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Sample records for establishing molecular tools

  1. Reevaluating establishment and potential hybridization of different biotypes of the biological control agent Longitarsus jacobaeae using molecular tools

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Evaluation of past and current biological control programs using molecular tools can clarify establishment success of agent biotypes, and can contribute to our understanding of best practice for natural enemy importations. The flea beetle, Longitarsus jacobaeae has been quite successful at controlli...

  2. Peak-bridges due to in-column analyte transformations as a new tool for establishing molecular connectivities by comprehensive two-dimensional gas chromatography-mass spectrometry.

    PubMed

    Filippi, Jean-Jacques; Cocolo, Nicolas; Meierhenrich, Uwe J

    2015-02-27

    Comprehensive two-dimensional gas chromatography-mass spectrometry (GC×GC-MS) has been shown to permit for the unprecedented chromatographic resolution of volatile analytes encompassing various families of organic compounds. However, peak identification based on retention time, two-dimensional mapping, and mass spectrometric fragmentation only, is not a straightforward task yet. The possibility to establish molecular links between constituents is of crucial importance to understand the overall chemistry of any sample, especially in natural extracts where biogenetically related isomeric structures are often abundant. We here present a new way of using GC×GC that allows searching for those molecular connectivities. Analytical investigations of essential oil constituents by means of GC×GC-MS permitted to observe in real time the thermally-induced transformations of various sesquiterpenic derivatives. These transformations generated a series of well-defined two-dimensional peak bridges within the 2D-chromatograms connecting parent and daughter molecules, thus permitting to build a clear scheme of structural relationship between the different constituents. GC×GC-MS appears here as a tool for investigating chromatographic phenomena and analyte transformations that could not be understood with conventional GC-MS only.

  3. Molecular tools for chemical biotechnology

    PubMed Central

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

    2013-01-01

    Biotechnological production of high value chemical products increasingly involves engineering in vivo multi-enzyme pathways and host metabolism. Recent approaches to these engineering objectives have made use of molecular tools to advance de novo pathway identification, tunable enzyme expression, and rapid pathway construction. Molecular tools also enable optimization of single enzymes and entire genomes through diversity generation and screening, whole cell analytics, and synthetic metabolic control networks. In this review, we focus on advanced molecular tools and their applications to engineered pathways in host organisms, highlighting the degree to which each tool is generalizable. PMID:23528237

  4. Molecular tools used in agriculture

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A summary of molecular tools used for research in agriculture were presented. Examples of DNA sequencing, library preparation, use of fingerprinting for pathogens and plant crops, high throughput sequencing, whole-genome amplification, reporter genes, and other methods....

  5. Establishing molecular microbiology facilities in developing countries.

    PubMed

    Ahmed, Salman S; Alp, Emine; Ulu-Kilic, Aysegul; Doganay, Mehmet

    2015-01-01

    Microbiology laboratories play an important role in epidemiology and infection control programs. Within microbiology laboratories, molecular microbiology techniques have revolutionized the identification and surveillance of infectious diseases. The combination of excellent sensitivity, specificity, low contamination levels and speed has made molecular techniques appealing methods for the diagnosis of many infectious diseases. In a well-equipped microbiology laboratory, the facility designated for molecular techniques remains indiscrete. However, in most developing countries, poor infrastructure and laboratory mismanagement have precipitated hazardous consequences. The establishment of a molecular microbiology facility within a microbiology laboratory remains fragmented. A high-quality laboratory should include both conventional microbiology methods and molecular microbiology techniques for exceptional performance. Furthermore, it should include appropriate laboratory administration, a well-designed facility, laboratory procedure standardization, a waste management system, a code of practice, equipment installation and laboratory personnel training. This manuscript lays out fundamental issues that need to be addressed when establishing a molecular microbiology facility in developing countries.

  6. Web tools for molecular epidemiology of tuberculosis.

    PubMed

    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.

  7. Developing molecular tools for Chlamydomonas reinhardtii

    NASA Astrophysics Data System (ADS)

    Noor-Mohammadi, Samaneh

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

  8. Improved molecular tools for sugar cane biotechnology.

    PubMed

    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.

  9. A Teaching Tool for Molecular Kinetics

    ERIC Educational Resources Information Center

    Imai, Izumi; Kamata, Masahiro; Miura, Naosuke

    2003-01-01

    Kinetic models of a gas can be hard for students to understand. Typical tools do not display events at the microscopic level, yet computer simulations of the molecules lack a hands-on aspect. Here a new tool is described that combines the squeezing of a syringe with a computer simulation, and it is shown that this has worked well in class for both…

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

    PubMed

    Bai, Shiyang; Lu, Benzhuo

    2014-05-01

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

  11. DockingShop: A Tool for Interactive Molecular Docking

    SciTech Connect

    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.

  12. [Establishing IAQ Metrics and Baseline Measures.] "Indoor Air Quality Tools for Schools" Update #20

    ERIC Educational Resources Information Center

    US Environmental Protection Agency, 2009

    2009-01-01

    This issue of "Indoor Air Quality Tools for Schools" Update ("IAQ TfS" Update) contains the following items: (1) News and Events; (2) IAQ Profile: Establishing Your Baseline for Long-Term Success (Feature Article); (3) Insight into Excellence: Belleville Township High School District #201, 2009 Leadership Award Winner; and (4) Have Your Questions…

  13. Establishing Natural Nootropics: Recent Molecular Enhancement Influenced by Natural Nootropic.

    PubMed

    Suliman, Noor Azuin; Mat Taib, Che Norma; Mohd Moklas, Mohamad Aris; Adenan, Mohd Ilham; Hidayat Baharuldin, Mohamad Taufik; Basir, Rusliza

    2016-01-01

    Nootropics or smart drugs are well-known compounds or supplements that enhance the cognitive performance. They work by increasing the mental function such as memory, creativity, motivation, and attention. Recent researches were focused on establishing a new potential nootropic derived from synthetic and natural products. The influence of nootropic in the brain has been studied widely. The nootropic affects the brain performances through number of mechanisms or pathways, for example, dopaminergic pathway. Previous researches have reported the influence of nootropics on treating memory disorders, such as Alzheimer's, Parkinson's, and Huntington's diseases. Those disorders are observed to impair the same pathways of the nootropics. Thus, recent established nootropics are designed sensitively and effectively towards the pathways. Natural nootropics such as Ginkgo biloba have been widely studied to support the beneficial effects of the compounds. Present review is concentrated on the main pathways, namely, dopaminergic and cholinergic system, and the involvement of amyloid precursor protein and secondary messenger in improving the cognitive performance.

  14. From morphologic to molecular: established and emerging molecular diagnostics for breast carcinoma.

    PubMed

    Portier, Bryce P; Gruver, Aaron M; Huba, Michael A; Minca, Eugen C; Cheah, Alison L; Wang, Zhen; Tubbs, Raymond R

    2012-09-15

    Diagnostics in the field of breast carcinoma are constantly evolving. The recent wave of molecular methodologies, both microscope and non-microscope based, have opened new ways to gain insight into this disease process and have moved clinical diagnostics closer to a 'personalized medicine' approach. In this review we highlight some of the advancements that laboratory medicine technology is making toward guiding the diagnosis, prognosis, and therapy selection for patients affected by breast carcinoma. The content of the article is largely structured by methodology, with a distinct emphasis on both microscope based and non-microscope based diagnostic formats. Where possible, we have attempted to emphasize the potential benefits as well as limitations to each of these technologies. Successful molecular diagnostics, applied in concert within the morphologic context of a patient's tumor, are what will lay the foundation for personalized therapy and allow a more sophisticated approach to clinical trial stratification. The future of breast cancer diagnostics looks challenging, but it is also a field of great opportunity. Never before have there been such a plethora of new tools available for disease investigation or candidate therapy selection.

  15. Establishing Natural Nootropics: Recent Molecular Enhancement Influenced by Natural Nootropic

    PubMed Central

    Adenan, Mohd Ilham; Hidayat Baharuldin, Mohamad Taufik

    2016-01-01

    Nootropics or smart drugs are well-known compounds or supplements that enhance the cognitive performance. They work by increasing the mental function such as memory, creativity, motivation, and attention. Recent researches were focused on establishing a new potential nootropic derived from synthetic and natural products. The influence of nootropic in the brain has been studied widely. The nootropic affects the brain performances through number of mechanisms or pathways, for example, dopaminergic pathway. Previous researches have reported the influence of nootropics on treating memory disorders, such as Alzheimer's, Parkinson's, and Huntington's diseases. Those disorders are observed to impair the same pathways of the nootropics. Thus, recent established nootropics are designed sensitively and effectively towards the pathways. Natural nootropics such as Ginkgo biloba have been widely studied to support the beneficial effects of the compounds. Present review is concentrated on the main pathways, namely, dopaminergic and cholinergic system, and the involvement of amyloid precursor protein and secondary messenger in improving the cognitive performance. PMID:27656235

  16. How to Train a Cell–Cutting-Edge Molecular Tools

    PubMed Central

    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.

    PubMed

    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. A tool to assess potential for alien plant establishment and expansion under climate change.

    PubMed

    Roger, Erin; Duursma, Daisy Englert; Downey, Paul O; Gallagher, Rachael V; Hughes, Lesley; Steel, Jackie; Johnson, Stephen B; Leishman, Michelle R

    2015-08-15

    Predicting the influence of climate change on the potential distribution of naturalised alien plant species is an important and challenging task. While prioritisation of management actions for alien plants under current climatic conditions has been widely adopted, very few systems explicitly incorporate the potential of future changes in climate conditions to influence the distribution of alien plant species. Here, we develop an Australia-wide screening tool to assess the potential of naturalised alien plants to establish and spread under both current and future climatic conditions. The screening tool developed uses five spatially explicit criteria to establish the likelihood of alien plant population establishment and expansion under baseline climate conditions and future climates for the decades 2035 and 2065. Alien plants are then given a threat rating according to current and future threat to enable natural resource managers to focus on those species that pose the largest potential threat now and in the future. To demonstrate the screening tool, we present results for a representative sample of approximately 10% (n = 292) of Australia's known, naturalised alien plant species. Overall, most alien plant species showed decreases in area of habitat suitability under future conditions compared to current conditions and therefore the threat rating of most alien plant species declined between current and future conditions. Use of the screening tool is intended to assist natural resource managers in assessing the threat of alien plant establishment and spread under current and future conditions and thus prioritise detailed weed risk assessments for those species that pose the greatest threat. The screening tool is associated with a searchable database for all 292 alien plant species across a range of spatial scales, available through an interactive web-based portal at http://weedfutures.net/.

  19. Establishing a molecular relationship between chondritic and cometary organic solids

    PubMed Central

    Cody, George D.; Heying, Emily; Alexander, Conel M. O.; Nittler, Larry R.; Kilcoyne, A. L. David; Sandford, Scott A.

    2011-01-01

    Multidimensional solid-state NMR spectroscopy is used to refine the identification and abundance determination of functional groups in insoluble organic matter (IOM) isolated from a carbonaceous chondrite (Murchison, CM2). It is shown that IOM is composed primarily of highly substituted single ring aromatics, substituted furan/pyran moieties, highly branched oxygenated aliphatics, and carbonyl groups. A pathway for producing an IOM-like molecular structure through formaldehyde polymerization is proposed and tested experimentally. Solid-state 13C NMR analysis of aqueously altered formaldehyde polymer reveals considerable similarity with chondritic IOM. Carbon X-ray absorption near edge structure spectroscopy of formaldehyde polymer reveals the presence of similar functional groups across certain Comet 81P/Wild 2 organic solids, interplanetary dust particles, and primitive IOM. Variation in functional group concentration amongst these extraterrestrial materials is understood to be a result of various degrees of processing in the parent bodies, in space, during atmospheric entry, etc. These results support the hypothesis that chondritic IOM and cometary refractory organic solids are related chemically and likely were derived from formaldehyde polymer. The fine-scale morphology of formaldehyde polymer produced in the experiment reveals abundant nanospherules that are similar in size and shape to organic nanoglobules that are ubiquitous in primitive chondrites. PMID:21464292

  20. Tools for Modeling & Simulation of Molecular and Nanoelectronics Devices

    DTIC Science & Technology

    2012-06-14

    1) Tools for Modeling & Simulation of Molecular and Nanoelectronics Devices 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S...parallel algorithms to allow for simulations of realistic device structures. In Phase II, these methods will be developed and will be integrated into...the integration of other simulation engines into the ATK package. This allows these codes, which are all of academic origin to date, to be driven from

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

    PubMed

    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. Polymerase chain reaction: A molecular diagnostic tool in periodontology

    PubMed Central

    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. PMID:27143822

  3. Molecular diagnostic and surveillance tools for global malaria control.

    PubMed

    Erdman, Laura K; Kain, Kevin C

    2008-01-01

    Malaria is the most devastating parasitic infection in the world, annually causing over 1 million deaths and extensive morbidity. The global burden of malaria has increased over the last several decades, as have rates of imported malaria into non-endemic regions. Rapid and accurate diagnostics are a crucial component of malaria control strategies, and epidemiological surveillance is required to monitor trends in malaria prevalence and antimalarial drug resistance. Conventional malaria diagnostic and surveillance tools can be cumbersome and slow with limitations in both sensitivity and specificity. New molecular techniques have been developed in an attempt to overcome these restrictions. These molecular techniques are discussed with regard to their technical advantages and disadvantages, with an emphasis on the practicality of implementation in malaria-endemic and non-endemic regions.

  4. Yada: a novel tool for molecular docking calculations

    NASA Astrophysics Data System (ADS)

    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.

  5. Yada: a novel tool for molecular docking calculations.

    PubMed

    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 .

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

    PubMed

    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.

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

    PubMed

    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.

  8. Plasmid vectors and molecular building blocks for the development of genetic manipulation tools for Trypanosoma cruzi.

    PubMed

    Bouvier, León A; Cámara, María de los Milagros; Canepa, Gaspar E; Miranda, Mariana R; Pereira, Claudio A

    2013-01-01

    The post genomic era revealed the need for developing better performing, easier to use and more sophisticated genetic manipulation tools for the study of Trypanosoma cruzi, the etiological agent of Chagas disease. In this work a series of plasmids that allow genetic manipulation of this protozoan parasite were developed. First of all we focused on useful tools to establish selection strategies for different strains and which can be employed as expression vectors. On the other hand molecular building blocks in the form of diverse selectable markers, modifiable fluorescent protein and epitope-tag coding sequences were produced. Both types of modules were harboured in backbone molecules conceived to offer multiple construction and sub-cloning strategies. These can be used to confer new properties to already available genetic manipulation tools or as starting points for whole novel designs. The performance of each plasmid and building block was determined independently. For illustration purposes, some simple direct practical applications were conducted.

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

    PubMed

    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.

  10. ms2: A molecular simulation tool for thermodynamic properties

    NASA Astrophysics Data System (ADS)

    Deublein, Stephan; Eckl, Bernhard; Stoll, Jürgen; Lishchuk, Sergey V.; Guevara-Carrion, Gabriela; Glass, Colin W.; Merker, Thorsten; Bernreuther, Martin; Hasse, Hans; Vrabec, Jadran

    2011-11-01

    This work presents the molecular simulation program ms2 that is designed for the calculation of thermodynamic properties of bulk fluids in equilibrium consisting of small electro-neutral molecules. ms2 features the two main molecular simulation techniques, molecular dynamics (MD) and Monte-Carlo. It supports the calculation of vapor-liquid equilibria of pure fluids and multi-component mixtures described by rigid molecular models on the basis of the grand equilibrium method. Furthermore, it is capable of sampling various classical ensembles and yields numerous thermodynamic properties. To evaluate the chemical potential, Widom's test molecule method and gradual insertion are implemented. Transport properties are determined by equilibrium MD simulations following the Green-Kubo formalism. ms2 is designed to meet the requirements of academia and industry, particularly achieving short response times and straightforward handling. It is written in Fortran90 and optimized for a fast execution on a broad range of computer architectures, spanning from single processor PCs over PC-clusters and vector computers to high-end parallel machines. The standard Message Passing Interface (MPI) is used for parallelization and ms2 is therefore easily portable to different computing platforms. Feature tools facilitate the interaction with the code and the interpretation of input and output files. The accuracy and reliability of ms2 has been shown for a large variety of fluids in preceding work. Program summaryProgram title:ms2 Catalogue identifier: AEJF_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEJF_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Special Licence supplied by the authors No. of lines in distributed program, including test data, etc.: 82 794 No. of bytes in distributed program, including test data, etc.: 793 705 Distribution format: tar.gz Programming language: Fortran90 Computer: The

  11. Molecular Genetic Tools and Techniques in Fission Yeast.

    PubMed

    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.

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

    PubMed

    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.

  13. Establishing a Novel Modeling Tool: A Python-Based Interface for a Neuromorphic Hardware System

    PubMed Central

    Brüderle, Daniel; Müller, Eric; Davison, Andrew; Muller, Eilif; Schemmel, Johannes; Meier, Karlheinz

    2008-01-01

    Neuromorphic hardware systems provide new possibilities for the neuroscience modeling community. Due to the intrinsic parallelism of the micro-electronic emulation of neural computation, such models are highly scalable without a loss of speed. However, the communities of software simulator users and neuromorphic engineering in neuroscience are rather disjoint. We present a software concept that provides the possibility to establish such hardware devices as valuable modeling tools. It is based on the integration of the hardware interface into a simulator-independent language which allows for unified experiment descriptions that can be run on various simulation platforms without modification, implying experiment portability and a huge simplification of the quantitative comparison of hardware and simulator results. We introduce an accelerated neuromorphic hardware device and describe the implementation of the proposed concept for this system. An example setup and results acquired by utilizing both the hardware system and a software simulator are demonstrated. PMID:19562085

  14. Molecular Targeted Viral Nanoparticles as Tools for Imaging Cancer

    PubMed Central

    Cho, C.F.; Sourabh, S.; Simpson, E.J.; Steinmetz, N.F.; Luyt, L.G.; Lewis, J.D.

    2015-01-01

    Viral nanoparticles (VNPs) are a novel class of bionanomaterials that harness the natural biocompatibility of viruses for the development of therapeutics, vaccines, and imaging tools. The plant virus, cowpea mosaic virus (CPMV), has been successfully engineered to create novel cancer-targeted imaging agents by incorporating fluorescent dyes, polyethylene glycol (PEG) polymers, and targeting moieties. Using straightforward conjugation strategies, VNPs with high selectivity for cancer-specific molecular targets can be synthesized for in vivo imaging of tumors. Here we describe the synthesis and purification of CPMV-based VNPs, the functionalization of these VNPs using click chemistry, and their use for imaging xenograft tumors in animal models. VNPs decorated with fluorescent dyes, PEG, and targeting ligands can be synthesized in one day, and imaging studies can be performed over hours, days, or weeks, depending on the application. PMID:24243252

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

    NASA Astrophysics Data System (ADS)

    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

  16. Establishment of an accurate and fast detection method using molecular beacons in loop-mediated isothermal amplification assay

    PubMed Central

    Liu, Wei; Huang, Simo; Liu, Ningwei; Dong, Derong; Yang, Zhan; Tang, Yue; Ma, Wen; He, Xiaoming; Ao, Da; Xu, Yaqing; Zou, Dayang; Huang, Liuyu

    2017-01-01

    This study established a constant-temperature fluorescence quantitative detection method, combining loop-mediated isothermal amplification (LAMP) with molecular beacons. The advantages of LAMP are its convenience and efficiency, as it does not require a thermocycler and results are easily visualized by the naked eye. However, a major disadvantage of current LAMP techniques is the use of indirect evaluation methods (e.g., electrophoresis, SYBR Green I dye, precipitation, hydroxynaphthol blue dye, the turbidimetric method, calcein/Mn2+ dye, and the composite probe method), which cannot distinguish between the desired products and products of nonspecific amplification, thereby leading to false positives. Use of molecular beacons avoids this problem because molecular beacons produce fluorescence signals only when binding to target DNA, thus acting as a direct indicator of amplification products. Our analyses determined the optimal conditions for molecular beacons as an evaluation tool in LAMP: beacon length of 25–45 bp, beacon concentration of 0.6–1 pmol/μL, and reaction temperature of 60–65 °C. In conclusion, we validated a novel molecular beacon loop-mediated isothermal amplification method (MB-LAMP), realizing the direct detection of LAMP product. PMID:28059137

  17. Development and Application of Camelid Molecular Cytogenetic Tools

    PubMed Central

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

    2014-01-01

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

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

    PubMed

    Delpech, M

    1993-01-01

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

  19. MLP Tools: a PyMOL plugin for using the molecular lipophilicity potential in computer-aided drug design

    NASA Astrophysics Data System (ADS)

    Oberhauser, Nils; Nurisso, Alessandra; Carrupt, Pierre-Alain

    2014-05-01

    The molecular lipophilicity potential (MLP) is a well-established method to calculate and visualize lipophilicity on molecules. We are here introducing a new computational tool named MLP Tools, written in the programming language Python, and conceived as a free plugin for the popular open source molecular viewer PyMOL. The plugin is divided into several sub-programs which allow the visualization of the MLP on molecular surfaces, as well as in three-dimensional space in order to analyze lipophilic properties of binding pockets. The sub-program Log MLP also implements the virtual log P which allows the prediction of the octanol/water partition coefficients on multiple three-dimensional conformations of the same molecule. An implementation on the recently introduced MLP GOLD procedure, improving the GOLD docking performance in hydrophobic pockets, is also part of the plugin. In this article, all functions of the MLP Tools will be described through a few chosen examples.

  20. Establishing a community-wide DNA barcode library as a new tool for arctic research.

    PubMed

    Wirta, H; Várkonyi, G; Rasmussen, C; Kaartinen, R; Schmidt, N M; Hebert, P D N; Barták, M; Blagoev, G; Disney, H; Ertl, S; Gjelstrup, P; Gwiazdowicz, D J; Huldén, L; Ilmonen, J; Jakovlev, J; Jaschhof, M; Kahanpää, J; Kankaanpää, T; Krogh, P H; Labbee, R; Lettner, C; Michelsen, V; Nielsen, S A; Nielsen, T R; Paasivirta, L; Pedersen, S; Pohjoismäki, J; Salmela, J; Vilkamaa, P; Väre, H; von Tschirnhaus, M; Roslin, T

    2016-05-01

    DNA sequences offer powerful tools for describing the members and interactions of natural communities. In this study, we establish the to-date most comprehensive library of DNA barcodes for a terrestrial site, including all known macroscopic animals and vascular plants of an intensively studied area of the High Arctic, the Zackenberg Valley in Northeast Greenland. To demonstrate its utility, we apply the library to identify nearly 20 000 arthropod individuals from two Malaise traps, each operated for two summers. Drawing on this material, we estimate the coverage of previous morphology-based species inventories, derive a snapshot of faunal turnover in space and time and describe the abundance and phenology of species in the rapidly changing arctic environment. Overall, 403 terrestrial animal and 160 vascular plant species were recorded by morphology-based techniques. DNA barcodes (CO1) offered high resolution in discriminating among the local animal taxa, with 92% of morphologically distinguishable taxa assigned to unique Barcode Index Numbers (BINs) and 93% to monophyletic clusters. For vascular plants, resolution was lower, with 54% of species forming monophyletic clusters based on barcode regions rbcLa and ITS2. Malaise catches revealed 122 BINs not detected by previous sampling and DNA barcoding. The insect community was dominated by a few highly abundant taxa. Even closely related taxa differed in phenology, emphasizing the need for species-level resolution when describing ongoing shifts in arctic communities and ecosystems. The DNA barcode library now established for Zackenberg offers new scope for such explorations, and for the detailed dissection of interspecific interactions throughout the community.

  1. The need for novel informatics tools for integrating and planning research in molecular and cellular cognition.

    PubMed

    Silva, Alcino J; Müller, Klaus-Robert

    2015-09-01

    The sheer volume and complexity of publications in the biological sciences are straining traditional approaches to research planning. Nowhere is this problem more serious than in molecular and cellular cognition, since in this neuroscience field, researchers routinely use approaches and information from a variety of areas in neuroscience and other biology fields. Additionally, the multilevel integration process characteristic of this field involves the establishment of experimental connections between molecular, electrophysiological, behavioral, and even cognitive data. This multidisciplinary integration process requires strategies and approaches that originate in several different fields, which greatly increases the complexity and demands of this process. Although causal assertions, where phenomenon A is thought to contribute or relate to B, are at the center of this integration process and key to research in biology, there are currently no tools to help scientists keep track of the increasingly more complex network of causal connections they use when making research decisions. Here, we propose the development of semiautomated graphical and interactive tools to help neuroscientists and other biologists, including those working in molecular and cellular cognition, to track, map, and weight causal evidence in research papers. There is a great need for a concerted effort by biologists, computer scientists, and funding institutions to develop maps of causal information that would aid in integration of research findings and in experiment planning.

  2. The need for novel informatics tools for integrating and planning research in molecular and cellular cognition

    PubMed Central

    Müller, Klaus-Robert

    2015-01-01

    The sheer volume and complexity of publications in the biological sciences are straining traditional approaches to research planning. Nowhere is this problem more serious than in molecular and cellular cognition, since in this neuroscience field, researchers routinely use approaches and information from a variety of areas in neuroscience and other biology fields. Additionally, the multilevel integration process characteristic of this field involves the establishment of experimental connections between molecular, electrophysiological, behavioral, and even cognitive data. This multidisciplinary integration process requires strategies and approaches that originate in several different fields, which greatly increases the complexity and demands of this process. Although causal assertions, where phenomenon A is thought to contribute or relate to B, are at the center of this integration process and key to research in biology, there are currently no tools to help scientists keep track of the increasingly more complex network of causal connections they use when making research decisions. Here, we propose the development of semiautomated graphical and interactive tools to help neuroscientists and other biologists, including those working in molecular and cellular cognition, to track, map, and weight causal evidence in research papers. There is a great need for a concerted effort by biologists, computer scientists, and funding institutions to develop maps of causal information that would aid in integration of research findings and in experiment planning. PMID:26286658

  3. Photorejuvenation: still not a fully established clinical tool for cosmetic treatment

    NASA Astrophysics Data System (ADS)

    Gong, Wei; Xie, Shusen; Li, Hui

    2006-01-01

    Several methods have been used to improve the esthetic appearance of photodamaged skin including dermabrasion, chemical peels and laser resurfacing using CO2 and Er:YAG laser. These procedures sacrifice epidermis, resulting in a long recuperation period and potential complications including persistent scarring, infection, hyperpigmentation, etc. Compared to ablative CO2 or Er:YAG laser resurfacing, non-ablative photorejuvenation technologies are playing an increasing role in the treatment of photodamaged skin. The clinical objective of which is to maximize thermal damage to upper dermis while minimizing injury to overlying skin. A variety of laser and non-laser systems have been used in the initial stage for this treatment. In our review, different treatment modalities have resulted in varying degrees of clinical effects. The basic mechanisms relate to improvement in employing non-ablative technologies are also discussed. Photorejuvenation is still not a fully established clinical tool for cosmetic treatment according to our review, therefore more research on basic mechanisms should be made.

  4. MBS measurement tool for swallow impairment--MBSImp: establishing a standard.

    PubMed

    Martin-Harris, Bonnie; Brodsky, Martin B; Michel, Yvonne; Castell, Donald O; Schleicher, Melanie; Sandidge, John; Maxwell, Rebekah; Blair, Julie

    2008-12-01

    The aim of this study was to test reliability, content, construct, and external validity of a new modified barium swallowing study (MBSS) tool (MBSImp) that is used to quantify swallowing impairment. Multiple regression, confirmatory factor, and correlation analyses were used to analyze 300 in- and outpatients with heterogeneous medical and surgical diagnoses who were sequentially referred for MBS exams at a university medical center and private tertiary care community hospital. Main outcome measures were the MBSImp and index scores of aspiration, health status, and quality of life. Inter- and intrarater concordance were 80% or greater for blinded scoring of MBSSs. Regression analysis revealed contributions of eight of nine swallow types to impressions of overall swallowing impairment (p < or = 0.05). Factor analysis revealed 13 significant components (loadings >/= 0.5) that formed two impairment groupings (oral and pharyngeal). Significant correlations were found between Oral and Pharyngeal Impairment scores and Penetration-Aspiration Scale scores, and indexes of intake status, nutrition, health status, and quality of life. The MBSImp demonstrated clinical practicality, favorable inter- and intrarater reliability following standardized training, content, and external validity. This study reflects potential for establishment of a new standard for quantification and comparison of oropharyngeal swallowing impairment across patient diagnoses as measured on MBSS.

  5. MBS Measurement Tool for Swallow Impairment—MBSImp: Establishing a Standard

    PubMed Central

    Martin-Harris, Bonnie; Brodsky, Martin B.; Michel, Yvonne; Castell, Donald O.; Schleicher, Melanie; Sandidge, John; Maxwell, Rebekah; Blair, Julie

    2014-01-01

    The aim of this study was to test reliability, content, construct, and external validity of a new modified barium swallowing study (MBSS) tool (MBSImp) that is used to quantify swallowing impairment. Multiple regression, confirmatory factor, and correlation analyses were used to analyze 300 in- and outpatients with heterogeneous medical and surgical diagnoses who were sequentially referred for MBS exams at a university medical center and private tertiary care community hospital. Main outcome measures were the MBSImp and index scores of aspiration, health status, and quality of life. Inter- and intrarater concordance were 80% or greater for blinded scoring of MBSSs. Regression analysis revealed contributions of eight of nine swallow types to impressions of overall swallowing impairment (p ≤ 0.05). Factor analysis revealed 13 significant components (loadings ≥ 0.5) that formed two impairment groupings (oral and pharyngeal). Significant correlations were found between Oral and Pharyngeal Impairment scores and Penetration-Aspiration Scale scores, and indexes of intake status, nutrition, health status, and quality of life. The MBSImp demonstrated clinical practicality, favorable inter- and intrarater reliability following standardized training, content, and external validity. This study reflects potential for establishment of a new standard for quantification and comparison of oropharyngeal swallowing impairment across patient diagnoses as measured on MBSS. PMID:18855050

  6. Established and Adapted Diagnostic Tools for Investigation of a Special Twin-Wire Arc Spraying Process

    NASA Astrophysics Data System (ADS)

    König, Johannes; Lahres, Michael; Zimmermann, Stephan; Schein, Jochen

    2016-10-01

    In the LDS® ( Lichtbogendrahtspritzen) process, a twin-wire arc spraying (TWAS) process developed by Daimler AG, the gas injection and feed to the arc play a crucial role in separating the molten particles from the wire ends. This paper describes an investigation of the gas and particle behavior according to individual LDS® process parameters. Coating problems are not considered. The measurements are separated into two different parts: "cold" (without arc and particles) and "hot" (with arc and particles). The results provide the first detailed understanding of the effect of different LDS® process parameters. A correlation between the gas parameter settings and the particle beam properties was found. Using established and adapted diagnostic tools, as also applied for conventional TWAS processes, this special LDS® process was investigated and the results (gas and particle behavior) validated, thereby allowing explanation and comparison of the diagnostic methods, which is the main focus of this paper. Based on error analysis, individual instabilities, limits, and deviations during the gas determinations and particle measurements are explained in more detail. The paper concludes with presentation of the first particle-shadow diagnostic results and main statements regarding these investigations.

  7. Molecular Tools for Exploring Polyploid Genomes in Plants

    PubMed Central

    Aversano, Riccardo; Ercolano, Maria Raffaella; Caruso, Immacolata; Fasano, Carlo; Rosellini, Daniele; Carputo, Domenico

    2012-01-01

    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. PMID:22949863

  8. Molecular tools for the detection of nitrogen cycling Archaea.

    PubMed

    Rusch, Antje

    2013-01-01

    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.

  9. Established and emerging variants of glioblastoma multiforme: review of morphological and molecular features.

    PubMed

    Karsy, Michael; Gelbman, Marshall; Shah, Paarth; Balumbu, Odessa; Moy, Fred; Arslan, Erol

    2012-01-01

    Since the recent publication of the World Health Organization brain tumour classification guidelines in 2007, a significant expansion in the molecular understanding of glioblastoma multiforme (GBM) and its pathological as well as genomic variants has been evident. The purpose of this review article is to evaluate the histopathological, molecular and clinical features surrounding emerging and currently established GBM variants. The tumours discussed include classic glioblastoma multiforme and its four genomic variants, proneural, neural, mesenchymal, classical, as well as gliosarcoma (GS), and giant cell GBM (gcGBM). Furthermore, the emerging variants include fibrillary/epithelial GBM, small cell astrocytoma (SCA), GBM with oligodendroglial component (GBMO), GBM with primitive neuroectodermal features (GBM-PNET), gemistocytic astrocytoma (GA), granular cell astrocytoma (GCA), and paediatric high-grade glioma (HGG) as well as diffuse intrinsic pontine glioma (DIPG). Better understanding of the heterogeneous nature of GBM may provide improved treatment paradigms, prognostic classification, and approaches towards molecularly targeted treatments.

  10. Establishing a High School on a College Campus: A Planning Tool

    ERIC Educational Resources Information Center

    Corallo, Christopher; Redfield, Doris; Jordan, Will; Cavalluzzo, Linda

    2004-01-01

    The purpose of this planning tool is to provide educators with a road map for developing a high school/college collaborative program on a college campus. The tool is designed to guide the user through decisions about building a high school/postsecondary education partnership, developing a planning team, building a program of study, developing a…

  11. Semantic Differential as One of the Research Tools Suitable for Establishing the Attitudes of Pupils to Old Age and Seniors

    ERIC Educational Resources Information Center

    Divilová, Sona

    2016-01-01

    The paper presents the results of the pre-research conducted under the project entitled "Seniors in the Eyes of Children". The main objective of the project was to create and test a research tool in order to establish what the attitudes of pupils to old age and seniors were. Semantic differential was chosen for these purposes. Semantic…

  12. Equipping Every Student with Psychological Tools: A Vygotskian Guide to Establishing the Goals of Education

    ERIC Educational Resources Information Center

    Eun, Barohny

    2016-01-01

    The present conceptual analysis begins with an assertion that the most fundamental act in any educational endeavors is establishing their goals. The discussion proceeds to reviewing recent pertinent literature that presents Vygotsky's theory of development as a useful source in providing guidance to establishing the goals of education in rapidly…

  13. Connectivity research in Iceland - using scientific tools to establish sustainable water management strategies

    NASA Astrophysics Data System (ADS)

    Finger, David

    2015-04-01

    Since the ninth century when the first settlers arrived in Iceland the island has undergone deforestation and subsequent vegetation degradation and soil erosion. Almost the entire birch forest and woodland, which originally covered ~ 25% of the nation, have been deforested through wood cutting and overgrazing. Consequently, soil erosion seriously affects over 40% of the country. During the last 50 years extensive drainage of wetlands has taken place. Furthermore, about 75% of Iceland electricity production comes from hydropower plants, constructed along the main rivers. Along with seismic and volcanic activities the above mentioned anthropogenic impacts continuously altered the hydro-geomorphic connectivity in many parts of the island. In the framework of ongoing efforts to restore ecosystems and their services in Iceland a thorough understanding of the hydro-geomorphic processes is essential. Field observations and numerical models are crucial tools to adopt appropriate management strategies and help decision makers establish sustainable governance strategies. Sediment transport models have been used in the past to investigate the impacts of hydropower dams on sediment transport in downstream rivers (Finger et al., 2006). Hydropower operations alter the turbidity dynamics in downstream freshwater systems, affecting visibility and light penetration into the water, leading to significant changes in primary production (Finger et al., 2007a). Overall, the interruption of connectivity by physical obstructions can affect the entire food chain, hampering the fishing yields in downstream waters (Finger et al., 2007b). In other locations hydraulic connectivity through retreating glaciers assures water transfer from upstream to downstream areas. The drastically retreat of glaciers can raise concerns of future water availability in remote mountain areas (Finger et al., 2013). Furthermore, the drastic reduction of glacier mass also jeopardizes the water availability for

  14. Establishing a Web-based DICOM teaching file authoring tool using open-source public software.

    PubMed

    Lee, Wen-Jeng; Yang, Chung-Yi; Liu, Kao-Lang; Liu, Hon-Man; Ching, Yu-Tai; Chen, Shyh-Jye

    2005-09-01

    Online teaching files are an important source of educational and referential materials in the radiology community. The commonly used Digital Imaging and Communications in Medicine (DICOM) file format of the radiology community is not natively supported by common Web browsers. The ability of the Web server to convert and parse DICOM is important when the DICOM-converting tools are not available. In this paper, we describe our approach to develop a Web-based teaching file authoring tool. Our server is built using Apache Web server running on FreeBSD operating system. The dynamic page content is produced by Hypertext Preprocessor (PHP). Digital Imaging and Communications in Medicine images are converted by ImageMagick into Joint Photographic Experts Group (JPEG) format. Digital Imaging and Communications in Medicine attributes are parsed by dicom3tools and stored in PostgreSQL database. Using free software available from the Internet, we build a Web service that allows radiologists to create their own online teaching file cases with a common Web browser.

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

    PubMed

    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.

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

    NASA Astrophysics Data System (ADS)

    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).

  17. WWW Entrez: A Hypertext Retrieval Tool for Molecular Biology.

    ERIC Educational Resources Information Center

    Epstein, Jonathan A.; Kans, Jonathan A.; Schuler, Gregory D.

    This article describes the World Wide Web (WWW) Entrez server which is based upon the National Center for Biotechnology Information's (NCBI) Entrez retrieval database and software. Entrez is a molecular sequence retrieval system that contains an integrated view of portions of Medline and all publicly available nucleotide and protein databases,…

  18. [Molecular mechanism for the establishment of blood-vessel gateway for immune cells in the CNS.

    PubMed

    Murakami, Masaaki

    2017-01-01

    We have been studying about the molecular mechanism responsible for the establishment of the blood-vessel gateway through which immune cells enter the CNS. We have discovered three kinds of gateways in a multiple sclerosis model, EAE, based on the neural stimulations and named them the gravity-gateway reflex, electric-gateway reflex, and pain-gateway reflex, respectively. All gateway reflexes are involved in specific crosstalk between sensory-sympathetic pathways. For example, in the gravity-gateway reflex, gravity-mediated sensory stimulation via the soleus muscles activates fifth lumber(L5)dorsal loot ganglions to activate L5 sympathetic ganglions, which express norepinephrine at specific vessels of the L5 cord. We explain these three types of gateway reflexes in this chapter.

  19. Molecular tools for investigating ANME community structure and function

    SciTech Connect

    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

  20. Using GP trainees as role players as a teaching/training tool for established GP trainers.

    PubMed

    Emerson, Kim; Moore, Penny; Edwards, Jill

    2017-02-16

    This work aimed to evaluate the effectiveness of using GP trainees in place of professional actors, to role-play trainees with 'difficulties' or various challenging characteristics, as an educational tool for skills development of experienced GP trainers. The context was a residential experienced GP trainers' course and the role players were local ST3 GP trainees. Professional actors have been used for this purpose for many years in medical education at all levels, particularly in teaching communication and consultation skills in the Thames Valley area of the UK. We wanted to trial and evaluate whether using GP trainees themselves, with their own more authentic 'hinterland' of experience, (but no acting training) would be as, or more, effective than using actors. The exercise was successful and showed, through post-course feedback (immediate written feedback and later on-line questionnaire), that the use of trainees was considered by the delegates to be an effective, adaptable and realistic training tool, and more so than using professional actors. The trainees also reported educational benefit from the experience.

  1. Molecular signals required for the establishment and maintenance of ectomycorrhizal symbioses.

    PubMed

    Garcia, Kevin; Delaux, Pierre-Marc; Cope, Kevin R; Ané, Jean-Michel

    2015-10-01

    Ectomycorrhizal (ECM) symbioses are among the most widespread associations between roots of woody plants and soil fungi in forest ecosystems. These associations contribute significantly to the sustainability and sustainagility of these ecosystems through nutrient cycling and carbon sequestration. Unfortunately, the molecular mechanisms controlling the mutual recognition between both partners are still poorly understood. Elegant work has demonstrated that effector proteins from ECM and arbuscular mycorrhizal (AM) fungi regulate host defenses by manipulating plant hormonal pathways. In parallel, genetic and evolutionary studies in legumes showed that a 'common symbiosis pathway' is required for the establishment of the ancient AM symbiosis and has been recruited for the rhizobia-legume association. Given that genes of this pathway are present in many angiosperm trees that develop ectomycorrhizas, we propose their potential involvement in some but not all ECM associations. The maintenance of a successful long-term relationship seems strongly regulated by resource allocation between symbiotic partners, suggesting that nutrients themselves may serve as signals. This review summarizes our current knowledge on the early and late signal exchanges between woody plants and ECM fungi, and we suggest future directions for decoding the molecular basis of the underground dance between trees and their favorite fungal partners.

  2. Establishment and molecular characterization of cell lines from Japanese patients with malignant pleural mesothelioma

    PubMed Central

    SUZAWA, KEN; YAMAMOTO, HIROMASA; MURAKAMI, TOMOYUKI; KATAYAMA, HIDEKI; FURUKAWA, MASASHI; SHIEN, KAZUHIKO; HASHIDA, SHINSUKE; OKABE, KAZUNORI; AOE, KEISUKE; SOH, JUNICHI; ASANO, HIROAKI; TSUKUDA, KAZUNORI; MIMURA, YUSUKE; TOYOOKA, SHINICHI; MIYOSHI, SHINICHIRO

    2016-01-01

    Malignant pleural mesothelioma (MPM) is an aggressive disease that is resistant to conventional therapies. Cell lines are useful models for studying the biological characteristics of tumors; therefore, the establishment of MPM cell lines is valuable for exploring novel therapeutic strategies for MPM. In the present study, 4 MPM cell lines (YUMC8, YUMC44, YUMC63, and YUMC64) were established, which consisted of 2 epithelioid and 2 sarcomatoid mesothelioma histological subtypes, from Japanese patients with MPM. The DNA methylation status, mutations, copy number gains, protein expression of representative genes, and the sensitivity to several drugs were examined in these 4 cell lines. Methylation of P16 was demonstrated in 3/4 cell lines, in which the protein expression of p16 was lost. Methylation of RASSF1A was observed in 3/4 cell lines. Copy number gains of EGFR, HER2 or MET were not detected in the 4 cell lines. Mutations in various genes, including EGFR, KRAS, HER2, BRAF, and PIK3CA, which are frequently detected in non-small cell lung cancer, were not detected in the 4 cell lines. microRNA-34b/c is a direct transcriptional target of p53 and is often silenced in MPM by promoter methylation. In the present study, miR-34b/c was heavily methylated in 2/4 established MPM cell lines. For cell adhesion molecules, E-cadherin expression was detected in the 2 epithelioid MPM cell lines, whereas N-cadherin expression was detected in all 4 established cell lines by western blotting. Vimentin was strongly expressed in the 2 sarcomatoid MPM cell lines. None of the established MPM cell lines demonstrated significant responses to the drugs tested, including NVP-AUY922, 17-DMAG, Trichostatin A, and Vorinostat. Although novel molecular findings were not observed in the current characterization of these MPM cell lines, these lines will be useful for future extensive analyses of the biological behavior of MPM and the development of novel therapeutic strategies. PMID:26870271

  3. Mutants of Arabidopsis as tools for physiology and molecular biology

    SciTech Connect

    Somerville, C.R.; Artus, N.; Browse, J.; Caspar, T.; Estelle, M.; Haughn, G.; Kunst, L.; Martinez, J.; McCourt, P.; Moffatt, B.

    1986-04-01

    The authors discuss the importance of developing a facile system for genetic analysis in higher plants which can be used to approach problems specific to plant biology in much the same way that molecular genetic approaches have been used in other classes of organisms such as yeast and Drosophila. Toward this end, they have developed methods for the isolation and analysis of mutants of Arabidopsis with specific alterations in photosynthesis, photorespiration, starch metabolism, lipid metabolism, purine metabolism, amino acid metabolism and phytohormone responses. The utility of this collection of mutants for studying problems in physiology and biochemistry is illustrated with selected examples.

  4. Graphene nanoribbon thermopower as a tool for molecular spectroscopy

    NASA Astrophysics Data System (ADS)

    Rosales, L.; Nunez, C. D.; Pacheco, M.; Latgé, A.; Orellana, P. A.

    2013-10-01

    In this work, we study thermoelectric properties of graphene nanoribbons with side-attached organic molecules. By adopting a single-band tight binding Hamiltonian and the Green's function formalism, we calculated the transmission and Seebeck coefficients for different hybrid systems. The corresponding thermopower profiles exhibit a series of sharp peaks at the eigenenergies of the isolated molecule indicating that the system can be proposed as a molecular thermo-device. We have studied the effects of the temperature on the thermoelectric response, and considered random configurations of molecule distributions, in different disorder regimes. We have found that the main features of the thermopower are robust under temperature and disorder.

  5. Design droughts as planning tool for ecosystem establishment in post-mining landscapes

    NASA Astrophysics Data System (ADS)

    Halwatura, D.; Lechner, A. M.; Arnold, S.

