa, Diego; Boggild, Andrea K; Deborggraeve, Stijn; Laurent, Thierry; Valencia, Cristian; Pacheco, Rosa; Miranda-Verástegui, César; Llanos-Cuentas, Alejandro; Leclipteux, Thierry; Dujardin, Jean-Claude; Büscher, Philippe; Arévalo, Jorge

    2009-08-01

    Molecular methods such as PCR have become attractive tools for diagnosis of cutaneous leishmaniasis (CL), both for their high sensitivity and for their specificity. However, their practical use in routine diagnosis is limited due to the infrastructural requirements and the lack of any standardization. Recently, a simplified and standardized PCR format for molecular detection of Leishmania was developed. The Leishmania OligoC-TesT is based on simple and rapid detection using a dipstick with PCR-amplified Leishmania DNA. In this study, we estimated the diagnostic accuracy of the Leishmania OligoC-TesT for 61 specimens from 44 CL-suspected patients presenting at the leishmaniasis clinic of the Instituto de Medicina Tropical Alexander von Humboldt, Peru. On the basis of parasitological detection and the leishmanin skin test (LST), patients were classified as (i) confirmed CL cases, (ii) LST-positive cases, and (iii) LST-negative cases. The sensitivities of the Leishmania OligoC-TesT was 74% (95% confidence interval (CI), 60.5% to 84.1%) for lesion aspirates and 92% (95% CI, 81.2% to 96.9%) for scrapings. A significantly higher sensitivity was observed with a conventional PCR targeting the kinetoplast DNA on the aspirates (94%) (P = 0.001), while there was no significant difference in sensitivity for the lesion scrapings (88%) (P = 0.317). In addition, the Leishmania OligoC-TesT was evaluated for 13 CL-suspected patients in two different peripheral health centers in the central jungle of Peru. Our findings clearly indicate the high accuracy of the Leishmania OligoC-TesT for lesion scrapings for simple and rapid molecular diagnosis of CL in Peru.

  14. Molecular diagnostic tools for detection and differentiation of phytoplasmas based on chaperonin-60 reveal differences in host plant infection patterns.

    Directory of Open Access Journals (Sweden)

    Tim J Dumonceaux

    Full Text Available Phytoplasmas ('Candidatus Phytoplasma' spp. are insect-vectored bacteria that infect a wide variety of plants, including many agriculturally important species. The infections can cause devastating yield losses by inducing morphological changes that dramatically alter inflorescence development. Detection of phytoplasma infection typically utilizes sequences located within the 16S-23S rRNA-encoding locus, and these sequences are necessary for strain identification by currently accepted standards for phytoplasma classification. However, these methods can generate PCR products >1400 bp that are less divergent in sequence than protein-encoding genes, limiting strain resolution in certain cases. We describe a method for accessing the chaperonin-60 (cpn60 gene sequence from a diverse array of 'Ca.Phytoplasma' spp. Two degenerate primer sets were designed based on the known sequence diversity of cpn60 from 'Ca.Phytoplasma' spp. and used to amplify cpn60 gene fragments from various reference samples and infected plant tissues. Forty three cpn60 sequences were thereby determined. The cpn60 PCR-gel electrophoresis method was highly sensitive compared to 16S-23S-targeted PCR-gel electrophoresis. The topology of a phylogenetic tree generated using cpn60 sequences was congruent with that reported for 16S rRNA-encoding genes. The cpn60 sequences were used to design a hybridization array using oligonucleotide-coupled fluorescent microspheres, providing rapid diagnosis and typing of phytoplasma infections. The oligonucleotide-coupled fluorescent microsphere assay revealed samples that were infected simultaneously with two subtypes of phytoplasma. These tools were applied to show that two host plants, Brassica napus and Camelina sativa, displayed different phytoplasma infection patterns.

  15. Methods and Tools to allow molecular flow simulations to be coupled to higher level continuum descriptions of flows in porous/fractured media and aerosol/dust dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Loyalka, Sudarshan [Univ. of Missouri, Columbia, MO (United States)

    2015-04-09

    The purpose of this project was to develop methods and tools that will aid in safety evaluation of nuclear fuels and licensing of nuclear reactors relating to accidents.The objectives were to develop more detailed and faster computations of fission product transport and aerosol evolution as they generally relate to nuclear fuel and/or nuclear reactor accidents. The two tasks in the project related to molecular transport in nuclear fuel and aerosol transport in reactor vessel and containment. For both the tasks, explorations of coupling of Direct Simulation Monte Carlo with Navier-Stokes solvers or the Sectional method were not successful. However, Mesh free methods for the Direct Simulation Monte Carlo method were successfully explored.These explorations permit applications to porous and fractured media, and arbitrary geometries.The computations were carried out in Mathematica and are fully parallelized. The project has resulted in new computational tools (algorithms and programs) that will improve the fidelity of computations to actual physics, chemistry and transport of fission products in the nuclear fuel and aerosol in reactor primary and secondary containments.

  16. 1H NMR Metabolomics: A New Molecular Level Tool for Assessment of Organic Contaminant Bioavailability to Earthworms in Soil

    Science.gov (United States)

    McKelvie, J. R.; Wolfe, D. M.; Celejewski, M. A.; Simpson, A. J.; Simpson, M. J.

    2009-05-01

    extractable using cyclodextrin. Hence, while cyclodextrin extraction may serve as a good proxy for microbial bioavailability, our results suggest that it may not serve as a good proxy for earthworm bioavailability. 1H NMR metabolomics therefore offers considerable promise as a novel, molecular-level method to directly monitor earthworm bioavailability of potentially toxic and persistent compounds in the environment.

  17. Bringing Rad52 foci into focus

    Science.gov (United States)

    Alvaro, David; Lisby, Michael

    2011-01-01

    In 2007, we published the results of a genome-wide screen for ORFs that affect the frequency of Rad52 foci in yeast. That paper was published within the constraints of conventional online publishing tools, and it provided only a glimpse into the actual screen data. New tools in the JCB DataViewer now show how these data can—and should—be shared. PMID:21893595

  18. Bringing Pulsed Laser Welding into Production

    DEFF Research Database (Denmark)

    Olsen, Flemmming Ove

    1996-01-01

    In this paper, some research and develop-ment activities within pulsed laser welding technology at the Tech-nical University of Denmark will be described. The laser group at the Insti-tute for Manufacturing Technology has nearly 20 years of experience in laser materials process-ing. Inter......-nationally the group is mostly known for its contri-butions to the development of the laser cutting process, but further it has been active within laser welding, both in assisting industry in bringing laser welding into production in several cases and in performing fundamental R & D. In this paper some research...... activities concerning the weldability of high alloyed austenitic stainless steels for mass production industry applying industrial lasers for fine welding will be described. Studies on hot cracking sensitivity of high alloyed austenitic stainless steel applying both ND-YAG-lasers and CO2-lasers has been...

  19. The molecular genetic linkage map of the model legume Medicago truncatula: an essential tool for comparative legume genomics and the isolation of agronomically important genes

    Science.gov (United States)

    Thoquet, Philippe; Ghérardi, Michele; Journet, Etienne-Pascal; Kereszt, Attila; Ané, Jean-Michel; Prosperi, Jean-Marie; Huguet, Thierry

    2002-01-01

    Background The legume Medicago truncatula has emerged as a model plant for the molecular and genetic dissection of various plant processes involved in rhizobial, mycorrhizal and pathogenic plant-microbe interactions. Aiming to develop essential tools for such genetic approaches, we have established the first genetic map of this species. Two parental homozygous lines were selected from the cultivar Jemalong and from the Algerian natural population (DZA315) on the basis of their molecular and phenotypic polymorphism. Results An F2 segregating population of 124 individuals between these two lines was obtained using an efficient manual crossing technique established for M. truncatula and was used to construct a genetic map. This map spans 1225 cM (average 470 kb/cM) and comprises 289 markers including RAPD, AFLP, known genes and isoenzymes arranged in 8 linkage groups (2n = 16). Markers are uniformly distributed throughout the map and segregation distortion is limited to only 3 linkage groups. By mapping a number of common markers, the eight linkage groups are shown to be homologous to those of diploid alfalfa (M. sativa), implying a good level of macrosynteny between the two genomes. Using this M. truncatula map and the derived F3 populations, we were able to map the Mtsym6 symbiotic gene on linkage group 8 and the SPC gene, responsible for the direction of pod coiling, on linkage group 7. Conclusions These results demonstrate that Medicago truncatula is amenable to diploid genetic analysis and they open the way to map-based cloning of symbiotic or other agronomically-important genes using this model plant. PMID:11825338

  20. SYBR Green Real-Time PCR-RFLP Assay Targeting the Plasmodium Cytochrome B Gene – A Highly Sensitive Molecular Tool for Malaria Parasite Detection and Species Determination

    Science.gov (United States)

    Xu, Weiping; Morris, Ulrika; Aydin-Schmidt, Berit; Msellem, Mwinyi I.; Shakely, Delér; Petzold, Max; Björkman, Anders; Mårtensson, Andreas

    2015-01-01

    A prerequisite for reliable detection of low-density Plasmodium infections in malaria pre-elimination settings is the availability of ultra-sensitive and high-throughput molecular tools. We developed a SYBR Green real-time PCR restriction fragment length polymorphism assay (cytb-qPCR) targeting the cytochrome b gene of the four major human Plasmodium species (P. falciparum, P. vivax, P. malariae, and P. ovale) for parasite detection and species determination with DNA extracted from dried blood spots collected on filter paper. The performance of cytb-qPCR was first compared against four reference PCR methods using serially diluted Plasmodium samples. The detection limit of the cytb-qPCR was 1 parasite/μl (p/μl) for P. falciparum and P. ovale, and 2 p/μl for P. vivax and P. malariae, while the reference PCRs had detection limits of 0.5–10 p/μl. The ability of the PCR methods to detect low-density Plasmodium infections was then assessed using 2977 filter paper samples collected during a cross-sectional survey in Zanzibar, a malaria pre-elimination setting in sub-Saharan Africa. Field samples were defined as ‘final positive’ if positive in at least two of the five PCR methods. Cytb-qPCR preformed equal to or better than the reference PCRs with a sensitivity of 100% (65/65; 95%CI 94.5–100%) and a specificity of 99.9% (2910/2912; 95%CI 99.7–100%) when compared against ‘final positive’ samples. The results indicate that the cytb-qPCR may represent an opportunity for improved molecular surveillance of low-density Plasmodium infections in malaria pre-elimination settings. PMID:25774805

  1. SYBR Green real-time PCR-RFLP assay targeting the plasmodium cytochrome B gene--a highly sensitive molecular tool for malaria parasite detection and species determination.

    Science.gov (United States)

    Xu, Weiping; Morris, Ulrika; Aydin-Schmidt, Berit; Msellem, Mwinyi I; Shakely, Delér; Petzold, Max; Björkman, Anders; Mårtensson, Andreas

    2015-01-01

    A prerequisite for reliable detection of low-density Plasmodium infections in malaria pre-elimination settings is the availability of ultra-sensitive and high-throughput molecular tools. We developed a SYBR Green real-time PCR restriction fragment length polymorphism assay (cytb-qPCR) targeting the cytochrome b gene of the four major human Plasmodium species (P. falciparum, P. vivax, P. malariae, and P. ovale) for parasite detection and species determination with DNA extracted from dried blood spots collected on filter paper. The performance of cytb-qPCR was first compared against four reference PCR methods using serially diluted Plasmodium samples. The detection limit of the cytb-qPCR was 1 parasite/μl (p/μl) for P. falciparum and P. ovale, and 2 p/μl for P. vivax and P. malariae, while the reference PCRs had detection limits of 0.5-10 p/μl. The ability of the PCR methods to detect low-density Plasmodium infections was then assessed using 2977 filter paper samples collected during a cross-sectional survey in Zanzibar, a malaria pre-elimination setting in sub-Saharan Africa. Field samples were defined as 'final positive' if positive in at least two of the five PCR methods. Cytb-qPCR preformed equal to or better than the reference PCRs with a sensitivity of 100% (65/65; 95%CI 94.5-100%) and a specificity of 99.9% (2910/2912; 95%CI 99.7-100%) when compared against 'final positive' samples. The results indicate that the cytb-qPCR may represent an opportunity for improved molecular surveillance of low-density Plasmodium infections in malaria pre-elimination settings.

  2. The molecular genetic linkage map of the model legume Medicago truncatula: an essential tool for comparative legume genomics and the isolation of agronomically important genes

    Directory of Open Access Journals (Sweden)

    Ané Jean-Michel

    2002-01-01

    Full Text Available Abstract Background The legume Medicago truncatula has emerged as a model plant for the molecular and genetic dissection of various plant processes involved in rhizobial, mycorrhizal and pathogenic plant-microbe interactions. Aiming to develop essential tools for such genetic approaches, we have established the first genetic map of this species. Two parental homozygous lines were selected from the cultivar Jemalong and from the Algerian natural population (DZA315 on the basis of their molecular and phenotypic polymorphism. Results An F2 segregating population of 124 individuals between these two lines was obtained using an efficient manual crossing technique established for M. truncatula and was used to construct a genetic map. This map spans 1225 cM (average 470 kb/cM and comprises 289 markers including RAPD, AFLP, known genes and isoenzymes arranged in 8 linkage groups (2n = 16. Markers are uniformly distributed throughout the map and segregation distortion is limited to only 3 linkage groups. By mapping a number of common markers, the eight linkage groups are shown to be homologous to those of diploid alfalfa (M. sativa, implying a good level of macrosynteny between the two genomes. Using this M. truncatula map and the derived F3 populations, we were able to map the Mtsym6 symbiotic gene on linkage group 8 and the SPC gene, responsible for the direction of pod coiling, on linkage group 7. Conclusions These results demonstrate that Medicago truncatula is amenable to diploid genetic analysis and they open the way to map-based cloning of symbiotic or other agronomically-important genes using this model plant.

  3. Nested-PCR real time as alternative molecular tool for detection of Borrelia burgdorferi compared to the classical serological diagnosis of the blood.

    Science.gov (United States)

    Sroka-Oleksiak, Agnieszka; Ufir, Krzysztof; Salamon, Dominika; Bulanda, Malgorzata; Gosiewski, Tomasz

    Lyme disease, caused by Borrelia burgdorferi, is a multisystem disease that often makes difficulties to recognize caused by their genetic heterogenity. Currently, the gold standard for the detection of Lyme disease (LD) is serologic diagnostics based mainly on tests: ELISA and Western blot (WB). These methods, however, are subject to consider- able defect, especially in the initial phase of infection due to the occurrence of so-called serological window period and low specificity. For this reason, they might be replaced by molecular methods, for example polymerase chain reaction (PCR), which should be more sensitivity and specificity. In the present study we attempt to optimize the PCR reaction conditions and enhance existing test sensitivity by applying the equivalent of real time PCR - nested PCR for detection B. burgdorferi DNA in the patient's blood. The study involved 94 blood samples of patients with suspected LD. From each sample, 1.5 ml of blood was used for the isolation of bacterial DNA and PCR real time am- plification and its equivalent, in nested version. The remaining part earmarked for serologi- cal testing. Optimization of the reaction conditions made experimentally, using gradient of the temperature and gradient of the magnesium ions concentration for reaction real time in nested-PCR and PCR version. The results show that the nested-PCR real time, has a much higher sensitivity 45 (47.8%) of positive results for the detection of B. burgdorferi compared to the single- variety, without a preceding pre-amplification 2 (2.1%). Serological methods allowed the detection of infection in 41 (43.6%) samples. These results support of the nested PCR method as a better molecular tool for the detection of B. burgdorferi infection than classical PCR real time reaction. The nested-PCR real time method may be considered as a complement to ELISA and WB mainly in the early stages of infection, when in the blood circulating B. burgdorferi cells. By contrast, the

  4. Information brings progress to Vietnam's communes

    International Development Research Centre (IDRC) Digital Library (Canada)

    vaccinate the animals, and trains them to use the tools. And the data is useful when disaster strikes. Nho Quan district is the poorest in the province, says Ms Thanh. When it suffered from flooding in 2007, the government provided assistance. The CBMS data was used to identify communes and people who should benefit ...

  5. GPCR-SSFE 2.0-a fragment-based molecular modeling web tool for Class A G-protein coupled receptors.

    Science.gov (United States)

    Worth, Catherine L; Kreuchwig, Franziska; Tiemann, Johanna K S; Kreuchwig, Annika; Ritschel, Michele; Kleinau, Gunnar; Hildebrand, Peter W; Krause, Gerd

    2017-07-03

    G-protein coupled receptors (GPCRs) are key players in signal transduction and therefore a large proportion of pharmaceutical drugs target these receptors. Structural data of GPCRs are sparse yet important for elucidating the molecular basis of GPCR-related diseases and for performing structure-based drug design. To ameliorate this problem, GPCR-SSFE 2.0 (http://www.ssfa-7tmr.de/ssfe2/), an intuitive web server dedicated to providing three-dimensional Class A GPCR homology models has been developed. The updated web server includes 27 inactive template structures and incorporates various new functionalities. Uniquely, it uses a fingerprint correlation scoring strategy for identifying the optimal templates, which we demonstrate captures structural features that sequence similarity alone is unable to do. Template selection is carried out separately for each helix, allowing both single-template models and fragment-based models to be built. Additionally, GPCR-SSFE 2.0 stores a comprehensive set of pre-calculated and downloadable homology models and also incorporates interactive loop modeling using the tool SL2, allowing knowledge-based input by the user to guide the selection process. For visual analysis, the NGL viewer is embedded into the result pages. Finally, blind-testing using two recently published structures shows that GPCR-SSFE 2.0 performs comparably or better than other state-of-the art GPCR modeling web servers. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  6. GPCR-SSFE 2.0—a fragment-based molecular modeling web tool for Class A G-protein coupled receptors

    Science.gov (United States)

    Kreuchwig, Franziska; Tiemann, Johanna K.S.; Kreuchwig, Annika; Ritschel, Michele; Kleinau, Gunnar; Hildebrand, Peter W.; Krause, Gerd

    2017-01-01

    Abstract G-protein coupled receptors (GPCRs) are key players in signal transduction and therefore a large proportion of pharmaceutical drugs target these receptors. Structural data of GPCRs are sparse yet important for elucidating the molecular basis of GPCR-related diseases and for performing structure-based drug design. To ameliorate this problem, GPCR-SSFE 2.0 (http://www.ssfa-7tmr.de/ssfe2/), an intuitive web server dedicated to providing three-dimensional Class A GPCR homology models has been developed. The updated web server includes 27 inactive template structures and incorporates various new functionalities. Uniquely, it uses a fingerprint correlation scoring strategy for identifying the optimal templates, which we demonstrate captures structural features that sequence similarity alone is unable to do. Template selection is carried out separately for each helix, allowing both single-template models and fragment-based models to be built. Additionally, GPCR-SSFE 2.0 stores a comprehensive set of pre-calculated and downloadable homology models and also incorporates interactive loop modeling using the tool SL2, allowing knowledge-based input by the user to guide the selection process. For visual analysis, the NGL viewer is embedded into the result pages. Finally, blind-testing using two recently published structures shows that GPCR-SSFE 2.0 performs comparably or better than other state-of-the art GPCR modeling web servers. PMID:28582569

  7. Combining MOSCED with molecular simulation free energy calculations or electronic structure calculations to develop an efficient tool for solvent formulation and selection.

    Science.gov (United States)

    Cox, Courtney E; Phifer, Jeremy R; Ferreira da Silva, Larissa; Gonçalves Nogueira, Gabriel; Ley, Ryan T; O'Loughlin, Elizabeth J; Pereira Barbosa, Ana Karolyne; Rygelski, Brett T; Paluch, Andrew S

    2017-02-01

    Solubility parameter based methods have long been a valuable tool for solvent formulation and selection. Of these methods, the MOdified Separation of Cohesive Energy Density (MOSCED) has recently been shown to correlate well the equilibrium solubility of multifunctional non-electrolyte solids. However, before it can be applied to a novel solute, a limited amount of reference solubility data is required to regress the necessary MOSCED parameters. Here we demonstrate for the solutes methylparaben, ethylparaben, propylparaben, butylparaben, lidocaine and ephedrine how conventional molecular simulation free energy calculations or electronic structure calculations in a continuum solvent, here the SMD or SM8 solvation model, can instead be used to generate the necessary reference data, resulting in a predictive flavor of MOSCED. Adopting the melting point temperature and enthalpy of fusion of these compounds from experiment, we are able to predict equilibrium solubilities. We find the method is able to well correlate the (mole fraction) equilibrium solubility in non-aqueous solvents over four orders of magnitude with good quantitative agreement.

  8. Molecular bioelectricity in developmental biology: new tools and recent discoveries: control of cell behavior and pattern formation by transmembrane potential gradients.

    Science.gov (United States)

    Levin, Michael

    2012-03-01

    Significant progress in the molecular investigation of endogenous bioelectric signals during pattern formation in growing tissues has been enabled by recently developed techniques. Ion flows and voltage gradients produced by ion channels and pumps are key regulators of cell proliferation, migration, and differentiation. Now, instructive roles for bioelectrical gradients in embryogenesis, regeneration, and neoplasm are being revealed through the use of fluorescent voltage reporters and functional experiments using well-characterized channel mutants. Transmembrane voltage gradients (V(mem) ) determine anatomical polarity and function as master regulators during appendage regeneration and embryonic left-right patterning. A state-of-the-art recent study reveals that they can also serve as prepatterns for gene expression domains during craniofacial patterning. Continued development of novel tools and better ways to think about physical controls of cell-cell interactions will lead to mastery of the morphogenetic information stored in physiological networks. This will enable fundamental advances in basic understanding of growth and form, as well as transformative biomedical applications in regenerative medicine. Copyright © 2012 WILEY Periodicals, Inc.

  9. Integrated Computational Tools for Identification of CCR5 Antagonists as Potential HIV-1 Entry Inhibitors: Homology Modeling, Virtual Screening, Molecular Dynamics Simulations and 3D QSAR Analysis

    Directory of Open Access Journals (Sweden)

    Suri Moonsamy

    2014-04-01

    Full Text Available Using integrated in-silico computational techniques, including homology modeling, structure-based and pharmacophore-based virtual screening, molecular dynamic simulations, per-residue energy decomposition analysis and atom-based 3D-QSAR analysis, we proposed ten novel compounds as potential CCR5-dependent HIV-1 entry inhibitors. Via validated docking calculations, binding free energies revealed that novel leads demonstrated better binding affinities with CCR5 compared to maraviroc, an FDA-approved HIV-1 entry inhibitor and in clinical use. Per-residue interaction energy decomposition analysis on the averaged MD structure showed that hydrophobic active residues Trp86, Tyr89 and Tyr108 contributed the most to inhibitor binding. The validated 3D-QSAR model showed a high cross-validated rcv2 value of 0.84 using three principal components and non-cross-validated r2 value of 0.941. It was also revealed that almost all compounds in the test set and training set yielded a good predicted value. Information gained from this study could shed light on the activity of a new series of lead compounds as potential HIV entry inhibitors and serve as a powerful tool in the drug design and development machinery.

  10. Combining MOSCED with molecular simulation free energy calculations or electronic structure calculations to develop an efficient tool for solvent formulation and selection

    Science.gov (United States)

    Cox, Courtney E.; Phifer, Jeremy R.; Ferreira da Silva, Larissa; Gonçalves Nogueira, Gabriel; Ley, Ryan T.; O'Loughlin, Elizabeth J.; Pereira Barbosa, Ana Karolyne; Rygelski, Brett T.; Paluch, Andrew S.

    2017-02-01

    Solubility parameter based methods have long been a valuable tool for solvent formulation and selection. Of these methods, the MOdified Separation of Cohesive Energy Density (MOSCED) has recently been shown to correlate well the equilibrium solubility of multifunctional non-electrolyte solids. However, before it can be applied to a novel solute, a limited amount of reference solubility data is required to regress the necessary MOSCED parameters. Here we demonstrate for the solutes methylparaben, ethylparaben, propylparaben, butylparaben, lidocaine and ephedrine how conventional molecular simulation free energy calculations or electronic structure calculations in a continuum solvent, here the SMD or SM8 solvation model, can instead be used to generate the necessary reference data, resulting in a predictive flavor of MOSCED. Adopting the melting point temperature and enthalpy of fusion of these compounds from experiment, we are able to predict equilibrium solubilities. We find the method is able to well correlate the (mole fraction) equilibrium solubility in non-aqueous solvents over four orders of magnitude with good quantitative agreement.

  11. Bringing science to the policy table

    CERN Multimedia

    2014-01-01

    “They shall beat their swords into plowshares, and their spears into pruning hooks. Nation shall not lift up sword against nation. Neither shall they learn war anymore." So says Isaiah 2:4, as transcribed on the famous wall in Ralph Bunche park, just the other side of 1st Avenue from the UN’s New York headquarters, where we held a celebration of our 60th anniversary year on Monday 20 October. I used the quotation in my opening address, since it is such a perfect fit to the theme of 60 years of science for peace and development.   The event was organised with the United Nations Economic and Social Council, ECOSOC, in the framework of CERN’s observer status at the UN, and although focused on CERN, its aim was broader. Presentations used CERN as an example to bring out the vital importance of science in general to the themes of peace and development. The event was presided over by Martin Sajdik, President of ECOSOC, and we were privileged to have presentat...

  12. Poster power brings together electronics community

    CERN Multimedia

    2006-01-01

    An 'Electronics at CERN' poster session was displayed on the mezzanine in building 500 for two days from 30 November. The display consisted of 20 posters and brought together a wide range of electronic projects designed and assembled by CERN teams and other collaborators involved in the building of the LHC. This was the first time this event had been held. As its organiser John Evans (IT/DES) explained, 'the idea came from the experience of attending conferences outside CERN, where you may find projects from CERN you didn't know about. It's nice to bring them together so we can all benefit from the efforts made.' The work on show spanned different departments and experiments, ranging from microelectronics to equipment designed for giant magnets. The invited audience was equally broad and included engineers, physicists as well as the electronics community at CERN. An informal gathering of all the exhibitors also offered an opportunity to view and discuss the work over a cup of coffee. 'The poster session acts...

  13. Bring NASA Scientific Data into GIS

    Science.gov (United States)

    Xu, H.

    2016-12-01

    NASA's Earth Observation System (EOS) and many other missions produce data of huge volume and near real time which drives the research and understanding of climate change. Geographic Information System (GIS) is a technology used for the management, visualization and analysis of spatial data. Since it's inception in the 1960s, GIS has been applied to many fields at the city, state, national, and world scales. People continue to use it today to analyze and visualize trends, patterns, and relationships from the massive datasets of scientific data. There is great interest in both the scientific and GIS communities in improving technologies that can bring scientific data into a GIS environment, where scientific research and analysis can be shared through the GIS platform to the public. Most NASA scientific data are delivered in the Hierarchical Data Format (HDF), a format is both flexible and powerful. However, this flexibility results in challenges when trying to develop supported GIS software - data stored with HDF formats lack a unified standard and convention among these products. The presentation introduces an information model that enables ArcGIS software to ingest NASA scientific data and create a multidimensional raster - univariate and multivariate hypercubes - for scientific visualization and analysis. We will present the framework how ArcGIS leverages the open source GDAL (Geospatial Data Abstract Library) to support its raster data access, discuss how we overcame the GDAL drivers limitations in handing scientific products that are stored with HDF4 and HDF5 formats and how we improve the way in modeling the multidimensionality with GDAL. In additional, we will talk about the direction of ArcGIS handling NASA products and demonstrate how the multidimensional information model can help scientists work with various data products such as MODIS, MOPPIT, SMAP as well as many data products in a GIS environment.

  14. Bringing nature-based solutions to scale

    Science.gov (United States)

    Jongman, Brenden; Lange, Glenn-Marie; Balog, Simone; van Wesenbeeck, Bregje

    2017-04-01

    Coastal communities in developing countries are highly exposed and vulnerable to coastal flood risk, and are likely to suffer from climate change induced changes in risk. Over the last decade, strong evidence has surfaced that nature-based solutions or ecosystem-based approaches are efficient and effective alternatives for flood risk reduction and climate change adaptation. In developing countries, numerous projects have therefore been implemented, often driven by international donors and NGOs. Some of these projects have been successful in reducing risk while improving environmental and socioeconomic conditions. However, the feasibility assessment, design and implementation of nature-based solutions is a multifaceted process, which needs to be well-understood before such solutions can be effectively implemented as an addition or alternative to grey infrastructure. This process has not always been followed. As a result, many projects have failed to deliver positive outcomes. The international community therefore has a challenge in bringing nature-based solutions to scale in an effective way. In this presentation, we will present best practice guidelines on nature-based solution implementation that are currently being discussed by the international community. Furthermore, we will present the alpha version of a new web platform being developed by the World Bank that will serve as a much-needed central repository for project information on nature-based solutions, and that will host actionable implementation guidelines. The presentation will also serve as an invitation to the scientific community to share their experience and lessons learned, and contribute to the outlining of best practice guidance.

  15. Conformational flexibility in designing peptides for immunology: the molecular dynamics approach.

    Science.gov (United States)

    Stavrakoudis, Athanassios

    2010-09-01

    Computational modeling techniques and computer simulations have become a routine in biological sciences and have gained great attention from researchers. Molecular dynamics simulation is a valuable tool towards an understanding of the complex structure of biological systems, especially in the study of the flexibility of the biological molecules such as peptides or proteins. Peptides play a very important role in human physiology and control many of the processes involved in the immune system response. Designing new and optimal peptide vaccines is one of the hottest challenges of the 21(st) century science and it brings together researchers from different fields. Molecular dynamics simulations have proven to be a helpful tool assisting laboratory work, saving financial sources and opening possibilities for exploring properties of the molecular systems that are hardly accessible by conventional experimental methods. Present review is dedicated to the recent contributions in applications of molecular dynamics simulations in peptide design for immunological purposes, such as B or T cell epitopes.

  16. Bringing values and deliberation to science communication.

    Science.gov (United States)

    Dietz, Thomas

    2013-08-20

    Decisions always involve both facts and values, whereas most science communication focuses only on facts. If science communication is intended to inform decisions, it must be competent with regard to both facts and values. Public participation inevitably involves both facts and values. Research on public participation suggests that linking scientific analysis to public deliberation in an iterative process can help decision making deal effectively with both facts and values. Thus, linked analysis and deliberation can be an effective tool for science communication. However, challenges remain in conducting such process at the national and global scales, in enhancing trust, and in reconciling diverse values.

  17. Mitochondrial DNA Fragmentation as a Molecular Tool to Monitor Thermal Processing of Plant-Derived, Low-Acid Foods, and Biomaterials.

