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. Intrageneric Primer Design: Bringing Bioinformatics Tools to the Class

    Science.gov (United States)

    Lima, Andre O. S.; Garces, Sergio P. S.

    2006-01-01

    Bioinformatics is one of the fastest growing scientific areas over the last decade. It focuses on the use of informatics tools for the organization and analysis of biological data. An example of their importance is the availability nowadays of dozens of software programs for genomic and proteomic studies. Thus, there is a growing field (private…

  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. Web tools for molecular epidemiology of tuberculosis.

    Science.gov (United States)

    Shabbeer, Amina; Ozcaglar, Cagri; Yener, Bülent; Bennett, Kristin P

    2012-06-01

    In this study we explore publicly available web tools designed to use molecular epidemiological data to extract information that can be employed for the effective tracking and control of tuberculosis (TB). The application of molecular methods for the epidemiology of TB complement traditional approaches used in public health. DNA fingerprinting methods are now routinely employed in TB surveillance programs and are primarily used to detect recent transmissions and in outbreak investigations. Here we present web tools that facilitate systematic analysis of Mycobacterium tuberculosis complex (MTBC) genotype information and provide a view of the genetic diversity in the MTBC population. These tools help answer questions about the characteristics of MTBC strains, such as their pathogenicity, virulence, immunogenicity, transmissibility, drug-resistance profiles and host-pathogen associativity. They provide an integrated platform for researchers to use molecular epidemiological data to address current challenges in the understanding of TB dynamics and the characteristics of MTBC.

  5. Bringing the Tools of Big Science to Bear on Local Environmental Challenges

    Science.gov (United States)

    Bronson, Scott; Jones, Keith W.; Brown, Maria

    2013-01-01

    We describe an interactive collaborative environmental education project that makes advanced laboratory facilities at Brookhaven National Laboratory accessible for one-year or multi-year science projects for the high school level. Cyber-enabled Environmental Science (CEES) utilizes web conferencing software to bring multi-disciplinary,…

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

    NARCIS (Netherlands)

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

    2013-01-01

    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 glo

  7. MDMovie: a molecular dynamics viewing tool.

    Science.gov (United States)

    Greenberg, J P

    1996-10-01

    The graphics program MDMovie (Molecular Dynamics Movie), written in C using IRIS GL graphics library calls, is designed to facilitate the visualization and interpretation of empirical force field data. MDMovie was created and initially adapted in accord with the needs of physical chemists and thereafter became an expandable analysis tool. Capabilities include the display of chemical structure, animation of molecular dynamics and Monte Carlo trajectories, and the visual representation of various vector and scalar dynamical properties. In addition to being a research tool, MDMovie has features for creating presentation videos and hardcopy output. A library is also available for linking to Fortran simulation codes running on a remote machine and connecting to MDMovie via a socket connection. MDMovie continues to be an ongoing research project and new features are actively being added in collaboration with various research groups. Future plans include porting to OpenGL and the design of an XII-based user interface.

  8. RZ: a tool for bringing constructive and computable mathematics closer to programming practice

    OpenAIRE

    Stone, Christopher A.; Bauer, Andrej

    2015-01-01

    Realizability theory can produce interfaces for the data structure corresponding to a mathematical theory. Our tool, called RZ, serves as a bridge between constructive mathematics and programming by translating specifications in constructive logic into annotated interface code in Objective Caml. The system supports a rich input language allowing descriptions of complex mathematical structures. RZ does not extract code from proofs, but allows any implementation method, from handwritten code to...

  9. 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.

  10. Healthcare, molecular tools and applied genome research.

    Science.gov (United States)

    Groves, M

    2000-11-01

    Biotechnology 2000 offered a rare opportunity for scientists from academia and industry to present and discuss data in fields as diverse as environmental biotechnology and applied genome research. The healthcare section of the meeting encompassed a number of gene therapy delivery systems that are successfully treating genetic disorders. Beta-thalassemia is being corrected in mice by continous erythropoeitin delivery from engineered muscles cells, and from naked DNA electrotransfer into muscles, as described by Dr JM Heard (Institut Pasteur, Paris, France). Dr Reszka (Max-Delbrueck-Centrum fuer Molekulare Medizin, Berlin, Germany), meanwhile, described a treatment for liver metastasis in the form of a drug carrier emolization system, DCES (Max-Delbrueck-Centrum fuer Molekulare Medizin), composed of surface modified liposomes and a substance for chemo-occlusion, which drastically reduces the blood supply to the tumor and promotes apoptosis, necrosis and antiangiogenesis. In the molecular tools section, Willem Stemmer (Maxygen Inc, Redwood City, CA, USA) gave an insight into the importance that techniques, such as molecular breeding (DNA shuffling), have in the evolution of molecules with improved function, over a range of fields including pharmaceuticals, vaccines, agriculture and chemicals. Technologies, such as ribosome display, which can incorporate the evolution and the specific enrichment of proteins/peptides in cycles of selection, could play an enormous role in the production of novel therapeutics and diagnostics in future years, as explained by Andreas Plückthun (Institute of Biochemistry, University of Zurich, Switzerland). Applied genome research offered technologies, such as the 'in vitro expression cloning', described by Dr Zwick (Promega Corp, Madison, WI, USA), are providing a functional analysis for the overwhelming flow of data emerging from high-throughput sequencing of genomes and from high-density gene expression microarrays (DNA chips). The

  11. Molecular Tools for Exploring Polyploid Genomes in Plants

    Directory of Open Access Journals (Sweden)

    Domenico Carputo

    2012-08-01

    Full Text Available Polyploidy is a very common phenomenon in the plant kingdom, where even diploid species are often described as paleopolyploids. The polyploid condition may bring about several advantages compared to the diploid state. Polyploids often show phenotypes that are not present in their diploid progenitors or exceed the range of the contributing species. Some of these traits may play a role in heterosis or could favor adaptation to new ecological niches. Advances in genomics and sequencing technology may create unprecedented opportunities for discovering and monitoring the molecular effects of polyploidization. Through this review, we provide an overview of technologies and strategies that may allow an in-depth analysis of polyploid genomes. After introducing some basic aspects on the origin and genetics of polyploids, we highlight the main tools available for genome and gene expression analysis and summarize major findings. In the last part of this review, the implications of next generation sequencing are briefly discussed. The accumulation of knowledge on polyploid formation, maintenance, and divergence at whole-genome and subgenome levels will not only help plant biologists to understand how plants have evolved and diversified, but also assist plant breeders in designing new strategies for crop improvement.

  12. 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.

  13. 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.

  14. Molecular tools for the characterisation of antibiotic-resistant bacteria

    NARCIS (Netherlands)

    Aarts, H.J.M.; Boumedine, K.S.; Nesme, X.; Cloeckaert, A.

    2001-01-01

    This review will discuss a number of molecular tools which are currently used as well as some innovative approaches for the characterisation of antibiotic-resistant bacterial strains. Various methods involved in the detection and characterisation of genes and mutations associated with antibiotic res

  15. Bringing the light to high throughput screening: use of optogenetic tools for the development of recombinant cellular assays

    Science.gov (United States)

    Agus, Viviana; Di Silvio, Alberto; Rolland, Jean Francois; Mondini, Anna; Tremolada, Sara; Montag, Katharina; Scarabottolo, Lia; Redaelli, Loredana; Lohmer, Stefan

    2015-03-01

    The use of light-activated proteins represents a powerful tool to control biological processes with high spatial and temporal precision. These so called "optogenetic" technologies have been successfully validated in many recombinant systems, and have been widely applied to the study of cellular mechanisms in intact tissues or behaving animals; to do that, complex, high-intensity, often home-made instrumentations were developed to achieve the optimal power and precision of light stimulation. In our study we sought to determine if this optical modulation can be obtained also in a miniaturized format, such as a 384-well plate, using the instrumentations normally dedicated to fluorescence analysis in High Throughput Screening (HTS) activities, such as for example the FLIPR (Fluorometric Imaging Plate Reader) instrument. We successfully generated optogenetic assays for the study of different ion channel targets: the CaV1.3 calcium channel was modulated by the light-activated Channelrhodopsin-2, the HCN2 cyclic nucleotide gated (CNG) channel was modulated by the light activated bPAC adenylyl cyclase, and finally the genetically encoded voltage indicator ArcLight was efficiently used to measure potassium, sodium or chloride channel activity. Our results showed that stable, robust and miniaturized cellular assays can be developed using different optogenetic tools, and efficiently modulated by the FLIPR instrument LEDs in a 384-well format. The spatial and temporal resolution delivered by this technology might enormously advantage the early stages of drug discovery, leading to the identification of more physiological and effective drug molecules.

  16. 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. PMID:28344971

  17. Lightweight object oriented structure analysis: tools for building tools to analyze molecular dynamics simulations.

    Science.gov (United States)

    Romo, Tod D; Leioatts, Nicholas; Grossfield, Alan

    2014-12-15

    LOOS (Lightweight Object Oriented Structure-analysis) is a C++ library designed to facilitate making novel tools for analyzing molecular dynamics simulations by abstracting out the repetitive tasks, allowing developers to focus on the scientifically relevant part of the problem. LOOS supports input using the native file formats of most common biomolecular simulation packages, including CHARMM, NAMD, Amber, Tinker, and Gromacs. A dynamic atom selection language based on the C expression syntax is included and is easily accessible to the tool-writer. In addition, LOOS is bundled with over 140 prebuilt tools, including suites of tools for analyzing simulation convergence, three-dimensional histograms, and elastic network models. Through modern C++ design, LOOS is both simple to develop with (requiring knowledge of only four core classes and a few utility functions) and is easily extensible. A python interface to the core classes is also provided, further facilitating tool development.

  18. genepopedit: a simple and flexible tool for manipulating multilocus molecular data in R.

    Science.gov (United States)

    Stanley, Ryan R E; Jeffery, Nicholas W; Wringe, Brendan F; DiBacco, Claudio; Bradbury, Ian R

    2017-01-01

    Advances in genetic sequencing technologies and techniques have made large, genome-wide data sets comprised of hundreds or even thousands of individuals and loci the norm rather than the exception even for nonmodel organisms. While such data present new opportunities for evaluating population structure and demographic processes, the large size of these genomic data sets brings new computational challenges for researchers needing to parse, convert and manipulate data often into a variety of software-specific formats required of genomic analyses. We developed genepopedit as a flexible tool for the manipulation of multilocus molecular data sets. Functionality can be divided among diagnostic-, manipulation-, sampling-, simulation-, and transformation-based tools. Metadata from large genomic data sets can be efficiently extracted, without the need to view data in a text-editing program. genepopedit provides tools to manipulate loci, individual samples and populations included in genomic data sets, in addition to the ability to convert directly to a variety of software formats. Functions are compiled as an R package, which can integrate into existing analysis workflows. Importantly, genepopedit provides a simple yet robust code-based tool for repeatable genomic data manipulation, which has been proven to be stable for data sets in excess of 200 000 SNPs. The latest version of the package and associated documentation are available on Github (github.com/rystanley/genepopedit).

  19. 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

  20. 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.

  1. 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.

  2. Yada: a novel tool for molecular docking calculations

    Science.gov (United States)

    Piotto, S.; Di Biasi, L.; Fino, R.; Parisi, R.; Sessa, L.; Concilio, S.

    2016-09-01

    Molecular docking is a computational method employed to estimate the binding between a small ligand (the drug candidate) and a protein receptor that has become a standard part of workflow in drug discovery. Generally, when the binding site is known and a molecule is similar to known ligands, the most popular docking methods are rather accurate in the prediction of the geometry. Unfortunately, when the binding site is unknown, the blind docking analysis requires large computational resources and the results are often not accurate. Here we present Yada, a new tool for molecular docking that is capable to distribute efficiently calculations onto general purposes computer grid and that combines biological and structural information of the receptor. Yada is available for Windows and Linux and it is free to download at >www.yada.unisa.it.

  3. Molecular imaging of rheumatoid arthritis: emerging markers, tools, and techniques.

    Science.gov (United States)

    Put, Stéphanie; Westhovens, René; Lahoutte, Tony; Matthys, Patrick

    2014-04-15

    Early diagnosis and effective monitoring of rheumatoid arthritis (RA) are important for a positive outcome. Instant treatment often results in faster reduction of inflammation and, as a consequence, less structural damage. Anatomical imaging techniques have been in use for a long time, facilitating diagnosis and monitoring of RA. However, mere imaging of anatomical structures provides little information on the processes preceding changes in synovial tissue, cartilage, and bone. Molecular imaging might facilitate more effective diagnosis and monitoring in addition to providing new information on the disease pathogenesis. A limiting factor in the development of new molecular imaging techniques is the availability of suitable probes. Here, we review which cells and molecules can be targeted in the RA joint and discuss the advances that have been made in imaging of arthritis with a focus on such molecular targets as folate receptor, F4/80, macrophage mannose receptor, E-selectin, intercellular adhesion molecule-1, phosphatidylserine, and matrix metalloproteinases. In addition, we discuss a new tool that is being introduced in the field, namely the use of nanobodies as tracers. Finally, we describe additional molecules displaying specific features in joint inflammation and propose these as potential new molecular imaging targets, more specifically receptor activator of nuclear factor κB and its ligand, chemokine receptors, vascular cell adhesion molecule-1, αVβ₃ integrin, P2X7 receptor, suppression of tumorigenicity 2, dendritic cell-specific transmembrane protein, and osteoclast-stimulatory transmembrane protein.

  4. Development of molecular tools to monitor conjugative transfer in rhizobia.

    Science.gov (United States)

    Tejerizo, Gonzalo Torres; Bañuelos, Luis Alfredo; Cervantes, Laura; Gaytán, Paul; Pistorio, Mariano; Romero, David; Brom, Susana

    2015-10-01

    Evolution of bacterial populations has been extensively driven by horizontal transfer events. Conjugative plasmid transfer is considered the principal contributor to gene exchange among bacteria. Several conjugative and mobilizable plasmids have been identified in rhizobia, and two major molecular mechanisms that regulate their transfer have been described, under laboratory conditions. The knowledge of rhizobial plasmid transfer regulation in natural environments is very poor. In this work we developed molecular tools to easily monitor the conjugative plasmid transfer in rhizobia by flow cytometry (FC) or microscopy. 24 cassettes were constructed by combining a variety of promotors, fluorescent proteins and antibiotic resistance genes, and used to tag plasmids and chromosome of donor strains. We were able to detect plasmid transfer after conversion of non-fluorescent recipients into fluorescent transconjugants. Flow cytometry (FC) was optimized to count donor, recipient and transconjugant strains to determine conjugative transfer frequencies. Results were similar, when determined either by FC or by viable counts. Our constructions also allowed the visualization of transconjugants in crosses performed on bean roots. The tools presented here may also be used for other purposes, such as analysis of transcriptional fusions or single-cell tagging. Application of the system will allow the survey of how different environmental conditions or other regulators modulate plasmid transfer in rhizobia.

  5. Molecular Genetic Tools and Techniques in Fission Yeast.

    Science.gov (United States)

    Murray, Johanne M; Watson, Adam T; Carr, Antony M

    2016-05-02

    The molecular genetic tools used in fission yeast have generally been adapted from methods and approaches developed for use in the budding yeast, Saccharomyces cerevisiae Initially, the molecular genetics of Schizosaccharomyces pombe was developed to aid gene identification, but it is now applied extensively to the analysis of gene function and the manipulation of noncoding sequences that affect chromosome dynamics. Much current research using fission yeast thus relies on the basic processes of introducing DNA into the organism and the extraction of DNA for subsequent analysis. Targeted integration into specific genomic loci is often used to create site-specific mutants or changes to noncoding regulatory elements for subsequent phenotypic analysis. It is also regularly used to introduce additional sequences that generate tagged proteins or to create strains in which the levels of wild-type protein can be manipulated through transcriptional regulation and/or protein degradation. Here, we draw together a collection of core molecular genetic techniques that underpin much of modern research using S. pombe We summarize the most useful methods that are routinely used and provide guidance, learned from experience, for the successful application of these methods.

  6. 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.

  7. Molecular cytogenetics: an indispensable tool for cancer diagnosis.

    Science.gov (United States)

    Wan, Thomas Sk; Ma, Edmond Sk

    2012-01-01

    Cytogenetic aberrations may escape detection or recognition in traditional karyotyping. The past decade has seen an explosion of methodological advances in molecular cytogenetics technology. These cytogenetics techniques add color to the black and white world of conventional banding. Fluorescence in-situ hybridization (FISH) study has emerged as an indispensable tool for both basic and clinical research, as well as diagnostics, in leukemia and cancers. FISH can be used to identify chromosomal abnormalities through fluorescent labeled DNA probes that target specific DNA sequences. Subsequently, FISH-based tests such as multicolor karyotyping, comparative genomic hybridization (CGH) and array CGH have been used in emerging clinical applications as they enable resolution of complex karyotypic aberrations and whole global scanning of genomic imbalances. More recently, crossspecies array CGH analysis has also been employed in cancer gene identification. The clinical impact of FISH is pivotal, especially in the diagnosis, prognosis and treatment decisions for hematological diseases, all of which facilitate the practice of personalized medicine. This review summarizes the methodology and current utilization of these FISH techniques in unraveling chromosomal changes and highlights how the field is moving away from conventional methods towards molecular cytogenetics approaches. In addition, the potential of the more recently developed FISH tests in contributing information to genetic abnormalities is illustrated.

  8. Monitoring bioremediation of atrazine in soil microcosms using molecular tools.

    Science.gov (United States)

    Sagarkar, Sneha; Mukherjee, Shinjini; Nousiainen, Aura; Björklöf, Katarina; Purohit, Hemant J; Jørgensen, Kirsten S; Kapley, Atya

    2013-01-01

    Molecular tools in microbial community analysis give access to information on catabolic potential and diversity of microbes. Applied in bioremediation, they could provide a new dimension to improve pollution control. This concept has been demonstrated in the study using atrazine as model pollutant. Bioremediation of the herbicide, atrazine, was analyzed in microcosm studies by bioaugmentation, biostimulation and natural attenuation. Genes from the atrazine degrading pathway atzA/B/C/D/E/F, trzN, and trzD were monitored during the course of treatment and results demonstrated variation in atzC, trzD and trzN genes with time. Change in copy number of trzN gene under different treatment processes was demonstrated by real-time PCR. The amplified trzN gene was cloned and sequence data showed homology to genes reported in Arthrobacter and Nocardioides. Results demonstrate that specific target genes can be monitored, quantified and correlated to degradation analysis which would help in predicting the outcome of any bioremediation strategy.

  9. 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.

  10. 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...

  11. 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 trajector

  12. Bring Your Own Toy: Socialisation of Two-Year-Olds through Tool-Mediated Activities in an Australian Early Childhood Education Context

    Science.gov (United States)

    Kultti, Anne; Pramling, Niklas

    2015-01-01

    The study focuses on how young children are socialised in early childhood education practice in activities with and around toys. A premise of this study is the theoretical notion of sociocultural theory that people do things with artefacts and other cultural tools, and tools do things with people. This is captured in the unit of analysis,…

  13. Molecular dynamics simulation: A tool for exploration and discovery

    Science.gov (United States)

    Rapaport, Dennis C.

    2009-03-01

    The exploratory and didactic aspects of science both benefit from the ever-growing role played by computer simulation. One particularly important simulational approach is the molecular dynamics method, used for studying the nature of matter from the molecular to much larger scales. The effectiveness of molecular dynamics can be enhanced considerably by employing visualization and interactivity during the course of the computation and afterwards, allowing the modeler not only to observe the detailed behavior of the systems simulated in different ways, but also to steer the computations in alternative directions by manipulating parameters that govern the actual behavior. This facilitates the creation of potentially rich simulational environments for examining a multitude of complex phenomena, as well as offering an opportunity for enriching the learning process. A series of relatively advanced examples involving molecular dynamics will be used to demonstrate the value of this approach, in particular, atomistic simulations of spontaneously emergent structured fluid flows (the classic Rayleigh--B'enard and Taylor--Couette problems), supramolecular self-assembly of highly symmetric shell structures (involved in the formation of viral capsids), and that most counterintuitive of phenomena, granular segregation (e.g., axial and radial separation in a rotating cylinder).

  14. Molecular tools for investigating ANME community structure and function

    Energy Technology Data Exchange (ETDEWEB)

    Hallam, Steven J.; Page, Antoine P.; Constan, Lea; Song, Young C.; Norbeck, Angela D.; Brewer, Heather M.; Pasa-Tolic, Ljiljana

    2011-05-20

    Methane production and consumption in anaerobic marine sediments 1 is catalyzed by a series of reversible tetramethanopterin (H4MPT)-linked C1 transfer reactions. Although many of these reactions are conserved between one-carbon compound utilizing microorganisms, two remain diagnostic for archaeal methane metabolism. These include reactions catalyzed by N5-methyltetrahydromethanopterin: coenzyme M methyltransferase and methyl coenzyme M reductase. The latter enzyme is central to C-H bond formation and cleavage underlying methanogenic and reverse methanogenic phenotypes. Here we describe a set of novel tools for the detection and functional analysis of H4MPT-linked C1 transfer reactions mediated by uncultivated anaerobic methane oxidizing archaea (ANME). These tools include polymerase chain reaction primers targeting ANME methyl coenzyme M reductase subunit A subgroups and protein extraction methods from marine sediments compatible with high-resolution mass spectrometry for profiling population structure and functional dynamics. [910, 1,043

  15. Laser induced electron diffraction: a tool for molecular orbital imaging

    CERN Document Server

    Peters, Michel; Charron, Eric; Keller, Arne; Atabek, Osman

    2012-01-01

    We explore the laser-induced ionization dynamics of N2 and CO2 molecules subjected to a few-cycle, linearly polarized, 800\\,nm laser pulse using effective two-dimensional single active electron time-dependent quantum simulations. We show that the electron recollision process taking place after an initial tunnel ionization stage results in quantum interference patterns in the energy resolved photo-electron signals. If the molecule is initially aligned perpendicular to the field polarization, the position and relative heights of the associated fringes can be related to the molecular geometrical and orbital structure, using a simple inversion algorithm which takes into account the symmetry of the initial molecular orbital from which the ionized electron is produced. We show that it is possible to extract inter-atomic distances in the molecule from an averaged photon-electron signal with an accuracy of a few percents.

  16. Stable Isotopic and Molecular Biological Tools to Validate Biodegradation of 1,4-Dioxane

    OpenAIRE

    2014-01-01

    1,4-Dioxane, a probable human carcinogen, is a heterocyclic ether increasingly found as a contaminant in water supplies. Recent studies have reported that 1,4-dioxane can be biodegraded by a variety of microorganisms, and bioremediation may be an effective strategy for 1,4-dioxane contaminated sites. However, reliable monitoring tools to validate biodegradation of 1,4-dioxane are still lacking. Molecular biological tools and stable isotope-based tools have been previously applied as diagno...

  17. 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

    2002-01-01

    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 microsphere

  18. 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.

  19. Molecular Genetic Tools and Techniques for Marchantia polymorpha Research.

    Science.gov (United States)

    Ishizaki, Kimitsune; Nishihama, Ryuichi; Yamato, Katsuyuki T; Kohchi, Takayuki

    2016-02-01

    Liverworts occupy a basal position in the evolution of land plants, and are a key group to address a wide variety of questions in plant biology. Marchantia polymorpha is a common, easily cultivated, dioecious liverwort species, and is emerging as an experimental model organism. The haploid gametophytic generation dominates the diploid sporophytic generation in its life cycle. Genetically homogeneous lines in the gametophyte generation can be established easily and propagated through asexual reproduction, which aids genetic and biochemical experiments. Owing to its dioecy, male and female sexual organs are formed in separate individuals, which enables crossing in a fully controlled manner. Reproductive growth can be induced at the desired times under laboratory conditions, which helps genetic analysis. The developmental process from a single-celled spore to a multicellular body can be observed directly in detail. As a model organism, molecular techniques for M. polymorpha are well developed; for example, simple and efficient protocols of Agrobacterium-mediated transformation have been established. Based on them, various strategies for molecular genetics, such as introduction of reporter constructs, overexpression, gene silencing and targeted gene modification, are available. Herein, we describe the technologies and resources for reverse and forward genetics in M. polymorpha, which offer an excellent experimental platform to study the evolution and diversity of regulatory systems in land plants.

  20. Molecular tools in understanding the evolution of Vibrio cholerae.

    Science.gov (United States)

    Rahaman, Md Habibur; Islam, Tarequl; Colwell, Rita R; Alam, Munirul

    2015-01-01

    Vibrio cholerae, the etiological agent of cholera, has been a scourge for centuries. Cholera remains a serious health threat for developing countries and has been responsible for millions of deaths globally over the past 200 years. Identification of V. cholerae has been accomplished using a variety of methods, ranging from phenotypic strategies to DNA based molecular typing and currently whole genomic approaches. This array of methods has been adopted in epidemiological investigations, either singly or in the aggregate, and more recently for evolutionary analyses of V. cholerae. Because the new technologies have been developed at an ever increasing pace, this review of the range of fingerprinting strategies, their relative advantages and limitations, and cholera case studies was undertaken. The task was challenging, considering the vast amount of the information available. To assist the study, key references representative of several areas of research are provided with the intent to provide readers with a comprehensive view of recent advances in the molecular epidemiology of V. cholerae. Suggestions for ways to obviate many of the current limitations of typing techniques are also provided. In summary, a comparative report has been prepared that includes the range from traditional typing to whole genomic strategies.

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

    Science.gov (United States)

    Monroy-Contreras, Ricardo; Vaca, Luis

    2011-01-01

    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. PMID:21876785

  2. 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.

  3. Culture-Independent Molecular Tools for Soil and Rhizosphere Microbiology

    Directory of Open Access Journals (Sweden)

    Peer M. Schenk

    2013-08-01

    Full Text Available Soil microbial communities play an important role in plant health and soil quality. Researchers have developed a wide range of methods for studying the structure, diversity, and activity of microbes to better understand soil biology and plant-microbe interactions. Functional microbiological analyses of the rhizosphere have given new insights into the role of microbial communities in plant nutrition and plant protection against diseases. In this review, we present the most commonly used traditional as well as new culture-independent molecular methods to assess the diversity and function of soil microbial communities. Furthermore, we discuss advantages and disadvantages of these techniques and provide a perspective on emerging technologies for soil microbial community profiling.

  4. 2. Molecular Biology as a Tool in Cancer Epidemiology

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    @@There can be little doubt that we are entering a new era in our understanding of the origins of human cancer. Unfortunately from the point of view of the cancer epidemiology community, some of the more recent advances in the molecular biology of cancer (once fully assimilated) will tend to make the talk of the up-to-date cancer epidemiologist a great deal less straightforward than many of us had previously envisaged it to be, There may still be a few cancers that will prove to result from only a few distinctive types of mutation in a relatively small number of genes, but I strongly suspect that the great majority of human cancers that we wish to study will prove to have their origins in a complex set of DNA changes whose precise

  5. 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

  6. 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. PMID:26240527

  7. Using reflexive tools for coping and bringing closure in pediatric palliative care: A music therapist's story of working with a terminally ill child.

    Directory of Open Access Journals (Sweden)

    Maeve Rigney

    2011-11-01

    Full Text Available This paper outlines the therapeutic journey of a newly qualified music therapist and a young girl with terminal cancer. As well as describing the clinical sessions with this young girl and her family, it includes personal reflections from the journal of the therapist, used as a method of self-review and clarification of thoughts and feelings following each session. The aim of this paper is to narrate the music therapy journey with Tina * from the music therapist's perspective, and to share my thoughts and feelings on coping while working with terminally ill children. In addition to outlining the significance of using reflexive tools for this type of work as a way to improve coping skills and to work more effectively when the future with your client is uncertain, I hope to encourage further others to share their work in pediatric palliative care.

  8. 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.

  9. 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

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

    DEFF Research Database (Denmark)

    Cock, Peter J A; Antao, Tiago; Chang, Jeffrey T

    2009-01-01

    , 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. AVAILABILITY: Biopython is freely available, with documentation and source code at (www...

  11. Molecular genealogy tools for white-tailed deer with chronic wasting disease.

    Science.gov (United States)

    Ernest, Holly B; Hoar, Bruce R; Well, Jay A; O'Rourke, Katherine I

    2010-04-01

    Molecular genetic data provide powerful tools for genealogy reconstruction to reveal mechanisms underlying disease ecology. White-tailed deer (Odocoileus virginianus) congregate in matriarchal groups; kin-related close social spacing may be a factor in the spread of infectious diseases. Spread of chronic wasting disease (CWD), a prion disorder of deer and their cervid relatives, is presumed to be associated with direct contact between individuals and by exposure to shared food and water sources contaminated with prions shed by infected deer. Key aspects of disease ecology are yet unknown. DNA tools for pedigree reconstruction were developed to fill knowledge gaps in disease dynamics in prion-infected wild animals. Kinship indices using data from microsatellite loci and sequence haplotypes of mitochondrial DNA were employed to assemble genealogies. Molecular genealogy tools will be useful for landscape-level population genetic research and monitoring, in addition to epidemiologic studies examining transmission of CWD in captive and free-ranging cervids.

  12. 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.

  13. Microbiology and Molecular Biology Tools for Biogas Process Analysis, Diagnosis and Control.

    Science.gov (United States)

    Lebuhn, Michael; Weiß, Stefan; Munk, Bernhard; Guebitz, Georg M

    2015-01-01

    Many biotechnological processes such as biogas production or defined biotransformations are carried out by microorganisms or tightly cooperating microbial communities. Process breakdown is the maximum credible accident for the operator. Any time savings that can be provided by suitable early-warning systems and allow for specific countermeasures are of great value. Process disturbance, frequently due to nutritional shortcomings, malfunction or operational deficits, is evidenced conventionally by process chemistry parameters. However, knowledge on systems microbiology and its function has essentially increased in the last two decades, and molecular biology tools, most of which are directed against nucleic acids, have been developed to analyze and diagnose the process. Some of these systems have been shown to indicate changes of the process status considerably earlier than the conventionally applied process chemistry parameters. This is reasonable because the triggering catalyst is determined, activity changes of the microbes that perform the reaction. These molecular biology tools have thus the potential to add to and improve the established process diagnosis system. This chapter is dealing with the actual state of the art of biogas process analysis in practice, and introduces molecular biology tools that have been shown to be of particular value in complementing the current systems of process monitoring and diagnosis, with emphasis on nucleic acid targeted molecular biology systems.

  14. A global indicator as a tool to follow airborne molecular contamination in a controlled environment.

    Science.gov (United States)

    Cariou, Stéphane; Guillot, Jean-Michel; Pépin, Laurence; Kaluzny, Pascal; Faure, Louis-Paul

    2005-02-01

    The impact of pollutants on production quality in nanotechnology necessitates reduction of contaminant levels in cleanrooms. So, devising a global airborne-pollutant indicator (GAPI) for rapid determination of the level of pollution and its danger to the process is justified. This tool used relative impact weights of the different molecules to quantify the pollution. A calculation of impact weight is proposed in this paper. Impact weights could take into account several characteristics of the molecules (molecular volume, sticking coefficient, ...). They could also be combined to be as close as possible to reality. An example of calculations of the impact of molecular volumes on air quality is given.

  15. Molecular genealogy tools for white-tailed deer with chronic wasting disease

    OpenAIRE

    Holly B Ernest; Hoar, Bruce R; Well, Jay A.; O’Rourke, Katherine I

    2010-01-01

    Molecular genetic data provide powerful tools for genealogy reconstruction to reveal mechanisms underlying disease ecology. White-tailed deer (Odocoileus virginianus) congregate in matriarchal groups; kin-related close social spacing may be a factor in the spread of infectious diseases. Spread of chronic wasting disease (CWD), a prion disorder of deer and their cervid relatives, is presumed to be associated with direct contact between individuals and by exposure to shared food and water sourc...

  16. Bring Life to Learning.

    Science.gov (United States)

    Graves, Donald H.

    2000-01-01

    A focus on people--whether community members, students, historical figures, or fictional characters--and their motivations brings excitement to learning. A community's experts on everything from jazz music and Chinese tapestries to building construction can help students move inside history and other subjects. (MLH)

  17. eMovie: a storyboard-based tool for making molecular movies.

    Science.gov (United States)

    Hodis, Eran; Schreiber, Gideon; Rother, Kristian; Sussman, Joel L

    2007-05-01

    The 3D structures of macromolecules are difficult to grasp and also to communicate. By their nature, movies or animations are particularly useful for highlighting key features by offering a 'guided tour' of structures and conformation changes. However, high-quality movies are rarely seen because they are currently difficult and time consuming to make. By adopting the traditional movie 'storyboard' concept, which gives guidance and direction to filming, eMovie makes the creation of lengthy molecular animations much easier. This tool is a plug-in for the open-source molecular graphics program PyMOL, and enables experts and novices alike to produce informative and high-quality molecular animations.

  18. Theoretical descriptions of electron transport through single molecules: Developing design tools for molecular electronic devices

    Science.gov (United States)

    Carroll, Natalie R.

    There are vast numbers of organic compounds that could be considered for use in molecular electronics. Hence there is a need for efficient and economical screening tools. Here we develop theoretical methods to describe electron transport through individual molecules, the ultimate goal of which is to establish design tools for molecular electronic devices. To successfully screen a compound for its use as a device component requires a proper representation of the quantum mechanics of electron transmission. In this work we report the development of tools for the description of electron transmission that are: Charge self-consistent, valid in the presence of a finite applied potential field and (in some cases) explicitly time-dependent. In addition, the tools can be extended to any molecular system, including biosystems, because they are free of restrictive parameterizations. Two approaches are explored: (1) correlation of substituent parameter values (sigma), (commonly found in organic chemistry textbooks) to properties associated with electron transport, (2) explicit tracking of the time evolution of the wave function of a nonstationary electron. In (1) we demonstrate that the a correlate strongly with features of the charge migration process, establishing them as useful indicators of electronic properties. In (2) we employ a time-dependent description of electron transport through molecular junctions. To date, the great majority of theoretical treatments of electron transport in molecular junctions have been of the time-independent variety. Time dependence, however, is critical to such properties as switching speeds in binary computer components and alternating current conductance, so we explored methods based on time-dependent quantum mechanics. A molecular junction is modeled as a single molecule sandwiched between two clusters of close-packed metal atoms or other donor and acceptor groups. The time dependence of electron transport is investigated by initially

  19. 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.

  20. DETERMINACIÓN DE SEXO EN AVES MEDIANTE HERRAMIENTAS MOLECULARES Sex Determination In Birds By Molecular Tools

    Directory of Open Access Journals (Sweden)

    NUBIA E MATTA CAMACHO

    Full Text Available La ausencia de dimorfismo sexual en los estadios juveniles y durante la edad adulta de gran cantidad de especies de aves, dificulta o imposibilita la determinación del sexo basados en el fenotipo. El empleo de marcadores moleculares para determinar el sexo de las aves es una herramienta útil debido a la exactitud y rapidez de los resultados y a su vez se constituye en un método que minimiza el estrés durante la toma de muestra, comparado con otras técnicas invasivas que pudieran afectar la salud o estabilidad biológica del animal. La determinación temprana del sexo en aves resulta de especial relevancia cuando se consideran programas de conservación ex situ, producción, explotación y estudios de ecología de poblaciones. Esta revisión presenta las metodologías usadas para determinar el sexo, haciendo especial énfasis en herramientas moleculares, presentando sus ventajas y limitaciones.The lack of sexual dimorphism in nestling, juvenile or adult birds of large number of avian species, makes it difficult or impossible sex determination based on phenotipic characteristics. To use molecular markers for bird sex determination is a rapid and safe procedure; moreover this methodology minimizes the stress during sampling, compared to other invasive techniques that could affect the health or biological stability of the animal. The early sex determination in birds is of particular importance when considering ex situ conservation programs, production, exploitation or population ecology studies. This review presents the methodologies used to sex determination, making emphasize on molecular tools, showing its advantages and limitations

  1. 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.