    2014-05-01

    Eastern Australia has considerable mineral and energy resources and areas of high biodiversity value co-occurring over a broad range of agro-climatic environments. Water is the primary abiotic stressor for (agro)ecosystems in many parts of Eastern Australia. In the context of mined land rehabilitation quantifying the severity-duration-frequency (SDF) of droughts is crucial for successful ecosystem rehabilitation to overcome challenges of early vegetation establishment and long-term ecosystem resilience. The objective of this study was to quantify the SDF of short-term and long-term drought events of 11 selected locations across a broad range of agro-climatic environments in Eastern Australia by using three drought indices at different time scales: the Standardized Precipitation Index (SPI), the Reconnaissance Drought Index (RDI), and the Standardized Precipitation-Evapotranspiration Index (SPEI). Based on the indices we derived bivariate distribution functions of drought severity and duration, and estimated the recurrence intervals of drought events at different time scales. The correlation between the simple SPI and the more complex SPEI or RDI was stronger for the tropical and temperate locations than for the arid locations, indicating that SPEI or RDI can be replaced by SPI if evaporation plays a minor role for plant available water. Both short-term and long-term droughts were most severe and prolonged, and occurred most frequently in arid regions, but were relatively rare in tropical and temperate regions. Our approach is similar to intensity-duration-frequency (IDF) analyses of rainfall crucial to design infrastructure. In this regard, we propose to apply SDF analyses of droughts to design ecosystem components in post-mining landscapes. Together with design rainfalls, design droughts should be used to assess rehabilitation strategies and ecological management based on drought recurrence intervals, thereby minimising the risk of failure of initial ecosystem

  6. Design droughts as planning tool for ecosystem establishment in post-mining landscapes

    NASA Astrophysics Data System (ADS)

    Halwatura, Devanmini; Lechner, Alex; Baumgartl, Thomas; McIntyre, Neil; Arnold, Sven

    2015-04-01

    Eastern Australia has considerable mineral and energy resources and areas of high biodiversity value co-occurring over a broad range of agro-climatic environments. Water is the primary abiotic stressor for (agro)ecosystems in many parts of Eastern Australia. In the context of mined land rehabilitation quantifying the severity-duration-frequency (SDF) of droughts is crucial for successful ecosystem rehabilitation to overcome challenges of early vegetation establishment and long-term ecosystem resilience. The objective of this study was to quantify the SDF of short-term and long-term drought events of 11 selected locations across a broad range of agro-climatic environments in Eastern Australia by using three drought indices at different time scales: the Standardized Precipitation Index (SPI), the Reconnaissance Drought Index (RDI), and the Standardized Precipitation-Evapotranspiration Index (SPEI). Based on the indices we derived bivariate distribution functions of drought severity and duration, and estimated the recurrence intervals of drought events at different time scales. The correlation between the simple SPI and the more complex SPEI or RDI was stronger for the tropical and temperate locations than for the arid locations, indicating that SPEI or RDI can be replaced by SPI if evaporation plays a minor role for plant available water. Both short-term and long-term droughts were most severe and prolonged, and occurred most frequently in arid regions, but were relatively rare in tropical and temperate regions. Our approach is similar to intensity-duration-frequency (IDF) analyses of rainfall crucial to design infrastructure. In this regard, we propose to apply SDF analyses of droughts to design ecosystem components in post-mining landscapes. Together with design rainfalls, design droughts should be used to assess rehabilitation strategies and ecological management based on drought recurrence intervals, thereby minimising the risk of failure of initial ecosystem

  7. Molecular tools in understanding the evolution of Vibrio cholerae

    PubMed Central

    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. PMID:26500613

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

    PubMed Central

    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

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

    PubMed

    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.

  10. Seniority and orbital symmetry as tools for establishing a full configuration interaction hierarchy.

    PubMed

    Bytautas, Laimutis; Henderson, Thomas M; Jiménez-Hoyos, Carlos A; Ellis, Jason K; Scuseria, Gustavo E

    2011-07-28

    We explore the concept of seniority number (defined as the number of unpaired electrons in a determinant) when applied to the problem of electron correlation in atomic and molecular systems. Although seniority is a good quantum number only for certain model Hamiltonians (such as the pairing Hamiltonian), we show that it provides a useful partitioning of the electronic full configuration interaction (FCI) wave function into rapidly convergent Hilbert subspaces whose weight diminishes as its seniority number increases. The primary focus of this study is the adequate description of static correlation effects. The examples considered are the ground states of the helium, beryllium, and neon atoms, the symmetric dissociation of the N(2) and CO(2) molecules, as well as the symmetric dissociation of an H(8) hydrogen chain. It is found that the symmetry constraints that are normally placed on the spatial orbitals greatly affect the convergence rate of the FCI expansion. The energy relevance of the seniority zero sector (determinants with all paired electrons) increases dramatically if orbitals of broken spatial symmetry (as those commonly used for Hubbard Hamiltonian studies) are allowed in the wave function construction.

  11. Molecular simulation as a tool for studying lignin

    SciTech Connect

    Sangha, Amandeep K; Petridis, Loukas; Smith, Jeremy C; Ziebell, Angela L; Parks, Jerry M

    2012-01-01

    Lignocellulosic biomass provides a sustainable source of sugars for biofuel and biomaterial production. However, biomass resistance to degradation imposes difficulties for economical conversion of plant carbohydrates to fermentable sugars. One of the key contributors to recalcitrance is lignin. Understanding the properties of lignin macromolecules in the cell wall matrix is useful for manipulating biomass structure to generate more easily degradable biomass. Along with experimental techniques such as 2D-NMR and mass spectrometry, computational techniques can be useful for characterizing the structural and energetic properties of the biomass assembly and its individual constituents. Here, we provide a brief introduction to lignin, review some of the recent, relevant scientific literature, and give our perspectives on the role of molecular simulation in understanding lignin structure.

  12. Web-based cheminformatics and molecular property prediction tools supporting drug design and development at Novartis.

    PubMed

    Ertl, P; Mühlbacher, J; Rohde, B; Selzer, P

    2003-01-01

    Web-based tools offer many advantages for processing chemical information, most notably ease of use and high interactivity. Therefore more and more pharmaceutical companies are using web technology to deliver sophisticated molecular processing tools directly to the desks of their chemists, to assist them in the process of designing and developing new drugs. In this paper, the web-based cheminformatics system developed at Novartis and currently used by more than thousand users is described. The system allows various molecular modeling and molecular processing tasks, including the calculation of molecular and substituent properties, property-based virtual screening, visualization of molecules, bioisosteric design, diversity analysis, and support of combinatorial chemistry. The methodology to calculate various molecular properties relevant to drug design is described, including the prediction of intestinal absorption, blood-brain barrier penetration, efflux, and water solubility. Information about the web technology used is also provided.

  13. Simulation as a New Tool to Establish Benchmark Outcome Measures in Obstetrics

    PubMed Central

    2015-01-01

    Background There are not enough clinical data from rare critical events to calculate statistics to decide if the management of actual events might be below what could reasonably be expected (i.e. was an outlier). Objectives In this project we used simulation to describe the distribution of management times as an approach to decide if the management of a simulated obstetrical crisis scenario could be considered an outlier. Design Twelve obstetrical teams managed 4 scenarios that were previously developed. Relevant outcome variables were defined by expert consensus. The distribution of the response times from the teams who performed the respective intervention was graphically displayed and median and quartiles calculated using rank order statistics. Results Only 7 of the 12 teams performed chest compressions during the arrest following the ‘cannot intubate/cannot ventilate’ scenario. All other outcome measures were performed by at least 11 of the 12 teams. Calculation of medians and quartiles with 95% CI was possible for all outcomes. Confidence intervals, given the small sample size, were large. Conclusion We demonstrated the use of simulation to calculate quantiles for management times of critical event. This approach could assist in deciding if a given performance could be considered normal and also point to aspects of care that seem to pose particular challenges as evidenced by a large number of teams not performing the expected maneuver. However sufficiently large sample sizes (i.e. from a national data base) will be required to calculate acceptable confidence intervals and to establish actual tolerance limits. PMID:26107661

  14. The ATLS(®) classification of hypovolaemic shock: a well established teaching tool on the edge?

    PubMed

    Mutschler, M; Paffrath, T; Wölfl, C; Probst, C; Nienaber, U; Schipper, I B; Bouillon, B; Maegele, M

    2014-10-01

    Uncontrolled bleeding is the leading cause of shock in trauma patients and delays in recognition and treatment have been linked to adverse outcomes. For prompt detection and management of hypovolaemic shock, ATLS(®) suggests four shock classes based upon vital signs and an estimated blood loss in percent. Although this classification has been widely implemented over the past decades, there is still no clear prospective evidence to fully support this classification. In contrast, it has recently been shown that this classification may be associated with substantial deficits. A retrospective analysis of data derived from the TraumaRegister DGU(®) indicated that only 9.3% of all trauma patients could be allocated into one of the ATLS(®) shock classes when a combination of the three vital signs heart rate, systolic blood pressure and Glasgow Coma Scale was assessed. Consequently, more than 90% of all trauma patients could not be classified according to the ATLS(®) classification of hypovolaemic shock. Further analyses including also data from the UK-based TARN registry suggested that ATLS(®) may overestimate the degree of tachycardia associated with hypotension and underestimate mental disability in the presence of hypovolaemic shock. This finding was independent from pre-hospital treatment as well as from the presence or absence of a severe traumatic brain injury. Interestingly, even the underlying trauma mechanism (blunt or penetrating) had no influence on the number of patients who could be allocated adequately. Considering these potential deficits associated with the ATLS(®) classification of hypovolaemic shock, an online survey among 383 European ATLS(®) course instructors and directors was performed to assess the actual appreciation and confidence in this tool during daily clinical trauma care. Interestingly, less than half (48%) of all respondents declared that they would assess a potential circulatory depletion within the primary survey according to the

  15. Differential Molecular Responses of Rapeseed Cotyledons to Light and Dark Reveal Metabolic Adaptations toward Autotrophy Establishment

    PubMed Central

    He, Dongli; Damaris, Rebecca N.; Fu, Jinlei; Tu, Jinxing; Fu, Tingdong; Xi, Chen; Yi, Bin; Yang, Pingfang

    2016-01-01

    Photosynthesis competent autotrophy is established during the postgerminative stage of plant growth. Among the multiple factors, light plays a decisive role in the switch from heterotrophic to autotrophic growth. Under dark conditions, the rapeseed hypocotyl extends quickly with an apical hook, and the cotyledon is yellow and folded, and maintains high levels of the isocitrate lyase (ICL). By contrast, in the light, the hypocotyl extends slowly, the cotyledon unfolds and turns green, the ICL content changes in parallel with cotyledon greening. To reveal metabolic adaptations during the establishment of postgerminative autotrophy in rapeseed, we conducted comparative proteomic and metabolomic analyses of the cotyledons of seedlings grown under light versus dark conditions. Under both conditions, the increase in proteases, fatty acid β-oxidation and glyoxylate-cycle related proteins was accompanied by rapid degradation of the stored proteins and lipids with an accumulation of the amino acids. While light condition partially retarded these conversions. Light significantly induced the expression of chlorophyll-binding and photorespiration related proteins, resulting in an increase in reducing-sugars. However, the levels of some chlorophyllide conversion, Calvin-cycle and photorespiration related proteins also accumulated in dark grown cotyledons, implying that the transition from heterotrophy to autotrophy is programmed in the seed rather than induced by light. Various anti-stress systems, e.g., redox related proteins, salicylic acid, proline and chaperones, were employed to decrease oxidative stress, which was mainly derived from lipid oxidation or photorespiration, under both conditions. This study provides a comprehensive understanding of the differential molecular responses of rapeseed cotyledons to light and dark conditions, which will facilitate further study on the complex mechanism underlying the transition from heterotrophy to autotrophy. PMID:27471506

  16. Discovery of an in Vivo Tool to Establish Proof-of-Concept for MAP4K4-Based Antidiabetic Treatment

    PubMed Central

    2015-01-01

    Recent studies in adipose tissue, pancreas, muscle, and macrophages suggest that MAP4K4, a serine/threonine protein kinase may be a viable target for antidiabetic drugs. As part of the evaluation of MAP4K4 as a novel antidiabetic target, a tool compound, 16 (PF-6260933) and a lead 17 possessing excellent kinome selectivity and suitable properties were delivered to establish proof of concept in vivo. The medicinal chemistry effort that led to the discovery of these lead compounds is described herein together with in vivo pharmacokinetic properties and activity in a model of insulin resistance. PMID:26617966

  17. Dopamine receptor genes: new tools for molecular psychiatry.

    PubMed Central

    Niznik, H B; Van Tol, H H

    1992-01-01

    For over a decade it has been generally assumed that all the pharmacological and biochemical actions of dopamine within the central nervous system and periphery were mediated by two distinct dopamine receptors. These receptors, termed D1 and D2, were defined as those coupled to the stimulation or inhibition of adenylate cyclase, respectively, and by their selectivity and avidity for various drugs and compounds. The concept that two dopamine receptors were sufficient to account for all the effects mediated by dopamine was an oversimplification. Recent molecular biological studies have identified five distinct genes which encode at least eight functional dopamine receptors. The members of the expanded dopamine receptor family, however, can still be codifed by way of the original D1 and D2 receptor dichotomy. These include two genes encoding dopamine D1-like receptors (D1 [D1A]/D5 [D1B]) and three genes encoding D2-like receptors (D2/D3/D4). We review here our recent work on the cloning and characterization of some of the members of the dopamine receptor gene family (D1, D2, D4, D5), their relationship to neuropsychiatric disorders and their potential role in antipsychotic drug action. Images Fig. 1 PMID:1450188

  18. Acetylenic Coupling: A Powerful Tool in Molecular Construction.

    PubMed

    Siemsen; Livingston; Diederich

    2000-08-04

    Acetylenic coupling is currently experiencing some of the most intensive study of its long history. Rigid and sterically undemanding di- and oligoacetylene moieties, which are frequently encountered in natural products, are finding increasing application as key structural elements in synthetic receptors for molecular recognition. Interesting electronic and optical properties of extensively pi-conjugated systems have spurred research into new linear oligoalkynes and acetylenic carbon allotropes. The synthetic challenges associated with these efforts have in turn spawned new methods. While classical Glaser conditions are still frequently used for homocoupling, the demand for increasingly selective heterocoupling conditions has provided the focus of research over the past decades. These efforts have undoubtedly been hampered by a relatively poor mechanistic understanding of these processes. More recently, palladium-catalyzed coupling methods have led to improvements in both the selectivity and reliability of acetylenic homo- and heterocouplings and paved the way for their application to ever more complicated systems. The variety of acetylenic coupling protocols, the current mechanistic understanding, and their application in natural product and targeted synthesis are discussed comprehensively for the first time in this review, with an emphasis on the most recently developed methods, and their application to the synthesis of complex macromolecular structures.

  19. Molecular Phylogeny and Identification of the Peach Fruit Fly, Bactrocera zonata, Established in Egypt

    PubMed Central

    Abd-El-Samie, Emtithal M.; El Fiky, Zaki A.

    2011-01-01

    The genetic structure of the Egyptian peach fruit fly (Bactrocera zonata (Saunders) (Diptera: Tephritidae)) population was analyzed using total RNA from adult females. A portion of mitochondrial cytochrome oxidase I (COI), 369 bp was amplified using RT-PCR, and was sequenced and analyzed to clarify the phylogenetic relationship of B. zonata established in Egypt. The data suggested that the gene shared a similarity in sequence compared to Bactrocera COI gene found in GenBank. Molecular phylogenetic analyses were performed based on nucleotide sequences in order to examine the position of the Egyptian population among many other species of fruit flies. The results indicate that four accession numbers of B. zonata (three from New Zealand and one from India) are closely related, while the Egyptian B. zonata are close to the 71 accession numbers of Bactrocera include one B. zonata from New Zealand. These two B. zonata from Egypt and New Zealand showed a close relationship in neighbor—joining analysis using the seven accession numbers of B. zonata. In addition, a theoretical restriction map of the homology portion of the COI gene was constructed using 212 restriction enzymes obtained from the restriction enzyme database to identify the Egyptian and New Zealand B. zonata. PMID:22958094

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

    PubMed

    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.

  1. Establishment of replacement batches for heparin low-molecular-mass for calibration CRS, and the International Standard Low Molecular Weight Heparin for Calibration.

    PubMed

    Mulloy, B; Heath, A; Behr-Gross, M-E

    2007-12-01

    An international collaborative study involving fourteen laboratories has taken place, organised by the European Directorate for the Quality of Medicines & HealthCare (EDQM) with National Institute for Biological Standards & Control (NIBSC) (in its capacity as a World Health Organisation (WHO) Laboratory for Biological Standardisation) to provide supporting data for the establishment of replacement batches of Heparin Low-Molecular-Mass (LMM) for Calibration Chemical Reference Substance (CRS), and of the International Reference Reagent (IRR) Low Molecular Weight Heparin for Molecular Weight Calibration. A batch of low-molecular-mass heparin was donated to the organisers and candidate preparations of freeze-dried heparin were produced at NIBSC and EDQM. The establishment study was organised in two phases: a prequalification (phase 1, performed in 3 laboratories in 2005) followed by an international collaborative study (phase 2). In phase 2, started in March 2006, molecular mass parameters were determined for seven different LMM heparin samples using the current CRS batch and two batches of candidate replacement material with a defined number average relative molecular mass (Mn) of 3,700, determined in phase 1. The values calculated using the candidates as standard were systematically different from values calculated using the current batch with its assigned number-average molecular mass (Mna) of 3,700. Using raw data supplied by participants, molecular mass parameters were recalculated using the candidates as standard with values for Mna of 3,800 and 3,900. Values for these parameters agreed more closely with those calculated using the current batch supporting the fact that the candidates, though similar to batch 1 in view of the production processes used, differ slightly in terms of molecular mass distribution. Therefore establishment of the candidates was recommended with an assigned Mna value of 3,800 that is both consistent with phase 1 results and guarantees

  2. Clinical Significance of Molecular Diagnostic Tools for Bacterial Bloodstream Infections: A Systematic Review

    PubMed Central

    Nyirahabimana, Therese

    2016-01-01

    Bacterial bloodstream infection (bBSI) represents any form of invasiveness of the blood circulatory system caused by bacteria and can lead to death among critically ill patients. Thus, there is a need for rapid and accurate diagnosis and treatment of patients with septicemia. So far, different molecular diagnostic tools have been developed. The majority of these tools focus on amplification based techniques such as polymerase chain reaction (PCR) which allows the detection of nucleic acids (both DNA and small RNAs) that are specific to bacterial species and sequencing or nucleic acid hybridization that allows the detection of bacteria in order to reduce delay of appropriate antibiotic therapy. However, there is still a need to improve sensitivity of most molecular techniques to enhance their accuracy and allow exact and on time antibiotic therapy treatment. In this regard, we conducted a systematic review of the existing studies conducted in molecular diagnosis of bBSIs, with the main aim of reporting on clinical significance and benefits of molecular diagnosis to patients. We searched both Google Scholar and PubMed. In total, eighteen reviewed papers indicate that shift from conventional diagnostic methods to molecular tools is needed and would lead to accurate diagnosis and treatment of bBSI. PMID:27974890

  3. [18F]-FDG positron emission tomography--an established clinical tool opening a new window into exercise physiology.

    PubMed

    Rudroff, Thorsten; Kindred, John H; Kalliokoski, Kari K

    2015-05-15

    Positron emission tomography (PET) with [(18)F]-fluorodeoxyglucose (FDG) is an established clinical tool primarily used to diagnose and evaluate disease status in patients with cancer. PET imaging using FDG can be a highly valuable tool to investigate normal human physiology by providing a noninvasive, quantitative measure of glucose uptake into various cell types. Over the past years it has also been increasingly used in exercise physiology studies to identify changes in glucose uptake, metabolism, and muscle activity during different exercise modalities. Metabolically active cells transport FDG, an (18)fluorine-labeled glucose analog tracer, from the blood into the cells where it is then phosphorylated but not further metabolized. This metabolic trapping process forms the basis of this method's use during exercise. The tracer is given to a participant during an exercise task, and the actual PET imaging is performed immediately after the exercise. Provided the uptake period is of sufficient duration, and the imaging is performed shortly after the exercise; the captured image strongly reflects the metabolic activity of the cells used during the task. When combined with repeated blood sampling to determine tracer blood concentration over time, also known as the input function, glucose uptake rate of the tissues can be quantitatively calculated. This synthesis provides an accounting of studies using FDG-PET to measure acute exercise-induced skeletal muscle activity, describes the advantages and limitations of this imaging technique, and discusses its applications to the field of exercise physiology.

  4. Collaborative study to establish human immunoglobulin BRP batch 3 and human immunoglobulin (molecular size) BRP batch 1.

    PubMed

    Sandberg, E; Daas, A; Behr-Gross, M-E

    2006-11-01

    A study was carried out by the European Directorate for the Quality of Medicines (EDQM) as part of the joint Biological Standardisation Programme of the Council of Europe and the European Commission with the aim to establish replacement batches of the European Pharmacopoeia (Ph. Eur.) human immunoglobulin Biological Reference Preparation (BRP) batch 2. Twenty-eight laboratories participated in this study. The suitability of the candidate reference preparations to serve as working references in the tests for distribution of the molecular size, anticomplementary activity and Fc function, in accordance with the specifications of the Ph. Eur. monographs Human normal immunoglobulin for intravenous administration (0918), Human normal immunoglobulin (0338) and Anti-T lymphocyte immunoglobulin for human use, animal (1928) was demonstrated. The candidates were therefore established as human immunoglobulin BRP batch 3 and Human immunoglobulin (molecular size) BRP batch 1. The prescribed use of the latter BRP is limited to the test for distribution of molecular size.

  5. Advances in Coupling of Kinetics and Molecular Scale Tools to Shed Light on Soil Biogeochemical Processes

    SciTech Connect

    Sparks, Donald

    2014-09-02

    Biogeochemical processes in soils such as sorption, precipitation, and redox play critical roles in the cycling and fate of nutrients, metal(loid)s and organic chemicals in soil and water environments. Advanced analytical tools enable soil scientists to track these processes in real-time and at the molecular scale. Our review focuses on recent research that has employed state-of-the-art molecular scale spectroscopy, coupled with kinetics, to elucidate the mechanisms of nutrient and metal(loid) reactivity and speciation in soils. We found that by coupling kinetics with advanced molecular and nano-scale tools major advances have been made in elucidating important soil chemical processes including sorption, precipitation, dissolution, and redox of metal(loids) and nutrients. Such advances will aid in better predicting the fate and mobility of nutrients and contaminants in soils and water and enhance environmental and agricultural sustainability.

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

    PubMed Central

    2014-01-01

    Among Australian endemic tephritid fruit flies, the sibling species Bactrocera tryoni and Bactrocera neohumeralis have been serious horticultural pests since the introduction of horticulture in the nineteenth century. More recently, Bactrocera jarvisi has also been declared a pest in northern Australia. After several decades of genetic research there is now a range of classical and molecular genetic tools that can be used to develop improved Sterile Insect Technique (SIT) strains for control of these pests. Four-way crossing strategies have the potential to overcome the problem of inbreeding in mass-reared strains of B. tryoni. The ability to produce hybrids between B. tryoni and the other two species in the laboratory has proved useful for the development of genetically marked strains. The identification of Y-chromosome markers in B. jarvisi means that male and female embryos can be distinguished in any strain that carries a B. jarvisi Y chromosome. This has enabled the study of homologues of the sex-determination genes during development of B jarvisi and B. tryoni, which is necessary for the generation of genetic-sexing strains. Germ-line transformation has been established and a draft genome sequence for B. tryoni released. Transcriptomes from various species, tissues and developmental stages, to aid in identification of manipulation targets for improving SIT, have been assembled and are in the pipeline. Broad analyses of the microbiome have revealed a metagenome that is highly variable within and across species and defined by the environment. More specific analyses detected Wolbachia at low prevalence in the tropics but absent in temperate regions, suggesting a possible role for this endosymbiont in future control strategies. PMID:25470996

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

    PubMed

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

    2013-12-01

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

  8. Molecular tools for differentiation of non-typeable Haemophilus influenzae from Haemophilus haemolyticus

    PubMed Central

    Pickering, Janessa; Richmond, Peter C.; Kirkham, Lea-Ann S.

    2014-01-01

    Non-typeable Haemophilus influenzae (NTHi) and Haemophilus haemolyticus are closely related bacteria that reside in the upper respiratory tract. NTHi is associated with respiratory tract infections that frequently result in antibiotic prescription whilst H. haemolyticus is rarely associated with disease. NTHi and H. haemolyticus can be indistinguishable by traditional culture methods and molecular differentiation has proven difficult. This current review chronologically summarizes the molecular approaches that have been developed for differentiation of NTHi from H. haemolyticus, highlighting the advantages and disadvantages of each target and/or technique. We also provide suggestions for the development of new tools that would be suitable for clinical and research laboratories. PMID:25520712

  9. Whole Genome Sequence Analysis Using JSpecies Tool Establishes Clonal Relationships between Listeria monocytogenes Strains from Epidemiologically Unrelated Listeriosis Outbreaks

    PubMed Central

    Burall, Laurel S.; Grim, Christopher J.; Mammel, Mark K.; Datta, Atin R.

    2016-01-01

    In an effort to build a comprehensive genomic approach to food safety challenges, the FDA has implemented a whole genome sequencing effort, GenomeTrakr, which involves the sequencing and analysis of genomes of foodborne pathogens. As a part of this effort, we routinely sequence whole genomes of Listeria monocytogenes (Lm) isolates associated with human listeriosis outbreaks, as well as those isolated through other sources. To rapidly establish genetic relatedness of these genomes, we evaluated tetranucleotide frequency analysis via the JSpecies program to provide a cursory analysis of strain relatedness. The JSpecies tetranucleotide (tetra) analysis plots standardized (z-score) tetramer word frequencies of two strains against each other and uses linear regression analysis to determine similarity (r2). This tool was able to validate the close relationships between outbreak related strains from four different outbreaks. Included in this study was the analysis of Lm strains isolated during the recent caramel apple outbreak and stone fruit incident in 2014. We identified that many of the isolates from these two outbreaks shared a common 4b variant (4bV) serotype, also designated as IVb-v1, using a qPCR protocol developed in our laboratory. The 4bV serotype is characterized by the presence of a 6.3 Kb DNA segment normally found in serotype 1/2a, 3a, 1/2c and 3c strains but not in serotype 4b or 1/2b strains. We decided to compare these strains at a genomic level using the JSpecies Tetra tool. Specifically, we compared several 4bV and 4b isolates and identified a high level of similarity between the stone fruit and apple 4bV strains, but not the 4b strains co-identified in the caramel apple outbreak or other 4b or 4bV strains in our collection. This finding was further substantiated by a SNP-based analysis. Additionally, we were able to identify close relatedness between isolates from clinical cases from 1993–1994 and a single case from 2011 as well as links between

  10. Solvation thermodynamic mapping of molecular surfaces in AmberTools: GIST.

    PubMed

    Ramsey, Steven; Nguyen, Crystal; Salomon-Ferrer, Romelia; Walker, Ross C; Gilson, Michael K; Kurtzman, Tom

    2016-08-05

    The expulsion of water from surfaces upon molecular recognition and nonspecific association makes a major contribution to the free energy changes of these processes. In order to facilitate the characterization of water structure and thermodynamics on surfaces, we have incorporated Grid Inhomogeneous Solvation Theory (GIST) into the CPPTRAJ toolset of AmberTools. GIST is a grid-based implementation of Inhomogeneous Fluid Solvation Theory, which analyzes the output from molecular dynamics simulations to map out solvation thermodynamic and structural properties on a high-resolution, three-dimensional grid. The CPPTRAJ implementation, called GIST-cpptraj, has a simple, easy-to-use command line interface, and is open source and freely distributed. We have also developed a set of open-source tools, called GISTPP, which facilitate the analysis of GIST output grids. Tutorials for both GIST-cpptraj and GISTPP can be found at ambermd.org. © 2016 Wiley Periodicals, Inc.

  11. Use of computational fluid dynamics as a tool for establishing process design space for mixing in a bioreactor.

    PubMed

    Rathore, A S; Sharma, C; Persad, And A

    2012-01-01

    The concept of "design space" plays an integral part in implementation of quality by design for pharmaceutical products. ICH Q8 defines design space as "the multidimensional combination and interaction of input variables (e.g., material attributes) and process parameters that have been demonstrated to provide assurance of quality. Working within the design space is not considered as a change. Movement out of the design space is considered to be a change and would normally initiate a regulatory post-approval change process. Design space is proposed by the applicant and is subject to regulatory assessment and approval." Computational fluid dynamics (CFD) is increasingly being used as a tool for modeling of hydrodynamics and mass transfer. In this study, a laboratory-scale aerated bioreactor is modeled using CFD. Eulerian-Eulerian multiphase model is used along with dispersed k-ε turbulent model. Population balance model is incorporated to account for bubble breakage and coalescence. Multiple reference frame model is used for the rotating region. We demonstrate the usefulness of CFD modeling for evaluating the effects of typical process parameters like impeller speed, gas flow rate, and liquid height on the mass transfer coefficient (k(L)a). Design of experiments is utilized to establish a design space for the above mentioned parameters for a given permissible range of k(L)a.

  12. Establishing whether the structural feature controlling the mechanical properties of starch films is molecular or crystalline.

    PubMed

    Li, Ming; Xie, Fengwei; Hasjim, Jovin; Witt, Torsten; Halley, Peter J; Gilbert, Robert G

    2015-03-06

    The effects of molecular and crystalline structures on the tensile mechanical properties of thermoplastic starch (TPS) films from waxy, normal, and high-amylose maize were investigated. Starch structural variations were obtained through extrusion and hydrothermal treatment (HTT). The molecular and crystalline structures were characterized using size-exclusion chromatography and X-ray diffractometry, respectively. TPS from high-amylose maize showed higher elongation at break and tensile strength than those from normal maize and waxy maize starches when processed with 40% plasticizer. Within the same amylose content, the mechanical properties were not affected by amylopectin molecular size or the crystallinity of TPS prior to HTT. This lack of correlation between the molecular size, crystallinity and mechanical properties may be due to the dominant effect of the plasticizer on the mechanical properties. Further crystallization of normal maize TPS by HTT increased the tensile strength and Young's modulus, while decreasing the elongation at break. The results suggest that the crystallinity from the remaining ungelatinized starch granules has less significant effect on the mechanical properties than that resulting from starch recrystallization, possibly due to a stronger network from leached-out amylose surrounding the remaining starch granules.

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

    PubMed

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

    2011-10-01

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

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

    PubMed

    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.

  15. A Molecular Analysis of Training Multiple versus Single Manipulations to Establish a Generalized Manipulative Imitation Repertoire

    ERIC Educational Resources Information Center

    Hartley, Breanne K.

    2009-01-01

    This study evaluates the necessity of training multiple versus single manipulative-imitations per object in order to establish generalized manipulative-imitation. Training took place in Croyden Avenue School's Early Childhood Developmental Delay preschool classroom in Kalamazoo, MI. Two groups of 3 children each were trained to imitate in order to…

  16. Moving from Histopathology to Molecular Tools in the Diagnosis of Molluscs Diseases of Concern under EU Legislation

    PubMed Central

    Aranguren, Raquel; Figueras, Antonio

    2016-01-01

    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 possible. Molluscs 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. PMID:27895595

  17. Moving from Histopathology to Molecular Tools in the Diagnosis of Molluscs Diseases of Concern under EU Legislation.

    PubMed

    Aranguren, Raquel; Figueras, Antonio

    2016-01-01

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

    PubMed

    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.

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

    SciTech Connect

    Charlieu, J.P.; Marcais, B.; Laurent, A.M.; Roizes, G.

    1993-12-31

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

  20. Establishing a reference group for distal 18q-: Clinical description and molecular basis

    PubMed Central

    Cody, Jannine D.; Hasi, Minire; Soileau, Bridgette; Heard, Patricia; Carter, Erika; Sebold, Courtney; O’Donnell, Louise; Perry, Brian; Stratton, Robert F.; Hale, Daniel E.

    2013-01-01

    Although constitutional chromosome abnormalities have been recognized since the 1960s, clinical characterization and development of treatment options have been hampered by their obvious genetic complexity and relative rarity. Additionally, deletions of 18q are particularly heterogeneous, with no two people having the same breakpoints. We identified sixteen individuals with deletions that, despite unique breakpoints, encompass the same set of genes within a 17.6 Mb region. This group represents the most genotypically similar group yet identified with distal 18q deletions. As the deletion is of average size when compared with other 18q deletions, this group can serve as a reference point for the clinical and molecular description of this condition. We performed a thorough medical record review as well as a series of clinical evaluations on 14 of the 16 individuals. Common functional findings included developmental delays, hypotonia, growth hormone deficiency, and hearing loss. Structural anomalies included foot anomalies, ear canal atresia/stenosis, and hypospadias. The majority of individuals performed within the low normal range of cognitive ability but had more serious deficits in adaptive abilities. Of interest, the hemizygous region contains 38 known genes, 26 of which are sufficiently understood to tentatively determine dosage sensitivity. Published data suggest that 20 are unlikely to cause an abnormal phenotype in the hemizygous state and five are likely to be dosage sensitive: TNX3, NETO1, ZNF407, TSHZ1, and NFATC. A sixth gene, ATP9B, may be conditionally dosage sensitive. Not all distal 18q- phenotypes can be attributed to these six genes; however, this is an important advance in the molecular characterization of 18q deletions. PMID:24092497

  1. Pulmonary Arterial Hypertension: A Current Perspective on Established and Emerging Molecular Genetic Defects

    PubMed Central

    Machado, Rajiv D.; Southgate, Laura; Eichstaedt, Christina A.; Aldred, Micheala A.; Austin, Eric D.; Best, D. Hunter; Chung, Wendy K.; Benjamin, Nicola; Elliott, C. Gregory; Eyries, Mélanie; Fischer, Christine; Gräf, Stefan; Hinderhofer, Katrin; Humbert, Marc; Keiles, Steven B.; Loyd, James E.; Morrell, Nicholas W.; Newman, John H.; Soubrier, Florent; Trembath, Richard C.; Viales, Rebecca Rodríguez; Grünig, Ekkehard

    2016-01-01

    Pulmonary arterial hypertension (PAH) is an often fatal disorder resulting from several causes including heterogeneous genetic defects. While mutations in the bone morphogenetic protein receptor type II (BMPR2) gene are the single most common causal factor for hereditary cases, pathogenic mutations have been observed in approximately 25% of idiopathic PAH patients without a prior family history of disease. Additional defects of the transforming growth factor beta (TGF-β) pathway have been implicated in disease pathogenesis. Specifically, studies have confirmed activin A receptor type II-like 1 (ACVRL1), endoglin (ENG) and members of the SMAD family as contributing to PAH both with and without associated clinical phenotypes. Most recently, next-generation sequencing has identified novel, rare genetic variation implicated in the PAH disease spectrum. Of importance, several identified genetic factors converge on related pathways and provide significant insight into the development, maintenance and pathogenetic transformation of the pulmonary vascular bed. Together, these analyses represent the largest comprehensive compilation of BMPR2 and associated genetic risk factors for PAH, comprising known and novel variation. Additionally, with the inclusion of an allelic series of locus-specific variation in BMPR2, these data provide a key resource in data interpretation and development of contemporary therapeutic and diagnostic tools. PMID:26387786

  2. Pulmonary Arterial Hypertension: A Current Perspective on Established and Emerging Molecular Genetic Defects.

    PubMed

    Machado, Rajiv D; Southgate, Laura; Eichstaedt, Christina A; Aldred, Micheala A; Austin, Eric D; Best, D Hunter; Chung, Wendy K; Benjamin, Nicola; Elliott, C Gregory; Eyries, Mélanie; Fischer, Christine; Gräf, Stefan; Hinderhofer, Katrin; Humbert, Marc; Keiles, Steven B; Loyd, James E; Morrell, Nicholas W; Newman, John H; Soubrier, Florent; Trembath, Richard C; Viales, Rebecca Rodríguez; Grünig, Ekkehard

    2015-12-01

    Pulmonary arterial hypertension (PAH) is an often fatal disorder resulting from several causes including heterogeneous genetic defects. While mutations in the bone morphogenetic protein receptor type II (BMPR2) gene are the single most common causal factor for hereditary cases, pathogenic mutations have been observed in approximately 25% of idiopathic PAH patients without a prior family history of disease. Additional defects of the transforming growth factor beta pathway have been implicated in disease pathogenesis. Specifically, studies have confirmed activin A receptor type II-like 1 (ACVRL1), endoglin (ENG), and members of the SMAD family as contributing to PAH both with and without associated clinical phenotypes. Most recently, next-generation sequencing has identified novel, rare genetic variation implicated in the PAH disease spectrum. Of importance, several identified genetic factors converge on related pathways and provide significant insight into the development, maintenance, and pathogenetic transformation of the pulmonary vascular bed. Together, these analyses represent the largest comprehensive compilation of BMPR2 and associated genetic risk factors for PAH, comprising known and novel variation. Additionally, with the inclusion of an allelic series of locus-specific variation in BMPR2, these data provide a key resource in data interpretation and development of contemporary therapeutic and diagnostic tools.

  3. Biliary tract cancers: molecular profiling as a tool for treatment decisions. A literature review.

    PubMed

    Berardi, Rossana; Rossana, Berardi; Scartozzi, Mario; Mario, Scartozzi; Freddari, Federica; Federica, Freddari; Squadroni, Michela; Michela, Squadroni; Santinelli, Alfredo; Alfredo, Santinelli; Bearzi, Italo; Italo, Bearzi; Fabris, Guidalberto; Guidalberto, Fabris; Cascinu, Stefano; Stefano, Cascinu

    2006-08-01

    Biliary tract cancer is a quite rare disease; despite recent significant advances in imaging modalities, most of the patients have advanced disease at presentation thus making radical surgery not feasible. Many different chemotherapeutic regimens have been investigated in small uncontrolled studies, with generally disappointing results. We extensively reviewed the literature on this topic trying to give an explanation to chemoresistance in this setting of patients and considering the molecular profiling as a tool for treatment decision. This review is divided in two parts, in the first one we illustrated chemotherapy results and possible mechanisms of resistance. In the second part we analysed the new molecular targets developing an hypothesis about the future therapeutics perspectives.

  4. Molecular phylogenetic and zoospore ultrastructural analyses of Chytridium olla establish the limits of a monophyletic Chytridiales.

    PubMed

    Vélez, Carlos G; Letcher, Peter M; Schultz, Sabina; Powell, Martha J; Churchill, Perry F

    2011-01-01

    Chytridium olla A. Braun, the first described chytrid and an obligate algal parasite, is the type for the genus and thus the foundation of family Chytridiaceae, order Chytridiales, class Chytridiomycetes and phylum Chytridiomycota. Chytridium olla was isolated in coculture with its host, Oedogonium capilliforme. DNA was extracted from the coculture, and 18S, 28S and ITS1-5.8S-ITS2 rDNA were amplified with universal fungal primers. Free swimming zoospores and zoospores in mature sporangia were examined with electron microscopy. Molecular analyses placed C. olla in a clade in Chytridiales with isolates of Chytridium lagenaria and Phlyctochytrium planicorne. Ultrastructural analysis revealed C. olla to have a Group II-type zoospore, previously described for Chytridium lagenaria and Phlyctochytrium planicorne. On the basis of zoospore ultrastructure, family Chytridiaceae is emended to include the type of Chytridium and other species with a Group II-type zoospore, and the new family Chytriomycetaceae is delineated to include members of Chytridiales with a Group I-type zoospore.

  5. Compartmentalization and molecular traffic in secondary metabolism: a new understanding of established cellular processes

    PubMed Central

    Roze, Ludmila V.; Chanda, Anindya; Linz, John E.

    2010-01-01

    Great progress has been made in understanding the regulation of expression of genes involved in secondary metabolism. Less is known about the mechanisms that govern the spatial distribution of the enzymes, cofactors, and substrates that mediate catalysis of secondary metabolites within the cell. Filamentous fungi in the genus Aspergillus synthesize an array of secondary metabolites and provide useful systems to analyze the mechanisms that mediate the temporal and spatial regulation of secondary metabolism in eukaryotes. For example, aflatoxin biosynthesis in A. parasiticus has been studied intensively because this mycotoxin is highly toxic, mutagenic, and carcinogenic in humans and animals. Using aflatoxin synthesis to illustrate key concepts, this review focuses on the mechanisms by which sub-cellular compartmentalization and intra-cellular molecular traffic contribute to the initiation and completion of secondary metabolism within the cell. We discuss the recent discovery of aflatoxisomes, specialized trafficking vesicles that participate in the compartmentalization of aflatoxin synthesis and export of the toxin to the cell exterior; this work provides a new and clearer understanding of how cells integrate secondary metabolism into basic cellular metabolism via the intracellular trafficking machinery. PMID:20519149

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

    PubMed

    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).

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

    PubMed

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

    2015-04-06

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

  8. Fungal Identification Using Molecular Tools: A Primer for the Natural Products Research Community

    PubMed Central

    2017-01-01

    Fungi are morphologically, ecologically, metabolically, and phylogenetically diverse. They are known to produce numerous bioactive molecules, which makes them very useful for natural products researchers in their pursuit of discovering new chemical diversity with agricultural, industrial, and pharmaceutical applications. Despite their importance in natural products chemistry, identification of fungi remains a daunting task for chemists, especially those who do not work with a trained mycologist. The purpose of this review is to update natural products researchers about the tools available for molecular identification of fungi. In particular, we discuss (1) problems of using morphology alone in the identification of fungi to the species level; (2) the three nuclear ribosomal genes most commonly used in fungal identification and the potential advantages and limitations of the ITS region, which is the official DNA barcoding marker for species-level identification of fungi; (3) how to use NCBI-BLAST search for DNA barcoding, with a cautionary note regarding its limitations; (4) the numerous curated molecular databases containing fungal sequences; (5) the various protein-coding genes used to augment or supplant ITS in species-level identification of certain fungal groups; and (6) methods used in the construction of phylogenetic trees from DNA sequences to facilitate fungal species identification. We recommend that, whenever possible, both morphology and molecular data be used for fungal identification. Our goal is that this review will provide a set of standardized procedures for the molecular identification of fungi that can be utilized by the natural products research community. PMID:28199101

  9. NACE: A web-based tool for prediction of intercompartmental efficiency of human molecular genetic networks.

    PubMed

    Popik, Olga V; Ivanisenko, Timofey V; Saik, Olga V; Petrovskiy, Evgeny D; Lavrik, Inna N; Ivanisenko, Vladimir A

    2016-06-15

    Molecular genetic processes generally involve proteins from distinct intracellular localisations. Reactions that follow the same process are distributed among various compartments within the cell. In this regard, the reaction rate and the efficiency of biological processes can depend on the subcellular localisation of proteins. Previously, the authors proposed a method of evaluating the efficiency of biological processes based on the analysis of the distribution of protein subcellular localisation (Popik et al., 2014). Here, NACE is presented, which is an open access web-oriented program that implements this method and allows the user to evaluate the intercompartmental efficiency of human molecular genetic networks. The method has been extended by a new feature that provides the evaluation of the tissue-specific efficiency of networks for more than 2800 anatomical structures. Such assessments are important in cases when molecular genetic pathways in different tissues proceed with the participation of various proteins with a number of intracellular localisations. For example, an analysis of KEGG pathways, conducted using the developed program, showed that the efficiencies of many KEGG pathways are tissue-specific. Analysis of efficiencies of regulatory pathways in the liver, linking proteins of the hepatitis C virus with human proteins involved in the KEGG apoptosis pathway, showed that intercompartmental efficiency might play an important role in host-pathogen interactions. Thus, the developed tool can be useful in the study of the effectiveness of functioning of various molecular genetic networks, including metabolic, regulatory, host-pathogen interactions and others taking into account tissue-specific gene expression. The tool is available via the following link: http://www-bionet.sscc.ru/nace/.

  10. [Molecular markers: an important tool in the diagnosis, treatment and epidemiology of invasive aspergillosis].

    PubMed

    Frías-de León, María Guadalupe; Acosta-Altamirano, Gustavo; Duarte-Escalante, Esperanza; Martínez-Hernández, José Enrique; Martínez-Rivera, María de Los Ángeles; Reyes-Montes, María Del Rocío

    2014-01-01

    Increase in the incidence of invasive aspergillosis has represented a difficult problem for management of patients with this infection due to its high rate of mortality, limited knowledge concerning its diagnosis, and therapeutic practice. The difficulty in management of patients with aspergillosis initiates with detection of the fungus in the specimens of immunosuppressed patients infected with Aspergillus fumigatus; in addition, difficulty exists in terms of the development of resistance to antifungals as a consequence of their indiscriminate use in prophylactic and therapeutic practice and to ignorance concerning the epidemiological data of aspergillosis. With the aim of resolving these problems, molecular markers is employed at present with specific and accurate results. However, in Mexico, the use of molecular markers has not yet been implemented in the routine of intrahospital laboratories; despite the fact that these molecular markers has been widely referred in the literature, it is necessary for it to validated and standardized to ensure that the results obtained in any laboratory would be reliable and comparable. In the present review, we present an update on the usefulness of molecular markers in accurate identification of A. fumigatus, detection of resistance to antifugal triazoles, and epidemiological studies for establishing the necessary measures for prevention and control of aspergillosis.

  11. Primer: genomic and proteomic tools for the molecular dissection of disease.

    PubMed

    Walker, Erin J; Siminovitch, Katherine A

    2007-10-01

    Completion of the Human Genome Project has been rapidly followed by the emergence of high-throughput technologies that combine automation, miniaturization, and many other strategies and tools to enable systematic surveys of genome composition and gene expression. Of particular relevance to the prevention and management of disease are technologies such as high-throughput DNA genotyping, microarray-based gene-expression profiling, and mass spectrometry-facilitated protein profiling--platforms that collectively support the comprehensive analysis of DNA sequence variants across the genome and the global gene and protein expression changes that distinguish health from disease. Now used extensively in all facets of biomedical investigation, genomic and proteomic tools are already beginning to pinpoint molecular variants that influence risk and outcome in common diseases, and to thereby inform and direct development of novel molecular biomarkers and drug targets. As evidenced by recent advances in DNA sequencing methods, continued improvements in the scope, power, and cost efficiency of genomic and proteomic technologies should ensure their capacity to provide the scale and depth of knowledge required for translating genome sequence information into major medical impact.

  12. Using molecular visualization to explore protein structure and function and enhance student facility with computational tools.