    Science.gov (United States)

    Caldwell, Jane M; Pérez-Díaz, Ilenys M; Sandeep, K P; Simunovic, Josip; Harris, Keith; Osborne, Jason A; Hassan, Hosni M

    2015-08-01

    Cycle threshold (Ct) increase, quantifying plant-derived DNA fragmentation, was evaluated for its utility as a time-temperature integrator. This novel approach to monitoring thermal processing of fresh, plant-based foods represents a paradigm shift. Instead of using quantitative polymerase chain reaction (qPCR) to detect pathogens, identify adulterants, or authenticate ingredients, this rapid technique was used to quantify the fragmentation of an intrinsic plant mitochondrial DNA (mtDNA) gene over time-temperature treatments. Universal primers were developed which amplified a mitochondrial gene common to plants (atp1). These consensus primers produced a robust qPCR signal in 10 vegetables, 6 fruits, 3 types of nuts, and a biofuel precursor. Using sweet potato (Ipomoea batatas) puree as a model low-acid product and simple linear regression, Ct value was highly correlated to time-temperature treatment (R(2) = 0.87); the logarithmic reduction (log CFU/mL) of the spore-forming Clostridium botulinum surrogate, Geobacillus stearothermophilus (R(2) = 0.87); and cumulative F-value (min) in a canned retort process (R(2) = 0.88), all comparisons conducted at 121 °C. D121 and z-values were determined for G. stearothermophilus ATCC 7953 and were 2.71 min and 11.0 °C, respectively. D121 and z-values for a 174-bp universal plant amplicon were 11.3 min and 9.17 °C, respectively, for mtDNA from sweet potato puree. We present these data as proof-of-concept for a molecular tool that can be used as a rapid, presumptive method for monitoring thermal processing in low-acid plant products. © 2015 Institute of Food Technologists®

  18. De novo assembly of the ringed seal (Pusa hispida) blubber transcriptome: A tool that enables identification of molecular health indicators associated with PCB exposure.

    Science.gov (United States)

    Brown, Tanya M; Hammond, S Austin; Behsaz, Bahar; Veldhoen, Nik; Birol, Inanç; Helbing, Caren C

    2017-04-01

    The ringed seal, Pusa hispida, is a keystone species in the Arctic marine ecosystem, and is proving a useful marine mammal for linking polychlorinated biphenyl (PCB) exposure to toxic injury. We report here the first de novo assembled transcriptome for the ringed seal (342,863 transcripts, of which 53% were annotated), which we then applied to a population of ringed seals exposed to a local PCB source in Arctic Labrador, Canada. We found an indication of energy metabolism imbalance in local ringed seals (n=4), and identified five significant gene transcript targets: plasminogen receptor (Plg-R(KT)), solute carrier family 25 member 43 receptor (Slc25a43), ankyrin repeat domain-containing protein 26-like receptor (Ankrd26), HIS30 (not yet annotated) and HIS16 (not yet annotated) that may represent indicators of PCB exposure and effects in marine mammals. The abundance profiles of these five gene targets were validated in blubber samples collected from 43 ringed seals using a qPCR assay. The mRNA transcript levels for all five gene targets, (Plg-R(KT), r(2)=0.43), (Slc25a43, r(2)=0.51), (Ankrd26, r(2)=0.43), (HIS30, r(2)=0.39) and (HIS16, r(2)=0.31) correlated with increasing levels of blubber PCBs. Results from the present study contribute to our understanding of PCB associated effects in marine mammals, and provide new tools for future molecular and toxicology work in pinnipeds. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. Using multi-compartment ensemble modeling as an investigative tool of spatially distributed biophysical balances: application to hippocampal oriens-lacunosum/moleculare (O-LM cells.

    Directory of Open Access Journals (Sweden)

    Vladislav Sekulić

    Full Text Available Multi-compartmental models of neurons provide insight into the complex, integrative properties of dendrites. Because it is not feasible to experimentally determine the exact density and kinetics of each channel type in every neuronal compartment, an essential goal in developing models is to help characterize these properties. To address biological variability inherent in a given neuronal type, there has been a shift away from using hand-tuned models towards using ensembles or populations of models. In collectively capturing a neuron's output, ensemble modeling approaches uncover important conductance balances that control neuronal dynamics. However, conductances are never entirely known for a given neuron class in terms of its types, densities, kinetics and distributions. Thus, any multi-compartment model will always be incomplete. In this work, our main goal is to use ensemble modeling as an investigative tool of a neuron's biophysical balances, where the cycling between experiment and model is a design criterion from the start. We consider oriens-lacunosum/moleculare (O-LM interneurons, a prominent interneuron subtype that plays an essential gating role of information flow in hippocampus. O-LM cells express the hyperpolarization-activated current (Ih. Although dendritic Ih could have a major influence on the integrative properties of O-LM cells, the compartmental distribution of Ih on O-LM dendrites is not known. Using a high-performance computing cluster, we generated a database of models that included those with or without dendritic Ih. A range of conductance values for nine different conductance types were used, and different morphologies explored. Models were quantified and ranked based on minimal error compared to a dataset of O-LM cell electrophysiological properties. Co-regulatory balances between conductances were revealed, two of which were dependent on the presence of dendritic Ih. These findings inform future experiments that

  20. Bringing ayahuasca to the clinical research laboratory.

    Science.gov (United States)

    Riba, Jordi; Barbanoj, Manel J

    2005-06-01

    Since the winter of 1999, the authors and their research team have been conducting clinical studies involving the administration of ayahuasca to healthy volunteers. The rationale for conducting this kind of research is twofold. First, the growing interest of many individuals for traditional indigenous practices involving the ingestion of natural psychotropic drugs such as ayahuasca demands the systematic study of their pharmacological profiles in the target species, i.e., human beings. The complex nature of ayahuasca brews combining a large number of pharmacologically active compounds requires that research be carried out to establish the safety and overall pharmacological profile of these products. Second, the authors believe that the study of psychedelics in general calls for renewed attention. Although the molecular and electrophysiological level effects of these drugs are relatively well characterized, current knowledge of the mechanisms by which these compounds modify the higher order cognitive processes in the way they do is still incomplete, to say the least. The present article describes the development of the research effort carried out at the Autonomous University of Barcelona, commenting on several methodological aspects and reviewing the basic clinical findings. It also describes the research currently underway in our laboratory, and briefly comments on two new studies we plan to undertake in order to further our knowledge of the pharmacology of ayahuasca.

  1. New genome sequence data and molecular tools promote the use of photosynthetic and edible cyanobacteria in bioregenerative systems to support human space exploration.

    Science.gov (United States)

    Leys, Natalie; Morin, Nicolas; Janssen, Paul; Mergeay, Max

    Cyanobacteria are daily used as nutritional supplements (e.g. Spirulina) and are considered for promising applications beyond Earth, in space, where they can play a crucial role in closed miniaturised biological waste recycling systems that are currently developed to support future long-term space missions. Cyanobacteria can be cultured with artificial light in controllable photobioreactors, and used for the efficient removal of CO2 from and production of O2 in the at-mosphere of the confined spacecraft, for removal of nitrate from waste water that is recycled to potable water, and as complementary food source. In this context, the filamentous cyanobac-terium Arthrospira sp. PCC 8005 was selected as part of the bio-regenerative life-support system MELiSSA from the European Space Agency. For bioprocess control and optimisation, the access to its genetic information and the development of molecular tools is crucial. Here we report on our efforts to determine the full genome of the cyanobacterium Arthrospira sp. PCC 8005. The obtained sequence data were analysed in detail to gain a better insight in the photosynthetic, nutritive, or potential toxic potential of this strain. In addition, the sensitivity of PCC 8005 to ionizing radiation was investigated because prolonged exposure of PCC 8005 to cosmic radiation in space might have a deleterious effect on its metabolism and oxygenic properties. To our knowledge, of the 6 different research groups across the globe trying to sequence Arthrospira strains, none of them, including us, were yet able to obtain a complete genome sequence. For Arthrospira sp. strain PCC 8005, we obtained 119 contigs (assembled in 16 scaffolds), representing 6,3 Mb, with 5,856 predicted protein-coding sequences (CDSs) and 176 genes encoding RNA. The PCC 8005 genome displays an unusual high number of large repeated sequences, covering around 8% of the genome, which likely hampered the sequenc-ing. The PCC 8005 genome is also ridden by mobile

  2. AASERT: Software Tools for Experimentation in Computational Geometry

    National Research Council Canada - National Science Library

    Dobkin, David

    2001-01-01

    This research has considered problems in computer graphics and visualization. The work has aimed to bring theoretical tools to practical problems as well as to develop tools with which to aid in the building of geometric software...

  3. Modelagem Molecular: Uma Ferramenta para o Planejamento Racional de Fármacos em Química Medicinal Molecular modeling: a tool for rational drug design in medicinal chemistry

    Directory of Open Access Journals (Sweden)

    Eliezer J. Barreiro

    1997-06-01

    Full Text Available The molecular basis of modern therapeutics consist in the modulation of cell function by the interaction of microbioactive molecules as drug cells macromolecules structures. Molecular modeling is a computational technique developed to access the chemical structure. This methodology, by means of the molecular similarity and complementary paradigm, is the basis for the computer-assisted drug design universally employed in pharmaceutical research laboratories to obtain more efficient, more selective, and safer drugs. In this work, we discuss some methods for molecular modeling and some approaches to evaluate new bioactive structures in development by our research group.

  4. [Genital herpes and pregnancy: Serological and molecular diagnostic tools. Guidelines for clinical practice from the French College of Gynecologists and Obstetricians (CNGOF)].

    Science.gov (United States)

    Vauloup-Fellous, C

    2017-12-01

    To describe serological and molecular tools available for genital and neonatal herpes, and their use in different clinical situations. Bibliographic investigations from MedLine database and consultation of international clinical practice guidelines. Virological confirmation of genital herpes during pregnancy or neonatal herpes must rely on PCR (Professional consensus). HSV type-specific serology (IgG) will allow determining the immune status of a patient (in the absence of clinical lesions). However, there is currently no evidence to justify universal HSV serological testing during pregnancy (Professional consensus). In case of genital lesions in a pregnant woman that do not report any genital herpes before, it is recommended to perform a virological confirmation by PCR and HSV type-specific IgG in order to distinguish a true primary infection, a non-primary infection associated with first genital manifestation, from a recurrence (Grade C). HSV IgM is useless for diagnosis of genital herpes (Grade C). If a pregnant woman has personal history of genital herpes but no lesions, whatever the gestational age, it is not recommended to perform genital sampling nor serology (Professional consensus). In case of recurrence, if the lesion is characteristic of herpes, virological confirmation is not necessary (Professional Agreement). However, if the lesion is not characteristic, virological confirmation by PCR should be performed (Professional consensus). At birth, HSV PCR samples should be collected as soon as neonatal herpes is suspected (symptomatic neonate) (best before beginning antiviral treatment but must not delay the treatment), or after 24hours of life in case of asymptomatic neonate born to a mother with herpes lesions at delivery (Professional consensus). Clinical samples for virological confirmation should include at least blood and a peripheral location. In case of clinical manifestations of herpes in the neonate, first samples PCR positive, preterm birth, or

  5. Bringing Science Public Outreach to Elementary Schools

    Science.gov (United States)

    Miller, Lucas; Speck, A.; Tinnin, A.

    2012-01-01

    Many science "museums” already offer fantastic programs for the general public, and even some aimed at elementary school kids. However, these venues are usually located in large cities and are only occasionally used as tools for enriching science education in public schools. Here we present preliminary work to establish exciting educational enrichment environments for public schools that do not easily have access to such facilities. This program is aimed at motivating children's interest in science beyond what they learn in the classroom setting. In this program, we use the experience and experiments/demonstrations developed at a large science museum (in this case, The St. Louis Science Center) and take them into a local elementary school. At the same time, students from the University of Missouri are getting trained on how to present these outreach materials and work with the local elementary schools. Our pilot study has started with implementation of presentations/demonstrations at Benton Elementary School within the Columbia Public School district, Missouri. The school has recently adopted a STEM (Science, Technology, Engineering, and Mathematics) centered learning system throughout all grade levels (K-5), and is therefore receptive to this effort. We have implemented a program in which we have given a series of scientific demonstrations at each grade level's lunch hour. Further enrichment ideas and plans include: addition demonstrations, hands-on experiments, and question and answer sessions. However, the application of these events would be to compliment the curriculum for the appropriate grade level at that time. The focus of this project is to develop public communications which links science museums, college students and local public schools with an emphasis on encouraging college science majors to share their knowledge and to strengthen their ability to work in a public environment.

  6. Bring your own device (BYOD) to work trend report

    CERN Document Server

    Hayes, Bob

    2013-01-01

    Bring Your Own Device (BYOD) to Work examines the emerging BYOD (Bring Your Own Device to work) trend in corporate IT. BYOD is the practice of employees bringing personally-owned mobile devices (e.g., smartphones, tablets, laptops) to the workplace, and using those devices to access company resources such as email, file servers, and databases. BYOD presents unique challenges in data privacy, confidentiality, security, productivity, and acceptable use that must be met proactively by information security professionals. This report provides solid background on the practice, original res

  7. Can Smartphone Use Bring on Carpal Tunnel Syndrome?

    Science.gov (United States)

    ... https://medlineplus.gov/news/fullstory_166847.html Can Smartphone Use Bring on Carpal Tunnel Syndrome? Maybe, especially ... People who spend lots of time on their smartphones may be scrolling, tapping and swiping their way ...

  8. Dubna at Play Exhibition Science Bringing Nations Together

    CERN Multimedia

    1999-01-01

    The small town of Dubna brings together the advantages of urban and country lifestyles. Dubna people spend a large part of their time outdoors taking part in all kind of sports or simply enjoying the beautiful surroundings.

  9. Dubna at Play Exhibition Science Bringing Nations Together

    CERN Multimedia

    1997-01-01

    The small town of Dubna brings together the advantages of urban and country lifestyles. Dubna people spend a large part of their time outdoors taking part in all kind of sports or simply enjoying the beautiful surroundings.

  10. What to bring to your labor and delivery

    Science.gov (United States)

    Prenatal care - what to bring ... underwear, and basic toiletries. While it is nice to have your own clothes with you, labor and ... very messy time, so you may not want to wear your brand-new lingerie. Items you should ...

  11. Molecular modeling

    Directory of Open Access Journals (Sweden)

    Aarti Sharma

    2009-01-01

    Full Text Available The use of computational chemistry in the development of novel pharmaceuticals is becoming an increasingly important tool. In the past, drugs were simply screened for effectiveness. The recent advances in computing power and the exponential growth of the knowledge of protein structures have made it possible for organic compounds to be tailored to decrease the harmful side effects and increase the potency. This article provides a detailed description of the techniques employed in molecular modeling. Molecular modeling is a rapidly developing discipline, and has been supported by the dramatic improvements in computer hardware and software in recent years.

  12. Quinoxaline-substituted chalcones as new inhibitors of breast cancer resistance protein ABCG2: polyspecificity at B-ring position

    Science.gov (United States)

    Winter, Evelyn; Gozzi, Gustavo Jabor; Chiaradia-Delatorre, Louise Domeneghini; Daflon-Yunes, Nathalia; Terreux, Raphael; Gauthier, Charlotte; Mascarello, Alessandra; Leal, Paulo César; Cadena, Silvia M; Yunes, Rosendo Augusto; Nunes, Ricardo José; Creczynski-Pasa, Tania Beatriz; Di Pietro, Attilio

    2014-01-01

    A series of chalcones substituted by a quinoxaline unit at the B-ring were synthesized and tested as inhibitors of breast cancer resistance protein-mediated mitoxantrone efflux. These compounds appeared more efficient than analogs containing other B-ring substituents such as 2-naphthyl or 3,4-methylenedioxyphenyl while an intermediate inhibitory activity was obtained with a 1-naphthyl group. In all cases, two or three methoxy groups had to be present on the phenyl A-ring to produce a maximal inhibition. Molecular modeling indicated both electrostatic and steric positive contributions. A higher potency was observed when the 2-naphthyl or 3,4-methylenedioxyphenyl group was shifted to the A-ring and methoxy substituents were shifted to the phenyl B-ring, indicating preferences among polyspecificity of inhibition. PMID:24920885

  13. Bringing New Tools and Techniques to Bear on Earthquake Hazard Analysis and Mitigation

    Science.gov (United States)

    Willemann, R. J.; Pulliam, J.; Polanco, E.; Louie, J. N.; Huerta-Lopez, C.; Schmitz, M.; Moschetti, M. P.; Huerfano Moreno, V.; Pasyanos, M.

    2013-12-01

    During July 2013, IRIS held an Advanced Studies Institute in Santo Domingo, Dominican Republic, that was designed to enable early-career scientists who already have mastered the fundamentals of seismology to begin collaborating in frontier seismological research. The Institute was conceived of at a strategic planning workshop in Heredia, Costa Rica, that was supported and partially funded by USAID, with a goal of building geophysical capacity to mitigate the effects of future earthquakes. To address this broad goal, we drew participants from a dozen different countries of Middle America. Our objectives were to develop understanding of the principles of earthquake hazard analysis, particularly site characterization techniques, and to facilitate future research collaborations. The Institute was divided into three main sections: overviews on the fundamentals of earthquake hazard analysis and lectures on the theory behind methods of site characterization; fieldwork where participants acquired new data of the types typically used in site characterization; and computer-based analysis projects in which participants applied their newly-learned techniques to the data they collected. This was the first IRIS institute to combine an instructional short course with field work for data acquisition. Participants broke into small teams to acquire data, analyze it on their own computers, and then make presentations to the assembled group describing their techniques and results.Using broadband three-component seismometers, the teams acquired data for Spatial Auto-Correlation (SPAC) analysis at seven array locations, and Horizontal to Vertical Spectral Ratio (HVSR) analysis at 60 individual sites along six profiles throughout Santo Domingo. Using a 24-channel geophone string, the teams acquired data for Refraction Microtremor (SeisOptReMi™ from Optim) analysis at 11 sites, with supplementary data for active-source Multi-channel Spectral Analysis of Surface Waves (MASW) analysis at five of them. The results showed that teams quickly learned to collect high-quality data for each method of analysis. SPAC and refraction microtremor analysis each demonstrated that dispersion relations based on ambient noise and from arrays with an aperture of less than 200 meters could be used to determine the depth of a weak, disaggregated layer known to underlie the fast near-surface limestone terraces on which Santo Domingo is situated, and indicated the presence of unexpectedly strong rocks below. All three array methods concurred that most Santo Domingo sites has relatively high VS30 (average shear velocity to a depth of 30 m), generally at the B-C NEHRP hazard class boundary or higher. HVSR analysis revealed that the general pattern of resonance was short periods close to the coast, and an increase with distance from the shore line. In the east-west direction, significant variations were also evident at the highest elevation terrace, and near the Ozama River. In terms of the sub-soil conditions, the observed pattern of HVSR values, departs form the expected increase of sediments thickness close to the coast.

  14. GLOBE Observer: A new tool to bring science activities and measurements home

    Science.gov (United States)

    Riebeek Kohl, H.; Murphy, T.

    2016-12-01

    The Global Learning and Observations to Benefit the Environment (GLOBE) Program is an international science and education program that provides students and the public worldwide with the opportunity to participate in data collection and the scientific process, and contribute meaningfully to our understanding of the Earth system and global environment. For more than 20 years, GLOBE-trained teachers have been leading environmental data collection and student research in the classroom. In 2016, GLOBE expanded to invite data collection from citizen scientists of all ages through a simple smart phone app. The app makes it possible for students to take GLOBE data (environmental observations) outside of school with their families. It enables a museum, park, youth organization, or other informal institution to provide a simple take-home activity that will keep patrons engaged in environmental science from home. This presentation will provide a demonstration of the app and will provide examples of its use in informal settings.

  15. What can Design Bring to Strategy? Designing Thinking as a Tool for Innovation and Change

    NARCIS (Netherlands)

    Kathryn Best

    2011-01-01

    This publication by Kathryn Best accompanied the Lector’s inauguration as head of the research group Cross-media, Brand, Reputation & Design Management (CBRD) in January 2011. The book outlines current debates around the Creative Industries, business and design education and the place of ’well

  16. Evaluation of Molecular Tools for Detection and Drug Susceptibility Testing of Mycobacterium tuberculosis in Stool Specimens from Patients with Pulmonary Tuberculosis ▿

    OpenAIRE

    Cordova, Julianna; Shiloh, Ron; Gilman, Robert H.; Sheen, Patricia; Martin, Laura; Arenas, Fanny; Caviedes, Luz; Kawai, Vivian; Soto, Giselle; Williams, Diana L.; Zimic, Mirko; Escombe, A. Roderick; Evans, Carlton A.

    2010-01-01

    Pulmonary tuberculosis diagnosis is difficult when patients cannot produce sputum. Most sputum is swallowed, and tuberculosis DNA can survive intestinal transit. We therefore evaluated molecular testing of stool specimens for detecting tuberculosis originating from the lungs. Paired stool and sputum samples (n = 159) were collected from 89 patients with pulmonary tuberculosis. Control stool samples (n = 47) were collected from patients without tuberculosis symptoms. Two techniques for DNA ext...

  17. Practical ways of bringing innovations and creativity into the school ...

    African Journals Online (AJOL)

    This article describes the practical ways of bringing innovations and creativity into the school library media programme in Nigeria. Discussion focused on areas on creativity and innovations such as environmental design, staffing, outreach activities, library cooperation, and introduction of ICT system. Keywords: Innovations ...

  18. "Bring Your Own Device": Considering Potential Risks to Student Health

    Science.gov (United States)

    Merga, Margaret K.

    2016-01-01

    Background and context: Schools in Australia and internationally are increasingly adopting a Bring Your Own Device (BYOD) approach to teaching and learning. The review: While discussion of a BYOD approach has taken place, there is a dearth of consideration of the potential impact of BYOD policy on student health. Implementation of a BYOD policy…

  19. Bringing climate change into natural resource management: proceedings.

    Science.gov (United States)

    L. Joyce; R. Haynes; R. White; R.J. Barbour

    2007-01-01

    These are the proceedings of the 2005 workshop titled implications of bringing climate into natural resource management in the Western United States. This workshop was an attempt to further the dialogue among scientists, land managers, landowners, interested stakeholders and the public about how individuals are addressing climate change in natural resource management....

  20. High School Academies Bring Inner-City Youth into Mainstream.

    Science.gov (United States)

    Koning, Hendrik B.

    1983-01-01

    Describes the Philadelphia High School Academies, vocational schools in the inner city that are jointly operated and funded by the public schools and local business and labor leaders. Discusses the program's growth and the reasons for its success in bringing inner city youth into the mainstream. (JOW)

  1. CASE STUDY: Vietnam — Information brings progress to Vietnam's ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    2010-12-16

    CASE STUDY: Vietnam — Information brings progress to Vietnam's communes. December 16, 2010. Image. Michelle Hibler. In Vietnam, a .... The strategy, he says, is to concentrate assistance on vulnerable groups, like women-headed households, widows, and invalids. There are 41 such deprived households in Gia Son.

  2. Model Testing - Bringing the Ocean into the Laboratory

    DEFF Research Database (Denmark)

    Aage, Christian

    2000-01-01

    Hydrodynamic model testing, the principle of bringing the ocean into the laboratory to study the behaviour of the ocean itself and the response of man-made structures in the ocean in reduced scale, has been known for centuries. Due to an insufficient understanding of the physics involved, however...

  3. Bringing Critical Thinking to the Education of Developing Country Professionals

    Science.gov (United States)

    Richmond, Jonathan E. D.

    2007-01-01

    Cultural differences between Asia and the West and their influence on teaching, are reviewed along with previous experiments in bringing critical thinking to Asian education, and recognition of needs for and barriers to achieving change. Principles driving design and implementation of a two-course sequence in professional transportation studies…

  4. Bringing Curriculum Theory and Didactics Together: A Deweyan Perspective

    Science.gov (United States)

    Deng, Zongyi

    2016-01-01

    Using Dewey's method of resolution for resolving a dualism exemplified in "The Child and the Curriculum," this article reconciles and brings together two rival schools of thought--curriculum theory and didactics--in China. The central thesis is that the rapprochement requires a reconceptualisation of curriculum theory and didactics in…

  5. Bringing the LHC and ATLAS to a regional planetarium

    CERN Document Server

    Schwienhorst, Reinhard

    2011-01-01

    An outreach effort has started at Michigan State University to bring particle physics, the Large Hadron Collider, and the ATLAS experiment to a general audience at the Abrams planetarium on the MSU campus. A team of undergraduate students majoring in physics, communications arts & sciences, and journalism are putting together short clips about ATLAS and the LHC to be shown at the planetarium.

  6. Bringing golf into sport psychology sessions through technology ...

    African Journals Online (AJOL)

    Bringing golf into sport psychology sessions through technology (video footage) ... sessions through technology (video footage). L Human, D Kriek, T Bezuidenhout ... psychology sessions informed by narrative practice with the six golfers respectively, during which the identified material from Stage 2 was discussed. During ...

  7. Bringing connectivity to rural Zambia using a collaborative approach

    CSIR Research Space (South Africa)

    Matthee, K

    2007-12-01

    Full Text Available This paper presents an initiative to bring connectivity to rural Zambia using a collaborative approach. In particular, it focuses on a proof-of-concept Internet service that has been implemented in rural Macha located in the Southern Province...

  8. High-field NMR spectroscopy and FTICR mass spectrometry: powerful discovery tools for the molecular level characterization of marine dissolved organic matter

    Directory of Open Access Journals (Sweden)

    N. Hertkorn

    2013-03-01

    Full Text Available High-performance, non-target, high-resolution organic structural spectroscopy was applied to solid phase extracted marine dissolved organic matter (SPE-DOM isolated from four different depths in the open South Atlantic Ocean off the Angola coast (3° E, 18° S; Angola Basin and provided molecular level information with extraordinary coverage and resolution. Sampling was performed at depths of 5 m (Angola Current; near-surface photic zone, 48 m (Angola Current; fluorescence maximum, 200 m (still above Antarctic Intermediate Water, AAIW; upper mesopelagic zone and 5446 m (North Atlantic Deep Water, NADW; abyssopelagic, ~30 m above seafloor and produced SPE-DOM with near 40% carbon yield and beneficial nuclear magnetic resonance (NMR relaxation properties, a crucial prerequisite for the acquisition of NMR spectra with excellent resolution. 1H and 13C NMR spectra of all four marine SPE-DOM showed smooth bulk envelopes, reflecting intrinsic averaging from massive signal overlap, with a few percent of visibly resolved signatures and variable abundances for all major chemical environments. The abundance of singly oxygenated aliphatics and acetate derivatives in 1H NMR spectra declined from surface to deep marine SPE-DOM, whereas C-based aliphatics and carboxyl-rich alicyclic molecules (CRAM increased in abundance. Surface SPE-DOM contained fewer methyl esters than all other samples, likely a consequence of direct exposure to sunlight. Integration of 13C NMR spectra revealed continual increase of carboxylic acids and ketones from surface to depth, reflecting a progressive oxygenation, with concomitant decline of carbohydrate-related substructures. Aliphatic branching increased with depth, whereas the fraction of oxygenated aliphatics declined for methine, methylene and methyl carbon. Lipids in the oldest SPE-DOM at 5446 m showed a larger share of ethyl groups and methylene carbon than observed in the other samples. Two-dimensional NMR spectra showed

  9. Characterization of natural anaerobic dechlorination of TCE and 1,1,1-TCA in clay till including isotope fractionation and molecular biological tools

    DEFF Research Database (Denmark)

    Damgaard, Ida; Bælum, J.; Hunkeler, D.

    2010-01-01

    One of the major challenges when using enhanced reductive dechlorination (ERD) as a remediation technology at clay till sites is to obtain good contact between added agents such as donor, bacteria and the contamination. It is unclear whether degradation only takes place in fractures and/or sand...... including the location of degradation in the fracture matrix geology. An extensive field collection of cores and discrete soil sampling has been conducted and samples have been analysed using state of the art microbial and chemical tools including isotope fractionation....

  10. Molecularly imprinted polymer applied to the selective isolation of urinary steroid hormones: an efficient tool in the control of natural steroid hormones abuse in cattle.

    Science.gov (United States)

    Doué, Mickael; Bichon, Emmanuelle; Dervilly-Pinel, Gaud; Pichon, Valérie; Chapuis-Hugon, Florence; Lesellier, Eric; West, Caroline; Monteau, Fabrice; Le Bizec, Bruno

    2012-12-28

    The use of anabolic substances to promote growth in livestock is prohibited within the European Union as laid down in Directive 96/22/EC. Nowadays, efficient methods such as steroid profiling or isotopic deviation measurements allow to control natural steroid hormones abuse. In both cases, urine is often selected as the most relevant matrix and, due to its relatively high content of potential interferents, its preparation before analysis is considered as a key step. In this context, the use of a selective sorbent such as molecularly imprinted polymer (MIP) was investigated. A MIP was synthesized based on 17β-estradiol, methacrylic acid and acetonitrile as template, monomer and porogen, respectively. Two approaches were then tested for non-conjugated (aglycons and glucuronides deconjugated) steroid purification: (i) molecularly imprinted solid phase extraction (MISPE) and (ii) semi-preparative supercritical fluid chromatography with a commercial MIP as stationary phase (SFC-MIP). Parameters for both approaches were optimized based on the main bovine metabolites of testosterone, estradiol, nandrolone and boldenone. The MISPE protocol developed for screening purposes allowed satisfactory recoveries (upper 65% for the 12 target steroids) with sufficient purification for gas chromatography-mass spectrometry (GC-MS) analysis. For confirmatory purposes, the use of isotopic ratio mass spectrometry (IRMS) requires a higher degree of purity of the target compounds, which can be reached by the SFC-MIP protocol with three steps less compared to the official and current method. Purity, concentration and absence of isotopic fractionation of target steroids extracted from urine of treated cattle (treated with testosterone, estradiol, androstenedione, and boldenone) allowed the measurement of (13)C/(12)C isotopic ratios of corresponding metabolites and endogenous reference compounds (ERC) and proved the relevance of the strategy. Copyright © 2012 Elsevier B.V. All rights

  11. Non-invasive Drosophila ECG recording by using eutectic gallium-indium alloy electrode: a feasible tool for future research on the molecular mechanisms involved in cardiac arrhythmia.