  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. ms2: A molecular simulation tool for thermodynamic properties, new version release

    CERN Document Server

    Glass, Colin W; Rutkai, Gábor; Deublein, Stephan; Köster, Andreas; Carrión, Gabriela Guevara; Wafai, Amer; Horsch, Martin; Bernreuther, Martin F; Windmann, Thorsten; Hasse, Hans; Vrabec, Jadran

    2015-01-01

    A new version release (2.0) of the molecular simulation tool ms2 [S. Deublein et al., Comput. Phys. Commun. 182 (2011) 2350] is presented. Version 2.0 of ms2 features a hybrid parallelization based on MPI and OpenMP for molecular dynamics simulation to achieve higher scalability. Furthermore, the formalism by Lustig [R. Lustig, Mol. Phys. 110 (2012) 3041] is implemented, allowing for a systematic sampling of Massieu potential derivatives in a single simulation run. Moreover, the Green-Kubo formalism is extended for the sampling of the electric conductivity and the residence time. To remove the restriction of the preceding version to electro-neutral molecules, Ewald summation is implemented to consider ionic long range interactions. Finally, the sampling of the radial distribution function is added.

  4. 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.

  5. Synthesis of Novel Hydrocarbon Soluble Multifunctional Anionic Initiators: Tools for Synthesis of Novel Dendrimer and Molecular Brush Polymer Architectures

    Science.gov (United States)

    2015-02-09

    SECURITY CLASSIFICATION OF: A novel hydrocarbon -soluble trifunctional organolithium initiator, with no polar-additive requirements, has been synthesized...Approved for Public Release; Distribution Unlimited Final Report: Synthesis of Novel Hydrocarbon Soluble Multifunctional Anionic Initiators: Tools for...journals: Final Report: Synthesis of Novel Hydrocarbon Soluble Multifunctional Anionic Initiators: Tools for Synthesis of Novel Dendrimer and Molecular

  6. Fluorescent protein-scorpion toxin chimera is a convenient molecular tool for studies of potassium channels.

    Science.gov (United States)

    Kuzmenkov, Alexey I; Nekrasova, Oksana V; Kudryashova, Kseniya S; Peigneur, Steve; Tytgat, Jan; Stepanov, Alexey V; Kirpichnikov, Mikhail P; Grishin, Eugene V; Feofanov, Alexey V; Vassilevski, Alexander A

    2016-09-21

    Ion channels play a central role in a host of physiological and pathological processes and are the second largest target for existing drugs. There is an increasing need for reliable tools to detect and visualize particular ion channels, but existing solutions suffer from a number of limitations such as high price, poor specificity, and complicated protocols. As an alternative, we produced recombinant chimeric constructs (FP-Tx) consisting of fluorescent proteins (FP) fused with potassium channel toxins from scorpion venom (Tx). In particular, we used two FP, eGFP and TagRFP, and two Tx, OSK1 and AgTx2, to create eGFP-OSK1 and RFP-AgTx2. We show that these chimeras largely retain the high affinity of natural toxins and display selectivity to particular ion channel subtypes. FP-Tx are displaced by other potassium channel blockers and can be used as an imaging tool in ion channel ligand screening setups. We believe FP-Tx chimeras represent a new efficient molecular tool for neurobiology.

  7. MOLECULAR TOOL FOR SEX IDENTIFICATION (FEMALE IN MOMORDICA DIOICA ROXB WITH REFERENCE TO MEDICINAL VALUES

    Directory of Open Access Journals (Sweden)

    Baratakke R.C.

    2013-08-01

    Full Text Available Spine gourd (Momordica dioica Roxb. is an important vegetable with high food value and sex specific versatile medicinal value. Momordica dioica, a perennial, rhizomatous, distinctly dioecious climber belongs to family cucurbitaceae. As there are no distinguished morphological markers to identify sex, an easy, rapid and reliable molecular method for female plant identification at pre-flowering stage in Momordica dioica is reported in this paper. Molecular tool like Random amplification of polymorphic DNA was used to identify female plants before pre-flowering stage. A total of 50 random decamer primers were used for screening of specific Random amplification of polymorphic DNA markers in male and female populations. Only one primer OPA-15 amplified genomic DNA in different patterns in male and female genotypes. This sex specific band OPA-15900 was identified only in female lines but not in male lines. This marker may be efficiently used as effective, convenient and reliable molecular markers for female identification in Momordica dioica at pre-flowering stages so that it can be cultivated and utilized for its medicinal purpose.

  8. 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

    2016-01-01

    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. PMID:26879404

  9. Molecular typing of Mycobacterium tuberculosis strains: a fundamental tool for tuberculosis control and elimination

    Directory of Open Access Journals (Sweden)

    Angela Cannas

    2016-06-01

    Full Text Available Tuberculosis (TB is still an important cause of morbidity and mortality worldwide. An improvement of the strategies for disease control is necessary in both low- and high-incidence TB countries. Clinicians, epidemiologists, laboratory specialists, and public health players should work together in order to achieve a significant reduction in TB transmission and spread of drug-resistant strains. Effective TB surveillance relies on early diagnosis of new cases, appropriate therapy, and accurate detection of outbreaks in the community, in order to implement proper TB control strategies. To achieve this goal, information from classical and molecular epidemiology, together with patient clinical data need to be combined. In this review, we summarize the methodologies currently used in molecular epidemiology, namely molecular typing. We will discuss their efficiency to phylogenetically characterize Mycobacterium tuberculosis isolates, and their ability to provide information that can be useful for disease control. We will also introduce next generation sequencing as the methodology that potentially could provide in a short time both, detection of new outbreaks and identification of resistance patterns. This could envision a potential of next generation sequencing as an important tool for accurate patient management and disease control.

  10. Molecular Typing of Mycobacterium Tuberculosis Strains: A Fundamental Tool for Tuberculosis Control and Elimination

    Science.gov (United States)

    Cannas, Angela; Mazzarelli, Antonio; Di Caro, Antonino; Delogu, Giovanni; Girardi, Enrico

    2016-01-01

    Tuberculosis (TB) is still an important cause of morbidity and mortality worldwide. An improvement of the strategies for disease control is necessary in both low- and high-incidence TB countries. Clinicians, epidemiologists, laboratory specialists, and public health players should work together in order to achieve a significant reduction in TB transmission and spread of drug-resistant strains. Effective TB surveillance relies on early diagnosis of new cases, appropriate therapy, and accurate detection of outbreaks in the community, in order to implement proper TB control strategies. To achieve this goal, information from classical and molecular epidemiology, together with patient clinical data need to be combined. In this review, we summarize the methodologies currently used in molecular epidemiology, namely molecular typing. We will discuss their efficiency to phylogenetically characterize Mycobacterium tuberculosis isolates, and their ability to provide information that can be useful for disease control. We will also introduce next generation sequencing as the methodology that potentially could provide in a short time both, detection of new outbreaks and identification of resistance patterns. This could envision a potential of next generation sequencing as an important tool for accurate patient management and disease control. PMID:27403266

  11. Molecular cytogenetics in solid tumors: laboratorial tool for diagnosis, prognosis, and therapy.

    Science.gov (United States)

    Varella-Garcia, Marileila

    2003-01-01

    The remarkable progress in the understanding of leukemogenesis was soundly sustained by methodological developments in the cytogenetic field. Nonrandom chromosomal abnormalities frequently associated with specific types of hematological disease play a major role in their diagnosis and have been demonstrated as independent prognostic indicators. Molecular pathways altered by chimeric or deregulated proteins as a consequence of chromosomal abnormalities have also significantly contributed to the development of targeted therapies, and cytogenetic assays are valuable for selecting patients for treatment and monitoring outcome. In solid tumors, significantly high levels of chromosome abnormalities have been detected, but distinction between critical and irrelevant events has been a major challenge. Consequently, the application of cytogenetic technology as diagnostic, prognostic, or therapeutic tools for these malignancies remains largely under appreciated. The emergence of molecular-based techniques such as fluorescence in situ hybridization was particularly useful for solid malignancies, and the spectrum of their application is rapidly expanding to improve efficiency and sensitivity in cancer prevention, diagnosis, prognosis, and therapy selection, alone or in combination with other diagnostic methods. This overview illustrates current uses and outlines potential applications for molecular cytogenetics in clinical oncology.

  12. 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.

  13. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

  15. Advanced microscopic and histochemical techniques: diagnostic tools in the molecular era of myology

    Directory of Open Access Journals (Sweden)

    G Meola

    2009-06-01

    Full Text Available Over the past two centuries, myology (i.e. the basic and clinical science of muscle and muscle disease has passed through 3 stages of development: the classical period, the modern stage and the molecular era. The classical period spans the last part of nineteenth century and the earlier part of the twentieth century. During this time, several major muscle disease were clinically and pathologically characterized, including Duchenne muscular dystrophy (DMD, myotonic dystrophy (DM and facioscapulohumeral dystrophy (FSHD. The modern stage in the second half of the twentieth century is characterized by the adaptation of histo and cytochemical techniques to the study of muscle biopsies. These tools improved the diagnostic accuracy and made possible the identification of new changes and structures (Engel and Cunningham, 1963; Scarlato, 1975.

  16. Explaining reaction mechanisms using the dual descriptor: a complementary tool to the molecular electrostatic potential.

    Science.gov (United States)

    Martínez-Araya, Jorge Ignacio

    2013-07-01

    The intrinsic reactivity of cyanide when interacting with a silver cation was rationalized using the dual descriptor (DD) as a complement to the molecular electrostatic potential (MEP) in order to predict interactions at the local level. It was found that DD accurately explains covalent interactions that cannot be explained by MEP, which focuses on essentially ionic interactions. This allowed the rationalization of the reaction mechanism that yields silver cyanide in the gas phase. Other similar reaction mechanisms involving a silver cation interacting with water, ammonia, and thiosulfate were also explained by the combination of MEP and DD. This analysis provides another example of the usefulness of DD as a tool for gaining a deeper understanding of any reaction mechanism that is mainly governed by covalent interactions.

  17. Bio-AIMS Collection of Chemoinformatics Web Tools based on Molecular Graph Information and Artificial Intelligence Models.

    Science.gov (United States)

    Munteanu, Cristian R; Gonzalez-Diaz, Humberto; Garcia, Rafael; Loza, Mabel; Pazos, Alejandro

    2015-01-01

    The molecular information encoding into molecular descriptors is the first step into in silico Chemoinformatics methods in Drug Design. The Machine Learning methods are a complex solution to find prediction models for specific biological properties of molecules. These models connect the molecular structure information such as atom connectivity (molecular graphs) or physical-chemical properties of an atom/group of atoms to the molecular activity (Quantitative Structure - Activity Relationship, QSAR). Due to the complexity of the proteins, the prediction of their activity is a complicated task and the interpretation of the models is more difficult. The current review presents a series of 11 prediction models for proteins, implemented as free Web tools on an Artificial Intelligence Model Server in Biosciences, Bio-AIMS (http://bio-aims.udc.es/TargetPred.php). Six tools predict protein activity, two models evaluate drug - protein target interactions and the other three calculate protein - protein interactions. The input information is based on the protein 3D structure for nine models, 1D peptide amino acid sequence for three tools and drug SMILES formulas for two servers. The molecular graph descriptor-based Machine Learning models could be useful tools for in silico screening of new peptides/proteins as future drug targets for specific treatments.

  18. 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.

  19. Practical tools to implement massive parallel pyrosequencing of PCR products in next generation molecular diagnostics.

    Directory of Open Access Journals (Sweden)

    Kim De Leeneer

    Full Text Available Despite improvements in terms of sequence quality and price per basepair, Sanger sequencing remains restricted to screening of individual disease genes. The development of massively parallel sequencing (MPS technologies heralded an era in which molecular diagnostics for multigenic disorders becomes reality. Here, we outline different PCR amplification based strategies for the screening of a multitude of genes in a patient cohort. We performed a thorough evaluation in terms of set-up, coverage and sequencing variants on the data of 10 GS-FLX experiments (over 200 patients. Crucially, we determined the actual coverage that is required for reliable diagnostic results using MPS, and provide a tool to calculate the number of patients that can be screened in a single run. Finally, we provide an overview of factors contributing to false negative or false positive mutation calls and suggest ways to maximize sensitivity and specificity, both important in a routine setting. By describing practical strategies for screening of multigenic disorders in a multitude of samples and providing answers to questions about minimum required coverage, the number of patients that can be screened in a single run and the factors that may affect sensitivity and specificity we hope to facilitate the implementation of MPS technology in molecular diagnostics.

  20. [Consideration on molecular imaging technology as a tool for drug research and development].

    Science.gov (United States)

    Yajima, Kazuyoshi; Nishimura, Shintaro

    2009-03-01

    Molecular imaging technology such as positron emission tomography (PET) and magnetic resonance imaging (MRI) are known as powerful tools for clinical diagnosis in neurology, oncology and so on. As applications to new drug research and development, there are three methodologies which are PK (Pharmacokinetics study), PD (Pharmacodynamic study), and efficacy study. When we use these methodologies for the drug research, we must consider construction of technological environment (tracer, animal model, imaging analysis software, and clinical database) and regulatory environment for GMP (Good Manufacturing Practice) and GCP (Good Clinical Practice) level. Additionally, concept of microdosing and exploratory clinical study was proposed in western countries and the guidance on microdosing study was also announced by Health, Labor and Welfare Ministry on June 3rd 2008. However they may be still in learning phase, we must meet with complexity, high cost, and indigestion. To promote molecular imaging technology into the drug research, integration of the scientists between academia and industry is important because it needs much type of the advanced technologies and skills.

  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. Molecular surveillance as monitoring tool for drug-resistant Plasmodium falciparum in Suriname.

    Science.gov (United States)

    Adhin, Malti R; Labadie-Bracho, Mergiory; Bretas, Gustavo

    2013-08-01

    The aim of this translational study was to show the use of molecular surveillance for polymorphisms and copy number as a monitoring tool to track the emergence and dynamics of Plasmodium falciparum drug resistance. A molecular baseline for Suriname was established in 2005, with P. falciparum chloroquine resistance transporter (pfcrt) and P. falciparum multidrug resistance (pfmdr1) markers and copy number in 40 samples. The baseline results revealed the existence of a uniformly distributed mutated genotype corresponding with the fully mefloquine-sensitive 7G8-like genotype (Y184F, S1034C, N1042D, and D1246Y) and a fixed pfmdr1 N86 haplotype. All samples harbored the pivotal pfcrtK76T mutation, showing that chloroquine reintroduction should not yet be contemplated in Suriname. After 5 years, 40 samples were assessed to trace temporal changes in the status of pfmdr1 polymorphisms and copy number and showed minor genetic alterations in the pfmdr1 gene and no significant changes in copy number, thus providing scientific support for prolongation of the current drug policy in Suriname.

  3. Windowed R-PDLF recoupling: a flexible and reliable tool to characterize molecular dynamics.

    Science.gov (United States)

    Gansmüller, Axel; Simorre, Jean-Pierre; Hediger, Sabine

    2013-09-01

    This work focuses on the improvement of the R-PDLF heteronuclear recoupling scheme, a method that allows quantification of molecular dynamics up to the microsecond timescale in heterogeneous materials. We show how the stability of the sequence towards rf-imperfections, one of the main sources of error of this technique, can be improved by the insertion of windows without irradiation into the basic elements of the symmetry-based recoupling sequence. The impact of this modification on the overall performance of the sequence in terms of scaling factor and homonuclear decoupling efficiency is evaluated. This study indicates the experimental conditions for which precise and reliable measurement of dipolar couplings can be obtained using the popular R18(1)(7) recoupling sequence, as well as alternative symmetry-based R sequences suited for fast MAS conditions. An analytical expression for the recoupled dipolar modulation has been derived that applies to a whole class of sequences with similar recoupling properties as R18(1)(7). This analytical expression provides an efficient and precise way to extract dipolar couplings from the experimental dipolar modulation curves. We hereby provide helpful tools and information for tailoring R-PDLF recoupling schemes to specific sample properties and hardware capabilities. This approach is particularly well suited for the study of materials with strong and heterogeneous molecular dynamics where a precise measurement of dipolar couplings is crucial.

  4. DINAMO: a coupled sequence alignment editor/molecular graphics tool for interactive homology modeling of proteins.

    Science.gov (United States)

    Hansen, M; Bentz, J; Baucom, A; Gregoret, L

    1998-01-01

    Gaining functional information about a novel protein is a universal problem in biomedical research. With the explosive growth of the protein sequence and structural databases, it is becoming increasingly common for researchers to attempt to build a three-dimensional model of their protein of interest in order to gain information about its structure and interactions with other molecules. The two most reliable methods for predicting the structure of a protein are homology modeling, in which the novel sequence is modeled on the known three-dimensional structure of a related protein, and fold recognition (threading), where the sequence is scored against a library of fold models, and the highest scoring model is selected. The sequence alignment to a known structure can be ambiguous, and human intervention is often required to optimize the model. We describe an interactive model building and assessment tool in which a sequence alignment editor is dynamically coupled to a molecular graphics display. By means of a set of assessment tools, the user may optimize his or her alignment to satisfy the known heuristics of protein structure. Adjustments to the sequence alignment made by the user are reflected in the displayed model by color and other visual cues. For instance, residues are colored by hydrophobicity in both the three-dimensional model and in the sequence alignment. This aids the user in identifying undesirable buried polar residues. Several different evaluation metrics may be selected including residue conservation, residue properties, and visualization of predicted secondary structure. These characteristics may be mapped to the model both singly and in combination. DINAMO is a Java-based tool that may be run either over the web or installed locally. Its modular architecture also allows Java-literate users to add plug-ins of their own design.

  5. Circulating tumor cells (CTCs) in breast cancer: a diagnostic tool for prognosis and molecular analysis

    Institute of Scientific and Technical Information of China (English)

    Xiaoshen Dong; R.Katherine Alpaugh; Massimo Cristofanilli

    2012-01-01

    Metastatic breast cancer (MBC) is characterized by a combination of tumor growth,proliferation and metastatic progression and is typically managed with palliative intent.The benefit of standard systemic therapies is relatively limited and the disease is considered incurable suggesting the need to investigate the biological drivers of the various phases of the metastatic process in order to improve the selection of molecularly driven therapies.The detection,enumeration and molecular analysis of circulating tumor cells (CTCs) provide an intriguing opportunity to advance this knowledge.CTCs enumerated by the Food and Drugs Administration-cleared CellSearchTM system are an independent prognostic factor of progression-free survival (PFS) and overall survival (OS) in MBC patients.Several published papers demonstrated the poor prognosis for MBC patients that presented basal CTC count ≥5 in 7.5 mL of blood.Therefore,the enumeration of CTCs during treatment for MBC provides a tool with the ability to predict progression of disease earlier than standard timing of anatomical assessment using conventional radiological tests.During the metastatic process cancer cells exhibit morphological and phenotypic plasticity undergoing epithelial-mesenchymal transition (EMT).This important phenomenon is associated with down regulation of epithelial marker (e.g.,EpCAM) with potential limitations in the applicability of current CTCs enrichment methods.Such observations translated in a number of investigations aimed at improving our capabilities to enumerate and perform molecular characterization of CTCs.Theoretically,the phenotypic analysis of CTCs can represent a "liquid" biopsy of breast tumor that is able to identify a new potential target against the metastatic disease and advance the development and monitoring of personalized therapies.

  6. Fluorescent resonance energy transfer: A tool for probing molecular cell-biomaterial interactions in three dimensions.

    Science.gov (United States)

    Huebsch, Nathaniel D; Mooney, David J

    2007-05-01

    The current paradigm in designing biomaterials is to optimize material chemical and physical parameters based on correlations between these parameters and downstream biological responses, whether in vitro or in vivo. Extensive developments in molecular design of biomaterials have facilitated identification of several biophysical and biochemical variables (e.g. adhesion peptide density, substrate elastic modulus) as being critical to cell response. However, these empirical observations do not indicate whether different parameters elicit cell responses by modulating redundant variables of the cell-material interface (e.g. number of cell-material bonds, cell-matrix mechanics). Recently, fluorescence resonance energy transfer (FRET) has been applied to quantitatively analyze parameters of the cell-material interface for both two- and three-dimensional adhesion substrates. Tools based on FRET have been utilized to quantify several parameters of the cell-material interface relevant to cell response, including molecular changes in matrix proteins induced by interactions both with surfaces and cells, the number of bonds between integrins and their adhesion ligands, and changes in the crosslink density of hydrogel synthetic extracellular matrix analogs. As such techniques allow both dynamic and 3-D analyses they will be useful to quantitatively relate downstream cellular responses (e.g. gene expression) to the composition of this interface. Such understanding will allow bioengineers to fully exploit the potential of biomaterials engineered on the molecular scale, by optimizing material chemical and physical properties to a measurable set of interfacial parameters known to elicit a predictable response in a specific cell population. This will facilitate the rational design of complex, multi-functional biomaterials used as model systems for studying diseases or for clinical applications.

  7. Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study.

    Science.gov (United States)

    Villaveces, J M; Jiménez, R C; Porras, P; Del-Toro, N; Duesbury, M; Dumousseau, M; Orchard, S; Choi, H; Ping, P; Zong, N C; Askenazi, M; Habermann, B H; Hermjakob, Henning

    2015-01-01

    The evidence that two molecules interact in a living cell is often inferred from multiple different experiments. Experimental data is captured in multiple repositories, but there is no simple way to assess the evidence of an interaction occurring in a cellular environment. Merging and scoring of data are commonly required operations after querying for the details of specific molecular interactions, to remove redundancy and assess the strength of accompanying experimental evidence. We have developed both a merging algorithm and a scoring system for molecular interactions based on the proteomics standard initiative-molecular interaction standards. In this manuscript, we introduce these two algorithms and provide community access to the tool suite, describe examples of how these tools are useful to selectively present molecular interaction data and demonstrate a case where the algorithms were successfully used to identify a systematic error in an existing dataset.

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

    Directory of Open Access Journals (Sweden)

    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.

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

    Directory of Open Access Journals (Sweden)

    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 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

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

    Science.gov (United States)

    Cai, Yindi; Chen, Yuan-Liu; Shimizu, Yuki; Ito, So; Gao, Wei; Zhang, Liangchi

    2016-04-01

    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.

  12. Molecular markers and imaging tools to identify malignant potential in Barrett’s esophagus

    Institute of Scientific and Technical Information of China (English)

    Michael; Bennett; Hiroshi; Mashimo

    2014-01-01

    Due to its rapidly rising incidence and high mortality, esophageal adenocarcinoma is a major public health concern, particularly in Western countries. The steps involved in the progression from its predisposing condition, gastroesophageal reflux disease, to its premalignant disorder, Barrett’s esophagus, and to cancer, are incompletely understood. Current screening and surveillance methods are limited by the lack of population-wide utility, incomplete sampling of standard biopsies, and subjectivity of evaluation. Advances in endoscopic ablation have raised the hope of effective therapy for eradication of high-risk Barrett’s lesions, but improvements are needed in determining when to apply this treatment and how to follow patients clinically. Researchers have evaluated numerous potential molecular biomarkers with the goal of detecting dysplasia, with varying degrees of success. The combination of biomarker panels with epidemiologic risk factors to yield clinical risk scoring systems is promising. New approaches to sample tissue may also be combined with these biomarkers for less invasive screening and sur-veillance. The development of novel endoscopic imaging tools in recent years has the potential to markedly improve detection of small foci of dysplasia in vivo. Current and future efforts will aim to determine the combination of markers and imaging modalities that will most effectively improve the rate of early detection of highrisk lesions in Barrett’s esophagus.

  13. Monocyte-targeting supramolecular micellar assemblies: a molecular diagnostic tool for atherosclerosis.

    Science.gov (United States)

    Chung, Eun Ji; Mlinar, Laurie B; Nord, Kathryn; Sugimoto, Matthew J; Wonder, Emily; Alenghat, Francis J; Fang, Yun; Tirrell, Matthew

    2015-02-18

    Atherosclerosis is a multifactorial inflammatory disease that can progress silently for decades and result in myocardial infarction, stroke, and death. Diagnostic imaging technologies have made great strides to define the degree of atherosclerotic plaque burden through the severity of arterial stenosis. However, current technologies cannot differentiate more lethal "vulnerable plaques," and are not sensitive enough for preventive medicine. Imaging early molecular markers and quantifying the extent of disease progression continues to be a major challenge in the field. To this end, monocyte-targeting, peptide amphiphile micelles (PAMs) are engineered through the incorporation of the chemokine receptor CCR2-binding motif of monocyte chemoattractant protein-1 (MCP-1) and MCP-1 PAMs are evaluated preclinically as diagnostic tools for atherosclerosis. Monocyte-targeting is desirable as the influx of monocytes is a marker of early lesions, accumulation of monocytes is linked to atherosclerosis progression, and rupture-prone plaques have higher numbers of monocytes. MCP-1 PAMs bind to monocytes in vitro, and MCP-1 PAMs detect and discriminate between early- and late-stage atherosclerotic aortas. Moreover, MCP-1 PAMs are found to be eliminated via renal clearance and the mononuclear phagocyte system (MPS) without adverse side effects. Thus, MCP-1 PAMs are a promising new class of diagnostic agents capable of monitoring the progression of atherosclerosis.

  14. 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

  15. 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.

  16. 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.

  17. 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.

  18. Potential molecular tools for assessing the public health risk associated with waterborne Cryptosporidium oocysts.

    Science.gov (United States)

    Kothavade, Rajendra J

    2012-08-01

    The use of multiple barrier stages at water and wastewater treatment facilities allows for the effective removal of the vast majority of coliforms and other enteric and non-enteric microbes. Subsequent disinfection steps (chlorine, ozone and UV irradiation) are utilized to inactivate microbes that escape the preceding treatment stages. Most viruses, bacteria and protozoa, such as Giardia, are effectively inactivated by chlorination; however, Cryptosporidium is relatively more resistant to environmental conditions and to chlorination. Therefore, UV disinfection has been introduced at many water and wastewater treatment plants to increase log inactivation. Any accidental treatment failure may pose a significant risk to public health. Waterborne transmission of coccidian parasites such as Cryptosporidium and Giardia continues to be a major public health concern. No effective therapies currently exist to treat cryptosporidiosis and the global increase in immunocompromised populations has emphasized the need for water utilities and public health laboratories to have immediate and reliable access to highly sensitive test methods that can determine the host specificity, viability and infectivity of protozoa in the water supply. The most common method used for monitoring Cryptosporidium oocysts and Giardia cysts at intermediate treatment stages and in finished drinking water is the US EPA Method 1623. Although Cryptosporidium species are morphologically indistinguishable, they differ greatly in their host specificity and infectivity. Method 1623 provides quantitative information about Cryptosporidium and Giardia contamination but cannot distinguish between species for intervention purposes in outbreak situations, nor is this method reliable for determining whether the oocyst on the slide is infective for humans. Molecular methods have proven valuable in diagnosing infectious diseases, especially those for which the causative agent is difficult to grow in culture, and

  19. MST (Molecular Serotyping Tool): a Program for Computer-Assisted Molecular Identification of Escherichia coli and Shigella O Antigens▿

    OpenAIRE

    2010-01-01

    Escherichia coli and Shigella O antigens can be inferred using the rfb-restriction fragment length polymorphism (RFLP) molecular test. We present herein a dynamic programming algorithm-based software to compare the rfb-RFLP patterns of clinical isolates with those in a database containing the 171 previously published patterns corresponding to all known E. coli/Shigella O antigens.

  20. 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.

  1. 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.

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

    Science.gov (United States)

    Cock, Peter J A; Grüning, Björn A; Paszkiewicz, Konrad; Pritchard, Leighton

    2013-01-01

    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).

  3. 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.

  4. Humans, dogs and parasitic zoonoses--unravelling the relationships in a remote endemic community in northeast India using molecular tools.

    Science.gov (United States)

    Traub, R J; Robertson, I D; Irwin, P; Mencke, N; Monis, P; Thompson, R C A

    2003-07-01

    Canine parasitic zoonoses pose a continuing public health problem, especially in developing countries and communities that are socioeconomically disadvantaged. Our study combined the use of conventional and molecular epidemiological tools to determine the role of dogs in transmission of gastrointestinal (GI) parasites such as hookworms, Giardiaand Ascarisin a parasite endemic tea-growing community in northeast India. A highly sensitive and specific PCR-RFLP was developed to detect and differentiate the zoonotic species of canine hookworm eggs directly from faeces. This allowed epidemiological screening of canine hookworm species in this community to be conducted with ease and accuracy. Seventy two percent of dogs were found to harbour A. caninum, 60% A. braziliense and 37% harboured mixed infections with both hookworms. No A. ceylanicum was detected in the dog population. The zoonotic potential of canine Giardiawas also investigated by characterising Giardia duodenalisrecovered from humans and dogs living in the same locality and households, at three different loci. Phylogenetic and epidemiological analysis provided compelling evidence to support the zoonotic transmission of canine Giardia. Molecular tools were also used to identify the species of Ascarisegg present in over 30% of dog faecal samples. The results demonstrated the role of dogs as a significant disseminator and environmental contaminator of Ascaris lumbricoidesin communities where promiscuous defecation practices exist. Our study demonstrated the usefulness of combining conventional and molecular parasitological and epidemiological tools to help solve unresolved relationships with regards to parasitic zoonoses.

  5. Genetic tools for wildlife management: New TWS Working Group focuses on molecular ecology

    Science.gov (United States)

    Latch, Emily; Crowhurst, Rachel S.; Oyler-McCance, Sara J.; Robinson, Stacie

    2014-01-01

    Granted interim status in November, 2013, The Wildlife Society’s (TWS) Molecular Ecology Working Group aims to promote scientific advancement by applying molecular techniques to wildlife ecology, management, and conservation. The working group—composed of sci - entists from diverse backgrounds—met for the first time in Pittsburgh at the TWS Annual Conference held in October. Our overarching goal is to enhance awareness of molecular ecology and genetic applica - tions to wildlife biology and act as an informational and networking resource. During the group’s interim status, which runs for three years, we intend to focus on a broad scope of molecular ecology that is applicable to wildlife including genetic and ge - nomic methods, conservation genetics, non-invasive genetic population monitoring, landscape genetics, evolutionary genetics, and molecular forensics

  6. 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...

  7. A new tool for the molecular identification of Culicoides species of the Obsoletus group: the glass slide microarray approach.

    Science.gov (United States)

    Deblauwe, I; de Witte, J C; de Deken, G; de Deken, R; Madder, M; van Erk, S; Hoza, F A; Lathouwers, D; Geysen, D

    2012-03-01

    Culicoides species of the Obsoletus group (Diptera: Ceratopogonidae) are potential vectors of bluetongue virus serotype 8 (BTV 8), which was introduced into central Western Europe in 2006. Correct morphological species identification of Obsoletus group females is especially difficult and molecular identification is the method of choice. In this study we present a new molecular tool based on probe hybridization using a DNA microarray format to identify Culicoides species of the Obsoletus group. The internal transcribed spacer 1 (ITS1) gene sequences of 55 Culicoides belonging to 13 different species were determined and used, together with 19 Culicoides ITS1 sequences sourced from GenBank, to design species-specific probes for the microarray test. This test was evaluated using the amplified ITS1 sequences of another 85 Culicoides specimens, belonging to 11 species. The microarray test successfully identified all samples (100%) of the Obsoletus group, identifying each specimen to species level within the group. This test has several advantages over existing polymerase chain reaction (PCR)-based molecular tools, including possible capability for parallel analysis of many species, high sensitivity and specificity, and low background signal noise. Hand-spotting of the microarray slide and the use of detection chemistry make this alternative technique affordable and feasible for any diagnostic laboratory with PCR facilities.

  8. 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.

  9. 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.

  10. Selective photodissociation of tailored molecular tags as a tool for quantum optics

    Science.gov (United States)

    Sezer, Ugur; Geyer, Philipp; Kriegleder, Moritz; Debiossac, Maxime; Shayeghi, Armin; Arndt, Markus; Felix, Lukas

    2017-01-01

    Recent progress in synthetic chemistry and molecular quantum optics has enabled demonstrations of the quantum mechanical wave–particle duality for complex particles, with masses exceeding 10 kDa. Future experiments with even larger objects will require new optical preparation and manipulation methods that shall profit from the possibility to cleave a well-defined molecular tag from a larger parent molecule. Here we present the design and synthesis of two model compounds as well as evidence for the photoinduced beam depletion in high vacuum in one case. PMID:28243571

  11. 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.

  12. FDA Bioinformatics Tool for Microbial Genomics Research on Molecular Characterization of Bacterial Foodborne Pathogens Using Microarrays

    Science.gov (United States)

    Background: Advances in microbial genomics and bioinformatics are offering greater insights into the emergence and spread of foodborne pathogens in outbreak scenarios. The Food and Drug Administration (FDA) has developed the genomics tool ArrayTrackTM, which provides extensive functionalities to man...

  13. Global and local properties used as analyses tools for molecular-dynamics simulations

    Science.gov (United States)

    Bachlechner, Martina E.; Anderson, Jonas T.; Cao, Deng; Leonard, Robert H.; Owens, Eli T.; Schiffbauer, Jarrod E.; Burky, Melissa R.; Ducatman, Samuel C.; Guffey, Eric J.; Serrano Ramos2, Fernando

    2006-03-01

    Molecular dynamics simulations have been used to study mechanical failure in realistic interface materials. Averaging over the individual atoms' contributions yields local and global information including displacements, bond angles, strains, stress tensor components, and pair distribution functions. A combined analysis of global and local properties facilitates detailed insight in the mechanisms of failure, which will eventually guide on how to prevent failure of interfaces.

  14. 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.

  15. Application of Machine Learning tools to recognition of molecular patterns in STM images

    Science.gov (United States)

    Maksov, Artem; Ziatdinov, Maxim; Fujii, Shintaro; Kiguchi, Manabu; Higashibayashi, Shuhei; Sakurai, Hidehiro; Kalinin, Sergei; Sumpter, Bobby

    The ability to utilize individual molecules and molecular assemblies as data storage elements has motivated scientist for years, concurrent with the continuous effort to shrink a size of data storage devices in microelectronics industry. One of the critical issues in this effort lies in being able to identify individual molecular assembly units (patterns), on a large scale in an automated fashion of complete information extraction. Here we present a novel method of applying machine learning techniques for extraction of positional and rotational information from scanning tunneling microscopy (STM) images of π-bowl sumanene molecules on gold. We use Markov Random Field (MRF) model to decode the polar rotational states for each molecule in a large scale STM image of molecular film. We further develop an algorithm that uses a convolutional Neural Network combined with MRF and input from density functional theory to classify molecules into different azimuthal rotational classes. Our results demonstrate that a molecular film is partitioned into distinctive azimuthal rotational domains consisting typically of 20-30 molecules. In each domain, the ``bowl-down'' molecules are generally surrounded by six nearest neighbor molecules in ``bowl-up'' configuration, and the resultant overall structure form a periodic lattice of rotational and polar states within each domain. Research was supported by the US Department of Energy.