    PubMed

    Terrell, Cassidy R; Listenberger, Laura L

    2017-02-01

    Recognizing that undergraduate students can benefit from analysis of 3D protein structure and function, we have developed a multiweek, inquiry-based molecular visualization project for Biochemistry I students. This project uses a virtual model of cyclooxygenase-1 (COX-1) to guide students through multiple levels of protein structure analysis. The first assignment explores primary structure by generating and examining a protein sequence alignment. Subsequent assignments introduce 3D visualization software to explore secondary, tertiary, and quaternary structure. Students design an inhibitor, based on scrutiny of the enzyme active site, and evaluate the fit of the molecule using computed binding energies. In the last assignment, students introduce a point mutation to model the active site of the related COX-2 enzyme and analyze the impact of the mutation on inhibitor binding. With this project we aim to increase knowledge about, and confidence in using, online databases and computational tools. Here, we share results of our mixed methods pre- and postsurvey demonstrating student gains in knowledge about, and confidence using, online databases and computational tools. © 2017 by The International Union of Biochemistry and Molecular Biology, 2017.

  13. Rheological and molecular weight comparisons of approved hyaluronic acid products - preliminary standards for establishing class III medical device equivalence.

    PubMed

    Braithwaite, Gavin J C; Daley, Michael J; Toledo-Velasquez, David

    2016-01-01

    Hyaluronic acid of various molecular weights has been in use for the treatment of osteoarthritis knee pain for decades. Worldwide, these products are regulated as either as drugs or devices and in some countries as both. In the US, this class of products is regulated as Class III medical devices, which places specific regulatory requirements on developers of these materials under a Pre-Market Approval process, typically requiring data from prospective randomized controlled clinical studies. In 1984 pharmaceutical manufacturers became able to file an Abbreviated New Drug Application for approval of a generic drug, thus establishing standards for demonstrating equivalence to an existing chemical entity. Recently, the first biosimilar, or 'generic biologic', was approved. Biosimilars are biological products that are approved by the FDA because they are 'highly similar' to a reference product, and have been shown to have no clinically meaningful differences from the reference product. For devices, Class II medical devices have a pathway for declaring equivalence to an existing product by filing a 510 k application for FDA clearance. However, until recently no equivalent regulatory pathway was available to Class III devices. In this paper, we consider the critical mechanical performance parameters for intra-articular hyaluronic products to demonstrate indistinguishable characteristics. Analogous to the aforementioned pathways that allow for a demonstration of equivalence, we examine these parameters for an existing, marketed device and compare molecular weight and rheological properties of multiple batches of a similar product. We propose that this establishes a scientific rationale for establishing Class III medical device equivalence.

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

    PubMed

    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

  15. Malignant pleural mesothelioma and mesothelial hyperplasia: A new molecular tool for the differential diagnosis.

    PubMed

    Bruno, Rossella; Alì, Greta; Giannini, Riccardo; Proietti, Agnese; Lucchi, Marco; Chella, Antonio; Melfi, Franca; Mussi, Alfredo; Fontanini, Gabriella

    2017-01-10

    Malignant pleural mesothelioma (MPM) is a rare asbestos related cancer, aggressive and unresponsive to therapies. Histological examination of pleural lesions is the gold standard of MPM diagnosis, although it is sometimes hard to discriminate the epithelioid type of MPM from benign mesothelial hyperplasia (MH).This work aims to define a new molecular tool for the differential diagnosis of MPM, using the expression profile of 117 genes deregulated in this tumour.The gene expression analysis was performed by nanoString System on tumour tissues from 36 epithelioid MPM and 17 MH patients, and on 14 mesothelial pleural samples analysed in a blind way. Data analysis included raw nanoString data normalization, unsupervised cluster analysis by Pearson correlation, non-parametric Mann Whitney U-test and molecular classification by the Uncorrelated Shrunken Centroid (USC) Algorithm.The Mann-Whitney U-test found 35 genes upregulated and 31 downregulated in MPM. The unsupervised cluster analysis revealed two clusters, one composed only of MPM and one only of MH samples, thus revealing class-specific gene profiles. The Uncorrelated Shrunken Centroid algorithm identified two classifiers, one including 22 genes and the other 40 genes, able to properly classify all the samples as benign or malignant using gene expression data; both classifiers were also able to correctly determine, in a blind analysis, the diagnostic categories of all the 14 unknown samples.In conclusion we delineated a diagnostic tool combining molecular data (gene expression) and computational analysis (USC algorithm), which can be applied in the clinical practice for the differential diagnosis of MPM.

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

    PubMed Central

    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.

    2016-01-01

    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. PMID:27650866

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed

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

    2016-06-24

    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.

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

    PubMed Central

    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

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

    PubMed

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

    2016-02-16

    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.

  1. Fluorescent Resonance Energy Transfer: A Tool for Probing Molecular Cell-Biomaterial Interactions in Three Dimensions

    PubMed Central

    Huebsch, Nathaniel D.; Mooney, David J.

    2007-01-01

    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, a molecular fluorescence technique, 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 3D 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. PMID:17270268

  2. Paraholcoglossum and Tsiorchis, Two New Orchid Genera Established by Molecular and Morphological Analyses of the Holcoglossum Alliance

    PubMed Central

    Chen, Sing-Chi; Cai, Jing; Tsai, Wen-Chieh; Hsiao, Yu-Yun; Rao, Wen-Hui; Ma, Xue-Yong; Zhang, Guo-Qiang

    2011-01-01

    Background Holcoglossum is a small orchid genus of 12 species ranging from SW China to Thailand and NE India. Although molecular and morphological analyses have been performed to establish the phylogenetic relationships within this genus, the interspecific relations and its relations with allied genera, such as Rhynchostylis, Aerides and Vanda, remain unclear. Methodology/Principal Findings In addition to morphological analysis, maximum parsimony, maximum likelihood, and Bayesian inference analyses were performed based on fragments of the nuclear ITS and chloroplast trnL-F and matK genes of 31 taxa (15 Holcoglossum, 14 Aeridinae, 2 outgroups) representing all major clades of the Holcoglossum alliance. The results suggest that Holcoglossum is triphyletic, comprising three clades: the Holcoglossum clade, its sister clade, and a distant clade more closely related to Rhynchostylis, Aerides, and Vanda than to the Holcoglossum clade. The Holcoglossum clade is further divided into three subclades; the genetic distances between these three subclades also support this delimitation. The molecular conclusion is consistent with their distinct morphological characters. Conclusions We propose that the latter two clades comprise two new genera, Paraholcoglossum and Tsiorchis, and Holcoglossum clade divides into three sections. In addition, a new section, Holcoglossum sect. Nujiangensia, and a new species, Holcoglossum linearifolium, are proposed. Some new combinations are made, and a new scheme is provided for the classification of all species of Holcoglossum, Paraholcoglossum, and Tsiorchis. PMID:22016762

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

    PubMed

    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.

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

    PubMed

    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.

  5. CRISPR/Cas9: a powerful genetic engineering tool for establishing large animal models of neurodegenerative diseases.

    PubMed

    Tu, Zhuchi; Yang, Weili; Yan, Sen; Guo, Xiangyu; Li, Xiao-Jiang

    2015-08-04

    Animal models are extremely valuable to help us understand the pathogenesis of neurodegenerative disorders and to find treatments for them. Since large animals are more like humans than rodents, they make good models to identify the important pathological events that may be seen in humans but not in small animals; large animals are also very important for validating effective treatments or confirming therapeutic targets. Due to the lack of embryonic stem cell lines from large animals, it has been difficult to use traditional gene targeting technology to establish large animal models of neurodegenerative diseases. Recently, CRISPR/Cas9 was used successfully to genetically modify genomes in various species. Here we discuss the use of CRISPR/Cas9 technology to establish large animal models that can more faithfully mimic human neurodegenerative diseases.

  6. Implementation of new tools in molecular epidemiology studies of Echinococcus granulosus sensu lato in South America.

    PubMed

    Avila, Héctor G; Santos, Guilherme B; Cucher, Marcela A; Macchiaroli, Natalia; Pérez, Matías G; Baldi, Germán; Jensen, Oscar; Pérez, Verónica; López, Raúl; Negro, Perla; Scialfa, Exequiel; Zaha, Arnaldo; Ferreira, Henrique B; Rosenzvit, Mara; Kamenetzky, Laura

    2017-06-01

    The aim of this work was to determine Echinococcus granulosus sensu lato species and genotypes in intermediate and definitive hosts and in human isolates from endemic regions of Argentina and Brazil including those where no molecular data is available by a combination of classical and alternative molecular tools. A total of 227 samples were isolated from humans, natural intermediate and definitive hosts. Amplification of cytochrome c oxidase subunit I gene fragment was performed and a combination of AluI digestion assay, High Resolution Melting analysis (HRM) assay and DNA sequencing was implemented for Echinococcus species/genotype determination. E. granulosus sensu stricto (G1) was found in sheep (n=35), cattle (n=67) and dogs (n=5); E. ortleppi (G5) in humans (n=3) and cattle (n=108); E. canadensis (G6) in humans (n=2) and E. canadensis (G7) in pigs (n=7). We reported for the first time the presence of E. ortleppi (G5) and E. canadensis (G6) in humans from San Juan and Catamarca Argentinean provinces and E. canadensis (G7) in pigs from Cordoba Argentinean province. In this work, we widened molecular epidemiology studies of E. granulosus s. l. in South America by analyzing several isolates from definitive and intermediate hosts, including humans from endemic regions were such information was scarce or unavailable. The presence of different species/genotypes in the same region and host species reinforce the need of rapid and specific techniques for accurate determination of Echinococcus species such as the ones proposed in this work.

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

    PubMed Central

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

    2016-01-01

    With the advance of next generation sequencing techniques, whole genome sequencing (WGS) is expected to become the optimal method for molecular subtyping of bacterial isolates. To use WGS as a general subtyping method for disease outbreak investigation and surveillance, the layout of WGS-based typing must be comparable among laboratories. Whole genome multilocus sequence typing (wgMLST) is an approach that achieves this requirement. To apply wgMLST as a standard subtyping approach, a pan-genome allele database (PGAdb) for the population of a bacterial organism must first be established. We present a free web service tool, PGAdb-builder (http://wgmlstdb.imst.nsysu.edu.tw), for the construction of bacterial PGAdb. The effectiveness of PGAdb-builder was tested by constructing a pan-genome allele database for Salmonella enterica serovar Typhimurium, with the database being applied to create a wgMLST tree for a panel of epidemiologically well-characterized S. Typhimurium isolates. The performance of the wgMLST-based approach was as high as that of the SNP-based approach in Leekitcharoenphon’s study used for discerning among epidemiologically related and non-related isolates. PMID:27824078

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

    PubMed

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

    2016-03-22

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

  9. Transmission of lungworms of harbour porpoises and harbour seals: molecular tools determine potential vertebrate intermediate hosts.

    PubMed

    Lehnert, K; von Samson-Himmelstjerna, G; Schaudien, D; Bleidorn, C; Wohlsein, P; Siebert, U

    2010-06-01

    Harbour porpoises (Phocoena phocoena) and harbour seals (Phoca vitulina) from German waters are infected by six species of lungworms (Metastrongyloidea). These nematodes parasitise the respiratory tract, are pathogenic and often cause secondary bacterial infections. In spite of their clinical and epidemiological significance, the life cycle and biology of lungworms in the marine environment is still largely unknown. Regions of ribosomal DNA (ITS-2) of all lungworms parasitising harbour porpoises and harbour seals in German waters were sequenced to characterise and compare the different species. The phylogenetic relationship among the lungworm species was analysed by means of their ITS-2 nucleotide sequences and the species-specific traits of the ITS-2 were used to screen wild fish as possible intermediate hosts for larval lungworms. Molecular markers were developed to identify larval nematodes via in-situ hybridisation of tissues of harbour porpoise and harbour seal prey fish. Potential wild intermediate fish hosts from the North Sea were dissected and found to harbour larval nematodes. Histological examination and in-situ hybridisation of tissue samples from these fish showed lungworm larvae within the intestinal wall. Based on larval ITS-2 nucleotide sequences, larval nematodes were identified as Pseudalius inflexus and Parafilaroides gymnurus. Turbot (Psetta maxima) bred and raised in captivity were experimentally infected with live L1s of Otostrongylus circumlitus and ensheathed larvae were recovered from the gastrointestinal tract of turbot and identified using molecular tools. Our results show that fish intermediate hosts play a role in the transmission of metastrongyloid nematodes of harbour porpoises and harbour seals.

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

    NASA Astrophysics Data System (ADS)

    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. An air quality management system as a tool for establishing a SO 2- and NOx-policy

    NASA Astrophysics Data System (ADS)

    Bovenkerk, M.; Builtjes, P. J. H.; Zwerver, S.

    A description is given of the development and use of an Air Quality Management System (AQMS) directed to the support of policy decisions made with respect to the conservation and improvement of clean air in the Netherlands. The AQMS consists of three separate modules oriented to economy, transmission and impact assessment. Application of the AQMS to SO 2 has led to the construction of an environmental decision scheme, in which maximum acceptable emission levels are given as a function of the primary and secondary SO 2-air quality standard, the S import-export balance and acidification. Together with information on the socio-economic impacts and the energy options this formed the basis for the political decision to limit future SO 2-emissions in the Netherlands to a value not higher than 500 × 10 6 kg y -1, in fact to establish a ceiling value for the emissions of SO 2. For NOx the AQMS is still under development, so at the moment it is not possible to formulate a complete NOx-environmental decision scheme. Up till now the emphasis has been on the development of the transmission module of the AQMS for NOx, i.e. the impact of domestic and foreign emissions. The results of this module are presented in the paper. The (partly preliminary) results of the AQMS-calculations point out the importance of long-range transport of NOx and photochemical precursors and products for the countrywide NO 2-pattern. The results emphasize the need for the abatement of NOx [and especially hydrocarbons (HC)] on a European scale. Also abatement of automobile exhaust is needed in order to prevent violation of the NO 2-standard at sites with high circulation of traffic.

  12. Optimization of preservation and processing of sea anemones for microbial community analysis using molecular tools

    PubMed Central

    Rocha, Joana; Coelho, Francisco J. R. C.; Peixe, Luísa; Gomes, Newton C. M.; Calado, Ricardo

    2014-01-01

    For several years, knowledge on the microbiome associated with marine invertebrates was impaired by the challenges associated with the characterization of bacterial communities. With the advent of culture independent molecular tools it is possible to gain new insights on the diversity and richness of microorganisms associated with marine invertebrates. In the present study, we evaluated if different preservation and processing methodologies (prior to DNA extraction) can affect the bacterial diversity retrieved from snakelocks anemone Anemonia viridis. Denaturing gradient gel electrophoresis (DGGE) community fingerprints were used as proxy to determine the bacterial diversity retrieved (H′). Statistical analyses indicated that preservation significantly affects H′. The best approach to preserve and process A. viridis biomass for bacterial community fingerprint analysis was flash freezing in liquid nitrogen (preservation) followed by the use of a mechanical homogenizer (process), as it consistently yielded higher H′. Alternatively, biomass samples can be processed fresh followed by cell lyses using a mechanical homogenizer or mortar & pestle. The suitability of employing these two alternative procedures was further reinforced by the quantification of the 16S rRNA gene; no significant differences were recorded when comparing these two approaches and the use of liquid nitrogen followed by processing with a mechanical homogenizer. PMID:25384534

  13. UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy.

    PubMed

    Smith, Tom; Heger, Andreas; Sudbery, Ian

    2017-03-01

    Unique Molecular Identifiers (UMIs) are random oligonucleotide barcodes that are increasingly used in high-throughput sequencing experiments. Through a UMI, identical copies arising from distinct molecules can be distinguished from those arising through PCR amplification of the same molecule. However, bioinformatic methods to leverage the information from UMIs have yet to be formalized. In particular, sequencing errors in the UMI sequence are often ignored or else resolved in an ad hoc manner. We show that errors in the UMI sequence are common and introduce network-based methods to account for these errors when identifying PCR duplicates. Using these methods, we demonstrate improved quantification accuracy both under simulated conditions and real iCLIP and single-cell RNA-seq data sets. Reproducibility between iCLIP replicates and single-cell RNA-seq clustering are both improved using our proposed network-based method, demonstrating the value of properly accounting for errors in UMIs. These methods are implemented in the open source UMI-tools software package.

  14. UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy

    PubMed Central

    2017-01-01

    Unique Molecular Identifiers (UMIs) are random oligonucleotide barcodes that are increasingly used in high-throughput sequencing experiments. Through a UMI, identical copies arising from distinct molecules can be distinguished from those arising through PCR amplification of the same molecule. However, bioinformatic methods to leverage the information from UMIs have yet to be formalized. In particular, sequencing errors in the UMI sequence are often ignored or else resolved in an ad hoc manner. We show that errors in the UMI sequence are common and introduce network-based methods to account for these errors when identifying PCR duplicates. Using these methods, we demonstrate improved quantification accuracy both under simulated conditions and real iCLIP and single-cell RNA-seq data sets. Reproducibility between iCLIP replicates and single-cell RNA-seq clustering are both improved using our proposed network-based method, demonstrating the value of properly accounting for errors in UMIs. These methods are implemented in the open source UMI-tools software package. PMID:28100584

  15. [Use of molecular typing tools for the study of hospital outbreaks of candidemia].

    PubMed

    Marcos-Zambrano, Laura Judith; Escribano, Pilar; Bouza, Emilio; Guinea, Jesús

    2014-01-01

    Candidemia is an infectious complication mainly affecting hospitalized patients, particularly those admitted to intensive care units. Patient mortality can reach up to 40%. Candidemia is typically nosocomially-acquired, and horizontal transmission of Candida spp. can lead to the presence of outbreaks of candidemia. Genotyping of isolates of Candida causing candidemia can help us to understand the source of the infection, detect the hospital wards with active Candida spp. transmission and, consequently, improve the prevention of the infection. Several genotyping tools have been used for the molecular characterization of Candida isolates involved in outbreaks of candidemia. Genotyping procedures based on microsatellites are reproducible and show a high discriminatory power. Microsatellites are recommended for the study of outbreaks of candidemia. In most hospital outbreaks of candidemia, patients admitted to intensive care units are involved, mostly neonatal patients. The role of genotyping Candida isolates causing candidemia for the study of nosocomial outbreaks of candidemia is reviewed, as well as the patients more commonly affected by epidemic strains.

  16. Malaria parasite mutants with altered erythrocyte permeability: a new drug resistance mechanism and important molecular tool

    PubMed Central

    Hill, David A; Desai, Sanjay A

    2010-01-01

    Erythrocytes infected with plasmodia, including those that cause human malaria, have increased permeability to a diverse collection of organic and inorganic solutes. While these increases have been known for decades, their mechanistic basis was unclear until electrophysiological studies revealed flux through one or more ion channels on the infected erythrocyte membrane. Current debates have centered on the number of distinct ion channels, which channels mediate the transport of each solute and whether the channels represent parasite-encoded proteins or human channels activated after infection. This article reviews the identification of the plasmodial surface anion channel and other proposed channels with an emphasis on two distinct channel mutants generated through in vitro selection. These mutants implicate parasite genetic elements in the parasite-induced permeability, reveal an important new antimalarial drug resistance mechanism and provide tools for molecular studies. We also critically examine the technical issues relevant to the detection of ion channels by electrophysiological methods; these technical considerations have general applicability for interpreting studies of various ion channels proposed for the infected erythrocyte membrane. PMID:20020831

  17. Molecular markers and imaging tools to identify malignant potential in Barrett's esophagus

    PubMed Central

    Bennett, Michael; Mashimo, Hiroshi

    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 surveillance. 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 high-risk lesions in Barrett’s esophagus. PMID:25400987

  18. Single-stranded DNA phages: from early molecular biology tools to recent revolutions in environmental microbiology.

    PubMed

    Székely, Anna J; Breitbart, Mya

    2016-03-01

    Single-stranded DNA (ssDNA) phages are profoundly different from tailed phages in many aspects including the nature and size of their genome, virion size and morphology, mutation rate, involvement in horizontal gene transfer, infection dynamics and cell lysis mechanisms. Despite the importance of ssDNA phages as molecular biology tools and model systems, the environmental distribution and ecological roles of these phages have been largely unexplored. Viral metagenomics and other culture-independent viral diversity studies have recently challenged the perspective of tailed, double-stranded DNA (dsDNA) phages, dominance by demonstrating the prevalence of ssDNA phages in diverse habitats. However, the differences between ssDNA and dsDNA phages also substantially limit the efficacy of simultaneously assessing the abundance and diversity of these two phage groups. Here we provide an overview of the major differences between ssDNA and tailed dsDNA phages that may influence their effects on bacterial communities. Furthermore, through the analysis of 181 published metaviromes we demonstrate the environmental distribution of ssDNA phages and present an analysis of the methodological biases that distort their study through metagenomics.

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

    PubMed

    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.

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

    NASA Astrophysics Data System (ADS)

    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.

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

    PubMed

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

    2014-01-01

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

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

    PubMed Central

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

    2015-01-01

    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. PMID:26006124

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

    PubMed

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

    2015-05-22

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

  4. Molecular Mechanisms of Chemosensory Receptors, Signal Transducers, and the Activation of Gene Expression Controlling Establishment of a Marine Symbiosis

    DTIC Science & Technology

    1989-07-01

    Our most significant advance in this area this year has been in the molecular cloning and analysis of cDNAs corresponding to the novel serine protease...Biological Chemistry (in preparation). 4. Groppe, J. and D.E. Morse. 1989. Molecular cloning of novel serine protease cDNAs from abalone. For: Proc...phycoerythrin gene. (Poster -- d Abstract) Northwest Algal Symposium, Seattle, WA. 8. Groppe, J.C. and D.E. Morse. 1989. Molecular cloning of novel serine

  5. Gene profiling approach to establish the molecular bases for partial versus full activation of naïve CD8 T lymphocytes.

    PubMed

    Verdeil, Gréory; Puthier, Denis; Nguyen, Catherine; Schmitt-Verhulst, Anne-Marie; Auphan-Anezin, Nathalie

    2002-12-01

    When initial antigen encounter involves optimal antigenic and costimulatory stimuli, naïve CD8 T cells undergo a developmental program that leads to their activation, expansion and acquisition of effector functions (including production of IL-2, IFNgamma and expression of cytolytic effector molecules). A subset of the activated CD8 T cells thrives as long-lived memory cells. Encounter of tissue-associated, and in particular tumor-associated antigen, may often be suboptimal in terms of antigenicity and costimulation, however. We previously developed a model of naïve CD8 T cells from transgenic mice expressing an alloreactive TCR for which a mutant alloantigen behaved as a partial agonist, inducing only some of the effector functions induced by the native alloantigen. To ascertain the molecular bases for the establishment of divergent fates within the same naïve CD8 T cells, we have used cDNA microarrays to monitor sequential gene expression patterns in conditions of full or partial response of these naïve CD8 T cells. Of the 5000 different genes monitored on the array, 18% showed changes in expression in activated versus naïve CD8 T cells, independent of whether stimulation was with full or partial agonist. These included antigen-induced upregulated as well as downregulated genes. Clusters of genes that were differentially expressed were also identified, being either (i) weakly versus strongly, or (ii) transiently versus stably expressed in response to partial and full agonist, respectively. They included (i) genes encoding costimulatory molecules and (ii) genes controlling cytolytic function, cytokine production, and chemokines. Therefore, the cDNA microarray approach was a sensitive tool to provide an exhaustive picture of T cell activation as it could discriminate quantitative, qualitative and dynamic differences in mRNA expression profiles between fully or partially activated T cells.

  6. Assessment of chloroethene biodegradation in the subsurface by microbiological, molecular and isotopic tools

    NASA Astrophysics Data System (ADS)

    Schmidt, K. R.; Kranzioch, I.; Heidinger, M.; Ertl, S.; Tiehm, A.

    2012-04-01

    methods is continuously increasing. For example, microbiological and molecular tools showed the presence and activity of halorespiring bacteria in sediment samples of the Yangtze river, China. PCR-detection demonstrated the presence of five different halorespiring bacterial groups as well as of four different dechlorinating enzymes of Dehalococcoides. In conclusion, our study demonstrates that (i) multiple lines of evidence approaches result in a profound understanding of the biodegradation processes occurring in the field, (ii) stable isotope fractionation is suitable for assessing and quantifying anaerobic and aerobic chloroethene degradation and (iii) detection and quantification of dechlorinating bacteria and enzymes by PCR methods provide more insight into biodegradation processes. Acknowledgement The authors gratefully acknowledge financial support by the German Ministry of Education and Research (BMBF, grant no 02WN0446, 02WN0447 and 02WT1130), the German Ministry of Economics and Technology (BMWi, grant no KF2265705AK9 and KF2285302AK9) and the federal state of Rhineland-Palatinate. We thank all project partners for fruitful cooperation.

  7. Molecular Mechanisms of Chemosensory Receptors, Signal Transducers, and the Activation of Gene Expression Controlling Establishment of a Marine Symbiosis

    DTIC Science & Technology

    1990-10-31

    filed.. ........... 0oDt . PUBLICATIONS AND REPORTS: Publications and Manuscripts: I. Groppe, J. and D.E. Morse. 1989. Molecular cloning of novel...Morse. 1989. Molecular cloning of novel serine protease cDNAs from abalone. (Abstract) Proc. First Intl. Symp. Marine Biotechnology, Tokyo. 6. Roell

  8. Establishing Tools for Computing Hybrids

    DTIC Science & Technology

    2006-10-01

    amorphous/#research. Link working as of August 14, 2006 3. Birge, Robert . 1997. Protein-Based Branched-Photocycle Three-Dimensional Optical...Memories. Final Report RL-TR-96-274, April, DTIC Accession Number ADA327063. 4. Birge, Robert . 1997. Branched-Photocycle Three-Dimensional Memory...Final Report RL-TR-97-194, October, DTIC Accession Number ADA339787. 5. Birge, Robert , 2003. Prototype Protein-Based Three-Dimensional Memory. Final

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

    PubMed

    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.

  10. Integrative genomics--a basic and essential tool for the development of molecular medicine.

    PubMed

    Ostrowski, Jerzy

    2008-01-01

    Understanding the molecular mechanisms of disease requires the introduction of molecular diagnostics into medical practice. Current medicine employs only elements of molecular diagnostics, and usually on the scale of single genes. Medicine in the post-genomic era will utilize thousands of molecular markers associated with disease that are provided by high-throughput sequencing and functional genomic, proteomic and metabolomic studies. Such a spectrum of techniques will link clinical medicine based on molecularly oriented diagnostics with the prediction and prevention of disease. To achieve this task, large-scale and genome-wide biological and medical data must be combined with biostatistical analyses and bioinformatic modeling of biological systems. The collecting, cataloging and comparison of data from molecular studies and the subsequent development of conclusions create the fundamentals of systems biology. This highly complex analytical process reflects a new scientific paradigm called integrative genomics.

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

    PubMed

    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).

  12. Turbulence in molecular clouds - A new diagnostic tool to probe their origin

    NASA Technical Reports Server (NTRS)

    Canuto, V. M.; Battaglia, A.

    1985-01-01

    A method is presented to uncover the instability responsible for the type of turbulence observed in molecular clouds and the value of the physical parameters of the 'placental medium' from which turbulence originated. The method utilizes the observational relation between velocities and sizes of molecular clouds, together with a recent model for large-scale turbulence (constructed by Canuto and Goldman, 1985).

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

    USGS Publications Warehouse

    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

  14. Molecular Tools for Plant Protection, True-to-Name Verification and Parentage Analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    DNA-based tools are available to improve ornamental plant cultivars through accelerated breeding and other practical applications. Highlights include examples where DNA fingerprints identified mislabeled cultivars, verified the renaming of cultivars and demonstrated some similar-looking cultivars ar...

  15. Sex chromosomal abnormalities associated with equine infertility: validation of a simple molecular screening tool in the Purebred Spanish Horse.

    PubMed

    Anaya, G; Molina, A; Valera, M; Moreno-Millán, M; Azor, P; Peral-García, P; Demyda-Peyrás, S

    2017-02-22

    Chromosomal abnormalities in the sex chromosome pair (ECAX and ECAY) are widely associated with reproductive problems in horses. However, a large proportion of these abnormalities remains undiagnosed due to the lack of an affordable diagnostic tool that allows for avoiding karyotyping tests. Hereby, we developed an STR (single-tandem-repeat)-based molecular method to determine the presence of the main sex chromosomal abnormalities in horses in a fast, cheap and reliable way. The frequency of five ECAX-linked (LEX026, LEX003, TKY38, TKY270 and UCDEQ502) and two ECAY-linked (EcaYH12 and SRY) markers was characterized in 261 Purebred Spanish Horses to determine the efficiency of the methodology developed to be used as a chromosomal diagnostic tool. All the microsatellites analyzed were highly polymorphic, with a sizeable number of alleles (polymorphic information content > 0.5). Based on this variability, the methodology showed 100% sensitivity and 99.82% specificity to detect the most important sex chromosomal abnormalities reported in horses (chimerism, Turner's syndrome and sex reversal syndromes). The method was also validated with 100% efficiency in 10 individuals previously diagnosed as chromosomally aberrant. This STR screening panel is an efficient and reliable molecular-cytogenetic tool for the early detection of sex chromosomal abnormalities in equines that could be included in breeding programs to save money, effort and time of veterinary practitioners and breeders.

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

    PubMed

    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.

  17. Development of molecular tools for characterization and genetic diversity analysis in Tunisian fig (Ficus carica) cultivars.

    PubMed

    Chatti, Khaled; Baraket, Ghada; Ben Abdelkrim, Ahmed; Saddoud, Olfa; Mars, Messaoud; Trifi, Mokhtar; Salhi Hannachi, Amel

    2010-10-01

    Fig, Ficus carica L., is a useful genetic resource for commercial cultivation. In this study, RAPD (60), ISSR (48), RAMPO (63), and SSR (34) markers were compared to detect polymorphism and to establish genetic relationships among Tunisian fig tree cultivars. The statistical procedures conducted on the combined data show considerable genetic diversity, and the tested markers discriminated all fig genotypes studied. The identification key established on the basis of SSR permitted the unambiguous discrimination of cultivars and confirmed the reliability of SSR for fingerprinting fig genotypes. The study findings are discussed in relation to the establishment of a national reference collection that will aid in the conservation of Tunisian fig resources.

  18. Application of Campylobacter molecular classification and typing techniques in veterinary medicine: old-established methods and new perspectives.

    PubMed

    Laturnus, Claudia; Wieler, Lothar H

    2007-01-01

    In this review the application and usefulness of Campylobacter genotypical classification and typing in veterinary medicine will be discussed.While there is a large area of overlapping applications between the veterinary and the medical field, several differences exist, as the spectrum of veterinary pathogens is different from the human and contaminated food of healthy animal origin may cause disease in man. In general, genotyping in the veterinary field can be applied in three different areas: (a) purely diagnostic purposes for classification of Campylobacter species and subspecies, (b) typing methods useful for monitoring or surveillance of animals as well as food products of animal origin, and (c) typing methods that can be applied during outbreaks and for source tracing. In addition, typing methods applied in areas (b) and (c) should be distinguished in regard to local short-term and global long-term epidemiology, respectively. While a whole plethora of discriminative typing methods are available, classification tools of certain species and subspecies are still missing. Perspectively, as the genomes of many relevant Campylobacter species have now been sequenced, this will help to identify several species specific loci, the products of which should be available to develop easy and fast applicable diagnostic tools. Global cooperation, sharing of strains and databases should close the currently existing gaps in Campylobacter identification tools.

  19. Transposable elements and two other molecular markers as typing tools for the genus Paracoccidioides.

    PubMed

    Alves, Fernanda Lourenço; Ribeiro, Mariceli Araújo; Hahn, Rosane Christine; de Melo Teixeira, Marcus; de Camargo, Zoilo Pires; Cisalpino, Patrícia Silva; Marini, Marjorie Mendes

    2015-02-01

    Studies comparing Paracoccidioides brasiliensis and Paracoccidioides lutzii have shown that these fungi have significant genomic differences that may have implications in the clinical manifestation, diagnosis, and treatment of paracoccidioidomycosis caused by them. Thus, molecular typing methods are required that can distinguish between various species of Paracoccidioides. The aim of this study was to explore the potential use as molecular markers of the transposable elements Trem A-H recently identified and characterized in the genus Paracoccidioides as a means of differentiating the species. We take advantage of the abundance and distribution of these transposons in the Paracoccidioides genomes to develop a simple and highly reproducible polymerase chain reaction (PCR)-based technique. Furthermore we compare the performance of this test with two other molecular markers already in use to identify these fungi.

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

    PubMed Central

    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. PMID:27390530

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

    PubMed Central

    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

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

    PubMed

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

    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.

  3. Molecular imprinting: a tool of modern chemistry for the preparation of highly selective monolithic sorbents

    NASA Astrophysics Data System (ADS)

    Vlakh, E. G.; Korzhikov, V. A.; Hubina, A. V.; Tennikova, T. B.

    2015-09-01

    Characteristic features of the synthesis of molecularly imprinted polymer systems used as sorbents for separation of complex mixtures into components are discussed. The data about the molecules imprinted in monoliths of various natures and shapes are integrated. Examples of application of new-generation separating media are discussed. Data on the utilization of the molecular imprinting principle for the fabrication of supermacroporous monolithic cryogels specific to particular molecules, which is important for the design of smart biomaterials, are analyzed. The bibliography includes 293 references.

  4. The supersonic molecular beam injector as a reliable tool for plasma fueling and physics experiment on HL-2A.

    PubMed

    Chen, C Y; Yu, D L; Feng, B B; Yao, L H; Song, X M; Zang, L G; Gao, X Y; Yang, Q W; Duan, X R

    2016-09-01

    On HL-2A tokamak, supersonic molecular beam injection (SMBI) has been developed as a routine refueling method. The key components of the system are an electromagnetic valve and a conic nozzle. The valve and conic nozzle are assembled to compose the simplified Laval nozzle for generating the pulsed beam. The appurtenance of the system includes the cooling system serving the cooled SMBI generation and the in situ calibration component for quantitative injection. Compared with the conventional gas puffing, the SMBI features prompt response and larger fueling flux. These merits devote the SMBI a good fueling method, an excellent plasma density feedback control tool, and an edge localized mode mitigation resource.

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

    PubMed

    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.

  6. The supersonic molecular beam injector as a reliable tool for plasma fueling and physics experiment on HL-2A

    NASA Astrophysics Data System (ADS)

    Chen, C. Y.; Yu, D. L.; Feng, B. B.; Yao, L. H.; Song, X. M.; Zang, L. G.; Gao, X. Y.; Yang, Q. W.; Duan, X. R.

    2016-09-01

    On HL-2A tokamak, supersonic molecular beam injection (SMBI) has been developed as a routine refueling method. The key components of the system are an electromagnetic valve and a conic nozzle. The valve and conic nozzle are assembled to compose the simplified Laval nozzle for generating the pulsed beam. The appurtenance of the system includes the cooling system serving the cooled SMBI generation and the in situ calibration component for quantitative injection. Compared with the conventional gas puffing, the SMBI features prompt response and larger fueling flux. These merits devote the SMBI a good fueling method, an excellent plasma density feedback control tool, and an edge localized mode mitigation resource.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

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

    NASA Astrophysics Data System (ADS)

    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.

  9. Spatiotemporal Fluctuation Analysis: A Powerful Tool for the Future Nanoscopy of Molecular Processes.

    PubMed

    Di Rienzo, Carmine; Gratton, Enrico; Beltram, Fabio; Cardarelli, Francesco

    2016-08-23

    The enormous wealth of information available today from optical microscopy measurements on living samples is often underexploited. We argue that spatiotemporal analysis of fluorescence fluctuations using multiple detection channels can enhance the performance of current nanoscopy methods and provide further insight into dynamic molecular processes of high biological relevance.

  10. A new molecular diagnostic tool for quantitatively detecting and genotyping “Candidatus Liberibacter species”

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A new molecular diagnostic method was developed for quantitative detection of “Candidatus Liberibacter” species associated with citrus Huanglongbing (“Ca. Liberibacter asiaticus”, “Ca. Liberibacter africanus” and “Ca. Liberibacter americanus”) and potato zebra chip disorder (“Ca. Liberibacter solana...

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

    NASA Astrophysics Data System (ADS)

    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.

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

    ERIC Educational Resources Information Center

    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…

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

    ERIC Educational Resources Information Center

    Crouch, R. David; And Others

    1996-01-01

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

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

    ERIC Educational Resources Information Center

    Silva, Alcino J.; Müller, Klaus-Robert

    2015-01-01

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

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

    PubMed

    Serpente, Norberto

    2013-02-01

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

  16. Establishment of an in silico phospholipidosis prediction method using descriptors related to molecular interactions causing phospholipid-compound complex formation.

    PubMed

    Haranosono, Yu; Nemoto, Shingo; Kurata, Masaaki; Sakaki, Hideyuki

    2016-04-01

    Although phospholipidosis (PLD) often affects drug development, there is no convenient in vitro or in vivo test system for PLD detection. In this study, we developed an in silico PLD prediction method based on the PLD-inducing mechanism. We focused on phospholipid (PL)-compound complex formation, which inhibits PL degradation by phospholipase. Thus, we used some molecular interactions, such as electrostatic interactions, hydrophobic interactions, and intermolecular forces, between PL and compounds as descriptors. First, we performed descriptor screening for intermolecular force and then developed a new in silico PLD prediction using descriptors related to molecular interactions. Based on the screening, we identified molecular refraction (MR) as a descriptor of intermolecular force. It is known that ClogP and most-basic pKa can be used for PLD prediction. Thereby, we developed an in silico prediction method using ClogP, most-basic pKa, and MR, which were related to hydrophobic interactions, electrostatic interactions, and intermolecular forces. In addition, a resampling method was used to determine the cut-off values for each descriptor. We obtained good results for 77 compounds as follows: sensitivity = 95.8%, specificity = 75.9%, and concordance = 88.3%. Although there is a concern regarding false-negative compounds for pKa calculations, this predictive ability will be adequate for PLD screening. In conclusion, the mechanism-based in silico PLD prediction method provided good prediction ability, and this method will be useful for evaluating the potential of drugs to cause PLD, particularly in the early stage of drug development, because this method only requires knowledge of the chemical structure.

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

    DTIC Science & Technology

    2012-09-10

    species they are not readily available for algae that are being identified as potential biofuel production strains . Our work was focused on developing...the genetic tools required to enable green algae to become efficient biofuel production strains . Being able to efficiently apply genetic...transformation techniques to green algae species will allow us to generate strains that contain ideal traits for maximally efficient fuel production, and will

  18. Surface-enhanced Raman spectroscopy as a tool for characterizing nanostructures containing molecular components

    NASA Astrophysics Data System (ADS)

    Xu, Ke; Abell, Justin; Zhao, Yiping; Qian, Jun; Brenneman, Kimber; Meshik, Xenia; Dutta, Mitra; Stroscio, Michael

    2012-12-01

    Raman spectroscopy, which is based on inelastic scattering of light that interacts with phonons or molecular vibrations in the nanostructure, has been widely used to identify chemical and biological molecules. Surface-Enhanced Raman Spectroscopy (SERS) greatly enhanced the sensitivity of conventional Raman spectroscopy by a factor of >106 through the use of a plasmon-generating substrate [1, 2]. This study investigated the use of Raman spectroscopy/SERS to verify that synthesized nanostructures contain active molecular components critical to their functioning. In particular, this study uses SERS to identify the signature spectrum of Methylene Blue (MB) and uses standard Raman spectroscopy to verify the fictionalization of a DNA aptamer terminated with MB.

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

    PubMed

    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.

  20. Chromatibody, a novel non-invasive molecular tool to explore and manipulate chromatin in living cells

    PubMed Central

    Jullien, Denis; Vignard, Julien; Fedor, Yoann; Béry, Nicolas; Olichon, Aurélien; Crozatier, Michèle; Erard, Monique; Cassard, Hervé; Ducommun, Bernard; Salles, Bernard

    2016-01-01

    ABSTRACT Chromatin function is involved in many cellular processes, its visualization or modification being essential in many developmental or cellular studies. Here, we present the characterization of chromatibody, a chromatin-binding single-domain, and explore its use in living cells. This non-intercalating tool specifically binds the heterodimer of H2A–H2B histones and displays a versatile reactivity, specifically labeling chromatin from yeast to mammals. We show that this genetically encoded probe, when fused to fluorescent proteins, allows non-invasive real-time chromatin imaging. Chromatibody is a dynamic chromatin probe that can be modulated. Finally, chromatibody is an efficient tool to target an enzymatic activity to the nucleosome, such as the DNA damage-dependent H2A ubiquitylation, which can modify this epigenetic mark at the scale of the genome and result in DNA damage signaling and repair defects. Taken together, these results identify chromatibody as a universal non-invasive tool for either in vivo chromatin imaging or to manipulate the chromatin landscape. PMID:27206857

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

    DTIC Science & Technology

    2014-02-01

    not well understood, but several studies have linked E. coli from retail meat—particularly poultry —to extraintestinal human infections [16, 17...sequencing data analysis To validate our assays we used a collection of 174 E. coli isolates; 133 were recovered from retail poultry products and 41 were...isolates from retail poultry products met the molecular definition of ExPEC. Further studies must be conducted to quantify the risk of colonization and

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

    NASA Astrophysics Data System (ADS)

    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

  3. Molecular imprinting of proteins emerging as a tool for protein recognition.

    PubMed

    Takeuchi, Toshifumi; Hishiya, Takayuki

    2008-07-21

    This article gives the recent developments in molecular imprinting for proteins. Currently bio-macromolecules such as antibodies and enzymes are mainly employed for protein recognition purposes. However, such bio-macromolecules are sometimes difficult to find and/or produce, therefore, receptor-like synthetic materials such as protein-imprinted polymers have been intensively studied as substitutes for natural receptors. Recent advances in protein imprinting shown here demonstrate the possibility of this technique as a future technology of protein recognition.

  4. phenix.mr_rosetta: a new tool for difficult molecular replacement problems

    SciTech Connect

    Terwilliger, Thomas C; Read, Randy; De Maio, Frank; Baker, David

    2011-01-12

    The PHENIX development team is working with the Baker laboratory at the University of Washington to combine the power of Rosetta structure modeling with PHENIX automated molecular replacement (MR), model-building, density modification, and refinement. The basic idea is to find MR solutions with phenix. automr, rebuild them with Rosetta, including electron density map information, then rebuild those models with phenix. autobuild. The combination of Rosetta rebuilding and phenix rebuilding is the key part of this method. MR solutions are found with phenix. automr (Phaser), scored with LLG (optionally following Rosetta relaxation), the best solutions are picked and rebuilt with Rosetta including map information, the resulting models are scored with Rosetta, and then rescored with LLG, and the top models are rebuilt with phenix. autobuild. It can be very useful for cases where the search model used in molecular replacement is slightly too distant to rebuild successfully with phenix. autobuild. It can also be useful in cases where the model is too distant to even find a molecular replacement solution, and prerefinement with Rosetta can yield an improved search model.

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

    PubMed Central

    Jaeger, Lauren Hubert; Iñiguez, Alena Mayo

    2014-01-01

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

  6. Molecularly imprinted polymers: an analytical tool for the determination of benzimidazole compounds in water samples.

    PubMed

    Cacho, Carmen; Turiel, Esther; Pérez-Conde, Concepción

    2009-05-15

    Molecularly imprinted polymers (MIPs) for benzimidazole compounds have been synthesized by precipitation polymerization using thiabendazole (TBZ) as template, methacrylic acid as functional monomer, ethyleneglycol dimethacrylate (EDMA) and divinylbenzene (DVB) as cross-linkers and a mixture of acetonitrile and toluene as porogen. The experiments carried out by molecularly imprinted solid phase extraction (MISPE) in cartridges demonstrated the imprint effect in both imprinted polymers. MIP-DVB enabled a much higher breakthrough volume than MIP-EDMA, and thus was selected for further experiments. The ability of this MIP for the selective recognition of other benzimidazole compounds (albendazole, benomyl, carbendazim, fenbendazole, flubendazole and fuberidazole) was evaluated. The obtained results revealed the high selectivity of the imprinted polymer towards all the selected benzimidazole compounds. An off-line analytical methodology based on a MISPE procedure has been developed for the determination of benzimidazole compounds in tap, river and well water samples at concentration levels below the legislated maximum concentration levels (MCLs) with quantitative recoveries. Additionally, an on-line preconcentration procedure based on the use of a molecularly imprinted polymer as selective stationary phase in HPLC is proposed as a fast screening method for the evaluation of the presence of benzimidazole compounds in water samples.

  7. Comparison of molecular and metabolomic methods as characterization tools of Debaryomyces hansenii cheese isolates.

    PubMed

    Del Bove, Marzia; Lattanzi, Monia; Rellini, Paolo; Pelliccia, Cristina; Fatichenti, Fabrizio; Cardinali, Gianluigi

    2009-08-01

    Debaryomyces hansenii is one of the yeast species most frequently isolated from cheese and salty foods, however little is known about the phenotypic and molecular variability of its strains. In order to explore the possibilities of a large study on its biodiversity, some D. hansenii strains were selectively isolated from pecorino cheese sampled in ten different Italian regions. All isolates were identified as D. hansenii on the basis of conventional and molecular taxonomic analysis. The D1/D2 domain sequences of the 26S-rDNA did not show any variation, confirming the extreme homogeneity of this species. PCR-duplex-RAPD banding patterns analyzed with PCoA showed interesting clustering related to the geographic areas of isolation, although some overlapping between strains derived from different districts could be observed. A FTIR (Fourier Transform Infrared Spectroscopy) metabolomic fingerprint produced groupings weakly related to those observed with RAPD and less associated with the isolation locales. The discriminatory power of metabolomic fingerprint was able to discriminate strains otherwise considered identical. This preliminary study showed that, in spite of the homogeneity at the 26S-rDNA level, the D. hansenii strains exhibit high molecular and metabolomic variability somehow linked to the places of isolation. Further studies will be necessary to better investigate on the link between terroir and strain variability, as well as on the relation between genotypic and metabolomic fingerprints.