    Directory of Open Access Journals (Sweden)

    Po-Hung Kuo

    Full Text Available BACKGROUND: Drosophila heart tube is a feasible model for cardiac physiological research. However, obtaining Drosophila electrocardiograms (ECGs is difficult, due to the weak signals and limited contact area to apply electrodes. This paper presents a non-invasive Gallium-Indium (GaIn based recording system for Drosophila ECG measurement, providing the heart rate and heartbeat features to be observed. This novel, high-signal-quality system prolongs the recording time of insect ECGs, and provides a feasible platform for research on the molecular mechanisms involved in cardiovascular diseases. METHODS: In this study, two types of electrode, tungsten needle probes and GaIn electrodes, were used respectively to noiselessly conduct invasive and noninvasive ECG recordings of Drosophila. To further analyze electrode properties, circuit models were established and simulated. By using electromagnetic shielded heart signal acquiring system, consisted of analog amplification and digital filtering, the ECG signals of three phenotypes that have different heart functions were recorded without dissection. RESULTS AND DISCUSSION: The ECG waveforms of different phenotypes of Drosophila recorded invasively and repeatedly with n value (n>5 performed obvious difference in heart rate. In long period ECG recordings, non-invasive method implemented by GaIn electrodes acts relatively stable in both amplitude and period. To analyze GaIn electrode, the correctness of GaIn electrode model established by this paper was validated, presenting accuracy, stability, and reliability. CONCLUSIONS: Noninvasive ECG recording by GaIn electrodes was presented for recording Drosophila pupae ECG signals within a limited contact area and signal strength. Thus, the observation of ECG changes in normal and SERCA-depleted Drosophila over an extended period is feasible. This method prolongs insect survival time while conserving major ECG features, and provides a platform for

  12. Massive sequencing of Ulmus minor's transcriptome provides new molecular tools for a genus under the constant threat of Dutch elm disease

    Directory of Open Access Journals (Sweden)

    Pedro ePerdiguero

    2015-07-01

    Full Text Available Elms, especially Ulmus minor and Ulmus americana, are carrying out a hard battle against Dutch elm disease (DED. This vascular wilt disease, caused by Ophiostoma ulmi and O. novo-ulmi, appeared in the twentieth century and killed millions of elms across North America and Europe. Elm breeding and conservation programmes have identified a reduced number of DED tolerant genotypes. In this study, three U. minor genotypes with contrasted levels of tolerance to DED were exposed to several biotic and abiotic stresses in order to (i obtain a de novo assembled transcriptome of U. minor using 454 pyrosequencing, (ii perform a functional annotation of the assembled transcriptome, (iii identify genes potentially involved in the molecular response to environmental stress, and (iv develop gene-based markers to support breeding programmes. A total of 58,429 putative unigenes were identified after assembly and filtering of the transcriptome. 32,152 of these unigenes showed homology with proteins identified in the genome from the most common plant model species. Well-known family proteins and transcription factors involved in abiotic, biotic or both stresses were identified after functional annotation. A total of 30,693 polymorphisms were identified in 7,125 isotigs, a large number of them corresponding to SNPs (27,359. In a subset randomly selected for validation, 87 % of the SNPs were confirmed. The material generated may be valuable for future Ulmus gene expression, population genomics and association genetics studies, especially taking into account the scarce molecular information available for this genus and the great impact that DED has on elm populations.

  13. Molecular Dynamics and Protein Function

    National Research Council Canada - National Science Library

    M. Karplus; J. Kuriyan; Bruce J. Berne

    2005-01-01

    .... Molecular dynamics simulations provide powerful tools for the exploration of the conformational energy landscape accessible to these molecules, and the rapid increase in computational power coupled...

  14. Befriending Everyday Life When Bringing Technology Into the Private Sphere.

    Science.gov (United States)

    Lindberg, Catharina; Fagerström, Cecilia; Willman, Ania; Sivberg, Bengt

    2017-05-01

    We present the findings of our phenomenological interview study concerning the meaning of being an autonomous person while dependent on advanced medical technology at home. This was elucidated in the participants' narratives as befriending everyday life when bringing technology into the private sphere. We discovered four constituents of the phenomenon: befriending the lived body, depending on good relationships, keeping the home as a private sphere, and managing time. The most important finding was the overall position of the lived body by means of the illness limiting the control over one's life. We found that the participants wanted to be involved in and have influence over their care to be able to enjoy autonomy. We therefore stress the importance of bringing the patients into the care process as chronic illness will be a part of their everyday life for a long time to come, hence challenging patient autonomy.

  15. Framework for Bringing Data Streams to the Grid

    Directory of Open Access Journals (Sweden)

    Beth Plale

    2004-01-01

    Full Text Available Data streams are a prevalent and growing source of timely data, particularly in the scientific domain. Just as it is common today to read starting conditions such as initial weather conditions, for a scientific simulation from a file, it should be equally as easy to draw starting conditions on-demand from live data streams. But efforts to date to bring streaming data to the grid have lacked generality. In this article we introduce a new model for bringing existing data streams systems onto the grid. The model is predicated on the ability to identify stream systems that meet the criteria of being a "data resource". We establish the criteria in this article, and define a grid service architecture for a data streams resource that leverages standardization efforts in the Global Grid Forum. We discuss key research issues in realizing the data streams model. We are currently developing a prototype of this architecture using our dQUOB system.

  16. Foreign Aided: Why Democratization Brings Growth When Democracy Does Not

    DEFF Research Database (Denmark)

    Hariri, Jacob Gerner

    2015-01-01

    There is an unresolved puzzle in research on the economics of democracy. While there is consensus that democracy is not generally associated with higher rates of economic growth, recent studies have found that democratization is followed by growth. But why should becoming a democracy bring growth...... if being one does not? This article shows that a substantial and immediate influx of foreign aid into new democracies accounts for the positive growth effect of democratization. The domestic regime characteristics of neither democracy nor democratization therefore seems to bring growth. The importance...... of aid in explaining the democratization-growth nexus underscores that democratizations do not occur in vacuum and cannot be fully understood from internal factors alone...

  17. S'Cool Tools: 5 Great Tools to Perk Up Your Classroom and Engage Your Students

    Science.gov (United States)

    Yoder, Maureen Brown

    2009-01-01

    For a kindergarten teacher trying to find a new way to help his/her students learn about shapes and patterns or a high school science teacher hoping to bring ecology alive, there is a tool that could be just right for them. This article presents five learning tools that have the potential to transform lessons: (1) Lego Education's WeDo Robotics…

  18. MANU Building – Bringing together Manufacturing Automation and Building Automation

    OpenAIRE

    Bratukhin, Aleksey; Treytl, Albert; Sauter, Thilo

    2012-01-01

    Part IV: ICT and Emerging Technologies in Production Management; International audience; Up to now, production systems only concern was to minimize production costs or optimize the utilization of production resources. But with the increasing energy prices and the growing concern over the environmental impact of production systems (industrial systems consume a quarter of all energy), efficient use of energy in manufacturing environment cannot be ignored any longer.MANUbuilding concept brings t...

  19. [Psychological features of mothers bringing up disabled children].

    Science.gov (United States)

    Kocherova, O Iu; Fil'kina, O M; Dolotova, N V; Malyshkina, A I; Antysheva, E N

    2014-01-01

    Research objective was to define psychological makers of mothers bringing up disabled children for scientific justification of the family psychotherapy branches. 60 mothers bringing up children of early age with infantile cerebral palsy and 50 mothers of children with compensation of perinatal affections of the central nervous system by the 1 life year are surveyed. Personal characteristics, family orientations of mothers, child and mother relations, awareness of mothers on the children health state and the attitude to their rehabilitation were studied by means of psychological techniques. It is found out that the mothers bringing up disabled children more often have emotional disorders, negative attitude to divorce and give the leading role in a family to the husband less often they show hypoguardianship of the child than the mothers of children with compensation of perinatal affections of the central nervous system. Mothers are less satisfied with the child development, they are more often worried about disorders of development of movements, speech and mental development delay, small appetite of the child, they feel helplessness in rehabilitation more often, note the ambiguity of its prospects. They understand that their child needs the help of the qualified experts: neurologist, orthopaedist, logopedist, psychologist, but they aren't satisfied with communication with them more often, underestimate own role in rehabilitation. The revealed characteristics prove the necessity and define the main directions of family psychotherapy--correction of mother's emotional disorders, child and parental relations, increase of medical and psychological competence that allows to increase efficiency of rehabilitation.

  20. Could molecular assessment of calcium metabolism be a useful tool to early screen patients at risk for pre-eclampsia complicated pregnancy? Proposal and rationale.

    Science.gov (United States)

    Gizzo, Salvatore; Noventa, Marco; Di Gangi, Stefania; Saccardi, Carlo; Cosmi, Erich; Nardelli, Giovanni Battista; Plebani, Mario

    2015-06-01

    One of the most frequent causes of maternal and perinatal morbidity is represented by hypertensive disorders during pregnancy. Women at high risk must be subjected to a more intensive antenatal surveillance and prophylactic treatments. Many genetic risk factors, clinical features and biomarkers have been proposed but none of these seems able to prevent pre-eclampsia onset. English literature review of manuscripts focused on calcium intake and hypertensive disorders during pregnancy was performed. We performed a critical analysis of evidences about maternal calcium metabolism pattern in pregnancy analyzing all possible bias affecting studies. Calcium supplementation seems to give beneficial effects on women with low calcium intake. Some evidence reported that calcium supplementation may drastically reduce the percentage of pre-eclampsia onset consequently improving the neonatal outcome. Starting from this evidence, it is intuitive that investigations on maternal calcium metabolism pattern in first trimester of pregnancy could represent a low cost, large scale tool to screen pregnant women and to identify those at increased risk of pre-eclampsia onset. We propose a biochemical screening of maternal calcium metabolism pattern in first trimester of pregnancy to discriminate patients who potentially may benefit from calcium supplementation. In a second step we propose to randomly allocate the sub-cohort of patients with calcium metabolism disorders in a treatment group (calcium supplementation) or in a control group (placebo) to define if calcium supplementation may represent a dietary mean to reduce pre-eclampsia onset and to improve pregnancy outcome.

  1. Banana MaMADS Transcription Factors Are Necessary for Fruit Ripening and Molecular Tools to Promote Shelf-Life and Food Security1[OPEN

    Science.gov (United States)

    Elitzur, Tomer; Yakir, Esther; Quansah, Lydia; Zhangjun, Fei; Vrebalov, Julia; Khayat, Eli; Giovannoni, James J.

    2016-01-01

    Genetic solutions to postharvest crop loss can reduce cost and energy inputs while increasing food security, especially for banana (Musa acuminata), which is a significant component of worldwide food commerce. We have functionally characterized two banana E class (SEPALLATA3 [SEP3]) MADS box genes, MaMADS1 and MaMADS2, homologous to the tomato (Solanum lycopersicum) RIN-MADS ripening gene. Transgenic banana plants repressing either gene (via antisense or RNA interference [RNAi]) were created and exhibited specific ripening delay and extended shelf-life phenotypes, including delayed color development and softening. The delay in fruit ripening is associated with a delay in climacteric respiration and reduced synthesis of the ripening hormone ethylene; in the most severe repressed lines, no ethylene was produced and ripening was most delayed. Unlike tomato rin mutants, banana fruits of all transgenic repression lines responded to exogenous ethylene by ripening normally, likely due to incomplete transgene repression and/or compensation by other MADS box genes. Our results show that, although MADS box ripening gene necessity is conserved across diverse taxa (monocots to dicots), unlike tomato, banana ripening requires at least two necessary members of the SEPALLATA MADS box gene group, and either can serve as a target for ripening control. The utility of such genes as tools for ripening control is especially relevant in important parthenocarpic crops such as the vegetatively propagated and widely consumed Cavendish banana, where breeding options for trait improvement are severely limited. PMID:26956665

  2. Banana MaMADS Transcription Factors Are Necessary for Fruit Ripening and Molecular Tools to Promote Shelf-Life and Food Security.

    Science.gov (United States)

    Elitzur, Tomer; Yakir, Esther; Quansah, Lydia; Zhangjun, Fei; Vrebalov, Julia; Khayat, Eli; Giovannoni, James J; Friedman, Haya

    2016-05-01

    Genetic solutions to postharvest crop loss can reduce cost and energy inputs while increasing food security, especially for banana (Musa acuminata), which is a significant component of worldwide food commerce. We have functionally characterized two banana E class (SEPALLATA3 [SEP3]) MADS box genes, MaMADS1 and MaMADS2, homologous to the tomato (Solanum lycopersicum) RIN-MADS ripening gene. Transgenic banana plants repressing either gene (via antisense or RNA interference [RNAi]) were created and exhibited specific ripening delay and extended shelf-life phenotypes, including delayed color development and softening. The delay in fruit ripening is associated with a delay in climacteric respiration and reduced synthesis of the ripening hormone ethylene; in the most severe repressed lines, no ethylene was produced and ripening was most delayed. Unlike tomato rin mutants, banana fruits of all transgenic repression lines responded to exogenous ethylene by ripening normally, likely due to incomplete transgene repression and/or compensation by other MADS box genes. Our results show that, although MADS box ripening gene necessity is conserved across diverse taxa (monocots to dicots), unlike tomato, banana ripening requires at least two necessary members of the SEPALLATA MADS box gene group, and either can serve as a target for ripening control. The utility of such genes as tools for ripening control is especially relevant in important parthenocarpic crops such as the vegetatively propagated and widely consumed Cavendish banana, where breeding options for trait improvement are severely limited. © 2016 American Society of Plant Biologists. All Rights Reserved.

  3. Molecular Modelling

    Directory of Open Access Journals (Sweden)

    Aarti Sharma

    2009-12-01

    Full Text Available

    The use of computational chemistry in the development of novel pharmaceuticals is becoming an increasingly important
    tool. In the past, drugs were simply screened for effectiveness. The recent advances in computing power and
    the exponential growth of the knowledge of protein structures have made it possible for organic compounds to tailored to
    decrease harmful side effects and increase the potency. This article provides a detailed description of the techniques
    employed in molecular modeling. Molecular modelling is a rapidly developing discipline, and has been supported from
    the dramatic improvements in computer hardware and software in recent years.

  4. Bringing Next-Generation Sequencing into the Classroom through a Comparison of Molecular Biology Techniques

    Science.gov (United States)

    Bowling, Bethany; Zimmer, Erin; Pyatt, Robert E.

    2014-01-01

    Although the development of next-generation (NextGen) sequencing technologies has revolutionized genomic research and medicine, the incorporation of these topics into the classroom is challenging, given an implied high degree of technical complexity. We developed an easy-to-implement, interactive classroom activity investigating the similarities…

  5. A molecular diagnostic tool for the preliminary assessment of host-parasitoid associations in biological control programmes for a new invasive pest.

    Science.gov (United States)

    Gariepy, T D; Haye, T; Zhang, J

    2014-08-01

    Evaluation of host-parasitoid associations can be tenuous using conventional methods. Molecular techniques are well placed to identify trophic links and resolve host-parasitoid associations. Establishment of the highly invasive brown marmorated stink bug, Halyomorpha halys (Hemiptera: Pentatomidae), outside Asia has prompted interest in the use of egg parasitoids (Hymenoptera: Scelionidae) as biological control agents. However, little is known regarding their host ranges. To address this, a DNA barcoding approach was taken wherein general PCR primers for Scelionidae and Pentatomidae were developed to amplify and sequence >500-bp products within the DNA barcoding region of the cytochrome oxidase I (COI) gene that would permit the identification of key players in this association. Amplification of DNA from Pentatomidae and Scelionidae was consistent across a broad range of taxa within these families, and permitted the detection of Scelionidae eggs within H. halys 1 h following oviposition. In laboratory assays, amplification and sequencing of DNA from empty, parasitized eggs was successful for both host (100% success) and parasitoid (50% success). When applied to field-collected, empty egg masses, the primers permitted host identification in 50-100% of the eggs analysed, and yielded species-level identifications. Parasitoid identification success ranged from 33 to 67% among field-collected eggs, with genus-level identification for most specimens. The inability to obtain species-level identities for these individuals is due to the lack of coverage of this taxonomic group in public DNA sequence databases; this situation is likely to improve as more species are sequenced and recorded in these databases. These primers were able to detect and identify both pentatomid host and scelionid parasitoid in a hyperparasitized egg mass, thereby clarifying trophic links otherwise unresolved by conventional methodology. © 2013 John Wiley & Sons Ltd.

  6. DG-AMMOS: A New tool to generate 3D conformation of small molecules using Distance Geometry and Automated Molecular Mechanics Optimization for in silico Screening

    Directory of Open Access Journals (Sweden)

    Villoutreix Bruno O

    2009-11-01

    Full Text Available Abstract Background Discovery of new bioactive molecules that could enter drug discovery programs or that could serve as chemical probes is a very complex and costly endeavor. Structure-based and ligand-based in silico screening approaches are nowadays extensively used to complement experimental screening approaches in order to increase the effectiveness of the process and facilitating the screening of thousands or millions of small molecules against a biomolecular target. Both in silico screening methods require as input a suitable chemical compound collection and most often the 3D structure of the small molecules has to be generated since compounds are usually delivered in 1D SMILES, CANSMILES or in 2D SDF formats. Results Here, we describe the new open source program DG-AMMOS which allows the generation of the 3D conformation of small molecules using Distance Geometry and their energy minimization via Automated Molecular Mechanics Optimization. The program is validated on the Astex dataset, the ChemBridge Diversity database and on a number of small molecules with known crystal structures extracted from the Cambridge Structural Database. A comparison with the free program Balloon and the well-known commercial program Omega generating the 3D of small molecules is carried out. The results show that the new free program DG-AMMOS is a very efficient 3D structure generator engine. Conclusion DG-AMMOS provides fast, automated and reliable access to the generation of 3D conformation of small molecules and facilitates the preparation of a compound collection prior to high-throughput virtual screening computations. The validation of DG-AMMOS on several different datasets proves that generated structures are generally of equal quality or sometimes better than structures obtained by other tested methods.

  7. Evaluation of molecular tools for detection and drug susceptibility testing of Mycobacterium tuberculosis in stool specimens from patients with pulmonary tuberculosis.

    Science.gov (United States)

    Cordova, Julianna; Shiloh, Ron; Gilman, Robert H; Sheen, Patricia; Martin, Laura; Arenas, Fanny; Caviedes, Luz; Kawai, Vivian; Soto, Giselle; Williams, Diana L; Zimic, Mirko; Escombe, A Roderick; Evans, Carlton A

    2010-05-01

    Pulmonary tuberculosis diagnosis is difficult when patients cannot produce sputum. Most sputum is swallowed, and tuberculosis DNA can survive intestinal transit. We therefore evaluated molecular testing of stool specimens for detecting tuberculosis originating from the lungs. Paired stool and sputum samples (n=159) were collected from 89 patients with pulmonary tuberculosis. Control stool samples (n=47) were collected from patients without tuberculosis symptoms. Two techniques for DNA extraction from stool samples were compared, and the diagnostic accuracy of the PCR in stool was compared with the accuracy of sputum testing by PCR, microscopy, and culture. A heminested IS6110-PCR was used for tuberculosis detection, and IS6110-PCR-positive stool samples then underwent rifampin sensitivity testing by universal heteroduplex generator PCR (heteroduplex-PCR) assay. For newly diagnosed pulmonary tuberculosis patients, stool IS6110-PCR had 86% sensitivity and 100% specificity compared with results obtained by sputum culture, and stool PCR had similar sensitivities for HIV-positive and HIV-negative patients (P=0.3). DNA extraction with commercially available spin columns yielded greater stool PCR sensitivity than DNA extraction with the in-house Chelex technique (P=0.007). Stool heteroduplex-PCR had 98% agreement with the sputum culture determinations of rifampin resistance and multidrug resistance. Tuberculosis detection and drug susceptibility testing by stool PCR took 1 to 2 days compared with an average of 9 weeks to obain those results by traditional culture-based testing. Stool PCR was more sensitive than sputum microscopy and remained positive for most patients for more than 1 week of treatment. In conclusion, stool PCR is a sensitive, specific, and rapid technique for the diagnosis and drug susceptibility testing of pulmonary tuberculosis and should be considered when sputum samples are unavailable.

  8. Evolution of molecular weight and fluorescence of effluent organic matter (EfOM) during oxidation processes revealed by advanced spectrographic and chromatographic tools.

    Science.gov (United States)

    Chen, Zhiqiang; Li, Mo; Wen, Qinxue; Ren, Nanqi

    2017-11-01

    Effluent organic matter (EfOM) is an emerging concern to receiving aquatic environment due to its refractory property. The degradation of EfOM in ozonation and other two advanced oxidation processes (AOPs), UV/H2O2 and UV/persulfate (PS), was investigated in this study. Fluorescence spectra coupled with parallel factor analysis (PARAFAC) and two-dimensional correlation gel permeation chromatography (2D-GPC) were used to track the evolution of EfOM during each oxidation process. Results showed that the degradation of EfOM indicated by dissolved organic carbon (DOC), UV254 and fluorescence components, fitted well with pseudo-first-order kinetic model during the oxidation processes. Ozonation showed higher degradation efficiency than AOPs, while UV/PS was more effective than UV/H2O2 with equimolar oxidants dosage. Ozone and SO·4- were more reactive with terrestrial humic-like substances, while hydroxyl radical preferentially reacted with protein-like substances. Organic molecules with higher molecular weight (MW) were susceptible to ozone or radicals. Ozonation could transform higher MW (MW of 3510 and 575) organic matters into lower MW organic matters (MW of 294), while reductions of all the organics were observed in both AOPs. Due to the higher reaction rates between ozone and EfOM, ozonation maybe serve as a pre-treatment for AOPs to reduce the radical and energy consumption and improve mineralization of EfOM by AOPs. The decline in DOC, UV254, fluorescence and reduction in oxidants increased with the increase of oxidants dosage, and linear correlations among them were found during the ozonation and AOPs. Copyright © 2017. Published by Elsevier Ltd.

  9. Human hair follicle transcriptome profiling: a minimally invasive tool to assess molecular adaptations upon low-volume, high-intensity interval training.

    Science.gov (United States)

    Zhang, Jing; Wallace, Sarah J; Shiu, Maria Y; Smith, Ingrid; Rhind, Shawn G; Langlois, Valerie S

    2017-12-01

    High-intensity interval training (HIIT) has become a popular fitness training approach under both civilian and military settings. Consisting of brief and intense exercise intervals, HIIT requires less time commitment yet is able to produce the consistent targeted physical adaptations as conventional endurance training. To effectively characterize and monitor HIIT-induced cellular and molecular responses, a highly accessible yet comprehensive biomarker discovery source is desirable. Both gene differential expression (DE) and gene set (GS) analyses were conducted using hair follicle transcriptome established from pre and postexercise subjects upon a 10-day HIIT program by RNA-Seq, Comparing between pre and posttraining groups, differentially expressed protein coding genes were identified. To interpret the functional significance of the DE results, a comprehensive GS analysis approach featuring multiple algorithms was used to enrich gene ontology (GO) terms and KEGG pathways. The GS analysis revealed enriched themes such as energy metabolism, cell proliferation/growth/survival, muscle adaptations, and cytokine-cytokine interaction, all of which have been previously proposed as HIIT responses. Moreover, related cell signaling pathways were also measured. Specifically, G-protein-mediated signal transduction, phosphatidylinositide 3-kinases (PI3K) - protein kinase B (PKB) and Janus kinase (JAK) - Signal Transducer and Activator of Transcription (STAT) signaling cascades were over-represented. Additionally, the RNA-Seq analysis also identified several HIIT-responsive microRNAs (miRNAs) that were involved in regulating hair follicle-specific processes, such as miR-99a For the first time, this study demonstrated that both existing and new biomarkers like miRNA can be explored for HIIT using the transcriptomic responses exhibited by the hair follicle. © 2017 The Authors. Physiological Reports published by Wiley Periodicals, Inc. on behalf of The Physiological Society and

  10. Combined parasitological and molecular-based diagnostic tools improve the detection of Trypanosoma cruzi in single peripheral blood samples from patients with Chagas disease

    Directory of Open Access Journals (Sweden)

    Fabiana Caroline Zempulski Volpato

    Full Text Available Abstract INTRODUCTION In order to detect Trypanosoma cruzi and determine the genetic profiles of the parasite during the chronic phase of Chagas disease (ChD, parasitological and molecular diagnostic methods were used to assess the blood of 91 patients without specific prior treatment. METHODS Blood samples were collected from 68 patients with cardiac ChD and 23 patients with an indeterminate form of ChD, followed by evaluation using blood culture and polymerase chain reaction. T . cruzi isolates were genotyped using three different genetic markers. RESULTS: Blood culture was positive in 54.9% of all patients, among which 60.3% had the cardiac form of ChD, and 39.1% the indeterminate form of ChD. There were no significant differences in blood culture positivity among patients with cardiac and indeterminate forms. Additionally, patient age and clinical forms did not influence blood culture results. Polymerase chain reaction (PCR was positive in 98.9% of patients, although comparisons between blood culture and PCR results showed that the two techniques did not agree. Forty-two T . cruzi stocks were isolated, and TcII was detected in 95.2% of isolates. Additionally, one isolate corresponded to TcIII or TcIV, and another corresponded to TcV or TcVI. CONCLUSIONS Blood culture and PCR were both effective for identifying T. cruzi using a single blood sample, and their association did not improve parasite detection. However, we were not able to establish an association between the clinical form of ChD and the genetic profile of the parasite.

  11. Computational methods for molecular imaging

    CERN Document Server

    Shi, Kuangyu; Li, Shuo

    2015-01-01

    This volume contains original submissions on the development and application of molecular imaging computing. The editors invited authors to submit high-quality contributions on a wide range of topics including, but not limited to: • Image Synthesis & Reconstruction of Emission Tomography (PET, SPECT) and other Molecular Imaging Modalities • Molecular Imaging Enhancement • Data Analysis of Clinical & Pre-clinical Molecular Imaging • Multi-Modal Image Processing (PET/CT, PET/MR, SPECT/CT, etc.) • Machine Learning and Data Mining in Molecular Imaging. Molecular imaging is an evolving clinical and research discipline enabling the visualization, characterization and quantification of biological processes taking place at the cellular and subcellular levels within intact living subjects. Computational methods play an important role in the development of molecular imaging, from image synthesis to data analysis and from clinical diagnosis to therapy individualization. This work will bring readers fro...

  12. Molecular characterization and properties of (R)-specific enoyl-CoA hydratases from Pseudomonas aeruginosa: metabolic tools for synthesis of polyhydroxyalkanoates via fatty acid beta-oxidation.

    Science.gov (United States)

    Tsuge, Takeharu; Taguchi, Kazunori; Seiichi, Taguchi; Doi, Yoshiharu

    2003-01-15

    The use of (R)-specific enoyl-coenzyme A (CoA) hydratase (PhaJ) provides a powerful tool for polyhydroxyalkanoate (PHA) synthesis from fatty acids or plant oils in recombinant bacteria. PhaJ provides monomer units for PHA synthesis from the fatty acid ss-oxidation cycle. Previously, two phaJ genes (phaJ1(Pa) and phaJ2(Pa)) were identified in Pseudomonas aeruginosa. This report identifies two new phaJ genes (phaJ3(Pa) and phaJ4(Pa)) in P. aeruginosa through a genomic database search. The abilities of the four PhaJ(Pa) proteins and the (R)-3-hydroxyacyl-acyl carrier protein [(R)-3HA-ACP] dehydrases, FabA(Pa) and FabZ(Pa), to supply monomers from enoyl-CoA substrates for PHA synthesis were determined. The presence of either PhaJ1(Pa) or PhaJ4(Pa) in recombinant Escherichia coli led to the high levels of PHA accumulation (as high as 36-41 wt.% in dry cells) consisting of mainly short- (C4-C6) and medium-chain-length (C6-C10) 3HA units, respectively. Furthermore, detailed characterizations of PhaJ1(Pa) and PhaJ4(Pa) were performed using purified samples. Kinetic analysis revealed that only PhaJ4(Pa) exhibits almost constant maximum reaction rates (V(max)) irrespective of the chain length of the substrates. The assay for stereospecific hydration revealed that, unlike PhaJ1(Pa), PhaJ4(Pa) has relatively low (R)-specificity. These hydratases may be very useful as monomer-suppliers for the synthesis of designed PHAs in recombinant bacteria.

  13. Ultrasound in Radiology: from Anatomic, Functional, Molecular Imaging to Drug Delivery and Image-Guided Therapy

    Science.gov (United States)

    Klibanov, Alexander L.; Hossack, John A.

    2015-01-01

    During the past decade, ultrasound has expanded medical imaging well beyond the “traditional” radiology setting - a combination of portability, low cost and ease of use makes ultrasound imaging an indispensable tool for radiologists as well as for other medical professionals who need to obtain imaging diagnosis or guide a therapeutic intervention quickly and efficiently. Ultrasound combines excellent ability for deep penetration into soft tissues with very good spatial resolution, with only a few exceptions (i.e. those involving overlying bone or gas). Real-time imaging (up to hundreds and thousands frames per second) enables guidance of therapeutic procedures and biopsies; characterization of the mechanical properties of the tissues greatly aids with the accuracy of the procedures. The ability of ultrasound to deposit energy locally brings about the potential for localized intervention encompassing: tissue ablation, enhancing penetration through the natural barriers to drug delivery in the body and triggering drug release from carrier micro- and nanoparticles. The use of microbubble contrast agents brings the ability to monitor and quantify tissue perfusion, and microbubble targeting with ligand-decorated microbubbles brings the ability to obtain molecular biomarker information, i.e., ultrasound molecular imaging. Overall, ultrasound has become the most widely used imaging modality in modern medicine; it will continue to grow and expand. PMID:26200224

  14. Draft de novo transcriptome assembly and proteome characterization of the electric lobe of Tetronarce californica: a molecular tool for the study of cholinergic neurotransmission in the electric organ.

    Science.gov (United States)

    Stavrianakou, Maria; Perez, Ricardo; Wu, Cheng; Sachs, Matthew S; Aramayo, Rodolfo; Harlow, Mark

    2017-08-14

    information was used to predict the position in human pathways of the conserved members of the T. californica MetaProteome. We found proteins not detected before in T. californica, corresponding to processes involved in synaptic vesicle biology. Finally, we identified 42 transporter proteins in TCDB that were detected by the T. californica MetaProteome (electric fish) and not selected by a control proteome consisting of the combined proteomes of 12 widely diverse non-electric fishes by Reverse-Blast-Hit Blast. Combined, the information provided here is not only a unique tool for the study of cholinergic neurotransmission, but it is also a starting point for understanding the evolution of early vertebrates.

  15. International Career Development in Education: What Teachers Bring Home

    Directory of Open Access Journals (Sweden)

    Mustafa Altun

    2017-09-01

    Full Text Available Working abroad helps teachers have a global perspective and enable them to become aware of global affairs. Teachers with international experience stands a better chance for professional and personal development. They not only enhance their teaching skills but also become more social. The skills they develop while working abroad make a difference in the lives of their students. Through transferring what they have learnt abroad to their home country, they can enhance the success of their students. This article presents the reasons why teachers need international experience and what changes they bring home.