  16. 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…

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

    NARCIS (Netherlands)

    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 fluoresc

  18. Afterschool Universe - Bringing Astronomy Down to Earth

    Science.gov (United States)

    Krishnamurthi, Anita; Eyermann, S. E.; Mitchell, S.

    2010-01-01

    Bring the universe beyond the solar system to middle-schoolers in your community! Afterschool Universe (AU) is a 12-session out-of-school-time astronomy program that explores astronomy concepts through engaging hands-on activities. It introduces participants to the tools of astronomy and takes them on a journey through the universe beyond the solar system. Afterschool programs reach a very diverse population and are offered in a variety of settings where the students go when the school day is over. The afterschool community is looking for quality science programming that will engage the children. AU offers just such an opportunity to bring science and astronomy to this under-served population. The afterschool community all over the country has received this well-tested curriculum very enthusiastically. It recently passed the rigorous NASA Product Review with flying colors. Help us disseminate it far and wide by working with afterschool program providers in your community. AU is ideally run as a partnership between astronomers or EPO professionals and local afterschool program providers. The former contribute content expertise to help train the program leaders while the latter have a deep understanding of their target audience. This program addresses several IYA themes as it works with an audience that doesn't typically get much exposure to astronomy. The adult afterschool program leaders do not usually have science backgrounds and middle school students do not normally get to explore the topics in Afterschool Universe despite their interest in this content. Bring the universe down to earth by engaging adults and children in your community through an Afterschool Universe partnership!

  19. 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.

  20. A divergent synthetic approach to diverse molecular scaffolds: assessment of lead-likeness using LLAMA, an open-access computational tool.

    Science.gov (United States)

    Colomer, Ignacio; Empson, Christopher J; Craven, Philip; Owen, Zachary; Doveston, Richard G; Churcher, Ian; Marsden, Stephen P; Nelson, Adam

    2016-06-07

    Complementary cyclisation reactions of hex-2-ene-1,6-diamine derivatives were exploited in the synthesis of alternative molecular scaffolds. The value of the synthetic approach was analysed using LLAMA, an open-access computational tool for assessing the lead-likeness and novelty of molecular scaffolds.

  1. 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.

  2. 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.

  3. Laboratory Molecular Astrophysics as an Invaluable Tool in understanding Astronomical Observations.

    Science.gov (United States)

    Fraser, Helen Jane

    2015-08-01

    We are entering the decade of molecular astrochemistry: spectroscopic data pertaining to the interactions between baryonic matter and electromagnetic radiation are now at the forefront of astronomical observations. Elucidating such data is reliant on inputs from laboratory experiments, modeling, and theoretical chemistry / physics, a field that is intended to be a key focus for the proposed new commission in Laboratory Astrophysics.Here, we propose a “tour de force” review of some recent successes since the last GA in molecular astrophysics, particularly those that have been directly facilitated by laboratory data in Astrochemistry. It is vital to highlight to the astronomers that the absence of laboratory data from the literature would otherwise have precluded advances in our astronomical understanding, e.g:the detection of gas-phase water deep in pre-stellar cores,the detection of water and other molecular species in gravitationally lensed galaxies at z~6“Jumps” in the appearance or disappearance of molecules, including the very recent detection of the first branched organic molecule in the ISM, iso-propyl-cyanide,disentangling dense spectroscopic features in the sub-mm as measured by ALMA, Herschel and SOFIA, the so-called “weeds” and “flowers”,the first ''image'' of a CO snow-line in a protoplanetary disk.Looking forward, the advent of high spatial and spectral resolution telescopes, particularly ALMA, SKA E-ELT and JWST, will continue to drive forward the needs and interests of laboratory astrochemistry in the coming decade. We will look forward to five key areas where advances are expected, and both observational and laboratory techniques are evolving:-(a) understanding star forming regions at very high spatial and spectral senstivity and resolution(b) extragalactic astrochemistry(c) (exo-)planetary atmospheres, surfaces and Solar System sample return - linkinginterstellar and planetary chemistry(d) astrobiology - linking simple molecular

  4. Using molecular tools to identify the geographical origin of a case of human brucellosis.

    Science.gov (United States)

    Muchowski, J K; Koylass, M S; Dainty, A C; Stack, J A; Perrett, L; Whatmore, A M; Perrier, C; Chircop, S; Demicoli, N; Gatt, A B; Caruana, P A; Gopaul, K K

    2015-10-01

    Although Malta is historically linked with the zoonosis brucellosis, there had not been a case of the disease in either the human or livestock population for several years. However, in July 2013 a case of human brucellosis was identified on the island. To determine whether this recent case originated in Malta, four isolates from this case were subjected to molecular analysis. Molecular profiles generated using multilocus sequence analysis and multilocus variable number tandem repeat for the recent human case isolates and 11 Brucella melitensis strains of known Maltese origin were compared with others held on in-house and global databases. While the 11 isolates of Maltese origin formed a distinct cluster, the recent human isolation was not associated with these strains but instead clustered with isolates originating from the Horn of Africa. These data was congruent with epidemiological trace-back showed that the individual had travelled to Malta from Eritrea. This work highlights the potential of using molecular typing data to aid in epidemiological trace-back of Brucella isolations and assist in monitoring of the effectiveness of brucellosis control schemes.

  5. Molecular diversity and tools for deciphering the methanogen community structure and diversity in freshwater sediments.

    Science.gov (United States)

    Chaudhary, Prem Prashant; Brablcová, Lenka; Buriánková, Iva; Rulík, Martin

    2013-09-01

    Methanogenic archaeal communities existing in freshwater sediments are responsible for approximately 50 % of the total global emission of methane. This process contributes significantly to global warming and, hence, necessitates interventional control measures to limit its emission. Unfortunately, the diversity and functional interactions of methanogenic populations occurring in these habitats are yet to be fully characterized. Considering several disadvantages of conventional culture-based methodologies, in recent years, impetus is given to molecular biology approaches to determine the community structure of freshwater sedimentary methanogenic archaea. 16S rRNA and methyl coenzyme M reductase (mcrA) gene-based cloning techniques are the first choice for this purpose. In addition, electrophoresis-based (denaturing gradient gel electrophoresis, temperature gradient gel electrophoresis, and terminal restriction fragment length polymorphism) and quantitative real-time polymerase chain reaction techniques have also found extensive applications. These techniques are highly sensitive, rapid, and reliable as compared to traditional culture-dependent approaches. Molecular diversity studies revealed the dominance of the orders Methanomicrobiales and Methanosarcinales of methanogens in freshwater sediments. The present review discusses in detail the status of the diversity of methanogens and the molecular approaches applied in this area of research.

  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. 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…

  8. Molecular tools for epidemiological investigations into Legionella pneumophila environmental diffusion: applications for the prevention

    Directory of Open Access Journals (Sweden)

    Stefania Boccia

    2004-12-01

    Full Text Available

    Microbiological typing is a useful tool in the epidemiological investigations of infectious diseases, given that it allows for the identification of specific clones among a set of isolates.

     In the last ten years several studies have demonstrated how genotyping methods can be useful in Legionella spp investigations in hospital setting (e.g., epidemic events. Pulsed field gel electrophoresis and amplified fragment length polymorphisms are the current typing methods of choice, even though multilocus sequence typing will probably be the gold standard of the future.

  9. In vivo recombination as a tool to generate molecular diversity in phage antibody libraries.

    Science.gov (United States)

    Sblattero, D; Lou, J; Marzari, R; Bradbury, A

    2001-06-01

    The creation of diversity in populations of polypeptides has become an important tool in the derivation of polypeptides with useful characteristics. This requires efficient methods to create diversity coupled with methods to select polypeptides with desired properties. In this review we describe the use of in vivo recombination as a powerful way to generate diversity. The novel principles for the recombination process and several applications of this process for the creation of phage antibody libraries are described. The advantage and disadvantages are discussed and possible future exploitation presented.

  10. A Tool for Brain-Wide Quantitative Analysis of Molecular Data upon Projection into a Planar View of Choice

    Science.gov (United States)

    Vreysen, Samme; Scheyltjens, Isabelle; Laramée, Marie-Eve; Arckens, Lutgarde

    2017-01-01

    Several techniques, allowing the reconstruction and visualization of functional, anatomical or molecular information from tissue and organ slices, have been developed over the years. Yet none allow direct comparison without reprocessing the same slices. Alternative methods using publicly available reference maps like the Allen Brain Atlas lack flexibility with respect to age and species. We propose a new approach to reconstruct a segmented region of interest from serial slices by projecting the optical density values representing a given molecular signal to a plane of view of choice, and to generalize the results into a reference map, which is built from the individual maps of all animals under study. Furthermore, to allow quantitative comparison between experimental conditions, a non-parametric pseudo t-test has been implemented. This new mapping tool was applied, optimized and validated making use of an in situ hybridization dataset that represents the spatiotemporal expression changes for the neuronal activity reporter gene zif268, in relation to cortical plasticity induced by monocular enucleation, covering the entire mouse visual cortex. The created top view maps of the mouse brain allow precisely delineating and interpreting 11 extrastriate areas surrounding mouse V1. As such, and because of the opportunity to create a planar projection of choice, these molecular maps can in the future easily be compared with functional or physiological imaging maps created with other techniques such as Ca2+, flavoprotein and optical imaging. PMID:28144216

  11. Fundamental Limits:. Developing New Tools for a Better Understanding of Second-Order Molecular Nonlinear Optics

    Science.gov (United States)

    Pérez-Moreno, Javier; Clays, Koen

    The generalized Thomas-Kuhn sum rules are used to characterize the nonlinear optical response of organic chromophores in terms of fundamental parameters that can be measured experimentally. The nonlinear optical performance of organic molecules is evaluated from the combination of hyper-Rayleigh scattering measurements and the analysis in terms of the fundamental limits. Different strategies for the enhancement of nonlinear optical behavior at the molecular and supramolecular level are evaluated and new paradigms for the design of more efficient nonlinear optical molecules are proposed and investigated.

  12. 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.

  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

    2015-01-01

    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. PMID:25856580

  14. 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 ...

  15. IROme, a New High-Throughput Molecular Tool for the Diagnosis of Inherited Retinal Dystrophies

    Directory of Open Access Journals (Sweden)

    Daniel F. Schorderet

    2013-01-01

    Full Text Available The molecular diagnosis of retinal dystrophies is difficult because of the very important number of genes implicated and is rarely helped by genotype-phenotype correlations. This prompted us to develop IROme, a custom designed in solution-based targeted exon capture assay (SeqCap EZ Choice library, Roche NimbleGen for 60 retinitis pigmentosa-linked genes and three candidate genes (942 exons. Pyrosequencing was performed on a Roche 454 GS Junior benchtop high-throughput sequencing platform. In total, 23 patients affected by retinitis pigmentosa were analyzed. Per patient, 39.6 Mb were generated, and 1111 sequence variants were detected on average, at a median coverage of 17-fold. After data filtering and sequence variant prioritization, disease-causing mutations were identified in ABCA4, CNGB1, GUCY2D, PROM1, PRPF8, PRPF31, PRPH2, RHO, RP2, and TULP1 for twelve patients (55%, ten mutations having never been reported previously. Potential mutations were identified in 5 additional patients, and in only 6 patients no molecular diagnosis could be established (26%. In conclusion, targeted exon capture and next-generation sequencing are a valuable and efficient approach to identify disease-causing sequence variants in retinal dystrophies.

  16. 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.

  17. IROme, a new high-throughput molecular tool for the diagnosis of inherited retinal dystrophies.

    Science.gov (United States)

    Schorderet, Daniel F; Iouranova, Alexandra; Favez, Tatiana; Tiab, Leila; Escher, Pascal

    2013-01-01

    The molecular diagnosis of retinal dystrophies is difficult because of the very important number of genes implicated and is rarely helped by genotype-phenotype correlations. This prompted us to develop IROme, a custom designed in solution-based targeted exon capture assay (SeqCap EZ Choice library, Roche NimbleGen) for 60 retinitis pigmentosa-linked genes and three candidate genes (942 exons). Pyrosequencing was performed on a Roche 454 GS Junior benchtop high-throughput sequencing platform. In total, 23 patients affected by retinitis pigmentosa were analyzed. Per patient, 39.6 Mb were generated, and 1111 sequence variants were detected on average, at a median coverage of 17-fold. After data filtering and sequence variant prioritization, disease-causing mutations were identified in ABCA4, CNGB1, GUCY2D, PROM1, PRPF8, PRPF31, PRPH2, RHO, RP2, and TULP1 for twelve patients (55%), ten mutations having never been reported previously. Potential mutations were identified in 5 additional patients, and in only 6 patients no molecular diagnosis could be established (26%). In conclusion, targeted exon capture and next-generation sequencing are a valuable and efficient approach to identify disease-causing sequence variants in retinal dystrophies.

  18. 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.

  19. An efficient tool to calculate two-dimensional optical spectra for photoactive molecular complexes

    CERN Document Server

    Duan, Hong-Guang; Nalbach, Peter; Thorwart, Michael

    2015-01-01

    We combine the coherent modified Redfield theory (CMRT) with the equation of motion-phase matching approach (PMA) to calculate two-dimensional photon echo spectra for photoactive molecular complexes with an intermediate strength of the coupling to their environment. Both techniques are highly efficient, yet they involve approximations at different levels. By explicitly comparing with the numerically exact quasi-adiabatic path integral approach, we show for the Fenna-Matthews-Olson complex that the CMRT describes the decay rates in the population dynamics well, but final stationary populations and the oscillation frequencies differ slightly. In addition, we use the combined CMRT+PMA to calculate two-dimensional photon-echo spectra for a simple dimer model. We find excellent agreement with the exact path integral calculations at short waiting times where the dynamics is still coherent. For long waiting times, differences occur due to different final stationary states, specifically for strong system-bath couplin...

  20. Oscillating Magnet Array−Based Nanomagnetic Gene Transfection: A Valuable Tool for Molecular Neurobiology Studies

    Science.gov (United States)

    Subramanian, Mahendran; Tyler, Aimee-Jayne; Luther, Eva Maria; Daniel, Elena Di; Lim, Jenson; Dobson, Jon

    2017-01-01

    To develop treatments for neurodegenerative disorders, it is critical to understand the biology and function of neurons in both normal and diseased states. Molecular studies of neurons involve the delivery of small biomolecules into cultured neurons via transfection to study genetic variants. However, as cultured primary neurons are sensitive to temperature change, stress, and shifts in pH, these factors make biomolecule delivery difficult, particularly non-viral delivery. Herein we used oscillating nanomagnetic gene transfection to successfully transfect SH-SY5Y cells as well as primary hippocampal and cortical neurons on different days in vitro. This novel technique has been used to effectively deliver genetic material into various cell types, resulting in high transfection efficiency and viability. From these observations and other related studies, we suggest that oscillating nanomagnetic gene transfection is an effective method for gene delivery into hard-to-transfect neuronal cell types. PMID:28336862

  1. 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.

  2. Generation of mouse mutants as tools in dissecting the molecular clock.

    Science.gov (United States)

    Anand, Sneha N; Edwards, Jessica K; Nolan, Patrick M

    2012-01-01

    Elucidation of the molecular basis of mammalian circadian rhythms has progressed dramatically in recent years through the characterization of mouse mutants. With the implementation of numerous mouse genetics programs, comprehensive sets of mutations in genes affecting circadian output measures have been generated. Although incomplete, existing arrays of mutants have been instrumental in our understanding of how the internal SCN clock interacts with the environment and how it conveys its rhythm to remote oscillators. The use of ENU mutagenesis has proven to be a significant contributor, generating mutations leading to subtle and distinct alterations in circadian protein function. In parallel, progress with mouse gene targeting allows one to study gene function in depth by ablating it entirely, in specific tissues at specific times, or by targeting specific functional domains. This has culminated in worldwide efforts to target every gene in the mouse genome allowing researchers to study multiple gene targeting effects systematically.

  3. Current Tools and Methods in Molecular Dynamics (MD) Simulations for Drug Design.

    Science.gov (United States)

    Hernández-Rodríguez, Maricarmen; Rosales-Hernández, Martha C; Mendieta-Wejebe, Jessica E; Martínez-Archundia, Marlet; Basurto, José Correa

    2016-01-01

    Molecular Dynamics (MD) simulations is a computational method that employs Newton's laws to evaluate the motions of water, ions, small molecules, and macromolecules or more complex systems, for example, whole viruses, to reproduce the behavior of the biological environment, including water molecules and lipid membranes. Specifically, structural motions, such as those that are dependent of the temperature and solute/ solvent are very important to study the recognition pattern of ligandprotein or protein-protein complexes, in that sense, MD simulations are very useful because these motions can be modeled using this methodology. Furthermore, MD simulations for drug design provide insights into the structural cavities required to design novel structures with higher affinity to the target. Also, the employment of MD simulations to drug design can help to refine the three-dimensional (3D) structure of targets in order to obtain a better sampling of the binding poses and more reliable affinity values with better structural advantages, because they incorporate some biological conditions that include structural motions compared to traditional docking procedures. This work analyzes the concepts and applicability of MD simulations for drug design because molecular structural motions are considered, and these help to identify hot spots, decipher structural details in the reported protein sites, as well as to eliminate sites that could be structural artifacts which could be originated from the structural characterization conditions from MD. Moreover, better free energy values for protein ligand recognition can also be obtained, and these can be validated under experimental procedures due to the robustness of the MD simulation methods.

  4. 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.

  5. Molecularly Characterised Xenograft Tumour Mouse Models: Valuable Tools for Evaluation of New Therapeutic Strategies for Secondary Liver Cancers

    Directory of Open Access Journals (Sweden)

    2009-03-01

    Full Text Available To develop and evaluate new therapeutic strategies for the treatment of human cancers, well-characterised preclinical model systems are a prerequisite. To this aim, we have established xenotransplantation mouse models and corresponding cell cultures from surgically obtained secondary human liver tumours. Established xenograft tumours were patho- and immunohistologically characterised, and expression levels of cancer-relevant genes were quantified in paired original and xenograft tumours and the derivative cell cultures applying RT-PCR-based array technology. Most of the characteristic morphological and immunohistochemical features of the original tumours were shown to be maintained. No differences were found concerning expression of genes involved in cell cycle regulation and oncogenesis. Interestingly, cytokine and matrix metalloproteinase encoding genes appeared to be expressed differentially. Thus, the established models are closely reflecting pathohistological and molecular characteristics of the selected human tumours and may therefore provide useful tools for preclinical analyses of new antitumour strategies in vivo.

  6. Molecular tools and protocols for engineering the acid-tolerant yeast Zygosaccharomyces bailii as a potential cell factory.

    Science.gov (United States)

    Branduardi, Paola; Dato, Laura; Porro, Danilo

    2014-01-01

    Microorganisms offer a tremendous potential as cell factories, and they are indeed used by humans for centuries for biotransformations. Among them, yeasts combine the advantage of unicellular state with a eukaryotic organization, and, in the era of biorefineries, their biodiversity can offer solutions to specific process constraints. Zygosaccharomyces bailii, an ascomycetales budding yeast, is widely known for its peculiar tolerance to various stresses, among which are organic acids. Despite the possibility to apply with this yeast some of the molecular tools and protocols routinely used to manipulate Saccharomyces cerevisiae, adjustments and optimizations are necessary. Here, we describe in detail protocols for transformation, for target gene disruption or gene integration, and for designing episomal expression plasmids helpful for developing and further studying the yeast Z. bailii.

  7. 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.

  8. Major intercontinentally distributed sequence types of Kingella kingae and development of a rapid molecular typing tool.

    Science.gov (United States)

    Basmaci, Romain; Bidet, Philippe; Yagupsky, Pablo; Muñoz-Almagro, Carmen; Balashova, Nataliya V; Doit, Catherine; Bonacorsi, Stéphane

    2014-11-01

    Although Kingella kingae is the most common etiology of osteoarticular infections in young children, is a frequent cause of bacteremia in those younger than 4 years, and has been involved in clusters of invasive infections among daycare center attendees, the population structure of the species has not been systematically studied. Using multilocus sequence typing, we investigated the genetic diversity of the largest intercontinental collection of K. kingae strains to date. To facilitate typing of bacterial isolates, we developed a novel genotyping tool that targets the DNA uptake sequence (DUS). Among 324 strains isolated from asymptomatic carriers and patients from Israel, Europe, North America, and Australia with various invasive forms of the disease from 1960 to 2013, we identified 64 sequence types (STs) and 12 ST complexes (STcs). Five predominant STcs, comprising 72.2% of all strains, were distributed intercontinentally. ST-6 was the most frequent, showing a worldwide distribution, and appeared genotypically isolated by exhibiting few neighboring STs, suggesting an optimal fitness. ST-14 and ST-23 appeared to be the oldest groups of bacteria, while ST-25 probably emerged more recently from the highly evolutive ST-23. Using the DUS typing method, randomly chosen isolates were correctly classified to one of the major STcs. The comprehensive description of K. kingae evolution would help to detect new emerging clones and decipher virulence and fitness mechanisms. The rapid and reproducible DUS typing method may serve in the initial investigation of K. kingae outbreaks.

  9. 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.

  10. Serological and molecular tools to detect neurologic parasitic zoonoses in rural Cameroon.

    Science.gov (United States)

    Nkouawa, Agathe; Sako, Yasuhito; Moyou-Somo, Roger; Ito, Akira

    2011-11-01

    Parasitic helminthiases, such as toxocariasis, cysticercosis and paragonimiasis are a public health threat, since they can affect the brain leading to neurological disorders. Epilepsy and paragonimiasis are common in southwestern Cameroon. We reviewed the literature for studies using antigens to diagnose toxocariasis, cysticercosis, and paragonimiasis. Serology revealed that 61 (36.3%), 26 (15.5%) and 2 (1.2%) of 168 persons examined [78 males (15.2 +/- 8.2 years old), 90 females (12.9 +/- 5.9 years old), 143 persons < 20 years old] had antibody responses to toxocariasis, paragonimiasis and cysticercosis, respectively. Of the 14 people with epilepsy, 5 were seropositive for Toxocara antigens and 1 was positive for both Toxocara and Paragonimus antigens. Two children were serologically confirmed to have cysticercosis. Serologic screening for cysticercosis may be feasible to detect asymptomatic cysticercosis in children in endemic areas leading to early treatment. The causative Paragonimus species was confirmed to be P. africanus by molecular sequencing. Education, screening and confirmation test for these diseases may be needed for control in Cameroon.

  11. 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.)

  12. 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.

  13. 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.

  14. 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.

  15. Multilocus sequence typing as a tool for studying the molecular epidemiology and population structure of Brachyspira hyodysenteriae.

    Science.gov (United States)

    La, Tom; Phillips, Nyree D; Harland, Belinda L; Wanchanthuek, Phatthanaphong; Bellgard, Matthew I; Hampson, David J

    2009-09-18

    The purpose of this study was to develop and apply a multilocus sequence typing (MLST) scheme to study the molecular epidemiology of Brachyspira hyodysenteriae, the aetiological agent of swine dysentery. Sequences of seven conserved genomic loci were examined in 111 B. hyodysenteriae strains. Fifty-eight of these previously had been analysed by multilocus enzyme electrophoresis (MLEE), and for some the results of pulsed field gel electrophoresis (PFGE), restriction endonuclease analysis (REA) and/or serotyping also were available. The discriminatory power of these methods was compared. The strains were divided into 67 sequence types (STs) and 46 amino acid types (AATs) by MLST. The Index of Association value was significantly different from zero, indication that the population was clonal. Eleven clonal complexes (Cc) comprising between 2 and 10 STs were recognised. A population snapshot based on AATs placed 77.5% of the isolates from 30 of the AATs into one major cluster. The founder type AAT9 included 13 strains from nine STs that were isolated in Australia, Sweden, Germany and Belgium, including one from a mallard. The MLST results were generally comparable to those produced by MLEE. The MLST system had a similar discriminatory power to PFGE, but was more discriminatory than REA, MLEE or serotyping. MLST data provided evidence for likely transmission of strains between farms, but also for the occurrence of temporal "micro-evolution" of strains on individual farms. Overall, the MLST system proved to be a useful new tool for investigating the molecular epidemiology and diversity of B. hyodysenteriae.

  16. Electrochemical reverse engineering: A systems-level tool to probe the redox-based molecular communication of biology.

    Science.gov (United States)

    Li, Jinyang; Liu, Yi; Kim, Eunkyoung; March, John C; Bentley, William E; Payne, Gregory F

    2016-12-29

    The intestine is the site of digestion and forms a critical interface between the host and the outside world. This interface is composed of host epithelium and a complex microbiota which is "connected" through an extensive web of chemical and biological interactions that determine the balance between health and disease for the host. This biology and the associated chemical dialogues occur within a context of a steep oxygen gradient that provides the driving force for a variety of reduction and oxidation (redox) reactions. While some redox couples (e.g., catecholics) can spontaneously exchange electrons, many others are kinetically "insulated" (e.g., biothiols) allowing the biology to set and control their redox states far from equilibrium. It is well known that within cells, such non-equilibrated redox couples are poised to transfer electrons to perform reactions essential to immune defense (e.g., transfer from NADH to O2 for reactive oxygen species, ROS, generation) and protection from such oxidative stresses (e.g., glutathione-based reduction of ROS). More recently, it has been recognized that some of these redox-active species (e.g., H2O2) cross membranes and diffuse into the extracellular environment including lumen to transmit redox information that is received by atomically-specific receptors (e.g., cysteine-based sulfur switches) that regulate biological functions. Thus, redox has emerged as an important modality in the chemical signaling that occurs in the intestine and there have been emerging efforts to develop the experimental tools needed to probe this modality. We suggest that electrochemistry provides a unique tool to experimentally probe redox interactions at a systems level. Importantly, electrochemistry offers the potential to enlist the extensive theories established in signal processing in an effort to "reverse engineer" the molecular communication occurring in this complex biological system. Here, we review our efforts to develop this

  17. 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.

  18. 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.

  19. 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

  20. Molecular Probes: A Tool for Studying Toxicity of VOCs to P.Putida F1

    Science.gov (United States)

    Singh, R.; Olson, M. S.

    2007-12-01

    Volatile Organic Compounds (VOCs) are of great concern in ground water remediation, and are generally present in the form of NAPLs in subsurface environments. Among the various treatment technologies, in situ bioremediation is one of the most effective and low-cost treatment options. Many soil bacteria are reported to degrade these organic contaminants via metabolism (using them as a source of carbon to derive energy) or co- metabolism up to certain concentrations. However, larger concentrations of these contaminants are toxic to bacteria. Thus, in order to achieve successful bioremediation, it is important to determine the optimal concentrations of various contaminants that is beneficial for the activity and survival of degrading bacteria. The purpose of this study is to develop a novel method for toxicity analyses of VOC contaminants to the soil bacteria that degrade them. The present study is based on a two-color fluorescence assay of bacterial viability which facilitates actual counting of live and dead bacteria. Pseudomonas putida F1 cells were labeled with a LIVE/DEAD® BacLightTM bacterial viability kit (Invitrogen), which consists of a mixture of two dyes, SYTO 9 and propidium iodide, each with a different ability to penetrate healthy bacterial cells. Live cells stain green whereas propidium iodide (red dye) only penetrates cells with compromised membranes that are considered dead or dying. Stained cells were exposed to different concentrations of trichloroethylene (TCE) and toluene in sealed vials. Change in the concentrations of green and red cells were monitored over the time using fluorescence microscopy. UTHSCSA ImageTool software was used to count the live and dead cells in the images. It was observed that live (green) cell concentrations decreased and dead/damaged (red) cell concentrations increased over time when cells were exposed to TCE. No significant changes were observed in control experiments. Death rate constants calculated based on live cell

  1. 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.

  2. Evaluation of a gp63-PCR based assay as a molecular diagnosis tool in canine leishmaniasis in Tunisia.

    Directory of Open Access Journals (Sweden)

    Souheila Guerbouj

    Full Text Available A gp63PCR method was evaluated for the detection and characterization of Leishmania (Leishmania (L. parasites in canine lymph node aspirates. This tool was tested and compared to other PCRs based on the amplification of 18S ribosomal genes, a L. infantum specific repetitive sequence and kinetoplastic DNA minicircles, and to classical parasitological (smear examination and/or culture or serological (IFAT techniques on a sample of 40 dogs, originating from different L. infantum endemic regions in Tunisia. Sensitivity and specificity of all the PCR assays were evaluated on parasitologically confirmed dogs within this sample (N = 18 and control dogs (N = 45 originating from non-endemic countries in northern Europe and Australia. The gp63 PCR had 83.5% sensitivity and 100% specificity, a performance comparable to the kinetoplast PCR assay and better than the other assays. These assays had comparable results when the gels were southern transferred and hybridized with a radioactive probe. As different infection rates were found according to the technique, concordance of the results was estimated by (κ test. Best concordance values were between the gp63PCR and parasitological methods (74.6%, 95% confidence intervals CI: 58.8-95.4% or serology IFAT technique (47.4%, 95% CI: 23.5-71.3%. However, taken together Gp63 and Rib assays covered most of the samples found positive making of them a good alternative for determination of infection rates. Potential of the gp63PCR-RFLP assay for analysis of parasite genetic diversity within samples was also evaluated using 5 restriction enzymes. RFLP analysis confirmed assignment of the parasites infecting the dogs to L. infantum species and illustrated occurrence of multiple variants in the different endemic foci. Gp63 PCR assay thus constitutes a useful tool in molecular diagnosis of L. infantum infections in dogs in Tunisia.

  3. Evaluation of a gp63–PCR Based Assay as a Molecular Diagnosis Tool in Canine Leishmaniasis in Tunisia

    Science.gov (United States)

    Guerbouj, Souheila; Djilani, Fattouma; Bettaieb, Jihene; Lambson, Bronwen; Diouani, Mohamed Fethi; Ben Salah, Afif; Ben Ismail, Riadh; Guizani, Ikram

    2014-01-01

    A gp63PCR method was evaluated for the detection and characterization of Leishmania (Leishmania) (L.) parasites in canine lymph node aspirates. This tool was tested and compared to other PCRs based on the amplification of 18S ribosomal genes, a L. infantum specific repetitive sequence and kinetoplastic DNA minicircles, and to classical parasitological (smear examination and/or culture) or serological (IFAT) techniques on a sample of 40 dogs, originating from different L. infantum endemic regions in Tunisia. Sensitivity and specificity of all the PCR assays were evaluated on parasitologically confirmed dogs within this sample (N = 18) and control dogs (N = 45) originating from non–endemic countries in northern Europe and Australia. The gp63 PCR had 83.5% sensitivity and 100% specificity, a performance comparable to the kinetoplast PCR assay and better than the other assays. These assays had comparable results when the gels were southern transferred and hybridized with a radioactive probe. As different infection rates were found according to the technique, concordance of the results was estimated by (κ) test. Best concordance values were between the gp63PCR and parasitological methods (74.6%, 95% confidence intervals CI: 58.8–95.4%) or serology IFAT technique (47.4%, 95% CI: 23.5–71.3%). However, taken together Gp63 and Rib assays covered most of the samples found positive making of them a good alternative for determination of infection rates. Potential of the gp63PCR-RFLP assay for analysis of parasite genetic diversity within samples was also evaluated using 5 restriction enzymes. RFLP analysis confirmed assignment of the parasites infecting the dogs to L. infantum species and illustrated occurrence of multiple variants in the different endemic foci. Gp63 PCR assay thus constitutes a useful tool in molecular diagnosis of L. infantum infections in dogs in Tunisia. PMID:25153833

  4. Bringing Planctomycetes into pure culture

    Directory of Open Access Journals (Sweden)

    Olga Maria Lage

    2012-12-01

    Full Text Available Planctomycetes have been known since the description of Planctomyces bekefii by Gimesi at the beginning of the twentieth century (1924, although the first axenic cultures were only obtained in the 1970s. Since then, eleven genera with fourteen species have been validly named and five candidatus genera belonging to the anaerobic ammonium oxidation, anammox bacteria have also been discovered. However, Planctomycetes diversity is much broader than these numbers indicate, as shown by environmental molecular studies. In recent years the authors have attempted to isolate and cultivate additional strains of Planctomycetes. This paper provides a summary of the isolation work that was carried out to obtain in pure culture Planctomycetes from several environmental sources. The following strains and planctomycetes have been successfully isolated: two freshwater strains from the sediments of an aquarium, which were described as a new genus and species, Aquisphaera giovannonii; several Rhodopirellula strains from the sediments of a water treatment recycling tank of a marine fish farm; and more than 140 planctomycetes from the biofilm community of macroalgae. This collection comprises several novel taxa that are being characterized and described. Improvements in the isolation methodology were made in order to optimize and enlarge the number of Planctomycetes isolated from the macroalgae. The existence of an intimate and an important relationship between planctomycetes and macroalgae reported before by molecular studies is therefore supported by culture dependent methods.

  5. Molecular tools for bathing water assessment in Europe: Balancing social science research with a rapidly developing environmental science evidence-base.

    Science.gov (United States)

    Oliver, David M; Hanley, Nick D; van Niekerk, Melanie; Kay, David; Heathwaite, A Louise; Rabinovici, Sharyl J M; Kinzelman, Julie L; Fleming, Lora E; Porter, Jonathan; Shaikh, Sabina; Fish, Rob; Chilton, Sue; Hewitt, Julie; Connolly, Elaine; Cummins, Andy; Glenk, Klaus; McPhail, Calum; McRory, Eric; McVittie, Alistair; Giles, Amanna; Roberts, Suzanne; Simpson, Katherine; Tinch, Dugald; Thairs, Ted; Avery, Lisa M; Vinten, Andy J A; Watts, Bill D; Quilliam, Richard S

    2016-02-01

    The use of molecular tools, principally qPCR, versus traditional culture-based methods for quantifying microbial parameters (e.g., Fecal Indicator Organisms) in bathing waters generates considerable ongoing debate at the science-policy interface. Advances in science have allowed the development and application of molecular biological methods for rapid (~2 h) quantification of microbial pollution in bathing and recreational waters. In contrast, culture-based methods can take between 18 and 96 h for sample processing. Thus, molecular tools offer an opportunity to provide a more meaningful statement of microbial risk to water-users by providing near-real-time information enabling potentially more informed decision-making with regard to water-based activities. However, complementary studies concerning the potential costs and benefits of adopting rapid methods as a regulatory tool are in short supply. We report on findings from an international Working Group that examined the breadth of social impacts, challenges, and research opportunities associated with the application of molecular tools to bathing water regulations.

  6. 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

    Thermal tetrachloroethene (PCE) remediation by steam injection in a sandy aquifer led to the release of dissolved organic carbon (DOC) from aquifer sediments resulting in more reduced redox conditions, accelerated PCE biodegradation, and changes in microbial populations. These changes were docume...... with molecular biology tools to evaluate which biogeochemical processes are taking place in an aquifer contaminated with chlorinated ethenes....

  7. 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.

  8. 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

  9. 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.