  8. In vivo Cerenkov luminescence imaging: a new tool for molecular imaging.

    PubMed

    Mitchell, Gregory S; Gill, Ruby K; Boucher, David L; Li, Changqing; Cherry, Simon R

    2011-11-28

    Cerenkov radiation is a phenomenon where optical photons are emitted when a charged particle moves faster than the speed of light for the medium in which it travels. Recently, we and others have discovered that measurable visible light due to the Cerenkov effect is produced in vivo following the administration of β-emitting radionuclides to small animals. Furthermore, the amounts of injected activity required to produce a detectable signal are consistent with small-animal molecular imaging applications. This surprising observation has led to the development of a new hybrid molecular imaging modality known as Cerenkov luminescence imaging (CLI), which allows the spatial distribution of biomolecules labelled with β-emitting radionuclides to be imaged in vivo using sensitive charge-coupled device cameras. We review the physics of Cerenkov radiation as it relates to molecular imaging, present simulation results for light intensity and spatial distribution, and show an example of CLI in a mouse cancer model. CLI allows many common radiotracers to be imaged in widely available in vivo optical imaging systems, and, more importantly, provides a pathway for directly imaging β(-)-emitting radionuclides that are being developed for therapeutic applications in cancer and that are not readily imaged by existing methods.

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

    PubMed Central

    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

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

    NASA Astrophysics Data System (ADS)

    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.

  11. The Advanced Light Source: A new tool for research in atomic and molecular physics

    NASA Astrophysics Data System (ADS)

    Schlachter, F.; Robinson, A.

    1991-04-01

    The Advanced Light Source at the Lawrence Berkeley Laboratory will be the world's brightest synchrotron radiation source in the extreme ultraviolet and soft x-ray regions of the spectrum when it begins operation in 1993. It will be available as a national user facility to researchers in a broad range of disciplines, including materials science, atomic and molecular physics, chemistry, biology, imaging, and technology. The high brightness of the ALS will be particularly well suited to high-resolution studies of tenuous targets, such as excited atoms, ions, and clusters.

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

    PubMed

    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. Anthropogenic Molecular Markers: Tools to Identify the Sources and Transport Pathways of Pollutants

    USGS Publications Warehouse

    Takada, H.; Satoh, F.; Bothner, Michael H.; Tripp, B.W.; Johnson, C.G.; Farrington, J.W.

    1997-01-01

    The activities of modern civilization have released to the oceans a wide variety of both mobilized natural compounds and synthetic compounds not found prior to modern times. Many of these compounds provide a means of identifying sources of inputs and pathways of movement of chemicals through oceanic ecosystems and serve as molecular markers of human activities. A coastal ocean (Tokyo Bay) and a deep ocean (Deep Water Dump Site 106 in the Western North Atlantic Ocean) example are presented. In the deep ocean study, the correlation between potential sewage marker, i.e. linear alkylbenzenes (LABs), and polychlorinated biphenyls (PCBs) concentrations indicates a contribution of sewage sludge PCBs to the dump site sediments.

  14. The Virtual Cell Animation Collection: Tools for Teaching Molecular and Cellular Biology

    PubMed Central

    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

  15. Computational and molecular tools for scalable rAAV-mediated genome editing

    PubMed Central

    Stoimenov, Ivaylo; Ali, Muhammad Akhtar; Pandzic, Tatjana; Sjöblom, Tobias

    2015-01-01

    The rapid discovery of potential driver mutations through large-scale mutational analyses of human cancers generates a need to characterize their cellular phenotypes. Among the techniques for genome editing, recombinant adeno-associated virus (rAAV)-mediated gene targeting is suited for knock-in of single nucleotide substitutions and to a lesser degree for gene knock-outs. However, the generation of gene targeting constructs and the targeting process is time-consuming and labor-intense. To facilitate rAAV-mediated gene targeting, we developed the first software and complementary automation-friendly vector tools to generate optimized targeting constructs for editing human protein encoding genes. By computational approaches, rAAV constructs for editing ∼71% of bases in protein-coding exons were designed. Similarly, ∼81% of genes were predicted to be targetable by rAAV-mediated knock-out. A Gateway-based cloning system for facile generation of rAAV constructs suitable for robotic automation was developed and used in successful generation of targeting constructs. Together, these tools enable automated rAAV targeting construct design, generation as well as enrichment and expansion of targeted cells with desired integrations. PMID:25488813

  16. Establishment of the onset of host specificity in four phyllobothriid tapeworm species (Cestoda: Tetraphyllidea) using a molecular approach.

    PubMed

    Randhawa, H S; Saunders, G W; Burt, M D B

    2007-08-01

    A parasitological survey in the Bay of Fundy, Canada, resulted in the recovery of mature specimens from 5 species of phyllobothriid tapeworms (Cestoda: Tetraphyllidea) from 4 rajid skates: Echeneibothrium canadensis and E. dubium abyssorum specimens from Amblyraja radiata; E. vernetae and Pseudanthobothrium n.sp. from Leucoraja erinacea and L. ocellata; and P. hanseni from A. radiata and Malacoraja senta. Partial sequence data of a variable region (D2) from the large subunit ribosomal DNA (LSU) were used here to determine the host distribution of immature specimens for 4 of these 5 species (E. d. abyssorum was not included in the analyses). Immature specimens from both Pseudanthobothrium spp. were identified in the same hosts as recorded previously for mature specimens, thus suggesting that there are mechanisms that prevent the attachment of the parasite in an 'unsuitable' host species. Immature E. canadensis specimens were recovered exclusively from A. radiata, whereas immature E. vernetae specimens were recovered from L. erinacea and A. radiata, despite the latter host species not harbouring mature E. vernetae specimens. Their presence in the latter host species may be explained by host restriction or resistance, which allows the attachment of the parasites in the 'wrong' host species, but not establishment or development.

  17. Extreme Heterogeneity in the Molecular Events Leading to the Establishment of Chiasmata during Meiosis I in Human Oocytes

    PubMed Central

    Lenzi, Michelle L.; Smith, Jenetta; Snowden, Timothy; Kim, Mimi; Fishel, Richard; Poulos, Bradford K.; Cohen, Paula E.

    2005-01-01

    In humans, ∼50% of conceptuses are chromosomally aneuploid as a consequence of errors in meiosis, and most of these aneuploid conceptuses result in spontaneous miscarriage. Of these aneuploidy events, 70% originate during maternal meiosis, with the majority proposed to arise as a direct result of defective crossing over during meiotic recombination in prophase I. By contrast, <1%–2% of mouse germ cells exhibit prophase I–related nondisjunction events. This disparity among mammalian species is surprising, given the conservation of genes and events that regulate meiotic progression. To understand the mechanisms that might be responsible for the high error rates seen in human females, we sought to further elucidate the regulation of meiotic prophase I at the molecular cytogenetic level. Given that these events occur during embryonic development in females, samples were obtained during a defined period of gestation (17–24 weeks). Here, we demonstrate that human oocytes enter meiotic prophase I and progress through early recombination events in a similar temporal framework to mice. However, at pachynema, when chromosomes are fully paired, we find significant heterogeneity in the localization of the MutL homologs, MLH1 and MLH3, among human oocyte populations. MLH1 and MLH3 have been shown to mark late-meiotic nodules that correlate well with—and are thought to give rise to—the sites of reciprocal recombination between homologous chromosomes, which suggests a possible 10-fold variation in the processing of nascent recombination events. If such variability persists through development and into adulthood, these data would suggest that as many as 30% of human oocytes are predisposed to aneuploidy as a result of prophase I defects in MutL homolog–related events. PMID:15558497

  18. The porphyrias: clinic, diagnostics, novel investigative tools and evolving molecular therapeutic strategies.

    PubMed

    van Serooskerken, A-M van Tuyll; Poblete-Gutiérrez, P; Frank, J

    2010-01-01

    The porphyrias are clinically and genetically heterogeneous metabolic disorders resulting from a predominantly hereditary dysfunction of specific enzymes involved in heme biosynthesis. Today, the clinical, biochemical, and genetic characteristics of this fascinating group of diseases are well established. Recently, different in vitro and animal models have facilitated the investigation of etiopathologic mechanisms in the different types of porphyria and the development of causal treatment strategies such as pathway interference, enzyme replacement, and gene therapy. The continuous progress in basic science has made an invaluable contribution to the rapid translation of discoveries made in the laboratory into new diagnostics and therapeutics in the near future.

  19. Network Based Approach in the Establishment of the Relationship between Type 2 Diabetes Mellitus and Its Complications at the Molecular Level Coupled with Molecular Docking Mechanism

    PubMed Central

    Rampogu Lemuel, Mary

    2016-01-01

    Diabetes mellitus (DM) is one of the major metabolic disorders that is currently threatening the world. DM is seen associated with obesity and diabetic retinopathy (DR). In the present paper we tried to evaluate the relationship between the three aliments at the gene level and further performed the molecular docking to identify the common drug for all the three diseases. We have adopted several software programs such as Phenopedia, VennViewer, and CDOCKER to accomplish the objective. Our results revealed six genes that commonly associated and are involved in the signalling pathway. Furthermore, evaluation of common gene association from the selected set of genes projected the presence of SIRT1 in all the three aliments. Therefore, we targeted protein 4KXQ which was produced from the gene SIRT1 and challenged it with eight phytochemicals, adopting the CDOCKER. C1 compound has displayed highest -CDOCKER energy and -CDOCKER interaction energy of 43.6905 and 43.3953, respectively. Therefore, this compound is regarded as the most potential lead molecule. PMID:27699170

  20. Molecular tools for investigating microbial community structure and function in oxygen-deficient marine waters.

    PubMed

    Hawley, Alyse K; Kheirandish, Sam; Mueller, Andreas; Leung, Hilary T C; Norbeck, Angela D; Brewer, Heather M; Pasa-Tolic, Ljiljana; Hallam, Steven J

    2013-01-01

    Water column oxygen (O2)-deficiency shapes food-web structure by progressively directing nutrients and energy away from higher trophic levels into microbial community metabolism resulting in fixed nitrogen loss and greenhouse gas production. Although respiratory O2 consumption during organic matter degradation is a natural outcome of a productive surface ocean, global-warming-induced stratification intensifies this process leading to oxygen minimum zone (OMZ) expansion. Here, we describe useful tools for detection and quantification of potential key microbial players and processes in OMZ community metabolism including quantitative polymerase chain reaction primers targeting Marine Group I Thaumarchaeota, SUP05, Arctic96BD-19, and SAR324 small-subunit ribosomal RNA genes and protein extraction methods from OMZ waters compatible with high-resolution mass spectrometry for profiling microbial community structure and functional dynamics.

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

    PubMed

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

    PubMed Central

    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

  3. New Tools and New Biology: Recent Miniaturized Systems for Molecular and Cellular Biology

    PubMed Central

    Hamon, Morgan; Hong, Jong Wook

    2013-01-01

    Recent advances in applied physics and chemistry have led to the development of novel microfluidic systems. Microfluidic systems allow minute amounts of reagents to be processed using μm-scale channels and offer several advantages over conventional analytical devices for use in biological sciences: faster, more accurate and more reproducible analytical performance, reduced cell and reagent consumption, portability, and integration of functional components in a single chip. In this review, we introduce how microfluidics has been applied to biological sciences. We first present an overview of the fabrication of microfluidic systems and describe the distinct technologies available for biological research. We then present examples of microsystems used in biological sciences, focusing on applications in molecular and cellular biology. PMID:24305843

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

    PubMed

    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.

  5. Establishing a Methodology for Evaluation and Selecting Computer Aided Software Engineering Tools for a Defined Software Engineering Environment at the Air Force Institute of Technology School of Engineering

    DTIC Science & Technology

    1991-12-01

    F. Lecouat, and V. Ambriola. "A Tool to Coordinate Tools," IEEE Software: 17-25 (November 1988). 6. Bruce , T. A., J. Fuller, and T. Moriarty, "So You...34 Journal of Systems Management, 40-5: 29-32 (May 1989). BIB.1 14. Dart, S. A., R. J. Ellison, P. H. Feiler , and A. N. Habermann, "Software

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

    PubMed

    Echeverría, Pablo C; Bernthaler, Andreas; Dupuis, Pierre; Mayer, Bernd; Picard, Didier

    2011-01-01

    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.

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

    PubMed

    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.

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

    PubMed

    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. Major Intercontinentally Distributed Sequence Types of Kingella kingae and Development of a Rapid Molecular Typing Tool

    PubMed Central

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

    2014-01-01

    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. PMID:25143574

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

    PubMed Central

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

    2016-01-01

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

  11. The Molecular Bronchoscope: A Tool for Measurement of Spatially Dependent CO2 Concentrations in the Lungs.

    PubMed

    Ciaffoni, Luca; Couper, John H; Richmond, Graham; Hancock, Gus; Ritchie, Grant A D

    2016-09-06

    Respiratory physicians use bronchoscopy for visual assessment of the lungs' topography and collecting tissue samples for external analysis. We propose a novel bronchoscope tool that would enable spatially dependent measurements of the functioning of the lungs by determining local concentrations of carbon dioxide, which will be produced by healthy parts of the lung at rates that are higher than from portions where gas exchange is impaired. The gas analyzer is based on a compact laser absorption spectrometer making use of fiber optics for delivery and return of low intensity diode laser radiation to and from the measurement chamber at the distal end of a flexible conduit. The appropriate optical wavelength was chosen such that light is selectively absorbed only by gaseous CO2. The optical absorption takes place over a short path (8.8 mm) within a rigid, 12 mm long, perforated probe tip. Wavelength modulation spectroscopy was adopted as the analytical technique to reduce the noise on the optical signal and yield measurements of relative CO2 concentration every 180 ms with a precision as low as 600 part-per-million by volume. The primary objective of such a device is to see if additional spatial information about the lungs functionality can be gathered, which will complement visual observation.

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

    PubMed

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

    2015-06-01

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

  13. Efficient tool to calculate two-dimensional optical spectra for photoactive molecular complexes

    NASA Astrophysics Data System (ADS)

    Duan, Hong-Guang; Dijkstra, Arend G.; Nalbach, Peter; Thorwart, Michael

    2015-10-01

    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 quasiadiabatic 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 coupling. For weak to intermediate system-bath couplings, which is most important for natural photosynthetic complexes, the combined CMRT+PMA gives reasonable results with acceptable computational efforts.

  14. Evaluation of the Illumigene Malaria LAMP: A Robust Molecular Diagnostic Tool for Malaria Parasites

    PubMed Central

    Lucchi, Naomi W.; Gaye, Marie; Diallo, Mammadou Alpha; Goldman, Ira F.; Ljolje, Dragan; Deme, Awa Bineta; Badiane, Aida; Ndiaye, Yaye Die; Barnwell, John W.; Udhayakumar, Venkatachalam; Ndiaye, Daouda

    2016-01-01

    Isothermal nucleic acid amplification assays such as the loop mediated isothermal amplification (LAMP), are well suited for field use as they do not require thermal cyclers to amplify the DNA. To further facilitate the use of LAMP assays in remote settings, simpler sample preparation methods and lyophilized reagents are required. The performance of a commercial malaria LAMP assay (Illumigene Malaria LAMP) was evaluated using two sample preparation workflows (simple filtration prep (SFP)) and gravity-driven filtration prep (GFP)) and pre-dispensed lyophilized reagents. Laboratory and clinical samples were tested in a field laboratory in Senegal and the results independently confirmed in a reference laboratory in the U.S.A. The Illumigene Malaria LAMP assay was easily implemented in the clinical laboratory and gave similar results to a real-time PCR reference test with limits of detection of ≤2.0 parasites/μl depending on the sample preparation method used. This assay reliably detected Plasmodium sp. parasites in a simple low-tech format, providing a much needed alternative to the more complex molecular tests for malaria diagnosis. PMID:27827432

  15. Advances in developing molecular-diagnostic tools for strongyloid nematodes of equids: fundamental and applied implications.

    PubMed

    Gasser, Robin B; Hung, Guo-Chiuan; Chilton, Neil B; Beveridge, Ian

    2004-02-01

    Infections of equids with parasitic nematodes of the order Strongylida (subfamilies Strongylinae and Cyathostominae) are of major veterinary importance. In last decades, the widespread use of drugs against these parasites has led to problems of resistance within the Cyathostominae, and to an increase in their prevalence and intensity of infection. Novel control strategies, based on improved knowledge of parasite biology and epidemiology, have thus become important. However, there are substantial limitations in the understanding of fundamental biological and systematic aspects of these parasites, which have been due largely to limitations in their specific identification and diagnosis using traditional, morphological approaches. Recently, there has been progress in the development of DNA-based approaches for the specific identification of strongyloids of equids for systematic studies and disease diagnosis. The present article briefly reviews information on the classification, biology, pathogenesis, epidemiology of equine strongyloids and the diagnosis of infections, highlights knowledge gaps in these areas, describes recent advances in the use of molecular techniques for the genetic characterisation, specific identification and differentiation of strongyloids of equids as a basis for fundamental investigations of the systematics, population biology and ecology.

  16. Imaging Mass Spectrometry: A New Tool for Pathology in a Molecular Age

    PubMed Central

    Norris, Jeremy L.; Caprioli, Richard M.

    2014-01-01

    Mass spectrometry provides unique advantages for the analysis of clinical specimens, and these capabilities have been critical to the advancement of diagnostic medicine. To date, liquid chromatography mass spectrometry (LC-MS) is the platform most commonly used for diagnostics; however, LC-MS based proteomics is very labor intensive and costly to implement for high volume assays. Furthermore, when analyzing tissue samples, additional laborious sample preparation steps must be employed (e.g., extraction methods or laser microdissection). The direct analysis of cells and tissues by matrix assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS) has developed significant momentum for applications that have diagnostic potential. MALDI IMS provides molecular information from specific cell types within tissue sections; however, this laser-based approach significantly reduces the analysis time for each location sampled. This Viewpoint discusses the technologies for direct analysis of tissues, the potential for diagnostic applications using MALDI IMS, and the challenges faced in the transfer of the technology to the clinical laboratory. PMID:24178781

  17. Assessment of changes in microbial community structure during operation of an ammonia biofilter with molecular tools

    NASA Technical Reports Server (NTRS)

    Sakano, Y.; Kerkhof, L.; Janes, H. W. (Principal Investigator)

    1998-01-01

    Biofiltration has been used for two decades to remove odors and various volatile organic and inorganic compounds in contaminated off-gas streams. Although biofiltration is widely practiced, there have been few studies of the bacteria responsible for the removal of air contaminants in biofilters. In this study, molecular techniques were used to identify bacteria in a laboratory-scale ammonia biofilter. Both 16S rRNA and ammonia monooxygenase (amoA) genes were used to characterize the heterotrophic and ammonia-oxidizing bacteria collected from the biofilter during a 102-day experiment. The overall diversity of the heterotrophic microbial population appeared to decrease by 38% at the end of the experiment. The community structure of the heterotrophic population also shifted from predominantly members of two subdivisions of the Proteobacteria (the beta and gamma subdivisions) to members of one subdivision (the gamma subdivision). An overall decrease in the diversity of ammonia monooxygenase genes was not observed. However, a shift from groups dominated by organisms containing Nitrosomonas-like and Nitrosospira-like amoA genes to groups dominated by organisms containing only Nitrosospira-like amoA genes was observed. In addition, a new amoA gene was discovered. This new gene is the first freshwater amoA gene that is closely affiliated with Nitrosococcus oceanus and the particulate methane monooxygenase gene from the methane oxidizers belonging to the gamma subdivision of the Proteobacteria.

  18. A Molecular Fraction Collecting Tool for the ABI 310 Automated Sequencer

    PubMed Central

    Lin, Ming-Tseh; Rich, Roy G.; Shipley, Royce F.; Hafez, Michael J.; Tseng, Li-Hui; Murphy, Kathleen M.; Gocke, Christopher D.; Eshleman, James R.

    2007-01-01

    Several methods exist to retrieve and purify DNA fragments after agarose or polyacrylamide gel electrophoresis for subsequent analyses. However, molecules present in low concentration and molecules similar in size to their neighbors are difficult to purify. Capillary electrophoresis has become popular in molecular diagnostic laboratories because of its automation, excellent resolution, and high sensitivity. In the current study, the ABI Prism 310 Genetic Analyzer was reconfigured into a fraction collector by adapting the standard gel block to accommodate a collection tube at the distal end of capillary. The time to collect the desired peaks was estimated by extrapolating from standard capillary electrophoresis using the original gel block. Fraction collection from a mixture of DNA fragments amplified from wild type and several internal tandem duplication mutations of the FMS-like tyrosine kinase 3 (Flt3) gene yielded highly purified DNA fragments containing internal tandem duplication mutations and predictable electrokinetics using the reconstructed gel block. The reconfigured instrument could successfully isolate DNA amplicons from extremely low-amplitude peaks (110 relative fluorescent units), which were undetectable using polyacrylamide gel electrophoresis. In addition, we successfully isolated bands that were only three bases apart that comigrated on polyacrylamide gel electrophoresis. DNA sequencing was used to confirm that the correct peaks were recovered at sufficient purity. PMID:17916601

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

    PubMed Central

    Sharma, Sanjib Kumar; Kuch, Ulrich; Höde, Patrick; Bruhse, Laura; Pandey, Deb P.; Ghimire, Anup; Chappuis, François; Alirol, Emilie

    2016-01-01

    Snakebite is an important medical emergency in rural Nepal. Correct identification of the biting species is crucial for clinicians to choose appropriate treatment and anticipate complications. This is particularly important for neurotoxic envenoming which, depending on the snake species involved, may not respond to available antivenoms. Adequate species identification tools are lacking. This study used a combination of morphological and molecular approaches (PCR-aided DNA sequencing from swabs of bite sites) to determine the contribution of venomous and non-venomous species to the snakebite burden in southern Nepal. Out of 749 patients admitted with a history of snakebite to one of three study centres, the biting species could be identified in 194 (25.9%). Out of these, 87 had been bitten by a venomous snake, most commonly the Indian spectacled cobra (Naja naja; n = 42) and the common krait (Bungarus caeruleus; n = 22). When both morphological identification and PCR/sequencing results were available, a 100% agreement was noted. The probability of a positive PCR result was significantly lower among patients who had used inadequate “first aid” measures (e.g. tourniquets or local application of remedies). This study is the first to report the use of forensic genetics methods for snake species identification in a prospective clinical study. If high diagnostic accuracy is confirmed in larger cohorts, this method will be a very useful reference diagnostic tool for epidemiological investigations and clinical studies. PMID:27105074

  20. Evaluation of four molecular typing methodologies as tools for determining taxonomy relations and for identifying species among Yersinia isolates.

    PubMed

    Souza, Roberto A; Pitondo-Silva, André; Falcão, Deise P; Falcão, Juliana P

    2010-08-01

    In the last few decades, molecular typing has become an important tool in taxonomic, phylogenetic and identification studies of numerous groups of bacteria, including the yersiniae. In this study, Enterobacterial Repetitive Intergenic Consensus PCR (ERIC-PCR), Pulsed-Field Gel Electrophoresis (PFGE), 16S rRNA gene sequencing and Multilocus Sequence Analysis (MLSA) were performed to determine the ability of these techniques to be used in taxonomy and identification of Yersinia strains. A total of 60 Yersinia strains were genotyped by ERIC-PCR and PFGE. Moreover, an in silico analysis was carried out for 16S rRNA gene sequencing and MLSA, using 68 and 49 Yersinia strains, respectively. A phylogenetic tree constructed from the ERIC-PCR, 16S rRNA gene sequencing and MLSA data grouped most of the Yersinia species into distinct species-specific clusters. In the PFGE assay these clusters were not observed. On this basis, ERIC-PCR, 16S rRNA gene sequencing and MLSA seem to be valuable techniques for use in taxonomic and identification studies of the genus Yersinia, whereas PFGE does not. Furthermore, ERIC-PCR has the advantage of being a cheaper, easier and faster assay than 16S rRNA gene sequencing or MLSA, and for these reasons can be considerate an alternative tool in taxonomic studies of yersiniae.

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

    PubMed

    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.

  2. Recent insights into the epidemiology and genetics of Ascaris in China using molecular tools.

    PubMed

    Peng, W; Yuan, K; Hu, M; Gasser, R B

    2007-03-01

    Ascaris is a large parasitic roundworm (nematode) of the small intestine of humans and pigs, which causes the socio-economically important disease, ascariasis. To better understand the relationship of Ascaris between the 2 host species, recent studies in China have focused on investigating the genetics and epidemiology of Ascaris from humans and pigs using a mutation scanning-based approach. Findings provided support for a low level of gene flow between the human and porcine Ascaris populations. Extending the studies of genotypic variability within Ascaris from humans and pigs, experimental infections of mice and pigs with selected genotypes of Ascaris were carried out. Initial results indicate that there is a significant difference in the ability of Ascaris eggs of genotype G1 (derived from human) and G3 (derived from pig) to infect and establish as adults in pigs, supporting the difference in the frequencies of these genotypes in natural Ascaris populations between pigs and humans in China. Taken together, current information supports that there is limited cross-infection of Ascaris between humans and pigs in endemic regions and that pigs are not a significant reservoir of human infection with the adult nematode in such areas.

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

    PubMed Central

    Kasahara, Kota; Kinoshita, Kengo

    2016-01-01

    Ion conduction mechanisms of ion channels are a long-standing conundrum. Although the molecular dynamics (MD) method has been extensively used to simulate ion conduction dynamics at the atomic level, analysis and interpretation of MD results are not straightforward due to complexity of the dynamics. In our previous reports, we proposed an analytical method called ion-binding state analysis to scrutinize and summarize ion conduction mechanisms by taking advantage of a variety of analytical protocols, e.g., the complex network analysis, sequence alignment, and hierarchical clustering. This approach effectively revealed the ion conduction mechanisms and their dependence on the conditions, i.e., ion concentration and membrane voltage. Here, we present an easy-to-use computational toolkit for ion-binding state analysis, called IBiSA_tools. This toolkit consists of a C++ program and a series of Python and R scripts. From the trajectory file of MD simulations and a structure file, users can generate several images and statistics of ion conduction processes. A complex network named ion-binding state graph is generated in a standard graph format (graph modeling language; GML), which can be visualized by standard network analyzers such as Cytoscape. As a tutorial, a trajectory of a 50 ns MD simulation of the Kv1.2 channel is also distributed with the toolkit. Users can trace the entire process of ion-binding state analysis step by step. The novel method for analysis of ion conduction mechanisms of ion channels can be easily used by means of IBiSA_tools. This software is distributed under an open source license at the following URL: http://www.ritsumei.ac.jp/~ktkshr/ibisa_tools/ PMID:27907142

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

    NASA Astrophysics Data System (ADS)

    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

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

    PubMed

    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.

  6. Perspective on post-menopausal osteoporosis: establishing an interdisciplinary understanding of the sequence of events from the molecular level to whole bone fractures

    PubMed Central

    McNamara, L. M.

    2010-01-01

    Current drug treatments for post-menopausal osteoporosis cannot eliminate bone fractures, possibly because the mechanisms responsible for bone loss are not fully understood. Although research within various disciplines has significantly advanced the state of knowledge, fundamental findings are not widely understood between different disciplines. For that reason, this paper presents noteworthy experimental findings from discrete disciplines focusing on post-menopausal osteoporosis. These studies have established that, in addition to bone loss, significant changes in bone micro-architecture, tissue composition and micro-damage occur. Cellular processes and molecular signalling pathways governing pathological bone resorption have been identified to a certain extent. Ongoing studies endeavour to determine how such changes are initiated at the onset of oestrogen deficiency. It emerges that, because of the discrete nature of previous research studies, the sequence of events that lead to bone fracture is not fully understood. In this paper, two sequences of multi-scale changes are proposed and the experimental challenges that need to be overcome to fully define this sequence are outlined. Future studies must comprehensively characterize the time sequence of molecular-, cellular- and tissue-level changes to attain a coherent understanding of the events that ultimately lead to bone fracture and inform the future development of treatments for post-menopausal osteoporosis. PMID:19846441

  7. Assessment of microscopic and molecular tools for the diagnosis and follow-up of cryptosporidiosis in patients at risk.

    PubMed

    Le Govic, Y; Guyot, K; Certad, G; Deschildre, A; Novo, R; Mary, C; Sendid, B; Viscogliosi, E; Favennec, L; Dei-Cas, E; Fréalle, E; Dutoit, E

    2016-01-01

    Cryptosporidiosis is an important though underreported public health concern. Molecular tools might be helpful in improving its diagnosis. In this study, ZR Fecal DNA MiniPrep™ Kit (ZR) and NucliSens® easyMAG® (EM) were compared using four Cryptosporidium-seeded feces and 29 Cryptosporidium-positive stools. Thereafter, ZR was selected for prospective evaluation of Cryptosporidium detection by 18S rDNA and LAXER quantitative PCR (qPCR) in 69 stools from 56 patients after Cryptosporidium detection by glycerin, modified Ziehl-Neelsen (ZN) and auramine-phenol (AP) stainings. The combination of any of the two extraction methods with 18S qPCR yielded adequate detection of Cryptosporidium in seeded stools, but the ZR kit showed the best performance. All 29 Cryptosporidium-positive samples were positive with 18S qPCR, after both ZR and EM extraction. However, false-negative results were found with LAXER qPCR or nested PCR. Cryptosporidiosis was diagnosed in 7/56 patients. All the microscopic methods enabled the initial diagnosis, but Cryptosporidium was detected in 12, 13, and 14 samples from these seven patients after glycerin, ZN, and AP staining respectively. Among these samples, 14 and 12 were positive with 18S and LAXER qPCR respectively. In two patients, Cryptosporidium DNA loads were found to be correlated with clinical evolution. Although little known, glycerin is a sensitive method for the initial detection of Cryptosporidium. When combined with 18S qPCR, ZR extraction, which had not been evaluated so far for Cryptosporidium, was an accurate tool for detecting Cryptosporidium and estimating the oocyst shedding in the course of infection.

  8. A Powerful Molecular Engineering Tool Provided Efficient Chlamydomonas Mutants as Bio-Sensing Elements for Herbicides Detection

    PubMed Central

    Lambreva, Maya D.; Giardi, Maria Teresa; Rambaldi, Irene; Antonacci, Amina; Pastorelli, Sandro; Bertalan, Ivo; Husu, Ivan; Johanningmeier, Udo; Rea, Giuseppina

    2013-01-01

    This study was prompted by increasing concerns about ecological damage and human health threats derived by persistent contamination of water and soil with herbicides, and emerging of bio-sensing technology as powerful, fast and efficient tool for the identification of such hazards. This work is aimed at overcoming principal limitations negatively affecting the whole-cell-based biosensors performance due to inadequate stability and sensitivity of the bio-recognition element. The novel bio-sensing elements for the detection of herbicides were generated exploiting the power of molecular engineering in order to improve the performance of photosynthetic complexes. The new phenotypes were produced by an in vitro directed evolution strategy targeted at the photosystem II (PSII) D1 protein of Chlamydomonas reinhardtii, using exposures to radical-generating ionizing radiation as selection pressure. These tools proved successful to identify D1 mutations conferring enhanced stability, tolerance to free-radical-associated stress and competence for herbicide perception. Long-term stability tests of PSII performance revealed the mutants capability to deal with oxidative stress-related conditions. Furthermore, dose-response experiments indicated the strains having increased sensitivity or resistance to triazine and urea type herbicides with I50 values ranging from 6×10−8 M to 2×10−6 M. Besides stressing the relevance of several amino acids for PSII photochemistry and herbicide sensing, the possibility to improve the specificity of whole-cell-based biosensors, via coupling herbicide-sensitive with herbicide-resistant strains, was verified. PMID:23613953

  9. Molecular fingerprinting of Salmonella typhimurium by IS200-typing as a tool for epidemiological and evolutionary studies.

    PubMed

    Soria, G; Barbé, J; Gibert, I

    1994-01-01

    The aim of this work was to develop and evaluate a molecular typing strategy for Salmonella based on hybridization of chromosomal DNA with two different probes derived from insertion sequence IS200. Probe IS200-TT was specifically constructed for this study as a trimer of a 112 pb TaqI-TaqI fragment of IS200. Among several restriction enzymes evaluated, two were selected: EcoRI, which cuts the insertion sequence in two pieces, each one complementary to one of the probes used, and PstI, a restriction enzyme with no recognition site into IS200. With several combinations of these restrictions enzymes and probes, 43 Salmonella typhimurium strains were analyzed for copy number and location of IS200, as well as reproducibility and stability of the patterns. IS200 types have been shown to be stable, both in strains isolated from different patients implicated in the same salmonellosis outbreak and in strains isolated from the same patient at different times or from different specimens. The discriminatory power of the method has been 0.91 to 0.94. As a comparison, S. typhimurium strains were also ribotyped. Discriminatory power of the ribotypes oscillated between 0.44 and 0.55, depending on the enzyme used, and achieved a 0.78 value when the information obtained with two restriction enzymes was combined. Moreover, IS200 typing was able to differentiate among a group of S. typhimurium strains which were identical by ribotype and enzymatic electrophoretic mobility. These results enable us to conclude that, for the stability, reproducibility and discriminatory power of the patterns generated, IS200 probes can be a very useful tool in the molecular typing of S. typhimurium.

  10. Evaluation of conjunctival swab as a mass-screening tool for molecular diagnosis of canine visceral leishmaniasis.

    PubMed

    Leite, Rodrigo Souza; Souza, Natalia Alves; Barbosa, Amanda Duarte; Ferreira, Aline Leandra Carvalho; de Andrade, Antero Silva Ribeiro

    2015-06-01

    The canine visceral leishmaniasis (CVL) diagnosis is an important step of visceral leishmaniasis control program in Brazil once the dog is the main reservoir host of the disease. The aim of this study was to evaluate the conjunctival swab (CS) as a mass-screening tool for CVL molecular diagnosis in an endemic area classified as priority for the Brazilian Ministry of Healthy for surveillance action. A total of 1350 domiciled dogs were screened. The animals were evaluated by serological tests (enzyme-linked immunosorbent assay (ELISA) as screening and immunofluorescence antibody test (IFAT) for confirmation) and by CS associated to real-time PCR, using primers addressed to kinetoplast DNA (kDNA) minicircles and SYBR Green. Canine β-globin gene amplification was used to evaluate the sample DNA integrity. A subgroup of 484 animals was also submitted to clinical evaluation. Among the 1350 dogs screened, 369 (27.3%) were positive by CS real-time PCR and 126 (9.3%) tested positive by ELISA. Thirty-one percent (39/126) of the ELISA-positive dogs were confirmed by IFAT. CS real-time PCR was able to detect infection in dogs independently of the symptomatology degree (p > 0.05), while ELISA was more sensitive in the group of dogs that present three or more clinical signs related to CVL. The results demonstrated that CS real-time PCR was able to detect a higher number of infected dogs than ELISA and that the prevalence of canine infections has been underestimated by the serological assays. The use of sensitive molecular diagnostic methods like CS real-time PCR, mainly in endemic areas, could greatly contribute to disease control.

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

    PubMed Central

    Zhu, Yanmin; Fazio, Gennaro; Mazzola, Mark

    2014-01-01

    Apple replant disease (ARD) is a major limitation to the establishment of economically viable orchards on replant sites due to the buildup and long-term survival of pathogen inoculum. Several soilborne necrotrophic fungi and oomycetes are primarily responsible for ARD, and symptoms range from serious inhibition of growth to the death of young trees. Chemical fumigation has been the primary method used for control of ARD, and manipulating soil microbial ecology to reduce pathogen density and aggressiveness is being investigated. To date, innate resistance of apple rootstocks as a means to control this disease has not been carefully explored, partly due to the complex etiology and the difficulty in phenotyping the disease resistance. Molecular defense responses of plant roots to soilborne necrotrophic pathogens are largely elusive, although considerable progress has been achieved using foliar disease systems. Plant defense responses to necrotrophic pathogens consist of several interacting modules and operate as a network. Upon pathogen detection by plants, cellular signals such as the oscillation of Ca2+ concentration, reactive oxygen species (ROS) burst and protein kinase activity, lead to plant hormone biosynthesis and signaling. Jasmonic acid (JA) and ethylene (ET) are known to be fundamental to the induction and regulation of defense mechanisms toward invading necrotrophic pathogens. Complicated hormone crosstalk modulates the fine-tuning of transcriptional reprogramming and metabolic redirection, resulting in production of antimicrobial metabolites, enzyme inhibitors and cell wall refortification to restrict further pathogenesis. Transcriptome profiling of apple roots in response to inoculation with Pythium ultimum demonstrated that there is a high degree of conservation regarding the molecular framework of defense responses compared with those observed with foliar tissues. It is conceivable that the timing and intensity of genotype-specific defense responses

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

    PubMed

    Zhu, Yanmin; Fazio, Gennaro; Mazzola, Mark

    2014-01-01

    Apple replant disease (ARD) is a major limitation to the establishment of economically viable orchards on replant sites due to the buildup and long-term survival of pathogen inoculum. Several soilborne necrotrophic fungi and oomycetes are primarily responsible for ARD, and symptoms range from serious inhibition of growth to the death of young trees. Chemical fumigation has been the primary method used for control of ARD, and manipulating soil microbial ecology to reduce pathogen density and aggressiveness is being investigated. To date, innate resistance of apple rootstocks as a means to control this disease has not been carefully explored, partly due to the complex etiology and the difficulty in phenotyping the disease resistance. Molecular defense responses of plant roots to soilborne necrotrophic pathogens are largely elusive, although considerable progress has been achieved using foliar disease systems. Plant defense responses to necrotrophic pathogens consist of several interacting modules and operate as a network. Upon pathogen detection by plants, cellular signals such as the oscillation of Ca(2+) concentration, reactive oxygen species (ROS) burst and protein kinase activity, lead to plant hormone biosynthesis and signaling. Jasmonic acid (JA) and ethylene (ET) are known to be fundamental to the induction and regulation of defense mechanisms toward invading necrotrophic pathogens. Complicated hormone crosstalk modulates the fine-tuning of transcriptional reprogramming and metabolic redirection, resulting in production of antimicrobial metabolites, enzyme inhibitors and cell wall refortification to restrict further pathogenesis. Transcriptome profiling of apple roots in response to inoculation with Pythium ultimum demonstrated that there is a high degree of conservation regarding the molecular framework of defense responses compared with those observed with foliar tissues. It is conceivable that the timing and intensity of genotype-specific defense responses

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

    PubMed Central

    Jroundi, Fadwa; Gonzalez-Muñoz, Maria Teresa; Sterflinger, Katja; Piñar, Guadalupe

    2015-01-01

    . The molecular strategy employed here is suggested as an efficient monitoring tool to assess the impact on the stone-autochthonous microbiota of the application of biomineralization processes as a restoration/conservation procedure. PMID:26222040

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

    PubMed

    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.

  15. Comparison of biotyping methods as alternative identification tools to molecular typing of pathogenic Cryptococcus species in sub-Saharan Africa.

    PubMed

    Nyazika, Tinashe K; Robertson, Valerie J; Nherera, Brenda; Mapondera, Prichard T; Meis, Jacques F; Hagen, Ferry

    2016-03-01

    Cryptococcal meningitis is the leading fungal infection and AIDS defining opportunistic illness in patients with late stage HIV infection, particularly in South-East Asia and sub-Saharan Africa. Given the high mortality, clinical differences and the extensive ecological niche of Cryptococcus neoformans and Cryptococcus gattii species complexes, there is need for laboratories in sub-Sahara African countries to adopt new and alternative reliable diagnostic algorithms that rapidly identify and distinguish these species. We biotyped 74 and then amplified fragment length polymorphism (AFLP) genotyped 66 Cryptococcus isolates from a cohort of patients with HIV-associated cryptococcal meningitis. C. gattii sensu lato was isolated at a prevalence of 16.7% (n = 11/66) and C. neoformans sensu stricto was responsible for 83.3% (n = 55/66) of the infections. l-Canavanine glycine bromothymol blue, yeast-carbon-base-d-proline-d-tryptophan and creatinine dextrose bromothymol blue thymine were able to distinguish pathogenic C. gattii sensu lato from C. neoformans sensu stricto species when compared with AFLP genotyping. This study demonstrates high C. gattii sensu lato prevalence in Zimbabwe. In addition, biotyping methods can be used as alternative diagnostic tools to molecular typing in resource-limited areas for differentiating pathogenic Cryptococcus species.

  16. Comparison of biotyping methods as alternative identification tools to molecular typing of pathogenic Cryptococcus species in sub-Saharan Africa

    PubMed Central

    Nyazika, Tinashe K.; Robertson, Valerie J.; Nherera, Brenda; Mapondera, Prichard T.; Meis, Jacques F.; Hagen, Ferry

    2015-01-01

    Summary Cryptococcal meningitis is the leading fungal infection and AIDS defining opportunistic illness in patients with late stage HIV infection, particularly in South-East Asia and sub-Saharan Africa. Given the high mortality, clinical differences and the extensive ecological niche of Cryptococcus neoformans and Cryptococcus gattii species complexes, there is need for laboratories in sub-Sahara African countries to adopt new and alternative reliable diagnostic algorithms that rapidly identify and distinguish these species. We biotyped 74 and then amplified fragment length polymorphism (AFLP) genotyped 66 Cryptococcus isolates from a cohort of patients with HIV-associated cryptococcal meningitis. Cryptococcus gattii sensu lato was isolated at a prevalence of 16.7% (n = 11/66) and C. neoformans sensu stricto was responsible for 83.3% (n = 55/66) of the infections. l-Canavanine glycine bromothymol blue, yeast-carbon-base-d-proline-d-tryptophan and creatinine dextrose bromothymol blue thymine were able to distinguish pathogenic C. gattii sensu lato from C. neoformans sensu stricto species when compared with amplified fragment length polymorphism genotyping. This study demonstrates high C. gattii sensu lato prevalence in Zimbabwe. In addition, biotyping methods can be used as alternative diagnostic tools to molecular typing in resource-limited areas for differentiating pathogenic Cryptococcus species. PMID:26661484

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

    PubMed

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

    2010-01-01

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

  18. THE ESTABLISHMENT OF LOCAL DIAGNOSTIC REFERENCE LEVELS IN ENDOSCOPIC RETROGRADE CHOLANGIOPANCREATOGRAPHY: A PRACTICAL TOOL FOR THE OPTIMISATION AND FOR QUALITY ASSURANCE MANAGEMENT.

    PubMed

    Saukko, E; Henner, A; Nieminen, M T; Ahonen, S-M

    2016-02-29

    Fluoroscopic procedures are an area of special concern in relation to radiation protection. The aim of this study was to describe the current level of patient radiation doses in endoscopic retrograde cholangiopancreatography (ERCP) collected from a single centre, as well as to establish and review local diagnostic reference levels (DRLs) in ERCP. A total of 100 patients' radiation doses in ERCP were recorded, and the third-quartile method was adopted to establish local DRLs for ERCP. The mean dose area product (DAP) was 2.05 Gy cm(2), fluoroscopy time (FT) 1.7 min and the number of images was 3. The proposed local DRLs for ERCP were 3.00 Gy cm(2) and 3.0 min. Local DRLs were reviewed in a sample of 25 patients 5 y after they had been established. In reviewing data, the averages of DAP and FT were below the local DRLs. Local DRLs help in the optimisation process of fluoroscopic procedures and guides to a good clinical practice.

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

    PubMed Central

    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

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

    PubMed Central

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

    2016-01-01

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

  1. Molecular basis, applications and challenges of CRISPR/Cas9: a continuously evolving tool for genome editing.

    PubMed

    D'Agostino, Ylenia; D'Aniello, Salvatore

    2017-01-05

    The clustered regularly interspaced short palindromic repeats (CRISPR/Cas9) system is a recently discovered tool for genome editing that has quickly revolutionized the ability to generate site-specific mutations in a wide range of animal models, including nonhuman primates. Indeed, a significant number of scientific reports describing single or multiplex guide RNA microinjection, double-nicking strategies, site-specific knock-in and conditional knock-out have been published in less than three years. However, despite the great potential of this new technology, there are some limitations because of the presence of off-target genomic sites, which must be taken into consideration. To address this issue, various research teams have tried to improve the efficiency of the system through enzymatic modifications of the Cas9 protein or by the introduction of alternative strategies. Although several review articles are available that singly describe the molecular mechanism(s), applications and challenges of each of these strategies, a concise compilation of approaches is lacking. In the current review, we describe and evaluate most CRISPR/Cas9 approaches available at present, describing both mechanism of action, in addition to advantages or disadvantages. The primary goal of this work is to serve as a guide for not skilled researchers, facilitating the selection of the best strategy to target their gene of interest and allowing optimization of particular applications to the specific aims of the study. The present article also offers a unique perspective, focusing on the fact that CRISPR technology is opening a new genomic era, providing the means to manipulate specific genes in a targeted manner in all animal models, an endeavor previously considered to be difficult.

  2. New target prediction and visualization tools incorporating open source molecular fingerprints for TB Mobile 2.0

    PubMed Central

    2014-01-01

    Background We recently developed a freely available mobile app (TB Mobile) for both iOS and Android platforms that displays Mycobacterium tuberculosis (Mtb) active molecule structures and their targets with links to associated data. The app was developed to make target information available to as large an audience as possible. Results We now report a major update of the iOS version of the app. This includes enhancements that use an implementation of ECFP_6 fingerprints that we have made open source. Using these fingerprints, the user can propose compounds with possible anti-TB activity, and view the compounds within a cluster landscape. Proposed compounds can also be compared to existing target data, using a näive Bayesian scoring system to rank probable targets. We have curated an additional 60 new compounds and their targets for Mtb and added these to the original set of 745 compounds. We have also curated 20 further compounds (many without targets in TB Mobile) to evaluate this version of the app with 805 compounds and associated targets. Conclusions TB Mobile can now manage a small collection of compounds that can be imported from external sources, or exported by various means such as email or app-to-app inter-process communication. This means that TB Mobile can be used as a node within a growing ecosystem of mobile apps for cheminformatics. It can also cluster compounds and use internal algorithms to help identify potential targets based on molecular similarity. TB Mobile represents a valuable dataset, data-visualization aid and target prediction tool. PMID:25302078

  3. Drought severity-duration-frequency curves: a foundation for risk assessment and planning tool for ecosystem establishment in post-mining landscapes

    NASA Astrophysics Data System (ADS)

    Halwatura, D.; Lechner, A. M.; Arnold, S.