  16. Bring Your Own Device - Providing Reliable Model of Data Access

    Directory of Open Access Journals (Sweden)

    Stąpór Paweł

    2016-10-01

    Full Text Available The article presents a model of Bring Your Own Device (BYOD as a model network, which provides the user reliable access to network resources. BYOD is a model dynamically developing, which can be applied in many areas. Research network has been launched in order to carry out the test, in which as a service of BYOD model Work Folders service was used. This service allows the user to synchronize files between the device and the server. An access to the network is completed through the wireless communication by the 802.11n standard. Obtained results are shown and analyzed in this article.

  17. The Napping Company: bringing science to the workplace.

    Science.gov (United States)

    Anthony, William A; Anthony, Camille W

    2005-01-01

    Increasing emphasis is currently being given to the importance of bringing knowledge gained from science into places where people live and work, in order to increase the impact science has on the general public's quality of life. Scientific findings about the positive impact of napping on mood and performance are an example of research generated knowledge that needs to be brought to the workplace. A major goal of the Napping Company (www.napping.com) is to bring the science of napping to the workers and the workplace so that employees and employers can act on this knowledge and change worker napping behavior and employer napping policies. The present paper overviews the challenges inherent in making scientific knowledge useful to how we live our lives. The Napping Company is guided by five principles of knowledge transfer in the company's attempts to disseminate and increase utilization of napping research. Examples are given to illustrate how the Napping Company has used these principles to bridge the gap between napping science and nap behavior and policies in the workplace.

  18. A Review of Bring Your Own Device on Security Issues

    Directory of Open Access Journals (Sweden)

    Morufu Olalere

    2015-04-01

    Full Text Available Mobile computing has supplanted internet computing because of the proliferation of cloud-based applications and mobile devices (such as smartphones, palmtops, and tablets. As a result of this, workers bring their mobile devices to the workplace and use them for enterprise work. The policy of allowing the employees to work with their own personal mobile devices is called Bring Your Own Devices (BYOD. In this article, we discuss BYOD’s background, prevalence, benefits, challenges, and possible security attacks. We then review contributions of academic researchers on BYOD. The Universiti Putra Malaysia online databases (such as IEEE Xplore digital library, Elsevier, Springer, ACM digital library were used to search for peer-reviewed academic publications and other relevant publications on BYOD. The Google Scholar search engine was also used. Our thorough review shows that security issues comprise the most significant challenge confronting BYOD policy and that very little has been done to tackle this security challenge. It is our hope that this review will provide a theoretical background for future research and enable researchers to identify researchable areas of BYOD.

  19. Simulation tools

    CERN Document Server

    Jenni, F

    2006-01-01

    In the last two decades, simulation tools made a significant contribution to the great progress in development of power electronics. Time to market was shortened and development costs were reduced drastically. Falling costs, as well as improved speed and precision, opened new fields of application. Today, continuous and switched circuits can be mixed. A comfortable number of powerful simulation tools is available. The users have to choose the best suitable for their application. Here a simple rule applies: The best available simulation tool is the tool the user is already used to (provided, it can solve the task). Abilities, speed, user friendliness and other features are continuously being improved—even though they are already powerful and comfortable. This paper aims at giving the reader an insight into the simulation of power electronics. Starting with a short description of the fundamentals of a simulation tool as well as properties of tools, several tools are presented. Starting with simplified models ...

  20. NASA Applications of Molecular Nanotechnology

    Science.gov (United States)

    Globus, Al; Bailey, David; Han, Jie; Jaffe, Richard; Levit, Creon; Merkle, Ralph; Srivastava, Deepak

    1998-01-01

    Laboratories throughout the world are rapidly gaining atomically precise control over matter. As this control extends to an ever wider variety of materials, processes and devices, opportunities for applications relevant to NASA's missions will be created. This document surveys a number of future molecular nanotechnology capabilities of aerospace interest. Computer applications, launch vehicle improvements, and active materials appear to be of particular interest. We also list a number of applications for each of NASA's enterprises. If advanced molecular nanotechnology can be developed, almost all of NASA's endeavors will be radically improved. In particular, a sufficiently advanced molecular nanotechnology can arguably bring large scale space colonization within our grasp.

  1. Physical tools for textile creativity and invention

    DEFF Research Database (Denmark)

    Heimdal, Elisabeth Jacobsen; Lenau, Torben Anker

    2010-01-01

    Two textile research projects (one completed and one ongoing) are described, where physical inspirational tools are developed and tested with the aim of stimulating textile creativity and invention, i.e. the use of textile materials in new kinds of products, thus bringing textiles into new contexts...

  2. Sharing tools and know-how

    DEFF Research Database (Denmark)

    Saad-Sulonen, Joanna

    In this position paper I address the theme of designing for sharing in self-organized urban communities by bringing forward the aspect of sharing tools and know-how. I report the lessons learned from a case in Helsinki and open questions for discussion regarding some of the identified challenges...

  3. The modern molecular clock.

    Science.gov (United States)

    Bromham, Lindell; Penny, David

    2003-03-01

    The discovery of the molecular clock--a relatively constant rate of molecular evolution--provided an insight into the mechanisms of molecular evolution, and created one of the most useful new tools in biology. The unexpected constancy of rate was explained by assuming that most changes to genes are effectively neutral. Theory predicts several sources of variation in the rate of molecular evolution. However, even an approximate clock allows time estimates of events in evolutionary history, which provides a method for testing a wide range of biological hypotheses ranging from the origins of the animal kingdom to the emergence of new viral epidemics.

  4. Bringing indigenous ownership back to the private sector

    DEFF Research Database (Denmark)

    Kragelund, Peter

    to traditional Copperbelt rhetoric, have enforced a role as minority middlemen upon the Chinese investors. This further segregates Chinese investors from other investors and has been a driving force in the anti-Chinese campaign in Zambia. To curb the critique of the growing foreign dominance over the economy......Driven by across-the-board liberalizations and the commodity price boom, Zambia has recently experienced an upsurge in foreign ownership over key parts of its economy. Albeit investors from all over the world have sought to make the most of the current situation in Zambia, Chinese investors have...... been particularly present in all sectors of the Zambian economy. Foreign ownership, however, is not new to African societies and several African countries pursued indigenisation policies in the wake of independence to bring ownership back to their own citizens. Now indigenisation policies thrive again...

  5. Archaeopteryx: Bringing the Dino-Bird to Life

    Energy Technology Data Exchange (ETDEWEB)

    Bergmann, Uwe

    2011-01-25

    Some 150 million years ago, a strange creature died in a tropical lagoon that today is located in Bavaria, Germany. In 1861, a single feather of this creature was discovered. Not long afterward, a complete fossil was found with the same bird-like feathers but dinosaur-like anatomical features. Darwin had just published 'On the Origin of Species'; could this be the missing link that Darwin's supporters hoped to find? Recently, two of the now eleven discovered Archaeopteryx fossils, and that first feather, were brought to SLAC, where, using the intense X-ray beam, researchers searched for the chemical remains of the original living creatures. Please join us for this lecture, which will explain how the studies attempt to bring the original dino-bird back to life.

  6. [Multimedia (visual collaboration) brings true nature of human life].

    Science.gov (United States)

    Tomita, N

    2000-03-01

    Videoconferencing system, high-quality visual collaboration, is bringing Multimedia into a society. Multimedia, high quality media such as TV broadcast, looks expensive because it requires broadband network with 100-200 Mpbs bandwidth or 3,700 analog telephone lines. However, thanks to the existing digital-line called N-ISDN (Narrow Integrated Service Digital Network) and PictureTel's audio/video compression technologies, it becomes far less expensive. N-ISDN provides 128 Kbps bandwidth, over twice wider than analog line. PictureTel's technology instantly compress audio/video signal into 1/1,000 in size. This means, with ISDN and PictureTel technology. Multimedia is materialized over even single ISDN line. This will allow doctor to remotely meet face-to-face with a medical specialist or patients to interview, conduct physical examinations, review records, and prescribe treatments. Bonding multiple ISDN lines will further improve video quality that enables remote surgery. Surgeon can perform an operation on internal organ by projecting motion video from Endoscope's CCD camera to large display monitor. Also, PictureTel provides advanced technologies of eliminating background noise generated by surgical knives or scalpels during surgery. This will allow sound of the breath or heartbeat be clearly transmitted to the remote site. Thus, Multimedia eliminates the barrier of distance, enabling people to be just at home, to be anywhere in the world, to undergo up-to-date medical treatment by expertise. This will reduce medical cost and allow people to live in the suburbs, in less pollution, closer to the nature. People will foster more open and collaborative environment by participating in local activities. Such community-oriented life-style will atone for mass consumption, materialistic economy in the past, then bring true happiness and welfare into our life after all.

  7. Molecular Tools for Investigating the Gut Microbiota

    Science.gov (United States)

    Lay, Christophe

    The “microbial world within us” (Zoetendal et al., 2006) is populated by a complex society of indigenous microorganisms that feature different “ethnic” populations. Those microbial cells thriving within us are estimated to outnumber human body cells by a factor of ten to one. Insights into the relation between the intestinal microbial community and its host have been gained through gnotobiology. Indeed, the influence of the gut microbiota upon human development, physiology, immunity, and nutrition has been inferred by comparing gnotoxenic and axenic murine models (Hooper et al., 1998, 2002, 2003; Hooper and Gordon, 2001).

  8. Molecular biology - New tool for genome surgery

    NARCIS (Netherlands)

    Oost, van der J.

    2013-01-01

    Gene therapy is the holy grail of human medicine. Many diseases are caused by a defective gene, sometimes with a mutation as subtle as a single-nucleotide variation. Before restoration of such a mutation in a patient's genome can take place, the target nucleotide sequence has to be cleaved at a

  9. EarthObserver: Bringing the world to your fingertips

    Science.gov (United States)

    Ryan, W. B.; Goodwillie, A. M.; Coplan, J.; Carbotte, S. M.; Arko, R. A.; Ferrini, V.; O'hara, S. H.; Chan, S.; Bonczkowski, J.; Nitsche, F. O.; Morton, J. J.; McLain, K.; Weissel, R.

    2011-12-01

    EarthObserver (http://www.earth-observer.org/), developed by the Lamont-Doherty Earth Observatory of Columbia University, brings a wealth of geoscience data to Apple iPad, iPhone and iPod Touch mobile devices. Built around an easy-to-use interface, EarthObserver allows users to explore and visualise a wide range of data sets superimposed upon a detailed base map of land elevations and ocean depths - tapping the screen will instantly return the height or depth at that point. A simple transparency function allows direct comparison of built-in content. Data sets include high-resolution coastal bathymetry of bays, sounds, estuaries, harbors and rivers; geological maps of the US states and world - tapping the screen displays the rock type, and full legends can be viewed; US Topo sheets; and, geophysical content including seafloor crustal age and sediment thickness, earthquake and volcano data, gravity and magnetic anomalies, and plate boundary descriptions. The names of physiographic features are automatically displayed. NASA Visible Earth images along with ocean temperature, salinity and productivity maps and precipitation information expose data sets of interest to the atmospheric, oceanic and biological communities. Natural hazard maps, population information and political boundaries allow users to explore impacts upon society. EarthObserver, so far downloaded by more than 55,000 users, offers myriad ways for educators at all levels to bring research-quality geoscience data into the learning environment, whether for use as an in-class illustration or for extensive exploration of earth sciences data. By using cutting-edge mobile app technology, EarthObserver boosts access to relevant earth science content. The EarthObserver base map is the Global Multi-Resolution Topography digital elevation model (GMRT; http://www.marine-geo.org/portals/gmrt/), also developed at LDEO and updated regularly. It provides land elevations with horizontal resolution as high as 10m for

  10. Skynet Junior Scholars: Bringing Astronomy to Deaf and Hard of Hearing Youth

    Science.gov (United States)

    Meredith, Kate; Williamson, Kathryn; Gartner, Constance; Hoette, Vivian L.; Heatherly, Sue Ann

    2016-01-01

    Skynet Junior Scholars (SJS), funded by the National Science Foundation, aims to engage middle school youth from diverse audiences in investigating the universe with research quality robotic telescopes. SJS project development goals include: 1) Online access to optical and radio telescopes, data analysis tools, and professional astronomers, 2) An age-appropriate web-based interface for controlling remote telescopes, 3) Inquiry-based standards-aligned instructional modules. From an accessibility perspective, the goal of the Skynet Junior Scholars project is to facilitate independent access to the project by all youth including those with blindness or low vision and those who are Deaf or Hard of Hearing.Deaf and Hard of Hearing (DHH) students have long been an underserved population within STEM fields, including astronomy. Two main barriers include: (1) insufficient corpus of American Sign Language (ASL) for astronomy terminology, and (2) DHH education professionals who lack astronomy background. A suite of vocabulary, accessible hands-on activities, and interaction with trained professionals, are critical for enhancing the background experiences of DHH youth, as they may come to an astronomy lesson lacking the basic "incidental learning" that is often taken for granted with hearing peers (for example, from astronomy in the media).A collaboration between the Skynet Junior Scholars (SJS) project and the Wisconsin School for the Deaf is bringing astronomy to the DHH community in an accessible way for the first time. We follow a group of seven DHH youth over one semester as they interact with the SJS tools and curriculum to understand how they assimilate astronomy experiences and benefit from access to telescopes both directly (on school campus and at Yerkes Observatory) and through Skynet's robotic telescope network (optical and radio telescopes, inquiry-based modules, data analysis tools, and professional astronomers). We report on our first findings of resources and

  11. Bringing Internet-based education and intervention into mental health practice: afterdeployment.org

    Directory of Open Access Journals (Sweden)

    Josef I. Ruzek

    2011-11-01

    Full Text Available Internet-facilitated interventions may offer numerous advantages in reaching the large numbers of military service men and women exposed to traumatic events. The Internet is now a primary source of health-related information for consumers and research has shown the effectiveness of web-based interventions in addressing a range of mental health problems.Clinicians can learn how to bring Internet education and intervention into routine care, to help clients better understand mental health issues and learn skills for self-management of problems.The Afterdeployment.org (AD Internet site can be used by health care professionals serving U.S. military personnel returning from Iraq and Afghanistan, and their families. The site currently addresses 18 key domains of functioning, including post-traumatic stress, sleep, anger, alcohol and drugs, and military sexual trauma. It provides an extensive amount of client and family education that is suitable for immediate use by clients and providers, as well as the kinds of interactive workshop content and self-assessment tools that have been shown to be helpful in other treatment contexts. AD can be utilized in clinical practice in a variety of ways: as an adjunct to treatment for PTSD, to supplement existing treatments for a range of post-deployment problems, or as the primary focus of treatment for a client.AD represents a kind of service that is likely to become increasingly available in coming years and that is important for mental health providers to actively explore as a tool for extending their reach, improving their efficiency, and improving quality of care.For the abstract or full text in other languages, please see Supplementary files under Reading Tools online.

  12. The Quake-Catcher Network: Bringing Seismology to Homes and Schools

    Science.gov (United States)

    Lawrence, J. F.; Cochran, E. S.; Christensen, C. M.; Saltzman, J.; Taber, J.; Hubenthal, M.

    2011-12-01

    The Quake-Catcher Network (QCN) is a collaborative initiative for developing the world's largest, low-cost strong-motion seismic network by utilizing sensors in and attached to volunteer internet-connected computers. QCN is not only a research tool, but provides an educational tool for teaching earthquake science in formal and informal environments. A central mission of the Quake-Catcher Network is to provide scientific educational software and hardware so that K-12 teachers, students, and the general public can better understand and participate in the science of earthquakes and earthquake hazards. With greater understanding, teachers, students, and interested individuals can share their new knowledge, resulting in continued participation in the project, and better preparation for earthquakes in their homes, businesses, and communities. The primary educational outreach goals are 1) to present earthquake science and earthquake hazards in a modern and exciting way, and 2) to provide teachers and educators with seismic sensors, interactive software, and educational modules to assist in earthquake education. QCNLive (our interactive educational computer software) displays recent and historic earthquake locations and 3-axis real-time acceleration measurements. This tool is useful for demonstrations and active engagement for all ages, from K-college. QCN provides subsidized sensors at 49 for the general public and 5 for K-12 teachers. With your help, the Quake-Catcher Network can provide better understanding of earthquakes to a broader audience. Academics are taking QCN to classrooms across the United States and around the world. The next time you visit a K-12 classroom or teach a college class on interpreting seismograms, bring a QCN sensor and QCNLive software with you! To learn how, visit http://qcn.stanford.edu.

  13. Bringing Systems Thinking into Community-based Environmental Management

    Science.gov (United States)

    The U.S. EPA’s ‘Sustainable and Healthy Communities Research Program’ is developing methods and tools to assist communities in making decisions that lead to more just and environmentally sustainable outcomes. Work includes collaborative development of system...

  14. Bringing Domain-Specific Languages to Digital Forensics

    NARCIS (Netherlands)

    J. van den Bos (Jeroen); T. van der Storm (Tijs); R.N. Taylor; H. Gall; N. Medvidović

    2011-01-01

    textabstractDigital forensics investigations often consist of analyzing large quantities of data. The software tools used for analyzing such data are constantly evolved to cope with a multiplicity of versions and variants of data formats. This process of customization is time consuming and error

  15. CERN's Mighty Machines Exhibition Science Bringing Nations Together

    CERN Multimedia

    2000-01-01

    The Laboratory's tools, particle accelerators and detectors, are amongst the world's largest and most complex sci-entific instruments. Built at the leading edge of technology, they are some of the finest monuments of 20th centu-ry science. Nobel prizes have been awarded to CERN physicists for developments in both.

  16. Bringing the Science of JWST to the Public

    Science.gov (United States)

    Green, Joel D.; Smith, Denise A.; Lawton, Brandon L.; Meinke, Bonnie K.; Jirdeh, Hussein

    2017-01-01

    The James Webb Space Telescope is the successor to the Hubble Space Telescope. STScI and the Office of Public Outreach are committed to bringing awareness of the technology, the excitement, and the future science potential of this great observatory to the public and to the scientific community, prior to its 2018 launch. The challenges in ensuring the high profile of JWST (understanding the infrared, the vast distance to the telescope's final position, and the unfamiliar science territory) requires us to lay the proper background, particularly in the area of spectroscopy. We currently engage the full range of the public and scientific communities using a variety of high impact, memorable initiatives, in combination with modern technologies to extend reach, linking the science goals of Webb to the ongoing discoveries being made by Hubble. Webbtelescope.org, the public hub for scientific information related to JWST, is now open. We have injected Webb-specific content into ongoing outreach programs: for example, partnering with high impact science communicators such as MinutePhysics to produce timely and concise content; partnering with musicians and artists to link science and art. Augmented reality apps showcase NASA’s telescopes in a format usable by anyone with a smartphone, and visuals from increasingly affordable 3D VR technologies.

  17. Using Multimedia to Bring Science News to the Public

    Science.gov (United States)

    O'Riordan, C.; Stein, B.; Lorditch, E. M.

    2015-12-01

    Creative partnerships between scientists and journalists open new opportunities to bring the excitement of scientific discoveries to wider audiences. Research tells us that the majority of the general public now gets more science and technology news from the Internet than from TV sources (2014 NSF Science and Engineering Indicators). In order to reach these audiences news organizations must embrace multiple forms of multimedia. We will review recent research on how the new multimedia landscape is changing the way that science news is consumed and how news organizations are changing the way they deliver news. News programs like Inside Science, and other examples of new partnerships that deliver research news to journalists, teachers, students, and the general public will be examined. We will describe examples of successful collaborations including an article by a former Newsweek science reporter entitled "My 1975 'Cooling World' Story Doesn't Make Today's Climate Scientists Wrong," which got reprinted in Slate, RealClearScience, and mentioned in Factcheck.org and USA Today.

  18. Bringing gender sensitivity into healthcare practice: a systematic review.

    Science.gov (United States)

    Celik, Halime; Lagro-Janssen, Toine A L M; Widdershoven, Guy G A M; Abma, Tineke A

    2011-08-01

    Despite the body of literature on gender dimensions and disparities between the sexes in health, practical improvements will not be realized effectively as long as we lack an overview of the ways how to implement these ideas. This systematic review provides a content analysis of literature on the implementation of gender sensitivity in health care. Literature was identified from CINAHL, PsycINFO, Medline, EBSCO and Cochrane (1998-2008) and the reference lists of relevant articles. The quality and relevance of 752 articles were assessed and finally 11 original studies were included. Our results demonstrate that the implementation of gender sensitivity includes tailoring opportunities and barriers related to the professional, organizational and the policy level. As gender disparities are embedded in healthcare, a multiple track approach to implement gender sensitivity is needed to change gendered healthcare systems. Conventional approaches, taking into account one barrier and/or opportunity, fail to prevent gender inequality in health care. For gender-sensitive health care we need to change systems and structures, but also to enhance understanding, raise awareness and develop skills among health professionals. To bring gender sensitivity into healthcare practice, interventions should address a range of factors. Copyright © 2010. Published by Elsevier Ireland Ltd.

  19. Bringing solar light to the bottom of the pyramid

    Energy Technology Data Exchange (ETDEWEB)

    Graham, S. [SGA Energy Ltd., Ottawa, ON (Canada)

    2006-07-01

    This presentation described the efforts in bringing solar light to areas of Rwanda, Uganda and the Congo that are currently unserved by electricity. In particular, it highlighted the contributions made by Light Up the World Foundation (LUTW) and the International Gorilla Conservation Programme (IGCP) to improve the quality of life in periphery villages by introducing solar LED lighting in 6 pilot villages. Efficient, long-lasting white LED lamps combined with solar can provide a low cost alternative to the current light source, which is kerosene, diesel and candles. It was noted that the technology exists, but the challenge lies in reaching the market and making a sustainable intervention. The operating parameters of solar panels, LED lamps and batteries were listed with reference to output power, open circuit voltage, maximum power voltage, maximum power current, and capacity. The service life of these devices was also listed along with estimates of their operating costs. The project needs were also identified. It was emphasized that financial support of IGCP and LUTW is needed to support private sector development and market expansion to other areas of Africa. figs.

  20. Bringing Classroom-Based Assessment into the EFL classroom

    Directory of Open Access Journals (Sweden)

    Andrew Finch

    2012-01-01

    Full Text Available   This paper describes how English as a Foreign Language (EFL teachers can bring reliable, valid, user-friendly assessment into their classrooms, and thus improve the quality of learning that occurs there. Based on the experience of the author as a an EFL teacher and teacher-trainer, it is suggested that the promotion and development of autonomy, intrinsic motivation, and self-esteem that takes place in a Classroom-Based Assessment (CBA environment facilitates an holistic approach to language learning and prepares the students for the high-stakes tests that often determine their motivation for learning English. Rather than relying on the memorization of language code, form, lexis, and prepared answers, students who have learned in a CBA environment are able to self-assess, peer-assess, build portfolios, and edit their own work. Not only does this reduce the assessment burden on the teacher, but it also develops the skills of problem-solving, critical thinking, and summarization in the students, in addition to a heightened awareness of the language-learning process. By learning how to set goals, assess their achievements, and reflect on their future learning needs, students become more efficient language learners. While acknowledging the place of standardized, summative tests in contemporary society, it is suggested that CBA in the EFL classroom can enhance long-term learning and consequently enable and empower students to prepare for their future learning needs.

  1. Bringing nursing science to the classroom: a collaborative project.

    Science.gov (United States)

    Reams, Susan; Bashford, Carol

    2009-01-01

    This project resulted as a collaborative effort on the part of a public school system and nursing faculty. The fifth grade student population utilized in this study focused on the skeletal, muscular, digestive, circulatory, respiratory, and nervous systems as part of their school system's existing science and health curriculum. The intent of the study was to evaluate the impact on student learning outcomes as a result of nursing-focused, science-based, hands-on experiential activities provided by nursing faculty in the public school setting. An assessment tool was created for pretesting and posttesting to evaluate learning outcomes resulting from the intervention. Over a two day period, six classes consisting of 25 to 30 students each were divided into three equal small groups and rotated among three interactive stations. Students explored the normal function of the digestive system, heart, lungs, and skin. Improvement in learning using the pretest and posttest assessment tools were documented.

  2. Method for delivery of small molecules and proteins across the cell wall of algae using molecular transporters

    Science.gov (United States)

    Geihe, Erika; Trantow, Brian; Wender, Paul; Hyman, Joel M.; Parvin, Bahram

    2017-11-14

    The introduction of tools to study, control or expand the inner-workings of algae has been slow to develop. Provided are embodiments of a molecular method based on guanidinium-rich molecular transporters (GR-MoTrs) for bringing molecular cargos into algal cells. The methods of the disclosure have been shown to work in wild-type algae that have an intact cell wall. Developed using Chlamydomonas reinhardtii, this method is also successful with less studied algae, including Neochloris oleoabundans and Scenedesmus dimorphus, thus providing a new and versatile tool for algal research and modification. The method of delivering a cargo compound to an algal cell comprises contacting an algal cell with a guanidinium-rich delivery vehicle comprising a guanidinium-rich molecular transporter (GR-MoTr) linked to a cargo compound desired to be delivered to the algal cell, whereby the guanidinium-rich molecular transporter can traverse the algal cell wall, thereby delivering the cargo compound to the algal cell.

  3. Bringing good and bad Whistle-blowers to the Lab

    OpenAIRE

    Schikora, Jan Theodor

    2011-01-01

    Whistle-blowing is seen as a powerful tool in containing corruption, although theoretical findings and experimental evidence cast doubt on its effectiveness. We expand a standard corruption model by allowing both, briber and official to initiate corruption actively, in order to assess the full effect of whistle-blowing. In our laboratory experiment we find that the effect of symmetrically punished whistle-blowing is ambiguous since it reduces the impact of corruption on productive activity, b...

  4. Conceptualising International Peace Mediation - Bring Back the Law

    OpenAIRE

    Higgins, Noelle; Daly, Brenda

    2011-01-01

    Mediation has been acknowledged and utilised for a number of decades as an effective method of alternative dispute resolution in a variety of areas of law, including family law, commercial law and medical law. A uniform, standardised framework exists within legal discourse which clearly identifies and categorises three main styles of mediation as facilitative, evaluative and transformative mediation. In the post-Cold War period, mediation has also emerged as an important resolution tool in ar...

  5. Aqueduct Global Flood Analyzer - bringing risk information to practice

    Science.gov (United States)

    Ward, Philip

    2017-04-01

    The economic losses associated with flooding are huge and rising. As a result, there is increasing attention for strategic flood risk assessments at the global scale. In response, the last few years have seen a large growth in the number of global flood models. At the same time, users and practitioners require flood risk information in a format that is easy to use, understandable, transparent, and actionable. In response, we have developed the Aqueduct Global Flood Analyzer (wri.org/floods). The Analyzer is a free, online, easy to use, tool for assessing global river flood risk at the scale of countries, states, and river basins, using data generated by the state of the art GLOFRIS global flood risk model. The Analyzer allows users to assess flood risk on-the-fly in terms of expected annual urban damage, and expected annual population and GDP affected by floods. Analyses can be carried out for current conditions and under future scenarios of climate change and socioeconomic development. We will demonstrate the tool, and discuss several of its applications in practice. In the past 15 months, the tool has been visited and used by more than 12,000 unique users from almost every country, including many users from the World Bank, Pacific Disaster Center, Red Cross Climate Centre, as well as many journalists from major international news outlets. Use cases will be presented from these user communities. We will also present ongoing research to improve the user functionality of the tool in the coming year. This includes the inclusion of coastal flood risk, assessing the costs and benefits of adaptation, and assessing the impacts of land subsidence and urban extension on risk.

  6. WorldWideScience.org: Bringing Light to Grey

    OpenAIRE

    Hitson, Brian A. (OSTI-DOE); Johnson, Lorrie A. (OSTI-DOE); GreyNet, Grey Literature Network Service

    2008-01-01

    WorldWideScience.org and its governance structure, the WorldWideScience Alliance, are putting a brighter spotlight on grey literature. Through this new tool, grey literature is getting broader exposure to audiences all over the world. Improved access to and sharing of research information is the key to accelerating progress and breakthroughs in any field, especially science. Includes: Conference preprint, Powerpoint presentation, Abstract and Biographical notes, Pratt student commentary ...

  7. CERN@school: bringing CERN into the classroom

    Science.gov (United States)

    Whyntie, T.; Cook, J.; Coupe, A.; Fickling, R. L.; Parker, B.; Shearer, N.

    2016-04-01

    CERN@school brings technology from CERN into the classroom to aid with the teaching of particle physics. It also aims to inspire the next generation of physicists and engineers by giving participants the opportunity to be part of a national collaboration of students, teachers and academics, analysing data obtained from detectors based on the ground and in space to make new, curiosity-driven discoveries at school. CERN@school is based around the Timepix hybrid silicon pixel detector developed by the Medipix 2 Collaboration, which features a 300 μm thick silicon sensor bump-bonded to a Timepix readout ASIC. This defines a 256-by-256 grid of pixels with a pitch of 55 μm, the data from which can be used to visualise ionising radiation in a very accessible way. Broadly speaking, CERN@school consists of a web portal that allows access to data collected by the Langton Ultimate Cosmic ray Intensity Detector (LUCID) experiment in space and the student-operated Timepix detectors on the ground; a number of Timepix detector kits for ground-based experiments, to be made available to schools for both teaching and research purposes; and educational resources for teachers to use with LUCID data and detector kits in the classroom. By providing access to cutting-edge research equipment, raw data from ground and space-based experiments, CERN@school hopes to provide the foundation for a programme that meets the many of the aims and objectives of CERN and the project's supporting academic and industrial partners. The work presented here provides an update on the status of the programme as supported by the UK Science and Technology Facilities Council (STFC) and the Royal Commission for the Exhibition of 1851. This includes recent results from work with the GridPP Collaboration on using grid resources with schools to run GEANT4 simulations of CERN@school experiments.

  8. Imaginative ethics--bringing ethical praxis into sharper relief.

    Science.gov (United States)

    Hansson, Mats G

    2002-01-01

    The empirical basis for this article is three years of experience with ethical rounds at Uppsala University Hospital. Three standard approaches of ethical reasoning are examined as potential explanations of what actually occurs during the ethical rounds. For reasons given, these are not found to be satisfying explanations. An approach called "imaginative ethics", is suggested as a more satisfactory account of this kind of ethical reasoning. The participants in the ethical rounds seem to draw on a kind of moral competence based on personal life experience and professional competence and experience. By listening to other perspectives and other experiences related to one particular patient story, the participants imagine alternative horizons of moral experience and explore a multitude of values related to clinical practice that might be at stake. In his systematic treatment of aesthetics in the Critique of Judgement, Kant made use of an operation of thought that, if applied to ethics, will enable us to be more sensitive to the particulars of each moral situation. Based on this reading of Kant, an account of imaginative ethics is developed in order to bring the ethical praxis of doctors and nurses into sharper relief. The Hebraic and the Hellenic traditions of imagination are used in order to illuminate some of the experiences of ethical rounds. In conclusion, it is argued that imaginative ethics and principle-based ethics should be seen as complementary in order to endow a moral discourse with ethical authority. Kantian ethics will do the job if it is remembered that Kant suggested only a modest, negative role of principle-based deliberation.