  10. Integrated system brings hospital data together.

    Science.gov (United States)

    Johnson, K F

    1987-10-01

    Healthcare industry changes during the 1980s--increased competition and alterations in the Medicare payment methodology--place new and more complex demands on a hospital's information systems, which often fall short of meeting those demands. These systems were designed for financial reporting, billing, or providing clinical data, and few of them are capable of linking with other unrelated systems. Today's hospital manager needs timely and simultaneous access to data from a variety of sources within the hospital. All the elements to accomplish this are collected somewhere in the hospital, but finding them and bringing them together is difficult. The key to the efficient management and use of data bases is in understanding the fundamental concept of relational data bases, which is the capability of linking or joining separate data files through a common data element in each file. In this way, data files may be integrated into a "related" data base. Any number of separate files, or tables, may exist within a "relational" data base as long as a series of threads links them. A strategic management information data base includes the information necessary to analyze, understand, and manage the hospital's markets, products, resources, and profitability. The major components of this information system are the case mix and cost accounting, budgeting, and modeling systems. The case mix and cost accounting factors involve managing concrete pieces of data, whereas the budgeting and modeling factors manipulate data to create a scenario. The strategic management information data base is the foundation of a hospital's decision support system, which is rapidly moving into the category of a necessary tool of the hospital manager's trade.

  11. 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.

  12. Impact of gastrointestinal parasitic nematodes of sheep, and the role of advanced molecular tools for exploring epidemiology and drug resistance - an Australian perspective.

    Science.gov (United States)

    Roeber, Florian; Jex, Aaron R; Gasser, Robin B

    2013-05-27

    Parasitic nematodes (roundworms) of small ruminants and other livestock have major economic impacts worldwide. Despite the impact of the diseases caused by these nematodes and the discovery of new therapeutic agents (anthelmintics), there has been relatively limited progress in the development of practical molecular tools to study the epidemiology of these nematodes. Specific diagnosis underpins parasite control, and the detection and monitoring of anthelmintic resistance in livestock parasites, presently a major concern around the world. The purpose of the present article is to provide a concise account of the biology and knowledge of the epidemiology of the gastrointestinal nematodes (order Strongylida), from an Australian perspective, and to emphasize the importance of utilizing advanced molecular tools for the specific diagnosis of nematode infections for refined investigations of parasite epidemiology and drug resistance detection in combination with conventional methods. It also gives a perspective on the possibility of harnessing genetic, genomic and bioinformatic technologies to better understand parasites and control parasitic diseases.

  13. 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 ...

  14. Zika Infection May Bring Future Immunity

    Science.gov (United States)

    ... page: https://medlineplus.gov/news/fullstory_161496.html Zika Infection May Bring Future Immunity: Study Individuals, and ... HealthDay News) -- People who've been infected with Zika face a low risk for another bout with ...

  15. Bring Your Own Technology (BYOT) to Education

    OpenAIRE

    2014-01-01

    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 explore...

  16. Bringing Space Crisis Stability Down to Earth

    Science.gov (United States)

    2015-01-01

    JFQ 76, 1st Quarter 2015 Finch 15 Bringing Space Crisis Stability Down to Earth By James P. Finch T ensions in the South and East China seas have...0704-0188 Public reporting burden for the collection of information is estimated to average 1 hour per response, including the time for reviewing...2015 to 00-00-2015 4. TITLE AND SUBTITLE Bringing Space Crisis Stability Down to Earth 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT

  17. The innate antiviral immune system of the cat: molecular tools for the measurement of its state of activation.

    Science.gov (United States)

    Robert-Tissot, Céline; Rüegger, Vera L; Cattori, Valentino; Meli, Marina L; Riond, Barbara; Gomes-Keller, Maria Alice; Vögtlin, Andrea; Wittig, Burghardt; Juhls, Christiane; Hofmann-Lehmann, Regina; Lutz, Hans

    2011-10-15

    Poly IC, Resiquimod (R-848) and dSLIM™, a synthetic oligonucleotide containing several unmethylated CpG motifs. Stimulation of feline PBMCs with dSLIM™ and R-848 effectively enhanced expression of IFNα within 12h by factors of 6 and 12, respectively, and Poly IC induced an increase in Mx mRNA expression of 28-fold. Altogether, we describe new molecular tools and their successful use for the characterization of innate immune responses against viruses in the cat and provide evidence that feline cells can be stimulated by synthetic molecules to enhance their antiviral defence mechanisms.

  18. Bioinformatics in bacterial molecular epidemiology and public health : databases, tools and the next-generation sequencing revolution

    NARCIS (Netherlands)

    Carrico, J. A.; Sabat, A. J.; Friedrich, A. W.; Ramirez, M.

    2013-01-01

    Advances in typing methodologies have been the driving force in the field of molecular epidemiology of pathogens. The development of molecular methodologies, and more recently of DNA sequencing methods to complement and improve phenotypic identification methods, was accompanied by the generation of

  19. 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. T

  20. 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.

  1. 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…

  2. Bringing Research into Educational Practice: Lessons Learned

    Science.gov (United States)

    Hille, Katrin

    2011-01-01

    Bringing research into educational practice is necessary but does not happen automatically. The Transfercenter for Neuroscience and Learning, at the University of Ulm in Germany, is set up to transfer (neuro)scientific knowledge into educational practice. In doing so we have learned why this does not happen automatically, and have tried to make…

  3. Unexpected diversity of Anopheles species in Eastern Zambia: implications for evaluating vector behavior and interventions using molecular tools.

    Science.gov (United States)

    Lobo, Neil F; St Laurent, Brandyce; Sikaala, Chadwick H; Hamainza, Busiku; Chanda, Javan; Chinula, Dingani; Krishnankutty, Sindhu M; Mueller, Jonathan D; Deason, Nicholas A; Hoang, Quynh T; Boldt, Heather L; Thumloup, Julie; Stevenson, Jennifer; Seyoum, Aklilu; Collins, Frank H

    2015-12-09

    The understanding of malaria vector species in association with their bionomic traits is vital for targeting malaria interventions and measuring effectiveness. Many entomological studies rely on morphological identification of mosquitoes, limiting recognition to visually distinct species/species groups. Anopheles species assignments based on ribosomal DNA ITS2 and mitochondrial DNA COI were compared to morphological identifications from Luangwa and Nyimba districts in Zambia. The comparison of morphological and molecular identifications determined that interpretations of species compositions, insecticide resistance assays, host preference studies, trap efficacy, and Plasmodium infections were incorrect when using morphological identification alone. Morphological identifications recognized eight Anopheles species while 18 distinct sequence groups or species were identified from molecular analyses. Of these 18, seven could not be identified through comparison to published sequences. Twelve of 18 molecularly identified species (including unidentifiable species and species not thought to be vectors) were found by PCR to carry Plasmodium sporozoites - compared to four of eight morphological species. Up to 15% of morphologically identified Anopheles funestus mosquitoes in insecticide resistance tests were found to be other species molecularly. The comprehension of primary and secondary malaria vectors and bionomic characteristics that impact malaria transmission and intervention effectiveness are fundamental in achieving malaria elimination.

  4. "Mycobacterium tilburgii" Infection in Two Immunocompromised Children: Importance of Molecular Tools in Culture-Negative Mycobacterial Disease Diagnosis

    NARCIS (Netherlands)

    Hartwig, N.G.; Warris, A.; Vosse, E. van de; Zanden, A.G. van der; Schulin-Casonato, T.; Ingen, J. van; Hest, R. van

    2011-01-01

    "Mycobacterium tilburgii" is a nontuberculous mycobacterium that cannot be cultured by current techniques. It is described as causing disseminated disease in adults. We present the first cases of disseminated disease in 2 immunocompromised children. This paper stresses the importance of molecular te

  5. 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 u

  6. IS element IS16 as a molecular screening tool to identify hospital-associated strains of Enterococcus faecium

    NARCIS (Netherlands)

    Werner, Guido; Fleige, Carola; Geringer, Uta; van Schaik, Willem; Klare, Ingo; Witte, Wolfgang

    2011-01-01

    Background: Hospital strains of Enterococcus faecium could be characterized and typed by various molecular methods (MLST, AFLP, MLVA) and allocated to a distinct clonal complex known as MLST CC17. However, these techniques are laborious, time-consuming and cost-intensive. Our aim was to identify hos

  7. 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.

  8. In-Silico search of Tailored Cox-2 Inhibitors: Screening of Quinazolinone derivatives via molecular modeling Tools

    Directory of Open Access Journals (Sweden)

    Samad Abdul

    2014-06-01

    Full Text Available Novel Quinazoline derivatives were designed through in silico studies including Molecular properties prediction, Toxicity risk prediction and by Molecular Docking approaches. The hypothetically designed molecules were studied for Lipinski rule of 5 properties. The successful molecules were subjected to toxicity risk prediction by Osiris property calculator.The docking methodology applied in the study was first validated by redocking the celecoxib in cox-2 domain with the co-crystallized one. Cox-2 protein was explored for the residues imperative for activity by analyzing the binding pattern of celecoxib and selected compounds of quinazolinone derivatives in the active domain. All the selected molecules passed Lipinski rule of five successfully and they were safe. The docking results explored that compound IQ1, IQ2, IQ5, IQ8 and IQ12 have binding affinity -9.3, which indicated that these compounds may prove successful anti-inflammatory oral candidates.

  9. 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.

  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. Virtual Waterless Port:" BRING THE PORT FORWARD"

    Institute of Scientific and Technical Information of China (English)

    Wang Siyuan

    2009-01-01

    @@ To deal with the crisis,the central government of China carried out"ten major industries stimulating programme",which includes logistics and information industry.Lifting the development of logistics and information industry to a level of national strategy,it shows that the central governments is paying great attention to construct modern logistics service system,cut the costs and improve efficiency,bringing an opportunity for Chinese logistics industry.

  12. 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.

  13. China-Vietnam Friendship Bringing Light Tour

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    <正>At the invitation of the Vietnam Union of Friendship Organizations (VUFO),a delegation headed by CPAFFC Vice President Feng Zuoku and composed of a medical team from Beijing Tongren Hospital made a"China-Vietnam Friendship Bringing Light Tour to Vietnam"from November 13 to 20,2009 and gave free cataract surgery to about 100 patients in Bac Giang Province.

  14. Investigation of torsional potentials, molecular structure, vibrational properties, molecular characteristics and NBO analysis of some bipyridines using experimental and theoretical tools

    Science.gov (United States)

    Prashanth, J.; Reddy, B. Venkatram; Rao, G. Ramana

    2016-08-01

    The Fourier Transform Infrared (FTIR) and Fourier Transform Raman (FT-Raman) spectra of 2,2‧-bipyridine (2BPE); 4,4‧-bipyridine (4BPE); and 2,4‧-bipyridine (24BPE) were measured in the range 4000-450 cm-1 and 4000-50 cm-1, respectively. Torsional potentials were evaluated at various angles of rotation around the C-C inter-ring bond for the three molecules in order to arrive at the molecular conformation of lowest energy. This conformation was further optimized to get ground state geometry. Vibrational frequencies along with infrared and Raman intensities were computed. In the above calculations, DFT employing B3LYP functional with 6311++G(d,p) basis set was used. The rms error between observed and calculated frequencies was 10.0, 10.9 and 10.2 cm-1 for 2BPE, 4BPE and 24BPE, respectively. A 54-parameter modified valence force field was derived by solving inverse vibrational problem using Wilson's GF matrix method. The force constants were refined using 117 experimental frequencies of the three molecules in overlay least-squares technique. The average error between observed and computed frequencies was 12.44 cm-1. PED and eigen vectors calculated in the process were used to make unambiguous vibrational assignments of all the fundamental vibrations. The values of dipole moment, polarizability and hyperpolarizability were computed to determine the NLO behaviour of these molecules. The HOMO and LUMO energies, thermodynamic parameters and molecular electrostatic surface potentials (MESP) were also evaluated. Stability of the molecules arising from hyper conjugative interactions, charge delocalization have been analyzed using natural bond orbital (NBO) analysis.

  15. HBP Builder: A Tool to Generate Hyperbranched Polymers and Hyperbranched Multi-Arm Copolymers for Coarse-grained and Fully Atomistic Molecular Simulations

    Science.gov (United States)

    Yu, Chunyang; Ma, Li; Li, Shanlong; Tan, Haina; Zhou, Yongfeng; Yan, Deyue

    2016-05-01

    Computer simulation has been becoming a versatile tool that can investigate detailed information from the microscopic scale to the mesoscopic scale. However, the crucial first step of molecular simulation is model building, particularly for hyperbranched polymers (HBPs) and hyperbranched multi-arm copolymers (HBMCs) with complex and various topological structures. Unlike well-defined polymers, not only the molar weight of HBPs/HBMCs with polydispersity, but the HBPs/HBMCs with the same degree of polymerization (DP) and degree of branching (DB) also have many possible topological structures, thus making difficulties for user to build model in molecular simulation. In order to build a bridge between model building and molecular simulation of HBPs and HBMCs, we developed HBP Builder, a C language open source HBPs/HBMCs building toolkit. HBP Builder implements an automated protocol to build various coarse-grained and fully atomistic structures of HBPs/HBMCs according to user’s specific requirements. Meanwhile, coarse-grained and fully atomistic output structures can be directly employed in popular simulation packages, including HOOMD, Tinker and Gromacs. Moreover, HBP Builder has an easy-to-use graphical user interface and the modular architecture, making it easy to extend and reuse it as a part of other program.

  16. WI-38 cell long-term quiescence model system: a valuable tool to study molecular events that regulate growth.

    Science.gov (United States)

    Soprano, K J

    1994-04-01

    A number of cell culture model systems have been used to study the regulation of cell cycle progression at the molecular level. In this paper we describe the WI-38 cell long-term quiescence model system. By modulating the length of time that WI-38 cells are density arrested, it is possible to proportionately alter the length of the prereplicative or G-1 phase which the cell traverses after growth factor stimulation in preparation for entry into DNA synthesis. Through studies aimed at understanding the cause and molecular nature of the prolongation of the prereplicative phase, we have determined that gene expression plays an important role in establishing growth factor "competence" and that once the cell becomes "competent" there is a defined order to the molecular events that follow during the remainder of G-1. More specifically, we have determined that the prolongation represents a delay in the ability of long term quiescent cells to become fully "competent" to respond to growth factors which regulate progression through G-1 into S. This prolongation appears to occur as a result of changes during long term quiescence in the ability of immediate early G-1 specific genes (such as c-myc) to activate the expression of early G-1 specific genes (such as ornithine decarboxylase). While ODC is the first and thus far only growth associated gene identified as a target of c-myc (and the Myc/Max protein complex), it is likely that further studies in this model system will reveal other early G-1 growth regulatory genes. We anticipate that future follow-up studies in this model system will provide additional valuable information about the function of growth-regulatory genes in controlling growth factor responsiveness and cell cycle progression.

  17. Root gravitropism: an experimental tool to investigate basic cellular and molecular processes underlying mechanosensing and signal transmission in plants

    Science.gov (United States)

    Boonsirichai, K.; Guan, C.; Chen, R.; Masson, P. H.

    2002-01-01

    The ability of plant organs to use gravity as a guide for growth, named gravitropism, has been recognized for over two centuries. This growth response to the environment contributes significantly to the upward growth of shoots and the downward growth of roots commonly observed throughout the plant kingdom. Root gravitropism has received a great deal of attention because there is a physical separation between the primary site for gravity sensing, located in the root cap, and the site of differential growth response, located in the elongation zones (EZs). Hence, this system allows identification and characterization of different phases of gravitropism, including gravity perception, signal transduction, signal transmission, and curvature response. Recent studies support some aspects of an old model for gravity sensing, which postulates that root-cap columellar amyloplasts constitute the susceptors for gravity perception. Such studies have also allowed the identification of several molecules that appear to function as second messengers in gravity signal transduction and of potential signal transducers. Auxin has been implicated as a probable component of the signal that carries the gravitropic information between the gravity-sensing cap and the gravity-responding EZs. This has allowed the identification and characterization of important molecular processes underlying auxin transport and response in plants. New molecular models can be elaborated to explain how the gravity signal transduction pathway might regulate the polarity of auxin transport in roots. Further studies are required to test these models, as well as to study the molecular mechanisms underlying a poorly characterized phase of gravitropism that is independent of an auxin gradient.

  18. Computational Immunology Meets Bioinformatics: The Use of Prediction Tools for Molecular Binding in the Simulation of the Immune System

    DEFF Research Database (Denmark)

    Rapin, N.; Lund, Ole; Bernaschi, M.

    2010-01-01

    -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......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...

  19. New molecular tools for the identification of 2 endangered smooth-hound sharks, Mustelus mustelus and Mustelus punctulatus.

    Science.gov (United States)

    Marino, Ilaria A M; Riginella, Emilio; Cariani, Alessia; Tinti, Fausto; Farrell, Edward D; Mazzoldi, Carlotta; Zane, Lorenzo

    2015-01-01

    The smooth-hounds represent a significant proportion of the elasmobranch catch in the Adriatic basin of the Mediterranean Sea, where the common (Mustelus mustelus) and blackspotted (Mustelus punctulatus) smooth-hounds co-occur. The 2 species share several morphological and morphometric characters that lead to frequent misidentification. In order to provide information useful for their species identification, we performed a morphological identification of several Mustelus specimens to select individuals unambiguously attributed to 1 of the 2 species, and assayed these with 3 new molecular tests. First, we developed and validated a mitochondrial DNA assay based on species-specific amplification of the cytochrome c oxidase subunit 1 (COI). Second, a fragment analysis of 15 microsatellites cross-amplified from several triakid species was performed to identify diagnostic loci. Finally, a length difference was identified in the internal transcribed spacer 2 (ITS2) region and a diagnostic test based on its amplification was established. All the samples classified morphologically as M. mustelus and M. punctulatus showed a species-specific profile using all the 3 molecular tests. In addition, cross-amplification of microsatellites allowed identification of 9 highly polymorphic loci that will be useful for the study of the mating system and population differentiation of the 2 species.

  20. SignS: a parallelized, open-source, freely available, web-based tool for gene selection and molecular signatures for survival and censored data

    Directory of Open Access Journals (Sweden)

    Diaz-Uriarte Ramon

    2008-01-01

    Full Text Available Abstract Background Censored data are increasingly common in many microarray studies that attempt to relate gene expression to patient survival. Several new methods have been proposed in the last two years. Most of these methods, however, are not available to biomedical researchers, leading to many re-implementations from scratch of ad-hoc, and suboptimal, approaches with survival data. Results We have developed SignS (Signatures for Survival data, an open-source, freely-available, web-based tool and R package for gene selection, building molecular signatures, and prediction with survival data. SignS implements four methods which, according to existing reviews, perform well and, by being of a very different nature, offer complementary approaches. We use parallel computing via MPI, leading to large decreases in user waiting time. Cross-validation is used to asses predictive performance and stability of solutions, the latter an issue of increasing concern given that there are often several solutions with similar predictive performance. Biological interpretation of results is enhanced because genes and signatures in models can be sent to other freely-available on-line tools for examination of PubMed references, GO terms, and KEGG and Reactome pathways of selected genes. Conclusion SignS is the first web-based tool for survival analysis of expression data, and one of the very few with biomedical researchers as target users. SignS is also one of the few bioinformatics web-based applications to extensively use parallelization, including fault tolerance and crash recovery. Because of its combination of methods implemented, usage of parallel computing, code availability, and links to additional data bases, SignS is a unique tool, and will be of immediate relevance to biomedical researchers, biostatisticians and bioinformaticians.

  1. 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…

  2. Research and Service Support: Bringing Users to Data

    Science.gov (United States)

    Delgado Blasco, Jose Manuel; Sabatino, Giovanni; Cuccu, Roberto; Rivolta, Giancarlo; Marchetti, Pier Giorgio

    2016-08-01

    The ESA Research and Service Support (RSS) service has the mission to support the Earth Observation (EO) data exploitation, by an operational pilot of the new paradigm "bring users to data" [1]. This approach fits well the challenges posed by larger data availability, from more missions, more frequently. It dramatically lowers the barriers to perform research activities, to develop algorithms and downstream services reducing the effort and resources needed by the EO users. This objective is achieved by (i) offering tools and services to the EO community granting a fast and easy data access (i.e. without the need to transfer the data into the scientist "own" infrastructure) and real (offered by RSS) scalable processing resources , and (ii) by supporting the researchers in developing new algorithms, enabling results visualization, verification, validation and sharing.

  3. Bringing macromolecular machinery to life using 3D animation.

    Science.gov (United States)

    Iwasa, Janet H

    2015-04-01

    Over the past decade, there has been a rapid rise in the use of three-dimensional (3D) animation to depict molecular and cellular processes. Much of the growth in molecular animation has been in the educational arena, but increasingly, 3D animation software is finding its way into research laboratories. In this review, I will discuss a number of ways in which 3d animation software can play a valuable role in visualizing and communicating macromolecular structures and dynamics. I will also consider the challenges of using animation tools within the research sphere.

  4. Are Charge-State Distributions a Reliable Tool Describing Molecular Ensembles of Intrinsically Disordered Proteins by Native MS?

    Science.gov (United States)

    Natalello, Antonino; Santambrogio, Carlo; Grandori, Rita

    2017-01-01

    Native mass spectrometry (MS) has become a central tool of structural proteomics, but its applicability to the peculiar class of intrinsically disordered proteins (IDPs) is still object of debate. IDPs lack an ordered tridimensional structure and are characterized by high conformational plasticity. Since they represent valuable targets for cancer and neurodegeneration research, there is an urgent need of methodological advances for description of the conformational ensembles populated by these proteins in solution. However, structural rearrangements during electrospray-ionization (ESI) or after the transfer to the gas phase could affect data obtained by native ESI-MS. In particular, charge-state distributions (CSDs) are affected by protein conformation inside ESI droplets, while ion mobility (IM) reflects protein conformation in the gas phase. This review focuses on the available evidence relating IDP solution ensembles with CSDs, trying to summarize cases of apparent consistency or discrepancy. The protein-specificity of ionization patterns and their responses to ligands and buffer conditions suggests that CSDs are imprinted to protein structural features also in the case of IDPs. Nevertheless, it seems that these proteins are more easily affected by electrospray conditions, leading in some cases to rearrangements of the conformational ensembles.

  5. Are Charge-State Distributions a Reliable Tool Describing Molecular Ensembles of Intrinsically Disordered Proteins by Native MS?

    Science.gov (United States)

    Natalello, Antonino; Santambrogio, Carlo; Grandori, Rita

    2016-10-01

    Native mass spectrometry (MS) has become a central tool of structural proteomics, but its applicability to the peculiar class of intrinsically disordered proteins (IDPs) is still object of debate. IDPs lack an ordered tridimensional structure and are characterized by high conformational plasticity. Since they represent valuable targets for cancer and neurodegeneration research, there is an urgent need of methodological advances for description of the conformational ensembles populated by these proteins in solution. However, structural rearrangements during electrospray-ionization (ESI) or after the transfer to the gas phase could affect data obtained by native ESI-MS. In particular, charge-state distributions (CSDs) are affected by protein conformation inside ESI droplets, while ion mobility (IM) reflects protein conformation in the gas phase. This review focuses on the available evidence relating IDP solution ensembles with CSDs, trying to summarize cases of apparent consistency or discrepancy. The protein-specificity of ionization patterns and their responses to ligands and buffer conditions suggests that CSDs are imprinted to protein structural features also in the case of IDPs. Nevertheless, it seems that these proteins are more easily affected by electrospray conditions, leading in some cases to rearrangements of the conformational ensembles.

  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. Molecularly imprinted polymers as a tool for the study of the 4-ethylphenol metabolic pathway in red wines.

    Science.gov (United States)

    Garcia, Deiene; Gomez-Caballero, Alberto; Guerreiro, Antonio; Goicolea, M Aranzazu; Barrio, Ramon J

    2015-09-01

    A molecularly imprinted polymer (MIP) based methodology is described here for the determination of compounds that belong to the 4-ethylphenol (4EP) metabolic pathway in red wines. To this end, two MIP materials have been developed: a 4EP MIP as a class-selective material to extract phenols that belong to the 4EP metabolic pathway and a coumaric acid (CA) imprinted polymer as a MIP-based stationary phase capable of selectively separating these phenols on HPLC analysis, obtaining clean chromatograms. 4-vinyl pyridine and ethylene glycol dimethacrylate were respectively used as functional monomer and cross-linker for both MIPs. Once polymer compositions were optimised, the 4EP MIP was packed into SPE cartridges for wine sample clean-up and CA MIP was packed into HPLC columns to chromatographically separate the compounds present in the eluates obtained after SPE extraction. The accuracy of the proposed method was tested spiking wine samples with known concentrations of target compounds and subsequently, analytes were quantified by the standard addition method. Registered mean recoveries ranged from 95.2 to 109.2% and RSD values were below 10% in most cases. The described methodology was found to be suitable for the selective extraction and quantification of the compounds that belong to the 4EP metabolic pathway in red wines with minimal matrix effects and could be undoubtedly exploited to monitor 4EP and its precursors in wines.

  8. 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.

  9. 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.

  10. 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.

  11. Next-generation sequencing (NGS) as a fast molecular diagnosis tool for left ventricular noncompaction in an infant with compound mutations in the MYBPC3 gene.

    Science.gov (United States)

    Schaefer, Elise; Helms, Pauline; Marcellin, Luc; Desprez, Philippe; Billaud, Philippe; Chanavat, Valérie; Rousson, Robert; Millat, Gilles

    2014-03-01

    Left ventricular noncompaction (LVNC) is a clinically heterogeneous disorder characterized by a trabecular meshwork and deep intertrabecular myocardial recesses that communicate with the left ventricular cavity. LVNC is classified as a rare genetic cardiomyopathy. Molecular diagnosis is a challenge for the medical community as the condition shares morphologic features of hypertrophic and dilated cardiomyopathies. Several genetic causes of LVNC have been reported, with variable modes of inheritance, including autosomal dominant and X-linked inheritance, but relatively few responsible genes have been identified. In this report, we describe a case of a severe form of LVNC leading to death at 6 months of life. NGS sequencing using a custom design for hypertrophic cardiomyopathy panel allowed us to identify compound heterozygosity in the MYBPC3 gene (p.Lys505del, p.Pro955fs) in 3 days, confirming NGS sequencing as a fast molecular diagnosis tool. Other studies have reported neonatal presentation of cardiomyopathies associated with compound heterozygous or homozygous MYBPC3 mutations. In this family and in families in which parental truncating MYBPC3 mutations are identified, preimplantation or prenatal genetic screening should be considered as these genotypes leads to neonatal mortality and morbidity.

  12. Matrix-assisted laser desorption/ionization mass spectrometry imaging: a powerful tool for probing the molecular topology of plant cutin polymer.

    Science.gov (United States)

    Veličković, Dušan; Herdier, Hélène; Philippe, Glenn; Marion, Didier; Rogniaux, Hélène; Bakan, Bénédicte

    2014-12-01

    The cutin polymers of different fruit cuticles (tomato, apple, nectarine) were examined using matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) after in situ release of the lipid monomers by alkaline hydrolysis. The mass spectra were acquired from each coordinate with a lateral spatial resolution of approximately 100 μm. Specific monomers were released at their original location in the tissue, suggesting that post-hydrolysis diffusion can be neglected. Relative quantification of the species was achieved by introducing an internal standard, and the collection of data was subjected to non-supervised and supervised statistical treatments. The molecular images obtained showed a specific distribution of ions that could unambiguously be ascribed to cutinized and suberized regions observed at the surface of fruit cuticles, thus demonstrating that the method is able to probe some structural changes that affect hydrophobic cuticle polymers. Subsequent chemical assignment of the differentiating ions was performed, and all of these ions could be matched to cutin and suberin molecular markers. Therefore, this MALDI-MSI procedure provides a powerful tool for probing the surface heterogeneity of plant lipid polymers. This method should facilitate rapid investigation of the relationships between cuticle phenotypes and the structure of cutin within a large population of mutants.

  13. Bringing Pulsed Laser Welding into Production

    DEFF Research Database (Denmark)

    Olsen, Flemmming Ove

    1996-01-01

    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......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...

  14. Developing a web page: bringing clinics online.

    Science.gov (United States)

    Peterson, Ronnie; Berns, Susan

    2004-01-01

    Introducing clinical staff education, along with new policies and procedures, to over 50 different clinical sites can be a challenge. As any staff educator will confess, getting people to attend an educational inservice session can be difficult. Clinical staff request training, but no one has time to attend training sessions. Putting the training along with the policies and other information into "neat" concise packages via the computer and over the company's intranet was the way to go. However, how do you bring the clinics online when some of the clinical staff may still be reluctant to turn on their computers for anything other than to gather laboratory results? Developing an easy, fun, and accessible Web page was the answer. This article outlines the development of the first training Web page at the University of Wisconsin Medical Foundation, Madison, WI.

  15. 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.

  16. Bringing Reflections into the TEFL Classrooms

    Directory of Open Access Journals (Sweden)

    M Sri Samiati Tarjana

    2002-01-01

    Full Text Available Abstract: Reflective practice is defined by John Dewey as a proactive, ongoing examination of beliefs and practices, their origins and impacts. In the reflective practice, the teacher and learners are engaged in a continuous cycle of self-observation and self-evaluation in order to understand their own actions and reactions, and thereby develop the teaching-learning process on an on-going basis. While English is regarded as compulsory in the preparation of more qualified human resources for the country, there are still complaints about the low English mastery of the majority of secondary and tertiary education graduates in Indonesia. It seems likely that bringing the reflective practice in the TEFL classrooms will help improve the teaching-learning of English in a more caring and responsive manner. It is expected that this will not only improve the English mastery, but also develop personal talents and capacities of the learners. The features of reflective practice in TEFL and their advantages for personal and professional development will be further discussed.

  17. Bringing Technology into High School Physics Classrooms

    Science.gov (United States)

    Zettili, Nouredine

    2005-04-01

    In an effort to help high school physics teachers bring technology into their classrooms, we at JSU have been offering professional development to secondary education teachers. This effort is part of Project IMPACTSEED (IMproving Physics And Chemistry Teaching in SEcondary Education), a No-Child Left Behind (NCLB) grant funded by the Alabama Commission on Higher Education, serving high school physics teachers in Northeast Alabama. This project is motivated by a major pressing local need: A large number of high school physics teachers teach out of field. To achieve IMPACTSEED's goals, we have forged a functional collaboration with school districts from about ten counties. This collaboration is aimed at achieving a double aim: (a) to make physics and chemistry understandable and fun to learn within a hands-on, inquiry-based setting; (b) to overcome the fear- factor for physics and chemistry among students. Through a two-week long summer institute, a series of weekend technology workshops, and onsite support, we have been providing year-round support to the physics/chemistry teachers in this area. This outreach initiative has helped provide our students with a physics/chemistry education that enjoys a great deal of continuity and consistency from high school to college.

  18. 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...

  19. 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...

  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.

  1. 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.

  2. Health fairs bring wellness concepts to life.

    Science.gov (United States)

    Serina, M; Giove, S

    1991-01-01

    Incorporated into the nursing curriculum, the health fair is a stimulating, unique, nontraditional educational project that examines effective health education tools, leadership skills, and interaction with the community. Students test theories and collaborate with other school disciplines while planning, implementing, and evaluating health education and health fair promotion. Health fairs help students to identify positive lifestyles and create opportunities to test the skills needed to improve the population's wellness level.

  3. Elucidating the molecular responses of apple rootstock resistant to ARD pathogens: challenges and opportunities for development of genomics-assisted breeding tools.

    Science.gov (United States)

    Zhu, Yanmin; Fazio, Gennaro; Mazzola, Mark

    2014-01-01

    may lead to different outcomes between rootstocks in response to invasion by necrotrophic pathogens. Elucidation of host defense mechanisms is critical in developing molecular tools for genomics-assisted breeding of resistant apple rootstocks. Due to their perennial nature, use of resistant rootstocks as a component for disease management might offer a durable and cost-effective benefit to tree performance than the standard practice of soil fumigation for control of ARD.

  4. Combined Use of Morphological and Molecular Tools to Resolve Species Mis-Identifications in the Bivalvia The Case of Glycymeris glycymeris and G. pilosa

    Science.gov (United States)

    Holmes, Anna; Bušelić, Ivana; Thébault, Julien; Featherstone, Amy

    2016-01-01

    Morphological and molecular tools were combined to resolve the misidentification between Glycymeris glycymeris and Glycymeris pilosa from Atlantic and Mediterranean populations. The ambiguous literature on the taxonomic status of these species requires this confirmation as a baseline to studies on their ecology and sclerochronology. We used classical and landmark-based morphometric approaches and performed bivariate and multivariate analyses to test for shell character interactions at the individual and population level. Both approaches generated complementary information. The former showed the shell width to length ratio and the valve asymmetry to be the main discriminant characters between Atlantic and Mediterranean populations. Additionally, the external microsculpture of additional and finer secondary ribs in G. glycymeris discriminates it from G. pilosa. Likewise, landmark-based geometric morphometrics revealed a stronger opisthogyrate beak and prosodetic ligament in G. pilosa than G. glycymeris. Our Bayesian and maximum likelihood phylogenetic analyses based on COI and ITS2 genes identified that G. glycymeris and G. pilosa form two separate monophyletic clades with mean interspecific divergence of 11% and 0.9% for COI and ITS2, respectively. The congruent patterns of morphometric analysis together with mitochondrial and nuclear phylogenetic reconstructions indicated the separation of the two coexisting species. The intraspecific divergence occurred during the Eocene and accelerated during the late Pliocene and Pleistocene. Glycymeris pilosa showed a high level of genetic diversity, appearing as a more robust species whose tolerance of environmental conditions allowed its expansion throughout the Mediterranean. PMID:27669452

  5. Advances in molecular tools for the use of Zygosaccharomyces bailii as host for biotechnological productions and construction of the first auxotrophic mutant.

    Science.gov (United States)

    Dato, Laura; Branduardi, Paola; Passolunghi, Simone; Cattaneo, Davide; Riboldi, Luca; Frascotti, Gianni; Valli, Minoska; Porro, Danilo

    2010-11-01

    The nonconventional yeast Zygosaccharomyces bailii has been proposed as a new host for biotechnological processes due to convenient properties such as its resistance to high sugar concentrations, relatively high temperatures and especially to acidic environments. We describe a series of new expression vectors specific for Z. bailii and the resulting improvements in production levels. By exploiting the sequences of the endogenous plasmid pSB2, 2microm-like multicopy vectors were obtained, giving a fivefold increase in production. A specific integrative vector was developed which led to 100% stability in the absence of selective pressure; a multiple-integration vector was constructed, based on an rRNA gene unit portion cloned and sequenced for this purpose, driving the insertion of up to 80 copies of the foreign construct. Moreover, we show the construction of the first stable auxotrophic mutant of Z. bailii, obtained by targeted gene deletion applied to ZbLEU2. The development of molecular tools for the Z. bailii manipulation has now reached a level that may be compatible with its industrial exploitation; the production of organic acids is a prominent field of application.

  6. Bringing the Fuzzy Front End into Focus

    Energy Technology Data Exchange (ETDEWEB)

    Beck, D.F.; Boyack, K.W.; Bray, O.H.; Siemens, W.D.