    2015-02-01

    Eastern Australia has considerable mineral and energy resources, with areas of high biodiversity value co-occurring over a broad range of agro-climatic environments. Lack of water is the primary abiotic stressor for (agro)ecosystems in many parts of eastern Australia. In the context of mined land rehabilitation quantifying the severity-duration-frequency (SDF) of droughts is crucial for successful ecosystem rehabilitation to overcome challenges of early vegetation establishment and long-term ecosystem resilience. The objective of this study was to quantify the SDF of short-term and long-term drought events of 11 selected locations across a broad range of agro-climatic environments in eastern Australia by using three drought indices at different timescales: the Standardized Precipitation Index (SPI), the Reconnaissance Drought Index (RDI), and the Standardized Precipitation-Evapotranspiration Index (SPEI). Based on the indices we derived bivariate distribution functions of drought severity and duration, and estimated the recurrence intervals of drought events at different timescales. The correlation between the simple SPI and the more complex SPEI or RDI was stronger for the tropical and temperate locations than for the arid locations, indicating that SPEI or RDI can be replaced by SPI if evaporation plays a minor role for plant available water (tropics). Both short-term and long-term droughts were most severe and prolonged, and recurred most frequently in arid regions, but were relatively rare in tropical and temperate regions. Our approach is similar to intensity-duration-frequency (IDF) analyses of rainfall, which are crucial for the design of hydraulic infrastructure. In this regard, we propose to apply SDF analyses of droughts to design ecosystem components in post-mining landscapes. Together with design rainfalls, design droughts should be used to assess rehabilitation strategies and ecological management using drought recurrence intervals, thereby minimising

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

    PubMed

    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.

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

    PubMed Central

    2013-01-01

    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. PMID:23711194

  6. A Probabilistic Tool that Aids Logistics Engineers in the Establishment of High Confidence Repair Need-Dates at the NASA Shuttle Logistics Depot

    NASA Technical Reports Server (NTRS)

    Bullington, J. V.; Winkler, J. C.; Linton, D. G.; Khajenoori, S.

    1995-01-01

    The NASA Shuttle Logistics Depot (NSLD) is tasked with the responsibility for repair and manufacture of Line Replaceable Unit (LRU) hardware and components to support the Space Shuttle Orbiter. Due to shrinking budgets, cost effective repair of LRU's becomes a primary objective. To achieve this objective, is imperative that resources be assigned to those LRU's which have the greatest expectation of being needed as a spare. Forecasting the times at which spares are needed requires consideration of many significant factors including: failure rate, flight rate, spares availability, and desired level of support, among others. This paper summarizes the results of the research and development work that has been accomplished in producing an automated tool that assists in the assignment of effective repair start-times for LRU's at the NSLD. This system, called the Repair Start-time Assessment System (RSAS), uses probabilistic modeling technology to calculate a need date for a repair that considers the current repair pipeline status, as well as, serviceable spares and projections of future demands. The output from the system is a date for beginning the repair that has significantly greater confidence (in the sense that a desired probability of support is ensured) than times produced using other techniques. Since an important output of RSAS is the longest repair turn-around time that will ensure a desired probability of support, RSAS has the potential for being applied to operations at any repair depot where spares are on-hand and repair start-times are of interest. In addition, RSAS incorporates tenants of Just-in-Time (JIT) techniques in that the latest repair start-time (i.e., the latest time at which repair resources must be committed) may be calculated for every failed unit This could reduce the spares inventory for certain items, without significantly increasing the risk of unsatisfied demand.

  7. Molecular epidemiology of carbapenemase-producing Klebsiella pneumoniae in a hospital in Madrid: Successful establishment of an OXA-48 ST11 clone.

    PubMed

    Brañas, Patricia; Villa, Jennifer; Viedma, Esther; Mingorance, Jesús; Orellana, M Angeles; Chaves, Fernando

    2015-07-01

    Here we report a retrospective clinical and molecular study conducted in a tertiary care facility in southern Madrid, Spain, from January 2009 to February 2014 to investigate the epidemiology of carbapenemase-producing Klebsiella pneumoniae (CPKp). Carbapenemase genes were identified in 97 non-duplicate K. pneumoniae isolates, including 59 harbouring blaOXA-48, 37 harbouring blaVIM-1 and 1 harbouring blaKPC-2. Pulsed-field gel electrophoresis (PFGE) analysis verified the presence of 20 different clonal types, whilst multilocus sequence typing (MLST) assigned the isolates to eight sequence types (STs). A gradual increase was noted in the number of CPKp isolated, ranging from 0.8% in 2009 to 4.3% in 2013. A large outbreak was also identified, initiated in 2013 owing to a blaOXA-48 and blaCTX-M-15 co-producing ST11 clone and involving a total of 44 patients. Whole-genome sequencing was used to characterise the resistome of a representative isolate from this outbreak. Bioinformatics analysis revealed the presence of 121 genes related to antibiotic and antiseptic resistance, mutations in the ompk35 and ompk36 genes, and the presence of the blaOXA-48 gene on a 62 811bp IncL/M-type plasmid as part of a Tn1999.2 composite transposon. These results portray the increasing trend in carbapenemase-producing isolates in this hospital and highlight the successful establishment of a blaOXA-48 and blaCTX-M-15 co-producing ST11 clone that has led to the displacement of previous circulating clones.

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

    PubMed

    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.

  9. Molecular Descriptors

    NASA Astrophysics Data System (ADS)

    Consonni, Viviana; Todeschini, Roberto

    In the last decades, several scientific researches have been focused on studying how to encompass and convert - by a theoretical pathway - the information encoded in the molecular structure into one or more numbers used to establish quantitative relationships between structures and properties, biological activities, or other experimental properties. Molecular descriptors are formally mathematical representations of a molecule obtained by a well-specified algorithm applied to a defined molecular representation or a well-specified experimental procedure. They play a fundamental role in chemistry, pharmaceutical sciences, environmental protection policy, toxicology, ecotoxicology, health research, and quality control. Evidence of the interest of the scientific community in the molecular descriptors is provided by the huge number of descriptors proposed up today: more than 5000 descriptors derived from different theories and approaches are defined in the literature and most of them can be calculated by means of dedicated software applications. Molecular descriptors are of outstanding importance in the research fields of quantitative structure-activity relationships (QSARs) and quantitative structure-property relationships (QSPRs), where they are the independent chemical information used to predict the properties of interest. Along with the definition of appropriate molecular descriptors, the molecular structure representation and the mathematical tools for deriving and assessing models are other fundamental components of the QSAR/QSPR approach. The remarkable progress during the last few years in chemometrics and chemoinformatics has led to new strategies for finding mathematical meaningful relationships between the molecular structure and biological activities, physico-chemical, toxicological, and environmental properties of chemicals. Different approaches for deriving molecular descriptors here reviewed and some of the most relevant descriptors are presented in

  10. "LOVE TO HATE" pesticides: felicity or curse for the soil microbial community? An FP7 IAPP Marie Curie project aiming to establish tools for the assessment of the mechanisms controlling the interactions of pesticides with soil microorganisms.

    PubMed

    Karpouzas, D G; Tsiamis, G; Trevisan, M; Ferrari, F; Malandain, C; Sibourg, O; Martin-Laurent, F

    2016-09-01

    Pesticides end up in soil where they interact with soil microorganisms in various ways. On the Yin Side of the interaction, pesticides could exert toxicity on soil microorganisms, while on the Yang side of interaction, pesticides could be used as energy source by a fraction of the soil microbial community. The LOVE TO HATE project is an IAPP Marie Curie project which aims to study these complex interactions of pesticides with soil microorganisms and provide novel tools which will be useful both for pesticide regulatory purposes and agricultural use. On the Yin side of the interactions, a new regulatory scheme for assessing the soil microbial toxicity of pesticides will be proposed based on the use of advanced standardized tools and a well-defined experimental tiered scheme. On the Yang side of the interactions, advanced molecular tools like amplicon sequencing and functional metagenomics will be applied to define microbes that are involved in the rapid transformation of pesticides in soils and isolate novel pesticide biocatalysts. In addition, a functional microarray has been designed to estimate the biodegradation genetic potential of the microbial community of agricultural soils for a range of pesticide groups.

  11. High-precision frequency measurements: indispensable tools at the core of the molecular-level analysis of complex systems

    PubMed Central

    Ruecker, C.; Meringer, M.; Gugisch, R.; Frommberger, M.; Perdue, E. M.; Witt, M.; Schmitt-Kopplin, P.

    2007-01-01

    This perspective article provides an assessment of the state-of-the-art in the molecular-resolution analysis of complex organic materials. These materials can be divided into biomolecules in complex mixtures (which are amenable to successful separation into unambiguously defined molecular fractions) and complex nonrepetitive materials (which cannot be purified in the conventional sense because they are even more intricate). Molecular-level analyses of these complex systems critically depend on the integrated use of high-performance separation, high-resolution organic structural spectroscopy and mathematical data treatment. At present, only high-precision frequency-derived data exhibit sufficient resolution to overcome the otherwise common and detrimental effects of intrinsic averaging, which deteriorate spectral resolution to the degree of bulk-level rather than molecular-resolution analysis. High-precision frequency measurements are integral to the two most influential organic structural spectroscopic methods for the investigation of complex materials—NMR spectroscopy (which provides unsurpassed detail on close-range molecular order) and FTICR mass spectrometry (which provides unrivalled resolution)—and they can be translated into isotope-specific molecular-resolution data of unprecedented significance and richness. The quality of this standalone de novo molecular-level resolution data is of unparalleled mechanistic relevance and is sufficient to fundamentally advance our understanding of the structures and functions of complex biomolecular mixtures and nonrepetitive complex materials, such as natural organic matter (NOM), aerosols, and soil, plant and microbial extracts, all of which are currently poorly amenable to meaningful target analysis. The discrete analytical volumetric pixel space that is presently available to describe complex systems (defined by NMR, FT mass spectrometry and separation technologies) is in the range of 108–14 voxels, and is

  12. Molecular docking of opiates and opioid peptides, a tool for the design of selective agonists and antagonists, and for the investigation of atypical ligand-receptor interactions.

    PubMed

    Gentilucci, L; Tolomelli, A; De Marco, R; Artali, R

    2012-01-01

    In the last years, molecular docking emerged as a powerful tool to investigate the interactions between opioid ligands and their receptors, thus driving the design and development of new selective agonists or antagonists of therapeutic interest. This review especially covers the most representative and recent comparative molecular docking analyses of structurally related compounds, as well as of agonists and antagonists within the active and inactive states of the receptors. The comparative analyses gave important information on the structural determinants responsible for the affinity and selectivity of the ligands, and defined the features responsible for the activation of the receptors. A special section is dedicated to the analyses of recently discovered, unusual agonists lacking of the tyramine pharmacophore, such as Salvinorin A, and the cyclopeptides which comprise the D-Trp-Phe pharmacophoric motif. For the atypical structure of these compounds, the docking proved to be essential to disclose how they interact with and activate the receptors.

  13. FOXA1, GATA3 and PPARɣ Cooperate to Drive Luminal Subtype in Bladder Cancer: A Molecular Analysis of Established Human Cell Lines

    PubMed Central

    Warrick, Joshua I.; Walter, Vonn; Yamashita, Hironobu; Chung, Eunah; Shuman, Lauren; Amponsa, Vasty Osei; Zheng, Zongyu; Chan, Wilson; Whitcomb, Tiffany L.; Yue, Feng; Iyyanki, Tejaswi; Kawasawa, Yuka I.; Kaag, Matthew; Guo, Wansong; Raman, Jay D.; Park, Joo-Seop; DeGraff, David J.

    2016-01-01

    Discrete bladder cancer molecular subtypes exhibit differential clinical aggressiveness and therapeutic response, which may have significant implications for identifying novel treatments for this common malignancy. However, research is hindered by the lack of suitable models to study each subtype. To address this limitation, we classified bladder cancer cell lines into molecular subtypes using publically available data in the Cancer Cell Line Encyclopedia (CCLE), guided by genomic characterization of bladder cancer by The Cancer Genome Atlas (TCGA). This identified a panel of bladder cancer cell lines which exhibit genetic alterations and gene expression patterns consistent with luminal and basal molecular subtypes of human disease. A subset of bladder cancer cell lines exhibit in vivo histomorphologic patterns consistent with luminal and basal subtypes, including papillary architecture and squamous differentiation. Using the molecular subtype assignments, and our own RNA-seq analysis, we found overexpression of GATA3 and FOXA1 cooperate with PPARɣ activation to drive transdifferentiation of a basal bladder cancer cells to a luminial phenotype. In summary, our analysis identified a set of human cell lines suitable for the study of molecular subtypes in bladder cancer, and furthermore indicates a cooperative regulatory network consisting of GATA3, FOXA1, and PPARɣ drive luminal cell fate. PMID:27924948

  14. Establishing operations

    PubMed Central

    Michael, Jack

    1993-01-01

    The first two books on behavior analysis (Skinner, 1938; Keller & Schoenfeld, 1950) had chapter-length coverage of motivation. The next generation of texts also had chapters on the topic, but by the late 1960s it was no longer being given much treatment in the behavior-analytic literature. The present failure to deal with the topic leaves a gap in our understanding of operant functional relations. A partial solution is to reintroduce the concept of the establishing operation, defined as an environmental event, operation, or stimulus condition that affects an organism by momentarily altering (a) the reinforcing effectiveness of other events and (b) the frequency of occurrence of that part of the organism's repertoire relevant to those events as consequences. Discriminative and motivative variables can be distinguished as follows: The former are related to the differential availability of an effective form of reinforcement given a particular type of behavior; the latter are related to the differential reinforcing effectiveness of environmental events. An important distinction can also be made between unconditioned establishing operations (UEOs), such as food deprivation and painful stimulation, and conditioned establishing operations (CEOs) that depend on the learning history of the organism. One type of CEO is a stimulus that has simply been paired with a UEO and as a result may take on some of the motivative properties of that UEO. The warning stimulus in avoidance procedures is another important type of CEO referred to as reflexive because it establishes its own termination as a form of reinforcement and evokes the behavior that has accomplished such termination. Another CEO is closely related to the concept of conditional conditioned reinforcement and is referred to as a transitive CEO, because it establishes some other stimulus as a form of effective reinforcement and evokes the behavior that has produced that other stimulus. The multiple control of human

  15. A Sclerostin super-producer cell line derived from the human cell line SaOS-2: a new tool for the study of the molecular mechanisms driving Sclerostin expression.

    PubMed

    Pérez-Campo, Flor M; Sañudo, Carolina; Delgado-Calle, Jesús; Arozamena, Jana; Zarrabeitia, María T; Riancho, José A

    2014-08-01

    Sclerostin, the product of the SOST gene, is a key regulator of bone homeostasis. Sclerostin interferes with the Wnt signalling pathway and, therefore, has a negative effect on bone formation. Although the importance of sclerostin in bone homeostasis is well established, many aspects of its biology are still unknown. Due to its restricted pattern of expression, in vitro studies of SOST gene regulation are technically challenging. Furthermore, a more profound investigation of the molecular mechanism controlling sclerostin expression has been hampered by the lack of a good human in vitro model. Here, we describe two cell lines derived from the human osteosarcoma cell line SaOS-2 that produce elevated levels of sclerostin. Analysis of the super-producer cell lines showed that sclerostin levels were still reduced in response to parathyroid hormone treatment or in response to mechanical loading, indicating that these regulatory mechanisms were not affected in the presented cell lines. In addition, we did not find differences between the promoter or ECR5 sequences of our clones and the SaOS-2 parental line. However, the methylation of the proximal CpG island located at the SOST promoter was lower in the super-producer clones, in agreement with a higher level of SOST transcription. Although the underlying biological causes of the elevated levels of sclerostin production in this cell line are not yet clear, we believe that it could be an extremely useful tool to study the molecular mechanisms driving sclerostin expression in humans.

  16. The importance of molecular tools in classical biological control of weeds: Two case studies with yellow starthistle candidate biological agents

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Molecular analyses may play a primary role in the process of host-specificity evaluation at species and population levels; here are reported two examples of their application with new candidate biocontrol agents for yellow starthistle (YST). Ceratapion basicorne is a root-crown boring weevil that sh...

  17. How does a Mycobacterium change its spots? Applying molecular tools to track diverse strains of Mycobacterium avium subspecies paratuberculosis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Defining genetic diversity in the wake of the release of several Mycobacterium avium subsp. paratuberculosis (MAP) genome sequences has become a major emphasis in the molecular biology and epidemiology of Johne’s disease research. These data can now be used to define the extent of strain diversity ...

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

    PubMed

    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.

  19. Chromatography process development in the quality by design paradigm I: Establishing a high-throughput process development platform as a tool for estimating "characterization space" for an ion exchange chromatography step.

    PubMed

    Bhambure, R; Rathore, A S

    2013-01-01

    This article describes the development of a high-throughput process development (HTPD) platform for developing chromatography steps. An assessment of the platform as a tool for establishing the "characterization space" for an ion exchange chromatography step has been performed by using design of experiments. Case studies involving use of a biotech therapeutic, granulocyte colony-stimulating factor have been used to demonstrate the performance of the platform. We discuss the various challenges that arise when working at such small volumes along with the solutions that we propose to alleviate these challenges to make the HTPD data suitable for empirical modeling. Further, we have also validated the scalability of this platform by comparing the results from the HTPD platform (2 and 6 μL resin volumes) against those obtained at the traditional laboratory scale (resin volume, 0.5 mL). We find that after integration of the proposed correction factors, the HTPD platform is capable of performing the process optimization studies at 170-fold higher productivity. The platform is capable of providing semi-quantitative assessment of the effects of the various input parameters under consideration. We think that platform such as the one presented is an excellent tool for examining the "characterization space" and reducing the extensive experimentation at the traditional lab scale that is otherwise required for establishing the "design space." Thus, this platform will specifically aid in successful implementation of quality by design in biotech process development. This is especially significant in view of the constraints with respect to time and resources that the biopharma industry faces today.

  20. Enriching the molecular definition of the airway "field of cancerization:" establishing new paradigms for the patient at risk for lung cancer.

    PubMed

    Gomperts, Brigitte N; Walser, Tonya C; Spira, Avrum; Dubinett, Steven M

    2013-01-01

    The "field of cancerization" refers to histologically normal-appearing tissue adjacent to neoplastic tissue that displays molecular abnormalities, some of which are the same as those of the tumor. Improving our understanding of these molecular events is likely to increase our understanding of carcinogenesis. Kadara and colleagues attempt to characterize the molecular events occurring temporally and spatially within the field of cancerization of patients with early-stage non-small cell lung cancer (NSCLC) following definitive surgery. They followed patients with bronchoscopies annually after tumor resection and extracted RNA from the serial brushings from different endobronchial sites. They then conducted microarray analysis to identify gene expression differences over time and in different sites in the airway. Candidate genes were found that may have biologic relevance to the field of cancerization. For example, expression of phosphorylated AKT and ERK1/2 was found to increase in the airway epithelium with time. Although there are limitations in the study design, this investigation demonstrates the utility of identifying molecular changes in histologically normal airway epithelium in lung cancer. In addition to increasing our understanding of lung cancer biology, studying the field of cancerization has the potential to identify biomarkers from samples obtained in a minimally invasive manner.

  1. Application of a long-established molecular marker in larval teleosts to evaluate estrogenic potential in surface waters and wastewater effluents

    EPA Science Inventory

    In recent years molecular indicators, diagnostic for exposure in aquatic systems, have been developed using teleostean models in laboratory and field settings. Our laboratory has previously shown that the gene for vitellogenin, a protein precursor of egg yolk in oviparous animals...

  2. Fighting an old disease with modern tools: characteristics and molecular detection methods of drug-resistant Mycobacterium tuberculosis.

    PubMed

    Engström, Anna

    2016-01-01

    Tuberculosis (TB) is an ancient disease, but not a disease of the past. The increasing prevalence of drug-resistant strains of Mycobacterium tuberculosis, the causative agent of TB, demands new measures to combat the situation. Rapid and accurate detection of the pathogen, and its drug susceptibility pattern, is essential for timely initiation of treatment, and ultimately, control of the disease. Molecular-based methods offer a great chance to improve detection of drug-resistant TB; however, their development and usage should be accompanied with a profound understanding of drug resistance mechanisms and circulating M. tuberculosis strains in specific settings, as otherwise, the usefulness of such tests may be limited. This review gives an overview of the history of TB treatment and drug resistance, drug resistance mechanisms for the most commonly used drugs and molecular methods designed to detect drug-resistant strains.

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

    DTIC Science & Technology

    2015-02-09

    was performed in-situ using stoichiometric amounts of sec-BuLi. Three arm Polystyrene and Polyisoprene stars with narrow molecular weight...NALDI-TOF MS. Activation of initiator was performed in-situ using stoichiometric amounts of sec-BuLi. Three arm Polystyrene and Polyisoprene stars with...in good agreement with g’ values of three arm stars from the literature. (a) Papers published in peer-reviewed journals (N/A for none) Enter List of

  4. The Raman-Derived Carbonization Continuum: A Tool to Select the Best Preserved Molecular Structures in Archean Kerogens

    NASA Astrophysics Data System (ADS)

    Delarue, Frédéric; Rouzaud, Jean-Noël; Derenne, Sylvie; Bourbin, Mathilde; Westall, Frances; Kremer, Barbara; Sugitani, Kenichiro; Deldicque, Damien; Robert, François

    2016-06-01

    The search for indisputable traces of life in Archean cherts is of prime importance. However, their great age and metamorphic history pose constraints on the study of molecular biomarkers. We propose a quantitative criterion to document the thermal maturity of organic matter in rocks in general, and Archean rocks in particular. This is definitively required to select the best candidates for seeking non-altered sample remnants of life. Analysis of chemical (Raman spectroscopy, 13C NMR, elemental analysis) and structural (HRTEM) features of Archean and non-Archean carbonaceous matter (CM) that was submitted to metamorphic grades lower than, or equal to, that of greenschist facies showed that these features had all undergone carbonization but not graphitization. Raman-derived quantitative parameters from the present study and from literature spectra, namely, R1 ratio and FWHM-D1, were used to draw a carbonization continuum diagram showing two carbonization stages. While non-Archean samples can be seen to dominate the first stage, the second stage mostly consists of the Archean samples. In this diagram, some Archean samples fall at the boundary with non-Archean samples, which thus demonstrates a low degree of carbonization when compared to most Archean CM. As a result, these samples constitute candidates that may contain preserved molecular signatures of Archean CM. Therefore, with regard to the search for the oldest molecular traces of life on Earth, we propose the use of this carbonization continuum diagram to select the Archean CM samples.

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-01-01

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

  7. 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.

    PubMed

    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.

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

    PubMed Central

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

    2016-01-01

    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. PMID:27188541

  9. Molecular tools for species and sex identification in the mixed-species flocks of bean geese and white-fronted geese.

    PubMed

    Kim, Min-kyung; Lee, Sang-im; Lee, Hang; Lee, Sangdon

    2012-11-01

    Genetic studies on protected species can be difficult, particularly when they form a mixed-species flock with other species. The bean goose (Anser fabalis), which is internationally recognized as a threatened species, was observed to form overwintering foraging flocks with white-fronted goose (Anser albifrons) at agricultural lands to feed on the grains in Korea. Non-invasive samples such as feces and feather that are readily available in their foraging ground can be useful for understanding the structure and composition of populations, but they often require specific experimental conditions due to small amount or low quality of DNA. In this study, we designed sets of primers that would allow efficient molecular identification of species and sex of individuals of bean geese and white-fronted geese. Species-specific primers (WFG-F/BG-F and G-R), developed from ND2 region of mitochondrial DNA, produced PCR products with different sizes which allow easy species identification without further sequencing. Based on published CHD 1 sequences, we designed internal primers (Gsex-F and Gsex-R) for sex determination that can be used in nested PCR after applying P2/P8 primers, and our methods clearly showed high success rate of molecular sexing from non-invasive samples. These molecular tools open the possibilities for genetic studies using non-invasive samples collected from a mixed-species aggregation containing bean geese and white-fronted geese.

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

    NASA Astrophysics Data System (ADS)

    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.

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

    NASA Technical Reports Server (NTRS)

    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.

  12. The Raman-Derived Carbonization Continuum: A Tool to Select the Best Preserved Molecular Structures in Archean Kerogens

    PubMed Central

    Rouzaud, Jean-Noël; Derenne, Sylvie; Bourbin, Mathilde; Westall, Frances; Kremer, Barbara; Sugitani, Kenichiro; Deldicque, Damien; Robert, François

    2016-01-01

    Abstract The search for indisputable traces of life in Archean cherts is of prime importance. However, their great age and metamorphic history pose constraints on the study of molecular biomarkers. We propose a quantitative criterion to document the thermal maturity of organic matter in rocks in general, and Archean rocks in particular. This is definitively required to select the best candidates for seeking non-altered sample remnants of life. Analysis of chemical (Raman spectroscopy, 13C NMR, elemental analysis) and structural (HRTEM) features of Archean and non-Archean carbonaceous matter (CM) that was submitted to metamorphic grades lower than, or equal to, that of greenschist facies showed that these features had all undergone carbonization but not graphitization. Raman-derived quantitative parameters from the present study and from literature spectra, namely, R1 ratio and FWHM-D1, were used to draw a carbonization continuum diagram showing two carbonization stages. While non-Archean samples can be seen to dominate the first stage, the second stage mostly consists of the Archean samples. In this diagram, some Archean samples fall at the boundary with non-Archean samples, which thus demonstrates a low degree of carbonization when compared to most Archean CM. As a result, these samples constitute candidates that may contain preserved molecular signatures of Archean CM. Therefore, with regard to the search for the oldest molecular traces of life on Earth, we propose the use of this carbonization continuum diagram to select the Archean CM samples. Key Words: Archean—Early life—Kerogen—Raman spectroscopy—Carbonization. Astrobiology 16, 407–417. PMID:27186810

  13. Preset pivotal tool holder

    DOEpatents

    Asmanes, Charles

    1979-01-01

    A tool fixture is provided for precise pre-alignment of a radiused edge cutting tool in a tool holder relative to a fixed reference pivot point established on said holder about which the tool holder may be selectively pivoted relative to the fixture base member to change the contact point of the tool cutting edge with a workpiece while maintaining the precise same tool cutting radius relative to the reference pivot point.

  14. MoleculaRnetworks: an integrated graph theoretic and data mining tool to explore solvent organization in molecular simulation.

    PubMed

    Mooney, Barbara Logan; Corrales, L René; Clark, Aurora E

    2012-03-30

    This work discusses scripts for processing molecular simulations data written using the software package R: A Language and Environment for Statistical Computing. These scripts, named moleculaRnetworks, are intended for the geometric and solvent network analysis of aqueous solutes and can be extended to other H-bonded solvents. New algorithms, several of which are based on graph theory, that interrogate the solvent environment about a solute are presented and described. This includes a novel method for identifying the geometric shape adopted by the solvent in the immediate vicinity of the solute and an exploratory approach for describing H-bonding, both based on the PageRank algorithm of Google search fame. The moleculaRnetworks codes include a preprocessor, which distills simulation trajectories into physicochemical data arrays, and an interactive analysis script that enables statistical, trend, and correlation analysis, and other data mining. The goal of these scripts is to increase access to the wealth of structural and dynamical information that can be obtained from molecular simulations.

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

    PubMed Central

    Diaz-Uriarte, Ramon

    2008-01-01

    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. PMID:18208605

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

    PubMed

    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.

  17. Establishing Time for Professional Learning

    ERIC Educational Resources Information Center

    Journal of Staff Development, 2013

    2013-01-01

    Time for collaborative learning is an essential resource for educators working to implement college- and career-ready standards. The pages in this article include tools from the workbook "Establishing Time for Professional Learning." The tools support a complete process to help educators effectively find and use time. The following…

  18. Microbial monitoring by molecular tools of a two-phase anaerobic bioreactor treating fruit and vegetable wastes.

    PubMed

    Bouallagui, H; Torrijos, M; Godon, J J; Moletta, R; Cheikh, R Ben; Touhami, Y; Delgenes, J P; Hamdi, M

    2004-05-01

    Microbial consortia in a two-phase, anaerobic bioreactor using a mixture of fruit and vegetable wastes were established. Bacterial and archaeal communities obtained by a culture-independent approach based on single strand conformation polymorphism analysis of total 16S rDNA showed the adaptation of the microflora to the process parameters. Throughout the 90 d of the study, the species composition of the bacterial community changed significantly. Bacterial 16S rDNA showed at least 7 different major species with a very prominent one corresponding to a Megasphaera elsdenii whereas bacterial 16S rDNA of a methanization bioreactor showed 10 different major species. After two weeks, Prevotella ruminicola became major and its dominance increased continuously until day 50. After an acid shock at pH 5, the 16S rDNA archaeal patterns in the acidogenic reactor showed two major prominent species corresponding to Methanosphaera stadtmanii and Methanobrevibacter wolinii, a hydrogenotrophic bacterium.

  19. Molecular breeding

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Use of molecular and genomic tools to assist selection of parents or progeny has become an integral part of modern cotton breeding. In this chapter, the basic components of molecular cotton breeding are described. These components include: molecular marker development, genetic and physical map const...

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

    NASA Astrophysics Data System (ADS)

    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.

  1. Identification of low molecular weight pyroglutamate A{beta} oligomers in Alzheimer disease: a novel tool for therapy and diagnosis.

    PubMed

    Wirths, Oliver; Erck, Christian; Martens, Henrik; Harmeier, Anja; Geumann, Constanze; Jawhar, Sadim; Kumar, Sathish; Multhaup, Gerd; Walter, Jochen; Ingelsson, Martin; Degerman-Gunnarsson, Malin; Kalimo, Hannu; Huitinga, Inge; Lannfelt, Lars; Bayer, Thomas A

    2010-12-31

    N-terminally truncated Aβ peptides starting with pyroglutamate (AβpE3) represent a major fraction of all Aβ peptides in the brain of Alzheimer disease (AD) patients. AβpE3 has a higher aggregation propensity and stability and shows increased toxicity compared with full-length Aβ. In the present work, we generated a novel monoclonal antibody (9D5) that selectively recognizes oligomeric assemblies of AβpE3 and studied the potential involvement of oligomeric AβpE3 in vivo using transgenic mouse models as well as human brains from sporadic and familial AD cases. 9D5 showed an unusual staining pattern with almost nondetectable plaques in sporadic AD patients and non-demented controls. Interestingly, in sporadic and familial AD cases prominent intraneuronal and blood vessel staining was observed. Using a novel sandwich ELISA significantly decreased levels of oligomers in plasma samples from patients with AD compared with healthy controls were identified. Moreover, passive immunization of 5XFAD mice with 9D5 significantly reduced overall Aβ plaque load and AβpE3 levels, and normalized behavioral deficits. These data indicate that 9D5 is a therapeutically and diagnostically effective monoclonal antibody targeting low molecular weight AβpE3 oligomers.

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

    PubMed

    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.

  3. Molecular dynamics - potential of mean force calculations as a tool for understanding ion permeation and selectivity in narrow channels.

    PubMed

    Allen, Toby W; Andersen, Olaf S; Roux, Benoit

    2006-12-01

    Ion channels catalyze the permeation of charged molecules across cell membranes and are essential for many vital physiological functions, including nerve and muscle activity. To understand better the mechanisms underlying ion conduction and valence selectivity of narrow ion channels, we have employed free energy techniques to calculate the potential of mean force (PMF) for ion movement through the prototypical gramicidin A channel. Employing modern all-atom molecular dynamics (MD) force fields with umbrella sampling methods that incorporate one hundred 1-2 ns trajectories, we find that it is possible to achieve semi-quantitative agreement with experimental binding and conductance measurements. We also examine the sensitivity of the MD-PMF results to the choice of MD force field and compare PMFs for potassium, calcium and chloride ions to explore the basis for the valence selectivity of this narrow and uncharged ion channel. A large central barrier is observed for both anions and divalent ions, consistent with lack of experimental conductance. Neither anion or divalent cation is seen to be stabilized inside the channel relative to the bulk electrolyte and each leads to large disruptions to the protein and membrane structure when held deep inside the channel. Weak binding of calcium ions outside the channel corresponds to a free energy well that is too shallow to demonstrate channel blocking. Our findings emphasize the success of the MD-PMF approach and the sensitivity of ion energetics to the choice of biomolecular force field.

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

    PubMed Central

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

    2014-01-01

    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. PMID:25417711

  5. Multiple-locus variable number of tandem repeat analysis as a tool for molecular epidemiology of botulism: The Italian experience.

    PubMed

    Anniballi, Fabrizio; Fillo, Silvia; Giordani, Francesco; Auricchio, Bruna; Tehran, Domenico Azarnia; di Stefano, Enrica; Mandarino, Giuseppina; De Medici, Dario; Lista, Florigio

    2016-12-01

    Clostridium botulinum is the bacterial agent of botulism, a rare but severe neuro-paralytic disease. Because of its high impact, in Italy botulism is monitored by an ad hoc surveillance system. The National Reference Centre for Botulism, as part of this system, collects and analyzes all demographic, epidemiologic, microbiological, and molecular data recovered during cases and/or outbreaks occurred in Italy. A panel of 312 C. botulinum strains belonging to group I were submitted to MLVA sub-typing. Strains, isolated from clinical specimens, food and environmental samples collected during the surveillance activities, were representative of all forms of botulism from all Italian regions. Through clustering analysis isolates were grouped into 12 main clusters. No regional or temporal clustering was detected, demonstrating the high heterogeneity of strains circulating in Italy. This study confirmed that MLVA is capable of sub-typing C. botulinum strains. Moreover, MLVA is effective at tracing and tracking the source of contamination and is helpful for the surveillance system in terms of planning and upgrading of procedures, activities and data collection forms.

  6. Molecular detection of establishment and geographical distribution of Brazilian isolates of Neozygites tanajoae, a fungus pathogenic to cassava green mite, in Benin (West Africa).

    PubMed

    Agboton, Bonaventure V; Hanna, Rachid; von Tiedemann, Andreas

    2011-03-01

    Diagnostic PCR with two specific primer pairs (NEOSSU and 8DDC) were used to monitor the establishment and geographical distribution of Brazilian isolates of Neozygites tanajoae Delalibera, Hajek and Humber (Entomophthorales: Neozygitaceae) released in Benin for the biological control of the cassava green mite, Mononychellus tanajoa (Bondar) (Acari: Tetranychidae). A total of 141 cassava fields were visited and samples of M. tanajoa suspected to be infected by N. tanajoae were collected in 60 fields distributed between the coastal Southern Forest Mosaic (SFM) and the Northern Guinea Savanna (NGS) zones of Benin, West Africa. Analysis of DNA samples of dead mites using the species specific NEOSSU primers revealed the presence of N. tanajoae in 46 fields. The second country specific pair of primers 8DDC revealed the presence of Brazilian isolates of N. tanajoae in 36 fields, representing 78.3% of fields positive for N. tanajoae. Brazilian isolates occurred from SFM to NGS zones in Benin, however, they were concentrated in fields located within former release zones (e.g. Department of Ouémé in the South and Borgou in the North). In contrast, the indigenous African isolates of N. tanajoae were evenly distributed in the sub-humid and humid savannah zones of the country. The mean infection rate of M. tanajoa with indigenous isolates of N. tanajoae was relatively low (5.3%) compared to Brazilian isolates (28%), indicating a higher biocontrol potential of the latter. This first post-release monitoring using PCR techniques showed that the Brazilian strains of N. tanajoae is well established in Benin and spread effectively in this area.

  7. 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

    SciTech Connect

    Loyalka, Sudarshan

    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.

  8. The effect of tool geometry on subsurface damage and material removal in nanometric cutting single-crystal silicon by a molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Dai, Houfu; Chen, Genyu; Fang, Qihong; Yin, Jiu

    2016-09-01

    Molecular dynamics is employed to investigate the nanoscale cutting process of monocrystalline silicon with diamond tool. Materials removal behavior of workpiece through diamond cutting is studied. The effects of tool geometry on the deformation of material including rake angle, clearance angle and edge radius were carefully explored by analyzing the phase transformation, chips, hydrostatic stress, shear stress and workpiece deformation. The investigation shows that a positive rake angle tip, a larger clearance angle tip or a small edge radius tip would result in a smaller cutting force, a better subsurface and a larger chipping volume. Moreover, a bigger negative rake angle tip cutting has a larger hydrostatic stress and shear stress. However, a positive rake angle tip cutting has a larger average friction coefficient than a negative rake angle tip cutting, which means that negative rake angle tip cutting experiences a lower resistance rate. It is also found that a tip with positive rake angle or smaller edge radius will improve the smoothness of a ground surface. In addition, a bigger clearance angle tip cutting generates a lower temperature in workpiece.

  9. Molecular dermatology comes of age.

    PubMed

    Has, Cristina; Sitaru, Cassian

    2013-01-01

    Groundbreaking advances on the molecular and cellular physiological and physiopathological skin processes, including the complete sequencing of the genome of several species and the increased availability of gene-modified organisms, paved the way to firmly establishing molecular approaches and methods in experimental, translational, and clinical dermatology. As a result, newly developed experimental ex vivo assays and animal models prove exquisite tools for addressing fundamental physiological cutaneous processes and pathogenic mechanisms of skin diseases. A plethora of new findings that were generated using these experimental tools serve as a strong basis for intense translational research efforts aiming at developing new, specific, and sensitive diagnostic tests and efficient "personalized" therapies with less side-effects. Consequently, a broad array of molecular diagnostic tests and therapies for a wide spectrum of skin diseases ranging from genodermatoses through skin neoplasms, allergy, inflammatory and autoimmune diseases, are already routinely used in the clinical dermatology practice. This article highlights several major developments in molecular experimental and clinical dermatology.

  10. Computer aided identification of sodium channel blockers in the clinical treatment of epilepsy using molecular docking tools

    PubMed Central

    Shaheen, Uzma; Akka, Jyothy; Hinore, Jitendra Singh; Girdhar, Amandeep; Bandaru, Srinivas; Sumithnath, Tharaparambil Gangadharan; Nayarisseri, Anuraj; Munshi, Anjana

    2015-01-01

    Phenytoin (PHT) and Carbamazepine (CBZ) are excellent sodium channel blockers administered in clinical treatment of epileptic seizures. However, the narrow therapeutic range and limited pharmacokinetics of these drugs have raised serious concerns in the proper management of epilepsy. To overcome this, the present study attempts to identify a candidate molecule with superior pharmacological profile than PHT and CBZ through In silico approaches. PHT and CBZ served as query small molecules for Tanimoto based similarity search with a threshold of 95% against PubChem database. Aided by MolDock algorithm, high affinity similar compound against each query was retrieved. PHT and CBZ and their respective similar were further tested for toxicity profiles, LC 50 values and biological activity. Compounds, NSC403438 and AGN-PC-0BPCBP respectively similar to PHT and CBZ demonstrated higher affinity to sodium channel protein than their respective leads. Of particular relevance, NSC403438 demonstrated highest binding affinity bestowed with least toxicity, better LC 50 values and optimal bioactivity. NSC403438 was further mapped for its structure based pharmacophoric features. In the study, we report NSC403438 as potential sodium channel blocker as a better candidate than PHT and CBZ which can be put forth for pharmacodynamic and pharmacokinetic studies. Abbreviations AEDs - Antiepileptic drugs, BLAST - Basic Local Alignment Search Tool, CBZ - Carbamazepine, GEFS+ - Generalized Epilepsy with Febrile Seizures Plus, GPCR - G Protein Coupled Receptor, Nav - Sodium channel with specific voltage conduction, PDB - Protein Data Bank, PHT - Phenytoin, PIR - Protein Information resources, SAVES - Structural Analysis and Verification Server, VGSC - Voltage-gated Sodium channels. PMID:25914447

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

    PubMed Central

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

    2016-01-01

    Western blotting is one of the most widely used techniques in molecular biology and biochemistry. Prestained proteins are used as molecular weight standards in protein electrophoresis. In the chemiluminescent Western blot analysis, however, these colored protein markers are invisible leaving researchers with the unsatisfying situation that the signal for the protein of interest and the signal for the markers are not captured simultaneously and have to be merged in an error-prone step. To allow the simultaneous detection of marker proteins we generated monoclonal antibodies specific for the protein dyes. To elicit a dye rather than protein specific immune response we immunized mice sequentially with dye-carrier protein complexes, in which a new carrier protein was used for each subsequent immunization. Moreover, by sequentially immunizing with dye-carrier protein complexes, in which different but structurally related dyes were used, we could also generate an antibody, termed anti-RAINBOW, that cross-reacted even with structurally related dyes not used in the immunizations. Our novel antibodies represent convenient tools for the simultaneous Western blot detection of commercially available prestained marker proteins in combination with the detection of any specific protein of interest. These antibodies will render obsolete the anachronistic tradition of manually charting marker bands on film. PMID:27531616

  12. SEEKR: Simulation Enabled Estimation of Kinetic Rates, A Computational Tool to Estimate Molecular Kinetics and Its Application to Trypsin-Benzamidine Binding.

    PubMed

    Votapka, Lane W; Jagger, Benjamin R; Heyneman, Alexandra L; Amaro, Rommie E

    2017-03-03

    We present the Simulation Enabled Estimation of Kinetic Rates (SEEKR) package, a suite of open-source scripts and tools designed to enable researchers to perform multiscale computation of the kinetics of molecular binding, unbinding, and transport using a combination of molecular dynamics, Brownian dynamics, and milestoning theory. To demonstrate its utility, we compute the kon, koff, and ΔGbind for the protein trypsin with its noncovalent binder, benzamidine, and examine the kinetics and other results generated in the context of the new software, and compare our findings to previous studies performed on the same system. We compute a kon estimate of (2.1 ± 0.3) × 10(7) M(-1) s(-1), a koff estimate of 83 ± 14 s(-1), and a ΔGbind of -7.4 ± 0.1 kcal·mol(-1), all of which compare closely to the experimentally measured values of 2.9 × 10(7) M(-1) s(-1), 600 ± 300 s(-1), and -6.71 ± 0.05 kcal·mol(-1), respectively.

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

    PubMed

    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.

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

    PubMed

    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.

  15. Multi-objective optimization and design of experiments as tools to tailor molecularly imprinted polymers specific for glucuronic acid.

    PubMed

    Kunath, Stephanie; Marchyk, Nataliya; Haupt, Karsten; Feller, Karl-Heinz

    2013-02-15

    We present a multi-objective optimization of the binding properties of a molecularly imprinted polymer (MIP) which specifically binds glucuronic acid (GA). A design of experiments approach is used to improve four different parameters that describe the binding properties of the polymer. Eleven different methacrylamide-co-ethyleneglycol dimethacrylate polymers imprinted with GA were synthesized according to a full factorial experimental design plan with 3 influencing factors (degree of cross-linking, molar equivalent of monomer to template and initiator concentration). These polymers were characterized by adsorption of the radiolabeled target analyte in methanol:water 9:1. The binding parameters were computed to optimize the polymer composition, taking into account four objective variables: the maximum binding capacity at high (Bmax) and low (B2) analyte concentrations, the equilibrium constant K50, and the imprinting factor (IF, binding to MIP/binding to NIP). With the multi-objective optimization method based on a desirability approach the composition of a twelfth "ideal" polymer could be predicted. This predicted polymer with highest "desirability" was synthesized with a composition of 0.65 mol% of initiator and a 1:4:20 ratio of template:functional monomers:cross-linker (T:M:X) (80% of cross-linking), and found to be the overall best MIP. Improvements over the original starting polymer were a 6 times lower K50, which corresponds to higher affinity, 20% higher capacity at low analyte concentration (B2), 40% higher capacity (Bmax) and 1.3 times increased imprinting factor (IF). Binding assays were also performed in aqueous solvents. Good binding properties were obtained in pure water with an imprinting factor of 3.2. Thus, this polymer is potentially applicable to biological samples like urine where glucuronides occur.

  16. Molecular confirmation of the genomic constitution of Douglasdeweya (Triticeae: Poaceae): demonstration of the utility of the 5S rDNA sequence as a tool for haplome identification.

    PubMed

    Baum, Bernard R; Johnson, Douglas A

    2008-06-01

    A new genus Douglasdeweya containing the two species, Douglasdeweya deweyi and D. wangii was published in 2005 by Yen et al. based upon the results of cytogenetical and morphological findings. The genome constitution of Douglasdeweya-PPStSt-allowed its segregation from the genus Pseudoroegneria which contains the StSt or StStStSt genomes. Our previous work had demonstrated the utility of using 5S rDNA units, especially the non-transcribed spacer sequence variation, for the resolution of genomes (haplomes) previously established by cytology. Here, we show that sequence analysis of the 5S DNA units from these species strongly supports the proposed species relationships of Yen et al. (Can J Bot 83:413-419, 2005), i.e., the PP genome from Agropyron and the StSt genome from Pseudoroegneria. Analysis of the 5S rDNA units constitutes a powerful tool for genomic research especially in the Triticeae.

  17. 1H NMR Metabolomics: A New Molecular Level Tool for Assessment of Organic Contaminant Bioavailability to Earthworms in Soil

    NASA Astrophysics Data System (ADS)

    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.