  9. Equity and what secondary science teachers bring to the classroom

    Science.gov (United States)

    Austin, Barbara Anne

    The demographics of people working in science-based careers do not match the demographics of the larger society. In particular, people who self-identify as Hispanic are underrepresented among working scientists. One reason may be the influence of formal schooling and more specifically, the behaviors of teachers in secondary science classrooms. This study looks at the practices of eight secondary science teachers at two schools at which 62% of the enrolled students declare their ethnicity as Hispanic. All of the teachers have at least three years of experience. Through interviews with the teachers, classroom observation, and interviews with other faculty, this research elucidates typical behaviors and attitudes surrounding teaching science in these settings. In spite of having a deficit view of their students, they all express interest in and concern about the students they teach. Their characterizations of teaching practices and classroom behaviors do not incorporate strategies designed to promote content learning through culturally relevant curriculum. Instead, they use mainstream-situated approaches that develop science content knowledge, vocabulary, procedures, and skills targeted toward high achievement on state and district standardized tests leading toward graduation or success in college. These approaches are consistent with a view of equity that increases the participation of underrepresented groups in science based careers in that it gives students the skills and knowledge they will need in order to successfully pursue these careers. Additionally, they behave in ways that are consistent with equitable strategies such as using inquiry based teaching, serving as role models, and providing a structured learning environment. This research informs the literature base for instructional systems designers by identifying what that teachers situated in culturally diverse classrooms bring to professional development programs targeted toward making secondary science

  10. Gender equity and tobacco control: bringing masculinity into focus.

    Science.gov (United States)

    Morrow, Martha; Barraclough, Simon

    2010-03-01

    Gender is a key but often overlooked--determinant of tobacco use, especially in Asia, where sex-linked differences in prevalence rates are very large. In this article we draw upon existing data to consider the implications of these patterns for gender equity and propose approaches to redress inequity through gender-sensitive tobacco control activities. International evidence demonstrates that, in many societies, risk behaviours (including tobacco use) are practised substantially more by men and boys, and are also viewed as expressions of masculine identity. While gender equity focuses almost exclusively on the relative disadvantage of girls and women that exists in most societies, disproportionate male use of tobacco has profound negative consequences for men (as users) and for women (nonusers). Surprisingly, health promotion and tobacco control literature rarely focus on the role of gender in health risks among boys and men. However, tobacco industry marketing has masterfully incorporated gender norms, and also other important cultural values, to ensure its symbols are context-specific. By addressing gender-specific risks within the local cultural context--as countries are enjoined to do within the Framework Convention's Guiding Principles--it may be possible to accelerate the impact of mechanisms such as tobacco pricing, restrictions on marketing, smoking bans and provision of accurate information. It is essential that we construct a new research-to-policy framework for gender-sensitive tobacco control. Successful control of tobacco can only be strengthened by bringing males, and the concept of gender as social construction, back into our research and discussion on health and gender equity.

  11. Future clinical trials in DIPG: bringing epigenetics to the clinic

    Directory of Open Access Journals (Sweden)

    Andres E. Morales La Madrid

    2015-07-01

    Full Text Available In spite of major recent advances in DIPG molecular characterization, this body of knowledge has not yet translated into better treatments.To date,more than 250 clinical trials evaluating radiotherapy along with conventional cytotoxic chemotherapy as well as newer biologic agents,have failed to improve the dismal outcome when compared to palliative radiation alone.The biology of DIPG remained unknown until recently when the neurosurgical expertise along with the recognition by the scientific and clinical community of the importance of tissue sampling at diagnosis;ideally in the context of a clinical trial and by trained neurosurgical teams to maximize patient safety.These pre-treatment tumor samples,and others coming from tissue obtained post-mortem,have yielded new insights into DIPG molecular biology.We now know that DIPG comprises a heterogeneous disease with variable molecular phenotypes, different from adult high grade glioma,other non-pontine pediatric high grade gliomas and even between pontine gliomas.The discovery of histone H3.3 or H3.1 mutations has been an important step forward in understanding tumor formation,maintenance and progression.Pharmacologic reversal of DIPG histone demethylation therefore offers an important potential intervention strategy for the treatment of DIPG.To date,clinical trials of newly diagnosed or progressive DIPG with epigenetic modifiers have been unsuccessful.Whether this failure represents limited activity of the agents used,their CNS penetration,redundant pathways within the tumor,or the possibility that histone mutations are necessary only to initiate DIPGs but not maintain their growth,suggest that a great deal still needs to be elucidated in both the underlying biology of these pathways,and the drugs designed to target them.In this review, we discuss the role of both epigenetic and genetic mutations within DIPG and the development of treatment strategies directed against the unique abnormalities

  12. Bringing natural behaviors into the laboratory: a tribute to Paul MacLean.

    Science.gov (United States)

    Blanchard, Robert J; Blanchard, D Caroline

    2003-08-01

    Paul MacLean's work has exemplified and encouraged an approach in which natural behaviors are elicited and investigated in laboratory settings. Our own experiences with bringing natural behaviors into the laboratory indicate that this is best achieved by providing the social and environmental stimuli necessary to support these behaviors and by an initial process of ethological/observational analysis of them. Examples discussed in support of these suggestions include the development of more natural habitats, including visible burrow systems (VBS), for fossorial rodents such as rats and mice; analysis of aggressive and defensive behaviors among social groups in such habitats and to introduced predators; and the development of defense test batteries in which individual defensive behaviors may be elicited through manipulations of threat and environmental stimuli. These situations have proved useful in analysis of the effects of drugs active against anxiety-related psychopathologies. However, an equally important use for them is in the analysis of normal defensive and aggressive behaviors. Detailed analysis of natural behaviors in socially and environmentally adequate situations provides an important link between molecular findings and both normal and pathological behavior patterns. Investigation of natural behaviors in adequate stimulus contexts does not represent an antiexperimental stance but one that supplements and enhances the generalizability of more conventional experimental laboratory approaches.

  13. tRNA's modifications bring order to gene expression.

    Science.gov (United States)

    Gustilo, Estella M; Vendeix, Franck Ap; Agris, Paul F

    2008-04-01

    The posttranscriptional modification of RNA is a significant investment in genes, enzymes, substrates, and energy. Advances in molecular genetics and structural biology indicate strongly that modifications of tRNA's anticodon domain control gene expression. Modifications at the anticodon's wobble position are required for recognition of rarely used codons and restrict or expand codon recognition depending on their chemistries. A shift of the translational reading frame occurs in the absence of modifications at either wobble position-34 or the conserved purine-37, 3'-adjacent to the anticodon, causing expression of alternate protein sequences. These modifications have in common their contribution of order to tRNA's anticodon.

  14. Tool steels

    DEFF Research Database (Denmark)

    Højerslev, C.

    2001-01-01

    On designing a tool steel, its composition and heat treatment parameters are chosen to provide a hardened and tempered martensitic matrix in which carbides are evenly distributed. In this condition the matrix has an optimum combination of hardness andtoughness, the primary carbides provide...... resistance against abrasive wear and secondary carbides (if any) increase the resistance against plastic deformation. Tool steels are alloyed with carbide forming elements (Typically: vanadium, tungsten, molybdenumand chromium) furthermore some steel types contains cobalt. Addition of alloying elements...... serves primarily two purpose (i) to improve the hardenabillity and (ii) to provide harder and thermally more stable carbides than cementite. Assuming proper heattreatment, the properties of a tool steel depends on the which alloying elements are added and their respective concentrations....

  15. Molecular Modeling

    Science.gov (United States)

    Holmes, Jon L.

    1999-06-01

    Molecular modeling has trickled down from the realm of pharmaceutical and research laboratories into the realm of undergraduate chemistry instruction. It has opened avenues for the visualization of chemical concepts that previously were difficult or impossible to convey. I am sure that many of you have developed exercises using the various molecular modeling tools. It is the desire of this Journal to become an avenue for you to share these exercises among your colleagues. It is to this end that Ron Starkey has agreed to edit such a column and to publish not only the description of such exercises, but also the software documents they use. The WWW is the obvious medium to distribute this combination and so accepted submissions will appear online as a feature of JCE Internet. Typical molecular modeling exercise: finding conformation energies. Molecular Modeling Exercises and Experiments is the latest feature column of JCE Internet, joining Conceptual Questions and Challenge Problems, Hal's Picks, and Mathcad in the Chemistry Curriculum. JCE Internet continues to seek submissions in these areas of interest and submissions of general interest. If you have developed materials and would like to submit them, please see our Guide to Submissions for more information. The Chemical Education Resource Shelf, Equipment Buyers Guide, and WWW Site Review would also like to hear about chemistry textbooks and software, equipment, and WWW sites, respectively. Please consult JCE Internet Features to learn more about these resources at JCE Online. Email Announcements Would you like to be informed by email when the latest issue of the Journal is available online? when a new JCE Software title is shipping? when a new JCE Internet article has been published or is available for Open Review? when your subscription is about to expire? A new feature of JCE Online makes this possible. Visit our Guestbook to learn how. When you submit the form on this page, which includes your email address

  16. How can scientists bring research to use: the HENVINET experience

    Directory of Open Access Journals (Sweden)

    Bartonova Alena

    2012-06-01

    Full Text Available Abstract Background Health concerns have driven the European environmental policies of the last 25 years, with issues becoming more complex. Addressing these concerns requires an approach that is both interdisciplinary and engages scientists with society. In response to this requirement, the FP6 coordination action “Health and Environment Network” HENVINET was set up to create a permanent inter-disciplinary network of professionals in the field of health and environment tasked to bridge the communication gap between science and society. In this paper we describe how HENVINET delivered on this task. Methods The HENVINET project approached the issue of inter-disciplinary collaboration in four ways. (1 The Drivers-Pressures-State-Exposure-Effect-Action framework was used to structure information gathering, collaboration and communication between scientists in the field of health and the environment. (2 Interactive web-based tools were developed to enhance methods for knowledge evaluation, and use these methods to formulate policy advice. (3 Quantification methods were adapted to measure scientific agreement. And (4 Open architecture web technology was used to develop an information repository and a web portal to facilitate collaboration and communication among scientists. Results Twenty-five organizations from Europe and five from outside Europe participated in the Health and Environment Network HENVINET, which lasted for 3.5 years. The consortium included partners in environmental research, public health and veterinary medicine; included medical practitioners and representatives of local administrations; and had access to national policy making and EEA and WHO expertise. Dedicated web-based tools for visualisation of environmental health issues and knowledge evaluation allowed remote expert elicitation, and were used as a basis for developing policy advice in five health areas (asthma and allergies; cancer; neurodevelopmental disorders

  17. Selective hair therapy: bringing science to the fiction.

    Science.gov (United States)

    Vogt, Annika; Blume-Peytavi, Ulrike

    2014-02-01

    Investigations on carrier-based drug delivery systems for higher selectivity in hair therapy have clearly evolved from dye release and model studies to highly sophisticated approaches, many of which specifically tackle hair indications and the delivery of hair-relevant molecules. Here, we group recent hair disease-oriented work into efforts towards (i) improved delivery of conventional drugs, (ii) delivery of novel drug classes, for example biomolecules and (iii) targeted delivery on the cellular/molecular level. Considering the solid foundation of experimental work, it does not take a large step outside the current box of thinking to follow the idea of using large carriers (>500 nm, unlikely to penetrate as a whole) for follicular penetration, retention and protection of sensitive compounds. Yet, reports on particles <200 nm being internalized by keratinocytes and dendritic cells at sites of barrier disruption (e.g., hair follicles) combined with recent advances in nanodermatology add interesting new facets to the possibilities carrier technologies could offer, for example, unprecedented levels of selectivity. The authors provide thought-provoking ideas on how smart delivery technologies and advances in our molecular understanding of hair pathophysiology could result in a whole new era of hair therapeutics. As the field still largely remains in preclinical investigation, determined efforts towards production of medical grade material and truly translational work are needed to demonstrate surplus value of carrier systems for clinical applications. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  18. Molecular beacon sequence design algorithm.

    Science.gov (United States)

    Monroe, W Todd; Haselton, Frederick R

    2003-01-01

    A method based on Web-based tools is presented to design optimally functioning molecular beacons. Molecular beacons, fluorogenic hybridization probes, are a powerful tool for the rapid and specific detection of a particular nucleic acid sequence. However, their synthesis costs can be considerable. Since molecular beacon performance is based on its sequence, it is imperative to rationally design an optimal sequence before synthesis. The algorithm presented here uses simple Microsoft Excel formulas and macros to rank candidate sequences. This analysis is carried out using mfold structural predictions along with other free Web-based tools. For smaller laboratories where molecular beacons are not the focus of research, the public domain algorithm described here may be usefully employed to aid in molecular beacon design.

  19. Augmented Reality as a Technology Bringing Interactivity to Print Products

    DEFF Research Database (Denmark)

    Seisto, Anu; Aikala, Maiju; Vatrapu, Ravi

    2012-01-01

    Augmented Reality (AR) is the technique of superimposing virtual objects in the user's view of the real world, providing a novel visualization technology for a wide range of applications. Hence, it is a user interface technology that combines the perception of real environments with digital......, virtual information. AR is also a promising tool for creating playfulness connected to printed items. In this study we present one example of creating an interactive and playful advertisement for a printed magazine by innovating possible outcomes together with a publisher (Aller), an advertiser (brand...

  20. ISSLIVE! Bringing the Space Station to Every Generation

    Science.gov (United States)

    Harris, Philip D.; Price, Jennifer B.; Severance, Mark; Blue, Regina; Khan, Ahmed; Healy, Matthew D.; Ehlinger, Jesse B.

    2011-01-01

    traditional education system, ISSLive! provides a single, interactive, and engaging experience to learn about the ISS and its role in space exploration, international collaboration, and science. While traditional students are using ISSLive! in the classroom, their parents, grandparents, and friends are using it at home. ISSLive! truly brings the daily operations of the ISS into the daily lives of the public from every generation.

  1. Kaiserschnitten Wien - Let's bring the forest in the city

    Directory of Open Access Journals (Sweden)

    Ajda Primožič

    2012-01-01

    Full Text Available The location is part of the Vienna River Valley, known as "Wiental", one of the most dissonant, incongruous, and contested areas of Vienna. Depending on one’s perspective, the Vienna River Valley can be viewed as a transit corridor, an unresolved urban area, an urban interface, an inter- zone, an infrastructure bundle, an ugly wound in the urban landscape, a socially charged boundary, etc. We started the project with urban pattern analyses on different scales: the scale of the city, the scale of Wiental (from Schönbrunn to Hofburg and on a minor scale, i.e. the scale of the project.The analysis showed that Wiental constitutes the main connection between the city centre and suburbia and the countryside in the background of the city. With its clear morphological importance, it could become a green axis of the city, a pleasant place for people, rather than having only an infrastructural role. Our concept is to bring new character to Wiental by making it a pedestrian- and cyclist-friendly green axis. Our initial goal was to reduce car traffic. We proposed introducing a park-and-ride system, which would become a point of transfer where car traffic is replaced by public transport and cycle traffic. Through the afforestation of Wiental, the area could become a park or recreational route, and the quality of life in the area would improve.An important aspect of the project was dealing with the Danube. We proposed to manage the flood peaks by introducing a dam, and after the point of regulation, we arranged the River into two levels: an ambient upper flow and infrastructural lower flow in the existing channel. Also, by rearranging "Naschmarkt" with the Danube uncovered, we predicted an extension of tourism from the city centre to Schönbrunn by bicycle or on foot, which could be followed by an expansion of the public programme. We wanted to show that the Danube, with an appropriate environment, could become a significant element of the city structure.

  2. Issues and Solutions for Bringing Heterogeneous Water Cycle Data Sets Together

    Science.gov (United States)

    Acker, James; Kempler, Steven; Teng, William; Belvedere, Deborah; Liu, Zhong; Leptoukh, Gregory

    2010-01-01

    The water cycle research community has generated many regional to global scale products using data from individual NASA missions or sensors (e.g., TRMM, AMSR-E); multiple ground- and space-based data sources (e.g., Global Precipitation Climatology Project [GPCP] products); and sophisticated data assimilation systems (e.g., Land Data Assimilation Systems [LDAS]). However, it is often difficult to access, explore, merge, analyze, and inter-compare these data in a coherent manner due to issues of data resolution, format, and structure. These difficulties were substantiated at the recent Collaborative Energy and Water Cycle Information Services (CEWIS) Workshop, where members of the NASA Energy and Water cycle Study (NEWS) community gave presentations, provided feedback, and developed scenarios which illustrated the difficulties and techniques for bringing together heterogeneous datasets. This presentation reports on the findings of the workshop, thus defining the problems and challenges of multi-dataset research. In addition, the CEWIS prototype shown at the workshop will be presented to illustrate new technologies that can mitigate data access roadblocks encountered in multi-dataset research, including: (1) Quick and easy search and access of selected NEWS data sets. (2) Multi-parameter data subsetting, manipulation, analysis, and display tools. (3) Access to input and derived water cycle data (data lineage). It is hoped that this presentation will encourage community discussion and feedback on heterogeneous data analysis scenarios, issues, and remedies.

  3. Bringing 3D Printing to Geophysical Science Education

    Science.gov (United States)

    Boghosian, A.; Turrin, M.; Porter, D. F.

    2014-12-01

    3D printing technology has been embraced by many technical fields, and is rapidly making its way into peoples' homes and schools. While there is a growing educational and hobbyist community engaged in the STEM focused technical and intellectual challenges associated with 3D printing, there is unrealized potential for the earth science community to use 3D printing to communicate scientific research to the public. Moreover, 3D printing offers scientists the opportunity to connect students and the public with novel visualizations of real data. As opposed to introducing terrestrial measurements through the use of colormaps and gradients, scientists can represent 3D concepts with 3D models, offering a more intuitive education tool. Furthermore, the tactile aspect of models make geophysical concepts accessible to a wide range of learning styles like kinesthetic or tactile, and learners including both visually impaired and color-blind students.We present a workflow whereby scientists, students, and the general public will be able to 3D print their own versions of geophysical datasets, even adding time through layering to include a 4th dimension, for a "4D" print. This will enable scientists with unique and expert insights into the data to easily create the tools they need to communicate their research. It will allow educators to quickly produce teaching aids for their students. Most importantly, it will enable the students themselves to translate the 2D representation of geophysical data into a 3D representation of that same data, reinforcing spatial reasoning.

  4. Design tools

    Science.gov (United States)

    Anton TenWolde; Mark T. Bomberg

    2009-01-01

    Overall, despite the lack of exact input data, the use of design tools, including models, is much superior to the simple following of rules of thumbs, and a moisture analysis should be standard procedure for any building envelope design. Exceptions can only be made for buildings in the same climate, similar occupancy, and similar envelope construction. This chapter...

  5. tRNA’s Modifications Bring Order to Gene Expression

    Science.gov (United States)

    Gustilo, Estella M.; Vendeix, Franck A.P.; Agris, Paul F.

    2008-01-01

    Summary The posttranscriptional modification of RNA is a significant investment in genes, enzymes, substrates, and energy. Advances in molecular genetics and structural biology indicate strongly that modifications of tRNA’s anticodon domain control gene expression. Modifications at the anticodon’s wobble position are required for recognition of rarely used codons, and restrict or expand codon recognition depending on their chemistries. A shift of the translational reading frame occurs in the absence of modifications at either wobble position-34 or the conserved purine-37, 3’-adjacent to the anticodon, causing expression of alternate protein sequences. These modifications have in common their contribution of order to tRNA’s anticodon. PMID:18378185

  6. Dynamics of mathematical models in biology bringing mathematics to life

    CERN Document Server

    Zazzu, Valeria; Guarracino, Mario

    2016-01-01

    This volume focuses on contributions from both the mathematics and life science community surrounding the concepts of time and dynamicity of nature, two significant elements which are often overlooked in modeling process to avoid exponential computations. The book is divided into three distinct parts: dynamics of genomes and genetic variation, dynamics of motifs, and dynamics of biological networks. Chapters included in dynamics of genomes and genetic variation analyze the molecular mechanisms and evolutionary processes that shape the structure and function of genomes and those that govern genome dynamics. The dynamics of motifs portion of the volume provides an overview of current methods for motif searching in DNA, RNA and proteins, a key process to discover emergent properties of cells, tissues, and organisms. The part devoted to the dynamics of biological networks covers networks aptly discusses networks in complex biological functions and activities that interpret processes in cells. Moreover, chapters i...

  7. CSR – A marketing tool?

    Directory of Open Access Journals (Sweden)

    Silvia- Ştefania MIHALACHE

    2011-03-01

    Full Text Available Starting from the idea that investing in CSR creates value not only for the company’s stakeholders, but especially for the company itself, in this article, using secondary data analysis, we try to answer the question: is CSR a sign of responsibility or just a marketing tool for promoting the business? The purpose of this paper is to bring contributions in highlighting the nature of the connection between CSR and Marketing, using the secondary data analyze of the annual reports of some companies. Companies that usually use the annual report as a marketing or communication tool for voluntary disclosure of non financial information to their various stakeholders, including shareholders, employees, customers, suppliers, media and government, and to develop a particular brand image for the organization although the report is sometimes a financial one.

  8. From the Moon: Bringing Space Science to Diverse Audiences

    Science.gov (United States)

    Runyon, C. J.; Hall, C.; Joyner, E.; Meyer, H. M.; M3 Science; E/PO Team

    2011-12-01

    NASA's Apollo missions held a place in the mindset of many Americans - we dared to go someplace where humans had never set foot, a place unknown and beyond our imaginations. These early NASA missions and discoveries resulted in an enhanced public understanding of the Moon. Now, with the human element so far removed from space exploration, students must rely on textbooks, TV's, and computers to build their understanding of our Moon. However, NASA educational materials about the Moon are stale and out-of-date. In addition, they do not effectively address 21st Century Skills, an essential for today's classrooms. Here, we present a three-part model for developing opportunities in lunar science education professional development that is replicable and sustainable and integrates NASA mission-derived data (e.g., Moon Mineralogy Mapper (M3)/Chandrayaan-1). I) With the return of high resolution/high spatial data from M3/Chandrayaan-1, we can now better explore and understand the compositional variations on the lunar surface. Data and analysis techniques from the imaging spectrometer are incorporated into the M3 Educator's Guide: Seeing the Moon in a New Light. The guide includes an array of activities and lessons to help educators and students understand how NASA is currently exploring the Moon. The guide integrates NASA maps and data into the interactive lessons, bringing the excitement of scientific exploration and discovery into the classroom. II) Utilizing the M3 Educator's Guide as well as educational activities from more current NASA lunar missions, we offer two sustained professional development opportunities for educators to explore the Moon through interactive and creative strategies. 1) Geology of the Moon, an online course offered through Montana State University's National Teacher Enhancement Network, is a 3-credit graduate course. 2) Fly Me to the Moon, offered through the College of Charleston's Office of Professional Development in Education, is a two

  9. SciServer Compute brings Analysis to Big Data in the Cloud

    Science.gov (United States)

    Raddick, Jordan; Medvedev, Dmitry; Lemson, Gerard; Souter, Barbara

    2016-06-01

    SciServer Compute uses Jupyter Notebooks running within server-side Docker containers attached to big data collections to bring advanced analysis to big data "in the cloud." SciServer Compute is a component in the SciServer Big-Data ecosystem under development at JHU, which will provide a stable, reproducible, sharable virtual research environment.SciServer builds on the popular CasJobs and SkyServer systems that made the Sloan Digital Sky Survey (SDSS) archive one of the most-used astronomical instruments. SciServer extends those systems with server-side computational capabilities and very large scratch storage space, and further extends their functions to a range of other scientific disciplines.Although big datasets like SDSS have revolutionized astronomy research, for further analysis, users are still restricted to downloading the selected data sets locally - but increasing data sizes make this local approach impractical. Instead, researchers need online tools that are co-located with data in a virtual research environment, enabling them to bring their analysis to the data.SciServer supports this using the popular Jupyter notebooks, which allow users to write their own Python and R scripts and execute them on the server with the data (extensions to Matlab and other languages are planned). We have written special-purpose libraries that enable querying the databases and other persistent datasets. Intermediate results can be stored in large scratch space (hundreds of TBs) and analyzed directly from within Python or R with state-of-the-art visualization and machine learning libraries. Users can store science-ready results in their permanent allocation on SciDrive, a Dropbox-like system for sharing and publishing files. Communication between the various components of the SciServer system is managed through SciServer‘s new Single Sign-on Portal.We have created a number of demos to illustrate the capabilities of SciServer Compute, including Python and R scripts

  10. Bringing New Families to the Museum One Baby at a Time

    Science.gov (United States)

    Herman, Alicia

    2012-01-01

    "Bring Your Baby to the Danforth Museum of Art" is a program for mothers. Unlike other museum programs that focus on the needs of children, Bring Your Baby caters to the intellectual interests of the adult parent. Parents learn about artworks, play with babies in a beautiful environment, and socialize with other families. The program is…

  11. 36 CFR 1280.18 - May I bring guns or other weapons onto NARA property?

    Science.gov (United States)

    2010-07-01

    ... 36 Parks, Forests, and Public Property 3 2010-07-01 2010-07-01 false May I bring guns or other weapons onto NARA property? 1280.18 Section 1280.18 Parks, Forests, and Public Property NATIONAL ARCHIVES... Conduct on NARA Property? Prohibited Activities § 1280.18 May I bring guns or other weapons onto NARA...

  12. CEREBELLUM DEVELOPMENTAL CHALLENGES: FROM MORPHOLOGY TO MOLECULAR ISSUES

    Directory of Open Access Journals (Sweden)

    Andrei Cosma ¹

    2017-10-01

    Full Text Available INTRODUCTION: It is known that, throughout the development of the nervous system, the cellular migratory routes are an important part of its expansion; therefore, the cerebellum is ‘sprinkled’ with cellular changes during its growth. The aim of this study was to analyse the morphological features of the cerebellum cells in all the layers, during its development. MATERIAL AND METHODS: We examined 14 cases of human cerebellum, ranging between 1 month to 12 years by histopathology and immunohistochemistry. RESULTS: Haematoxylin and eosin staining method confirmed the age-linked migration of the cells from the external granular layer into the internal granular layer. Moreover, immunohistochemical evaluation using PROX1 and NFAP showed positivity for the Purkinje cells. However, these cells exposed negativity on NSE stained specimens. On the other hand, the transience of the EGL was analysed using OCT3/4, which showed the migration of the EGL cells through the molecular layer to the IGL. Also, GFAP and NFAP proved to be a useful tool for the identification of the climbing fibres and the variation of their density connected the age of the patient. CONCLUSIONS: The human cerebellum undergoes different morphological and molecular changes throughout its evolution during embryogenesis. The markers used in our study have proved to present a differential, stage-dependant reactivity and appeared as useful tools for the identification of different cerebellar structures. Our study is a challenging attempt to understand the basics of cerebellar development at a morphological and molecular level and may bring new perspectives for a better approach of cerebellar associated pathologies.

  13. Cerebellum developmental challenges: From morphology to molecular issues

    Directory of Open Access Journals (Sweden)

    Andrei Cosma

    2017-06-01

    Full Text Available Introduction: It is known that, throughout the development of the nervous system, the cellular migratory routes are an important part of its expansion; therefore, the cerebellum is ‘sprinkled’ with cellular changes during its growth. The aim of this study was to analyse the morphological features of the cerebellum cells in all the layers, during its development. Material and methods: We examined 14 cases of human cerebellum, ranging between 1 to 12 months by histopathology and immunohistochemistry. Results: Haematoxylin and eosin staining method confirmed the age-linked migration of the cells from the external granular layer into the internal granular layer. Moreover, immunohistochemical evaluation using PROX1 and NFAP showed positivity for the Purkinje cells. However, these cells exposed negativity on NSE stained specimens. On the other hand, the transience of the EGL was analyzed using OCT3/4, which showed the migration of the EGL cells through the molecular layer to the IGL. Also, GFAP and NFAP proved to be a useful tool for the identification of the climbing fibres and the variation of their density connected the age of the patient. Conclusions: The human cerebellum undergoes different morphological and molecular changes throughout its evolution during embryogenesis. The markers used in our study have proved to present a differential, stage-dependant reactivity and appeared as useful tools for the identification of different cerebellar structures. Our study is a challenging attempt to understand the basics of cerebellar development at a morphological and molecular level and may bring new perspectives for a better approach of cerebellar associated pathologies.

  14. Can mouse imaging studies bring order to autism connectivity chaos?

    Directory of Open Access Journals (Sweden)

    Adam Liska

    2016-11-01

    Full Text Available Functional Magnetic Resonance Imaging (fMRI has consistently highlighted impaired or aberrant functional connectivity across brain regions of autism spectrum disorder (ASD patients. However, the manifestation and neural substrates of these alterations are highly heterogeneous and often conflicting. Moreover, their neurobiological underpinnings and etiopathological significance remain largely unknown. A deeper understanding of the complex pathophysiological cascade leading to aberrant connectivity in ASD can greatly benefit from the use of model organisms where individual pathophysiological or phenotypic components of ASD can be recreated and investigated via approaches that are either off limits or confounded by clinical heterogeneity. Despite some obvious limitations in reliably modelling the full phenotypic spectrum of a complex developmental disorder like ASD, mouse models have played a central role in advancing our basic mechanistic and molecular understanding of this syndrome. Recent progress in mouse brain connectivity mapping via resting-state fMRI (rsfMRI offers the opportunity to generate and test mechanistic hypotheses about the elusive origin and significance of connectional aberrations observed in autism. Here we discuss recent progress towards this goal, and illustrate initial examples of how the approach can be employed to establish causal links between ASD-related mutations, developmental processes, and brain connectional architecture. As the spectrum of genetic and pathophysiological components of ASD modelled in the mouse is rapidly expanding, the use of rsfMRI can advance our mechanistic understanding of the origin and significance of the connectional alterations associated with autism, and their heterogeneous expression across patient cohorts.