    1999-03-03

    Technology planning is relatively straightforward for well-established research and development (R and D) areas--those areas in which an organization has a history, the competitors are well understood, and the organization clearly knows where it is going with that technology. What we are calling the fuzzy front-end in this paper is that condition in which these factors are not well understood--such as for new corporate thrusts or emerging areas where the applications are embryonic. While strategic business planning exercises are generally good at identifying technology areas that are key to future success, they often lack substance in answering questions like: (1) Where are we now with respect to these key technologies? ... with respect to our competitors? (2) Where do we want or need to be? ... by when? (3) What is the best way to get there? In response to its own needs in answering such questions, Sandia National Laboratories is developing and implementing several planning tools. These tools include knowledge mapping (or visualization), PROSPERITY GAMES and technology roadmapping--all three of which are the subject of this paper. Knowledge mapping utilizes computer-based tools to help answer Question 1 by graphically representing the knowledge landscape that we populate as compared with other corporate and government entities. The knowledge landscape explored in this way can be based on any one of a number of information sets such as citation or patent databases. PROSPERITY GAMES are high-level interactive simulations, similar to seminar war games, which help address Question 2 by allowing us to explore consequences of various optional goals and strategies with all of the relevant stakeholders in a risk-free environment. Technology roadmapping is a strategic planning process that helps answer Question 3 by collaboratively identifying product and process performance targets and obstacles, and the technology alternatives available to reach those targets.

  7. Bringing Vision-Based Measurements into our Daily Life: A Grand Challenge for Computer Vision Systems

    OpenAIRE

    Scharcanski, Jacob

    2016-01-01

    Bringing computer vision into our daily life has been challenging researchers in industry and in academia over the past decades. However, the continuous development of cameras and computing systems turned computer vision-based measurements into a viable option, allowing new solutions to known problems. In this context, computer vision is a generic tool that can be used to measure and monitor phenomena in wide range of fields. The idea of using vision-based measurements is appealing, since the...

  8. Disulfide Bridges: Bringing Together Frustrated Structure in a Bioactive Peptide.

    Science.gov (United States)

    Zhang, Yi; Schulten, Klaus; Gruebele, Martin; Bansal, Paramjit S; Wilson, David; Daly, Norelle L

    2016-04-26

    Disulfide bridges are commonly found covalent bonds that are usually believed to maintain structural stability of proteins. Here, we investigate the influence of disulfide bridges on protein dynamics through molecular dynamics simulations on the cysteine-rich trypsin inhibitor MCoTI-II with three disulfide bridges. Correlation analysis of the reduced cyclic peptide shows that two of the three disulfide distances (Cys(11)-Cys(23) and Cys(17)-Cys(29)) are anticorrelated within ∼1 μs of bridge formation or dissolution: when the peptide is in nativelike structures and one of the distances shortens to allow bond formation, the other tends to lengthen. Simulations over longer timescales, when the denatured state is less structured, do not show the anticorrelation. We propose that the native state contains structural elements that frustrate one another's folding, and that the two bridges are critical for snapping the frustrated native structure into place. In contrast, the Cys(4)-Cys(21) bridge is predicted to form together with either of the other two bridges. Indeed, experimental chromatography and nuclear magnetic resonance data show that an engineered peptide with the Cys(4)-Cys(21) bridge deleted can still fold into its near-native structure even in its noncyclic form, confirming the lesser role of the Cys(4)-Cys(21) bridge. The results highlight the importance of disulfide bridges in a small bioactive peptide to bring together frustrated structure in addition to maintaining protein structural stability.

  9. Defining life or bringing biology to life.

    Science.gov (United States)

    Ruiz-Mirazo, Kepa; Peretó, Juli; Moreno, Alvaro

    2010-04-01

    In the present, post-genomic times, systemic or holistic approaches to living phenomena are compulsory to overcome the limits of traditional strategies, such as the methodological reductionism of molecular biology. In this paper, we propose that theoretical and philosophical efforts to define life also contribute to those integrative approaches, providing a global theoretical framework that may help to deal with or interpret the huge amount of data being collected by current high-throughput technologies, in this so-called 'omics' revolution. We claim that two fundamental notions can capture the core of the living, (basic) autonomy and open-ended evolution, and that only the complementary combination of these two theoretical constructs offers an adequate solution to the problem of defining the nature of life in specific enough-but also encompassing enough-terms. This tentative solution should also illuminate, in its most elementary version, the leading steps towards living beings on Earth.

  10. De novo Transcriptome Sequencing and Development of Abscission Zone-Specific Microarray as a New Molecular Tool for Analysis of Tomato Organ Abscission

    Science.gov (United States)

    Sundaresan, Srivignesh; Philosoph-Hadas, Sonia; Riov, Joseph; Mugasimangalam, Raja; Kuravadi, Nagesh A.; Kochanek, Bettina; Salim, Shoshana; Tucker, Mark L.; Meir, Shimon

    2016-01-01

    Abscission of flower pedicels and leaf petioles of tomato (Solanum lycopersicum) can be induced by flower removal or leaf deblading, respectively, which leads to auxin depletion, resulting in increased sensitivity of the abscission zone (AZ) to ethylene. However, the molecular mechanisms that drive the acquisition of abscission competence and its modulation by auxin gradients are not yet known. We used RNA-Sequencing (RNA-Seq) to obtain a comprehensive transcriptome of tomato flower AZ (FAZ) and leaf AZ (LAZ) during abscission. RNA-Seq was performed on a pool of total RNA extracted from tomato FAZ and LAZ, at different abscission stages, followed by de novo assembly. The assembled clusters contained transcripts that are already known in the Solanaceae (SOL) genomics and NCBI databases, and over 8823 identified novel tomato transcripts of varying sizes. An AZ-specific microarray, encompassing the novel transcripts identified in this study and all known transcripts from the SOL genomics and NCBI databases, was constructed to study the abscission process. Multiple probes for longer genes and key AZ-specific genes, including antisense probes for all transcripts, make this array a unique tool for studying abscission with a comprehensive set of transcripts, and for mining for naturally occurring antisense transcripts. We focused on comparing the global transcriptomes generated from the FAZ and the LAZ to establish the divergences and similarities in their transcriptional networks, and particularly to characterize the processes and transcriptional regulators enriched in gene clusters that are differentially regulated in these two AZs. This study is the first attempt to analyze the global gene expression in different AZs in tomato by combining the RNA-Seq technique with oligonucleotide microarrays. Our AZ-specific microarray chip provides a cost-effective approach for expression profiling and robust analysis of multiple samples in a rapid succession. PMID:26834766

  11. De novo transcriptome sequencing and development of abscission zone-specific microarray as a new molecular tool for analysis of tomato organ abscission

    Directory of Open Access Journals (Sweden)

    Srivignesh eSundaresan

    2016-01-01

    Full Text Available Abscission of flower pedicels and leaf petioles of tomato (Solanum lycopersicum can be induced by flower removal or leaf deblading, respectively, leading to auxin depletion, which results in increased sensitivity of the abscission zone (AZ to ethylene. However, the molecular mechanisms that drive the acquisition of abscission competence and its modulation by auxin gradients are not yet known. We used RNA-Sequencing (RNA-Seq to obtain the comprehensive transcriptome of tomato flower AZ (FAZ and leaf AZ (LAZ during abscission. RNA-Seq was performed on a pool of total RNA extracted from different abscission stages of tomato FAZ and LAZ, followed by de novo assembly. The assembled clusters contained transcripts that are already known in Solanaceae (SOL genomics database and NCBI databases, and over 8,823 identified novel tomato transcripts of varying sizes. An AZ-specific microarray, encompassing these novel transcripts identified in this study and all known transcripts from the SOL genomics and NCBI databases, was constructed to study the abscission process. Multiple probes for longer genes and key AZ-specific genes, including antisense probes for all transcripts, make this array a unique tool for studying abscission with a comprehensive set of transcripts, and for mining for naturally occurring antisense transcripts. We focused on comparing the global transcriptomes generated from the FAZ and the LAZ to establish the divergences and similarities in their transcriptional networks, and particularly to characterize the processes and transcriptional regulators enriched in gene clusters that are differentially regulated in these two AZs. This study is the first attempt to analyze the global gene expression in different AZs in tomato by combining the RNA-Seq technique with oligonucleotide microarrays. Our AZ-specific microarray chip provides a cost-effective approach for expression profiling and robust analysis of multiple samples in a rapid succession.

  12. Work-Based Courses: Bringing College to the Production Line

    Science.gov (United States)

    Kobes, Deborah; Girardi, Amy

    2016-01-01

    Work-based courses are an innovative way to bring college to the production line by using the job as a learning lab. This toolkit provides guidance to community college administrators and faculty who are interested in bringing a work-based course model to their college. It contains video content and teaching tips that introduce the six steps of…

  13. 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.

  14. 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.

  15. Rice arbuscular mycorrhiza as a tool to study the molecular mechanisms of fungal symbiosis and a potential target to increase productivity.

    Science.gov (United States)

    Nakagawa, Tomomi; Imaizumi-Anraku, Haruko

    2015-12-01

    Rice (Oryza sativa L.) is a monocot model crop for cereal molecular biology. Following the emergence of molecular genetics of arbuscular mycorrhizal (AM) symbiosis in model legumes in the 1990s, studies on rice genetic resources have considerably contributed to our understanding of the molecular mechanisms and evolution of root intracellular symbioses.In this review, we trace the history of these studies and suggest the potential utility of AM symbiosis for improvement in rice productivity.

  16. 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

  17. Illuminating odors: when optogenetics brings to light unexpected olfactory abilities

    Science.gov (United States)

    Grimaud, Julien

    2016-01-01

    For hundreds of years, the sense of smell has generated great interest in the world literature, oenologists, and perfume makers but less of scientists. Only recently this sensory modality has gained new attraction in neuroscience when original tools issued from physiology, anatomy, or molecular biology were available to decipher how the brain makes sense of olfactory cues. However, this move was promptly dampened by the difficulties of developing quantitative approaches to study the relationship between the physical characteristics of stimuli and the sensations they create. An upswing of olfactory investigations occurred when genetic tools could be used in combination with devices borrowed from the physics of light (a hybrid technique called optogenetics) to scrutinize the olfactory system and to provide greater physiological precision for studying olfactory-driven behaviors. This review aims to present the most recent studies that have used light to activate components of the olfactory pathway, such as olfactory receptor neurons, or neurons located further downstream, while leaving intact others brain circuits. With the use of optogenetics to unravel the mystery of olfaction, scientists have begun to disentangle how the brain makes sense of smells. In this review, we shall discuss how the brain recognizes odors, how it memorizes them, and how animals make decisions based on odorants they are capable of sensing. Although this review deals with olfaction, the role of light will be central throughout. PMID:27194792

  18. 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.

  19. 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.

  20. 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 ...

  1. Climate Change May Bring More Tainted Shellfish to Northern Seas

    Science.gov (United States)

    ... page: https://medlineplus.gov/news/fullstory_160300.html Climate Change May Bring More Tainted Shellfish to Northern Seas ... must be monitored "in the light of ongoing climate change, especially in coastal areas most heavily affected by ...

  2. Use of molecular tools for the identification of males of some scale insects (Hemiptera: Coccoidea, in pheromone traps used for monitoring and comparison with females

    Directory of Open Access Journals (Sweden)

    István Tóbiás

    2010-11-01

    Full Text Available Species from Pseudococcidae family were studied. It was determined that the dry males of Planococcus citri, and Pseudococcus comstocki, collected by pheromone traps could be useful for the molecular analyses too. The ITS-2 sequences of males and females in case of Pl.citri, Planococcus ficus and Ps. comstocki were identical. This molecular method could differentiate the two mealybug species and this method can be useful to have idea specimens collected by pheromone traps.

  3. 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.

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

    NARCIS (Netherlands)

    Best, Kathryn

    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 being

  5. User’s Guide for T.E.S.T. (version 4.2) (Toxicity Estimation Software Tool) A Program to Estimate Toxicity from Molecular Structure

    Science.gov (United States)

    The user's guide describes the methods used by TEST to predict toxicity and physical properties (including the new mode of action based method used to predict acute aquatic toxicity). It describes all of the experimental data sets included in the tool. It gives the prediction res...

  6. Does Satisfaction with Teaching Quality Factors Bring Conceptual Change?

    Directory of Open Access Journals (Sweden)

    Saifur Rehman Khan

    2014-05-01

    Full Text Available The purpose of this study is to explore classroom teaching quality factors that determine the satisfaction level and ultimately bring conceptual change among students. This study tests the theories of customer satisfaction in educational psychology research on a sample of 972 respondents. Overwhelmingly the results point out that male students were highly dissatisfied and have little impact on conceptual change whereas female students were reported significant level of satisfaction and conceptual change. In conclusion, detailed empirical analyses promote the theory of learning-satisfaction with classroom teaching bring conceptual change.

  7. 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

  8. 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…

  9. The Chemedian Brings Laughter to the Chemistry Classroom

    Science.gov (United States)

    Weitkamp, Emma; Burnet, Frank

    2007-01-01

    "The Chemedian and the Crazy Football Match" is a comic strip developed by the authors to bring humor to aspects of the UK primary science curriculum. The comic strip was tested in six English primary school classes (years 3-5; ages 7-10); over 150 children participated in the project, together with six teachers. Children found the comic strip fun…

  10. Driven: Bringing German Auto Concepts to the Classroom

    Science.gov (United States)

    Adney, Cara

    2012-01-01

    A world away from the red dirt of Oklahoma, David Shields and Shelly Smith felt right at home. A national grant took the Meridian Technology Center automotive teachers on a trip to Germany that car lovers only dream about. The tour to the major automakers last summer has them geared up and bringing fresh ideas to the classroom. They spent four…

  11. 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.

  12. Bringing internet connectivity to rural Zambia using a collaborative approach

    NARCIS (Netherlands)

    Matthee, K.W.; Mweemba, G.; Pais, A.V.; Starn, G.V.; Rijken, M.

    2007-01-01

    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 of Zambia. The service operates using satellite terminals

  13. "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…

  14. 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...

  15. On Bringing Industry English Teaching into College English Course

    Institute of Scientific and Technical Information of China (English)

    魏圆圆

    2016-01-01

    With the development of global economy, it’s becoming increasingly important to bring industry English into College English Course. But there are still many problems about industry English teaching in most colleges. This paper will analyze these problems and put forward effective measures to promote industry English teaching.

  16. Excelsior: Bringing the Benefits of Modularisation to Excel

    CERN Document Server

    Paine, Jocelyn

    2008-01-01

    Excel lacks features for modular design. Had it such features, as do most programming languages, they would save time, avoid unneeded programming, make mistakes less likely, make code-control easier, help organisations adopt a uniform house style, and open business opportunities in buying and selling spreadsheet modules. I present Excelsior, a system for bringing these benefits to Excel.

  17. Molecular tools for studying the major malaria vector Anopheles funestus: improving the utility of the genome using a comparative poly(A) and Ribo-Zero RNAseq analysis

    OpenAIRE

    WEEDALL, GARETH D.; Irving, Helen; Hughes, Margaret A.; Wondji, Charles S.

    2015-01-01

    Background Next-generation sequencing (NGS) offers great opportunities for studying the biology of insect vectors of disease. Prerequisites for successful analyses include high quality annotated genome assemblies and that techniques designed for use with model organisms be tested and optimised for use with these insects. We aimed to test and improve genomic tools for studying the major malaria vector Anopheles funestus. Results To guide future RNAseq transcriptomic studies of An. funestus, we...

  18. Topological sub-structural molecular design (TOPS-MODE): a useful tool to explore key fragments of human A3 adenosine receptor ligands.

    Science.gov (United States)

    Saíz-Urra, Liane; Teijeira, Marta; Rivero-Buceta, Virginia; Helguera, Aliuska Morales; Celeiro, Maria; Terán, Ma Carmen; Besada, Pedro; Borges, Fernanda

    2016-02-01

    Adenosine regulates tissue function by activating four G-protein-coupled adenosine receptors (ARs). Selective agonists and antagonists for A3 ARs have been investigated for the treatment of a variety of immune disorders, cancer, brain, and heart ischemic conditions. We herein present a QSAR study based on a Topological sub-structural molecular design (TOPS-MODE) approach, intended to predict the A3 ARs of a diverse dataset of 124 (94 training set/ 30 prediction set) adenosine derivatives. The final model showed good fit and predictive capability, displaying 85.1 % of the experimental variance. The TOPS-MODE approach afforded a better understanding and interpretation of the developed model based on the useful information extracted from the analysis of the contribution of different molecular fragments to the affinity.

  19. Functional Genomics and Cell Biology of the Dolphin (Tursiops runcatus): Establishment of Novel Molecular Tools to Study Marine Mammals in Changing Environments

    OpenAIRE

    Mancia, Annalaura

    2010-01-01

    The dolphin (Tursiops truncatus) is a mammal that is adapted to life in a totally aquatic environment. Despite the popularity and even iconic status of the dolphin, our knowledge of its physiology, its unique adaptations and the effects on it of environmental stressors are limited. One approach to improve this limited understanding is the implementation of established cellular and molecular methods to provide sensitive and insightful information for dolphin biology. We initiated our studi...

  20. IROme, a new high-throughput molecular tool for the diagnosis of inherited retinal dystrophies-a price comparison with Sanger sequencing.

    Science.gov (United States)

    Schorderet, Daniel F; Bernasconi, Maude; Tiab, Leila; Favez, Tatiana; Escher, Pascal

    2014-01-01

    The molecular diagnosis of retinal dystrophies (RD) is difficult because of genetic and clinical heterogeneity. Previously, the molecular screening of genes was done one by one, sometimes in a scheme based on the frequency of sequence variants and the number of exons/length of the candidate genes. Payment for these procedures was complicated and the sequential billing of several genes created endless paperwork. We therefore evaluated the costs of generating and sequencing a hybridization-based DNA library enriched for the 64 most frequently mutated genes in RD, called IROme, and compared them to the costs of amplifying and sequencing these genes by the Sanger method. The production cost generated by the high-throughput (HT) sequencing of IROme was established at CHF 2,875.75 per case. Sanger sequencing of the same exons cost CHF 69,399.02. Turnaround time of the analysis was 3 days for IROme. For Sanger sequencing, it could only be estimated, as we never sequenced all 64 genes in one single patient. Sale cost for IROme calculated on the basis of the sale cost of one exon by Sanger sequencing is CHF 8,445.88, which corresponds to the sale price of 40 exons. In conclusion, IROme is cheaper and faster than Sanger sequencing and therefore represents a sound approach for the diagnosis of RD, both scientifically and economically. As a drop in the costs of HT sequencing is anticipated, target resequencing might become the new gold standard in the molecular diagnosis of RD.

  1. A petal-specific InMYB1 promoter from Japanese morning glory: a useful tool for molecular breeding of floricultural crops.

    Science.gov (United States)

    Azuma, Mirai; Morimoto, Reina; Hirose, Mana; Morita, Yasumasa; Hoshino, Atsushi; Iida, Shigeru; Oshima, Yoshimi; Mitsuda, Nobutaka; Ohme-Takagi, Masaru; Shiratake, Katsuhiro

    2016-01-01

    Production of novel transgenic floricultural crops with altered petal properties requires transgenes that confer a useful trait and petal-specific promoters. Several promoters have been shown to control transgenes in petals. However, all suffer from inherent drawbacks such as low petal specificity and restricted activity during the flowering stage. In addition, the promoters were not examined for their ability to confer petal-specific expression in a wide range of plant species. Here, we report the promoter of InMYB1 from Japanese morning glory as a novel petal-specific promoter for molecular breeding of floricultural crops. First, we produced stable InMYB1_1kb::GUS transgenic Arabidopsis and Eustoma plants and characterized spatial and temporal expression patterns under the control of the InMYB1 promoter by histochemical β-glucuronidase (GUS) staining. GUS staining patterns were observed only in petals. This result showed that the InMYB1 promoter functions as a petal-specific promoter. Second, we transiently introduced the InMYB1_1 kb::GUS construct into Eustoma, chrysanthemum, carnation, Japanese gentian, stock, rose, dendrobium and lily petals by particle bombardment. GUS staining spots were observed in Eustoma, chrysanthemum, carnation, Japanese gentian and stock. These results showed that the InMYB1 promoter functions in most dicots. Third, to show the InMYB1 promoter utility in molecular breeding, a MIXTA-like gene function was suppressed or enhanced under the control of InMYB1 promoter in Arabidopsis. The transgenic plant showed a conspicuous morphological change only in the form of wrinkled petals. Based on these results, the InMYB1 promoter can be used as a petal-specific promoter in molecular breeding of floricultural crops.

  2. Capillary electrophoresis, gas-phase electrophoretic mobility molecular analysis, and electron microscopy: effective tools for quality assessment and basic rhinovirus research.

    Science.gov (United States)

    Weiss, Victor U; Subirats, Xavier; Kumar, Mohit; Harutyunyan, Shushan; Gösler, Irene; Kowalski, Heinrich; Blaas, Dieter

    2015-01-01

    We describe standard methods for propagation, purification, quality control, and physicochemical characterization of human rhinoviruses, using HRV-A2 as an example. Virus is propagated in HeLa-OHIO cells grown in suspension culture and purified via sucrose density gradient centrifugation. Purity and homogeneity of the preparations are assessed with SDS-polyacrylamide gel electrophoresis (SDS-PAGE), capillary electrophoresis (CE), gas-phase electrophoretic mobility molecular analysis (GEMMA), and electron microscopy (EM). We also briefly describe usage of these methods for the characterization of subviral particles as well as for the analysis of their complexes with antibodies and soluble recombinant receptor mimics.

  3. Classical Molecular Tests Using Urine Samples as a Potential Screening Tool for Human Papillomavirus Detection in Human Immunodeficiency Virus-Infected Women

    OpenAIRE

    Munoz, Marina; Camargo, Milena; Soto-De Leon, Sara C.; Sanchez, Ricardo; Pineda-Peña, Andrea C.; Perez-Prados, Antonio; Patarroyo, Manuel E.; Patarroyo, Manuel A.

    2013-01-01

    Human papillomavirus (HPV) is the main risk factor associated with the development of cervical cancer (CC); however, there are other factors, such as immunosuppression caused by the human immunodeficiency virus (HIV), that favor progression of the illness. This study was thus aimed at evaluating the functionality of classical PCR-based molecular tests for the generic identification of HPV DNA (GP5+/GP6+, MY09/MY11, and pU1M/2R primers, individually or in combination) using cervical and urine ...

  4. 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

  5. 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 ...

  6. Time-resolved molecular imaging

    Science.gov (United States)

    Xu, Junliang; Blaga, Cosmin I.; Agostini, Pierre; DiMauro, Louis F.

    2016-06-01

    Time-resolved molecular imaging is a frontier of ultrafast optical science and physical chemistry. In this article, we review present and future key spectroscopic and microscopic techniques for ultrafast imaging of molecular dynamics and show their differences and connections. The advent of femtosecond lasers and free electron x-ray lasers bring us closer to this goal, which eventually will extend our knowledge about molecular dynamics to the attosecond time domain.

  7. Introduction to the special issue on molecular spectroscopy in traps

    Science.gov (United States)

    Schlemmer, Stephan; Willitsch, Stefan; Steimle, Tim

    2017-02-01

    Trapping is a very versatile tool in many aspects of physics and chemistry. Trapping techniques are very well suited for spectroscopy studies due to the localization of the species of interest. As a result the particle density and the interaction times with photons are substantially increased with respect to other techniques. Therefore, both sensitivity and resolution benefit from this peculiar environment. Buffer gas or sympathetic cooling and mass selection are additional features applied in many trapping experiments. Thanks to these possibilities the number of spectroscopy publications based on these techniques increased substantially in the last decade. This special issue brings together some of the recent advancements in the field of molecular spectroscopy, mainly in ion traps, and demonstrates the large variety of applications, the very broad range of frequency coverage and the great potential for the field of molecular spectroscopy in general.

  8. 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.

  9. Bringing History Home. Postcolonial Immigrants and the Dutch Cultural Arena

    Directory of Open Access Journals (Sweden)

    S. Legêne

    2011-01-01

    Full Text Available Bringing History Home: Postcolonial Immigrants and the Dutch Cultural ArenaThree Dutch-language monographs published in 2008-2009 by Ulbe Bosma, Lizzy van Leeuwen and Gert Oostindie in the context of the interdisciplinary research programme Bringing History Home, present a history of identity politics in relation to ‘postcolonial immigrants’. This term refers to some 500,000 people who since 1945 arrived in the Netherlands from Indonesia and the former Dutch New Guinea, Suriname or the Antillean islands in the Caribbean. Bosma traces the development of postcolonial immigrant organizations. In interaction with government policies, these organizations moved from mere socioeconomic emancipation struggles to mere cultural identity politics. Van Leeuwen takes such cultural identity politics as the starting point for her analysis of Indo-Dutch and Dutch Indies cultural initiatives and the competing interests at stake in the Indies heritage discourse. Oostindie discusses these developments in terms of community development and change within Dutch society at large. He introduces the notion of a ‘postcolonial bonus’. In postcolonial Netherlands, this bonus was available to immigrants on the grounds of a shared colonial past. Today, this bonus is (almost spent. The review discusses the three monographs, as well as the coherence of Bringing History Home as a research programme. Legêne argues, that notwithstanding valuable research outcomes, the very category of postcolonial immigrants does not constitute a convincing category of analysis.

  10. Construction of Two mCherry Plasmids (pXG-mCherry) for Transgenic Leishmania: Valuable Tools for Future Molecular Analysis

    Science.gov (United States)

    Sugden, Conor; Velasco-Rodriguez, Óscar; Algarabel-Olona, Miriam; Larrea, Esther; Fernández-Rubio, Celia

    2017-01-01

    Leishmania is the causative agent of leishmaniasis, a neglected tropical disease that affects more than 12 million people around the world. Current treatments are toxic and poorly effective due to the acquisition of resistance within Leishmania populations. Thus, the pursuit for new antileishmanial drugs is a priority. The available methods for drug screening based on colorimetric assays using vital dyes are time-consuming. Currently, the use of fluorescent reporter proteins is replacing the use of viability indicator dyes. We have constructed two plasmids expressing the red fluorescent protein mCherry with multiple cloning sites (MCS), adequate for N- and C-terminal fusion protein constructs. Our results also show that the improved pXG-mCherry plasmid can be employed for drug screening in vitro. The use of the red fluorescent protein, mCherry, is an easier tool for numerous assays, not only to test pharmacological compounds, but also to determine the subcellular localization of proteins. PMID:28286673

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

    Science.gov (United States)

    Hertkorn, N.; Harir, M.; Koch, B. P.; Michalke, B.; Schmitt-Kopplin, P.

    2013-03-01

    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 exceptional

  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. High field NMR spectroscopy and FTICR mass spectrometry: powerful discovery tools for the molecular level characterization of marine dissolved organic matter from the South Atlantic Ocean

    Science.gov (United States)

    Hertkorn, N.; Harir, M.; Koch, B. P.; Michalke, B.; Grill, P.; Schmitt-Kopplin, P.

    2012-01-01

    Non target high resolution organic structural spectroscopy of marine dissolved organic matter (DOM) isolated on 27 November 2008 by means of solid phase extraction (SPE) from four different depths in the South Atlantic Ocean off the Angola coast (3.1° E; -17.7° S; Angola basin) provided molecular level information of complex unknowns with unprecedented coverage and resolution. The sampling was intended to represent major characteristic oceanic regimes of general significance: 5 m (FISH; near surface photic zone), 48 m (FMAX; fluorescence maximum), 200 m (upper mesopelagic zone) and 5446 m (30 m above ground). 800 MHz proton (1H) nuclear magnetic resonance (NMR) 1H NMR, spectra were least affected by fast and differential transverse NMR relaxation and produced at first similar looking, rather smooth bulk NMR envelopes reflecting intrinsic averaging from massive signal overlap. Visibly resolved NMR signatures were most abundant in surface DOM but contributed at most a few percent to the total 1H NMR integral and were mainly limited to unsaturated and singly oxygenated carbon chemical environments. The relative abundance and variance of resolved signatures between samples was maximal in the aromatic region; in particular, the aromatic resolved NMR signature of the deep ocean sample at 5446 m was considerably different from that of all other samples. When scaled to equal total NMR integral, 1H NMR spectra of the four marine DOM samples revealed considerable variance in abundance for all major chemical environments across the entire range of chemical shift. Abundance of singly oxygenated CH units and acetate derivatives declined from surface to depth whereas aliphatics and carboxyl-rich alicyclic molecules (CRAM) derived molecules increased in abundance. Surface DOM contained a remarkably lesser abundance of methyl esters than all other marine DOM, likely a consequence of photodegradation from direct exposure to sunlight. All DOM showed similar overall 13C NMR

  14. High field NMR spectroscopy and FTICR mass spectrometry: powerful discovery tools for the molecular level characterization of marine dissolved organic matter from the South Atlantic Ocean

    Directory of Open Access Journals (Sweden)

    N. Hertkorn

    2012-01-01

    Full Text Available Non target high resolution organic structural spectroscopy of marine dissolved organic matter (DOM isolated on 27 November 2008 by means of solid phase extraction (SPE from four different depths in the South Atlantic Ocean off the Angola coast (3.1° E; −17.7° S; Angola basin provided molecular level information of complex unknowns with unprecedented coverage and resolution. The sampling was intended to represent major characteristic oceanic regimes of general significance: 5 m (FISH; near surface photic zone, 48 m (FMAX; fluorescence maximum, 200 m (upper mesopelagic zone and 5446 m (30 m above ground.

    800 MHz proton (1H nuclear magnetic resonance (NMR 1H NMR, spectra were least affected by fast and differential transverse NMR relaxation and produced at first similar looking, rather smooth bulk NMR envelopes reflecting intrinsic averaging from massive signal overlap. Visibly resolved NMR signatures were most abundant in surface DOM but contributed at most a few percent to the total 1H NMR integral and were mainly limited to unsaturated and singly oxygenated carbon chemical environments. The relative abundance and variance of resolved signatures between samples was maximal in the aromatic region; in particular, the aromatic resolved NMR signature of the deep ocean sample at 5446 m was considerably different from that of all other samples. When scaled to equal total NMR integral, 1H NMR spectra of the four marine DOM samples revealed considerable variance in abundance for all major chemical environments across the entire range of chemical shift. Abundance of singly oxygenated CH units and acetate derivatives declined from surface to depth whereas aliphatics and carboxyl-rich alicyclic molecules (CRAM derived molecules increased in abundance. Surface DOM contained a remarkably lesser abundance of methyl esters than all other marine DOM, likely a consequence of photodegradation from direct

  15. 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.

  16. Förster Resonance Energy Transfer (FRET as a Tool for Dissecting the Molecular Mechanisms for Maturation of the Shigella Type III Secretion Needle Tip Complex

    Directory of Open Access Journals (Sweden)

    William D. Picking

    2012-11-01

    Full Text Available Förster resonance energy transfer (FRET provides a powerful tool for monitoring intermolecular interactions and a sensitive technique for studying Å-level protein conformational changes. One system that has particularly benefited from the sensitivity and diversity of FRET measurements is the maturation of the Shigella type III secretion apparatus (T3SA needle tip complex. The Shigella T3SA delivers effector proteins into intestinal cells to promote bacterial invasion and spread. The T3SA is comprised of a basal body that spans the bacterial envelope and a needle with an exposed tip complex that matures in response to environmental stimuli. FRET measurements demonstrated bile salt binding by the nascent needle tip protein IpaD and also mapped resulting structural changes which led to the recruitment of the translocator IpaB. At the needle tip IpaB acts as a sensor for host cell contact but prior to secretion, it is stored as a heterodimeric complex with the chaperone IpgC. FRET analyses showed that chaperone binding to IpaB’s N-terminal domain causes a conformational change in the latter. These FRET analyses, with other biophysical methods, have been central to understanding T3SA maturation and will be highlighted, focusing on the details of the FRET measurements and the relevance to this particular system.

  17. Denaturing gradient electrophoresis (DGE) and single-strand conformation polymorphism (SSCP) molecular fingerprintings revisited by simulation and used as a tool to measure microbial diversity.

    Science.gov (United States)

    Loisel, Patrice; Harmand, Jérôme; Zemb, Olivier; Latrille, Eric; Lobry, Claude; Delgenès, Jean-Philippe; Godon, Jean-Jacques

    2006-04-01

    The exact extent of microbial diversity remains unknowable. Nevertheless, fingerprinting patterns [denaturing gradient electrophoresis (DGE), single-strand conformation polymorphism (SSCP)] provide an image of a microbial ecosystem and contain diversity data. We generated numerical simulation fingerprinting patterns based on three types of distribution (uniform, geometric and lognormal) with a range of units from 10 to 500,000. First, simulated patterns containing a diversity of around 1000 units or more gave patterns similar to those obtained in experiments. Second, the number of bands or peaks saturated quickly to about 35 and were unrelated to the degree of diversity. Finally, assuming lognormal distribution, we used an estimator of diversity on in silico and experimental fingerprinting patterns. Results on in silico patterns corresponded to the simulation inputs. Diversity results in experimental patterns were in the same range as those obtained from the same DNA sample in molecular inventories. Thus, fingerprinting patterns contain extractable data about diversity although not on the basis of a number of bands or peaks, as is generally assumed to be the case.

  18. Cathodic pseudopolarography: a new tool for the identification and quantification of cysteine, cystine and other low molecular weight thiols in seawater.

    Science.gov (United States)

    Laglera, Luis M; Downes, Javier; Tovar-Sánchez, Antonio; Monticelli, Damiano

    2014-07-11

    Thiols are compounds of paramount importance in the cellular metabolism due to their double detoxifying role as radical scavengers and trace metal ligands. However, we have scarce information about their extracellular cycling as limited data are available about their concentration, stability and speciation in the aquatic medium. In natural waters, they form part of the pool of reduced sulfur substance (RSS) whose presence has been documented by voltammetric and chromatographic methods. Traditional use of cathodic stripping voltammetry (CSV) for the analysis of RSS could only give an overall concentration due to the coalescence of their CSV peaks. Recently, it has been shown that the use of multiple deposition potentials could take voltammetry of RSS to a higher level, permitting the identification and quantification of the mixtures of RSS despite showing as a single coalescent peak. Here, due to its similarity with classical pseudopolarography, we propose to rename this analytical strategy as cathodic pseudopolarography (CP) and we present for the first time its use for the analysis of mixes of low molecular weight thiols (LMWT) at the nanomolar level. Despite limitations caused by the identical behavior of some LMWT, the CP allowed to isolate the contribution of cysteine and cystine from a coalescent signal in LMWT mixtures. Sample handling with clean protocols allowed the direct determination of the cystine:cysteine ratio without sample modification. Finally, we show the application of CP to identify LMWT in seawater samples extracted from benthic chambers and suggest future applications in other areas of environmental electroanalysis.

  19. 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...

  20. Conserved signature indels and signature proteins as novel tools for understanding microbial phylogeny and systematics: identification of molecular signatures that are specific for the phytopathogenic genera Dickeya, Pectobacterium and Brenneria.

    Science.gov (United States)

    Naushad, Hafiz Sohail; Lee, Brian; Gupta, Radhey S

    2014-02-01

    and one CSP that are specifically shared by members of the genera Pectobacterium and Brenneria, but absent in species of the genus Dickeya, indicating that the former two genera shared a common ancestor exclusive of Dickeya. The identified CSIs and CSPs provide novel tools for identification of members of the genera Dickeya and Pectobacterium and for delimiting these taxa in molecular terms. Descriptions of the genera Dickeya and Pectobacterium have been revised to provide information for these molecular markers. Biochemical studies on these CSIs and CSPs, which are specific for these genera, may lead to discovery of novel properties that are unique to these bacteria and which could be targeted to develop antibacterial agents that are specific for these plant-pathogenic bacteria.

  1. A molecular tool for detection and tracking of a potential indigenous Beauveria bassiana strain for managing emerald ash borer populations in Canada.