  18. Early Antiretroviral Therapy Is Associated with Lower HIV DNA Molecular Diversity and Lower Inflammation in Cerebrospinal Fluid but Does Not Prevent the Establishment of Compartmentalized HIV DNA Populations

    PubMed Central

    Oliveira, Michelli F.; Chaillon, Antoine; Nakazawa, Masato; Vargas, Milenka; Strain, Matthew C.; Morris, Sheldon; Little, Susan J.; Smith, Davey M.; Gianella, Sara

    2017-01-01

    Even when antiretroviral therapy (ART) is started early after infection, HIV DNA might persist in the central nervous system (CNS), possibly contributing to inflammation, brain damage and neurocognitive impairment. Paired blood and cerebrospinal fluid (CSF) were collected from 16 HIV-infected individuals on suppressive ART: 9 participants started ART <4 months of the estimated date of infection (EDI) (“early ART”), and 7 participants started ART >14 months after EDI (“late ART”). For each participant, neurocognitive functioning was measured by Global Deficit Score (GDS). HIV DNA levels were measured in peripheral blood mononuclear cells (PBMCs) and CSF cell pellets by droplet digital (dd)PCR. Soluble markers of inflammation (sCD163, IL-6, MCP-1, TNF-α) and neuronal damage (neurofilament light [NFL]) were measured in blood and CSF supernatant by immunoassays. HIV-1 partial C2V3 env deep sequencing data (Roche 454) were obtained for 8 paired PBMC and CSF specimens and used for phylogenetic and compartmentalization analysis. Median exposure to ART at the time of sampling was 2.6 years (IQR: 2.2–3.7) and did not differ between groups. We observed that early ART was significantly associated with lower molecular diversity of HIV DNA in CSF (p<0.05), and lower IL-6 levels in CSF (p = 0.02), but no difference for GDS, NFL, or HIV DNA detectability compared to late ART. Compartmentalization of HIV DNA populations between CSF and blood was detected in 6 out of 8 participants with available paired HIV DNA sequences (2 from early and 4 from late ART group). Phylogenetic analysis confirmed the presence of monophyletic HIV DNA populations within the CSF in 7 participants, and the same population was repeatedly sampled over a 5 months period in one participant with longitudinal sampling. Such compartmentalized provirus in the CNS needs to be considered for the design of future eradication strategies and might contribute to the neuropathogenesis of HIV. PMID:28046096

  19. Tracing the oxygen triple isotopic composition of tropospheric molecular oxygen in biogenic apatite - a new tool for palaeoclimatology

    NASA Astrophysics Data System (ADS)

    Pack, A.; Süssenberger, A.; Gehler, A.; Wotzlaw, J.

    2009-04-01

    It has been demonstrated that tropospheric molecular oxygen posses a significant isotope anomaly [1, 2 and refs. therein]. Relative to the rocks- and minerals-defined terrestrial fractionation line (TFL), tropospheric O2 has an anomaly of -0.35‰ [2]. Because almost all oxygen on Earth is contained in rocks, we suggest that the rocks- and minerals-defined TFL [3] should be used as reference when reporting isotope anomalies with ∆17O = δ'17OSMOW - βTFL δ'18OSMOW. We have developed a new technique for the determination of δ17O and δ18O of silicates by means of laser fluorination GC-CF-irmMS. We have determined βTFL to 0.5247 (N > 100), which is identical to the value reported by other laboratories and techniques [2, 3]. The uncertainty in ∆17O is ±0.03 (1σ) for a single analysis. It was suggested that ∆17O of tropospheric O2 can be used as proxy for the global bioactivity rate [GBR, 1] as well as for past atmospheric CO2 concentrations [4]. Past ∆17O of tropospheric O2 can be determined by analyzing O2 trapped in ice [1, 5] or by analyzing sulfates from terrestrial sulphide oxidation [4]. Disadvantage of ice core data is the limitation in time back <1 Myrs. The sulfate approach is used to trace ∆17O of air O2 back to Proterozoic times. Disadvantage of this technique is the uncertainty in the proportion of oxygen from O2 and oxygen from ambient water during oxidation of the sulphides. We suggest that oxygen from tooth and bone phosphate can be used as proxy for the ∆17O of air O2. Mass balance calculations [e.g. 6] suggest that a considerable portion of oxygen in biogenic apatite sources from respired air O2. We have analyzed tooth (enamel, dentine) and bone material by means of direct fluorination for their δ17O and δ18O. We have chosen material of mammals of different body mass (Mb) from Northern Germany (except Indian Elephant). The ∆17O of apatite varies between -0.16‰ for a wood mouse (Apodemus sylvaticus) and +0.04‰ for a wild boar

  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.

    PubMed

    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. Genotype characterization of the bacterium expressing the male-killing trait in the ladybird beetle Adalia bipunctata with specific rickettsial molecular tools.

    PubMed Central

    Balayeva, N M; Eremeeva, M E; Tissot-Dupont, H; Zakharov, I A; Raoult, D

    1995-01-01

    The male-killing ladybird beetle (LB) bacterium (AB bacterium) was analyzed with specific rickettsial molecular biology tools in the LB Adalia bipunctata strains. Eight phenotype-positive LB strains showing mortality of male embryos were amplified with rickettsial genus-specific primers from the gene for citrate synthase (CS) and the gene for a 17-kDa protein and spotted fever group-specific primers from the gene for the 120-kDa outer membrane protein (ompB). The specificity of amplification was confirmed by Southern hybridization and the absence of the above-listed gene products in three phenotype-negative LB strains. Restriction polymorphism patterns of three examined amplicons from the CS gene, 17-kDa-protein gene, and ompB gene were identical among the eight phenotype-positive LB strains and were unique among all known rickettsiae of the spotted fever and typhus groups. Amplified fragments of the CS genes of the AB bacterium, Rickettsia prowazekii Breinl, Rickettsia typhi Wilmington, Rickettsia canada 2678, and Rickettsia conorii 7 (Malish) were sequenced. The greatest differences among the above-listed rickettsial and AB bacterium CS gene sequences were between bp 1078 and 1110. Numerical analysis based on CS gene fragment sequences shows the close relationships of the AB bacterium to the genus Rickettsia. Expanding of knowledge about rickettsial arthropod vectors and participation of rickettsiae in the cytoplasmic maternal inheritance of arthropods is discussed. PMID:7747963

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

    NASA Astrophysics Data System (ADS)

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

    2017-02-01

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

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

    PubMed Central

    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

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

    PubMed

    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.

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

    PubMed

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

    2017-02-03

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

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

    PubMed

    Levin, Michael

    2012-03-01

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

  7. Molecular imaging for personalized cancer care.

    PubMed

    Kircher, Moritz F; Hricak, Hedvig; Larson, Steven M

    2012-04-01

    Molecular imaging is rapidly gaining recognition as a tool with the capacity to improve every facet of cancer care. Molecular imaging in oncology can be defined as in vivo characterization and measurement of the key biomolecules and molecularly based events that are fundamental to the malignant state. This article outlines the basic principles of molecular imaging as applied in oncology with both established and emerging techniques. It provides examples of the advantages that current molecular imaging techniques offer for improving clinical cancer care as well as drug development. It also discusses the importance of molecular imaging for the emerging field of theranostics and offers a vision of how molecular imaging may one day be integrated with other diagnostic techniques to dramatically increase the efficiency and effectiveness of cancer care.

  8. Establishing Time for Professional Learning

    ERIC Educational Resources Information Center

    Killion, Joyce

    2013-01-01

    Finding time for job-embedded professional learning is one of the most frequently cited challenges with implementing the Common Core State Standards (CCSS). With "Establishing Time for Professional Learning," practitioners and education leaders use tools to identify current allocations of time for professional learning, analyze how that…

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

    NASA Astrophysics Data System (ADS)

    Badin, Alice; Broholm, Mette M.; Jacobsen, Carsten S.; Palau, Jordi; Dennis, Philip; Hunkeler, Daniel

    2016-09-01

    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 documented by comparing data collected prior to the remediation event and eight years later. Based on the premise that dual C-Cl isotope slopes reflect ongoing degradation pathways, the slopes associated with PCE and TCE suggest the predominance of biotic reductive dechlorination near the source area. PCE was the predominant chlorinated ethene near the source area prior to thermal treatment. After thermal treatment, cDCE became predominant. The biotic contribution to these changes was supported by the presence of Dehalococcoides sp. DNA (Dhc) and Dhc targeted rRNA close to the source area. In contrast, dual C-Cl isotope analysis together with the almost absent VC 13C depletion in comparison to cDCE 13C depletion suggested that cDCE was subject to abiotic degradation due to the presence of pyrite, possible surface-bound iron (II) or reduced iron sulphides in the downgradient part of the plume. This interpretation is supported by the relative lack of Dhc in the downgradient part of the plume. The results of this study show that thermal remediation can enhance the biodegradation of chlorinated ethenes, and that this effect can be traced to the mobilisation of DOC due to steam injection. This, in turn, results in more reduced redox conditions which favor active reductive dechlorination and/or may lead to a series of redox reactions which may consecutively trigger biotically induced abiotic degradation. Finally, this study illustrates the valuable complementary application of compound-specific isotopic analysis combined with molecular biology tools to evaluate which biogeochemical processes are taking place in an aquifer contaminated with chlorinated ethenes.

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

    PubMed

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

    2015-08-01

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

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

    PubMed

    Sekulić, Vladislav; Lawrence, J Josh; Skinner, Frances K

    2014-01-01

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

  12. Infrared imaging as a cancer diagnostic tool: introducing a new concept of spectral barcodes for identifying molecular changes in colon tumors.

    PubMed

    Nallala, Jayakrupakar; Piot, Olivier; Diebold, Marie-Danièle; Gobinet, Cyril; Bouché, Olivier; Manfait, Michel; Sockalingum, Ganesh D

    2013-03-01

    Complementary diagnostic methods to conventional histopathology are under scrutiny for various types of cancers for rapid and molecular level diagnostics. In this perspective, a biophotonic approach based on infrared spectral micro-imaging combined with multivariate statistical analysis has been implemented on colon tissues. The ability of infrared imaging to investigate the intrinsic biochemical features of cells and tissues has been exploited to develop a new concept of spectral bar coding. To implement this concept, 10 frozen colon tissue samples (five nontumoral and tumoral pairs from five patients) were imaged using infrared spectral micro-imaging in a nondestructive manner. The spectral images were processed by a multivariate clustering method to identify the histological organization in a label-free manner. Spectral information from the epithelial components was then automatically recovered on the basis of their intrinsic biochemical composition, and compared using a statistical method (Mann-Whitney U-test) to construct spectral barcodes specific to each patient. The spectral barcodes representing the discriminant infrared spectral wavenumbers (900-1,800 cm(-1) ) enabled characterization of some of the malignancy-associated biochemical alterations associated with mucin, nucleotides, carbohydrates, and protein regions. This approach not only allowed the identification of common biochemical alterations among all the colon cancer patients, but also revealed a difference of gradient within individual patients. This new concept of spectral bar coding gives insight into the potential of infrared spectral micro-imaging as a complementary diagnostic tool to conventional histopathology, for biochemical level understanding of malignancy in colon cancers in an objective and label-free manner.

  13. Using Multi-Compartment Ensemble Modeling As an Investigative Tool of Spatially Distributed Biophysical Balances: Application to Hippocampal Oriens-Lacunosum/Moleculare (O-LM) Cells

    PubMed Central

    Sekulić, Vladislav; Lawrence, J. Josh; Skinner, Frances K.

    2014-01-01

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

  14. Reference Genes for qPCR Analysis in Resin-Tapped Adult Slash Pine As a Tool to Address the Molecular Basis of Commercial Resinosis

    PubMed Central

    de Lima, Júlio C.; de Costa, Fernanda; Füller, Thanise N.; Rodrigues-Corrêa, Kelly C. da Silva; Kerber, Magnus R.; Lima, Mariano S.; Fett, Janette P.; Fett-Neto, Arthur G.

    2016-01-01

    Pine oleoresin is a major source of terpenes, consisting of turpentine (mono- and sesquiterpenes) and rosin (diterpenes) fractions. Higher oleoresin yields are of economic interest, since oleoresin derivatives make up a valuable source of materials for chemical industries. Oleoresin can be extracted from living trees, often by the bark streak method, in which bark removal is done periodically, followed by application of stimulant paste containing sulfuric acid and other chemicals on the freshly wounded exposed surface. To better understand the molecular basis of chemically-stimulated and wound induced oleoresin production, we evaluated the stability of 11 putative reference genes for the purpose of normalization in studying Pinus elliottii gene expression during oleoresinosis. Samples for RNA extraction were collected from field-grown adult trees under tapping operations using stimulant pastes with different compositions and at various time points after paste application. Statistical methods established by geNorm, NormFinder, and BestKeeper softwares were consistent in pointing as adequate reference genes HISTO3 and UBI. To confirm expression stability of the candidate reference genes, expression profiles of putative P. elliottii orthologs of resin biosynthesis-related genes encoding Pinus contorta β-pinene synthase [PcTPS-(−)β-pin1], P. contorta levopimaradiene/abietadiene synthase (PcLAS1), Pinus taeda α-pinene synthase [PtTPS-(+)αpin], and P. taeda α-farnesene synthase (PtαFS) were examined following stimulant paste application. Increased oleoresin yields observed in stimulated treatments using phytohormone-based pastes were consistent with higher expression of pinene synthases. Overall, the expression of all genes examined matched the expected profiles of oleoresin-related transcript changes reported for previously examined conifers. PMID:27379135

  15. Molecular cytogenetic analyses of HIG, a novel human cell line carrying t(1;3)(p36.3;q25.3) established from a patient with chronic myelogenous leukemia in blastic crisis.

    PubMed

    Hosoya, Noriko; Ogawa, Seishi; Motokura, Tohru; Hangaishi, Akira; Wang, Lili; Qiao, Ying; Nannya, Yasuhito; Kogi, Mieko; Hirai, Hisamaru

    2003-12-01

    Chromosomal abnormalities involving 1p36, 3q21, and/or 3q26 have been reported in a subset of myeloid neoplasms having characteristic dysmegakaryopoiesis, and the overexpression of EVI1 on 3q26 or of MEL1 on 1p36 has been implicated in their pathogenesis. We describe molecular cytogenetic analyses of a novel human cell line, HIG, established from a unique case in which a novel translocation t(1;3)(p36;q26) appeared as the sole additional chromosomal abnormality at the time of blastic transformation of chronic myelogenous leukemia. The patient displayed clinical features resembling those of the 3q21q26 syndrome. The HIG cell line retained der(1)t(1;3)(p36;q26) but lost t(9;22)(q34;q11). To identify the relevant gene that would be deregulated by this translocation, we molecularly cloned the translocation's breakpoints. They were distant from the breakpoint cluster regions of the 3q21q26 syndrome or t(1;3)(p36;q21), and neither the EVI1 nor the MEL1 transcript was detected in the HIG cell line. None of the genes located within 150 kilobase pairs of the breakpoints were aberrantly expressed, suggesting that in this case other gene(s) more distant from the breakpoints are deregulated by possible remote effects. Further analyses of the deregulated genes in the HIG cell line should provide important insight into the mechanisms involved in these types of leukemias.

  16. The development of new molecular tools containing a chemically synthesized carbohydrate ligand for the elucidation of carbohydrate roles via photoaffinity labeling: carbohydrate-protein interactions are affected by the structures of the glycosidic bonds and the reducing-end sugar.

    PubMed

    Ohtsuka, Isao; Sadakane, Yutaka; Hada, Noriyasu; Higuchi, Mari; Atsumi, Toshiyuki; Kakiuchi, Nobuko

    2014-08-01

    Photoaffinity labeling technology is a highly efficient method for cloning carbohydrate-binding proteins. When the carbohydrate probes are synthesized according to conventional methods, however, the reducing terminus of the sugar is opened to provide an acyclic structure. Our continued efforts to solve this problem led to the development of new molecular tools with an oligosaccharide structure that contains a phenyldiazirine group for the elucidation of carbohydrate-protein interactions. We investigated whether carbohydrate-lectin interactions are affected by differences in the glycosidic formation and synthesized three types of molecular tools containing Galp-GlcpNAc disaccharide ligands and a photoreactive group (1, 2, 3). Photoaffinity labeling validated the recognition of the new ligand by different glycosidic bonds. Photoaffinity labeling also demonstrated that both the reducing end sugar and non-reducing end sugar recognized the Erythrina cristagalli agglutinin.

  17. MIiSR: Molecular Interactions in Super-Resolution Imaging Enables the Analysis of Protein Interactions, Dynamics and Formation of Multi-protein Structures

    PubMed Central

    Caetano, Fabiana A.; Dirk, Brennan S.; Tam, Joshua H. K.; Cavanagh, P. Craig; Goiko, Maria; Ferguson, Stephen S. G.; Pasternak, Stephen H.; Dikeakos, Jimmy D.; de Bruyn, John R.; Heit, Bryan

    2015-01-01

    Our current understanding of the molecular mechanisms which regulate cellular processes such as vesicular trafficking has been enabled by conventional biochemical and microscopy techniques. However, these methods often obscure the heterogeneity of the cellular environment, thus precluding a quantitative assessment of the molecular interactions regulating these processes. Herein, we present Molecular Interactions in Super Resolution (MIiSR) software which provides quantitative analysis tools for use with super-resolution images. MIiSR combines multiple tools for analyzing intermolecular interactions, molecular clustering and image segmentation. These tools enable quantification, in the native environment of the cell, of molecular interactions and the formation of higher-order molecular complexes. The capabilities and limitations of these analytical tools are demonstrated using both modeled data and examples derived from the vesicular trafficking system, thereby providing an established and validated experimental workflow capable of quantitatively assessing molecular interactions and molecular complex formation within the heterogeneous environment of the cell. PMID:26657340

  18. Establishment of a sandwich enzyme-linked immunosorbent assay for specific detection of Bacillus thuringiensis (Bt) Cry1Ab toxin utilizing a monoclonal antibody produced with a novel hapten designed with molecular model.

    PubMed

    Dong, Sa; Zhang, Xiao; Liu, Yuan; Zhang, Cunzheng; Xie, Yajing; Zhong, Jianfeng; Xu, Chongxin; Liu, Xianjin

    2017-03-01

    Cry1Ab toxin is commonly expressed in genetically modified crops in order to control chewing pests. At present, the detection method with enzyme-linked immunosorbent assay (ELISA) based on monoclonal antibody cannot specifically detect Cry1Ab toxin for Cry1Ab's amino acid sequence and spatial structure are highly similar to Cry1Ac toxin. In this study, based on molecular design, a novel hapten polypeptide was synthesized and conjugated to keyhole limpet hemocyanin (KLH). Then, through animal immunization with this antigen, a monoclonal antibody named 2C12, showing high affinity to Cry1Ab and having no cross reaction with Cry1Ac, was produced. The equilibrium dissociation constant (K D) value of Cry1Ab toxin with MAb 2C12 was 1.947 × 10(-8) M. Based on this specific monoclonal antibody, a sandwich enzyme-linked immunosorbent assay (DAS-ELISA) was developed for the specific determination of Cry1Ab toxin and the LOD and LOQ values were determined as 0.47 ± 0.11 and 2.43 ± 0.19 ng mL(-1), respectively. The average recoveries of Cry1Ab from spiked rice leaf and rice flour samples ranged from 75 to 115%, with coefficient of variation (CV) less than 8.6% within the quantitation range (2.5-100 ng mL(-1)), showing good accuracy for the quantitative detection of Cry1Ab toxin in agricultural samples. In conclusion, this study provides a new approach for the production of high specific antibody and the newly developed DAS-ELISA is a useful method for Cry1Ab monitoring in agriculture products. Graphical Abstract Establishment of a DAS-ELISA for the specific detecting of Bacillus thuringiensis (Bt) Cry1Ab toxin.

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

    NASA Astrophysics Data System (ADS)

    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

  20. I Cell Disease (Mucolipidosis II Alpha/Beta): From Screening to Molecular Diagnosis.

    PubMed

    Singh, Ankur; Prasad, Rajniti; Gupta, Aditya Kumar; Sharma, Anil; Alves, Sandra; Coutinho, Maria Francisca; Kapoor, Seema; Mishra, Om Prakash

    2017-02-01

    Mucopolysaccharidosis (MPS) and Mucolipidosis (ML) share common phenotypes (coarse facial features, organomegaly, dysostosis multiplex) despite having different molecular basis. Thus, they pose great diagnostic challenge to treating clinicians. Differentiating between the two conditions requires a battery of tests from screening to molecular diagnosis. Besides discussing differential diagnosis of MPS like features with negative urinary Glycosaminoglycans (GAG), the authors also discuss the utility of p-nitrocatechol sulphate based chemical test as an important screening tool, besides establishing molecular basis in index case.

  1. Establishing the colitis-associated cancer progression mouse models.

    PubMed

    Zheng, Haiming; Lu, Zhanjun; Wang, Ruhua; Chen, Niwei; Zheng, Ping

    2016-12-01

    Inflammatory bowel disease (IBD) has been reported as an important inducer of colorectal cancer (CRC). The most malignant IBD-associated CRC type has been highlighted as colitis-associated cancer (CAC). However, lack of CAC cases and difficulties of the long follow-up research have challenged researchers in molecular mechanism probing. Here, we established pre-CAC mouse models (dextran sulfate sodium [DSS] group and azoxymethane [AOM] group) and CAC mouse model (DSS/AOM group) to mimic human CAC development through singly or combinational treatment with DSS and AOM followed by disease activity index analysis. We found that these CAC mice showed much more severe disease phenotype, including serious diarrhea, body weight loss, rectal prolapse and bleeding, bloody stool, tumor burden, and bad survival. By detecting expression patterns of several therapeutic targets-Apc, p53, Kras, and TNF-α-in these mouse models through western blot, histology analysis, qRT-PCR, and ELISA methods, we found that the oncogene Kras expression remained unchanged, while the tumor suppressors-Apc and p53 expression were both significantly downregulated with malignancy progression from pre-CAC to CAC, and TNF-α level was elevated the most in CAC mice blood which is of potential clinical use. These data indicated the successful establishment of CAC development mouse models, which mimics human CAC well both in disease phenotype and molecular level, and highlighted the promoting role of inflammation in CAC progression. This useful tool will facilitate the further study in CAC molecular mechanism.

  2. KymographClear and KymographDirect: two tools for the automated quantitative analysis of molecular and cellular dynamics using kymographs

    PubMed Central

    Mangeol, Pierre; Prevo, Bram; Peterman, Erwin J. G.

    2016-01-01

    Dynamic processes are ubiquitous and essential in living cells. To properly understand these processes, it is imperative to measure them in a time-dependent way and analyze the resulting data quantitatively, preferably with automated tools. Kymographs are single images that represent the motion of dynamic processes and are widely used in live-cell imaging. Although they contain the full range of dynamics, it is not straightforward to extract this quantitative information in a reliable way. Here we present two complementary, publicly available software tools, KymographClear and KymographDirect, that have the power to reveal detailed insight in dynamic processes. KymographClear is a macro toolset for ImageJ to generate kymographs that provides automatic color coding of the different directions of movement. KymographDirect is a stand-alone tool to extract quantitative information from kymographs obtained from a wide range of dynamic processes in an automated way, with high accuracy and reliability. We discuss the concepts behind these software tools, validate them using simulated data, and test them on experimental data. We show that these tools can be used to extract motility parameters from a diverse set of cell-biological experiments in an automated and user-friendly way. PMID:27099372

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

    EPA Science Inventory

    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...

  4. Jetting tool

    SciTech Connect

    Szarka, D.D.; Schwegman, S.L.

    1991-07-09

    This patent describes an apparatus for hydraulically jetting a well tool disposed in a well, the well tool having a sliding member. It comprises positioner means for operably engaging the sliding member of the well tool; and a jetting means, connected at a rotatable connection to the positioner means so that the jetting means is rotatable relative to the positioner means and the well tool, for hydraulically jetting the well tool as the jetting means is rotated relative thereto.

  5. New integrated elemental and molecular strategies as a diagnostic tool for the quality of water soluble quantum dots and their bioconjugates

    NASA Astrophysics Data System (ADS)

    Trapiella-Alfonso, Laura; Montoro Bustos, Antonio R.; Encinar, Jorge Ruiz; Costa-Fernández, Jose M.; Pereiro, Rosario; Sanz-Medel, Alfredo

    2011-03-01

    Herein, we demonstrate that both qualitative molecular and quantitative elemental data obtained from size exclusion chromatography coupled online for the first time to both molecular fluorescence and elemental mass spectrometry, respectively, turned out to be critical to evaluate the quality of coatings of quantum dots. Moreover, such an instrumental approach also allowed us to study quantitatively the appropriated bioconjugation of quantum dots to antibodies, a critical step for QDs future use in quantitative fluorescence immunoassays.Herein, we demonstrate that both qualitative molecular and quantitative elemental data obtained from size exclusion chromatography coupled online for the first time to both molecular fluorescence and elemental mass spectrometry, respectively, turned out to be critical to evaluate the quality of coatings of quantum dots. Moreover, such an instrumental approach also allowed us to study quantitatively the appropriated bioconjugation of quantum dots to antibodies, a critical step for QDs future use in quantitative fluorescence immunoassays. Electronic supplementary information (ESI) available: Description of experimental section and Fig. S1 and S2. See DOI: 10.1039/c0nr00822b

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Apple Replant Disease (ARD) is one of the major limitations to the establishment of an economically viable orchard on replant sites due to the buildup and long-term survival of pathogen inoculum. Infection by several soilborne necrotrophic fungi and oomycetes is primarily responsible for ARD and res...

  7. Tool Carrier

    NASA Technical Reports Server (NTRS)

    1980-01-01

    Tool organizer accommodates a selection of hand tools on a waist or thigh belt or alternately on wall, work bench, or car trunk mountings. Tool caddy is widely used by industrial maintenance personnel, TV technicians, mechanics, artists, draftsmen, hobbyists and homeowners. Its innovative feature is rows of flexible vinyl "fingers" like the bristles of a hairbrush which mesh together to hold the tool securely in place yet allow easy insertion or withdrawal. Product is no longer commercially available.

  8. Percussion tool

    DOEpatents

    Reed, Teddy R.

    2006-11-28

    A percussion tool is described and which includes a housing mounting a tool bit; a reciprocally moveable hammer borne by the housing and which is operable to repeatedly strike the tool bit; and a reciprocally moveable piston enclosed within the hammer and which imparts reciprocal movement to the reciprocally moveable hammer.

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

    PubMed

    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.

  10. NMR chemical shifts as a tool to analyze first principles molecular dynamics simulations in condensed phases: the case of liquid water.

    PubMed

    Banyai, Douglas R; Murakhtina, Tatiana; Sebastiani, Daniel

    2010-12-01

    We present (1)H NMR chemical shift calculations of liquid water based on first principles molecular dynamics simulations under periodic boundary conditions. We focus on the impact of computational parameters on the structural and spectroscopic data, which is an important question for understanding how sensitive the computed (1)H NMR resonances are upon variation of the simulation setup. In particular, we discuss the influence of the exchange-correlation functional and the size of the basis set, the choice for the fictitious electronic mass and the use of pseudopotentials for the nuclear magnetic resonance (NMR) calculation on one hand and the underlying Car-Parrinello-type molecular dynamics simulations on the other hand. Our findings show that the direct effect of these parameters on (1)H shifts is not big, whereas the indirect dependence via the structural data is more important. The (1)H NMR chemical shifts clearly reflect the induced structural changes, illustrating once again the sensitivity of (1)H NMR observables on small changes in the local chemical structure of complex hydrogen-bonded liquids.

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

    NASA Astrophysics Data System (ADS)

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

    PubMed Central

    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

  13. The Protestant Establishment Revisited

    ERIC Educational Resources Information Center

    Baltzell, E. Digby

    1976-01-01

    The author's book, "The Protestant Establishment: Aristocracy and Caste in America", is highly critical of the WASP (White-Anglo-Saxon-Protestant) establishment and proposed the development and need for some sort of upper-class ruling-group. Here is a re-evaluation of his book, now thirteen years old, by the author. (Author/RK)

  14. Topological and quantum molecular descriptors as effective tools for analyzing cytotoxic activity achieved by a series of (diselanediyldibenzene-4,1-diylnide)biscarbamate derivatives.

    PubMed

    Font, María; Plano, Daniel; Sanmartín, Carmen; Palop, Juan Antonio

    2017-05-01

    A molecular modeling study has been carried out on a previously reported series of (diselanediyldibenzene-4,1-diylnide)biscarbamate derivatives that show cytotoxic and antiproliferative in vitro activity against MCF-7 human cell line; radical scavenging properties were also confirmed when these compounds were tested for their ability to scavenge DPPH and ABTS radicals. The data obtained allowed us to classify the compounds into two different groups: (a) aliphatic carbamates for which the activity could be related with a first nucleophilic attack (mediated by H2O, for example) on the selenium atoms of the central scaffold, followed by the release of the alkyl N-(4-selanylphenyl) and N-(4-selenenophenyl)carbamate moieties. Then, a second nucleophilic attack on the carbamate moiety, to yield 4-aminobenzeneselenol and 4-selenenoaniline respectively, which can ultimately be responsible for the activity of the compounds; (b) aromatic carbamates, for which we propose a preferred nucleophilic attack on the carbamate moiety, yielding 4-[(4-aminophenyl)diselanyl]aniline, the common structural fragment for this series, for which we have previously demonstrated its cytotoxic profile. Then, selenium atoms of the central fragment may later undergo a new nucleophilic attack, to yield 4-selenenoaniline and 4-aminobenzeneselenol. The phenolic moieties released in this process may also have a synergistic cytotoxic and redox activity. The data that support this connection include the conformational behavior and the molecular topography of the derivatives which can influence the accessibility of the hydrolysis points, and some quantum descriptors (bond order, atomic charges, total valences, ionization potential, electron affinity, HOMO 0 and LUMO 0 location, etc.) that have been related to the biological activity of the compounds.

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

    PubMed Central

    Perdiguero, Pedro; Venturas, Martin; Cervera, María Teresa; Gil, Luis; Collada, Carmen

    2015-01-01

    Elms, especially Ulmus minor and U. 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 single nucleotide polymorphisms (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. PMID:26257751

  16. Holistic Framework For Establishing Interoperability of Heterogeneous Software Development Tools

    DTIC Science & Technology

    2003-06-01

    requirements of the customer. In the Japanese application of QFD, this is termed as "going to the gemba ." As stated by [ZULT93]: We must not be content...form going to the gemba . Contextual Inquiry (CI) is another technique for gathering customer requirements at the customers’ workplace. [HRON93...34going to the gemba " and "CI": "In CI, a fundamental principle is that users are to be studied in their normal working context (’going to the gemba

  17. The Comparison of Expressed Candidate Secreted Proteins from Two Arbuscular Mycorrhizal Fungi Unravels Common and Specific Molecular Tools to Invade Different Host Plants

    PubMed Central

    Kamel, Laurent; Tang, Nianwu; Malbreil, Mathilde; San Clemente, Hélène; Le Marquer, Morgane; Roux, Christophe; Frei dit Frey, Nicolas

    2017-01-01

    Arbuscular mycorrhizal fungi (AMF), belonging to the fungal phylum Glomeromycota, form mutualistic symbioses with roots of almost 80% of land plants. The release of genomic data from the ubiquitous AMF Rhizophagus irregularis revealed that this species possesses a large set of putative secreted proteins (RiSPs) that could be of major importance for establishing the symbiosis. In the present study, we aimed to identify SPs involved in the establishment of AM symbiosis based on comparative gene expression analyses. We first curated the secretome of the R. irregularis DAOM 197198 strain based on two available genomic assemblies. Then we analyzed the expression patterns of the putative RiSPs obtained from the fungus in symbiotic association with three phylogenetically distant host plants—a monocot, a dicot and a liverwort—in comparison with non-symbiotic stages. We found that 33 out of 84 RiSPs induced in planta were commonly up-regulated in these three hosts. Most of these common RiSPs are small proteins of unknown function that may represent putative host non-specific effector proteins. We further investigated the expressed secretome of Gigaspora rosea, an AM fungal species phylogenetically distant from R. irregularis. G. rosea also presents original symbiotic features, a narrower host spectrum and a restrictive geographic distribution compared to R. irregularis. Interestingly, when analyzing up-regulated G. rosea SPs (GrSPs) in different hosts, a higher ratio of host-specific GrSPs was found compared to RiSPs. Such difference of expression patterns may mirror the restrained host spectrum of G. rosea compared to R. irregularis. Finally, we identified a set of conserved SPs, commonly up-regulated by both fungi in all hosts tested, that could correspond to common keys of AMF to colonize host plants. Our data thus highlight the specificities of two distant AM fungi and help in understanding their conserved and specific strategies to invade different hosts. PMID

  18. The Comparison of Expressed Candidate Secreted Proteins from Two Arbuscular Mycorrhizal Fungi Unravels Common and Specific Molecular Tools to Invade Different Host Plants.

    PubMed

    Kamel, Laurent; Tang, Nianwu; Malbreil, Mathilde; San Clemente, Hélène; Le Marquer, Morgane; Roux, Christophe; Frei Dit Frey, Nicolas

    2017-01-01

    Arbuscular mycorrhizal fungi (AMF), belonging to the fungal phylum Glomeromycota, form mutualistic symbioses with roots of almost 80% of land plants. The release of genomic data from the ubiquitous AMF Rhizophagus irregularis revealed that this species possesses a large set of putative secreted proteins (RiSPs) that could be of major importance for establishing the symbiosis. In the present study, we aimed to identify SPs involved in the establishment of AM symbiosis based on comparative gene expression analyses. We first curated the secretome of the R. irregularis DAOM 197198 strain based on two available genomic assemblies. Then we analyzed the expression patterns of the putative RiSPs obtained from the fungus in symbiotic association with three phylogenetically distant host plants-a monocot, a dicot and a liverwort-in comparison with non-symbiotic stages. We found that 33 out of 84 RiSPs induced in planta were commonly up-regulated in these three hosts. Most of these common RiSPs are small proteins of unknown function that may represent putative host non-specific effector proteins. We further investigated the expressed secretome of Gigaspora rosea, an AM fungal species phylogenetically distant from R. irregularis. G. rosea also presents original symbiotic features, a narrower host spectrum and a restrictive geographic distribution compared to R. irregularis. Interestingly, when analyzing up-regulated G. rosea SPs (GrSPs) in different hosts, a higher ratio of host-specific GrSPs was found compared to RiSPs. Such difference of expression patterns may mirror the restrained host spectrum of G. rosea compared to R. irregularis. Finally, we identified a set of conserved SPs, commonly up-regulated by both fungi in all hosts tested, that could correspond to common keys of AMF to colonize host plants. Our data thus highlight the specificities of two distant AM fungi and help in understanding their conserved and specific strategies to invade different hosts.

  19. 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

    NASA Astrophysics Data System (ADS)

    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

  20. Enhanced Diagnosis of Pneumococcal Bacteremia Using Antigen- and Molecular-Based Tools on Blood Specimens in Mali and Thailand: A Prospective Surveillance Study.

    PubMed

    Moïsi, Jennifer C; Moore, Matthew; Carvalho, Maria da Gloria; Sow, Samba O; Siludjai, Duangkamon; Knoll, Maria Deloria; Tapia, Milagritos; Baggett, Henry C

    2016-02-01

    Prior antibiotic use, contamination, limited blood volume, and processing delays reduce yield of blood cultures for detection of Streptococcus pneumoniae. We performed immunochromatographic testing (ICT) on broth from incubated blood culture bottles and real-time lytA polymerase chain reaction (PCR) on broth and whole blood and compared findings to blood culture in patients with suspected bacteremia. We selected 383 patients in Mali and 586 patients in Thailand based on their blood culture results: 75 and 31 were positive for pneumococcus, 100 and 162 were positive for other pathogens, and 208 and 403 were blood culture negative, respectively. ICT and PCR of blood culture broth were at least 87% sensitive and 97% specific compared with blood culture; whole blood PCR was 75-88% sensitive and 96-100% specific. Pneumococcal yields in children < 5 years of age increased from 2.9% to 10.7% in Mali with > 99% of additional cases detected by whole blood PCR, and from 0.07% to 5.1% in Thailand with two-thirds of additional cases identified by ICT. Compared with blood culture, ICT and lytA PCR on cultured broth were highly sensitive and specific but their ability to improve pneumococcal identification varied by site. Further studies of these tools are needed before widespread implementation.

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

    PubMed

    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.

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

    PubMed

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

    2015-06-01

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

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

    PubMed Central

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

    2016-01-01

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

  4. Calixarene derivative as a tool for highly sensitive detection and oriented immobilization of proteins in a microarray format through noncovalent molecular interaction.

    PubMed

    Oh, Sang Wook; Moon, Jung Dae; Lim, Hyo Jin; Park, Sang Yeol; Kim, Taisun; Park, JaeBum; Han, Moon Hi; Snyder, Michael; Choi, Eui Yul

    2005-08-01

    One important factor in fabricating protein microarray is to immobilize proteins without losing their activity on a solid phase. To keep them functional, it is necessary to immobilize proteins in a way that preserve their folded structural integrity. In a previous study, we developed novel Calixarene derivatives for the immobilization of proteins on the surface of a glass slide (1). In this study, we compared the sensitivity and the specificity of the linker molecules with those of five other protein attachment agents on glass slides using a prostate-specific antigen and its antibodies as a model system. The Calixcrown-coated protein chip showed a superior sensitivity and a much lower detection limit than those chips prepared by other methods. When we tested the capability of Calixcrown to immobilize antibody molecules, it appeared that Calixcrown makes arrangement of antibody be more regular with the vertical orientation than the covalent-bond agent. We also observed that the Calixcrown chip could be used for the diagnostic application with clinical samples from prostate cancer and HIV patients. Finally, we applied the Calixcrown chip using an antibody microarray to identify up- or down-regulated proteins in specific tissue and detected several up- or down-regulated proteins from a rat liver by administering toxin. Thus, the Calixcrown chip can be used as a powerful tool with a wide range of applications, including protein-protein interaction, protein-DNA interaction, and an enzyme activity assay.

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

    PubMed

    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.

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

    PubMed

    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.

  7. Promising Practices in Instruction of Discovery Tools

    ERIC Educational Resources Information Center

    Buck, Stefanie; Steffy, Christina

    2013-01-01

    Libraries are continually changing to meet the needs of users; this includes implementing discovery tools, also referred to as web-scale discovery tools, to make searching library resources easier. Because these tools are so new, it is difficult to establish definitive best practices for teaching these tools; however, promising practices are…

  8. Forming Tool Use Representations: A Neurophysiological Investigation into Tool Exposure

    ERIC Educational Resources Information Center

    Mizelle, John Christopher; Tang, Teresa; Pirouz, Nikta; Wheaton, Lewis A.

    2011-01-01

    Prior work has identified a common left parietofrontal network for storage of tool-related information for various tasks. How these representations become established within this network on the basis of different modes of exposure is unclear. Here, healthy subjects engaged in physical practice (direct exposure) with familiar and unfamiliar tools.…

  9. 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.

    PubMed

    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.

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

    PubMed

    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.

  11. Cell-permeable peptide-based disruption of endogenous PKA-AKAP complexes: a tool for studying the molecular roles of AKAP-mediated PKA subcellular anchoring.

    PubMed

    Faruque, Omar M; Le-Nguyen, Dung; Lajoix, Anne-Dominique; Vives, Eric; Petit, Pierre; Bataille, Dominique; Hani, El-Habib

    2009-02-01

    Stimulation of numerous G protein-coupled receptors leads to the elevation of intracellular concentrations of cAMP, which subsequently activates the PKA pathway. Specificity of the PKA signaling module is determined by a sophisticated subcellular targeting network that directs the spatiotemporal activation of the kinase. This specific compartmentalization mechanism occurs through high-affinity interactions of PKA with A-kinase anchoring proteins (AKAPs), the role of which is to target the kinase to discrete subcellular microdomains. Recently, a peptide designated "AKAPis" has been proposed to competitively inhibit PKA-AKAP interactions in vitro. We therefore sought to characterize a cell-permeable construct of the AKAPis inhibitor and use it as a tool to characterize the impact of PKA compartmentalization by AKAPs. Using insulin-secreting pancreatic beta-cells (INS-1 cells), we showed that TAT-AKAPis (at a micromolar range) dose dependently disrupted a significant fraction of endogenous PKA-AKAP interactions. Immunoflurescent analysis also indicated that TAT-AKAPis significantly affected PKA subcellular localization. Furthermore, TAT-AKAPis markedly attenuated glucagon-induced phosphorylations of p44/p42 MAPKs and cAMP response element binding protein, which are downstream effectors of PKA. In parallel, TAT-AKAPis dose dependently inhibited the glucagon-induced potentiation of insulin release. Therefore, AKAP-mediated subcellular compartmentalization of PKA represents a key mechanism for PKA-dependent phosphorylation events and potentiation of insulin secretion in intact pancreatic beta-cells. More interestingly, our data highlight the effectiveness of the cell-permeable peptide-mediated approach to monitoring in cellulo PKA-AKAP interactions and delineating PKA-dependent phosphorylation events underlying specific cellular responses.

  12. A rapid molecular diagnosis of cutaneous leishmaniasis by colorimetric malachite green-loop-mediated isothermal amplification (LAMP) combined with an FTA card as a direct sampling tool.

    PubMed

    Nzelu, Chukwunonso O; Cáceres, Abraham G; Guerrero-Quincho, Silvia; Tineo-Villafuerte, Edwin; Rodriquez-Delfin, Luis; Mimori, Tatsuyuki; Uezato, Hiroshi; Katakura, Ken; Gomez, Eduardo A; Guevara, Angel G; Hashiguchi, Yoshihisa; Kato, Hirotomo

    2016-01-01

    Leishmaniasis remains one of the world's most neglected diseases, and early detection of the infectious agent, especially in developing countries, will require a simple and rapid test. In this study, we established a quick, one-step, single-tube, highly sensitive loop-mediated isothermal amplification (LAMP) assay for rapid detection of Leishmania DNA from tissue materials spotted on an FTA card. An FTA-LAMP with pre-added malachite green was performed at 64°C for 60min using a heating block and/or water bath and DNA amplification was detected immediately after incubation. The LAMP assay had high detection sensitivity down to a level of 0.01 parasites per μl. The field- and clinic-applicability of the colorimetric FTA-LAMP assay was demonstrated with 122 clinical samples collected from patients suspected of having cutaneous leishmaniasis in Peru, from which 71 positives were detected. The LAMP assay in combination with an FTA card described here is rapid and sensitive, as well as simple to perform, and has great potential usefulness for diagnosis and surveillance of leishmaniasis in endemic areas.

  13. The utility of multiple molecular methods including whole genome sequencing as tools to differentiate Escherichia coli O157:H7 outbreaks.

    PubMed

    Berenger, Byron M; Berry, Chrystal; Peterson, Trevor; Fach, Patrick; Delannoy, Sabine; Li, Vincent; Tschetter, Lorelee; Nadon, Celine; Honish, Lance; Louie, Marie; Chui, Linda

    2015-01-01

    A standardised method for determining Escherichia coli O157:H7 strain relatedness using whole genome sequencing or virulence gene profiling is not yet established. We sought to assess the capacity of either high-throughput polymerase chain reaction (PCR) of 49 virulence genes, core-genome single nt variants (SNVs) or k-mer clustering to discriminate between outbreak-associated and sporadic E. coli O157:H7 isolates. Three outbreaks and multiple sporadic isolates from the province of Alberta, Canada were included in the study. Two of the outbreaks occurred concurrently in 2014 and one occurred in 2012. Pulsed-field gel electrophoresis (PFGE) and multilocus variable-number tandem repeat analysis (MLVA) were employed as comparator typing methods. The virulence gene profiles of isolates from the 2012 and 2014 Alberta outbreak events and contemporary sporadic isolates were mostly identical; therefore the set of virulence genes chosen in this study were not discriminatory enough to distinguish between outbreak clusters. Concordant with PFGE and MLVA results, core genome SNV and k-mer phylogenies clustered isolates from the 2012 and 2014 outbreaks as distinct events. k-mer phylogenies demonstrated increased discriminatory power compared with core SNV phylogenies. Prior to the widespread implementation of whole genome sequencing for routine public health use, issues surrounding cost, technical expertise, software standardisation, and data sharing/comparisons must be addressed.

  14. GRIPPING TOOL

    DOEpatents

    Sandrock, R.J.

    1961-12-12

    A self-actuated gripping tool is described for transferring fuel elements and the like into reactors and other inaccessible locations. The tool will grasp or release the load only when properly positioned for this purpose. In addition, the load cannot be released except when unsupported by the tool, so that jarring or contact will not bring about accidental release of the load. The gripping members or jaws of the device are cam-actuated by an axially slidable shaft which has two lockable positions. A spring urges the shaft into one position and a solenoid is provided to overcome the spring and move it into the other position. The weight of the tool operates a sleeve to lock the shaft in its existing position. Only when the cable supporting the tool is slack is the device capable of being actuated either to grasp or release its load. (AEC)

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

    PubMed

    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.