  15. Bringing patient centricity to diabetes medication access in Canada

    Directory of Open Access Journals (Sweden)

    Glennie JL

    2016-10-01

    “ahead of the curve” when it comes to diabetes care. Improving access to medications is one of the tools for getting there. Canada’s “call to action” for diabetes starts with effective implementation of existing best practices. A personalized approach to medication access, to meet individual needs and optimize outcomes, is also a key enabler. PWD and prescribers need reimbursement approaches that allow them to use existing tools (ie, medications and supplies to manage diabetes in a timely manner and to avoid and/or delay major downstream complications. Keywords: diabetes, patient-centered care, reimbursement, policy, pharmaceuticals, health technology assessment

  16. Magnetismo Molecular (Molecular Magentism)

    Energy Technology Data Exchange (ETDEWEB)

    Reis, Mario S [Universidade Federal Fluminense, Brasil; Moreira Dos Santos, Antonio F [ORNL

    2010-07-01

    The new synthesis processes in chemistry open a new world of research, new and surprising materials never before found in nature can now be synthesized and, as a wonderful result, observed a series of physical phenomena never before imagined. Among these are many new materials the molecular magnets, the subject of this book and magnetic properties that are often reflections of the quantum behavior of these materials. Aside from the wonderful experience of exploring something new, the theoretical models that describe the behavior these magnetic materials are, in most cases, soluble analytically, which allows us to know in detail the physical mechanisms governing these materials. Still, the academic interest in parallel this subject, these materials have a number of properties that are promising to be used in technological devices, such as in computers quantum magnetic recording, magnetocaloric effect, spintronics and many other devices. This volume will journey through the world of molecular magnets, from the structural description of these materials to state of the art research.

  17. Windows Developer Power Tools Turbocharge Windows development with more than 170 free and open source tools

    CERN Document Server

    Avery, James

    2007-01-01

    Software developers need to work harder and harder to bring value to their development process in order to build high quality applications and remain competitive. Developers can accomplish this by improving their productivity, quickly solving problems, and writing better code. A wealth of open source and free software tools are available for developers who want to improve the way they create, build, deploy, and use software. Tools, components, and frameworks exist to help developers at every point in the development process. Windows Developer Power Tools offers an encyclopedic guide to m

  18. Bringing ecosystem services into integrated water resources management.

    Science.gov (United States)

    Liu, Shuang; Crossman, Neville D; Nolan, Martin; Ghirmay, Hiyoba

    2013-11-15

    In this paper we propose an ecosystem service framework to support integrated water resource management and apply it to the Murray-Darling Basin in Australia. Water resources in the Murray-Darling Basin have been over-allocated for irrigation use with the consequent degradation of freshwater ecosystems. In line with integrated water resource management principles, Australian Government reforms are reducing the amount of water diverted for irrigation to improve ecosystem health. However, limited understanding of the broader benefits and trade-offs associated with reducing irrigation diversions has hampered the planning process supporting this reform. Ecosystem services offer an integrative framework to identify the broader benefits associated with integrated water resource management in the Murray-Darling Basin, thereby providing support for the Government to reform decision-making. We conducted a multi-criteria decision analysis for ranking regional potentials to provide ecosystem services at river basin scale. We surveyed the wider public about their understanding of, and priorities for, managing ecosystem services and then integrated the results with spatially explicit indicators of ecosystem service provision. The preliminary results of this work identified the sub-catchments with the greatest potential synergies and trade-offs of ecosystem service provision under the integrated water resources management reform process. With future development, our framework could be used as a decision support tool by those grappling with the challenge of the sustainable allocation of water between irrigation and the environment. Crown Copyright © 2013. Published by Elsevier Ltd. All rights reserved.

  19. Nanoinformatics knowledge infrastructures: bringing efficient information management to nanomedical research

    Science.gov (United States)

    de la Iglesia, D; Cachau, R E; García-Remesal, M; Maojo, V

    2014-01-01

    Nanotechnology represents an area of particular promise and significant opportunity across multiple scientific disciplines. Ongoing nanotechnology research ranges from the characterization of nanoparticles and nanomaterials to the analysis and processing of experimental data seeking correlations between nanoparticles and their functionalities and side effects. Due to their special properties, nanoparticles are suitable for cellular-level diagnostics and therapy, offering numerous applications in medicine, e.g. development of biomedical devices, tissue repair, drug delivery systems and biosensors. In nanomedicine, recent studies are producing large amounts of structural and property data, highlighting the role for computational approaches in information management. While in vitro and in vivo assays are expensive, the cost of computing is falling. Furthermore, improvements in the accuracy of computational methods (e.g. data mining, knowledge discovery, modeling and simulation) have enabled effective tools to automate the extraction, management and storage of these vast data volumes. Since this information is widely distributed, one major issue is how to locate and access data where it resides (which also poses data-sharing limitations). The novel discipline of nanoinformatics addresses the information challenges related to nanotechnology research. In this paper, we summarize the needs and challenges in the field and present an overview of extant initiatives and efforts. PMID:24932210

  20. Tangible display systems: bringing virtual surfaces into the real world

    Science.gov (United States)

    Ferwerda, James A.

    2012-03-01

    We are developing tangible display systems that enable natural interaction with virtual surfaces. Tangible display systems are based on modern mobile devices that incorporate electronic image displays, graphics hardware, tracking systems, and digital cameras. Custom software allows the orientation of a device and the position of the observer to be tracked in real-time. Using this information, realistic images of surfaces with complex textures and material properties illuminated by environment-mapped lighting, can be rendered to the screen at interactive rates. Tilting or moving in front of the device produces realistic changes in surface lighting and material appearance. In this way, tangible displays allow virtual surfaces to be observed and manipulated as naturally as real ones, with the added benefit that surface geometry and material properties can be modified in real-time. We demonstrate the utility of tangible display systems in four application areas: material appearance research; computer-aided appearance design; enhanced access to digital library and museum collections; and new tools for digital artists.

  1. THE OMC IN THE EUROPEAN EMPLOYMENT POLICY: BRINGING SOCIALISATION IN

    Directory of Open Access Journals (Sweden)

    Matia Vannoni

    2011-06-01

    Full Text Available This paper argues in favour of a more thorough analysis of a specific set of dynamics taking place in the Open Method of Coordination (OMC, the latter being conceived as an informal organizational framework aimed at mutual learning (de Burca and Zeitlin, 2003 and policy change (Dolowitz and Marsh, 2000; Radaelli, 2000. The aim of this paper is to uncover the missing link between these two elements, which has hitherto been black -boxed by the literature. Theoretical tools from International Relations (IR theories (i.e. constructivist institutionalism are borrowed in order to circumvent such a fallacy. The premises are the same as the ones hitherto employed by scholars studying the OMC (e.g. Jacobsson, 2004: can norms and values assume a binding character even outside the ‘territorially bounded democratic government’ (Héritier and Lehmkuhl, 2008 and thus leading to policy change? If so, how does this phenomenon take place? Nevertheless, the approach is different, in that it builds on two closely interrelated factors: the concept of socialisation with its micro-processes (Johnston, 2001; Johnston, 2008 and the institutional characteristics of social environments (Rogowski, 1999. Accordingly, this paper will address the question: is the OMC in European employment policy a social environment conducive of socialisation?

  2. Planetary Simulation Chambers bring Mars to laboratory studies

    Energy Technology Data Exchange (ETDEWEB)

    Mateo-Marti, E.

    2016-07-01

    Although space missions provide fundamental and unique knowledge for planetary exploration, they are always costly and extremely time-consuming. Due to the obvious technical and economical limitations of in-situ planetary exploration, laboratory simulations are among the most feasible research options for making advances in planetary exploration. Therefore, laboratory simulations of planetary environments are a necessary and complementary option to expensive space missions. Simulation chambers are economical, more versatile, and allow for a higher number of experiments than space missions. Laboratory-based facilities are able to mimic the conditions found in the atmospheres and on the surfaces of a majority of planetary objects. Number of relevant applications in Mars planetary exploration will be described in order to provide an understanding about the potential and flexibility of planetary simulation chambers systems: mainly, stability and presence of certain minerals on Mars surface; and microorganisms potential habitability under planetary environmental conditions would be studied. Therefore, simulation chambers will be a promising tools and necessary platform to design future planetary space mission and to validate in-situ measurements from orbital or rover observations. (Author)

  3. Bringing androgens up a NOTCH in breast cancer.

    Science.gov (United States)

    Tarulli, Gerard A; Butler, Lisa M; Tilley, Wayne D; Hickey, Theresa E

    2014-08-01

    While it has been known for decades that androgen hormones influence normal breast development and breast carcinogenesis, the underlying mechanisms have only been recently elucidated. To date, most studies have focused on androgen action in breast cancer cell lines, yet these studies represent artificial systems that often do not faithfully replicate/recapitulate the cellular, molecular and hormonal environments of breast tumours in vivo. It is critical to have a better understanding of how androgens act in the normal mammary gland as well as in in vivo systems that maintain a relevant tumour microenvironment to gain insights into the role of androgens in the modulation of breast cancer development. This in turn will facilitate application of androgen-modulation therapy in breast cancer. This is particularly relevant as current clinical trials focus on inhibiting androgen action as breast cancer therapy but, depending on the steroid receptor profile of the tumour, certain individuals may be better served by selectively stimulating androgen action. Androgen receptor (AR) protein is primarily expressed by the hormone-sensing compartment of normal breast epithelium, commonly referred to as oestrogen receptor alpha (ERa (ESR1))-positive breast epithelial cells, which also express progesterone receptors (PRs) and prolactin receptors and exert powerful developmental influences on adjacent breast epithelial cells. Recent lineage-tracing studies, particularly those focussed on NOTCH signalling, and genetic analysis of cancer risk in the normal breast highlight how signalling via the hormone-sensing compartment can influence normal breast development and breast cancer susceptibility. This provides an impetus to focus on the relationship between androgens, AR and NOTCH signalling and the crosstalk between ERa and PR signalling in the hormone-sensing component of breast epithelium in order to unravel the mechanisms behind the ability of androgens to modulate breast cancer

  4. Euarchontan Opsin Variation Brings New Focus to Primate Origins.

    Science.gov (United States)

    Melin, Amanda D; Wells, Konstans; Moritz, Gillian L; Kistler, Logan; Orkin, Joseph D; Timm, Robert M; Bernard, Henry; Lakim, Maklarin B; Perry, George H; Kawamura, Shoji; Dominy, Nathaniel J

    2016-04-01

    Debate on the adaptive origins of primates has long focused on the functional ecology of the primate visual system. For example, it is hypothesized that variable expression of short- (SWS1) and middle-to-long-wavelength sensitive (M/LWS) opsins, which confer color vision, can be used to infer ancestral activity patterns and therefore selective ecological pressures. A problem with this approach is that opsin gene variation is incompletely known in the grandorder Euarchonta, that is, the orders Scandentia (treeshrews), Dermoptera (colugos), and Primates. The ancestral state of primate color vision is therefore uncertain. Here, we report on the genes (OPN1SW and OPN1LW) that encode SWS1 and M/LWS opsins in seven species of treeshrew, including the sole nocturnal scandentian Ptilocercus lowii. In addition, we examined the opsin genes of the Central American woolly opossum (Caluromys derbianus), an enduring ecological analogue in the debate on primate origins. Our results indicate: 1) retention of ultraviolet (UV) visual sensitivity in C. derbianus and a shift from UV to blue spectral sensitivities at the base of Euarchonta; 2) ancient pseudogenization of OPN1SW in the ancestors of P. lowii, but a signature of purifying selection in those of C. derbianus; and, 3) the absence of OPN1LW polymorphism among diurnal treeshrews. These findings suggest functional variation in the color vision of nocturnal mammals and a distinctive visual ecology of early primates, perhaps one that demanded greater spatial resolution under light levels that could support cone-mediated color discrimination. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  5. [Molecular pathology: applications of molecular biology in pathological anatomy].

    Science.gov (United States)

    Wistuba, I I

    2001-07-01

    The rapid development of molecular biology techniques as well as recent progress in the understanding of genetic and molecular basis of human diseases have had enormous impact in the practice of clinical pathology. Since new diagnostic (molecular) tools are now available, the concept of Molecular Pathology is emerging. Molecular Pathology is defined by the use of molecular biology techniques and the type of specimens that are involved in its practice, basically ARN and ADN, extracted from cytological and tissue specimens. Although most methods used in molecular pathology and their applications are still under investigation and clinical validation they have great potential in several areas of pathological diagnosis, particularly on infectious and neoplastic diseases. Introduction of these techniques in pathology laboratories in our country should significantly enhance the diagnostic and research skills in the field.

  6. SeaView: bringing EarthCube to the Oceanographer

    Science.gov (United States)

    Stocks, K. I.; Diggs, S. C.; Arko, R. A.; Kinkade, D.; Shepherd, A.

    2016-12-01

    As new instrument types are developed, and new observational programs start, that support a growing community of "dry" oceanographers, the ability to find, access, and visualize existing data of interest becomes increasingly critical. Yet ocean data, when available, is are held in multiple data facilities, in different formats, and accessible through different pathways. This creates practical problems with integrating and working across different data sets. The SeaView project is building connections between the rich data resources in five major oceanographic data facilities - BCO-DMO, CCHDO, OBIS, OOI, and R2R* - creating a federated set of thematic data collections that are organized around common characteristics (geographic location, time, expedition, program, data type, etc.) and published online in Web Accessible Folders using standard file formats such as ODV and NetCDF. The work includes not simply reformatting data, but identifying and, where possible, addressing interoperability challenges: which common identifiers for core concepts can connect data across repositories, which terms a scientist may want to search that, if added to the data repositories, will increase discoverability; the presence of duplicate data across repositories, etc. We will present the data collections available to date, including data from the OOI Pioneer Array region, and seek scientists' input on the data types and formats they prefer, the tools they use to analyze and visualize data, and their specific recommendations for future data collections to support oceanographic science. * Biological and Chemical Oceanography Data Management Office (BCO-DMO), CLIVAR and Carbon Hydrographic Data Office (CCHDO), International Ocean Biogeographic Information System (iOBIS), Ocean Observatories Initiative (OOI), and Rolling Deck to Repository (R2R) Program.

  7. Molecular Programming with DNA

    Science.gov (United States)

    Winfree, Erik

    2009-05-01

    Information can be stored in molecules and processed by molecular reactions. Molecular information processing is at the heart of all biological systems; might it soon also be at the heart of non-biological synthetic chemical systems? Perhaps yes. One technological approach comes from DNA nanotechnology and DNA computing, where DNA is used as a non-biological informational polymer that can be rationally designed to create a rich class of molecular systems -- for example, DNA molecules that self-assemble precisely, that fold into complex nanoscale objects, that act as mechanical actuators and molecular motors, and that make decisions based on digital and analog logic. I will argue that to fully exploit their design potential, we will need to invent programming languages for specifying the behavior of information-based molecular systems, to create theoretical tools for understanding and analyzing the behavior of molecular programs, to develop compilers that automate the design of molecules with the desired behaviors, and to expand experimental techniques so that the implementation and debugging of complex molecular systems becomes as commonplace and practical as computer programming.

  8. Molecular hematology

    National Research Council Canada - National Science Library

    Provan, Drew; Gribben, John

    2010-01-01

    ... The molecular basis of hemophilia, 219 Paul LF Giangrande 4 The genetics of acute myeloid leukemias, 42 Carolyn J Owen & Jude Fitzgibbon 19 The molecular basis of von Willebrand disease, 233 Luciano Baronc...

  9. Reviewing Molecular Clouds

    Science.gov (United States)

    Fernandez Lopez, Manuel

    2017-07-01

    The star formation process involves a wide range of spatial scales, densities and temperatures. Herschel observations of the cold and low density molecular gas extending tens of parsecs, that constitutes the bulk of the molecular clouds of the Milky Way, have shown a network of dense structures in the shape of filaments. These filaments supposedly condense into higher density clumps to form individual stars or stellar clusters. The study of the kinematics of the filaments through single-dish observations suggests the presence of gas flows along the filaments, oscillatory motions due to gravity infall, and the existence of substructure inside filaments that may be threaded by twisted fibers. A few molecular clouds have been mapped with interferometric resolutions bringing more insight into the filament structure. Compression due to large-scale supersonic flows is the preferred mechanism to explain filament formation although the exact nature of the filaments, their origin and evolution are still not well understood. Determining the turbulence drivers behind the origin of the filaments, the relative importance of turbulence, gravity and magnetic fields on regulating the filament structure and evolution, and providing detailed insight on the substructure inside the filaments are among the current open questions in this research area.

  10. Beyond the shape: molecular systematics and phytopathological diagnostic

    Directory of Open Access Journals (Sweden)

    Giuseppe Firrao

    2008-04-01

    Full Text Available Crop protection can be implemented by several strategies, among them prophylaxis guarantees profitable productions and a slight environmental impact. Diagnosis of pathogens exploited different strategies, according to the organisms to be detected. Historically, fungi have been identified by morphological characters, bacteria by physiological tests and viruses by symptoms on indexing plants. Immunological assays (devised to detect bacteria and viruses at first, and nucleic acid based assays (available for all biotic pathogens later, reduced strategy discrepancies. The fast evolution in regulation and techniques that we are living nowadays, deeply changed the terms. It is, now,possible to identify all the pathogens affecting a crop in a single sample (multiplexing and to examine a high number of samples at a time.We can state that there is no pathogen that cannot be identified through assays that guarantee the sensitivity and the specificity required by certification schemes, eradication procedures and quarantine protocols. The same fast technical evolution renders the exploitation of the new sophisticate and powerful tools more and more cheap and simple. At the present stage, a deeper knowledge of the biology and the epidemiology of plant pathogens changes the problem from technical to conceptual. Conventional fungal taxonomy is no more apt to depict frameworks to house the biological complexity of fungal pathogens; molecular phylogeny opened new horizons and posed new questions. Molecular systematics can bring into harmony systematic schemes, biological complexity and phytopathological aspects. To explain concepts, examples including toxigenic Fusarium and Diaporthe helianthi, as a quarantine pathogen, will be discussed.

  11. Bringing Society to a Changing Polar Ocean: Polar Interdisciplinary Coordinated Education (ICE)

    Science.gov (United States)

    Schofield, O.

    2015-12-01

    Environmental changes in the Arctic and Antarctic appear to be accelerating and scientists are trying to understand both the patterns and the impacts of change. These changes will have profound impact on humanity and create a need for public education about these critical habitats. We have focused on a two-pronged strategy to increase public awareness as well as enable educators to discuss comfortably the implications of climate change. Our first focus is on entraining public support through the development of science documentaries about the science and people who conduct it. Antarctic Edge is a feature length award-winning documentary about climate change that has been released in May 2015 and has garnered interest in movie theatres and on social media stores (NetFlix, ITunes). This broad outreach is coupled with our group's interest assisting educators formally. The majority of current polar education is focused on direct educator engagement through personal research experiences that have impact on the participating educators' classrooms. Polar Interdisciplinary Coordinated Education (ICE) proposes to improve educator and student engagement in polar sciences through exposure to scientists and polar data. Through professional development and the creation of data tools, Polar ICE will reduce the logistical costs of bringing polar science to students in grades 6-16. We will provide opportunities to: 1) build capacity of polar scientists in communicating and engaging with diverse audiences; 2) create scalable, in-person and virtual opportunities for educators and students to engage with polar scientists and their research through data visualizations, data activities, educator workshops, webinars, and student research symposia; and 3) evaluate the outcomes of Polar ICE and contribute to our understanding of science education practices. We will use a blended learning approach to promote partnerships and cross-disciplinary sharing. This combined multi-pronged approach

  12. SEA Change: Bringing together Science, Engineering and the Arts at the University of Florida

    Science.gov (United States)

    Perfit, M. R.; Mertz, M. S.; Lavelli, L.

    2014-12-01

    A group of interested and multifaceted faculty, administrators and students created the Science, Engineering, Arts Committee (SEA Change) two years ago at the University of Florida (UF). Recognizing that innovative ideas arise from the convergence of divergent thinkers, the committee seeks to bring together faculty in Science, Engineering, the Arts and others across campus to develop and disseminate innovative ideas for research, teaching and service that will enhance the campus intellectual environment. We meet regularly throughout the year as faculty with graduate and undergraduate students to catalyze ideas that could lead to collaborative or interdisciplinary projects and make recommendations to support innovative, critical and creative work. As an example, the Department of Geological Sciences and the School of Art and Art History collaborated on a competition among UF undergraduate painting students to create artistic works that related to geoscience. Each student gathered information from Geological Sciences faculty members to use for inspiration in creating paintings along with site-specific proposals to compete for a commission. The winning work was three-story high painting representing rock strata and the Florida environment entitled "Prairie Horizontals" that is now installed in the Geoscience building entrance atrium. Two smaller paintings of the second place winner, depicting geologists in the field were also purchased and displayed in a main hallway. Other activities supported by SEA Change have included a collaborative work of UF engineering and dance professors who partnered for the Creative Storytelling and Choreography Lab, to introduce basic storytelling tools to engineering students. A campus-wide gathering of UF faculty and graduate students titled Creative Practices: The Art & Science of Discovery featured guest speakers Steven Tepper, Victoria Vesna and Benjamin Knapp in spring 2014. The Committee plans to develop and foster ideas that will

  13. Molecular mechanics application in inorganic Chemistry

    Directory of Open Access Journals (Sweden)

    Coelho Lilian Weitzel

    1999-01-01

    Full Text Available The present paper is a review about basic principles of the molecular mechanics that is the most important tool used in molecular modeling area, and their applications to the calculation of the relative stability and chemical reactivity of organometalic and coordination compounds. We show how molecular mechanics can be successfully applied to a wide variety of inorganic systems.

  14. Bringing Together Users and Developers of Forest Biomass Maps

    Science.gov (United States)

    Brown, Molly Elizabeth; Macauley, Molly K.

    2012-01-01

    Forests store carbon and thus represent important sinks for atmospheric carbon dioxide. Reducing uncertainty in current estimates of the amount of carbon in standing forests will improve precision of estimates of anthropogenic contributions to carbon dioxide in the atmosphere due to deforestation. Although satellite remote sensing has long been an important tool for mapping land cover, until recently aboveground forest biomass estimates have relied mostly on systematic ground sampling of forests. In alignment with fiscal year 2010 congressional direction, NASA has initiated work toward a carbon monitoring system (CMS) that includes both maps of forest biomass and total carbon flux estimates. A goal of the project is to ensure that the products are useful to a wide community of scientists, managers, and policy makers, as well as to carbon cycle scientists. Understanding the needs and requirements of these data users is helpful not just to the NASA CMS program but also to the entire community working on carbon-related activities. To that end, this meeting brought together a small group of natural resource managers and policy makers who use information on forests in their work with NASA scientists who are working to create aboveground forest biomass maps. These maps, derived from combining remote sensing and ground plots, aim to be more accurate than current inventory approaches when applied at local and regional scales. Meeting participants agreed that users of biomass information will look to the CMS effort not only to provide basic data for carbon or biomass measurements but also to provide data to help serve a broad range of goals, such as forest watershed management for water quality, habitat management for biodiversity and ecosystem services, and potential use for developing payments for ecosystem service projects. Participants also reminded the CMS group that potential users include not only public sector agencies and nongovernmental organizations but also the

  15. Bringing Science out of the Lab into the Classroom

    Science.gov (United States)

    2006-03-01

    Science is moving more rapidly than ever; one groundbreaking discovery chases the next at an incredible speed. School teachers have trouble keeping up with the pace, and many pupils call science classes "boring". Today, Europe's major research organisations launch Science in School, the first international, multidisciplinary journal for innovative science teaching, to provide a platform for communication between science teachers, practising scientists and other stakeholders in science education. ESO PR Photo 12/06 ESO PR Photo 12/06 First Issue! "Science is becoming increasingly international and interdisciplinary," says Eleanor Hayes, editor of the journal. "The most exciting development of the day may happen anywhere in any field: students may suddenly want to talk about a discovery on Mars, a medical breakthrough or a natural disaster. On such days it would be a shame not to put the textbooks aside and to capitalise on that curiosity." Published by EIROforum, a partnership between Europe's seven largest intergovernmental research organisations, Science in School will bridge the gap between the worlds of research and schools. One extremely powerful tool to achieve this is the journal's web-based discussion forum that will establish a direct dialogue between science teachers and researchers across national and subject boundaries. Science in School will appear quarterly online and in print and will feature news about the latest scientific discoveries, teaching materials, interviews with inspiring teachers and scientists, reviews of books, films and websites, suggestions for class trips, training opportunities and many other useful resources for science teachers. Contributors to the first issue include the world-renowned neurologist and author Oliver Sachs, and scientists and teachers from nine countries. "We urgently need to engage young people in science. This is why the research community and the European Commission are committed to outreach and education

  16. Pressure profiles of the BRing based on the simulation used in the CSRm

    Energy Technology Data Exchange (ETDEWEB)

    Wang, J.C., E-mail: wangjiachen@impcas.ac.cn [Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Li, P., E-mail: lipeng@impcas.ac.cn [Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China); Yang, J.C.; Yuan, Y.J. [Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China); Wu, B. [Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Chai, Z.; Luo, C. [Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China); Dong, Z.Q. [Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Zheng, W.H. [Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China); Zhao, H.; Ruan, S.; Wang, G.; Liu, J.; Chen, X.; Wang, K.D.; Qin, Z.M. [Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Yin, B. [Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China)

    2017-07-11

    HIAF-BRing, a new multipurpose accelerator facility of the High Intensity heavy-ion Accelerator Facility project, requires an extremely high vacuum lower than 10{sup −11} mbar to fulfill the requirements of radioactive beam physics and high energy density physics. To achieve the required process pressure, the bench-marked codes of VAKTRAK and Molflow+ are used to simulate the pressure profiles of the BRing system. In order to ensure the accuracy of the implementation of VAKTRAK, the computational results are verified by measured pressure data and compared with a new simulation code BOLIDE on the current synchrotron CSRm. Since the verification of VAKTRAK has been done, the pressure profiles of the BRing are calculated with different parameters such as conductance, out-gassing rates and pumping speeds. According to the computational results, the optimal parameters are selected to achieve the required pressure for the BRing.

  17. Interactive exploratory data analysis tool in Alzheimer’s disease

    Directory of Open Access Journals (Sweden)

    Diana Furcila

    2015-04-01

    Thus, MorExAn provide us the possibility to relate histopathological data with neuropsychological and clinical variables. The aid of this interactive visualization tool brings us the possibility to find unexpected conclusions beyond the insight provided by simple statistics analysis, as well as to improve neuroscientists’ productivity.

  18. Molecular and Morphological Tools to Distinguish Scyphophorus acupunctatus Gyllenhal, 1838 (Curculionidae: Dryophthorinae): A New Weevil Pest of the Endangered Century Plant, Agave eggersiana from St. Croix, U.S. Virgin Islands

    Science.gov (United States)

    M. Lourdes Chamorro; Joshua Persson; Christian W. Torres-Santana; Jeff Keularts; Sonja J. Scheffer; Matthew L. Lewis

    2016-01-01

    The agave snout weevil (AGW) or sisal weevil, Scyphophorus acupunctatus Gyllenhal is here reported for the first time in St. Croix, U.S. Virgin Islands (USVI) where it threatens Agave eggersiana Trel., a USVI endemic and endangered century-plant. We provide molecular, morphological, and behavioral characters to successfully distinguish the two known Scyphophorus...

  19. Combined normal-phase and reversed-phase liquid chromatography/ESI-MS as a tool to determine the molecular diversity of A-type procyanidins in peanut skins

    NARCIS (Netherlands)

    Appeldoorn, M.M.; Vincken, J.P.; Sanders, M.B.; Hollman, P.C.H.; Gruppen, H.

    2009-01-01

    Peanut skins, a byproduct of the peanut butter industry, are a rich source of proanthocyanidins, which might be used in food supplements. Data on the molecular diversity of proanthocyanidins in peanut skins is limited and conflicting with respect to the ratio of double- (A-type) versus single-linked

  20. Molecular imaging as a tool to investigate heterogeneity of advanced HER2-positive breast cancer and to predict patient outcome under trastuzumab emtansine (T-DM1) : the ZEPHIR trial

    NARCIS (Netherlands)

    Gebhart, G.; Lamberts, L. E.; Wimana, Z.; Garcia, C.; Emonts, P.; Ameye, L.; Stroobants, S.; Huizing, M.; Aftimos, P.; Tol, J.; Oyen, W. J. G.; Vugts, D. J.; Hoekstra, O. S.; Schroder, C. P.; van Oordt, C. W. Menke-van der Houven; Guiot, T.; Brouwers, A. H.; Awada, A.; de Vries, E. G. E.; Flamen, P.

    Molecular imaging of metastatic human epidermal growth factor receptor 2 (HER2)-positive breast cancer reveals marked intra- and interpatient heterogeneity in HER2 mapping, which correlates with clinical outcome under T-DM1 therapy.Only human epidermal growth factor receptor (HER)2 status determined

  1. Molecular imaging as a tool to investigate heterogeneity of advanced HER2-positive breast cancer and to predict patient outcome under trastuzumab emtansine (T-DM1): the ZEPHIR trial

    NARCIS (Netherlands)

    Gebhart, G.; Lamberts, L.E.; Wimana, Z.; Garcia, C.; Emonts, P.; Ameye, L.; Stroobants, S.; Huizing, M.; Aftimos, P.; Tol, J.; Oyen, W.J.G.; Vugts, D.J.; Hoekstra, O.S.; Schroder, C.P.; Oordt, C.W. Menke-van der H; Guiot, T.; Brouwers, A.H.; Awada, A.; Vries, E.G. de; Flamen, P.

    2016-01-01

    BACKGROUND: Only human epidermal growth factor receptor (HER)2 status determined by immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) has been validated to predict efficacy of HER2-targeting antibody-drug-conjugate trastuzumab emtansine (T-DM1). We propose molecular imaging to

  2. Workshop on the Application of Genomic Tools for the Rapid Molecular Characterization of Bacterial Isolates in Food-borne Disease Outbreak Investigations Ottawa, ON, February 24-25, 2014

    Science.gov (United States)

    2014-05-01

    and food/environmental isolate of Listeria monocytogenes collected in the U.S. Future plans include partnering with more organizations that have...and pathogenicity islands harbouring host colonization factors. There is evidence that other food pathogens such as Listeria monocytogenes strains...to MLVA, to WGS : How to Make Food Safer ........................................... 8 Use of Molecular Markers for Characterization of Food-Borne

  3. Software engineering methodologies and tools

    Science.gov (United States)

    Wilcox, Lawrence M.

    1993-01-01

    Over the years many engineering disciplines have developed, including chemical, electronic, etc. Common to all engineering disciplines is the use of rigor, models, metrics, and predefined methodologies. Recently, a new engineering discipline has appeared on the scene, called software engineering. For over thirty years computer software has been developed and the track record has not been good. Software development projects often miss schedules, are over budget, do not give the user what is wanted, and produce defects. One estimate is there are one to three defects per 1000 lines of deployed code. More and more systems are requiring larger and more complex software for support. As this requirement grows, the software development problems grow exponentially. It is believed that software quality can be improved by applying engineering principles. Another compelling reason to bring the engineering disciplines to software development is productivity. It has been estimated that productivity of producing software has only increased one to two percent a year in the last thirty years. Ironically, the computer and its software have contributed significantly to the industry-wide productivity, but computer professionals have done a poor job of using the computer to do their job. Engineering disciplines and methodologies are now emerging supported by software tools that address the problems of software development. This paper addresses some of the current software engineering methodologies as a backdrop for the general evaluation of computer assisted software engineering (CASE) tools from actual installation of and experimentation with some specific tools.