    Science.gov (United States)

    Johny, Shajahan; Kyei-Poku, George

    2014-10-01

    Emerald ash borer is an invasive species from Asia. Beauveria bassiana strain L49-1AA is being tested for the control of emerald ash borer in Canada, using an autocontamination trapping system. We have developed a simplified allele discrimination polymerase chain reaction (PCR) assay to screen B. bassiana strain, L49-1AA from other Beauveria species by targeting the inter-strain genetic differences in 5' end of EF1-α gene of the genus Beauveria. A single nucleotide polymorphism (SNP) site, T→C was identified only in L49-1AA and was used to develop a simplified allele discrimination polymerase chain reaction (PCR) assay based on a modified allelic inhibition of displacement activity (AIDA) approach for distinguishing B. bassiana L49-1AA from all background Beauveria isolates. The SNP site was employed to design inner primers but with a deliberate mismatch introduced at the 3' antepenultimate from the mutation site in order to maximize specificity and detection efficiency. Amplification was specific to L49-1AA without cross-reaction with DNA from other Beauveria strains. In addition, the designed primers were also tested against environmental samples in L49-1AA released plots and observed to be highly efficient in detecting and discriminating the target strain, L49-1AA from both pure and crude DNA samples. This new method can potentially allow for more discriminatory tracking and monitoring of released L49-1AA in our autocontamination and dissemination projects for managing EAB populations. Additionally, the modified-AIDA format has potential as a tool for simultaneously identifying and differentiating closely related Beauveria species, strains/isolates as well as general classification of other pathogens or organisms.

  2. The use of molecular and cytogenetic methods as a valuable tool in the detection of chromosomal abnormalities in horses: a case of sex chromosome chimerism in a Spanish purebred colt.

    Science.gov (United States)

    Demyda-Peyrás, S; Membrillo, A; Bugno-Poniewierska, M; Pawlina, K; Anaya, G; Moreno-Millán, M

    2013-01-01

    Chromosomal abnormalities associated to sex chromosomes are reported as a problem more common than believed to be in horses. Most of them remain undiagnosed due to the complexity of the horse karyotype and the lack of interest of breeders and veterinarians in this type of diagnosis. Approximately 10 years ago, the Spanish Purebred Breeders Association implemented a DNA paternity test to evaluate the pedigree of every newborn foal. All candidates who showed abnormal or uncertain results are routinely submitted to cytogenetical analysis to evaluate the presence of chromosomal abnormalities. We studied the case of a foal showing 3 and even 4 different alleles in several loci in the short tandem repeat (STR) -based DNA parentage test. To confirm these results, a filiation test was repeated using follicular hair DNA showing normal results. A complete set of conventional and molecular cytogenetic analysis was performed to determine their chromosomal complements. C-banding and FISH had shown that the foal presents a sex chimerism 64,XX/64,XY with a cellular percentage of approximately 70/30, diagnosed in blood samples. The use of a diagnostic approach combining routine parentage QF-PCR-based STR screening tested with classical or molecular cytogenetic analysis could be a powerful tool that allows early detection of foals that will have a poor or even no reproductive performance due to chromosomal abnormalities, saving time, efforts and breeders' resources.

  3. 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.

  4. High efficiency protocol of DNA extraction from Micromys minutus mandibles from owl pellets: a tool for molecular research of cryptic mammal species.

    Science.gov (United States)

    Buś, Magdalena M; Zmihorski, Michał; Romanowski, Jerzy; Balčiauskienė, Laima; Cichocki, Jan; Balčiauskas, Linas

    2014-01-01

    Owl pellets have high potential as a source of DNA. However, this noninvasive method of collecting DNA is rarely used, and its methodological aspects are poorly understood. We investigated the methodology for DNA extraction and amplification from owl pellets containing the smallest European rodent-the Harvest mouse Micromys minutus-as an example. We used mandibles identified in owl pellets for mitochondrial and nuclear DNA amplification. For DNA extraction, we tested two commercial protocols and utilized a protocol being a combination of two commercial kits which ensured high efficiency of DNA extraction. Additionally, we recorded that the amount of DNA was five times higher in extracts from teeth as compared to DNA extracts from jawbones derived from the same mandible. The quantity of DNA was significantly positively correlated with biological sample weight; however, the age of the pellet remains had an impact on the level of inhibition. We recorded inhibition in 40 % of mtDNA extracts derived from pellets older than 150 months, whereas in DNA extracts from pellets younger than 80 months, we did not observe a negative impact of inhibition on PCR efficiency. The amplification success rate was 89.9 % for the mitochondrial fragment and 39.4 % in the case of the nuclear fragment. We observed partial degradation of DNA evidenced by the fact that the longest fragments that we were able to amplify in the case of mtDNA were 450 and 200 bp for nuDNA. The study shows that pellets can be considered as a source of DNA and have high potential for molecular research in the case of threatened species and species that are difficult to study using standard field techniques.

  5. Molecular markers as a complementary tool in risk assessments: quantifying interspecific gene flow from triticale to spring wheat and durum wheat.

    Science.gov (United States)

    Kavanagh, Vanessa B; Hills, Melissa J; Goyal, Aakash; Randhawa, Harpinder S; Topinka, A Keith; Eudes, Francois; Hall, Linda M

    2013-08-01

    Triticale is being considered as a bioindustrial crop in Canada using genetic modification. Because related spring wheat (Triticum aestivum) and durum wheat (T. durum) may exhibit synchronous flowering and grow in proximity, determination of interspecific gene flow when triticale is the pollen donor is necessary to evaluate potential risk. Pollen-mediated gene flow risk assessments generally rely on phenotypic markers to detect hybridization but DNA markers could be powerful and less ambiguous in quantifying rare interspecific gene flow. Six cultivars representing four species [spring wheat, durum wheat, triticale and rye (Secale cereale)] were screened with 235 spring wheat and 27 rye SSR markers to evaluate transferability and polymorphism. Fifty-five polymorphic markers were used in conjunction with morphological characterization to quantify interspecific gene flow from a blue aleurone (BA) triticale line to two spring wheat cultivars (AC Barrie and AC Crystal) and one durum wheat cultivar (AC Avonlea). Approximately 1.9 Million seeds from small plot experiments were visually screened in comparison with known hybrid seed. In total 2031 putative hybrids were identified and 448 germinated. Morphological analysis of putative hybrid plants identified five hybrids while molecular analysis identified 11 hybrids and two were common to both. Combined, 14 hybrids were confirmed: 10 spring wheat × triticale (0.0008 % of harvested seed): seven AC Barrie × BA triticale (0.001 %) and three AC Crystal × BA triticale (0.0005 %); and four durum wheat × triticale (0.0006 %). The occurrence of rare hybrids does not present a substantial risk to the development of GM triticale.

  6. Combination of genetic screening and molecular dynamics as a useful tool for identification of disease-related mutations: ZASP PDZ domain G54S mutation case.

    Science.gov (United States)

    Fratev, Filip; Mihaylova, Elina; Pajeva, Ilza

    2014-05-27

    Cypher/ZASP (LDB3 gene) is known to interact with a network of proteins. It binds to α-actinin and the calcium voltage channels (LTCC) via its PDZ domain. Here we report the identification of a highly conserved ZASP G54S mutation classified as a variant of unknown significance in a sample of an adult with hypertrophic cardiomyopathy (HCM). The initial bioinformatics calculations strongly evaluated G54S as damaging. Furthermore, we employed accelerated and classical molecular dynamics and free energy calculations to study the structural impact of this mutation on the ZASP apo form and to address the question of whether it can be linked to HCM. Seventeen independent MD runs and simulations of 2.5 μs total were performed and showed that G54S perturbs the α2 helix position via destabilization of the adjacent loop linked to the β5 sheet. This also leads to the formation of a strong H-bond between peptide target residues Leu17 and Gln66, thus restricting both the α-actinin2 and LTCC C-terminal peptides to access their natural binding site and reducing in this way their binding capacity. On the basis of these observations and the adult's clinical data, we propose that ZASP(G54S) and presumably other ZASP PDZ domain mutations can cause HCM. To the best of our knowledge, this is the first reported ZASP PDZ domain mutation that might be linked to HCM. The integrated workflow used in this study can be applied for the identification and description of other mutations that might be related to particular diseases.

  7. 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.

  8. 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.

  9. BRINGING CIVILIZATION: SAVAGERY AND THE TAMING OF THE SAVAGE

    Directory of Open Access Journals (Sweden)

    Nicholas D. Newman

    2015-01-01

    Full Text Available “See, the Conqu’ring Hero Comes” goes the famous chorus from Handel’s Judas Maccabeus, but how does the hero conquer? Achilles defeats his enemies through his extraordinary prowess in battle, Odysseus by using his wit, but some heroes must abandon the trappings of civilization in order to conquer. This paper examines two examples of such heroes from Germanic and Greco-Roman myth: Beowulf and Herakles. In the texts analyzed, these heroes not only set aside their civilized veneer, but must journey into the territory of the monster they wish to destroy and there use savagery to defeat the savage, in order to bring civilization.

  10. 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…

  11. Bringing Technology into college and High School Physics Classrooms

    Science.gov (United States)

    Zettili, Nouredine

    2007-04-01

    We want to present ideas on ways of bringing technology to college and high school physics classrooms. We focus in particular on our outreach initiative in supporting a number of school districts with ways to improve high school physics education. This initiative is part of Project IMPACTSEED (IMproving Physics And Chemistry Teaching in SEcondary Education), a No-Child Left Behind grant funded by the Alabama Commission on Higher Education. This project is motivated by a major local need: A large number of high school physics teachers teach out of field. IMPACTSEED aims at helping high school teachers learn and master the various physics topics required by the Alabama course of study. Teachers are offered year-round support through a rich variety of programs: a two-week long summer institute, a series of five technology workshops, and onsite year-round support. Through our hands-on approach, we have identified a number of ways of bringing technology into physics classrooms. A number of technology projects were assigned to the teachers so as to show their students how physics connects to the technological devices around us. IMPACTSEED aims at providing our students with a physics education that enjoys continuity and consistency from high school to college.

  12. 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.

  13. Tool steels

    DEFF Research Database (Denmark)

    Højerslev, C.

    2001-01-01

    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...

  14. The Supernova Club: Bringing Space Science to Urban Youths

    Science.gov (United States)

    Sakimoto, P. J.; Pettit, R.; Balsara, D.; Garnavich, P.

    2008-06-01

    The Supernova Club is an experiment aimed at bringing space science to youths, almost all African Americans, from the most severely disadvantaged areas of the South Bend, Indiana, region. It leverages the National Youth Sports Program (NYSP) that, in Summer 2007, brought 100 children, ages 10-16 and living at or below the poverty level, to the Notre Dame campus for a 4-week non-residential summer program. Six contact hours of space science instruction were added to the core curriculum of nutrition, physical fitness, and academic study. At summer's end, 13 high interest/high potential youths were selected to form ``The Supernova Club''-a year-round, after-school, weekly follow-up program.

  15. BRING BACK THE SONICS西雅图夜未眠

    Institute of Scientific and Technical Information of China (English)

    2016-01-01

    2008年超音速离开之后,西雅图便没有了NBA球队,不过这座城市并没有就此放弃这个念头,他们一直在努力将一支NBA球队重新引入这座城市。作为西雅图人,快艇球员贾马尔·克劳福德饱含深情地发表了一篇名为《带超音速回来》(Bring Back The Sonics)的文章。他知道自己的家乡是一座非常热爱篮球的城市,西雅图球迷都希望在不远的将来看到一支新的超音速队。

  16. 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.

  17. Bringing history to life: simulating landmark experiments in psychology.

    Science.gov (United States)

    Boynton, David M; Smith, Laurence D

    2006-05-01

    The course in history of psychology can be challenging for students, many of whom enter it with little background in history and faced with unfamiliar names and concepts. The sheer volume of material can encourage passive memorization unless efforts are made to increase student involvement. As part of a trend toward experiential history, historians of science have begun to supplement their lectures with demonstrations of classic physics experiments as a way to bring the history of science to life. Here, the authors report on computer simulations of five landmark experiments from early experimental psychology in the areas of reaction time, span of attention, and apparent motion. The simulations are designed not only to permit hands-on replication of historically important results but also to reproduce the experimental procedures closely enough that students can gain a feel for the nature of early research and the psychological processes being studied.

  18. A Feasibility Study of Implementing a Bring-Your-Own-Computing-Device Policy

    Science.gov (United States)

    2013-12-01

    14. SUBJECT TERMS: Bring-your-own device ( BYOD ), hardware and software procurement plans, cost analysis, cloud...Full BYOC/ BYOD Policy for the GSBPP ....44 viii c. COA 3—Partial Secession of the Smart Classroom Construct...ACRONYMS AND ABBREVIATIONS AE academic edition BYOC bring your own computer BYOD bring your own device CA cost analysis CAL client access license

  19. Management Tools

    Science.gov (United States)

    1987-01-01

    Manugistics, Inc. (formerly AVYX, Inc.) has introduced a new programming language for IBM and IBM compatible computers called TREES-pls. It is a resource management tool originating from the space shuttle, that can be used in such applications as scheduling, resource allocation project control, information management, and artificial intelligence. Manugistics, Inc. was looking for a flexible tool that can be applied to many problems with minimal adaptation. Among the non-government markets are aerospace, other manufacturing, transportation, health care, food and beverage and professional services.

  20. How Can We Bring Public Health in All Policies? Strategies for Healthy Societies

    Science.gov (United States)

    Bert, Fabrizio; Scaioli, Giacomo; Gualano, Maria Rosaria; Siliquini, Roberta

    2015-01-01

    New scenarios are emerging in the European and worldwide context: the ageing of society, the climate changes, the increasing of health inequalities and the financial crisis. In this context, the scientific community and the decision-makers agree on the role of health in all policies (HiAP) strategy in improving the population’s health. The HiAP takes into account factors not strictly related to health but with important health consequences. To bring public health in all policies a change is needed, but there are some obstacles to overcome: for instance, the lack of evidence regarding the governance tools and frameworks for HiAP, the difficulty of convincing stakeholders and producing a cultural change in the political positioning of decision-makers. Consequently, it is necessary: i) to implement stronger and responsible decision-support approaches, such as health impact assessment and health technology assessment; ii) to encourage and coordinate all relevant sectors in playing their part in reducing health gaps within the European Union; iii) to strengthen cooperation and make better use of existing networks and existing public health and related institutions. The final aim will be to monitor the impact of the health determinants in order to promote the effective implementation of HiAP approach. Significance for public health This paper makes public health professionals aware of the pivotal role that they could play in reducing health inequalities and in helping to overcome the crisis of the European health systems. It discusses how, thanks to a systematic approach based on new instruments like health impact assessment and health technology assessment, and thanks also to a stronger cooperation among stakeholders and policy makers, it is possible to monitor the health determinants and consequently to bring health in all policies. PMID:25918692

  1. 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.

  2. 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

  3. 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.

  4. 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.

  5. 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...

  6. 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...

  7. 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

  8. Community Efforts Bringing Research on Learning to the Geosciences

    Science.gov (United States)

    Manduca, C. A.; Mogk, D. W.; Kastens, K. A.

    2009-12-01

    Individual, departmental and community efforts have all played a major role in developing a thriving research effort addressing thinking and learning in the geosciences. Community efforts have been effective in elevating the importance of the field, defining a research agenda, fostering collaborations with cognitive science and education communities, building capacity within the geosciences, and developing reviewer awareness of the importance and opportunities within geoscience education research. Important community efforts include a call for geoscience education research in the 1997 NSF report Geoscience Education: A Recommended Strategy and in the subsequent 2000 NSF report ‘Bridges: Connecting Research and Education in the Earth System Sciences’. A research agenda and supporting recommendations for collaboration and capacity building were jointly developed by geoscience educators, cognitive scientists and education researchers at the 2002 NSF/Johnson Foundation funded workshop Bringing Research on Learning to the Geosciences. This research agenda emphasized studies of geoscience expertise, learning pathways (and their challenges) that are critical to the development of that expertise, and materials and environments that support this learning, with a focus on learning in the field and from large data sets, complex systems and deep time, spatial skills, and the synthesis of understanding from multiple sources of incomplete data. Collaboration and capacity building have been further supported by the NAGT sponsored professional development program “On the Cutting Edge” with workshops bringing together cognitive scientists, educators and geoscientists on topics including developing on-line learning resources, teaching with visualizations, the role of the affective domain in geoscience learning, teaching metacognition, and teaching with data. 40 successful educational research proposals are attributed to participation in On the Cutting Edge. An NSF funded

  9. 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 sing

  10. 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).

  11. Molecular tools for contemporary cotton breeding

    Science.gov (United States)

    Among approximately 50 Gossypium (cotton) species are two tetraploids (G. hirsutum, G. barbadense) and two diploids (G. arboreum, and G. herbaceum) that are domesticated to produce raw materials for global textile and oilseed industries with an increasing demand for high-yield and high-quality of co...

  12. Bringing the fathead minnow into the genomic era

    Science.gov (United States)

    The fathead minnow is a well-established ecotoxicological model organism that has been widely used for regulatory ecotoxicity testing and research for over a half century. While a large amount of molecular information has been gathered on the fathead minnow over the years, the la...

  13. 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.

  14. Bringing the Universe into the Community: Afterschool Astronomy and You

    Science.gov (United States)

    Krishnamurthi, Anita; Mitchell, S.; Reynolds, C. S.; Lochner, J.

    2007-12-01

    We present a successful afterschool program that astronomers can adopt and implement within their local communities with minimal effort. Our program targets middle school students in out-of-school-time settings and introduces basic astronomy concepts through hands-on activities, with a focus on the Universe beyond the solar system. It provides an opportunity for astronomers to work within their communities to introduce students to topics which hold significant interest but are not typically studied in school. The program is ideally run as a partnership between astronomers and local afterschool program providers - astronomers contribute the content expertise, and program leaders bring it to the audience. This program was successfully pilot tested with several hundred participants in 2006 and 2007 as the Beyond Einstein Explorers’ Program (BEEP). A comprehensive manual provides detailed recipes for running the program sessions, background information, materials lists, and extension activities and resources. Activity topics include the scale and structure of the Universe, the electromagnetic spectrum, spectroscopy, telescopes, stellar evolution, galaxies, black holes, and more. A flexible structure allows the program to be run in a variety of settings, including astronomy days, summer camps, or year-long afterschool programming. Astronomers who are interested in deeper involvement can partner with us to run training sessions and also add new modules to the program.

  15. 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.

  16. Bringing Superconductor Digital Technology to the Market Place

    Science.gov (United States)

    Nisenoff, Martin

    The unique properties of superconductivity can be exploited to provide the ultimate in electronic technology for systems such as ultra-precise analogue-to-digital and digital-to-analogue converters, precise DC and AC voltage standards, ultra high speed logic circuits and systems (both digital and hybrid analogue-digital systems), and very high throughput network routers and supercomputers which would have superior electrical performance at lower overall electrical power consumption compared to systems with comparable performance which are fabricated using conventional room temperature technologies. This potential for high performance electronics with reduced power consumption would have a positive impact on slowing the increase in the demand for electrical utility power by the information technology community on the overall electrical power grid. However, before this technology can be successfully brought to the commercial market place, there must be an aggressive investment of resources and funding to develop the required infrastructure needed to yield these high performance superconductor systems, which will be reliable and available at low cost. The author proposes that it will require a concerted effort by the superconductor and cryogenic communities to bring this technology to the commercial market place or make it available for widespread use in scientific instrumentation.

  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. Mathematical tools

    Science.gov (United States)

    Capozziello, Salvatore; Faraoni, Valerio

    In this chapter we discuss certain mathematical tools which are used extensively in the following chapters. Some of these concepts and methods are part of the standard baggage taught in undergraduate and graduate courses, while others enter the tool-box of more advanced researchers. These mathematical methods are very useful in formulating ETGs and in finding analytical solutions.We begin by studying conformal transformations, which allow for different representations of scalar-tensor and f(R) theories of gravity, in addition to being useful in GR. We continue by discussing variational principles in GR, which are the basis for presenting ETGs in the following chapters. We close the chapter with a discussion of Noether symmetries, which are used elsewhere in this book to obtain analytical solutions.

  19. Navigating Towards Digital Tectonic Tools

    DEFF Research Database (Denmark)

    Schmidt, Anne Marie Due; Kirkegaard, Poul Henning

    2006-01-01

    The computer holds a great potential to break down the barriers between architecture and the technical aspects relating to architecture, thus supporting innovative architecture with an inner correspondence between form and technique. While the differing values in architecture and technique can seem...... like opposites, the term tectonics deals with creating a meaningful relationship between the two. The aim of this paper is to investigate what a digital tectonic tool could be and what relationship with technology it should represent. An understanding of this relationship can help us not only...... to understand the conflicts in architecture and the building industry but also bring us further into a discussion of how architecture can use digital tools. The investigation is carried out firstly by approaching the subject theoretically through the term tectonics and by setting up a model of the values...

  20. 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.

  1. Bringing the CMS distributed computing system into scalable operations

    CERN Document Server

    Belforte, S; Fisk, I; Flix, J; Hernández, J M; Kress, T; Letts, J; Magini, N; Miccio, V; Sciabà, A

    2010-01-01

    Establishing efficient and scalable operations of the CMS distributed computing system critically relies on the proper integration, commissioning and scale testing of the data and workload management tools, the various computing workflows and the underlying computing infrastructure, located at more than 50 computing centres worldwide and interconnected by the Worldwide LHC Computing Grid. Computing challenges periodically undertaken by CMS in the past years with increasing scale and complexity have revealed the need for a sustained effort on computing integration and commissioning activities. The Processing and Data Access (PADA) Task Force was established at the beginning of 2008 within the CMS Computing Program with the mandate of validating the infrastructure for organized processing and user analysis including the sites and the workload and data management tools, validating the distributed production system by performing functionality, reliability and scale tests, helping sites to commission, configure an...

  2. Tactile Sun: Bringing an Invisible Universe to the Visually Impaired

    Science.gov (United States)

    Isidro, G. M.; Pantoja, C. A.

    2014-07-01

    A tactile model of the Sun has been created as a strategy for communicating astronomy to the blind or visually impaired, and as a useful outreach tool for general audiences. The model design was a collaboration between an education specialist, an astronomy specialist and a sculptor. The tactile Sun has been used at astronomy outreach events in Puerto Rico to make activities more inclusive and to increase public awareness of the needs of those with disabilities.

  3. WorldWideScience.org: Bringing Light to Grey

    OpenAIRE

    Hitson, Brian A. (OSTI-DOE); Johnson, Lorrie A; 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 ...

  4. THE OMC IN THE EUROPEAN EMPLOYMENT POLICY: BRINGING SOCIALISATION IN

    OpenAIRE

    Matia Vannoni

    2011-01-01

    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...

  5. Bringing together components of the fly renal system.

    Science.gov (United States)

    Denholm, Barry; Skaer, Helen

    2009-10-01

    The function of all animal excretory systems is to rid the body of toxins and to maintain homeostatic balance. Although excretory organs in diverse animal species appear superficially different they are often built on two common principals: filtration and tubular secretion/reabsorbtion. The Drosophila excretory system is composed of filtration nephrocytes and Malpighian (renal) tubules. Here we review recent molecular genetic data on the development and differentiation of nephrocytes and renal tubules. We focus in particular on the molecular mechanisms that underpin key cell and tissue behaviours during morphogenesis, drawing parallels with other species where they exist. Finally we assess the implications of patterned tissue differentiation for the subsequent regulation of renal function. These studies highlight the continuing usefulness of the fly to provide fundamental insights into the complexities of organ formation.

  6. New tools and insights to assist with the molecular identification of Simulium guianense s.l., main Onchocerca volvulus vector within the highland areas of the Amazonia onchocerciasis focus.

    Science.gov (United States)

    Crainey, James L; Mattos-Glória, Aline; Hamada, Neusa; Luz, Sérgio L B

    2014-03-01

    .l. within individual ribosomal DNA variation and thus the first evidence that the species is not subject to the normal effects of concerted evolution. Collectively, these data illustrate the need for diverse sampling in the development of robust molecular tools for vector identification and suggest that ribosomal DNA might be able to assist with resolving S. guianense s.l. species substructuring that C01 barcoding has hitherto failed to.

  7. 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

  8. 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.

  9. 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.

  10. Workshop on molecular animation.

    Science.gov (United States)

    Bromberg, Sarina; Chiu, Wah; Ferrin, Thomas E

    2010-10-13

    From February 25 to 26, 2010, in San Francisco, the Resource for Biocomputing, Visualization, and Informatics (RBVI) and the National Center for Macromolecular Imaging (NCMI) hosted a molecular animation workshop for 21 structural biologists, molecular animators, and creators of molecular visualization software. Molecular animation aims to visualize scientific understanding of biomolecular processes and structures. The primary goal of the workshop was to identify the necessary tools for producing high-quality molecular animations, understanding complex molecular and cellular structures, creating publication supplementary materials and conference presentations, and teaching science to students and the public. Another use of molecular animation emerged in the workshop: helping to focus scientific inquiry about the motions of molecules and enhancing informal communication within and between laboratories.

  11. 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

  12. 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

  13. 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

  14. Bringing diagnostics to developing countries: an interview with Rosanna Peeling.

    Science.gov (United States)

    Peeling, Rosanna

    2015-01-01

    Interview with Professor Rosanna Peeling, PhD by Claire Raison (Commissioning Editor) Professor Rosanna Peeling is Chair of Diagnostic Research at the London School of Hygiene and Tropical Medicine (London, UK) and founded the International Diagnostics Centre at the institution. Professor Peeling previously worked for the WHO in Geneva, Switzerland, and continues to work on innovations for molecular diagnostics for point-of-care use in developing countries, addressing challenges posed by lack of funding and resources, regulatory issues and under-developed healthcare systems in these locations. Here, she discusses her career, recent progress in the field and how connectivity will affect global healthcare.

  15. Bringing the Coral to the Classroom: Using Clay Cores to Learn about Paleoceanography

    Science.gov (United States)

    Brenner, L. D.

    2014-12-01

    Scientists use myriad tools to reconstruct past surface ocean conditions to develop a comprehensive image of our Earth. Corals are often utilized to create high-resolution records of sea surface temperature, local salinity or precipitation, and overall reef health via geochemical analyses. Paleoceanography is often a completely foreign topic for younger students or is taught in an abstract way unaccompanied by lab experiences for older students. Additionally, it is quite rare for students to be regularly interacting with marine organisms and coastal processes, weakening their connection to the ocean. In order to strengthen this bond and help students to understand the global impacts of a distant ocean it is sometimes necessary to bring the coral reef to the classroom. Using modeling clay and large straws students can take their own coral cores and examine the alternating clay layers to create their own chronology. Different clay colors represent a spectrum of environmental conditions. Students can reconstruct the oceanic conditions according to their coral core and begin to appreciate the wealth of information stored in these reef structures. The goals of this activity are to introduce students to paleoceanography and teach just one of many ways that scientists can learn about the past. Ideally students will begin to cultivate an appreciation for the ocean and its role in the climate system.

  16. How can we bring public health in all policies? Strategies for healthy societies

    Directory of Open Access Journals (Sweden)

    Fabrizio Bert

    2015-04-01

    Full Text Available New scenarios are emerging in the European and worldwide context: the ageing of society, the climate changes, the increasing of health inequalities and the financial crisis. In this context, the scientific community and the decision-makers agree on the role of health in all policies (HiAP strategy in improving the population’s health. The HiAP takes into account factors not strictly related to health but with important health consequences. To bring public health in all policies a change is needed, but there are some obstacles to overcome: for instance, the lack of evidence regarding the governance tools and frameworks for HiAP, the difficulty of convincing stakeholders and producing a cultural change in the political positioning of decision-makers. Consequently, it is necessary: i to implement stronger and responsible decision-support approaches, such as health impact assessment and health technology assessment; ii to encourage and coordinate all relevant sectors in playing their part in reducing health gaps within the European Union; iii to strengthen cooperation and make better use of existing networks and existing public health and related institutions. The final aim will be to monitor the impact of the health determinants in order to promote the effective implementation of HiAP approach.

  17. Advances in e-health and telemedicine: strategy to bring health service users

    Directory of Open Access Journals (Sweden)

    Wilson Giovanni Jiménez Barbosa

    2015-08-01

    Full Text Available Background: The e-health and telemedicine have emerged as tools to facilitate access to health services, both populations far from the centres, and those who reside near them is not easily accessible or require constant controls by their professionals health traffickers. Objective: To reflect on the uses, progress and difficulties faced by Information and Communication Technologies (ICT as a strategy to bring health services to users. Methodology: qualitative hermeneutic research; advanced in two phases. The first, theoretical review by finding relevant articles in scientific databases. The second phase, critical analysis of literature found, in order to understand the dynamics generated from the use of ICT in the health sector, its current uses and prospected, and the risk that can generate its implementation for providers and patients. Results: The e-health and telemedicine have advanced in their development process andColombiahas not been outside, but there are still drawbacks of ethical, legal and operational order, which are not static and show great variation over time, becoming challenges are not independent but are associated with the dynamic progress of ICT. Conclusion: e-health and telemedicine are valid strategies to improve access to health services to communities. But require the development of processes to prevent, mitigate and / or exceed the inconveniences that may arise from its use. 

  18. 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.

  19. 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.

  20. 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 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.

  1. doit – Automation Tool

    Directory of Open Access Journals (Sweden)

    2010-09-01

    Full Text Available

    This article describes how traditional build-tools work, what are the shortcomings of this model for modern software development and finally how doit solve these problems. doit is written in python, it comes from the idea of bringing the power of build-tools to execute any kind of tasks.

  2. Bringing partial differential equations to life for students

    Science.gov (United States)

    José Cano, María; Chacón-Vera, Eliseo; Esquembre, Francisco

    2015-05-01

    Teaching partial differential equations (PDEs) carries inherent difficulties that an interactive visualization might help overcome in an active learning process. However, the generation of this kind of teaching material implies serious difficulties, mainly in terms of coding efforts. This work describes how to use an authoring tool, Easy Java Simulations, to build interactive simulations using FreeFem++ (Hecht F 2012 J. Numer. Math. 20 251) as a PDE solver engine. It makes possible to build simulations where students can change parameters, the geometry and the equations themselves getting an immediate feedback. But it is also possible for them to edit the simulations to set deeper changes. The process is ilustrated with some basic examples. These simulations show PDEs in a pedagogic manner and can be tuned by no experts in the field, teachers or students. Finally, we report a classroom experience and a survey from the third year students in the Degree of Mathematics at the University of Murcia.

  3. REALCAT: A New Platform to Bring Catalysis to the Lightspeed

    Directory of Open Access Journals (Sweden)

    Paul Sébastien

    2015-03-01

    Full Text Available Catalysis, irrespective of its form can be considered as one of the most important pillars of today’s chemical industry. The development of new catalysts with improved performances is therefore a highly strategic issue. However, the a priori theoretical design of the best catalyst for a desired reaction is not yet possible and a time- and money-consuming experimental phase is still needed to develop a new catalyst for a given reaction. The REALCAT platform described in this paper consists in a complete, unique, integrated and top-level high-throughput technologies workflow that allows a significant acceleration of this kind of research. This is illustrated by some preliminary results of optimization of the operating conditions of glycerol dehydration to acrolein over an heteropolyacid-based supported catalyst. It is shown that using REALCAT high-throughput tools a more than 10-fold acceleration of the operating conditions optimization process is obtained.

  4. 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...

  5. The making of a portrait--bringing it into focus.

    Science.gov (United States)

    Zeng, X

    2003-12-01

    The data generated by DNA arrays are often described as the molecular "portrait" of a particular physiological/pathological sample. Although the emotional reactions could range from revulsion to adoration when viewing those portraits, as it might be when viewing some contemporary art, array technology has fundamentally changed the way researchers approach many biomedical questions. With its ability to monitor the expression level of tens of thousands genes simultaneously, microarray technology has been able to identify "markers" for complex diseases such as cancer. While massive amounts of work lie ahead to validate those marker genes, many researchers are turning their attentions to the low-density, focused arrays. When incorporated with current knowledge on specific biological pathways, these specially tailored macroarrays may be better fitted for purposes such as diagnosis, drug discovery and validation, and prognostic assessment of clinical treatments.

  6. 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

  7. 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

  8. Bringing patient centricity to diabetes medication access in Canada

    Science.gov (United States)

    Glennie, Judith L; Kovacs Burns, Katharina; Oh, Paul

    2016-01-01

    Canada must become proactive in addressing type 2 diabetes. With the second highest rate of diabetes prevalence in the developed world, the number of Canadians living with diabetes will soon reach epidemic levels. Against international comparisons, Canada also performs poorly with respect to diabetes-related hospitalizations, mortality rates, and access to medications. Diabetes and its comorbidities pose a significant burden on people with diabetes (PWD) and their families, through out-of-pocket expenses for medications, devices, supplies, and the support needed to manage their illness. Rising direct and indirect costs of diabetes will become a drain on Canada’s economy and undermine the financial stability of our health care system. Canada’s approach to diabetes medication assessment and funding has created a patchwork of medication access across provinces. Access to treatments for those who rely on public programs is highly restricted compared to Canadians with private drug plans, as well in contrast with public payers in other countries. Each person living with diabetes has different needs, so a “patient-centric” approach ensures treatment focused on individual circumstances. Such tailoring is difficult to achieve, with the linear approach required by public payers. We may be undermining optimal care for PWD because of access policies that are not aligned with individualized approaches – and increasing overall health care costs in the process. The scope of Canada’s diabetes challenge demands holistic and proactive solutions. Canada needs to get out from “behind the eight ball” and get “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

  9. Molecular marker databases.

    Science.gov (United States)

    Lai, Kaitao; Lorenc, Michał Tadeusz; Edwards, David

    2015-01-01

    The detection and analysis of genetic variation plays an important role in plant breeding and this role is increasing with the continued development of genome sequencing technologies. Molecular genetic markers are important tools to characterize genetic variation and assist with genomic breeding. Processing and storing the growing abundance of molecular marker data being produced requires the development of specific bioinformatics tools and advanced databases. Molecular marker databases range from species specific through to organism wide and often host a variety of additional related genetic, genomic, or phenotypic information. In this chapter, we will present some of the features of plant molecular genetic marker databases, highlight the various types of marker resources, and predict the potential future direction of crop marker databases.

  10. 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...

  11. 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

  12. 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.

  13. 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?

  14. 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.

    2013-01-01

    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.

  15. 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.

  16. Manipulation of molecular structures with magnetic fields

    NARCIS (Netherlands)

    Boamfa, M.I.

    2003-01-01

    The present thesis deals with the use of magnetic fields as a handle to manipulate matter at a molecular level and as a tool to probe molecular properties or inter molecular interactions. The work consists of in situ optical studies of (polymer) liquid crystals and molecular aggregates in high magne

  17. Process for attaching molecular wires and devices to carbon nanotubes and compositions thereof

    Science.gov (United States)

    Tour, James M. (Inventor); Bahr, Jeffrey L. (Inventor); Yang, Jiping (Inventor)

    2008-01-01

    The present invention is directed towards processes for covalently attaching molecular wires and molecular electronic devices to carbon nanotubes and compositions thereof. Such processes utilize diazonium chemistry to bring about this marriage of wire-like nanotubes with molecular wires and molecular electronic devices.

  18. 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.