  16. Omics Tools

    SciTech Connect

    Schaumberg, Andrew

    2012-12-21

    The Omics Tools package provides several small trivial tools for work in genomics. This single portable package, the “omics.jar” file, is a toolbox that works in any Java-based environment, including PCs, Macs, and supercomputers. The number of tools is expected to grow. One tool (called cmsearch.hadoop or cmsearch.local), calls the external cmsearch program to predict non-coding RNA in a genome. The cmsearch program is part of the third-party Infernal package. Omics Tools does not contain Infernal. Infernal may be installed separately. The cmsearch.hadoop subtool requires Apache Hadoop and runs on a supercomputer, though cmsearch.local does not and runs on a server. Omics Tools does not contain Hadoop. Hadoop mat be installed separartely The other tools (cmgbk, cmgff, fastats, pal, randgrp, randgrpr, randsub) do not interface with third-party tools. Omics Tools is written in Java and Scala programming languages. Invoking the “help” command shows currently available tools, as shown below: schaumbe@gpint06:~/proj/omics$ java -jar omics.jar help Known commands are: cmgbk : compare cmsearch and GenBank Infernal hits cmgff : compare hits among two GFF (version 3) files cmsearch.hadoop : find Infernal hits in a genome, on your supercomputer cmsearch.local : find Infernal hits in a genome, on your workstation fastats : FASTA stats, e.g. # bases, GC content pal : stem-loop motif detection by palindromic sequence search (code stub) randgrp : random subsample without replacement, of groups randgrpr : random subsample with replacement, of groups (fast) randsub : random subsample without replacement, of file lines For more help regarding a particular command, use: java -jar omics.jar command help Usage: java -jar omics.jar command args

  17. Diagnostic Tools for Learning Organizations.

    ERIC Educational Resources Information Center

    Moilanen, Raili

    2001-01-01

    The Learning Organization Diamond Tool was designed for holistic analysis of 10 learning organization elements at the individual and organizational levels. A test in 25 Finnish organizations established validity. Comparison with existing tools showed that differences derive from their different purposes. (Contains 33 references.) (SK)

  18. Establishing Passing Scores.

    ERIC Educational Resources Information Center

    McLarty, Joyce R.

    The problem of establishing appropriate passing scores is one of evaluation rather than estimation and not amenable to exact solution. It must therefore be approached by (1) identifying criteria for judging the acceptability of the passing score, (2) collecting the data appropriate to assessing each relevant criterion, and (3) judging how well the…

  19. Establishing a Continuous Repertoire.

    ERIC Educational Resources Information Center

    Meadowcroft, Pamela; Holland, James G.

    Investigators in this study looked for conditions that can rapidly establish continuous stimulus control of continuous response variations, or "response mapping." Unlike previous research in stimulus control, where a single stimulus comes to control a single response, 36 5-year-old children received errorless discrimination training at…

  20. Establishing a University Foundation.

    ERIC Educational Resources Information Center

    Lemish, Donald L.

    A handbook on how to establish a university foundation is presented. It presupposes that a foundation will be used as the umbrella organization for receiving all private gifts, restricted and unrestricted, for the benefit of a public college or university; and hence it chiefly addresses readers from public colleges and universities. Information is…

  1. Molecular Epidemiology for Vector Research on Leishmaniasis

    PubMed Central

    Kato, Hirotomo; Gomez, Eduardo A; Cáceres, Abraham G; Uezato, Hiroshi; Mimori, Tatsuyuki; Hashiguchi, Yoshihisa

    2010-01-01

    Leishmaniasis is a protozoan disease caused by the genus Leishmania transmitted by female phlebotomine sand flies. Surveillance of the prevalence of Leishmania and responsive vector species in endemic and surrounding areas is important for predicting the risk and expansion of the disease. Molecular biological methods are now widely applied to epidemiological studies of infectious diseases including leishmaniasis. These techniques are used to detect natural infections of sand fly vectors with Leishmania protozoa and are becoming powerful tools due to their sensitivity and specificity. Recently, genetic analyses have been performed on sand fly species and genotyping using PCR-RFLP has been applied to the sand fly taxonomy. In addition, a molecular mass screening method has been established that enables both sand fly species and natural leishmanial infections to be identified simultaneously in hundreds of sand flies with limited effort. This paper reviews recent advances in the study of sand flies, vectors of leishmaniasis, using molecular biological approaches. PMID:20617005

  2. A fast and accurate method for the determination of total and soluble fluorine in toothpaste using high-resolution graphite furnace molecular absorption spectrometry and its comparison with established techniques.

    PubMed

    Gleisner, Heike; Einax, Jürgen W; Morés, Silvane; Welz, Bernhard; Carasek, Eduardo

    2011-04-05

    A fast and reliable method has been developed for the determination of total and soluble fluorine in toothpaste, important quality control parameters in dentifrices. The method is based on the molecular absorption of gallium mono-fluoride, GaF, using a commercially available high-resolution continuum source atomic absorption spectrometer. Transversely heated platform tubes with zirconium as permanent chemical modifier were used throughout. Before each sample injection, a palladium and zirconium modifier solution and a gallium reagent were deposited onto the graphite platform and thermally pretreated to transform them into their active forms. The samples were only diluted and introduced directly into the graphite tube together with additional gallium reagent. Under these conditions the fluoride was stable up to a pyrolysis temperature of 550 °C, and the optimum vaporization (molecule formation) temperature was 1550 °C. The GaF molecular absorption was measured at 211.248 nm, and the limits of detection and quantification were 5.2 pg and 17 pg, respectively, corresponding to a limit of quantification of about 30 μg g(-1) (ppm) F in the original toothpaste. The proposed method was used for the determination of total and soluble fluorine content in toothpaste samples from different manufactures. The samples contained different ionic fluoride species and sodium monofluorophosphate (MFP) with covalently bonded fluorine. The results for total fluorine were compared with those obtained with a modified conventional headspace gas chromatographic procedure. Accuracy and precision of the two procedures were comparable, but the proposed procedure was much less labor-intensive, and about five times faster than the latter one.

  3. DNA topology influences molecular machine lifetime in human serum.

    PubMed

    Goltry, Sara; Hallstrom, Natalya; Clark, Tyler; Kuang, Wan; Lee, Jeunghoon; Jorcyk, Cheryl; Knowlton, William B; Yurke, Bernard; Hughes, William L; Graugnard, Elton

    2015-06-21

    DNA nanotechnology holds the potential for enabling new tools for biomedical engineering, including diagnosis, prognosis, and therapeutics. However, applications for DNA devices are thought to be limited by rapid enzymatic degradation in serum and blood. Here, we demonstrate that a key aspect of DNA nanotechnology-programmable molecular shape-plays a substantial role in device lifetimes. These results establish the ability to operate synthetic DNA devices in the presence of endogenous enzymes and challenge the textbook view of near instantaneous degradation.

  4. Establishment of Intestinal Bacteriology

    PubMed Central

    MITSUOKA, Tomotari

    2014-01-01

    Research on intestinal bacteria began around the end of the 19th century. During the last 5 decades of the 20th century, research on the intestinal microbiota made rapid progress. At first, in my work, I first developed a method of comprehensive analysis of the intestinal microbiota, and then I established classification and identification methods for intestinal anaerobes. Using these methods I discovered a number of ecological rules governing the intestinal microbiota and the role of the intestinl microbiota in health and disease. Moreover, using germfree animals, it was proven that the intestinal microbiota has a role in carcinogenesis and aging in the host. Thus, a new interdisciplinary field, “intestinal bacteriology” was established. PMID:25032084

  5. Establishment of a multimarker qPCR panel for the molecular characterization of circulating tumor cells in blood samples of metastatic breast cancer patients during the course of palliative treatment

    PubMed Central

    Bredemeier, Maren; Edimiris, Philippos; Tewes, Mitra; Mach, Pawel; Aktas, Bahriye; Schellbach, Doreen; Wagner, Jenny; Kimmig, Rainer; Kasimir-Bauer, Sabine

    2016-01-01

    Background Circulating tumor cells (CTC) are discussed to be an ideal surrogate marker for individualized treatment in metastatic breast cancer (MBC) since metastatic tissue is often difficult to obtain for repeated analysis. We established a nine gene qPCR panel to characterize the heterogeneous CTC population in MBC patients including epithelial CTC, their receptors (EPCAM, ERBB2, ERBB3, EGFR) CTC in Epithelial-Mesenchymal-Transition [(EMT); PIK3CA, AKT2), stem cell-like CTC (ALDH1) as well as resistant CTC (ERCC1, AURKA] to identify individual therapeutic targets. Results At TP0, at least one marker was detected in 84%, at TP1 in 74% and at TP2 in 79% of the patients, respectively. The expression of ERBB2, ERBB3 and ERCC1 alone or in combination with AURKA was significantly associated with therapy failure. ERBB2 + CTC were only detected in patients not receiving ERBB2 targeted therapies which correlated with no response. Furthermore, patients responding at TP2 had a significantly prolonged overall-survival than patients never responding (p = 0.0090). Patients and Methods 2 × 5 ml blood of 62 MBC patients was collected at the time of disease progression (TP0) and at two clinical staging time points (TP1 and TP2) after 8–12 weeks of chemo-, hormone or antibody therapy for the detection of CTC (AdnaTest EMT-2/StemCell Select™, QIAGEN Hannover GmbH, Germany). After pre-amplification, multiplex qPCR was performed. Establishment was performed using various cancer cell lines. PTPRC (Protein tyrosine phosphatase receptor type C) and GAPDH served as controls. Conclusions Monitoring MBC patients using a multimarker qPCR panel for the characterization of CTC might help to treat patients accordingly in the future. PMID:27223437

  6. Robot Tools

    NASA Technical Reports Server (NTRS)

    1996-01-01

    Mecanotron, now division of Robotics and Automation Corporation, developed a quick-change welding method called the Automatic Robotics Tool-change System (ARTS) under Marshall Space Flight Center and Rockwell International contracts. The ARTS system has six tool positions ranging from coarse sanding disks and abrasive wheels to cloth polishing wheels with motors of various horsepower. The system is used by fabricators of plastic body parts for the auto industry, by Texas Instruments for making radar domes, and for advanced composites at Aerospatiale in France.

  7. Management Tools

    NASA Technical Reports Server (NTRS)

    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.

  8. Microsatellite mapping of the deletion in patients with hereditary neuropathy with liability to pressure palsies (HNPP): new molecular tools for the study of the region 17p12 --> p11 and for diagnosis.

    PubMed

    LeGuern, E; Ravise, N; Gouider, R; Gugenheim, M; Lopes, J; Bouche, P; Agid, Y; Brice, A

    1996-01-01

    Hereditary neuropathy with liability to pressure palsies (HNPP) is an autosomal dominant peripheral neuropathy characterized by recurrent episodes of nerve palsies. We have analyzed 11 microsatellite markers from chromosome 17p12 --> p11 in nine French families with HNPP. The three microsatellites D17S839 (afm200yb12), D17S955 (afm317ygl), and D17S921 (afm191xh12) were localized in the deleted region. In allele segregation analyses, the microsatellite D17S793 (afm165zd4) detected two chromosome 17-linked loci, one of which was deleted in HNPP patients. Using these STR markers, we found that the deletion coincided with the CMT1A/HNPP monomer unit in eight of the nine families. In the remaining pedigree, the deletion lay between the centromeric microsatellite D17S805 (afm234tal) and the telomeric marker D17S922 (afm197xh6), which flank the CMT1A monomer unit. Comparison of these data with the available genetic and physical maps of 17p12 --> p11 shows that this region, which is frequently subject to rearrangement-inducing diseases, such as Smith-Magenis syndrome, Charcot-Marie-Tooth type 1A, and HNPP, presents recombination hot spots. Finally, this study demonstrates the usefulness of the D17S122 (RM11GT) and D17S921 (afm191xh12) microsatellites as tools for the molecular diagnosis of HNPP.

  9. A numerical study of ultraprecision machining of monocrystalline silicon with laser nano-structured diamond tools by atomistic simulation

    NASA Astrophysics Data System (ADS)

    Dai, Houfu; Chen, Genyu; Zhou, Cong; Fang, Qihong; Fei, Xinjiang

    2017-01-01

    Three-dimension molecular dynamics (MD) simulations is employed to investigate the ultraprecision machining of single crystal silicon with structured nanoscale diamond tool fabricated by laser. The advantages and disadvantages of diamond machining using structured tools are discussed in comparison with those of using non-structured tools. The von Mises stress distribution, hydrostatic stress distribution, atomic displacement, stress, the radial distribution function, cutting forces, frictional coefficient, subsurface temperature and potential energy during the nanometric machining process are studied. A theoretical analysis model is also established to investigate the subsurface damage mechanism by analyzing the distribution of residual stress during the nanoscale machining process. The results show that a structured nanoscale tool in machining brittle material silicon causes a smaller hydrostatic stress, a less compressive normal stress σxx and σyy , a lower temperature and a smaller cutting force. However, the structured nanoscale tool machining results in smaller chip volume and more beta-silicon phase. Besides, the friction coefficient for tool with V-shape groove is smaller than those for non-structured tools and other structured nanoscale tools. This means that the tool with V-shape groove can reduce the resistance to cutting during the nanoscale machining process. In addition, the results also point out that the potential energy of subsurface atoms and the number of other atoms for pyramid-structured tool are much smaller than those of using non-structured tools and other structured nanoscale tools.

  10. Tools for fluorescent molecularly imprinted polymers.

    PubMed

    Rathbone, Daniel L; Bains, Ajeet

    2005-01-15

    A linear co-polymer of hexyl acrylate and quinine acrylate was prepared anchored to cellulose filtration membranes. These were used to probe quenching of the tethered fluorophore by test compounds in solution for the validation of imprinted polymer fluorescence studies. The results are compared with simple solution phase quenching studies and also for two membrane-bound imprinted polymers containing the same fluorophore.

  11. Molecular tools for contemporary cotton breeding

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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. Molecular tools for studying plant genetic diversity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The ubiquitous nature of DNA is a central theme for all biology. The nucleus of each cell that makes up an organism contains genomic DNA, which is the blueprint for life. The differential expression of genes within each cell gives rise to different tissues, organs and, ultimately, different organi...

  13. Molecular Tools for Studying Plant Pathogens

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The ubiquitous nature of DNA is a central theme for all biology. The nucleus of each cell that makes up an organism contains genomic DNA, which is the blueprint for life. The differential expression of genes within each cell gives rise to different tissues, organs and, ultimately, different organism...

  14. Molecular Tools for Investigating the Gut Microbiota

    NASA Astrophysics Data System (ADS)

    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).

  15. Establishing maintenance performance indicators

    SciTech Connect

    Baca, B.

    1994-10-01

    Maintenance Performance Indicators (PI) specify where the maintenance department is and which direction it is going allowing for a quick and accurate assessment of the performance of the Maintenance Management Program (MMP). Establishing PI`s for the maintenance department will allow a measure of productivity and a means of feedback for methods improvement. Effective performance of the maintenance department directly effects plant profitability. Improvements in the quality and productivity of the maintenance work force will significantly reduce maintenance costs. The level of performance attained by the maintenance work force is usually guessed at. Guessing will not identify areas needing improvement or help to initiate a corrective action. Maintenance PI`s are required for maintenance departments whose goal is to control maintenance costs while increasing productivity. The application of basic statistical methods will allow a maintenance department to know where they are and which direction they are going. The data presented in this paper is a representation of indicators used in industry as well as developed indicators to establish a complete maintenance performance indicator program. The methodology used in developing this program can be used as a way to manage a cost effective maintenance management program.

  16. Molecular diagnosis of acute myeloid leukemia.

    PubMed

    Watt, Christopher D; Bagg, Adam

    2010-11-01

    The diagnosis and classification of acute myeloid leukemia is multifaceted, requiring the integration of a variety of laboratory findings, with genetic approaches now firmly established as a central component. Molecular genetic technologies continue to evolve and provide additional tiers of both clarity and complexity. Many have rapidly moved into clinical laboratories; others remain as relevant discovery tools, while some are poised to take their place in diagnostic testing menus. Here, we attempt to synthesize the role of various testing modalities and exciting nascent fundamental discoveries, with a view as to how these might be integrated into the contemporary and future evaluation of this group of aggressive hematologic malignancies.

  17. On the establishment of thermal diffusion in binary Lennard-Jones liquids

    NASA Astrophysics Data System (ADS)

    Ferrario, M.; Bonella, S.; Ciccotti, G.

    2016-10-01

    The establishment of thermal diffusion in an Ar-Kr Lennard-Jones mixture is investigated via dynamical non equilibrium molecular dynamics [G. Ciccotti, G. Jacucci, Phys. Rev. Lett. 35, 789 (1975)]. We observe, in particular, the evolution of the density and temperature fields of the system following the onset of the thermal gradient. In stationary conditions, we also compute the Soret coefficient of the mixture. This study confirms that dynamical non equilibrium molecular dynamics is an effective tool to gather information on transient phenomena, even though the full evolution of the mass and energy fluxes associated to the temperature and density fields requires, in this case, a more substantial numerical effort than the one employed here.

  18. Establishing Substantial Equivalence: Transcriptomics

    NASA Astrophysics Data System (ADS)

    Baudo, María Marcela; Powers, Stephen J.; Mitchell, Rowan A. C.; Shewry, Peter R.

    Regulatory authorities in Western Europe require transgenic crops to be substantially equivalent to conventionally bred forms if they are to be approved for commercial production. One way to establish substantial equivalence is to compare the transcript profiles of developing grain and other tissues of transgenic and conventionally bred lines, in order to identify any unintended effects of the transformation process. We present detailed protocols for transcriptomic comparisons of developing wheat grain and leaf material, and illustrate their use by reference to our own studies of lines transformed to express additional gluten protein genes controlled by their own endosperm-specific promoters. The results show that the transgenes present in these lines (which included those encoding marker genes) did not have any significant unpredicted effects on the expression of endogenous genes and that the transgenic plants were therefore substantially equivalent to the corresponding parental lines.

  19. Establishing a Presence

    NASA Technical Reports Server (NTRS)

    McCandless, Jeffrey

    2005-01-01

    The basis for this successful collaboration was face-to-face communication. Though it was sometimes stressful being on the road so much, I really learned the importance of being present to work together and ask questions in person. Another measure of success was that in the midst of this project and traveling, my wife and I managed to start a family. My oldest boy got a real kick out of visiting Space Center Houston when he was two to learn all about the "face futtle" which goes way up in the sky. When practical, collocation and face-to-face communication on a project eliminate misunderstandings, establish relationships, make information more easily accessible, and promote a team atmosphere. Compromise is key to balancing both family and career goals. Knowing when to prioritize each is important to success in both aspects.

  20. On establishing reference values.

    PubMed Central

    Lumsden, J H; Mullen, K

    1978-01-01

    In order to establish a range of reference values for any characteristic one can use Gaussian or nonparametric techniques, whichever are most appropriate. One has the choice of calculating tolerance intervals or percentile intervals. A tolerance interval is said to contain, say 95% of the population with probability, say 0.90. A percentile interval simply simply calculates the values between which 95% of the observations fall. If the data can be said to have a Gaussian distribution, the same precision can be obtained with smaller sample sizes than using the nonparametric techniques. In some cases, data which are not Gaussian can be transformed into a Gaussian form and hence make use of the more efficient Gaussian techniques. In both cases, the data should be checked for outliers or rogue observations and these should be eliminated if the testing procedure fails to imply that they are an integral part of the data. PMID:688072

  1. Downhole tool

    DOEpatents

    Hall, David R.; Muradov, Andrei; Pixton, David S.; Dahlgren, Scott Steven; Briscoe, Michael A.

    2007-03-20

    A double shouldered downhole tool connection comprises box and pin connections having mating threads intermediate mating primary and secondary shoulders. The connection further comprises a secondary shoulder component retained in the box connection intermediate a floating component and the primary shoulders. The secondary shoulder component and the pin connection cooperate to transfer a portion of makeup load to the box connection. The downhole tool may be selected from the group consisting of drill pipe, drill collars, production pipe, and reamers. The floating component may be selected from the group consisting of electronics modules, generators, gyroscopes, power sources, and stators. The secondary shoulder component may comprises an interface to the box connection selected from the group consisting of radial grooves, axial grooves, tapered grooves, radial protrusions, axial protrusions, tapered protrusions, shoulders, and threads.

  2. 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.

    PubMed

    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.

  3. Establishing lunar resource viability

    NASA Astrophysics Data System (ADS)

    Carpenter, J.; Fisackerly, R.; Houdou, B.

    2016-11-01

    Recent research has highlighted the potential of lunar resources as an important element of space exploration but their viability has not been demonstrated. Establishing whether or not they can be considered in future plans is a multidisciplinary effort, requiring scientific expertise and delivering scientific results. To this end various space agencies and private entities are looking to lunar resources, extracted and processed in situ, as a potentially game changing element in future space architectures, with the potential to increase scale and reduce cost. However, before any decisions can be made on the inclusion of resources in exploration roadmaps or future scenarios some big questions need to be answered about the viability of different resource deposits and the processes for extraction and utilisation. The missions and measurements that will be required to answer these questions, and which are being prepared by agencies and others, can only be performed through the engagement and support of the science community. In answering questions about resources, data and knowledge will be generated that is of fundamental scientific importance. In supporting resource prospecting missions the science community will de facto generate new scientific knowledge. Science enables exploration and exploration enables science.

  4. Workshop on molecular animation.

    PubMed

    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.

  5. Workshop on Molecular Animation

    PubMed Central

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

    2011-01-01

    Summary February 25–26, 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. PMID:20947014

  6. Genomic Tools in Groundnut Breeding Program: Status and Perspectives

    PubMed Central

    Janila, P.; Variath, Murali T.; Pandey, Manish K.; Desmae, Haile; Motagi, Babu N.; Okori, Patrick; Manohar, Surendra S.; Rathnakumar, A. L.; Radhakrishnan, T.; Liao, Boshou; Varshney, Rajeev K.

    2016-01-01

    Groundnut, a nutrient-rich food legume, is cultivated world over. It is valued for its good quality cooking oil, energy and protein rich food, and nutrient-rich fodder. Globally, groundnut improvement programs have developed varieties to meet the preferences of farmers, traders, processors, and consumers. Enhanced yield, tolerance to biotic and abiotic stresses and quality parameters have been the target traits. Spurt in genetic information of groundnut was facilitated by development of molecular markers, genetic, and physical maps, generation of expressed sequence tags (EST), discovery of genes, and identification of quantitative trait loci (QTL) for some important biotic and abiotic stresses and quality traits. The first groundnut variety developed using marker assisted breeding (MAB) was registered in 2003. Since then, USA, China, Japan, and India have begun to use genomic tools in routine groundnut improvement programs. Introgression lines that combine foliar fungal disease resistance and early maturity were developed using MAB. Establishment of marker-trait associations (MTA) paved way to integrate genomic tools in groundnut breeding for accelerated genetic gain. Genomic Selection (GS) tools are employed to improve drought tolerance and pod yield, governed by several minor effect QTLs. Draft genome sequence and low cost genotyping tools such as genotyping by sequencing (GBS) are expected to accelerate use of genomic tools to enhance genetic gains for target traits in groundnut. PMID:27014312

  7. Genomic Tools in Groundnut Breeding Program: Status and Perspectives.

    PubMed

    Janila, P; Variath, Murali T; Pandey, Manish K; Desmae, Haile; Motagi, Babu N; Okori, Patrick; Manohar, Surendra S; Rathnakumar, A L; Radhakrishnan, T; Liao, Boshou; Varshney, Rajeev K

    2016-01-01

    Groundnut, a nutrient-rich food legume, is cultivated world over. It is valued for its good quality cooking oil, energy and protein rich food, and nutrient-rich fodder. Globally, groundnut improvement programs have developed varieties to meet the preferences of farmers, traders, processors, and consumers. Enhanced yield, tolerance to biotic and abiotic stresses and quality parameters have been the target traits. Spurt in genetic information of groundnut was facilitated by development of molecular markers, genetic, and physical maps, generation of expressed sequence tags (EST), discovery of genes, and identification of quantitative trait loci (QTL) for some important biotic and abiotic stresses and quality traits. The first groundnut variety developed using marker assisted breeding (MAB) was registered in 2003. Since then, USA, China, Japan, and India have begun to use genomic tools in routine groundnut improvement programs. Introgression lines that combine foliar fungal disease resistance and early maturity were developed using MAB. Establishment of marker-trait associations (MTA) paved way to integrate genomic tools in groundnut breeding for accelerated genetic gain. Genomic Selection (GS) tools are employed to improve drought tolerance and pod yield, governed by several minor effect QTLs. Draft genome sequence and low cost genotyping tools such as genotyping by sequencing (GBS) are expected to accelerate use of genomic tools to enhance genetic gains for target traits in groundnut.

  8. RSP Tooling Technology

    SciTech Connect

    2001-11-20

    RSP Tooling{trademark} is a spray forming technology tailored for producing molds and dies. The approach combines rapid solidification processing and net-shape materials processing in a single step. The general concept involves converting a mold design described by a CAD file to a tooling master using a suitable rapid prototyping (RP) technology such as stereolithography. A pattern transfer is made to a castable ceramic, typically alumina or fused silica (Figure 1). This is followed by spray forming a thick deposit of a tooling alloy on the pattern to capture the desired shape, surface texture, and detail. The resultant metal block is cooled to room temperature and separated from the pattern. The deposit's exterior walls are machined square, allowing it to be used as an insert in a standard mold base. The overall turnaround time for tooling is about 3 to 5 days, starting with a master. Molds and dies produced in this way have been used in high volume production runs in plastic injection molding and die casting. A Cooperative Research and Development Agreement (CRADA) between the Idaho National Engineering and Environmental Laboratory (INEEL) and Grupo Vitro has been established to evaluate the feasibility of using RSP Tooling technology for producing molds and dies of interest to Vitro. This report summarizes results from Phase I of this agreement, and describes work scope and budget for Phase I1 activities. The main objective in Phase I was to demonstrate the feasibility of applying the Rapid Solidification Process (RSP) Tooling method to produce molds for the manufacture of glass and other components of interest to Vitro. This objective was successfully achieved.

  9. State Analysis Database Tool

    NASA Technical Reports Server (NTRS)

    Rasmussen, Robert; Bennett, Matthew

    2006-01-01

    The State Analysis Database Tool software establishes a productive environment for collaboration among software and system engineers engaged in the development of complex interacting systems. The tool embodies State Analysis, a model-based system engineering methodology founded on a state-based control architecture (see figure). A state represents a momentary condition of an evolving system, and a model may describe how a state evolves and is affected by other states. The State Analysis methodology is a process for capturing system and software requirements in the form of explicit models and states, and defining goal-based operational plans consistent with the models. Requirements, models, and operational concerns have traditionally been documented in a variety of system engineering artifacts that address different aspects of a mission s lifecycle. In State Analysis, requirements, models, and operations information are State Analysis artifacts that are consistent and stored in a State Analysis Database. The tool includes a back-end database, a multi-platform front-end client, and Web-based administrative functions. The tool is structured to prompt an engineer to follow the State Analysis methodology, to encourage state discovery and model description, and to make software requirements and operations plans consistent with model descriptions.

  10. Tool Gear: Infrastructure for Parallel Tools

    SciTech Connect

    May, J; Gyllenhaal, J

    2003-04-17

    Tool Gear is a software infrastructure for developing performance analysis and other tools. Unlike existing integrated toolkits, which focus on providing a suite of capabilities, Tool Gear is designed to help tool developers create new tools quickly. It combines dynamic instrumentation capabilities with an efficient database and a sophisticated and extensible graphical user interface. This paper describes the design of Tool Gear and presents examples of tools that have been built with it.

  11. Sasquatch Footprint Tool

    NASA Technical Reports Server (NTRS)

    Bledsoe, Kristin

    2013-01-01

    The Crew Exploration Vehicle Parachute Assembly System (CPAS) is the parachute system for NASA s Orion spacecraft. The test program consists of numerous drop tests, wherein a test article rigged with parachutes is extracted or released from an aircraft. During such tests, range safety is paramount, as is the recoverability of the parachutes and test article. It is crucial to establish an aircraft release point that will ensure that the article and all items released from it will land in safe locations. A new footprint predictor tool, called Sasquatch, was created in MATLAB. This tool takes in a simulated trajectory for the test article, information about all released objects, and atmospheric wind data (simulated or actual) to calculate the trajectories of the released objects. Dispersions are applied to the landing locations of those objects, taking into account the variability of winds, aircraft release point, and object descent rate. Sasquatch establishes a payload release point (e.g., where the payload will be extracted from the carrier aircraft) that will ensure that the payload and all objects released from it will land in a specified cleared area. The landing locations (the final points in the trajectories) are plotted on a map of the test range. Sasquatch was originally designed for CPAS drop tests and includes extensive information about both the CPAS hardware and the primary test range used for CPAS testing. However, it can easily be adapted for more complex CPAS drop tests, other NASA projects, and commercial partners. CPAS has developed the Sasquatch footprint tool to ensure range safety during parachute drop tests. Sasquatch is well correlated to test data and continues to ensure the safety of test personnel as well as the safe recovery of all equipment. The tool will continue to be modified based on new test data, improving predictions and providing added capability to meet the requirements of more complex testing.

  12. Why You Should Establish a Connection to the Internet.

    ERIC Educational Resources Information Center

    Hill, Judy A.; Misic, Mark M.

    1996-01-01

    Provides the rationale for establishing a connection to the Internet. Describes Internet services, including e-mail, telnet, file transfer protocol (FTP), USENET, gopher, Archie, and World Wide Web. Identifies reasons why the Internet is a valuable tool. Outlines steps for establishing a connection and discusses the future of the Internet. A…

  13. Indispensable tool

    SciTech Connect

    Robinson, Arthur

    2001-08-10

    Synchrotron radiation has become an indispensable research tool for a growing number of scientists in a seemingly ever expanding number of disciplines. We can thank the European Synchrotron Research Facility (ESRF) in Grenoble for taking an innovative step toward achieving the educational goal of explaining the nature and benefits of synchrotron radiation to audiences ranging from the general public (including students) to government officials to scientists who may be unfamiliar with x-ray techniques and synchrotron radiation. ESRF is the driving force behind a new CD-ROM playable on both PCs and Macs titled Synchrotron light to explore matter. Published by Springer-Verlag, the CD contains both English and French versions of a comprehensive overview of the subject.

  14. Hydraulic tool

    SciTech Connect

    Gregory, J.T.

    1988-04-05

    A hydraulic force-delivering tool including a cylinder, a piston slidable in the cylinder and a hydraulic pump to deliver fluid under pressure to the cylinder the hydraulic pump is described, comprising: a pump body; means forming a cylindrical chamber in the pump body; at least one inlet port opening into one end of the chamber from outside the body; means forming an outlet port at the other end of the chamber; a check valve in the outlet port enabling outward flow only; a pump rod plunger reciprocable through a given stroke in the chamber; inner and outer concentric cylindrical surfaces in the chamber and on the plunger, respectively; an annular shoulder on the chamber inner cylindrical surface facing toward the other end of the chamber; an annular seal member slidable along the pump rod and conditioned to seal against the shoulder; and spring means biasing the seal member toward the shoulder.

  15. Optical Tools

    NASA Astrophysics Data System (ADS)

    Roncali, E.; Tavitian, B.; Texier, I. E.; Peltié, P.; Perraut, F.; Boutet, J.; Cognet, L.; Lounis, B.; Marguet, D.; Thoumine, O.; Tramier, M.

    Fluorescence is a physical phenomenon described for the first time in 1852 by the British scientist George G. Stokes, famous for his work in mathematics and hydrodynamics. He observed the light emitted by a mineral after excitation (absorption of light by the mineral) by UV light. He then formulated what has become known as Stokes’ law, which says that the wavelength of fluorescence emission is longer than the excitation wavelength used to generate it. Some phenomena departing from this rule were later discovered, but do not in fact invalidate it. The possibility of visible excitation was subsequently developed, with the discovery of many fluorescing aromaticmolecules, called fluorophores. The identification of these compounds and improved control over the physical phenomenon meant that by 1930 research tools had been developed in biology, e.g., labeling certain tissues and bacteria so as to observe them by fluorescence. The optical microscope as it had existed since the nineteenth century thus gave rise to the fluorescence microscope: a reflection system to supply the light required to excite the fluorophores was added to the standard microscope, together with a suitable filtering system. Fluorescence microscopy soon became an important tool for biological analysis both in vitro and ex vivo, and other applications of light emission were also devised (light-emission phenomena of which fluorescence is a special case, described further in Sect. 7.2). It became possible to study phenomena that could not be observed by standard optical microscopy. Among other things, the location of molecules inside cells, monitoring of intracellular processes, and detection of single molecules all become feasible by means of fluorescence microscopy.

  16. Zoonotic potential and molecular epidemiology of Giardia species and giardiasis.

    PubMed

    Feng, Yaoyu; Xiao, Lihua

    2011-01-01

    Molecular diagnostic tools have been used recently in assessing the taxonomy, zoonotic potential, and transmission of Giardia species and giardiasis in humans and animals. The results of these studies have firmly established giardiasis as a zoonotic disease, although host adaptation at the genotype and subtype levels has reduced the likelihood of zoonotic transmission. These studies have also identified variations in the distribution of Giardia duodenalis genotypes among geographic areas and between domestic and wild ruminants and differences in clinical manifestations and outbreak potentials of assemblages A and B. Nevertheless, our efforts in characterizing the molecular epidemiology of giardiasis and the roles of various animals in the transmission of human giardiasis are compromised by the lack of case-control and longitudinal cohort studies and the sampling and testing of humans and animals living in the same community, the frequent occurrence of infections with mixed genotypes and subtypes, and the apparent heterozygosity at some genetic loci for some G. duodenalis genotypes. With the increased usage of multilocus genotyping tools, the development of next-generation subtyping tools, the integration of molecular analysis in epidemiological studies, and an improved understanding of the population genetics of G. duodenalis in humans and animals, we should soon have a better appreciation of the molecular epidemiology of giardiasis, the disease burden of zoonotic transmission, the taxonomy status and virulences of various G. duodenalis genotypes, and the ecology of environmental contamination.

  17. Correlating tool wear, tool life, surface roughness and tool vibration in finish turning with coated carbide tools

    NASA Astrophysics Data System (ADS)

    Bonifacio, M. E. R.; Diniz, A. E.

    1994-04-01

    Experiments have been carried out in an attempt to monitor the change of workpiece surface roughness caused by the increase of tool wear, through the variation of the vibration in finish turning, under different cutting conditions. The vibration was measured by two accelerometers attached to the tool and the parameter used to make the correlation with surface roughness was the r.m.s. of the signal. The tool of one experiment was photographed at different stages of the cut in order to explain the wear formation and the behaviour of surface roughness as the cutting time elapsed. The material machined was AISI 4340 steel and the tool was coated carbide inserts. The results show that vibration of the tool can be a good way to monitor on-line the growth of surface roughness in finish turning and, therefore, it can be useful for establishing the end of tool life in these operations. Another conclusion is that, when coated tools are used, the behaviour of surface roughness as cutting time elapses is very different from that when uncoated tools are used.

  18. Establishing Chlamydomonas reinhardtii as an industrial biotechnology host

    PubMed Central

    Scaife, Mark A; Nguyen, Ginnie TDT; Rico, Juan; Lambert, Devinn; Helliwell, Katherine E; Smith, Alison G

    2015-01-01

    Microalgae constitute a diverse group of eukaryotic unicellular organisms that are of interest for pure and applied research. Owing to their natural synthesis of value-added natural products microalgae are emerging as a source of sustainable chemical compounds, proteins and metabolites, including but not limited to those that could replace compounds currently made from fossil fuels. For the model microalga, Chlamydomonas reinhardtii, this has prompted a period of rapid development so that this organism is poised for exploitation as an industrial biotechnology platform. The question now is how best to achieve this? Highly advanced industrial biotechnology systems using bacteria and yeasts were established in a classical metabolic engineering manner over several decades. However, the advent of advanced molecular tools and the rise of synthetic biology provide an opportunity to expedite the development of C. reinhardtii as an industrial biotechnology platform, avoiding the process of incremental improvement. In this review we describe the current status of genetic manipulation of C. reinhardtii for metabolic engineering. We then introduce several concepts that underpin synthetic biology, and show how generic parts are identified and used in a standard manner to achieve predictable outputs. Based on this we suggest that the development of C. reinhardtii as an industrial biotechnology platform can be achieved more efficiently through adoption of a synthetic biology approach. Significance Statement Chlamydomonas reinhardtii offers potential as a host for the production of high value compounds for industrial biotechnology. Synthetic biology provides a mechanism to generate generic, well characterised tools for application in the rational genetic manipulation of organisms: if synthetic biology principles were adopted for manipulation of C. reinhardtii, development of this microalga as an industrial biotechnology platform would be expedited. PMID:25641561

  19. Establishing Chlamydomonas reinhardtii as an industrial biotechnology host.

    PubMed

    Scaife, Mark A; Nguyen, Ginnie T D T; Rico, Juan; Lambert, Devinn; Helliwell, Katherine E; Smith, Alison G

    2015-05-01

    Microalgae constitute a diverse group of eukaryotic unicellular organisms that are of interest for pure and applied research. Owing to their natural synthesis of value-added natural products microalgae are emerging as a source of sustainable chemical compounds, proteins and metabolites, including but not limited to those that could replace compounds currently made from fossil fuels. For the model microalga, Chlamydomonas reinhardtii, this has prompted a period of rapid development so that this organism is poised for exploitation as an industrial biotechnology platform. The question now is how best to achieve this? Highly advanced industrial biotechnology systems using bacteria and yeasts were established in a classical metabolic engineering manner over several decades. However, the advent of advanced molecular tools and the rise of synthetic biology provide an opportunity to expedite the development of C. reinhardtii as an industrial biotechnology platform, avoiding the process of incremental improvement. In this review we describe the current status of genetic manipulation of C. reinhardtii for metabolic engineering. We then introduce several concepts that underpin synthetic biology, and show how generic parts are identified and used in a standard manner to achieve predictable outputs. Based on this we suggest that the development of C. reinhardtii as an industrial biotechnology platform can be achieved more efficiently through adoption of a synthetic biology approach.

  20. Establishing a new radiology residency research track.

    PubMed

    Costello, James R; Mullins, Mark E; Votaw, John R; Karolyi, Dan R; Kalb, Bobby; Gonzales, Patrick; Fornwalt, Brandon; Meltzer, Carolyn C

    2013-02-01

    The authors describe the establishment of a radiology residency research track at their institution. Based on growing biomedical technology needs and the tremendous increase in imaging-based research, the importance of training and cultivating future clinical investigators continues to grow. Within the framework of a supportive environment, a residency research track exposes motivated radiologists-in-training to the tools, challenges, and successes of a career in academics. The authors describe their program's design, admissions process, curriculum, and expectations. Lastly, the authors share the insight of their experience and seek feedback from readers who have been involved in similar endeavors.

  1. Establishing a successful home dialysis program.

    PubMed

    Diaz-Buxo, Jose A; Crawford-Bonadio, Terri L; St Pierre, Donna; Ingram, Katherine M

    2006-01-01

    The renewed interest in home dialysis therapies makes it pertinent to address the essentials of establishing and running a successful home dialysis program. The success of a home program depends on a clear understanding of the structure of the home program team, the physical plant, educational tool requirements, reimbursement sources and a business plan. A good command of the technical and economic aspects is important, but the primary drivers for the creation and growth of a home dialysis program are the confidence and commitment of the nephrological team.

  2. Molecular Biosignatures

    NASA Astrophysics Data System (ADS)

    Summons, Roger E.; Albrecht, Pierre; McDonald, Gene; Moldowan, J. Michael

    2008-03-01

    Life, as we know it, is based on carbon chemistry operating in an aqueous environment. Living organisms process chemicals, make copies of themselves, are autonomous and evolve in concert with the environment. All these characteristics are driven by, and operate through, carbon chemistry. The carbon chemistry of living systems is an exact branch of science and we have detailed knowledge of the basic metabolic and reproductive machinery of living organisms. We can recognise the residual biochemicals long after life has expired and otherwise lost most life-defining features. Carbon chemistry provides a tool for identifying extant and extinct life on Earth and, potentially, throughout the Universe. In recognizing that certain distinctive compounds isolable from living systems had related fossil derivatives, organic geochemists coined the term biological marker compound or biomarker (e.g. Eglinton et al. in Science 145:263-264, 1964) to describe them. In this terminology, biomarkers are metabolites or biochemicals by which we can identify particular kinds of living organisms as well as the molecular fossil derivatives by which we identify defunct counterparts. The terms biomarker and molecular biosignature are synonymous. A defining characteristic of terrestrial life is its metabolic versatility and adaptability and it is reasonable to expect that this is universal. Different physiologies operate for carbon acquisition, the garnering of energy and the storage and processing of information. As well as having a range of metabolisms, organisms build biomass suited to specific physical environments, habitats and their ecological imperatives. This overall ‘metabolic diversity’ manifests itself in an enormous variety of accompanying product molecules (i.e. natural products). The whole field of organic chemistry grew from their study and now provides tools to link metabolism (i.e. physiology) to the occurrence of biomarkers specific to, and diagnostic for, particular kinds

  3. New approaches to establish genetic causality.

    PubMed

    McNally, Elizabeth M; George, Alfred L

    2015-10-01

    Cardiovascular medicine has evolved rapidly in the era of genomics with many diseases having primary genetic origins becoming the subject of intense investigation. The resulting avalanche of information on the molecular causes of these disorders has prompted a revolution in our understanding of disease mechanisms and provided new avenues for diagnoses. At the heart of this revolution is the need to correctly classify genetic variants discovered during the course of research or reported from clinical genetic testing. This review will address current concepts related to establishing the cause and effect relationship between genomic variants and heart diseases. A survey of general approaches used for functional annotation of variants will also be presented.

  4. Molecular beacon sequence design algorithm.

    PubMed

    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.

  5. [Molecular bases of α-thalassemia in Argentina].

    PubMed

    Scheps, Karen G; Francipane, Liliana; Nash, Abigail; Cerrone, Gloria E; Copelli, Silvia B; Varela, Viviana

    2015-01-01

    The α-thalassemia is one of the most common hereditary disorders worldwide. Currently, molecular diagnostics is the only available tool to achieve an accurate diagnosis. The purpose of this study was to characterize the molecular bases of these syndromes in our environment and to establish genotype-phenotype associations. Through a combination of different molecular techniques and fluorescent in situ hybridization (FISH),we were able to find α-thalassemic mutations in 145 of the 184 patients (78.8%) studied with hematological parameters compatible with α-thalassemia. Deletions of the α-globin genes resulted the major molecular cause of the disease, and the most frequent mutation was -α(3.7), found in homozygous and heterozygous genotypes. In patients with α° phenotypes, other prevalent mutations were( _MED) and (_CAL/CAMP). The description of a sub-telomeric deletion in a patient with α-thalassemia and mental retardation was also achieved. β-thalassemic mutations in heterozygous state were found in 7.6% of the patients, who presented α-thalassemic clinical features (microcytosis and Hb A₂levels below 3.5%). Hematologic profiles for the α+ and α° genotypes were established for adult and pediatric patients. Hopefully, this work will provide guidelines for the detection of possible α-thalassemic carriers. It also highlights the collaborative work of hematologists, the biochemical and molecular biology laboratory and genetists, in order to provide appropriate genetic counseling.

  6. Tool to Prioritize Energy Efficiency Investments

    SciTech Connect

    Farese, Philip; Gelman, Rachel; Hendron, Robert

    2012-08-01

    To provide analytic support of the U.S. Department of Energy's Office of the Building Technology Program (BTP), NREL developed a Microsoft Excel-based tool to provide an open and objective comparison of the hundreds of investment opportunities available to BTP. This tool uses established methodologies to evaluate the energy savings and cost of those savings.

  7. Establishing Liver Bioreactors for In Vitro Research.

    PubMed

    Rebelo, Sofia P; Costa, Rita; Sousa, Marcos F Q; Brito, Catarina; Alves, Paula M

    2015-01-01

    In vitro systems that can effectively model liver function for long periods of time are fundamental tools for preclinical research. Nevertheless, the adoption of in vitro research tools at the earliest stages of drug development has been hampered by the lack of culture systems that offer the robustness, scalability, and flexibility necessary to meet industry's demands. Bioreactor-based technologies, such as stirred tank bioreactors, constitute a feasible approach to aggregate hepatic cells and maintain long-term three-dimensional cultures. These three-dimensional cultures sustain the polarity, differentiated phenotype, and metabolic performance of human hepatocytes. Culture in computer-controlled stirred tank bioreactors allows the maintenance of physiological conditions, such as pH, dissolved oxygen, and temperature, with minimal fluctuations. Moreover, by operating in perfusion mode, gradients of soluble factors and metabolic by-products can be established, aiming at resembling the in vivo microenvironment. This chapter provides a protocol for the aggregation and culture of hepatocyte spheroids in stirred tank bioreactors by applying perfusion mode for the long-term culture of human hepatocytes. This in vitro culture system is compatible with feeding high-throughput screening platforms for the assessment of drug elimination pathways, being a useful tool for toxicology research and drug development in the preclinical phase.

  8. Hydraulic release oil tool

    SciTech Connect

    Mims, M.G.; Mueller, M.D.; Ehlinger, J.C.

    1992-03-11

    This patent describes a hydraulic release tool. It comprises a setting assembly; a coupling member for coupling to drill string or petroleum production components, the coupling member being a plurality of sockets for receiving the dogs in the extended position and attaching the coupling member the setting assembly; whereby the setting assembly couples to the coupling member by engagement of the dogs in the sockets of releases from and disengages the coupling member in movement of the piston from its setting to its reposition in response to a pressure in the body in exceeding the predetermined pressure; and a relief port from outside the body into its bore and means to prevent communication between the relief port and the bore of the body axially of the piston when the piston is in the setting position and to establish such communication upon movement of the piston from the setting position to the release position and reduce the pressure in the body bore axially of the piston, whereby the reduction of the pressure signals that the tool has released the coupling member.

  9. Genetically modified animal models recapitulating molecular events altered in human hepatocarcinogenesis.

    PubMed

    Sánchez, Aránzazu; Fabregat, Isabel

    2009-04-01

    New advancements have been made in recent years in the understanding of the molecular mechanisms that govern human liver tumorigenesis. Experimental animal models have been widely used, especially mouse models. In this review we highlight some of the genetically engineered mouse models that have proved to be excellent tools to study the intracellular signalling pathways altered in hepatocarcinogenesis and establish potential correlations with data from humans, with special focus on hepatocellular carcinoma (HCC), the most common type of primary liver cancer. Information obtained from these animal models will help to design future therapeutic approaches to HCC, particularly those that explore drugs that specifically target the altered molecular pathways.