  4. Theoretical Molecular Biophysics

    CERN Document Server

    Scherer, Philipp

    2010-01-01

    "Theoretical Molecular Biophysics" is an advanced study book for students, shortly before or after completing undergraduate studies, in physics, chemistry or biology. It provides the tools for an understanding of elementary processes in biology, such as photosynthesis on a molecular level. A basic knowledge in mechanics, electrostatics, quantum theory and statistical physics is desirable. The reader will be exposed to basic concepts in modern biophysics such as entropic forces, phase separation, potentials of mean force, proton and electron transfer, heterogeneous reactions coherent and incoherent energy transfer as well as molecular motors. Basic concepts such as phase transitions of biopolymers, electrostatics, protonation equilibria, ion transport, radiationless transitions as well as energy- and electron transfer are discussed within the frame of simple models.

  5. Molecular pharmacognosy.

    Science.gov (United States)

    Huang, LuQi; Xiao, PeiGen; Guo, LanPing; Gao, WenYuan

    2010-06-01

    This article analyzes the background and significance of molecular pharmacognosy, including the molecular identification of medicinal raw materials, phylogenetic evolution of medicinal plants and animals, evaluation and preservation of germplasm resources for medicinal plants and animals, etiology of endangerment and protection of endangered medicinal plants and animals, biosynthesis and bioregulation of active components in medicinal plants, and characteristics and the molecular bases of top-geoherbs.

  6. Molecular Gastronomy

    OpenAIRE

    Burke, Roisin; This, Herve; Kelly, Alan

    2016-01-01

    Molecular gastronomy may be defined as the scientific discipline that explores the phenomena occurring during culinary transformations. In contrast with traditional approaches of food science and technology, which considered mostly the chemistry, physics, or biology of food ingredients and industrial transformations, the focus is on phenomena occurring during the preparation of dishes. Applications building on the principles of molecular gastronomy, such as ‘Molecular Cooking’ and ‘Note-by-No...

  7. VisANT: an online visualization and analysis tool for biological interaction data

    Directory of Open Access Journals (Sweden)

    DeLisi Charles

    2004-02-01

    Full Text Available Abstract Background New techniques for determining relationships between biomolecules of all types – genes, proteins, noncoding DNA, metabolites and small molecules – are now making a substantial contribution to the widely discussed explosion of facts about the cell. The data generated by these techniques promote a picture of the cell as an interconnected information network, with molecular components linked with one another in topologies that can encode and represent many features of cellular function. This networked view of biology brings the potential for systematic understanding of living molecular systems. Results We present VisANT, an application for integrating biomolecular interaction data into a cohesive, graphical interface. This software features a multi-tiered architecture for data flexibility, separating back-end modules for data retrieval from a front-end visualization and analysis package. VisANT is a freely available, open-source tool for researchers, and offers an online interface for a large range of published data sets on biomolecular interactions, including those entered by users. This system is integrated with standard databases for organized annotation, including GenBank, KEGG and SwissProt. VisANT is a Java-based, platform-independent tool suitable for a wide range of biological applications, including studies of pathways, gene regulation and systems biology. Conclusion VisANT has been developed to provide interactive visual mining of biological interaction data sets. The new software provides a general tool for mining and visualizing such data in the context of sequence, pathway, structure, and associated annotations. Interaction and predicted association data can be combined, overlaid, manipulated and analyzed using a variety of built-in functions. VisANT is available at http://visant.bu.edu.

  8. Molecular dynamics

    NARCIS (Netherlands)

    Bergstra, J.A.; Bethke, I.

    2002-01-01

    Molecular dynamics is a model for the structure and meaning of object based programming systems. In molecular dynamics the memory state of a system is modeled as a fluid consisting of a collection of molecules. Each molecule is a collection of atoms with bindings between them. A computation is

  9. Bringing Terra Science to the People: 10 years of education and public outreach

    Science.gov (United States)

    Riebeek, H.; Chambers, L. H.; Yuen, K.; Herring, D.

    2009-12-01

    The default image on Apple's iPhone is a blue, white, green and tan globe: the Blue Marble. The iconic image was produced using Terra data as part of the mission's education and public outreach efforts. As far-reaching and innovative as Terra science has been over the past decade, Terra education and public outreach efforts have been equally successful. This talk will provide an overview of Terra's crosscutting education and public outreach projects, which have reached into educational facilities—classrooms, museums, and science centers, across the Internet, and into everyday life. The Earth Observatory web site was the first web site designed for the public that told the unified story of what we can learn about our planet from all space-based platforms. Initially conceived as part of Terra mission outreach in 1999, the web site has won five Webby awards, the highest recognition a web site can receive. The Visible Earth image gallery is a catalogue of NASA Earth imagery that receives more than one million page views per month. The NEO (NASA Earth Observations) web site and WMS (web mapping service) tool serves global data sets to museums and science centers across the world. Terra educational products, including the My NASA Data web service and the Students' Cloud Observations Online (S'COOL) project, bring Terra data into the classroom. Both projects target multiple grade levels, ranging from elementary school to graduate school. S'COOL uses student observations of clouds to help validate Terra data. Students and their parents have puzzled over weekly "Where on Earth" geography quizzes published on line. Perhaps the most difficult group to reach is the large segment of the public that does not seek out science information online or in a science museum or classroom. To reach these people, EarthSky produced a series of podcasts and radio broadcasts that brought Terra science to more than 30 million people in 2009. Terra imagery, including the Blue Marble, have

  10. Bringing Legacy Visualization Software to Modern Computing Devices via Application Streaming

    Science.gov (United States)

    Fisher, Ward

    2014-05-01

    Planning software compatibility across forthcoming generations of computing platforms is a problem commonly encountered in software engineering and development. While this problem can affect any class of software, data analysis and visualization programs are particularly vulnerable. This is due in part to their inherent dependency on specialized hardware and computing environments. A number of strategies and tools have been designed to aid software engineers with this task. While generally embraced by developers at 'traditional' software companies, these methodologies are often dismissed by the scientific software community as unwieldy, inefficient and unnecessary. As a result, many important and storied scientific software packages can struggle to adapt to a new computing environment; for example, one in which much work is carried out on sub-laptop devices (such as tablets and smartphones). Rewriting these packages for a new platform often requires significant investment in terms of development time and developer expertise. In many cases, porting older software to modern devices is neither practical nor possible. As a result, replacement software must be developed from scratch, wasting resources better spent on other projects. Enabled largely by the rapid rise and adoption of cloud computing platforms, 'Application Streaming' technologies allow legacy visualization and analysis software to be operated wholly from a client device (be it laptop, tablet or smartphone) while retaining full functionality and interactivity. It mitigates much of the developer effort required by other more traditional methods while simultaneously reducing the time it takes to bring the software to a new platform. This work will provide an overview of Application Streaming and how it compares against other technologies which allow scientific visualization software to be executed from a remote computer. We will discuss the functionality and limitations of existing application streaming

  11. Molecular genetics in aquaculture

    Directory of Open Access Journals (Sweden)

    Liliana Di Stasio

    2010-01-01

    Full Text Available Great advances in molecular genetics have deeply changed the way of doing research in aquaculture, as it has already done in other fields. The molecular revolution started in the 1980’s, thanks to the widespread use of restriction enzymes and Polymerase Chain Reaction technology, which makes it possible to easily detect the genetic variability directly at the DNA level. In aquaculture, the molecular data are used for several purposes, which can be clustered into two main groups. The first one, focused on individuals, includes the sex identification and parentage assignment, while the second one, focused on populations, includes the wide area of the genetic characterization, aimed at solving taxonomic uncertainties, preserving genetic biodiversity and detecting genetic tags. For the future, the increase in the number of molecular markers and the construction of high density genetic maps, as well as the implementation of genomic resources (including genome sequencing, are expected to provide tools for the genetic improvement of aquaculture species through Marked Assisted Selection. In this review the characteristics of different types of molecular markers, along with their applications to a variety of aquaculture issues are presented.

  12. Molecular imaging. Fundamentals and applications

    Energy Technology Data Exchange (ETDEWEB)

    Tian, Jie (ed.) [Chinese Academy of Sciences, Beijing (China). Intelligent Medical Research Center

    2013-07-01

    Covers a wide range of new theory, new techniques and new applications. Contributed by many experts in China. The editor has obtained the National Science and Technology Progress Award twice. ''Molecular Imaging: Fundamentals and Applications'' is a comprehensive monograph which describes not only the theory of the underlying algorithms and key technologies but also introduces a prototype system and its applications, bringing together theory, technology and applications. By explaining the basic concepts and principles of molecular imaging, imaging techniques, as well as research and applications in detail, the book provides both detailed theoretical background information and technical methods for researchers working in medical imaging and the life sciences. Clinical doctors and graduate students will also benefit from this book.

  13. Value Innovation in Learner-Centered Design. How to Develop Valuable Learning Tools

    Science.gov (United States)

    Breuer, Henning; Schwarz, Heinrich; Feller, Kristina; Matsumoto, Mitsuji

    2014-01-01

    This paper shows how to address technological, cultural and social transformations with empirically grounded innovation. Areas in transition such as higher education and learning techniques today bring about new needs and opportunities for innovative tools and services. But how do we find these tools? The paper argues for using a strategy of…

  14. Sensitive Detection of Competitive Molecular Adsorption by Surface-Enhanced Raman Spectroscopy.

    Science.gov (United States)

    Altun, Ali O; Bond, Tiziana; Pronk, Wouter; Park, Hyung Gyu

    2017-07-18

    Surface adsorption plays a critical role in a wide variety of fields from surface catalysis to molecular separation. Despite the importance, limited access to simultaneously sensitive and selective detection mechanisms has hampered the acquisition of comprehensive and versatile experimental data needed to understand the complex aspects of mixture adsorption, calling for a molecular detection method capable of obtaining the surface adsorption isotherms over a wide range of concentrations as well as distinguishing the competitive adsorption of different adsorbates. Here, we test surface-enhanced Raman spectroscopy (SERS) as an effective analysis tool of surface adsorption phenomena. Using a sensitive SERS substrate, we characterize the adsorption isotherms of chemical species of various binding energies. We obtained the isotherms for strongly binding species in a concentration range from subpicomolar to micromolar. A log-sigmoidal dependency of the SERS signals to the analyte concentration could be modeled by surface binding theories accurately using molecular dynamics simulations, thereby bringing out the potential capability of sensitive SERS for describing a single-compound adsorption process. SERS also enabled the determination of competitive adsorption isotherms from a multiple-compound solution for the first time. The successful demonstration of the sensitive and selective characterization of surface adsorption lends SERS adaptability to a cheap, facile, and effective solution for chemical analysis.

  15. The Engaged Microbiologist: Bringing the Microbiological Sciences to the K–12 Community

    Directory of Open Access Journals (Sweden)

    David J. Westenberg

    2015-12-01

    Full Text Available Exposing K–12 students to cutting edge science that impacts their daily lives can bring classroom lessons to life. Citizen-science projects are an excellent way to bring high-level science to the classroom and help satisfy one of the cornerstone concepts of the Next Generation Science Standards (NGSS, “engaging in practices that scientists and engineers actually use.” This can be a daunting task for teachers who may lack the background or resources to integrate these projects into the classroom. This is where scientific societies such as the American Society for Microbiology (ASM can play a critical role. ASM encourages its members to engage with the K–12 community by providing networking opportunities and resources for ASM members and K–12 teachers to work together to bring microbiology into the classroom.

  16. Molecular geometry

    CERN Document Server

    Rodger, Alison

    1995-01-01

    Molecular Geometry discusses topics relevant to the arrangement of atoms. The book is comprised of seven chapters that tackle several areas of molecular geometry. Chapter 1 reviews the definition and determination of molecular geometry, while Chapter 2 discusses the unified view of stereochemistry and stereochemical changes. Chapter 3 covers the geometry of molecules of second row atoms, and Chapter 4 deals with the main group elements beyond the second row. The book also talks about the complexes of transition metals and f-block elements, and then covers the organometallic compounds and trans

  17. Molecular Haeckel.

    Science.gov (United States)

    Elinson, Richard P; Kezmoh, Lorren

    2010-07-01

    More than a century ago, Ernst Haeckel created embryo drawings to illustrate the morphological similarity of vertebrate early embryos. These drawings have been both widely presented and frequently criticized. At the same time that the idea of morphological similarity was recently attacked, there has been a growing realization of molecular similarities in the development of tissues and organs. We have surveyed genes expressed in vertebrate embryos, and we have used them to construct drawings that we call Molecular Haeckels. The Molecular Haeckels emphasize that, based on gene expression, there is a greater similarity among vertebrate embryos than even Haeckel might have imagined. (c) 2010 Wiley-Liss, Inc.

  18. Molecular electronic-structure theory

    CERN Document Server

    Helgaker, Trygve; Olsen, Jeppe

    2014-01-01

    Ab initio quantum chemistry has emerged as an important tool in chemical research and is appliced to a wide variety of problems in chemistry and molecular physics. Recent developments of computational methods have enabled previously intractable chemical problems to be solved using rigorous quantum-mechanical methods. This is the first comprehensive, up-to-date and technical work to cover all the important aspects of modern molecular electronic-structure theory. Topics covered in the book include: * Second quantization with spin adaptation * Gaussian basis sets and molecular-integral evaluati

  19. Data Redistribution through MY NASA DATA: Striving to bring authentic NASA data into education

    Science.gov (United States)

    Lewis, P. M.; Oostra, D.; Oots, P.; Chambers, L. H.; Moore, S.; Crecelius, S.; Taylor, J.

    2012-12-01

    The Mentoring and inquirY using NASA Data on Atmospheric and Earth science for Teachers and Amateurs (MY NASA DATA or MND) project was launched in 2004 to bring authentic data into K-12 education. The MND website features a Live Access Server (LAS), an open source tool which allows users to customize data sets to suit their individual needs, choosing from among 200 global Level 3 data sets. Approximately 120 lesson plans that utilize the available parameters are offered to help teachers and students get started with data exploration. Grade appropriate data documentation is also provided (with continual efforts to improve it to better meet the needs of this target audience). Through inquiry and lesson utilization, educators have several connection points to the data. As classrooms shift to problem-based and inquiry learning, the need for a data visualizer/server increases. Through numerous and growing connections to NASA satellite missions, and with access to data as a built-in feature, MND effectively fills this niche to provide a first level of data re-use that is friendly to the K-12 community. Offering a wide variety of data sets allows MND to support many science topics within the K-12 curriculum while extending the use of scientific data from NASA Earth science satellites. Lessons, created by educators across the country, allow MND to connect with the classroom teacher and to meet their data needs. As technology continues to evolve, a second level of data re-use becomes both interesting and possible. Thus, the MND team is now exploring new web and mobile platforms that can be built and distributed on an accelerated time cycle to keep up with information technology developments. With implementation of these new platforms come challenges in promoting new items to the education community, the public, and other potential users. Included in the list of challenges are: ever-evolving technology, prediction of the market, web/mobile platforms, and time-to-market for

  20. An introduction to Molecular Biology (Omics) in Food Microbiology

    NARCIS (Netherlands)

    Brul, S.; Batt, C.A.; Tortorello, M.L.

    2014-01-01

    Molecular biological tools are developing in biology at a dazzling pace. These omics tools cover full genome sequencing (originally coined genomics), genomewide transcript analysis (transcriptomics), full protein analysis (proteomics), as well as the analysis of cellular or organism metabolism

  1. Molecular Origami

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 5; Issue 9. Molecular Origami - Modular Construction of Platonic Solids as Models for Reversible Assemblies. Subramania Ranganathan. General Article Volume 5 Issue 9 September 2000 pp 82-91 ...

  2. CoC GIS Tools (GIS Tool)

    Data.gov (United States)

    Department of Housing and Urban Development — This tool provides a no-cost downloadable software tool that allows users to interact with professional quality GIS maps. Users access pre-compiled projects through...

  3. Molecular Evolution in Historical Perspective.

    Science.gov (United States)

    Suárez-Díaz, Edna

    2016-12-01

    In the 1960s, advances in protein chemistry and molecular genetics provided new means for the study of biological evolution. Amino acid sequencing, nucleic acid hybridization, zone gel electrophoresis, and immunochemistry were some of the experimental techniques that brought about new perspectives to the study of the patterns and mechanisms of evolution. New concepts, such as the molecular evolutionary clock, and the discovery of unexpected molecular phenomena, like the presence of repetitive sequences in eukaryotic genomes, eventually led to the realization that evolution might occur at a different pace at the organismic and the molecular levels, and according to different mechanisms. These developments sparked important debates between defendants of the molecular and organismic approaches. The most vocal confrontations focused on the relation between primates and humans, and the neutral theory of molecular evolution. By the 1980s and 1990s, the construction of large protein and DNA sequences databases, and the development of computer-based statistical tools, facilitated the coming together of molecular and evolutionary biology. Although in its contemporary form the field of molecular evolution can be traced back to the last five decades, the field has deep roots in twentieth century experimental life sciences. For historians of science, the origins and consolidation of molecular evolution provide a privileged field for the study of scientific debates, the relation between technological advances and scientific knowledge, and the connection between science and broader social concerns.

  4. Kinesiophobia – Introducing a New Diagnostic Tool

    Science.gov (United States)

    Knapik, Andrzej; Saulicz, Edward; Gnat, Rafał

    2011-01-01

    Technical development of human civilisation brings about a decrease of adaptation potential of an individual, which is directly linked to deficient motor activity. Only precise identification of factors leading to hypokinesia would make prophylactic and therapeutic actions possible. In this article, authors would like to introduce a new, original tool aiming at diagnosing limitations of motor activity in adults. They propose a synthetic diagnosis of hypokinesia in two domains: biological and psycho-social, which is based on the contemporary model of health. PMID:23487514

  5. Teaching molecular genetics: Chapter 1--Background principles and methods of molecular biology.

    Science.gov (United States)

    Knoers, Nine V A M; Monnens, Leo A H

    2006-02-01

    In this first chapter of the series "Teaching molecular genetics," an introduction to molecular genetics is presented. We describe the structure of DNA and genes and explain in detail the central dogma of molecular biology, that is, the flow of genetic information from DNA via RNA to polypeptide (protein). In addition, several basic and frequently used general molecular tools, such as restriction enzymes, Southern blotting, DNA amplification and sequencing are discussed, in order to lay the foundations for the forthcoming chapters.

  6. Scanning Electron Microscopy and Energy-Dispersive X-Ray Spectroscopy as a Valuable Tool to Investigate the Ultra-High-Molecular-Weight Polyethylene Wear Mechanisms and Debris in Hip Implants.

    Science.gov (United States)

    Schappo, Henrique; Gindri, Izabelle M; Cubillos, Patrícia O; Maru, Marcia M; Salmoria, Gean V; Roesler, Carlos R M

    2018-01-01

    The use of scanning electron microscopy (SEM) and energy-dispersive spectrometry (EDS) was investigated to understand the wear mechanisms from a metal-on-polyethylene bearing couple. Morphological features of femoral head acetabular liner, and isolated particles resulting from hip wear testing were evaluated. EDS was proposed to investigate the polymeric nature of the particles isolated from the wear testing. In this work, 28-mm conventional ultra-high-molecular-weight polyethylene acetabular liners paired with metallic heads were tested in a hip wear simulator over 2 million cycles. SEM-EDS was employed to investigate wear mechanisms on hip implant components and associated wear debris. SEM showed worn surfaces for both hip components, and a significant volume of ultra-high-molecular-weight polyethylene wear particles resulting from hip wear testing. Particles were classified into 3 groups, which were then correlated to wear mechanisms. Group I had particles with smooth surfaces, group II consisted of particles with rough surfaces, and group III comprised aggregate-like particles. Group I EDS revealed that particles from groups I and II had a high C/O ratio raising a concern about the particle source. On the other hand, particles from group III had a low C/O ratio, supporting the hypothesis that they resulted from the wear of acetabular liner. Most of particles identified in group III were in the biologically active size range (0.3 to 20 μm). The use of optical and electron microscopy enabled the morphological characterization of worn surfaces and wear debris, while EDS was essential to elucidate the chemical composition of isolated debris. Copyright © 2017 Elsevier Inc. All rights reserved.

  7. Bring Your Own Device Technology: Preliminary Results from a Mixed Methods Study to Explore Student Experience of In-Class Response Systems in Post-Secondary Education

    Directory of Open Access Journals (Sweden)

    Matthew Numer

    2015-02-01

    Full Text Available This research examines the effectiveness of Bring Your Own Device (BYOD technology in a postsecondary classroom. Despite recent advances in the technological tools available to educators, there is a significant gap in the literature regarding student efficacy, engagement and contribution to learning. This paper will present the preliminary findings of the first phases of an evaluation project measuring student interaction with BYOD technology in a large group setting. Employing a mixed methods design, the findings from two focus groups and two online surveys will be discussed. This project involved students in the Winter and Fall 2014 semesters of a fourth year Human Sexuality course which has enrolment of approximately 400 per semester. The findings suggest that BYOD technology contributes to student engagement and participation in the classroom setting. Further, the findings suggest that students are comfortable in using this tool, and perceived the experience as enjoyable.

  8. MIPs as Tools in Environmental Biotechnology.

    Science.gov (United States)

    Mattiasson, Bo

    2015-01-01

    Molecular imprints are potentially fantastic constructions. They are selective, robust, and nonbiodegradable if produced from stable polymers. A range of different applications has been presented, everything from separation of enantiomers, via adsorbents for sample preparation before analysis to applications in wastewater treatment. This chapter deals with molecularly imprinted polymers (MIPs) as tools in environmental biotechnology, a field that has the potential to become very important in the future.

  9. Designing molecular nano-architectures on metals and on graphene

    NARCIS (Netherlands)

    Gottardi, Stefano

    2015-01-01

    Nano-engineering of molecular two-dimensional materials brings exciting opportunities to achieve novel and tunable surface functionalities. Among these nanomaterials, graphene (a single-layer of carbon atoms) and supramolecular architectures on surfaces are the central topic of this thesis. Scanning

  10. Molecular fountain.

    Energy Technology Data Exchange (ETDEWEB)

    Strecker, Kevin E.; Chandler, David W.

    2009-09-01

    A molecular fountain directs slowly moving molecules against gravity to further slow them to translational energies that they can be trapped and studied. If the molecules are initially slow enough they will return some time later to the position from which they were launched. Because this round trip time can be on the order of a second a single molecule can be observed for times sufficient to perform Hz level spectroscopy. The goal of this LDRD proposal was to construct a novel Molecular Fountain apparatus capable of producing dilute samples of molecules at near zero temperatures in well-defined user-selectable, quantum states. The slowly moving molecules used in this research are produced by the previously developed Kinematic Cooling technique, which uses a crossed atomic and molecular beam apparatus to generate single rotational level molecular samples moving slowly in the laboratory reference frame. The Kinematic Cooling technique produces cold molecules from a supersonic molecular beam via single collisions with a supersonic atomic beam. A single collision of an atom with a molecule occurring at the correct energy and relative velocity can cause a small fraction of the molecules to move very slowly vertically against gravity in the laboratory. These slowly moving molecules are captured by an electrostatic hexapole guiding field that both orients and focuses the molecules. The molecules are focused into the ionization region of a time-of-flight mass spectrometer and are ionized by laser radiation. The new molecular fountain apparatus was built utilizing a new design for molecular beam apparatus that has allowed us to miniaturize the apparatus. This new design minimizes the volumes and surface area of the machine allowing smaller pumps to maintain the necessary background pressures needed for these experiments.

  11. Bring Your Own Device to Secondary School: The Perceptions of Teachers, Students and Parents

    Science.gov (United States)

    Parsons, David; Adhikar, Janak

    2016-01-01

    This paper reports on the first two years of a Bring Your Own Device (BYOD) initiative in a New Zealand secondary school, using data derived from a series of surveys of teachers, parents and students, who are the main stakeholders in the transformation to a BYOD school. In this paper we analyse data gathered from these surveys, which consists…

  12. Bring-Your-Own-Device: Turning Cell Phones into Forces for Good

    Science.gov (United States)

    Imazeki, Jennifer

    2014-01-01

    Over the last few years, classroom response systems (or "clickers") have become increasingly common. Although most systems require students to use a standalone handheld device, bring-your-own-device (BYOD) systems allow students to use devices they already own (e.g., a cell phone, tablet or laptop) to submit responses via text message or…

  13. Five Ways to Hack and Cheat with Bring-Your-Own-Device Electronic Examinations

    Science.gov (United States)

    Dawson, Phillip

    2016-01-01

    Bring-your-own-device electronic examinations (BYOD e-exams) are a relatively new type of assessment where students sit an in-person exam under invigilated conditions with their own laptop. Special software restricts student access to prohibited computer functions and files, and provides access to any resources or software the examiner approves.…

  14. An Empirical Study towards Understanding User Acceptance of Bring Your Own Device (BYOD) in Higher Education

    Science.gov (United States)

    Cheng, Gary; Guan, Yuanyuan; Chau, Juliana

    2016-01-01

    This paper discusses the findings of a research study investigating user acceptance of bring your own device (BYOD) practice to support teaching and learning in a Hong Kong university. Forty-four undergraduate students and two teachers participated in the study. To collect their ratings of agreement with respect to several BYOD-related issues,…

  15. The Wild-Card Character of "Bring Your Own:" A Panel Discussion

    Science.gov (United States)

    Campbell, W. Gardner; Fitch, Megan; German, Robert F., Jr.; Hulvey, Dale; McIntosh, Keith; McPherson, Michael R.; O'Keefe, John

    2013-01-01

    Panelists on the front lines of higher education information technology share their thoughts on Bring Your Own Device (BYOD) and what it could mean for colleges and universities. Five questions were asked of each panelist. These were: (1) How strategically important to higher education is the BYOD phenomenon? Is it simply a passing fad? (2) Should…

  16. Take heart in an initiative aiming to bring universal healthcare to ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    2017-12-04

    Take heart in an initiative aiming to bring universal healthcare to Pakistan. Heartfile has developed an innovative model of health financing that enrolls primarily public sector health facilities. December 04, 2017. Bano Bibi is 73 years old and she is raising her two young granddaughters alone. When her son died in 2005 ...

  17. Bringing Together Interactive Digital Storytelling with Tangible Interaction : Challenges and Opportunities

    NARCIS (Netherlands)

    Catala, Alejandro; Theune, Mariët; Sylla, Cristina; Ribeiro, Pedro; Nunes, Nuno; Oakley, Ian; Nisi, Valentina

    2017-01-01

    This workshop aims to explore challenges and potential opportunities in bringing interactive digital storytelling into the realm of tangible and embodied interaction. To this end, experts from both fields are invited to present and discuss their ideas. Besides fostering discussion and potential

  18. Ready for Robotics: Bringing Together the T and E of STEM in Early Childhood Teacher Education

    Science.gov (United States)

    Bers, Marina Umaschi; Seddighin, Safoura; Sullivan, Amanda

    2013-01-01

    Prior work has shown that early childhood educators demonstrate a lack of knowledge and understanding about technology and engineering, and about developmentally appropriate pedagogical approaches to bring those disciplines into the classrooms. This paper reports a study in which 32 early childhood educators participated in an intensive three-day…

  19. Descendit ad [in] inferna:'A matter of no small moment in bringing ...

    African Journals Online (AJOL)

    This article endorses Calvin's conviction that the 'descendit ad inferna' of the Apostles' Creed is part of the 'summary of doctrine' and a matter of 'no small moment in bringing about redemption' (Calvin 1960:Inst. II, xvi, 8). The reason for this role, however, is not Calvin's metaphorical interpretation of the clause. Instead, the ...

  20. Clickers in the Flipped Classroom: Bring Your Own Device (BYOD) to Promote Student Learning

    Science.gov (United States)

    Hung, Hsiu-Ting

    2017-01-01

    Flipped classrooms continue to grow in popularity across all levels of education. Following this pedagogical trend, the present study aimed to enhance the face-to-face instruction in flipped classrooms with the use of clickers. A game-like clicker application was implemented through a bring your own device (BYOD) model to gamify classroom dynamics…

  1. Contingent Commitments: Bringing Part-Time Faculty into Focus. Methodology Supplement

    Science.gov (United States)

    Center for Community College Student Engagement, 2014

    2014-01-01

    Center reporting prior to 2013 focused primarily on descriptive statistics (frequencies and means) of student and faculty behaviors. The goal of the analyses reported here and in "Contingent Commitments: Bringing Part-Time Faculty into Focus" is to understand the engagement of part-time or contingent faculty in various activities that…

  2. Bring Your Own Device--A Snapshot of Two Australian Primary Schools

    Science.gov (United States)

    Maher, Damian; Twining, Peter

    2017-01-01

    Background: The use of 1:1 and Bring Your Own Device strategies in schools is in its infancy and little is known about how mobile devices such as tablets are being used to support educational practice. Purpose: In this article, two suburban primary schools in Sydney, Australia were focused on with an aim to understand how mobile device strategies…

  3. Digital Natives: The Millennial Workforce's Intention to Adopt Bring Your Own Device

    Science.gov (United States)

    Fulton, Joel

    2017-01-01

    Bring your own device (BYOD) is the use of uncontrolled devices, which increases risks to business data and intellectual property. Like centralized and distributed computing adoption before it, the rapid proliferation of BYOD has outstripped security advances. The trend is growing due to the expectations of the Millennial workforce and its high…

  4. 29 CFR 779.110 - Employees in retailing whose activities may bring them under the Act.

    Science.gov (United States)

    2010-07-01

    ... individual activities ordinarily constitute engagement in commerce or in the production of goods for commerce... REGULATIONS THE FAIR LABOR STANDARDS ACT AS APPLIED TO RETAILERS OF GOODS OR SERVICES Employment to Which the... Production of Goods for Commerce § 779.110 Employees in retailing whose activities may bring them under the...