  19. OMICs Technologies Tools for Food Science

    CERN Document Server

    Benkeblia, Noureddine

    2012-01-01

    Since the completion of the Human Genome Project, food and nutrition sciences have undergone a fundamental molecular transformation. New discoveries in molecular biology, analytical chemistry, and biochemistry have led to the development of new tools that are likely to revolutionize the study of food. OMICS Technologies: Tools for Food Science explores how these tools reveal the fundamental pathways and biochemical processes that drive food and nutrition sciences. In this volume, an international panel of researchers examines the rise of these new technologies--including metabolomics, metageno

  20. Non-contact measurement and analysis of machine tool spindles

    OpenAIRE

    Clough, David A; Fletcher, Simon; Longstaff, Andrew P.

    2010-01-01

    Increasing demand on the manufacturing industry to produce tighter tolerance parts means it is\\ud necessary to gain a greater understanding of machine tool capabilities and error sources. A significant source of machine tool errors is down to spindle inaccuracies and performance, leading to part scrapping. Catastrophic spindle failure brings production to a standstill until a new spindle can be procured and installed, resulting in lost production time.\\ud This project aims to assess the effec...

  1. Downhole tool with replaceable tool sleeve sections

    Energy Technology Data Exchange (ETDEWEB)

    Case, W. A.

    1985-10-29

    A downhole tool for insertion in a drill stem includes elongated cylindrical half sleeve tool sections adapted to be non-rotatably supported on an elongated cylindrical body. The tool sections are mountable on and removable from the body without disconnecting either end of the tool from a drill stem. The half sleeve tool sections are provided with tapered axially extending flanges on their opposite ends which fit in corresponding tapered recesses formed on the tool body and the tool sections are retained on the body by a locknut threadedly engaged with the body and engageable with an axially movable retaining collar. The tool sections may be drivably engaged with axial keys formed on the body or the tool sections may be formed with flat surfaces on the sleeve inner sides cooperable with complementary flat surfaces formed on a reduced diameter portion of the body around which the tool sections are mounted.

  2. 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.

  3. Bring Hidden Hazards to the Publics Attention, Understanding, and Informed Decision by Coordinating Federal Education Initiatives

    Science.gov (United States)

    Niepold, F.; Karsten, J. L.; Wei, M.; Jadin, J.

    2010-12-01

    In the 2010 National Research Council’s America’s Climate Choices’ report on Informing Effective Decisions and Actions Related to Climate Change concluded; “Education and communication are among the most powerful tools the nation has to bring hidden hazards to public attention, understanding, and action.” They conclude that the “current and future students, the broader public, and policymakers need to understand the causes, consequences, and potential solutions to climate change, develop scientific thinking and problem-solving skills, and improve their ability to make informed decisions.” The U.S. Global Change Research Program (USGCRP) works to integrate the climate related activities of these different agencies, with oversight from the Office of Science and Technology Policy and other White House offices. USGCRP’s focus is now on evaluating optimal strategies for addressing climate change risks, improving coordination among the Federal agencies, engaging stakeholders (including national policy leaders and local resource managers) on the research results to all and improving public understanding and decision-making related to global change. Implicit to these activities is the need to educate the public about the science of climate change and its consequences, as well as coordinate Federal investments related to climate change education. In a broader sense, the implementation of the proposed Interagency Taskforce on Climate Change Communication and Education will serve the evolving USGCRP mandates around cross-cutting, thematic elements, as recommended by the National Research Council (NRC, 2009) and the U.S. Climate Change Science Program Revised Research Plan: An update to the 2003 Strategic Plan (USGCRP, 2008), to help the Federal government “capitalize on its investments and aid in the development of increased climate literacy for the Nation.” This session will update the participants on the work to date and the near term coordinated plans

  4. 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

  5. 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.

  6. Molecular physics

    CERN Document Server

    Williams, Dudley

    2013-01-01

    Methods of Experimental Physics, Volume 3: Molecular Physics focuses on molecular theory, spectroscopy, resonance, molecular beams, and electric and thermodynamic properties. The manuscript first considers the origins of molecular theory, molecular physics, and molecular spectroscopy, as well as microwave spectroscopy, electronic spectra, and Raman effect. The text then ponders on diffraction methods of molecular structure determination and resonance studies. Topics include techniques of electron, neutron, and x-ray diffraction and nuclear magnetic, nuclear quadropole, and electron spin reson

  7. 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

  8. 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

  9. ADAPTABLE DESIGN OF MACHINE TOOLS STRUCTURES

    Institute of Scientific and Technical Information of China (English)

    XU Yanshen; CHEN Yongliang; ZHANG Guojun; GU Peihua

    2008-01-01

    Adaptable design aims to extend the utilities of design and product. The specific methods are developed for practical applications of adaptable design in the design of mechanical structures, including adaptable platform, interface and module designs. Adaptable redesign problems are formulated as adaptable platform design under adaptability bound constraints. Analysis tools are then suggested for the implementation of the redesign of machine tool structures, including variation techniques based sensitivity analysis, similarity-based commonality analysis, performance improvement, and adaptability measures. The specific measure of adaptability for machine tool structures is measured through the quantification of the structural similarity and performance improvement gained from adaptable design. The method provides designers with an approach that brings adaptability into the design process, with considering the cost and benefits of such adaptability. The redesign of CNC spiral bevel gear cutting machine structures has been included to illustrate these concepts and methods.

  10. Bringing-Light Tour” ——Symbol of China-Pakistan Friendship

    Institute of Scientific and Technical Information of China (English)

    Our Staff Reporter

    2012-01-01

    <正>On April 26, 2012, the 1008th cataract operation conducted at the Civil Hospital Karachi by the medical team of the China-Pakistan Friendship Bringing-Light Tour brought the activity to a successfully conclusion.

  11. A Vehicle for Science and Exploration: Bringing Offshore Industry Advances and Experience to the Oceanographic Community

    Science.gov (United States)

    2007-01-01

    A Vehicle for Science and Exploration: Bringing Offshore Industry Advances and Experience to the Oceanographic Community Brent Evers...DATES COVERED 00-00-2007 to 00-00-2007 4. TITLE AND SUBTITLE A Vehicle for Science and Exploration: Bringing Offshore Industry Advances and...fiber, and thus the umbilical connecting the ROV to the ship. While the .680” electro-optical cable employed in the NOAA ROV system incorporates three

  12. 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...

  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. Lubricant characterization by molecular simulation

    Energy Technology Data Exchange (ETDEWEB)

    Moore, J.D.; Cui, S.T.; Cummings, P.T.; Cochran, H.D. [Univ. of Tennessee, Knoxville, TN (United States). Dept. of Chemical Engineering]|[Oak Ridge National Lab., TN (United States). Chemical Technology Div.

    1997-12-01

    The authors have reported the calculation of the kinematic viscosity index of squalane from nonequilibrium molecular dynamics simulations. This represents the first accurate quantitative prediction of this measure of lubricant performance by molecular simulation. Using the same general alkane potential model, this computational approach offers the possibility of predicting the performance of potential lubricants prior to synthesis. Consequently, molecular simulation is poised to become an important tool for future lubricant development.

  15. 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.

  16. 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.

  17. Tool Changer For Robot

    Science.gov (United States)

    Voellmer, George M.

    1992-01-01

    Mechanism enables robot to change tools on end of arm. Actuated by motion of robot: requires no additional electrical or pneumatic energy to make or break connection between tool and wrist at end of arm. Includes three basic subassemblies: wrist interface plate attached to robot arm at wrist, tool interface plate attached to tool, and holster. Separate tool interface plate and holster provided for each tool robot uses.

  18. 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

  19. 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

  20. Bringing Relief

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    China is mobilizing medical and epidemic prevention resources from around the country to ensure adequate levels of care for earthquake survivors"When the rescued people arrive, what we can do is to try our best to restore their health,"said Liu Xiaoguang,Deputy Principal of Peking University Third Hospital and head of Beijing’s medical rescue team for the Sichuan earthquake.As one of the first

  1. 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...

  2. Number of Hydroxyl Groups on the B-Ring of Flavonoids Affects Their Antioxidant Activity and Interaction with Phorbol Ester Binding Site of PKCδ C1B Domain: In Vitro and in Silico Studies.

    Science.gov (United States)

    Kongpichitchoke, Teeradate; Hsu, Jue-Liang; Huang, Tzou-Chi

    2015-05-13

    Although flavonoids have been reported for their benefits and nutraceutical potential use, the importance of their structure on their beneficial effects, especially on signal transduction mechanisms, has not been well clarified. In this study, three flavonoids, pinocembrin, naringenin, and eriodictyol, were chosen to determine the effect of hydroxyl groups on the B-ring of flavonoid structure on their antioxidant activity. In vitro assays, including DPPH scavenging activity, ROS quantification by flow cytometer, and proteins immunoblotting, and in silico analysis by molecular docking between the flavonoids and C1B domain of PKCδ phorbol ester binding site were both used to complete this study. Eriodictyol (10 μM), containing two hydroxyl groups on the B-ring, exhibited significantly higher (p groups on its B-ring, which consequently contributed to greater antioxidant activity over pinocembrin and naringenin.

  3. 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

  4. 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.

  5. [Future prospects of molecular epidemiology in tuberculosis].

    Science.gov (United States)

    Matsumoto, Tomoshige; Iwamoto, Tomotada

    2009-12-01

    Before the availability of high-resolution genotyping tools in 1990s, there was a prevailing dogma of little genomic sequence diversity in Mycobacterium tuberculosis. Due to the low levels of genetic variation, it was assumed that M. tuberculosis exhibit very little phenotypic variation in immunologic and virulence factors. The fingerprinting method based on restriction fragment length polymorphisms (RFLP) of IS6110 insertion sequences had unveiled the underestimation of the sequence variation in M. tuberculosis and the importance of strain-to-strain variation for understanding pathogenesis, immune mechanisms, bacterial evolution, and host adaptation. This method became a gold standard for strain differentiation in the molecular epidemiological study. It had lead to a profusion of studies in molecular epidemiology such as the detection of unsuspected transmission, the estimation of the extent of recent transmission, the identification of laboratory cross-contamination, the identification of outbreaks, and distinction between reinfection and relapse. This, in 1990s, is the opening of the molecular epidemiology of tuberculosis. After the completion of genome project of the M. tuberculosis laboratory strain H37Rv, some of the clinical isolates were completely sequenced. This prompted the in silico genome comparison and identified various genomic markers which can give a unifying framework for both epidemiology and evolutionary analysis of M. tuberculosis population. Of them, variable numbers of tandem repeats (VNTR) was found as the most promising PCR-based method which can provide adequate discrimination of M. tuberculosis strains in many cases, including the estimation of M. tuberculosis transmission and the identification of genetic lineages. PCR-based VNTR analysis is easy, rapid, and highly specific and can generate portable digit-based data, unlike the analog information obtained from IS6110 RFLP which is labor intensive. In this regards, investigators can

  6. 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.

  7. 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.

  8. Frontier Fields: A Cost-Effective Approach to Bringing Authentic Science to the Education Community

    Science.gov (United States)

    Eisenhamer, B.; Lawton, B.; Summers, F.; Ryer, H.

    2015-11-01

    For more than two decades, the Hubble EPO program has sought to bring the wonders of the universe to the education community and the public, and to engage audiences in the adventure of scientific discovery. Program components include standards-based, curriculum-support materials, exhibits and exhibit components, and professional development workshops. The main underpinnings of the program's infrastructure are scientist-educator development teams, partnerships, and an embedded program evaluation component. The Space Telescope Science Institute's Office of Public Outreach is leveraging this existing infrastructure to bring the Frontier Fields science program to the education community in a cost-effective way. Frontier Fields observations and results have been, and will continue to be, embedded into existing product lines and professional development offerings. We also are leveraging our new social media strategy to bring the science program to the public in the form of an ongoing blog.

  9. [Tuberculosis and molecular biology].

    Science.gov (United States)

    Andersen, Ase Bengård; Lillebaek, Troels; Søborg, Christian; Johansen, Isik Somuncu; Thomsen, Vibeke Østergaard

    2003-02-24

    Mycobacterium tuberculosis, the causative agent of tuberculosis (TB) hunting millions worldwide, is a challenge to work with in the laboratory. Modern molecular biology has provided extremely useful tools which have changed conventional diagnostic procedures in the TB laboratories. Research in molecular epidemiology is currently expanding our knowledge of the natural history of TB. Access to the genome sequence has opened new avenues for research in drug development and new vaccines. However, we are still awaiting the impact of these efforts in the resource-poor TB endemic countries.

  10. Bring Me Men: Intertextual Identity Formation at the US Air Force Academy

    Science.gov (United States)

    2008-09-01

    number of things from Contrails and are tested on their knowledge at the end of the week. With the Agenda for Change, the Class of 2007’s Contrails...place for women under "Bring Me Men..." even as role models; the Cadet Field House where each semester every cadet must pass the Physical Fitness Test is...hidden under the stairs. 53 CHAPTER 4 WORDS MATTER Bring me men to match my rivers Continent cleavers , flowing free, Drawn by the eternal madness To

  11. 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....... The first research project (completed) concerns how textile designers use new responsive materials and technologies, whereas the second (ongoing) concerns how architects and design engineers can use textile materials. In both projects, the developed inspirational tool is tested through workshops...... with the mentioned stakeholders. In these workshops, new ways of disseminating the results from research in textiles and textile design are experimented with. The submitted contribution therefore mainly addresses the role of interdisciplinarity in textile design research as well as the impact of new materials...

  12. New Tool Creates a Big Stir

    Science.gov (United States)

    2001-01-01

    A new self-adjusting, retractable pin tool for friction stir welding is now used in the manufacturing of components for NASA Space Shuttles. Friction stir welding is a process that makes straight-line welds without bringing the parent material to a liquid state. This is accomplished through high-speed rotation, which generates frictional heat between the welding tool and the piece being welded. This heat causes the material to soften to the point of plasticity without allowing it to melt. The plasticized material is then transferred from the front edge of the welding tool to the trail edge, where it joins the pieces being welded. However, a major flaw of this method is its reliance on a single-piece pin tool. The weld is left unfinished and a hole remains where the pin was inserted. The hole must be covered with a rivet in order to preserve the integrity of the weld. The NASA-developed pin tool, however, eliminates the need for this finishing step, as its retraction allows continuous rewelding at lesser depths, until the hole is completely closed. With this NASA technology, welding of higher strength alloys, as well as non-planer and variable thickness structures can be achieved.

  13. 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.

  14. Interface-assisted molecular spintronics

    Energy Technology Data Exchange (ETDEWEB)

    Raman, Karthik V. [Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012 (India)

    2014-09-15

    Molecular spintronics, a field that utilizes the spin state of organic molecules to develop magneto-electronic devices, has shown an enormous scientific activity for more than a decade. But, in the last couple of years, new insights in understanding the fundamental phenomena of molecular interaction on magnetic surfaces, forming a hybrid interface, are presenting a new pathway for developing the subfield of interface-assisted molecular spintronics. The recent exploration of such hybrid interfaces involving carbon based aromatic molecules shows a significant excitement and promise over the previously studied single molecular magnets. In the above new scenario, hybridization of the molecular orbitals with the spin-polarized bands of the surface creates new interface states with unique electronic and magnetic character. This study opens up a molecular-genome initiative in designing new handles to functionalize the spin dependent electronic properties of the hybrid interface to construct spin-functional tailor-made devices. Through this article, we review this subject by presenting a fundamental understanding of the interface spin-chemistry and spin-physics by taking support of advanced computational and spectroscopy tools to investigate molecular spin responses with demonstration of new interface phenomena. Spin-polarized scanning tunneling spectroscopy is favorably considered to be an important tool to investigate these hybrid interfaces with intra-molecular spatial resolution. Finally, by addressing some of the recent findings, we propose novel device schemes towards building interface tailored molecular spintronic devices for applications in sensor, memory, and quantum computing.

  15. Useful design tools?

    DEFF Research Database (Denmark)

    Jensen, Jesper Ole

    2005-01-01

    Tools for design management are on the agenda in building projects in order to set targets, to choose and prioritise between alternative environmental solutions, to involve stakeholders and to document, evaluate and benchmark. Different types of tools are available, but what can we learn from...... the use or lack of use of current tools in the development of future design tools for sustainable buildings? Why are some used while others are not? Who is using them? The paper deals with design management, with special focus on sustainable building in Denmark, and the challenge of turning the generally...... vague and contested concept of sustainability into concrete concepts and building projects. It describes a typology of tools: process tools, impact assessment tools, multi-criteria tools and tools for monitoring. It includes a Danish paradigmatic case study of stakeholder participation in the planning...

  16. GenomicScape: an easy-to-use web tool for gene expression data analysis. Application to investigate the molecular events in the differentiation of B cells into plasma cells.

    Science.gov (United States)

    Kassambara, Alboukadel; Rème, Thierry; Jourdan, Michel; Fest, Thierry; Hose, Dirk; Tarte, Karin; Klein, Bernard

    2015-01-01

    DNA microarrays have considerably helped to improve the understanding of biological processes and diseases. Large amounts of publicly available microarray data are accumulating, but are poorly exploited due to a lack of easy-to-use bioinformatics resources. The aim of this study is to build a free and convenient data-mining web site (www.genomicscape.com). GenomicScape allows mining dataset from various microarray platforms, identifying genes differentially expressed between populations, clustering populations, visualizing expression profiles of large sets of genes, and exporting results and figures. We show how easily GenomicScape makes it possible to construct a molecular atlas of the B cell differentiation using publicly available transcriptome data of naïve B cells, centroblasts, centrocytes, memory B cells, preplasmablasts, plasmablasts, early plasma cells and bone marrow plasma cells. Genes overexpressed in each population and the pathways encoded by these genes are provided as well as how the populations cluster together. All the analyses, tables and figures can be easily done and exported using GenomicScape and this B cell to plasma cell atlas is freely available online. Beyond this B cell to plasma cell atlas, the molecular characteristics of any biological process can be easily and freely investigated by uploading the corresponding transcriptome files into GenomicScape.

  17. 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…

  18. Bringing (Century-Old) Technology into the Classroom. Part I: Teaching Mechanics and Thermodynamics with Antiques

    Science.gov (United States)

    Jewett, John W., Jr.

    2015-01-01

    The notion of bringing technology into the classroom has been the subject of many recent presentations at conferences and papers in physics teaching journals. The use of devices such as laptops, smartphones, tablets, and clickers is rising in today's classrooms and laboratories. PhET simulations have been available online for over a decade. A…

  19. Echoes of the Past: Jackdaws and Historical Fiction Bring History to Life.

    Science.gov (United States)

    Dodd, Elizabeth L.

    1999-01-01

    Discusses the use of jackdaws, collections of artifacts generating a visual representation of a time period, and historical fiction in the classroom to bring history alive for students. Reports on the success of jackdaws in an early-childhood classroom and in a university setting with preservice teachers. Includes jackdaws and related historical…

  20. Bring Back "Das Kapital" Punishment! Credit Crunch and the Fall of the "Knowledge Economy"

    Science.gov (United States)

    Stronach, Ian; Clarke, John

    2010-01-01

    This article contrasts the collapse of the twin political certainties of the 20th century--"scientific socialism" (1989) and "scientific capitalism" (2008). Such a collapse restores Uncertainty to her throne, and brings back the need to radically rethink political possibilities for the future. (Contains 1 note.)

  1. 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…

  2. Bring Back Our Girls, Social Mobilization: Implications for Cross-Cultural Research

    Science.gov (United States)

    Olutokunbo, Adekalu Samuel; Suandi, Turiman; Cephas, Oluwaseyitan Rotimi; Abu-Samah, Irza Hanie

    2015-01-01

    Social mobilization is a proactive measure for community development that salvages the society from destruction and disaster. From sociological perspective, this paper discusses the concept of social mobilization and its implications for cross-cultural research. To do this, the study uses the "Bring Back Our Girls" Global Campaign, as…

  3. 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…

  4. 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…

  5. Learning a Third Language: What Learner Strategies Do Bilingual Students Bring?

    Science.gov (United States)

    Grenfell, Michael; Harris, Vee

    2015-01-01

    This article seeks to develop the research agenda of multilingualism and multicompetence by bringing together three research fields and their related methodologies: bilingualism, third language acquisition and language learner strategies. After a brief introduction to each area, it describes a study to explore whether bilingual adolescent students…

  6. 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.…

  7. 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,…

  8. 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…

  9. 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…

  10. 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…

  11. Bringing up condom use and using condoms with new sexual partners : Intentional or habitual?

    NARCIS (Netherlands)

    Yzer, MC; Siero, FW; Buunk, BP

    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: Aj

  12. Our Grandparents' Civil Rights Era: Family Letters Bring History to Life

    Science.gov (United States)

    McCormick, Willow

    2013-01-01

    This article describes second graders in a predominantly white suburban school who were assigned to ask their grandparents to write about their experiences during the Civil Rights Movement. The letters bring surprising wisdom--and some thought-provoking issues--to the classroom. The author found that the power of the primary source documents…

  13. Practitioner in the Classroom: Bringing Local Government Experience into the Public Administration Curriculum.

    Science.gov (United States)

    Milam, Donna M.

    2003-01-01

    A local government administrator used her work experiences to create simulation exercises for public administration students. Advantages that such practitioners bring to the classroom include "inside" information, organizational management skills, budget knowledge, and the ability to provide networking opportunities for students. (JOW)

  14. Bringing Work Home: Take-Home Pesticide Exposure Among Farm Families

    NARCIS (Netherlands)

    Curwin, B.D.

    2006-01-01

    In this thesis take-home pesticide exposure among farm families, with an emphasis on herbicides, was investigated. Take-home exposure occurs when a worker unwittingly brings home a substance on his or her clothing or shoes, thereby potentially exposing his or her family. The pesticides investigated

  15. LensTools: Weak Lensing computing tools

    Science.gov (United States)

    Petri, A.

    2016-02-01

    LensTools implements a wide range of routines frequently used in Weak Gravitational Lensing, including tools for image analysis, statistical processing and numerical theory predictions. The package offers many useful features, including complete flexibility and easy customization of input/output formats; efficient measurements of power spectrum, PDF, Minkowski functionals and peak counts of convergence maps; survey masks; artificial noise generation engines; easy to compute parameter statistical inferences; ray tracing simulations; and many others. It requires standard numpy and scipy, and depending on tools used, may require Astropy (ascl:1304.002), emcee (ascl:1303.002), matplotlib, and mpi4py.

  16. Novel gene expression tools for rice biotechnology

    Science.gov (United States)

    Biotechnology is an effective and important method of improving both quality and agronomic traits in rice. We are developing novel molecular tools for genetic engineering, with a focus on developing novel transgene expression control elements (i.e. promoters) for rice. A suite of monocot grass promo...

  17. Electronic Safety Resource Tools -- Supporting Hydrogen and Fuel Cell Commercialization

    Energy Technology Data Exchange (ETDEWEB)

    Barilo, Nick F.

    2014-09-29

    The Pacific Northwest National Laboratory (PNNL) Hydrogen Safety Program conducted a planning session in Los Angeles, CA on April 1, 2014 to consider what electronic safety tools would benefit the next phase of hydrogen and fuel cell commercialization. A diverse, 20-person team led by an experienced facilitator considered the question as it applied to the eight most relevant user groups. The results and subsequent evaluation activities revealed several possible resource tools that could greatly benefit users. The tool identified as having the greatest potential for impact is a hydrogen safety portal, which can be the central location for integrating and disseminating safety information (including most of the tools identified in this report). Such a tool can provide credible and reliable information from a trustworthy source. Other impactful tools identified include a codes and standards wizard to guide users through a series of questions relating to application and specific features of the requirements; a scenario-based virtual reality training for first responders; peer networking tools to bring users from focused groups together to discuss and collaborate on hydrogen safety issues; and a focused tool for training inspectors. Table ES.1 provides results of the planning session, including proposed new tools and changes to existing tools.

  18. Molecular Plasmonics

    Science.gov (United States)

    Wilson, Andrew J.; Willets, Katherine A.

    2016-06-01

    In this review, we survey recent advances in the field of molecular plasmonics beyond the traditional sensing modality. Molecular plasmonics is explored in the context of the complex interaction between plasmon resonances and molecules and the ability of molecules to support plasmons self-consistently. First, spectroscopic changes induced by the interaction between molecular and plasmonic resonances are discussed, followed by examples of how tuning molecular properties leads to active molecular plasmonic systems. Next, the role of the position and polarizability of a molecular adsorbate on surface-enhanced Raman scattering signals is examined experimentally and theoretically. Finally, we introduce recent research focused on using molecules as plasmonic materials. Each of these examples is intended to highlight the role of molecules as integral components in coupled molecule-plasmon systems, as well as to show the diversity of applications in molecular plasmonics.

  19. 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.

  20. Genetic tools and techniques for Chlamydomonas reinhardtii.

    Science.gov (United States)

    Mussgnug, Jan H

    2015-07-01

    The development of tools has always been a major driving force for the advancement of science. Optical microscopes were the first instruments that allowed discovery and descriptive studies of the subcellular features of microorganisms. Although optical and electron microscopes remained at the forefront of microbiological research tools since their inventions, the advent of molecular genetics brought about questions which had to be addressed with new "genetic tools". The unicellular green microalgal genus Chlamydomonas, especially the most prominent species C. reinhardtii, has become a frequently used model organism for many diverse fields of research and molecular genetic analyses of C. reinhardtii, as well as the available genetic tools and techniques, have become increasingly sophisticated throughout the last decades. The aim of this review is to provide an overview of the molecular key features of C. reinhardtii and summarize the progress related to the development of tools and techniques for genetic engineering of this organism, from pioneering DNA transformation experiments to state-of-the-art techniques for targeted nuclear genome editing and high-throughput screening approaches.

  1. 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)

  2. 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.

  3. Correlation of electronic transitions and redox potentials measured for pyrocatechol, resorcinol, hydroquinone, pyrogallol, and gallic acid with results of semi-empirical molecular orbital computations A useful interpretation tool

    Science.gov (United States)

    Carter, Melvin Keith

    2007-04-01

    Cyclic voltammogram (CV) electrochemical measurements for pyrocatechol, resorcinol, hydroquinone, pyrogallol, and gallic acid in strong alkaline solution produced observable oxidation-reduction potentials for each hydroxy group present except for resorcinol. UV absorption spectra were also observed for the diluted solutions. Semi-empirical molecular orbital computations were conducted for these molecules of C2 v point group symmetry to determine the character and energies to aid interpretation of the experimental results. CV oxidation removed a π-electron by a radiationless π-π* transition followed by an electron shift from a negative oxygen to the positive aromatic π-system indicated by an observable σ-π* transition. Simple semi-empirical computations correlated with measured excited electronic states during electron transfer.

  4. Personal Wellness Tools

    Science.gov (United States)

    ... Public Service Announcements Partnering with DBSA Personal Wellness Tools The Merriam-Webster dictionary gives several definitions for ... home to a wealth of customizable, personal wellness tools to help you live a full, healthy, and ...

  5. OOTW COST TOOLS

    Energy Technology Data Exchange (ETDEWEB)

    HARTLEY, D.S.III; PACKARD, S.L.

    1998-09-01

    This document reports the results of a study of cost tools to support the analysis of Operations Other Than War (OOTW). It recommends the continued development of the Department of Defense (DoD) Contingency Operational Support Tool (COST) as the basic cost analysis tool for 00TWS. It also recommends modifications to be included in future versions of COST and the development of an 00TW mission planning tool to supply valid input for costing.

  6. Software engineering tools.

    Science.gov (United States)

    Wear, L L; Pinkert, J R

    1994-01-01

    We have looked at general descriptions and illustrations of several software development tools, such as tools for prototyping, developing DFDs, testing, and maintenance. Many others are available, and new ones are being developed. However, you have at least seen some examples of powerful CASE tools for systems development.

  7. Pro Tools HD

    CERN Document Server

    Camou, Edouard

    2013-01-01

    An easy-to-follow guide for using Pro Tools HD 11 effectively.This book is ideal for anyone who already uses ProTools and wants to learn more, or is new to Pro Tools HD and wants to use it effectively in their own audio workstations.

  8. An Educational Tool for Interactive Parallel and Distributed Processing

    DEFF Research Database (Denmark)

    Pagliarini, Luigi; Lund, Henrik Hautop

    2011-01-01

    In this paper we try to describe how the Modular Interactive Tiles System (MITS) can be a valuable tool for introducing students to interactive parallel and distributed processing programming. This is done by providing an educational hands-on tool that allows a change of representation...... of the abstract problems related to designing interactive parallel and distributed systems. Indeed, MITS seems to bring a series of goals into the education, such as parallel programming, distributedness, communication protocols, master dependency, software behavioral models, adaptive interactivity, feedback...... parallel and distributed processing with different software behavioural models such as open loop, randomness based, rule based, user interaction based, AI and ALife based software....

  9. Scheme Program Documentation Tools

    DEFF Research Database (Denmark)

    Nørmark, Kurt

    2004-01-01

    This paper describes and discusses two different Scheme documentation tools. The first is SchemeDoc, which is intended for documentation of the interfaces of Scheme libraries (APIs). The second is the Scheme Elucidator, which is for internal documentation of Scheme programs. Although the tools...... are separate and intended for different documentation purposes they are related to each other in several ways. Both tools are based on XML languages for tool setup and for documentation authoring. In addition, both tools rely on the LAML framework which---in a systematic way---makes an XML language available...

  10. Machine tool structures

    CERN Document Server

    Koenigsberger, F

    1970-01-01

    Machine Tool Structures, Volume 1 deals with fundamental theories and calculation methods for machine tool structures. Experimental investigations into stiffness are discussed, along with the application of the results to the design of machine tool structures. Topics covered range from static and dynamic stiffness to chatter in metal cutting, stability in machine tools, and deformations of machine tool structures. This volume is divided into three sections and opens with a discussion on stiffness specifications and the effect of stiffness on the behavior of the machine under forced vibration c

  11. Molecular pharmacognosy

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    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.

  12. Molecular Spintronics

    OpenAIRE

    Shiraishi, Masashi; Ikoma, Tadaaki

    2011-01-01

    Molecular spintronics is recognized to as an attractive new research direction in a field of spintronics, following to metallic spintronics and inorganic semiconductor spintronics, and attracts many people in recent decades. The purpose of this manuscript is to describe the history of molecular spintronics by introducing important achievements and to show the current status of this field. In addition, the authors briefly introduce several theories for implementing studies in molecular spintro...

  13. Bringing the field into the classroom: an innovative methodology in global health teaching

    OpenAIRE

    Dr. M H Bryant, MBBS; J Wolff, MD

    2015-01-01

    Background: The practice of global health is difficult to teach from a US-based classroom. Students benefit from experiencing how theory becomes practice in the chaotic environments of under-resourced health programmes in developing countries. We could not take our students to the field during weekly course work, so we designed a course to bring the field to the students. We created innovative partnerships with locally based organisations that implement programmes in developing countries. Eac...

  14. Bringing the outside world to the remote mountains:the Nepal wireless networking project

    OpenAIRE

    Sein, Maung,; Thapa, Devinder; Säbö, Öystein

    2012-01-01

    This teaching case presents the story of the Nepal Wireless Networking Project (NWNP) and its effort to connect villages in remote areas of Nepal to the outside world. Despite lack of access to proper equipment, the fact that it was illegal to install wireless network, lack of technical competence and the difficult terrain in the Himalayan mountains, Mahabir Pun, the initiator of NWNP, suceeded in bringing Internet access to these villages which led to improvement in education, health service...

  15. An Internet Framework to Bring Coherence between WAP and HTTP Ensuring Better Mobile Internet Security

    OpenAIRE

    Pathan, Al-Mukaddim Khan; Mottalib, Md. Abdul; Zibran, Minhaz Fahim

    2006-01-01

    To bring coherence between Wireless Access Protocol (WAP) and Hyper Text Transfer Protocol (HTTP), in this paper, we have proposed an enhanced Internet framework, which incorporates a new markup language and a browser compatible with both of the access control protocols. This Markup Language and the browser enables co-existence of both Hyper Text Markup Language (HTML) and Wireless Markup Language (WML) contents in a single source file, whereas the browser incorporates the ability to hold con...

  16. Healthy birth practice #3: bring a loved one, friend, or doula for continuous support.

    Science.gov (United States)

    Green, Jeanne; Hotelling, Barbara A

    2014-01-01

    All women should be allowed and encouraged to bring a loved one, friend, or doula to their birth without financial or cultural barriers. Continuous labor support offers benefits to mothers and their babies with no known harm. This article is an updated evidence-based review of the "Lamaze International Care Practices that Promote Normal Birth, Care Practice #3: Continuous Labor Support," published in The Journal of Perinatal Education, 16(3), 2007.

  17. Healthy Birth Practice #3: Bring a Loved One, Friend, or Doula for Continuous Support

    OpenAIRE

    Green, Jeanne; Hotelling, Barbara A.

    2014-01-01

    All women should be allowed and encouraged to bring a loved one, friend, or doula to their birth without financial or cultural barriers. Continuous labor support offers benefits to mothers and their babies with no known harm. This article is an updated evidence-based review of the “Lamaze International Care Practices that Promote Normal Birth, Care Practice #3: Continuous Labor Support,” published in The Journal of Perinatal Education, 16(3), 2007.

  18. 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.

  19. 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

  20. Molecular epidemiology: a multidisciplinary approach to understanding parasitic zoonoses.

    Science.gov (United States)

    Traub, R J; Monis, P T; Robertson, I D

    2005-10-01

    Sound application of molecular epidemiological principles requires working knowledge of both molecular biological and epidemiological methods. Molecular tools have become an increasingly important part of studying the epidemiology of infectious agents. Molecular tools have allowed the aetiological agent within a population to be diagnosed with a greater degree of efficiency and accuracy than conventional diagnostic tools. They have increased the understanding of the pathogenicity, virulence, and host-parasite relationships of the aetiological agent, provided information on the genetic structure and taxonomy of the parasite and allowed the zoonotic potential of previously unidentified agents to be determined. This review describes the concept of epidemiology and proper study design, describes the array of currently available molecular biological tools and provides examples of studies that have integrated both disciplines to successfully unravel zoonotic relationships that would otherwise be impossible utilising conventional diagnostic tools. The current limitations of applying these tools, including cautions that need to be addressed during their application are also discussed.

  1. 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 model

  2. Rose George: Deep Sea and Foreign Going: Inside Shipping, the Invisible Industry that Brings you 90% of Everything

    DEFF Research Database (Denmark)

    Taudal Poulsen, René

    2014-01-01

    Book review of: Rose George: Deep Sea and Foreign Going: Inside Shipping, the Invisible Industry that Brings you 90% of Everything. London :Portobello Books, 2013. 320 pp. ISBN 9781846272639......Book review of: Rose George: Deep Sea and Foreign Going: Inside Shipping, the Invisible Industry that Brings you 90% of Everything. London :Portobello Books, 2013. 320 pp. ISBN 9781846272639...

  3. Lunar hand tools

    Science.gov (United States)

    Bentz, Karl F.; Coleman, Robert D.; Dubnik, Kathy; Marshall, William S.; Mcentee, Amy; Na, Sae H.; Patton, Scott G.; West, Michael C.

    1987-01-01

    Tools useful for operations and maintenance tasks on the lunar surface were determined and designed. Primary constraints are the lunar environment, the astronaut's space suit and the strength limits of the astronaut on the moon. A multipurpose rotary motion tool and a collapsible tool carrier were designed. For the rotary tool, a brushless motor and controls were specified, a material for the housing was chosen, bearings and lubrication were recommended and a planetary reduction gear attachment was designed. The tool carrier was designed primarily for ease of access to the tools and fasteners. A material was selected and structural analysis was performed on the carrier. Recommendations were made about the limitations of human performance and about possible attachments to the torque driver.