  5. Explore: An Action to Bring Science and Technology Closer to Secondary School

    Science.gov (United States)

    Torras-Melenchon, Nuria; Grau, M. Dolors; Font-Soldevila, Josep; Freixas, Josep

    2015-01-01

    This paper presents the experience of an initiative, the EXPLORE courses, designed to bring science and technology closer to secondary school. The EXPLORE courses, organised by "EXPLORATORI: Natural Resources" project, are particularly addressed to secondary school teachers and are conducted at Catalonia (North East of Spain). The main…

  6. Bringing up condom use and using condoms with new sexual partners : Intentional or habitual?

    NARCIS (Netherlands)

    Yzer, M.C; Siero, F.W.; Buunk, Abraham (Bram)

    2001-01-01

    A prospective study of 94 Dutch adults who have casual sexual partners examined whether two important aspects of safe sex. namely bringing up condom use (BCU) and actual condom use (ACU) are intentional or habitual. For each of these aspects, a model based on the Theory of Planned Behaviour (TPB:

  7. Bringing Preschoolers and the Institutionalized Elderly Together: How One Program Works.

    Science.gov (United States)

    Robbert, Lois

    In developing an intergenerational program bringing together preschool children and elderly adults in a retirement home/geriatric center complex, preschool staff had to discard three misconceptions. It was initially supposed that the elderly would like to visit the nursery school. It was assumed that people in the retirement home have nothing to…

  8. Crawl and crowd to bring machine translation to under-resourced languages

    NARCIS (Netherlands)

    Toral Ruiz, Antonio

    2017-01-01

    We present a widely applicable methodology to bring machine translation (MT) to under-resourced languages in a cost-effective and rapid manner. Our proposal relies on web crawling to automatically acquire parallel data to train statistical MT systems if any such data can be found for the language

  9. STUDY ON THE COMPULSORY BRINGING OF PERSONS IN FRONT OF THE JUDICIAL AUTHORITIES IN CRIMINAL MATTERS

    Directory of Open Access Journals (Sweden)

    Radu - Florin GEAMĂNU

    2014-05-01

    Full Text Available The study will try to perform an in-depth analysis of the measure of compulsory bringing, assessing both the national legislation and the legislation of some European countries, namely: Austria, Bulgaria, Poland and the Netherlands. Due attention will be granted to the provisions of the current Criminal Procedure Code, which entered into force on the 1st of February 2014, as this piece of legislation brings some important changes regarding the compulsory bringing, some of them being the consequence of the convictions of Romania in front of the Strasbourg Court. Also, the paper will focus on case-law established by the European Court of Human Rights regarding articles 3 and 5 relating to the compulsory bringing. To close with, the study will give some conclusions regarding the conformity of the current Criminal Procedure Code of Romania with the standards imposed by the European Convention for the Protection of Human Rights and Fundamental Freedoms and by the case-law of the European Court of Human Rights.

  10. Bringing Adam Smith's Pin Factory to Life: Field Trips and Discussions as Forms of Experiential Learning

    Science.gov (United States)

    Galizzi, Monica

    2014-01-01

    Educators are often aware of the need to implement a variety of teaching techniques to reach out to students with different learning styles. I describe an attempt to target multimodal learners by bringing classical economic texts and concepts to life through discussions, field visits and role playing exercises. In my Labor Economics class I…

  11. A Mobile Farmers' Market Brings Nutrition Education to Low-Income Students

    Science.gov (United States)

    Ellsworth, Devin; Ernst, Jenny; Snelling, Anastasia

    2015-01-01

    Purpose: The purpose of this paper is to examine the impact of a nutrition-education intervention delivered at low-income middle schools in Washington, DC in the USA, using a mobile farmers' market to bring hands-on lessons to schools. The program was a partnership between a local farm and university and was funded by the United States Department…

  12. Data Nuggets: Bringing Real Data into the Classroom to Unearth Students' Quantitative & Inquiry Skills

    Science.gov (United States)

    Schultheis, Elizabeth H.; Kjelvik, Melissa K.

    2015-01-01

    Current educational reform calls for increased integration between science and mathematics to overcome the shortcomings in students' quantitative skills. Data Nuggets (free online resource, http://datanuggets.org) are worksheets that bring data into the classroom, repeatedly guiding students through the scientific method and making claims…

  13. The Power of Questions to Bring Balance to the Curriculum in the Age of New Standards

    Science.gov (United States)

    del Prado, Pixita; McMillen, Susan E.; Friedland, Ellen S.

    2017-01-01

    The Common Core State Standards (CCSS); the Next Generation Science Standards (NGSS); and the College, Career, and Civic Life (C3) Framework for Social State Standards are bringing many changes to schools and classrooms across the United States. This article suggests using the power of questions to make connections across seemingly disparate…

  14. How Do Virtual World Experiences Bring about Learning? A Critical Review of Theories

    Science.gov (United States)

    Loke, Swee-Kin

    2015-01-01

    While students do learn real-world knowledge and skills in virtual worlds, educators have yet to adequately theorise how students' virtual world experiences bring about this learning. This paper critically reviewed theories currently used to underpin empirical work in virtual worlds for education. In particular, it evaluated how applicable these…

  15. Molecular biology in cardiovascular anaesthesia

    NARCIS (Netherlands)

    Weber, Nina C.; Schlack, Wolfgang; Preckel, Benedikt

    2008-01-01

    Purpose of review The last few years have seen rapid technical developments of methods in molecular biology which are increasingly used as powerful tools in experimental and clinical research. A basic knowledge of these techniques becomes increasingly important for the clinically working

  16. Photo fragmentation dynamics of small argon clusters and biological molecular: new tools by trapping and vectorial correlation; Dynamique de photofragmentation de petits agregats d'argon et de molecules biologiques: nouvel outil par piegeage et correlation vectorielle

    Energy Technology Data Exchange (ETDEWEB)

    Lepere, V

    2006-09-15

    The present work concerns the building up of a complex set-up whose aim being the investigation of the photo fragmentation of ionised clusters and biological molecules. This new tool is based on the association of several techniques. Two ion sources are available: clusters produced in a supersonic beam are ionised by 70 eV electrons while ions of biological interest are produced in an 'electro-spray'. Ro-vibrational cooling is achieved in a 'Zajfman' electrostatic ion trap. The lifetime of ions can also be measured using the trap. Two types of lasers are used to excite the ionised species: the femtosecond laser available at the ELYSE facilities and a nanosecond laser. Both lasers have a repetition rate of 1 kHz. The neutral and ionised fragments are detected in coincidence using a sophisticated detection system allowing time and localisation of the various fragments to be determined. With such a tool, I was able to investigate in details the fragmentation dynamics of ionised clusters and bio-molecules. The first experiments deal with the measurement of the lifetime of the Ar{sup 2+} dimer II(1/2)u metastable state. The relative population of this state was also determined. The Ar{sup 2+} and Ar{sup 3+} photo-fragmentation was then studied and electronic transitions responsible for their dissociation identified. The detailed analysis of our data allowed to distinguish the various fragmentation mechanisms. Finally, a preliminary investigation of the protonated tryptamine fragmentation is presented. (author)

  17. Molecular diagnostics in genodermatoses.

    Science.gov (United States)

    Schaffer, Julie V

    2012-12-01

    In recent years, there has been tremendous progress in elucidating the molecular bases of genodermatoses. The interface between genetics and dermatology has broadened with the identification of "new" heritable disorders, improved recognition of phenotypic spectrums, and integration of molecular and clinical data to simplify disease categorization and highlight relationships between conditions. With the advent of next-generation sequencing and other technological advances, dermatologists have promising new tools for diagnosis of genodermatoses. This article first addresses phenotypic characterization and classification with the use of online databases, considering concepts of clinical and genetic heterogeneity. Indications for genetic testing related to medical care and patient/family decision making are discussed. Standard genetic testing is reviewed, including resources for finding specialized laboratories, methods of gene analysis, and patient/family counseling. The benefits and challenges associated with multigene panels, array-based analysis (eg, copy number variation, linkage, and homozygosity), and whole-exome or whole-genome sequencing are then examined. Specific issues relating to molecular analysis of mosaic skin conditions and prenatal/preimplantation diagnosis are also presented. Use of the modern molecular diagnostics described herein enhance our ability to counsel, monitor, and treat patients and families affected by genodermatoses, with broader benefits of providing insights into cutaneous physiology and multifactorial skin disorders. Copyright © 2012 Frontline Medical Communications. Published by Elsevier Inc. All rights reserved.

  18. FORT Molecular Ecology Laboratory

    Science.gov (United States)

    Oyler-McCance, Sara J.; Stevens, P.D.

    2011-01-01

    The mission of the U.S. Geological Survey (USGS) at the Fort Collins Science Center Molecular Ecology Laboratory is to use the tools and concepts of molecular genetics to address a variety of complex management questions and conservation issues facing the management of the Nation's fish and wildlife resources. Together with our partners, we design and implement studies to document genetic diversity and the distribution of genetic variation among individuals, populations, and species. Information from these studies is used to support wildlife-management planning and conservation actions. Current and past studies have provided information to assess taxonomic boundaries, inform listing decisions made under the Endangered Species Act, identify unique or genetically depauperate populations, estimate population size or survival rates, develop management or recovery plans, breed wildlife in captivity, relocate wildlife from one location to another, and assess the effects of environmental change.

  19. Artificial Molecular Machines.

    Science.gov (United States)

    Balzani; Credi; Raymo; Stoddart

    2000-10-02

    The miniaturization of components used in the construction of working devices is being pursued currently by the large-downward (top-down) fabrication. This approach, however, which obliges solid-state physicists and electronic engineers to manipulate progressively smaller and smaller pieces of matter, has its intrinsic limitations. An alternative approach is a small-upward (bottom-up) one, starting from the smallest compositions of matter that have distinct shapes and unique properties-namely molecules. In the context of this particular challenge, chemists have been extending the concept of a macroscopic machine to the molecular level. A molecular-level machine can be defined as an assembly of a distinct number of molecular components that are designed to perform machinelike movements (output) as a result of an appropriate external stimulation (input). In common with their macroscopic counterparts, a molecular machine is characterized by 1) the kind of energy input supplied to make it work, 2) the nature of the movements of its component parts, 3) the way in which its operation can be monitored and controlled, 4) the ability to make it repeat its operation in a cyclic fashion, 5) the timescale needed to complete a full cycle of movements, and 6) the purpose of its operation. Undoubtedly, the best energy inputs to make molecular machines work are photons or electrons. Indeed, with appropriately chosen photochemically and electrochemically driven reactions, it is possible to design and synthesize molecular machines that do work. Moreover, the dramatic increase in our fundamental understanding of self-assembly and self-organizational processes in chemical synthesis has aided and abetted the construction of artificial molecular machines through the development of new methods of noncovalent synthesis and the emergence of supramolecular assistance to covalent synthesis as a uniquely powerful synthetic tool. The aim of this review is to present a unified view of the field

  20. Molecular beams with a tunable velocity

    NARCIS (Netherlands)

    Heiner, C.E.; Bethlem, H.L.; Meijer, G.

    2006-01-01

    The merging of molecular beam methods with those of accelerator physics has yielded new tools to manipulate the motion of molecules. Over the last few years, decelerators, lenses, bunchers, traps, and storage rings for neutral molecules have been demonstrated. Molecular beams with a tunable velocity

  1. Molecular Models: Construction of Models with Magnets

    Directory of Open Access Journals (Sweden)

    Kalinovčić P.

    2015-07-01

    Full Text Available Molecular models are indispensable tools in teaching chemistry. Beside their high price, commercially available models are generally too small for classroom demonstration. This paper suggests how to make space-filling (callote models from Styrofoam with magnetic balls as connectors and disc magnets for showing molecular polarity

  2. Dynamics and Thermodynamics of Molecular Machines

    DEFF Research Database (Denmark)

    Golubeva, Natalia

    2014-01-01

    to their microscopic size, molecular motors are governed by principles fundamentally different from those describing the operation of man-made motors such as car engines. In this dissertation the dynamic and thermodynamic properties of molecular machines are studied using the tools of nonequilibrium statistical...

  3. Molecular Electronics

    DEFF Research Database (Denmark)

    Jennum, Karsten Stein

    This thesis includes the synthesis and characterisation of organic compounds designed for molecular electronics. The synthesised organic molecules are mainly based on two motifs, the obigo(phenyleneethynylenes) (OPE)s and tetrathiafulvalene (TTF) as shown below. These two scaffolds (OPE and TTF...... transistors (Part 2). The synthetic protocols rely on stepwise Sonogashira coupling reactions. Conductivity studies on various OPE-based molecular wires reveal that mere OPE compounds have a higher electrical resistance compared to the cruciform based wires (up to 9 times higher). The most spectacular result...... be potential candidates for future molecular electronics Synthesis of a new donor-acceptor chromophore based on a benzoquinone- TTF motif (QuinoneDTF) is also described herein (Part 2). Reaction of this molecule with acid induces a colour change from purple to orange. The purple colour can be restored...

  4. Group therapy integrated with CAT: interactive Group therapy integrated with cognitive analytic therapy, understandings and tools

    OpenAIRE

    Ruppert, Margaret

    2013-01-01

    This qualitative study investigated bringing Cognitive Analytic Therapy (CAT) tools and understandings (Ryle & Kerr, 2002) into a time-limited (16 sessions) interactive, here-and-now, group therapy (Yalom,1985). Group members were not exposed to CAT or individual work with the two facilitators prior to the group. The study investigated the group members’ experience, particularly in respect of the CAT tools; the facilitators’ experience of integrating CAT tools and understandings into the grou...

  5. Route Availabililty Planning Tool -

    Data.gov (United States)

    Department of Transportation — The Route Availability Planning Tool (RAPT) is a weather-assimilated decision support tool (DST) that supports the development and execution of departure management...

  6. Molecular pathways

    DEFF Research Database (Denmark)

    Cox, Thomas R; Erler, Janine Terra

    2014-01-01

    that 45% of deaths in the developed world are linked to fibrotic disease. Fibrosis and cancer are known to be inextricably linked; however, we are only just beginning to understand the common and overlapping molecular pathways between the two. Here, we discuss what is known about the intersection...... of fibrosis and cancer, with a focus on cancer metastasis, and highlight some of the exciting new potential clinical targets that are emerging from analysis of the molecular pathways associated with these two devastating diseases. Clin Cancer Res; 20(14); 3637-43. ©2014 AACR....

  7. Molecular typing for detection of high-risk human papillomavirus is a useful tool for distinguishing primary bladder carcinoma from secondary involvement of uterine cervical carcinoma in the urinary bladder.

    Science.gov (United States)

    Kao, Hua-Lin; Lai, Chiung-Ru; Ho, Hsiang-Ling; Pan, Chin-Chen

    2016-03-01

    For patients with carcinoma of the urinary bladder and uterine cervix, distinguishing between metastasis and a second primary carcinoma has significant prognostic and therapeutic implications. The aim of this study was to investigate the prevalence of high-risk human papillomavirus (HR-HPV) in cervical carcinoma with secondary involvement of the bladder and primary bladder carcinoma, in order to explore whether the detection of HR-HPV could help to differentiate between the two. Paired bladder and cervix carcinoma specimens from 37 patients with cervical carcinoma with bladder involvement, four patients with bladder carcinoma with uterine cervical involvement and two patients with double primaries were studied with quantitative multiplex polymerase chain reaction and chromogenic in-situ hybridization. Three hundred and seventy-five bladder carcinomas and 220 cervical carcinomas were analysed as controls. All cases of cervical carcinoma with bladder involvement showed concordant HR-HPV-positive patterns. The four cases of bladder carcinoma with uterine involvement were negative for HR-HPV. HR-HPV was detected in the cervical carcinoma but not in the bladder carcinoma of the patients with double primaries. HR-HPV was detected in 91.9% of cervical carcinomas but in none of the bladder carcinomas in the control group. Molecular typing for HR-HPV detection is useful to distinguish bladder carcinoma from secondary involvement of cervical carcinoma. © 2015 John Wiley & Sons Ltd.

  8. Comparison of semi-automated commercial rep-PCR fingerprinting, spoligotyping, 12-locus MIRU-VNTR typing and single nucleotide polymorphism analysis of the embB gene as molecular typing tools for Mycobacterium bovis.

    Science.gov (United States)

    Armas, Federica; Camperio, Cristina; Coltella, Luana; Selvaggini, Serena; Boniotti, Maria Beatrice; Pacciarini, Maria Lodovica; Di Marco Lo Presti, Vincenzo; Marianelli, Cinzia

    2017-08-04

    Highly discriminatory genotyping strategies are essential in molecular epidemiological studies of tuberculosis. In this study we evaluated, for the first time, the efficacy of the repetitive sequence-based PCR (rep-PCR) DiversiLab Mycobacterium typing kit over spoligotyping, 12-locus mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing and embB single nucleotide polymorphism (SNP) analysis for Mycobacterium bovis typing. A total of 49 M. bovis animal isolates were used. DNA was extracted and genomic DNA was amplified using the DiversiLab Mycobacterium typing kit. The amplified fragments were separated and detected using a microfluidics chip with Agilent 2100. The resulting rep-PCR-based DNA fingerprints were uploaded to and analysed using web-based DiversiLab software through Pearson's correlation coefficient. Rep-PCR DiversiLab grouped M. bovis isolates into ten different clusters. Most isolates sharing identical spoligotype, MIRU-VNTR profile or embB gene polymorphism were grouped into different rep-PCR clusters. Rep-PCR DiversiLab displayed greater discriminatory power than spoligotyping and embB SNP analysis but a lower resolution power than the 12-locus MIRU-VNTR analysis. MIRU-VNTR confirmed that it is superior to the other PCR-based methods tested here. In combination with spoligotyping and 12-locus MIRU-VNTR analysis, rep-PCR improved the discriminatory power for M. bovis typing.

  9. The World Climate Project: Bringing the UN Climate Negotiations to Classrooms, Boardrooms, and Living Rooms Near You

    Science.gov (United States)

    Rath, K.; Rooney-varga, J. N.; Jones, A.; Johnston, E.; Sterman, J.

    2015-12-01

    As a simulation-based role-playing exercise, World Climate provides an opportunity for participants to have an immersive experience in which they learn first-hand about both the social dynamics of climate change decision-making, through role-play, and the geophysical dynamics of the climate system, through an interactive computer simulation. In June 2015, we launched the World Climate Project with the intent of bringing this powerful tool to students, citizens, and decision-makers across government, NGO, and private sectors around the world. Within a period of six weeks from the launch date, 440 educators from 36 states and 56 countries have enrolled in the initiative, offering the potential to reach tens of thousands of participants around the world. While this project is clearly in its infancy, we see several characteristics that may be contributing to widespread interest in it. These factors include the ease-of-use, real-world relevance, and scientific rigor of the decision-support simulation, C-ROADS, that frames the World Climate Exercise. Other characteristics of World Climate include its potential to evoke an emotional response that is arousing and inspirational and its use of positive framing and a call to action. Similarly, the World Climate Project takes a collaborative approach, enabling educators to be innovators and valued contributors and regularly communicating with people who join the initiative through webinars, social media, and resources.

  10. Adaptive Biomedical Innovation: Evolving Our Global System to Sustainably and Safely Bring New Medicines to Patients in Need.

    Science.gov (United States)

    Hirsch, G; Trusheim, M; Cobbs, E; Bala, M; Garner, S; Hartman, D; Isaacs, K; Lumpkin, M; Lim, R; Oye, K; Pezalla, E; Saltonstall, P; Selker, H

    2016-12-01

    The current system of biomedical innovation is unable to keep pace with scientific advancements. We propose to address this gap by reengineering innovation processes to accelerate reliable delivery of products that address unmet medical needs. Adaptive biomedical innovation (ABI) provides an integrative, strategic approach for process innovation. Although the term "ABI" is new, it encompasses fragmented "tools" that have been developed across the global pharmaceutical industry, and could accelerate the evolution of the system through more coordinated application. ABI involves bringing stakeholders together to set shared objectives, foster trust, structure decision-making, and manage expectations through rapid-cycle feedback loops that maximize product knowledge and reduce uncertainty in a continuous, adaptive, and sustainable learning healthcare system. Adaptive decision-making, a core element of ABI, provides a framework for structuring decision-making designed to manage two types of uncertainty - the maturity of scientific and clinical knowledge, and the behaviors of other critical stakeholders. © 2016 The Authors Clinical Pharmacology & Therapeutics published by Wiley Periodicals, Inc. on behalf of American Society for Clinical Pharmacology and Therapeutics.

  11. Molecular optoelectronics: the interaction of molecular conduction junctions with light.

    Science.gov (United States)

    Galperin, Michael; Nitzan, Abraham

    2012-07-14

    The interaction of light with molecular conduction junctions is attracting growing interest as a challenging experimental and theoretical problem on one hand, and because of its potential application as a characterization and control tool on the other. It stands at the interface between two important fields, molecular electronics and molecular plasmonics and has attracted attention as a challenging scientific problem with potentially important technological consequences. Here we review the present state of the art of this field, focusing on several key phenomena and applications: using light as a switching device, using light to control junction transport in the adiabatic and non-adiabatic regimes, light generation in biased junctions and Raman scattering from such systems. This field has seen remarkable progress in the past decade, and the growing availability of scanning tip configurations that can combine optical and electrical probes suggests that further progress towards the goal of realizing molecular optoelectronics on the nanoscale is imminent.

  12. QR Code: An Interactive Mobile Advertising Tool

    Directory of Open Access Journals (Sweden)

    Ela Sibel Bayrak Meydanoglu

    2013-10-01

    Full Text Available Easy and rapid interaction between consumers and marketers enabled by mobile technology prompted  an increase in the usage of mobile media as an interactive marketing tool in recent years. One of the mobile technologies that can be used in interactive marketing for advertising is QR code (Quick Response Code. Interactive advertising brings back some advantages for the companies that apply it. For example, interaction with consumers provides significant information about consumers' preferences. Marketers can use information obtained from consumers for various marketing activities such as customizing advertisement messages, determining  target audience, improving future products and services. QR codes used in marketing campaigns can provide links to specific websites in which through various tools (e.g. questionnaires, voting information about the needs and wants of customers are collected. The aim of this basic research is to illustrate the contribution of  QR codes to the realization of the advantages gained by interactive advertising.

  13. Molecular gastronomy

    Science.gov (United States)

    This, Hervé

    2005-01-01

    For centuries, cooks have been applying recipes without looking for the mechanisms of the culinary transformations. A scientific discipline that explores these changes from raw ingredients to eating the final dish, is developing into its own field, termed molecular gastronomy. Here, one of the founders of the discipline discusses its aims and importance.

  14. Molecular farming

    NARCIS (Netherlands)

    Merck, K.B.; Vereijken, J.M.

    2006-01-01

    Molecular Farming is a new and emerging technology that promises relatively cheap and flexible production of large quantities of pharmaceuticals in genetically modified plants. Many stakeholders are involved in the production of pharmaceuticals in plants, which complicates the discussion on the

  15. Molecular-based processing and transfer of information in the terahertz domain for military and security applications

    Science.gov (United States)

    Ma, Yuefei; Yan, Liuming; Seminario, Jorge M.

    2006-05-01

    An implementation and review of our recently proposed scenarios [1-13] for processing and transfer of information is presented. We will show how computing using molecular potentials and vibronics communications can be adapted to upgrade present charge-current approaches, which are already in the limits of their technical and perhaps physical limits because their immense heat dissipation problems. It has long been recognized the many advantages and potential payoffs that the development of THz based applications could bring to the military and security areas. We focus our implementation in the development of THz sensing and imaging for a wide range of military and security applications as systems operating at these frequencies have shown to have high sensitivity and selectivity when applied to the analysis of molecules. These are properties that are highly desirable in the design of sensing tools for the detection, identification and characterization of chemical and biological agents; and in the design of monitoring tools for the detection of these substances, both in closed and, with less selectivity, in open environments. Many materials of interest for security applications including explosives, and chemical and biological agents have characteristic THz fingerprints which set them apart from non-hazardous materials, thus allowing their identification. As molecular electronics techniques become available [14], they could sharply improve our present detection and sensing techniques.

  16. Drawing tool recognition by stroke ending analysis

    Science.gov (United States)

    Vill, Maria C.; Sablatnig, Robert

    2008-02-01

    The aim of our work is the development of image analysis tools and methods for the investigation of drawings and drawn drafts in order to investigate the authorship, to identify copies or more general to allow for a comparison of different types of drawings. It was and is common for artists to draw their design as several drafts on paper. These drawings can show how some elements were adjusted until the artist was satisfied with the composition. Therefore it can bring insights into the practice of artists and painting and/or drawing schools. This information is useful for art historians, because it can relate artists to each other. The goal of this paper is to describe a stroke classification algorithm which can recognize the drawing tool based on the shape of the endings of an open stroke. In this context, "open" means that both endings of a stroke are free-standing, uncovered and do not pass into another stroke. These endings are prominent features whose shape carries information about the drawing tool and are therefore used as features to distinguish different drawing tools. Our results show that it is possible to use these endings as input a drawing tool classificator.

  17. Three novel software tools for ASDEX Upgrade

    Energy Technology Data Exchange (ETDEWEB)

    Martinov, S. [Max-Planck-Institut für Plasmaphysik, Boltzmannstr. 2, D-85748 Garching bei München (Germany); Löbhard, T. [Conovum GmbH & Co. KG, Nymphenburger Straße 13, D-80335 München (Germany); Lunt, T. [Max-Planck-Institut für Plasmaphysik, Boltzmannstr. 2, D-85748 Garching bei München (Germany); Behler, K., E-mail: karl.behler@ipp.mpg.de [Max-Planck-Institut für Plasmaphysik, Boltzmannstr. 2, D-85748 Garching bei München (Germany); Drube, R.; Eixenberger, H.; Herrmann, A.; Lohs, A. [Max-Planck-Institut für Plasmaphysik, Boltzmannstr. 2, D-85748 Garching bei München (Germany); Lüddecke, K. [Unlimited Computer Systems GmbH, Seeshaupterstr. 15, D-82393 Iffeldorf (Germany); Merkel, R.; Neu, G.; ASDEX Upgrade Team [Max-Planck-Institut für Plasmaphysik, Boltzmannstr. 2, D-85748 Garching bei München (Germany); MPCDF Garching [Max Planck Compu ting and Data Facility, Boltzmannstr. 2, D-85748 Garching (Germany)

    2016-11-15

    Highlights: • Key features of innovative software tools for data visualization and inspection are presented to the nuclear fusion research community. • 3D animation of experiment geometry together with diagnostic data and images allow better understanding of measurements and influence of machine construction details behind them. • Multi-video viewer with fusion relevant image manipulation abilities and event database features allows faster and better decision making from video streams coming from various plasma and machine diagnostics. • Platform independant Web technologies enable the inspection of diagnostic raw signals with virtually any kind of display device. - Abstract: Visualization of measurements together with experimental settings is a general subject in experiments analysis. The complex engineering design, 3D geometry, and manifold of diagnostics in larger fusion research experiments justify the development of special analysis and visualization programs. Novel ASDEX Upgrade (AUG) software tools bring together virtual navigation through 3D device models and advanced play-back and interpretation of video streams from plasma discharges. A third little tool allows the web-based platform independent observation of real-time diagnostic signals. While all three tools stem from spontaneous development ideas and are not considered mission critical for the operation of a fusion device, they with time and growing completeness shaped up as valuable helpers to visualize acquired data in fusion research. A short overview on the goals, the features, and the design as well as the operation of these tools is given in this paper.

  18. Diagnostic Accuracy of Loop-mediated Isothermal Amplifica-tion Assay as a Field Molecular Tool for Rapid Mass Screening of Old World Leishmania Infections in Sand Flies and In Vitro Culture

    Directory of Open Access Journals (Sweden)

    Mehdi GHODRATI

    2017-12-01

    Full Text Available AbstractBackground: We employed a highly sensitive loop-mediated isothermal amplification (LAMP by targeting 18S rRNA gene to identify the rapid mass screening of Leishmania infections in captured sand flies of southwest Iran and In vitro culture. Methods: One hundred fifty sand flies were collected from 11 sites adjacent to Iraqi’s borders in southern parts of Khuzestan Province by using sticky sheets of paper and CDC miniature light traps during late May 2014 to Nov 2015. Following morphological identification of sand flies species, the DNA of infected samples was extracted and amplified by PCR and LAMP assays by targeting ITS-rDNA and 18S rRNA genes. The PCR amplicons were directly sequenced to conduct the phylogenetic analysis Results: Ten (6.6% Leishmania infections were identified by LAMP assay (detection limit 0.01 parasites DNA among infected Sergentomyia baghdadis, S. sintoni and Phlebotomus papatasi sand flies that was more sensitive than PCR (n=6.4%; (detection limit 101parasites DNA. LAMP can identify 101-106promastigotes/100 µl RPMI 1640 while PCR recognized104-106 promastigotes. The majority infection rate of sand flies was confirmed to L. major inferred by phylogenetic analysis. Conclusion: This is the first exploration characterized the Old World Leishmania infections by LAMP technique in both infected sand flies and In vitro conditions. The LAMP method because of its shorter reaction time, robustness, more sensitivity, lack of requirement of complicated equipment and visual discriminatory of positivity can be appeared a promising tool instead of PCR to identify low Leishmania loads and entomological monitoring of leishmaniasis in resource-limited endemic of the world.

  19. Possible room temperature superconductivity in conductors obtained by bringing alkanes into contact with a graphite surface

    Science.gov (United States)

    Kawashima, Yasushi

    2013-05-01

    Electrical resistances of conductors obtained by bringing alkanes into contact with a graphite surface have been investigated at room temperatures. Ring current in a ring-shaped container into which n-octane-soaked thin graphite flakes were compressed did not decay for 50 days at room temperature. After two HOPG plates were immersed into n-heptane and n-octane at room temperature, changes in resistances of the two samples were measured by four terminal technique. The measurement showed that the resistances of these samples decrease to less than the smallest resistance that can be measured with a high resolution digital voltmeter (0.1μV). The observation of persistent currents in the ring-shaped container suggests that the HOPG plates immersed in n-heptane and n-octane really entered zero-resistance state at room temperature. These results suggest that room temperature superconductor may be obtained by bringing alkanes into contact with a graphite surface.

  20. CASAS: A tool for composing automatically and semantically astrophysical services

    Science.gov (United States)

    Louge, T.; Karray, M. H.; Archimède, B.; Knödlseder, J.

    2017-07-01

    Multiple astronomical datasets are available through internet and the astrophysical Distributed Computing Infrastructure (DCI) called Virtual Observatory (VO). Some scientific workflow technologies exist for retrieving and combining data from those sources. However selection of relevant services, automation of the workflows composition and the lack of user-friendly platforms remain a concern. This paper presents CASAS, a tool for semantic web services composition in astrophysics. This tool proposes automatic composition of astrophysical web services and brings a semantics-based, automatic composition of workflows. It widens the services choice and eases the use of heterogeneous services. Semantic web services composition relies on ontologies for elaborating the services composition; this work is based on Astrophysical Services ONtology (ASON). ASON had its structure mostly inherited from the VO services capacities. Nevertheless, our approach is not limited to the VO and brings VO plus non-VO services together without the need for premade recipes. CASAS is available for use through a simple web interface.