  4. Open Health Tools: Tooling for Interoperable Healthcare

    Directory of Open Access Journals (Sweden)

    Skip McGaughey

    2008-11-01

    Full Text Available The Open Health Tools initiative is creating an ecosystem focused on the production of software tooling that promotes the exchange of medical information across political, geographic, cultural, product, and technology lines. At its core, OHT believes that the availability of high-quality tooling that interoperates will propel the industry forward, enabling organizations and vendors to build products and systems that effectively work together. This will ?raise the interoperability bar? as a result of having tools that just work. To achieve these lofty goals, careful consideration must be made to the constituencies that will be most affected by an OHT-influenced world. This document outlines a vision of OHT?s impact to these stakeholders. It does not explain the OHT process itself or how the OHT community operates. Instead, we place emphasis on the impact of that process within the health industry. The catchphrase ?code is king? underpins this document, meaning that the manifestation of any open source community lies in the products and technology it produces.

  5. Authoring tool evaluation

    Energy Technology Data Exchange (ETDEWEB)

    Wilson, A.L.; Klenk, K.S.; Coday, A.C.; McGee, J.P.; Rivenburgh, R.R.; Gonzales, D.M.; Mniszewski, S.M.

    1994-09-15

    This paper discusses and evaluates a number of authoring tools currently on the market. The tools evaluated are Visix Galaxy, NeuronData Open Interface Elements, Sybase Gain Momentum, XVT Power++, Aimtech IconAuthor, Liant C++/Views, and Inmark Technology zApp. Also discussed is the LIST project and how this evaluation is being used to fit an authoring tool to the project.

  6. Population Density Modeling Tool

    Science.gov (United States)

    2014-02-05

    194 POPULATION DENSITY MODELING TOOL by Davy Andrew Michael Knott David Burke 26 June 2012 Distribution...MARYLAND NAWCADPAX/TR-2012/194 26 June 2012 POPULATION DENSITY MODELING TOOL by Davy Andrew Michael Knott David Burke...Density Modeling Tool 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Davy Andrew Michael Knott David Burke 5d. PROJECT NUMBER

  7. CMS offline web tools

    CERN Document Server

    Metson, S; Bockelman, B; Dziedziniewicz, K; Egeland, R; Elmer, P; Eulisse, G; Evans, D; Fanfani, A; Feichtinger, D; Kavka, C; Kuznetsov, V; Van Lingen, F; Newbold, D; Tuura, L; Wakefield, S

    2008-01-01

    We describe a relatively new effort within CMS to converge on a set of web based tools, using state of the art industry techniques, to engage with the CMS offline computing system. CMS collaborators require tools to monitor various components of the computing system and interact with the system itself. The current state of the various CMS web tools is described along side current planned developments.

  8. Molecular detection technologies for arboviruses

    Science.gov (United States)

    Arthropod-borne animal viruses (arboviruses) cause significant livestock and economic losses to world agriculture. This paper discusses the current and potential impact of these viruses, as well as the current and developing molecular diagnostic tools for these emerging and re-emerging insect transm...

  9. Qlikview Audit Tool (QLIKVIEW) -

    Data.gov (United States)

    Department of Transportation — This tool supports the cyclical financial audit process. Qlikview supports large volumes of financial transaction data that can be mined, summarized and presented to...

  10. Instant Spring Tool Suite

    CERN Document Server

    Chiang, Geoff

    2013-01-01

    Filled with practical, step-by-step instructions and clear explanations for the most important and useful tasks. A tutorial guide that walks you through how to use the features of Spring Tool Suite using well defined sections for the different parts of Spring.Instant Spring Tool Suite is for novice to intermediate Java developers looking to get a head-start in enterprise application development using Spring Tool Suite and the Spring framework. If you are looking for a guide for effective application development using Spring Tool Suite, then this book is for you.

  11. Agreement Workflow Tool (AWT)

    Data.gov (United States)

    Social Security Administration — The Agreement Workflow Tool (AWT) is a role-based Intranet application used for processing SSA's Reimbursable Agreements according to SSA's standards. AWT provides...

  12. Java Power Tools

    CERN Document Server

    Smart, John

    2008-01-01

    All true craftsmen need the best tools to do their finest work, and programmers are no different. Java Power Tools delivers 30 open source tools designed to improve the development practices of Java developers in any size team or organization. Each chapter includes a series of short articles about one particular tool -- whether it's for build systems, version control, or other aspects of the development process -- giving you the equivalent of 30 short reference books in one package. No matter which development method your team chooses, whether it's Agile, RUP, XP, SCRUM, or one of many other

  13. A Biochemistry and Molecular Biology Course for Secondary School Teachers

    Science.gov (United States)

    Fernandez-Novell, J. M.; Cid, E.; Gomis, R.; Barbera, A.; Guinovart, J. J.

    2004-01-01

    This article describes a course for reinforcing the knowledge of biochemistry in secondary school science teachers. The Department of Biochemistry and Molecular Biology of the University of Barcelona designed a course to bring these teachers up to date with this discipline. In addition to updating their knowledge of biochemistry and molecular…

  14. Novel tools, classic techniques: evolutionary studies using primate pluripotent stem cells.

    Science.gov (United States)

    Hrvoj-Mihic, Branka; Marchetto, Maria C N; Gage, Fred H; Semendeferi, Katerina; Muotri, Alysson R

    2014-06-15

    Recent applications of genomic tools on the analysis of alterations unique to our species coupled with a growing number of neuroanatomical studies across primates provide an unprecedented opportunity to compile different levels of human brain evolution into a complex whole. Applications of induced pluripotent stem cell (iPSC) technology, capable of reprogramming somatic tissue of different species and generating species-specific neuronal phenotypes, for the first time offer an opportunity to test specific evolutionary hypotheses in a field of inquiry that has been long plagued by the limited availability of research specimens. In this review, we will focus specifically on the experimental role of iPSC technology as applied to the analysis of neocortical pyramidal neurons. Pyramidal neurons emerge as particularly suitable for testing evolutionary scenarios, since they form the most common morphological class of neurons in the cortex, display morphological variations across different cortical areas and cortical layers that appear species-specific, and express unique molecular signatures. Human and nonhuman primate iPSC-derived neurons may represent a unique biological resource to elucidate the phenotypic differences between humans and other hominids. As the typical morphology of pyramidal neurons tends to be compromised in neurological disorders, application of iPSC technology to the analysis of pyramidal neurons could not only bring new insights into human adaptation but also offer opportunities to link biomedical research with studies of the origins of the human species.

  15. The rebirth of the morphogenetic field as an explanatory tool in biology

    Directory of Open Access Journals (Sweden)

    Perović Slobodan

    2013-01-01

    Full Text Available I discuss two uses of the concept of the morphogenetic field, a tool of the 19th century biology motivated by particular ontological views of the time, which has been re-emerging and increasingly relevant in explaining microbiological phenomena. I also consider the relation of these uses to the Central Dogma of modern biology as well as Modern Synthesis of Darwinism and genetics. An induced morphogenetic field is determined by a physical (e.g., gravitational field, or it acquires a physical (e.g., visco-elastic field’s characteristics. Such a morphogenetic field presents only a weak challenge to the Central Dogma of Modern Synthesis by indirectly, albeit severely, constraining variability at the molecular level. I discuss explanations that introduce structural inheritance in ciliate protozoa, as well as the experimental evidence on which these arguments are based. The global cellular morphogenetic field is a unit of such inheritance. I discuss relevant cases of structural inheritance in ciliates that bring about internal cellular as well as functional changes and point out that DNA is absent in the cortex and that RNA controls neither intermediary nor the global level of the field. I go on to argue that utilizing knowledge of known physical fields may advance explanations and understanding of the morphogenetic field in ciliates as the unit of both development and inheritance. [Projekat Ministarstva nauke Republike Srbije, br. 179041: Dynamic Systems in nature and society: Philosophical and empirical aspects

  16. CSR as a Marketing Tool : a Case Study of Fast Food Restaurant in Malaysia

    OpenAIRE

    Abdul Razak, Armiza

    2014-01-01

    The use of corporate social responsibility (CSR) as being an efficient marketing tool would be matter that is being researched, especially with the increasing awareness of consumers about the importance of commercial organizations doing business in ways that do not harm the consumers or the environment. The aim of the research will be to obtain data from qualitative data in order to determine whether using CSR as being a marketing tool would bring a higher level of efficiency in the marketing...

  17. 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

  18. Alexander Meets Michotte: A Simulation Tool Based on Pattern Programming and Phenomenology

    Science.gov (United States)

    Basawapatna, Ashok

    2016-01-01

    Simulation and modeling activities, a key point of computational thinking, are currently not being integrated into the science classroom. This paper describes a new visual programming tool entitled the Simulation Creation Toolkit. The Simulation Creation Toolkit is a high level pattern-based phenomenological approach to bringing rapid simulation…

  19. Thinking Tools in Computer-Based Assessment: Technology Enhancements in Assessments for Learning

    Science.gov (United States)

    Rosen, Yigal

    2014-01-01

    One of the greatest concerns in schools today is how teachers can bring together assessment and learning in a way that is meaningful for students' thinking skills, while focusing on content standards. Better understanding of how different types of technology based thinking tools can be used for improving classroom teaching and learning,…

  20. Understanding Managers Decision Making Process for Tools Selection in the Core Front End of Innovation

    DEFF Research Database (Denmark)

    Appio, Francesco P.; Achiche, Sofiane; McAloone, Tim C.

    2011-01-01

    New product development (NPD) describes the process of bringing a new product or service to the market. The Fuzzy Front End (FFE) of Innovation is the term describing the activities happening before the product development phase of NPD. In the FFE of innovation, several tools are used to facilitate...

  1. Tools for characterizing biomembranes : final LDRD report.

    Energy Technology Data Exchange (ETDEWEB)

    Alam, Todd Michael; Stevens, Mark; Holland, Gregory P.; McIntyre, Sarah K.

    2007-10-01

    A suite of experimental nuclear magnetic resonance (NMR) spectroscopy tools were developed to investigate lipid structure and dynamics in model membrane systems. By utilizing both multinuclear and multidimensional NMR experiments a range of different intra- and inter-molecular contacts were probed within the membranes. Examples on pure single component lipid membranes and on the canonical raft forming mixture of DOPC/SM/Chol are presented. A unique gel phase pretransition in SM was also identified and characterized using these NMR techniques. In addition molecular dynamics into the hydrogen bonding network unique to sphingomyelin containing membranes were evaluated as a function of temperature, and are discussed.

  2. Maailma suurim tool

    Index Scriptorium Estoniae

    2000-01-01

    AS Tartu näitused, Tartu Kunstikool ja ajakiri 'Diivan' korraldavad 9.-11. III Tartu messikeskuse I paviljonis näituse 'Tool 2000'. Eksponeeritakse 2000 tooli, mille hulgast valitakse TOP 12. Messikeskuse territooriumile on kavas püstitada maailma suurim tool. Samal ajal II paviljonis kaksikmess 'Sisustus 2000' ja 'Büroo 2000'.

  3. Study of Tools Interoperability

    NARCIS (Netherlands)

    Krilavičius, T.

    2007-01-01

    Interoperability of tools usually refers to a combination of methods and techniques that address the problem of making a collection of tools to work together. In this study we survey different notions that are used in this context: interoperability, interaction and integration. We point out relation

  4. WATERS Expert Query Tool

    Data.gov (United States)

    U.S. Environmental Protection Agency — The Expert Query Tool is a web-based reporting tool using the EPA’s WATERS database.There are just three steps to using Expert Query:1. View Selection – Choose what...

  5. Coring Sample Acquisition Tool

    Science.gov (United States)

    Haddad, Nicolas E.; Murray, Saben D.; Walkemeyer, Phillip E.; Badescu, Mircea; Sherrit, Stewart; Bao, Xiaoqi; Kriechbaum, Kristopher L.; Richardson, Megan; Klein, Kerry J.

    2012-01-01

    A sample acquisition tool (SAT) has been developed that can be used autonomously to sample drill and capture rock cores. The tool is designed to accommodate core transfer using a sample tube to the IMSAH (integrated Mars sample acquisition and handling) SHEC (sample handling, encapsulation, and containerization) without ever touching the pristine core sample in the transfer process.

  6. 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......) are chemically merged together to form cruciform-like structures that are an essential part of the thesis. The cruciform molecules were subjected to molecular conductance measurements to explore their capability towards single-crystal field-effect transistors (Part 1), molecular wires, and single electron......, however, was obtained by a study of a single molecular transistor. The investigated OPE5-TTF compound was captured in a three-terminal experiment, whereby manipulation of the molecule’s electronic spin was possible in different charge states. Thus, we demonstrated how the cruciform molecules could...

  7. Language Management Tools

    DEFF Research Database (Denmark)

    Sanden, Guro Refsum

    may deploy in order to address the language needs of the organisation. Finally, front-line practices refer to the use of informal, emergent language management tools available to staff members. The language management tools taxonomy provides a framework for operationalising the management of language......This paper offers a review of existing literature on the topic of language management tools – the means by which language is managed – in multilingual organisations. By drawing on a combination of sociolinguistics and international business and management studies, a new taxonomy of language...... management tools is proposed, differentiating between three categories of tools. Firstly, corporate policies are the deliberate control of issues pertaining to language and communication developed at the managerial level of a firm. Secondly, corporate measures are the planned activities the firm’s leadership...

  8. Software Tool Issues

    Science.gov (United States)

    Hennell, Michael

    This chapter relies on experience with tool development gained over the last thirty years. It shows that there are a large number of techniques that contribute to any successful project, and that formality is always the key: a modern software test tool is based on a firm mathematical foundation. After a brief introduction, Section 2 recalls and extends the terminology of Chapter 1. Section 3 discusses the the design of different sorts of static and dynamic analysis tools. Nine important issues to be taken into consideration when evaluating such tools are presented in Section 4. Section 5 investigates the interplay between testing and proof. In Section 6, we call for developers to take their own medicine and verify their tools. Finally, we conclude in Section 7 with a summary of our main messages, emphasising the important role of testing.

  9. OOTW Force Design Tools

    Energy Technology Data Exchange (ETDEWEB)

    Bell, R.E.; Hartley, D.S.III; Packard, S.L.

    1999-05-01

    This report documents refined requirements for tools to aid the process of force design in Operations Other Than War (OOTWs). It recommends actions for the creation of one tool and work on other tools relating to mission planning. It also identifies the governmental agencies and commands with interests in each tool, from whom should come the user advisory groups overseeing the respective tool development activities. The understanding of OOTWs and their analytical support requirements has matured to the point where action can be taken in three areas: force design, collaborative analysis, and impact analysis. While the nature of the action and the length of time before complete results can be expected depends on the area, in each case the action should begin immediately. Force design for OOTWs is not a technically difficult process. Like force design for combat operations, it is a process of matching the capabilities of forces against the specified and implied tasks of the operation, considering the constraints of logistics, transport and force availabilities. However, there is a critical difference that restricts the usefulness of combat force design tools for OOTWs: the combat tools are built to infer non-combat capability requirements from combat capability requirements and cannot reverse the direction of the inference, as is required for OOTWs. Recently, OOTWs have played a larger role in force assessment, system effectiveness and tradeoff analysis, and concept and doctrine development and analysis. In the first Quadrennial Defense Review (QDR), each of the Services created its own OOTW force design tool. Unfortunately, the tools address different parts of the problem and do not coordinate the use of competing capabilities. These tools satisfied the immediate requirements of the QDR, but do not provide a long-term cost-effective solution.

  10. Bringing New Ph.D.s Together for Interdisciplinary Climate Change Research

    Science.gov (United States)

    Phelan, Liam; Jones, Holly; Marlon, Jennifer R.

    2013-01-01

    Climate change is complex and thus requires interdisciplinary research, and new scholars are rising to that challenge. The Dissertations Initiative for the Advancement of Climate Change Research (DISCCRS (pronounced "discourse"); see http://www.disccrs.org) brings together select groups of recent PhD graduates to encourage interdisciplinary work on climate change. The DISCCRS Symposium VII held just outside of Colorado Springs, Colo., brought together 33 graduates from fields as diverse as climatology, ecology, anthropology, and political science for an intensive week of cross-disciplinary engagement in activities like facilitation and leadership training, collaborative research development, peer networking, communication training, and analysis of working group processes.

  11. Strategies of bringing drug product marketing applications to meet current regulatory standards.

    Science.gov (United States)

    Wu, Yan; Freed, Anita; Lavrich, David; Raghavachari, Ramesh; Huynh-Ba, Kim; Shah, Ketan; Alasandro, Mark

    2015-08-01

    In the past decade, many guidance documents have been issued through collaboration of global organizations and regulatory authorities. Most of these are applicable to new products, but there is a risk that currently marketed products will not meet the new compliance standards during audits and inspections while companies continue to make changes through the product life cycle for continuous improvement or market demands. This discussion presents different strategies to bringing drug product marketing applications to meet current and emerging standards. It also discusses stability and method designs to meet process validation and global development efforts.

  12. Old Books Bring New Life to the Brick and Mortar Library

    Science.gov (United States)

    Bosken, S.

    2012-08-01

    If all the library books and journals can be viewed on your desk top, why come to the physical library? The USNO Library tried to bring the patrons inside the library. One method was to rotate rare book displays each month. As the library holds a fabulous collection of ancient astronomy books, including Copernicus, Kepler, Galileo, and Newton, we have abundant resources. The presentation will highlight the varied displays and offer a Rare Books 101 explanation of paper, printing, binding and a behind-the-scenes look at how old books are maintained and preserved.

  13. [Bring fruit at school: promotion of healthy food habit in primary school-children].

    Science.gov (United States)

    Panunzio, M F; Antoniciello, A; Ugolini, G; Dalton, S

    2009-01-01

    The many nutrition education guidelines formulated by different organizations and institutions are the frames for the program actions targeting nutrition awareness in the school-age population. But while the guidelines represent a solid starting block they still need to be backed up by programs giving concrete form to the guiding principles, a program whose efficacy is demonstrated by specific applications studies. The aim of the "Bring Fruit at School" nutrition education program is to encourage elementary school children to change their eating habits for the better. And in particular to eat more fruit, vegetables, legumes, and fish and to cut down on junk-food and sugar-sweetened drink.

  14. Vision implants: An electrical device will bring light to the blind

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Cochlear implant has been successfully applied in clinic. Recent research indicates vision implants may be the potential way to restore sight for the blind. Here, principle and common structure of vision implants are introduced. Main vision approaches of retinal, optic nerve, and cortical prosthesis are reviewed. In our progress, electrical response at visual cortex is recorded, when penetrating electrodes stimulate rabbit optic nerve, vision implants based on optic nerve stimulator chip (ONSC) and Chipcon radio frequency (RF) chip are under developing. Despite several obstacles to overcome, promising results in animal and human experiments give scientists confidence that artificial vision implants will bring light to the blind in the near future.

  15. Visualization of molecular fingerprints.

    Science.gov (United States)

    Owen, John R; Nabney, Ian T; Medina-Franco, José L; López-Vallejo, Fabian

    2011-07-25

    A visualization plot of a data set of molecular data is a useful tool for gaining insight into a set of molecules. In chemoinformatics, most visualization plots are of molecular descriptors, and the statistical model most often used to produce a visualization is principal component analysis (PCA). This paper takes PCA, together with four other statistical models (NeuroScale, GTM, LTM, and LTM-LIN), and evaluates their ability to produce clustering in visualizations not of molecular descriptors but of molecular fingerprints. Two different tasks are addressed: understanding structural information (particularly combinatorial libraries) and relating structure to activity. The quality of the visualizations is compared both subjectively (by visual inspection) and objectively (with global distance comparisons and local k-nearest-neighbor predictors). On the data sets used to evaluate clustering by structure, LTM is found to perform significantly better than the other models. In particular, the clusters in LTM visualization space are consistent with the relationships between the core scaffolds that define the combinatorial sublibraries. On the data sets used to evaluate clustering by activity, LTM again gives the best performance but by a smaller margin. The results of this paper demonstrate the value of using both a nonlinear projection map and a Bernoulli noise model for modeling binary data.

  16. Adapting JMARS for Earth: Blogging brings a new user community from the CAP LTER urban ecology research project

    Science.gov (United States)

    Webber, J.; Prashad, L. C.; Dickenshied, S.; Guha, A.; Burgess, E.; Metson, G.; Christensen, P. R.

    2010-12-01

    J-Earth is a Geographic Information Systems (GIS) application used for viewing and processing satellite and airborne remote sensing data and includes NASA imagery such as ASTER, Landsat, MODIS, TIMS, as well as other geological, ecological, and social datasets. The J-Earth team is working with the National Science Foundation-funded Central Arizona-Phoenix Long Term Ecological Research Project (CAP LTER) to incorporate its data and develop functionality for J-Earth. J-Earth was developed by the Arizona State University Mars Space Flight Facility as part of the JMARS (Java Mission-planning and Analysis for Remote Sensing) suite of open-source tools. J-Earth has been enhanced to support the needs of CAP LTER users with the use of web tutorials, social networking, user surveys and interviews. CAP LTER consists of an interdisciplinary urban ecology research group with different needs in the area of socio-ecological systems. Adapting J-Earth for the CAP LTER community has provided a test of J-Earth’s functionality for interdisciplinary datasets and has shown the potential for expanding J-Earth to include future users within the entire LTER network. This project could potentially be expanded to bring data from the other twenty-six LTER sites into J-Earth. J-Earth utilizes the analytical tools of JMARS and makes them available to a broad range of users. J-Earth utilizes a layered system to view data from different sources that can be exported, scaled, colored and superimposed for quick comparisons. The functionality of JMARS is focused on the planetary geology community, while J-Earth has the potential to be used by geologists, geographers, sociologists, and ecologists as well as policy makers. This presentation will provide an overview of information and feedback gathered from users of J-Earth, especially those of the CAP LTER. Collecting additional feedback in the form of social networking, interviews, trainings, and tutorials will help make J-Earth more functional and

  17. Revolutions in Neuroscience: Tool Development

    Directory of Open Access Journals (Sweden)

    John eBickle

    2016-03-01

    Full Text Available Thomas Kuhn’s famous model of the components and dynamics of scientific revolutions is still dominant to this day across science, philosophy, and history. The guiding philosophical theme of this paper is that, concerning actual revolutions in neuroscience over the past sixty years, Kuhn’s account is wrong. There have been revolutions, and new ones are brewing, but they do not turn on competing paradigms, anomalies, or the like. Instead, they turn exclusively on the development of new experimental tools. I adopt a metascientific approach and examine in detail the development of two recent neuroscience revolutions: the impact of engineered genetically mutated mammals in the search for causal mechanisms of higher cognitive functions; and the more recent impact of optogenetics (and DREADDs. The two key metascientific concepts I derive from these case studies are a revolutionary new tool’s motivating problem, and its initial and second-phase hook experiments. These concepts hardly exhaust a detailed metascience of Tool Development experiments in neuroscience, but they get that project off to a useful start and distinguish the subsequent account of neuroscience revolutions clearly from Kuhn’s famous model. I close with a brief remark about the general importance of molecular biology for a current philosophical understanding of science, as comparable to the place physics occupied when Kuhn formulated his famous theory of scientific revolutions.

  18. Advanced Characterization of Molecular Interactions in TALSPEAK-like Separations Systems

    Energy Technology Data Exchange (ETDEWEB)

    Nash, Kenneth [Washington State Univ., Pullman, WA (United States); Guelis, Artem [Argonne National Lab. (ANL), Argonne, IL (United States); Lumetta, Gregg J. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Sinkov, Sergey [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2015-10-21

    Combining unit operations in advanced aqueous reprocessing schemes brings obvious process compactness advantages, but at the same time greater complexity in process design and operation. Unraveling these interactions requires increasingly sophisticated analytical tools and unique approaches for adequate analysis and characterization that probe molecular scale interactions. Conventional slope analysis methods of solvent extraction are too indirect to provide much insight into such interactions. This project proposed the development and verification of several analytical tools based on studies of TALSPEAK-like aqueous processes. As such, the chemistry of trivalent fission product lanthanides, americium, curium, plutonium, neptunium and uranium figure prominently in these studies. As the project was executed, the primary focus fell upon the chemistry or trivalent lanthanides and actinides. The intent of the investigation was to compare and contrast the results from these various complementary techniques/studies to provide a stronger basis for predicting the performance of extractant/diluent mixtures as media for metal ion separations. As many/most of these techniques require the presence of metal ions at elevated concentrations, it was expected that these studies would take this investigation into the realm of patterns of supramolecular organization of metal complexes and extractants in concentrated aqueous/organic media. We expected to advance knowledge of the processes that enable and limit solvent extraction reactions as a result of the application of fundamental chemical principles to explaining interactions in complex media.

  19. Possible room temperature superconductivity in conductors obtained by bringing alkanes into contact with a graphite surface

    Directory of Open Access Journals (Sweden)

    Yasushi Kawashima

    2013-05-01

    Full Text Available 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. Cytotoxic non-aromatic B-ring flavanones from Piper carniconnectivum C. DC.

    Science.gov (United States)

    Freitas, Giovana C; Batista, João M; Franchi, Gilberto C; Nowill, Alexandre E; Yamaguchi, Lydia F; Vilcachagua, Janaina D; Favaro, Denize C; Furlan, Maysa; Guimarães, Elsie F; Jeffrey, Christopher S; Kato, Massuo J

    2014-01-01

    The EtOAc extract from the leaves of Piper carniconnectivum C. DC. was subjected to chromatographic separation to afford two non-aromatic B-ring flavanone compounds: 5-hydroxy-2-(1'-hydroxy-4'-oxo-cyclohex-2'-en-1'-yl)-6,7-dimethoxy-2,3-dihydro-4H-chromen-4-one (1) and 5-hydroxy-2-(1',2'-dihydroxy-4'-oxo-cyclohexyl)-6,7-dimethoxy-2,3-dihydro-4H-chromen-4-one (2). The absolute configuration of (+)-1 was unambiguously determined as 2S,1'R by electronic circular dichroism (ECD) spectroscopy and comparison to simulated spectra that were calculated using time-dependent density functional theory (TDDFT). This methodology allowed the assignment of the absolute configuration of (+)-2 also as 2S,1'R, except for the stereogenic center at C-2', which was assigned as R because of the evidence drawn from high resolution NMR experiments. The cytotoxic activity of both compounds and 3 (hydrogenated B-ring derivative of 1) was evaluated on twelve human leukemia cell lines, and the IC50 values (<10 μM) indicated the activity of 1 against seven cell lines.

  1. Machine Tool Software

    Science.gov (United States)

    1988-01-01

    A NASA-developed software package has played a part in technical education of students who major in Mechanical Engineering Technology at William Rainey Harper College. Professor Hack has been using (APT) Automatically Programmed Tool Software since 1969 in his CAD/CAM Computer Aided Design and Manufacturing curriculum. Professor Hack teaches the use of APT programming languages for control of metal cutting machines. Machine tool instructions are geometry definitions written in APT Language to constitute a "part program." The part program is processed by the machine tool. CAD/CAM students go from writing a program to cutting steel in the course of a semester.

  2. Benchmarking expert system tools

    Science.gov (United States)

    Riley, Gary

    1988-01-01

    As part of its evaluation of new technologies, the Artificial Intelligence Section of the Mission Planning and Analysis Div. at NASA-Johnson has made timing tests of several expert system building tools. Among the production systems tested were Automated Reasoning Tool, several versions of OPS5, and CLIPS (C Language Integrated Production System), an expert system builder developed by the AI section. Also included in the test were a Zetalisp version of the benchmark along with four versions of the benchmark written in Knowledge Engineering Environment, an object oriented, frame based expert system tool. The benchmarks used for testing are studied.

  3. Hierarchical virtual screening for the discovery of new molecular scaffolds in antibacterial hit identification.

    Science.gov (United States)

    Ballester, Pedro J; Mangold, Martina; Howard, Nigel I; Robinson, Richard L Marchese; Abell, Chris; Blumberger, Jochen; Mitchell, John B O

    2012-12-07

    One of the initial steps of modern drug discovery is the identification of small organic molecules able to inhibit a target macromolecule of therapeutic interest. A small proportion of these hits are further developed into lead compounds, which in turn may ultimately lead to a marketed drug. A commonly used screening protocol used for this task is high-throughput screening (HTS). However, the performance of HTS against antibacterial targets has generally been unsatisfactory, with high costs and low rates of hit identification. Here, we present a novel computational methodology that is able to identify a high proportion of structurally diverse inhibitors by searching unusually large molecular databases in a time-, cost- and resource-efficient manner. This virtual screening methodology was tested prospectively on two versions of an antibacterial target (type II dehydroquinase from Mycobacterium tuberculosis and Streptomyces coelicolor), for which HTS has not provided satisfactory results and consequently practically all known inhibitors are derivatives of the same core scaffold. Overall, our protocols identified 100 new inhibitors, with calculated K(i) ranging from 4 to 250 μM (confirmed hit rates are 60% and 62% against each version of the target). Most importantly, over 50 new active molecular scaffolds were discovered that underscore the benefits that a wide application of prospectively validated in silico screening tools is likely to bring to antibacterial hit identification.

  4. Characterizing Molecular Structure by Combining Experimental Measurements with Density Functional Theory Computations

    Science.gov (United States)

    Lopez-Encarnacion, Juan M.

    2016-06-01

    In this talk, the power and synergy of combining experimental measurements with density functional theory computations as a single tool to unambiguously characterize the molecular structure of complex atomic systems is shown. Here, we bring three beautiful cases where the interaction between the experiment and theory is in very good agreement for both finite and extended systems: 1) Characterizing Metal Coordination Environments in Porous Organic Polymers: A Joint Density Functional Theory and Experimental Infrared Spectroscopy Study 2) Characterization of Rhenium Compounds Obtained by Electrochemical Synthesis After Aging Process and 3) Infrared Study of H(D)2 + Co4+ Chemical Reaction: Characterizing Molecular Structures. J.M. López-Encarnación, K.K. Tanabe, M.J.A. Johnson, J. Jellinek, Chemistry-A European Journal 19 (41), 13646-13651 A. Vargas-Uscategui, E. Mosquera, J.M. López-Encarnación, B. Chornik, R. S. Katiyar, L. Cifuentes, Journal of Solid State Chemistry 220, 17-21

  5. Smart Growth Tools

    Science.gov (United States)

    This page describes a variety of tools useful to federal, state, tribal, regional, and local government staff and elected officials; community leaders; developers; and others interested in smart growth development.

  6. Neighborhood Mapping Tool

    Data.gov (United States)

    Department of Housing and Urban Development — This tool assists the public and Choice Neighborhoods applicants to prepare data to submit with their grant application by allowing applicants to draw the exact...

  7. TENCompetence tool demonstration

    NARCIS (Netherlands)

    Kluijfhout, Eric

    2010-01-01

    Kluijfhout, E. (2009). TENCompetence tool demonstration. Presented at Zorgacademie Parkstad (Health Academy Parkstad), Limburg Leisure Academy, Life Long Learning Limburg and a number of regional educational institutions. May, 18, 2009, Heerlen, The Netherlands: Open University of the Netherlands, T

  8. Tools and their uses

    CERN Document Server

    1973-01-01

    Teaches names, general uses, and correct operation of all basic hand and power tools, fasteners, and measuring devices you are likely to need. Also, grinding, metal cutting, soldering, and more. 329 illustrations.

  9. NWRS Survey Prioritization Tool

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — A SMART Tool and User's Guide for aiding NWRS Station staff when prioritizing their surveys for an Inventory and Monitoring Plan. This guide describes a process and...

  10. Smart tool holder

    Science.gov (United States)

    Day, Robert Dean; Foreman, Larry R.; Hatch, Douglas J.; Meadows, Mark S.

    1998-01-01

    There is provided an apparatus for machining surfaces to accuracies within the nanometer range by use of electrical current flow through the contact of the cutting tool with the workpiece as a feedback signal to control depth of cut.

  11. Game development tool essentials

    CERN Document Server

    Berinstein, Paula; Ardolino, Alessandro; Franco, Simon; Herubel, Adrien; McCutchan, John; Nedelcu, Nicusor; Nitschke, Benjamin; Olmstead, Don; Robinet, Fabrice; Ronchi, Christian; Turkowski, Rita; Walter, Robert; Samour, Gustavo

    2014-01-01

    Offers game developers new techniques for streamlining the critical game tools pipeline. Inspires game developers to share their secrets and improve the productivity of the entire industry. Helps game industry practitioners compete in a hyper-competitive environment.

  12. Mapping Medicare Disparities Tool

    Data.gov (United States)

    U.S. Department of Health & Human Services — The CMS Office of Minority Health has designed an interactive map, the Mapping Medicare Disparities Tool, to identify areas of disparities between subgroups of...

  13. ATO Resource Tool -

    Data.gov (United States)

    Department of Transportation — Cru-X/ART is a shift management tool designed for?use by operational employees in Air Traffic Facilities.? Cru-X/ART is used for shift scheduling, shift sign in/out,...

  14. Chatter and machine tools

    CERN Document Server

    Stone, Brian

    2014-01-01

    Focussing on occurrences of unstable vibrations, or Chatter, in machine tools, this book gives important insights into how to eliminate chatter with associated improvements in product quality, surface finish and tool wear. Covering a wide range of machining processes, including turning, drilling, milling and grinding, the author uses his research expertise and practical knowledge of vibration problems to provide solutions supported by experimental evidence of their effectiveness. In addition, this book contains links to supplementary animation programs that help readers to visualise the ideas detailed in the text. Advancing knowledge in chatter avoidance and suggesting areas for new innovations, Chatter and Machine Tools serves as a handbook for those desiring to achieve significant reductions in noise, longer tool and grinding wheel life and improved product finish.

  15. Chemical Data Access Tool

    Data.gov (United States)

    U.S. Environmental Protection Agency — This tool is intended to aid individuals interested in learning more about chemicals that are manufactured or imported into the United States. Health and safety...

  16. Recovery Action Mapping Tool

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The Recovery Action Mapping Tool is a web map that allows users to visually interact with and query actions that were developed to recover species listed under the...

  17. Cash Reconciliation Tool

    Data.gov (United States)

    US Agency for International Development — CART is a cash reconciliation tool that allows users to reconcile Agency cash disbursements with Treasury fund balances; track open unreconciled items; and create an...

  18. Friction stir welding tool

    Science.gov (United States)

    Tolle; Charles R. , Clark; Denis E. , Barnes; Timothy A.

    2008-04-15

    A friction stir welding tool is described and which includes a shank portion; a shoulder portion which is releasably engageable with the shank portion; and a pin which is releasably engageable with the shoulder portion.

  19. Autism Teaching Tool

    CERN Multimedia

    2014-01-01

    CERN pattern recognition technologies transferred to Austistic children learning tool. The state of the art of pattern recognition technology developed at CERN for High Energy Physics are transferred to Computer Vision domain and are used to develop a new

  20. Dienone-phenol Rearrangement of C-9 Oxygenated Decalinic Dienone and Analogs through B-Ring Cleavage

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    Dehydrogenation of 9-hydroxy decalinic enones and analogs with DDQ resulted in a formal dienone-phenol type rearrangement via B-ring cleavage, while the corresponding dienone acetates underwent base-catalyzed formal dienone-phenol type rearrangement analogously.