  10. 75 FR 36157 - Establishment of the Temporary Certification Program for Health Information Technology

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-06-24

    ... certification program to authorize organizations to test and certify Complete Electronic Health Records (EHRs... Management System b. Use of NIST Test Tools and Test Procedures i. Establishment of Test Tools and Test... establishment of a conformance testing infrastructure, including the development of technical test beds.''...

  11. Designing Molecular Printboards: A Photolithographic Platform for Recodable Surfaces.

    PubMed

    Abt, Doris; Schmidt, Bernhard V K J; Pop-Georgievski, Ognen; Quick, Alexander S; Danilov, Denis; Kostina, Nina Yu; Bruns, Michael; Wenzel, Wolfgang; Wegener, Martin; Rodriguez-Emmenegger, Cesar; Barner-Kowollik, Christopher

    2015-09-14

    A light induced strategy for the design of β-cyclodextrin (CD) based supramolecular devices is introduced, presenting a novel tool to fabricate multifunctional biointerfaces. Precision photolithography of a modified β-CD was established on a light sensitive tetrazole surface immobilized on a bioinspired polydopamine (PDA) anchor layer via various shadow masks, as well as via direct laser writing (DLW), in order to craft any desired printboard design. Interfacial molecular recognition provided by light generated cavitate domains was demonstrated via spatially resolved encoding, erasing, and recoding of distinct supramolecular guest patterns. Thus, the light directed shaping of receptor monolayers introduces a powerful path to control supramolecular assemblies on various surfaces.

  12. Establishment of a large panel of patient-derived preclinical models of human renal cell carcinoma

    PubMed Central

    Lang, Hervé; Béraud, Claire; Bethry, Audrey; Danilin, Sabrina; Lindner, Véronique; Coquard, Catherine; Rothhut, Sylvie; Massfelder, Thierry

    2016-01-01

    The objective of the present work was to establish a large panel of preclinical models of human renal cell carcinoma (RCC) directly from patients, faithfully reproducing the biological features of the original tumor. RCC tissues (all stages/subtypes) were collected for 8 years from 336 patients undergoing surgery, xenografted subcutaneously in nude mice, and serially passaged into new mice up to 13 passages. Tissue samples from the primary tumor and tumors grown in mice through passages were analyzed for biological tissue stability by histopathology, mRNA profiling, von Hippel-Lindau gene sequencing, STR fingerprinting, growth characteristics and response to current therapies. Metastatic models were also established by orthotopic implantation and analyzed by imagery. We established a large panel of 30 RCC models (passage > 3, 8.9% success rate). High tumor take rate was associated with high stage and grade. Histopathologic, molecular and genetic characteristics were preserved between original tumors and case-matched xenografts. The models reproduced the sensitivity to targeted therapies observed in the clinic. Overall, these models constitute an invaluable tool for the clinical design of efficient therapies, the identification of predictive biomarkers and translational research. PMID:27449081

  13. Molecular imaging in atherosclerosis.

    PubMed

    Glaudemans, Andor W J M; Slart, Riemer H J A; Bozzao, Alessandro; Bonanno, Elena; Arca, Marcello; Dierckx, Rudi A J O; Signore, Alberto

    2010-12-01

    Atherosclerosis is the major cause of cardiovascular disease, which still has the leading position in morbidity and mortality in the Western world. Many risk factors and pathobiological processes are acting together in the development of atherosclerosis. This leads to different remodelling stages (positive and negative) which are both associated with plaque physiology and clinical presentation. The different remodelling stages of atherosclerosis are explained with their clinical relevance. Recent advances in basic science have established that atherosclerosis is not only a lipid storage disease, but that also inflammation has a fundamental role in all stages of the disease. The molecular events leading to atherosclerosis will be extensively reviewed and described. Further on in this review different modalities and their role in the different stages of atherosclerosis will be discussed. Non-nuclear invasive imaging techniques (intravascular ultrasound, intravascular MRI, intracoronary angioscopy and intravascular optical coherence tomography) and non-nuclear non-invasive imaging techniques (ultrasound with Doppler flow, electron-bean computed tomography, coronary computed tomography angiography, MRI and coronary artery MR angiography) will be reviewed. After that we focus on nuclear imaging techniques for detecting atherosclerotic plaques, divided into three groups: atherosclerotic lesion components, inflammation and thrombosis. This emerging area of nuclear imaging techniques can provide measures of biological activity of atherosclerotic plaques, thereby improving the prediction of clinical events. As we will see in the future perspectives, at present, there is no special tracer that can be called the diagnostic tool to diagnose prospective stroke or infarction in patients. Nevertheless, we expect such a tracer to be developed in the next few years and maybe, theoretically, it could even be used for targeted therapy (in the form of a beta-emitter) to combat

  14. Precise Countersinking Tool

    NASA Technical Reports Server (NTRS)

    Jenkins, Eric S.; Smith, William N.

    1992-01-01

    Tool countersinks holes precisely with only portable drill; does not require costly machine tool. Replaceable pilot stub aligns axis of tool with centerline of hole. Ensures precise cut even with imprecise drill. Designed for relatively low cutting speeds.

  15. Your Health Priorities Tool

    MedlinePlus

    ... Care Explore Your Treatment Options: Your Health Priorities Tool Home Why Explore Your Options Start the Conversation ... Home > Your Health Priorities Tool Your Health Priorities Tool If you don’t share details about your ...

  16. Molecular imaging agents: impact on diagnosis and therapeutics in oncology

    PubMed Central

    Seaman, Marc E.; Contino, Gianmarco; Bardeesy, Nabeel; Kelly, Kimberly A.

    2011-01-01

    Imaging has become a crucial tool in oncology throughout the course of disease detection and management and is an integral part of clinical trials. Anatomic and functional imaging led the way, providing valuable information used in the diagnosis of disease, including data regarding the size and location of the tumor and on physiologic processes such as blood flow and perfusion. As understanding of cancer pathogenesis has advanced through the identification of genetic, biochemical, and cellular alterations in evolving tumors, emphasis has been made on developing methods to detect and serially monitor such alterations. This class of approaches is referred to as molecular imaging. Molecular imaging offers the potential for increasingly sensitive and specific visualization and quantification of biological processes at the cellular and molecular level. These approaches have become established as essential tools for cancer research, early cancer detection and staging and monitoring and predicting response to targeted therapies. Here, we will discuss recent advances in the development of molecular imaging agents and their implementation in basic cancer research as well as in more rationalized approaches to cancer care. PMID:20633310

  17. AutoFACT: An Automatic Functional Annotation and Classification Tool

    PubMed Central

    Koski, Liisa B; Gray, Michael W; Lang, B Franz; Burger, Gertraud

    2005-01-01

    Background Assignment of function to new molecular sequence data is an essential step in genomics projects. The usual process involves similarity searches of a given sequence against one or more databases, an arduous process for large datasets. Results We present AutoFACT, a fully automated and customizable annotation tool that assigns biologically informative functions to a sequence. Key features of this tool are that it (1) analyzes nucleotide and protein sequence data; (2) determines the most informative functional description by combining multiple BLAST reports from several user-selected databases; (3) assigns putative metabolic pathways, functional classes, enzyme classes, GeneOntology terms and locus names; and (4) generates output in HTML, text and GFF formats for the user's convenience. We have compared AutoFACT to four well-established annotation pipelines. The error rate of functional annotation is estimated to be only between 1–2%. Comparison of AutoFACT to the traditional top-BLAST-hit annotation method shows that our procedure increases the number of functionally informative annotations by approximately 50%. Conclusion AutoFACT will serve as a useful annotation tool for smaller sequencing groups lacking dedicated bioinformatics staff. It is implemented in PERL and runs on LINUX/UNIX platforms. AutoFACT is available at . PMID:15960857

  18. Tool Changer For Robot

    NASA Technical Reports Server (NTRS)

    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.

  19. Genetic and genomic tools for the marine annelid Platynereis dumerilii.

    PubMed

    Zantke, Juliane; Bannister, Stephanie; Rajan, Vinoth Babu Veedin; Raible, Florian; Tessmar-Raible, Kristin

    2014-05-01

    The bristle worm Platynereis dumerilii displays many interesting biological characteristics. These include its reproductive timing, which is synchronized to the moon phase, its regenerative capacity that is hormonally controlled, and a slow rate of evolution, which permits analyses of ancestral genes and cell types. As a marine annelid, Platynereis is also representative of the marine ecosystem, as well as one of the three large animal subphyla, the Lophotrochozoa. Here, we provide an overview of the molecular resources, functional techniques, and behavioral assays that have recently been established for the bristle worm. This combination of tools now places Platynereis in an excellent position to advance research at the frontiers of neurobiology, chronobiology, evo-devo, and marine biology.

  20. Genetic and Genomic Tools for the Marine Annelid Platynereis dumerilii

    PubMed Central

    Zantke, Juliane; Bannister, Stephanie; Rajan, Vinoth Babu Veedin; Raible, Florian; Tessmar-Raible, Kristin

    2014-01-01

    The bristle worm Platynereis dumerilii displays many interesting biological characteristics. These include its reproductive timing, which is synchronized to the moon phase, its regenerative capacity that is hormonally controlled, and a slow rate of evolution, which permits analyses of ancestral genes and cell types. As a marine annelid, Platynereis is also representative of the marine ecosystem, as well as one of the three large animal subphyla, the Lophotrochozoa. Here, we provide an overview of the molecular resources, functional techniques, and behavioral assays that have recently been established for the bristle worm. This combination of tools now places Platynereis in an excellent position to advance research at the frontiers of neurobiology, chronobiology, evo-devo, and marine biology. PMID:24807110

  1. The click reaction as an efficient tool for the construction of macrocyclic structures.

    PubMed

    Pasini, Dario

    2013-08-08

    The Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC, known as the click reaction) is an established tool used for the construction of complex molecular architectures. Given its efficiency it has been widely applied for bioconjugation, polymer and dendrimer synthesis. More recently, this reaction has been utilized for the efficient formation of rigid or shape-persistent, preorganized macrocyclic species. This strategy also allows the installment of useful functionalities, in the form of polar and function-rich 1,2,3-triazole moieties, directly embedded in the macrocyclic structures. This review analyzes the state of the art in this context, and provides some elements of perspective for future applications.

  2. Imaging mass spectrometry of the visual system: Advancing the molecular understanding of retina degenerations.

    PubMed

    Bowrey, Hannah E; Anderson, David M; Pallitto, Patrick; Gutierrez, Danielle B; Fan, Jie; Crouch, Rosalie K; Schey, Kevin L; Ablonczy, Zsolt

    2016-04-01

    Visual sensation is fundamental for quality of life, and loss of vision to retinal degeneration is a debilitating condition. The eye is the only part of the central nervous system that can be noninvasively observed with optical imaging. In the clinics, various spectroscopic methods provide high spatial resolution images of the fundus and the developing degenerative lesions. However, the currently utilized tools are not specific enough to establish the molecular underpinnings of retinal diseases. In contrast, mass spectrometric imaging (MSI) is a powerful tool to identify molecularly specific disease indicators and classification markers. This technique is particularly well suited to the eye, where molecular information can be correlated with clinical data collected via noninvasive diagnostic imaging modalities. Recent studies during the last few recent years have uncovered a plethora of new spatially defined molecular information on several vision-threatening diseases, including age-related macular degeneration, Stargardt disease, glaucoma, cataract, as well as lipid disorders. Even though MS inside the eye cannot be performed noninvasively, by linking diagnostic and molecular information, these studies are the first step toward the development of smart ophthalmic diagnostic and surgical tools. Here, we provide an overview of current approaches applying MSI technology to ocular pathology.

  3. Establishing "Green Schools" and Enhancing Teachers and Students' Environmental Awareness

    ERIC Educational Resources Information Center

    Zhongguo, Tang

    2004-01-01

    The environmental education and "green school" establishment at schools is an important means and basic tool to enhance students' environmental awareness. It is also one important aspect of the quality-oriented education at schools and the construction of spiritual aspect of civilization. This article discusses the importance of…

  4. Proposed Methodology for Establishing Area of Applicability

    SciTech Connect

    Broadhead, B.L.; Hopper, C.M.; Parks, C.V.

    1999-09-20

    This paper presents the application of sensitivity and uncertainty (S/U) analysis methodologies to the data validation tasks of a criticality safety computational study. The S/U methods presented are designed to provide a formal means of establishing the area (or range) of applicability for criticality safety data validation studies. The development of parameters that are analogous to the standard trending parameters form the key to the technique. These parameters are the so-called D parameters, which represent the differences by energy group of S/U-generated sensitivity profiles, and c parameters, which are the k correlation coefficients, each of which give information relative to the similarity between pairs of selected systems. The use of a Generalized Linear Least-Squares Methodology (GLLSM) tool is also described in this paper. These methods and guidelines are also applied to a sample validation for uranium systems with enrichments greater than 5 wt %.

  5. Databases and tools in glycobiology.

    PubMed

    Artemenko, Natalia V; McDonald, Andrew G; Davey, Gavin P; Rudd, Pauline M

    2012-01-01

    Glycans are crucial to the functioning of multicellular organisms. They may also play a role as mediators between host and parasite or symbiont. As many proteins (>50%) are posttranslationally modified by glycosylation, this mechanism is considered to be the most widespread posttranslational modification in eukaryotes. These surface modifications alter and regulate structure and biological activities/functions of proteins/biomolecules as they are largely involved in the recognition process of the appropriate structure in order to bind to the target cells. Consequently, the recognition of glycans on cellular surfaces plays a crucial role in the promotion or inhibition of various diseases and, therefore, glycosylation itself is considered to be a critical protein quality control attribute for commercial therapeutics, which is one of the fastest growing segments in the pharmaceutical industry. With the development of glycobiology as a separate discipline, a number of databases and tools became available in a similar way to other well-established "omics." Alleviating the recognized shortcomings of the available tools for data storage and retrieval is one of the highest priorities of the international glycoinformatics community. In the last decade, major efforts have been made, by leading scientific groups, towards the integration of a number of major databases and tools into a single portal, which would act as a centralized data repository for glycomics, equipped with a number of comprehensive analytical tools for data systematization, analysis, and comparison. This chapter provides an overview of the most important carbohydrate-related databases and glycoinformatic tools.

  6. Establishing an antimicrobial stewardship program.

    PubMed

    Morris, Andrew M; Stewart, Thomas E; Shandling, Maureen; McIntaggart, Scott; Liles, W Conrad

    2010-01-01

    Hospitals are faced with increasing challenges of antibiotic-resistant organisms and rising antimicrobial costs despite widespread attention to infection prevention and control measures. Government, professional organizations and accreditation bodies are all signalling an urgent need for the establishment of programs in hospitals to address antibiotic misuse. Although variations of such "antimicrobial stewardship programs" have been functioning in Canada for some time, a formal approach using change management and quality improvement principles has largely been lacking. We describe how we have established such a program in a teaching hospital, modelled on John Kotter's eight steps of leading change.

  7. Establishing operations and the mand.

    PubMed

    Michael, J

    1988-01-01

    In Verbal Behavior Skinner identifies a small number of elementary verbal relations, one of which is the mand. Because its introduction is at first in terms of unlearned motivative variables, and because the mand's relation to prior controlling events is quite complex, its general significance has probably been underestimated. An extensive treatment of establishing operations, including the warning and the blocked-response conditioned establishing operations is provided, followed by a description of the mand in terms of such operations. The importance of the mand for language training programs is suggested, as well as the reasons why it is typically neglected in such programs.

  8. MIPs as Tools in Environmental Biotechnology.

    PubMed

    Mattiasson, Bo

    2015-01-01

    Molecular imprints are potentially fantastic constructions. They are selective, robust, and nonbiodegradable if produced from stable polymers. A range of different applications has been presented, everything from separation of enantiomers, via adsorbents for sample preparation before analysis to applications in wastewater treatment. This chapter deals with molecularly imprinted polymers (MIPs) as tools in environmental biotechnology, a field that has the potential to become very important in the future.

  9. Molecular diagnosis of von Willebrand disease.

    PubMed

    Baronciani, L; Goodeve, A; Peyvandi, F

    2017-03-01

    The role of molecular characterization in the diagnosis of von Willebrand disease (VWD) is not essential if the patients have been extensively investigated using phenotypic analysis. On the other hand, if some of these phenotype assays are not available, the identification of the mutation causing the disease could be crucial for an accurate diagnosis. Nevertheless, there are several reasons for performing molecular analysis in patients phenotypically well characterized, e.g. to identify the mutation causing VWD can be useful for patients and their family members when prenatal diagnosis is required (type 3 or severe type 2). In this manuscript, we report the techniques used for the molecular characterization of suspected VWD patients. We describe the use of online von Willebrand factor database and online single nucleotide variation databases, the former to verify whether a candidate mutation has been previously identified in other VWD patients and the latter to ascertain whether a putative mutation has been reported earlier in healthy individuals. We listed the available in silico analysis tools, to determine the predicted pathogenicity of a sequence variant and to establish its possible negative effect on the normal splicing process. We also report the strategy that can be used to identify VWD type 2 patients' mutations in subjects who have been fully characterized using the phenotype assays.

  10. Magnetismo Molecular (Molecular Magentism)

    SciTech Connect

    Reis, Mario S; Moreira Dos Santos, Antonio F

    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.

  11. Application of high-rate cutting tools

    NASA Astrophysics Data System (ADS)

    Moriarty, John L., Jr.

    1989-03-01

    Widespread application of the newest high-rate cutting tools to the most appropriate jobs is slowed by the sheer magnitude of developments in tool types, materials, workpiece applications, and by the rapid pace of change. Therefore, a study of finishing and roughing sizes of coated carbide inserts having a variety of geometries for single point turning was completed. The cutting tools were tested for tool life, chip quality, and workpiece surface finish at various cutting conditions with medium alloy steel. An empirical wear-life data base was established, and a computer program was developed to facilitate technology transfer, assist selection of carbide insert grades, and provide machine operating parameters. A follow-on test program was implemented suitable for next generation coated carbides, rotary cutting tools, cutting fluids, and ceramic tool materials.

  12. Neurochemistry of dementia: establishing the links.

    PubMed

    Whitehouse, P J; Gambetti, P; Harik, S I; Kalaria, R N; Perry, G; Younkin, S I; Tabaton, M; Unnerstall, J R

    1989-01-01

    Neurochemical research in dementia needs to move beyond descriptive inventories of neurotransmitter systems affected in the specific disorders and to link to molecular studies of mechanism and clinical studies of cognition. New advances in Alzheimer's Disease (AD), Huntington's Disease (HD), and Parkinson's Disease (PD) are being guided by models of how nerve cells die in these disorders. Theories of pathophysiology which address the cellular level need to explain the selective vulnerability of neuronal populations in the different diseases. Clinically, the importance of neurochemical studies will be increased by understanding the bridges between neural and cognitive processes. Clinicians are concerned about the nosology of dementias, diagnostic tests, and more effective therapies. The value of neurochemical studies will be enhanced to the extent that they can contribute to understanding and modifying the clinical phenomenology of these disorders. In this paper, we will briefly review what is known about the neurochemistry of dementia but focus most of our attention on establishing the linkage between this level of description and the levels of description which are either "downstream" (molecular biology) or "upstream" (cognition) in terms of a reductionistic conception of understanding the disease process. We will explore how understanding neurochemistry relates to our understanding of disease mechanism and what constraints neurochemical studies place on understanding clinical aspects of disease. We will conclude by briefly discussing some of the problems with our current understanding of the neurochemistry of dementia and how we can address those problems in the future.

  13. Establishing a Suicide Prevention Program.

    ERIC Educational Resources Information Center

    Vidal, John A.

    1986-01-01

    Outlines important considerations for establishing suicide prevention programs in high schools. Teenage suicide rate has doubled since 1970. To deal with this crisis schools must develop procedures for detecting potential victims and for helping students and staff cope after a suicide. Schools must not be afraid to talk about suicide; avoiding the…

  14. Methods for improving PGPR establishment

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Plant growth-promoting rhizobacteria (PGPR) are often touted as a useful means to improve crop productivity and sustainability. However, field studies with PGPR inoculants often result in limited PGPR establishment and colonization, highlighting the need to better understand the factors involved in...

  15. On Establishing Underlying Tonal Contrast

    ERIC Educational Resources Information Center

    Snider, Keith

    2014-01-01

    Phonological field work is largely about establishing contrast in comparable environments. The notion of phonological contrast, however, can be confusing, particularly in its application to tone analysis. Does it mean phonemic contrast in the structuralist sense, or does it mean underlying contrast in the generative sense? Many linguists, in…

  16. Molecular Modeling

    NASA Astrophysics Data System (ADS)

    Holmes, Jon L.

    1999-06-01

    Molecular modeling has trickled down from the realm of pharmaceutical and research laboratories into the realm of undergraduate chemistry instruction. It has opened avenues for the visualization of chemical concepts that previously were difficult or impossible to convey. I am sure that many of you have developed exercises using the various molecular modeling tools. It is the desire of this Journal to become an avenue for you to share these exercises among your colleagues. It is to this end that Ron Starkey has agreed to edit such a column and to publish not only the description of such exercises, but also the software documents they use. The WWW is the obvious medium to distribute this combination and so accepted submissions will appear online as a feature of JCE Internet. Typical molecular modeling exercise: finding conformation energies. Molecular Modeling Exercises and Experiments is the latest feature column of JCE Internet, joining Conceptual Questions and Challenge Problems, Hal's Picks, and Mathcad in the Chemistry Curriculum. JCE Internet continues to seek submissions in these areas of interest and submissions of general interest. If you have developed materials and would like to submit them, please see our Guide to Submissions for more information. The Chemical Education Resource Shelf, Equipment Buyers Guide, and WWW Site Review would also like to hear about chemistry textbooks and software, equipment, and WWW sites, respectively. Please consult JCE Internet Features to learn more about these resources at JCE Online. Email Announcements Would you like to be informed by email when the latest issue of the Journal is available online? when a new JCE Software title is shipping? when a new JCE Internet article has been published or is available for Open Review? when your subscription is about to expire? A new feature of JCE Online makes this possible. Visit our Guestbook to learn how. When

  17. Establishing Ergonomics in Industrially Developing Countries

    SciTech Connect

    Stewart, K; Silverstein, B; Kiefer, M

    2005-08-29

    The introduction of ergonomics is an ongoing effort in industrially developing countries and will ultimately require an organized, programmatic approach spanning several countries and organizations. Our preliminary efforts with our partner countries of Viet Nam, Thailand, and Nicaragua have demonstrated that a one-time course is just the first step in a series of necessary events to provide skills and create an infrastructure that will have lasting impact for the host country. To facilitate that any sort of training has a lasting impact, it is recommended that host countries establish a 'contract' with class participants and the guest instructors for at least one follow-up visit so instructors can see the progress and support the participants in current and future efforts. With repeated exchanges, the class participants can become the 'in country experts' and the next generation of ergonomic trainers. Additionally, providing participants with an easy to use hazard assessment tool and methods for evaluating the financial impact of the project (cost/benefit analysis) will assist increase the likelihood of success and establish a foundation for future projects. In the future, developing trade and regionally/culturally specific 'ergonomics toolkits' can help promote broader implementation, especially where training resources may be limited.

  18. Molecular diagnosis of onychomycosis.

    PubMed

    Petinataud, D; Berger, S; Contet-Audonneau, N; Machouart, M

    2014-12-01

    Onychomycosis is a frequent cause of nail infections due to dermatophytes. Molds and yeast may also be responsible of these pathologies. Antifungal treatments are frequently given without a mycological diagnosis, partly because of the requisite time for obtaining the biological results. The mycological diagnosis requires a direct microscopic examination and a culture in order to accurately identify the fungal genus and species. Nevertheless, this conventional diagnosis is often time consuming due to the delay of fungal cultures and presents disadvantages that make it not sufficient enough to give a precise and confident response to the clinicians. Therefore additional tests have been developed to help distinguish onychomycosis from other nail disorders. Among them, molecular biology techniques offer modern and rapid tools to improve traditional microbiological diagnosis. In this review, we first present the conventional diagnosis methods for onychomycosis and then we describe the main molecular biology tools and the currently available commercial kits that allow a rapid detection of the pathology.

  19. Tools to assess tissue quality.

    PubMed

    Neumeister, Veronique M

    2014-03-01

    Biospecimen science has recognized the importance of tissue quality for accurate molecular and biomarker analysis and efforts are made to standardize tissue procurement, processing and storage conditions of tissue samples. At the same time the field has emphasized the lack of standardization of processes between different laboratories, the variability inherent in the analytical phase and the lack of control over the pre-analytical phase of tissue processing. The problem extends back into tissue samples in biorepositories, which are often decades old and where documentation about tissue processing might not be available. This review highlights pre-analytical variations in tissue handling, processing, fixation and storage and emphasizes the effects of these variables on nucleic acids and proteins in harvested tissue. Finally current tools for quality control regarding molecular or biomarker analysis are summarized and discussed.

  20. Interface-assisted molecular spintronics

    NASA Astrophysics Data System (ADS)

    Raman, Karthik V.

    2014-09-01

    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.

  1. Interface-assisted molecular spintronics

    SciTech Connect

    Raman, Karthik V.

    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.

  2. Numerical tools for atomistic simulations.

    SciTech Connect

    Fang, H.; Gullett, Philip Michael; Slepoy, Alexander; Horstemeyer, Mark F.; Baskes, Michael I.; Wagner, Gregory John; Li, Mo

    2004-01-01

    The final report for a Laboratory Directed Research and Development project entitled 'Parallel Atomistic Computing for Failure Analysis of Micromachines' is presented. In this project, atomistic algorithms for parallel computers were developed to assist in quantification of microstructure-property relations related to weapon micro-components. With these and other serial computing tools, we are performing atomistic simulations of various sizes, geometries, materials, and boundary conditions. These tools provide the capability to handle the different size-scale effects required to predict failure. Nonlocal continuum models have been proposed to address this problem; however, they are phenomenological in nature and are difficult to validate for micro-scale components. Our goal is to separately quantify damage nucleation, growth, and coalescence mechanisms to provide a basis for macro-scale continuum models that will be used for micromachine design. Because micro-component experiments are difficult, a systematic computational study that employs Monte Carlo methods, molecular statics, and molecular dynamics (EAM and MEAM) simulations to compute continuum quantities will provide mechanism-property relations associated with the following parameters: specimen size, number of grains, crystal orientation, strain rates, temperature, defect nearest neighbor distance, void/crack size, chemical state, and stress state. This study will quantify sizescale effects from nanometers to microns in terms of damage progression and thus potentially allow for optimized micro-machine designs that are more reliable and have higher fidelity in terms of strength. In order to accomplish this task, several atomistic methods needed to be developed and evaluated to cover the range of defects, strain rates, temperatures, and sizes that a material may see in micro-machines. Therefore we are providing a complete set of tools for large scale atomistic simulations that include pre-processing of

  3. Establishing Pluripotency in Early Development

    PubMed Central

    Paranjpe, Sarita S.; Veenstra, Gert Jan C.

    2015-01-01

    The earliest steps of embryonic development involve important changes in chromatin and transcription factor networks, which are orchestrated to establish pluripotent cells that will form the embryo. DNA methylation, histone modifications, the pluripotency regulatory network of transcription factors, maternal factors and newly translated proteins all contribute to these transitions in dynamic ways. Moreover, these dynamics are linked to the onset of zygotic transcription. We will review recent progress in our understanding of chromatin state and regulation of gene expression in the context of embryonic development in vertebrates, in particular mouse, Xenopus and zebrafish. We include work on mouse embryonic stem cells and highlight work that illustrates how early embryonic dynamics establish gene regulatory networks and the state of pluripotency. PMID:25857441

  4. Treatment of Established Status Epilepticus

    PubMed Central

    Falco-Walter, Jessica J.; Bleck, Thomas

    2016-01-01

    Status epilepticus is the most severe form of epilepsy, with a high mortality rate and high health care costs. Status epilepticus is divided into four stages: early, established, refractory, and super-refractory. While initial treatment with benzodiazepines has become standard of care for early status epilepticus, treatment after benzodiazepine failure (established status epilepticus (ESE)) is incompletely studied. Effective treatment of ESE is critical as morbidity and mortality increases dramatically the longer convulsive status epilepticus persists. Phenytoin/fosphenytoin, valproic acid, levetiracetam, phenobarbital, and lacosamide are the most frequently prescribed antiseizure medications for treatment of ESE. To date there are no class 1 data to support pharmacologic recommendations of one agent over another. We review each of these medications, their pharmacology, the scientific evidence in support and against each in the available literature, adverse effects and safety profiles, dosing recommendations, and limitations of the available evidence. We also discuss future directions including the established status epilepticus treatment trial (ESETT). Substantial further research is urgently needed to identify these patients (particularly those with non-convulsive status epilepticus), elucidate the most efficacious antiseizure treatment with head-to-head randomized prospective trials, and determine whether this differs for convulsive vs. non-convulsive ESE. PMID:27120626

  5. RFID as a Tool in Cyber Warfare

    DTIC Science & Technology

    2010-11-01

    RTO-MP-IST-091 P4 - 1 RFID as a Tool in Cyber Warfare Mikko Kiviharju P.O.Box 10 FIN-11311 Riihimaki FINLAND mikko.kiviharju@mil.fi...auditing existing systems and planning new establishments. 1 INTRODUCTION Cyber warfare , especially computer network operations (CNO) have a deep...SUBTITLE RFID as a Tool in Cyber Warfare 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER 5e. TASK

  6. DNA topology influences molecular machine lifetime in human serum

    NASA Astrophysics Data System (ADS)

    Goltry, Sara; Hallstrom, Natalya; Clark, Tyler; Kuang, Wan; Lee, Jeunghoon; Jorcyk, Cheryl; Knowlton, William B.; Yurke, Bernard; Hughes, William L.; Graugnard, Elton

    2015-06-01

    DNA nanotechnology holds the potential for enabling new tools for biomedical engineering, including diagnosis, prognosis, and therapeutics. However, applications for DNA devices are thought to be limited by rapid enzymatic degradation in serum and blood. Here, we demonstrate that a key aspect of DNA nanotechnology--programmable molecular shape--plays a substantial role in device lifetimes. These results establish the ability to operate synthetic DNA devices in the presence of endogenous enzymes and challenge the textbook view of near instantaneous degradation.DNA nanotechnology holds the potential for enabling new tools for biomedical engineering, including diagnosis, prognosis, and therapeutics. However, applications for DNA devices are thought to be limited by rapid enzymatic degradation in serum and blood. Here, we demonstrate that a key aspect of DNA nanotechnology--programmable molecular shape--plays a substantial role in device lifetimes. These results establish the ability to operate synthetic DNA devices in the presence of endogenous enzymes and challenge the textbook view of near instantaneous degradation. Electronic supplementary information (ESI) available: DNA sequences, fluorophore and quencher properties, equipment design, and degradation studies. See DOI: 10.1039/c5nr02283e

  7. Improved tool grinding machine

    DOEpatents

    Dial, C.E. Sr.

    The present invention relates to an improved tool grinding mechanism for grinding single point diamond cutting tools to precise roundness and radius specifications. The present invention utilizes a tool holder which is longitudinally displaced with respect to the remainder of the grinding system due to contact of the tool with the grinding surface with this displacement being monitored so that any variation in the grinding of the cutting surface such as caused by crystal orientation or tool thicknesses may be compensated for during the grinding operation to assure the attainment of the desired cutting tool face specifications.

  8. Tool grinding machine

    DOEpatents

    Dial, Sr., Charles E.

    1980-01-01

    The present invention relates to an improved tool grinding mechanism for grinding single point diamond cutting tools to precise roundness and radius specifications. The present invention utilizes a tool holder which is longitudinally displaced with respect to the remainder of the grinding system due to contact of the tool with the grinding surface with this displacement being monitored so that any variation in the grinding of the cutting surface such as caused by crystal orientation or tool thickness may be compensated for during the grinding operation to assure the attainment of the desired cutting tool face specifications.

  9. Molecular biology in physiology

    SciTech Connect

    Chien, S.; Gargus, J.J.

    1987-08-01

    The aim of this symposium on molecular biology in physiology was to introduce molecular biology to physiologists who had relatively little exposure to the new developments in this field, so that they can become conversant on this topic and contribute to the advancement of physiology by incorporating molecular biological approaches as a part of their research arsenal. This report is a review of the symposium, which consisted of two four-part sessions. Each session had four papers. After the discussion of the basic concepts, terminology, and methodology used in molecular biology, it was shown how these basic principles have been applied to the study of the genes encoding two membrane proteins that have important transport functions (band 3 and ATPase). The second half of the symposium consisted of papers on the state-of-the-art developments in the application of molecular biology to the studies of the atrial natriuretic factor and renin genes, adenylate cyclase-coupled adrenergic receptors, acetylcholine receptors and sodium channel, and long-term and short-term memories. The ultimate goal is that these examples will provide an impetus for the opening of new frontiers of research in physiology by taking advantage of the tools developed from recent advances in molecular biology.

  10. LensTools: Weak Lensing computing tools

    NASA Astrophysics Data System (ADS)

    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.

  11. Novel gene expression tools for rice biotechnology

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  12. Molecular Plasmonics.

    PubMed

    Wilson, Andrew J; Willets, Katherine A

    2016-06-12

    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.

  13. Genetic tools and techniques for Chlamydomonas reinhardtii.

    PubMed

    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.

  14. 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

    NASA Astrophysics Data System (ADS)

    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.

  15. Deliberate Establishment of Asymptomatic Bacteriuria—A Novel Strategy to Prevent Recurrent UTI

    PubMed Central

    Wullt, Björn; Svanborg, Catharina

    2016-01-01

    We have established a novel strategy to reduce the risk for recurrent urinary tract infection (UTI), where rapidly increasing antibiotic resistance poses a major threat. Epidemiologic studies have demonstrated that asymptomatic bacteriuria (ABU) protects the host against symptomatic infections with more virulent strains. To mimic this protective effect, we deliberately establish ABU in UTI-prone patients, who are refractory to conventional therapy. The patients are inoculated with Escherichia coli (E. coli) 83972, now widely used as a prototype ABU strain. Therapeutic efficacy has been demonstrated in a placebo-controlled trial, supporting the feasibility of using E. coli 83972 as a tool to prevent recurrent UTI and, potentially, to outcompete antibiotic-resistant strains from the human urinary tract. In addition, the human inoculation protocol offers unique opportunities to study host-parasite interaction in vivo in the human urinary tract. Here, we review the clinical evidence for protection using this approach as well as some molecular insights into the pathogenesis of UTI that have been gained during these studies. PMID:27483325

  16. Innovative Environmental Protection Tools

    EPA Pesticide Factsheets

    Local decision makers and citizens can make use of EPA tools for interacting with and learning about their local environments with tools that include green apps, My Environment, the National Stormwater Calculator, EPEAT, and EnvirFacts.

  17. Molecular similarity and property similarity.

    PubMed

    Barbosa, Frédérique; Horvath, Dragos

    2004-01-01

    This paper reviews the main efforts undertaken up to date in order to understand, rationalize and apply the similarity principle (similar compounds=>similar properties) as a computational tool in modern drug discovery. The best suited mathematical expression of this classical working hypothesis of medicinal chemistry needs to be carefully chosen (out of the virtually infinite possible implementations in terms of molecular descriptors and molecular similarity metrics), in order to achieve an optimal validation of the hypothesis that molecules that are neighbors in the Structural Space will also display similar properties. This overview will show why no single "absolute" measure of molecular similarity can be conceived, and why molecular similarity scores should be considered tunable tools that need to be adapted to each problem to solve.

  18. Engineering crystals by the strategy of molecular tectonics.

    PubMed

    Wuest, James D

    2005-12-21

    Detailed structures of molecular crystals cannot yet be predicted with consistent accuracy, but the strategy of molecular tectonics offers crystal engineers a powerful tool for designing molecules that are predisposed to form crystals with particular structural features and properties.

  19. Hand tools: A compilation

    NASA Technical Reports Server (NTRS)

    1972-01-01

    A selection of new hand tools, modifications of existing tools, and techniques developed in the course of NASA research and development projects are presented. The items are presented in two sections: tools for cable and connector applications, and tools for welding applications. Safety is emphasized, together with ease of operation and use in restricted areas or hazardous environments. The discussions are directed primarily toward the technician engaged in assembly or maintenance of mechanical or electrical equipment.

  20. OOTW COST TOOLS

    SciTech Connect

    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.

  1. Demand Response Dispatch Tool

    SciTech Connect

    2012-08-31

    The Demand Response (DR) Dispatch Tool uses price profiles to dispatch demand response resources and create load modifying profiles. These annual profiles are used as inputs to production cost models and regional planning tools (e.g., PROMOD). The tool has been effectively implemented in transmission planning studies conducted by the Western Electricity Coordinating Council via its Transmission Expansion Planning and Policy Committee. The DR Dispatch Tool can properly model the dispatch of DR resources for both reliability and economic conditions.

  2. Fluid sampling tool

    DOEpatents

    Garcia, Anthony R.; Johnston, Roger G.; Martinez, Ronald K.

    2000-01-01

    A fluid-sampling tool for obtaining a fluid sample from a container. When used in combination with a rotatable drill, the tool bores a hole into a container wall, withdraws a fluid sample from the container, and seals the borehole. The tool collects fluid sample without exposing the operator or the environment to the fluid or to wall shavings from the container.

  3. Standardized Procedures for Use of Nucleic Acid-Based Tools

    EPA Science Inventory

    Groundwater and soil samples are frequently analyzed using molecular biological tools (MBTs) to detect unique genetic biomarkers associated with Dehalococcoides (Dhc) and other environmentally relevant microorganisms. The results of these analyses are increasingly used b...

  4. Dose metrology for DUV lithographic tools

    NASA Astrophysics Data System (ADS)

    Kivenzor, Gregory J.; Zimmerman, Richard

    2001-04-01

    The semiconductor industry is investigating metrology methods and tools to ensure the high accuracy and stability required for chip making. Lithography equipment manufacturers are under constant pressure to provide in situ measurements that prevent wafer processing form slipping from the established parameters. This is especially true for DUV exposure tools utilizing excimer lasers with high repetition rates. Dose metrology is one of the key parameters for linewidth control in photolithography. This paper discusses current developments in dose metrology for 248, 193, and 157 nm wavelengths. Particular emphasis is placed on the methodology to support dose stability over the lifetime of the tool. Aspects of tool-to-self and tool-to- tool matching are examined in detail, as well as the implications of the mix-and-match use of lithography equipment. To ensure the long-term accuracy of present tools, strong cooperation is needed within the semiconductor industry from suppliers and end users; and beyond, from standards organizations and international consortia. This paper describes the tasks that have to be accomplished to sustain the dose metrology during the transition from the existing tools to future generations of optical micro lithographic tools.

  5. MOD Tool (Microwave Optics Design Tool)

    NASA Technical Reports Server (NTRS)

    Katz, Daniel S.; Borgioli, Andrea; Cwik, Tom; Fu, Chuigang; Imbriale, William A.; Jamnejad, Vahraz; Springer, Paul L.

    1999-01-01

    The Jet Propulsion Laboratory (JPL) is currently designing and building a number of instruments that operate in the microwave and millimeter-wave bands. These include MIRO (Microwave Instrument for the Rosetta Orbiter), MLS (Microwave Limb Sounder), and IMAS (Integrated Multispectral Atmospheric Sounder). These instruments must be designed and built to meet key design criteria (e.g., beamwidth, gain, pointing) obtained from the scientific goals for the instrument. These criteria are frequently functions of the operating environment (both thermal and mechanical). To design and build instruments which meet these criteria, it is essential to be able to model the instrument in its environments. Currently, a number of modeling tools exist. Commonly used tools at JPL include: FEMAP (meshing), NASTRAN (structural modeling), TRASYS and SINDA (thermal modeling), MACOS/IMOS (optical modeling), and POPO (physical optics modeling). Each of these tools is used by an analyst, who models the instrument in one discipline. The analyst then provides the results of this modeling to another analyst, who continues the overall modeling in another discipline. There is a large reengineering task in place at JPL to automate and speed-up the structural and thermal modeling disciplines, which does not include MOD Tool. The focus of MOD Tool (and of this paper) is in the fields unique to microwave and millimeter-wave instrument design. These include initial design and analysis of the instrument without thermal or structural loads, the automation of the transfer of this design to a high-end CAD tool, and the analysis of the structurally deformed instrument (due to structural and/or thermal loads). MOD Tool is a distributed tool, with a database of design information residing on a server, physical optics analysis being performed on a variety of supercomputer platforms, and a graphical user interface (GUI) residing on the user's desktop computer. The MOD Tool client is being developed using Tcl

  6. Electron localization following attosecond molecular photoionization.

    PubMed

    Sansone, G; Kelkensberg, F; Pérez-Torres, J F; Morales, F; Kling, M F; Siu, W; Ghafur, O; Johnsson, P; Swoboda, M; Benedetti, E; Ferrari, F; Lépine, F; Sanz-Vicario, J L; Zherebtsov, S; Znakovskaya, I; L'huillier, A; Ivanov, M Yu; Nisoli, M; Martín, F; Vrakking, M J J

    2010-06-10

    For the past several decades, we have been able to directly probe the motion of atoms that is associated with chemical transformations and which occurs on the femtosecond (10(-15)-s) timescale. However, studying the inner workings of atoms and molecules on the electronic timescale has become possible only with the recent development of isolated attosecond (10(-18)-s) laser pulses. Such pulses have been used to investigate atomic photoexcitation and photoionization and electron dynamics in solids, and in molecules could help explore the prompt charge redistribution and localization that accompany photoexcitation processes. In recent work, the dissociative ionization of H(2) and D(2) was monitored on femtosecond timescales and controlled using few-cycle near-infrared laser pulses. Here we report a molecular attosecond pump-probe experiment based on that work: H(2) and D(2) are dissociatively ionized by a sequence comprising an isolated attosecond ultraviolet pulse and an intense few-cycle infrared pulse, and a localization of the electronic charge distribution within the molecule is measured that depends-with attosecond time resolution-on the delay between the pump and probe pulses. The localization occurs by means of two mechanisms, where the infrared laser influences the photoionization or the dissociation of the molecular ion. In the first case, charge localization arises from quantum mechanical interference involving autoionizing states and the laser-altered wavefunction of the departing electron. In the second case, charge localization arises owing to laser-driven population transfer between different electronic states of the molecular ion. These results establish attosecond pump-probe strategies as a powerful tool for investigating the complex molecular dynamics that result from the coupling between electronic and nuclear motions beyond the usual Born-Oppenheimer approximation.

  7. Establishment of a transgenic hairy root system in wild and domesticated watermelon (Citrullus lanatus) for studying root vigor under drought.

    PubMed

    Kajikawa, Masataka; Morikawa, Kaoru; Abe, Yosuke; Yokota, Akiho; Akashi, Kinya

    2010-07-01

    Root vigor is an important trait for the growth of terrestrial plants, especially in water-deficit environments. Although deserts plants are known for their highly developed root architecture, the molecular mechanism responsible for this trait has not been determined. Here we established an efficient protocol for the genetic manipulation of two varieties of watermelon plants: a desert-grown wild watermelon that shows vigorous root growth under drought, and a domesticated cultivar showing retardation of root growth under drought stress. Agrobacterium rhizogenes-mediated transgenic hairy roots were efficiently induced and selected from the hypocotyls of these plants. Transgenic GUS expression was detected in the roots by RT-PCR and histochemical GUS staining. Moreover, a liquid culture system for evaluating their root growth was also established. Interestingly, growth of the hairy roots derived from domesticated variety of watermelon strongly inhibited under high osmotic condition, whereas the hairy roots derived from wild variety of watermelon retained substantial growth rates under the stress condition. The new protocol presented here offers a powerful tool for the comparative study of the molecular mechanism underlying drought-induced root growth in desert plants.

  8. Canine mammary tumour cell lines established in vitro.

    PubMed

    Hellmén, E

    1993-01-01

    Mammary tumours are the most common tumours in the female dog. The tumours have a complex histology and exist in epithelial, mixed and mesenchymal forms. To study the biology of canine mammary tumours, five cell lines have been established and characterized. The results indicate that canine mammary tumours might be derived from mammary stem cells and that the tumour growth is independent of oestrogens. The established canine mammary tumour cell lines will be valuable tools in further studies of the histogenesis and pathogenesis of these tumours.

  9. Establishment and characterization of a new human myxoid liposarcoma cell line (DL-221) with the FUS-DDIT3 translocation

    PubMed Central

    de Graaff, Marieke A.; Yu, Jamie S.E.; Cheung, Hannah C.; Ingram, Davis R.; Nguyen, Theresa; Liu, Jeffrey Juehui; Bolshakov, Svetlana; Szuhai, Károly; Åman, Pierre; Torres, Keila E.; Lev, Dina; Nielsen, Torsten O.; Bovée, Judith V.M.G.; Lazar, Alexander J.; Somaiah, Neeta

    2016-01-01

    Myxoid liposarcoma has the pathognomonic fusion oncogene FUS-DDIT3 encoding a chimeric transcription factor. Metastatic risk is higher with an increased round cell component and has been linked to aberrations involving the IGFR/PI3K/AKT pathway. These molecular insights have yet to translate to targeted therapies and the lack of experimental models is a major hindrance. We describe the initial in-depth characterization of a new cell line (DL-221) and establishment of a mouse xenograft model. The cell line DL-221 was derived from a metastatic pleural lesion showing myxoid and round cell histology. This newly established cell line was characterized for phenotypic properties and molecular cytogenetic profile, using PCR, COBRA-FISH and western blot. Next-generation whole exome sequencing was performed to further characterize the cell line and the parent tumor. NOD-SCID-IL2R gamma knockout mice were xenograft hosts. DL-221 cells grew an adhering monolayer and COBRA-FISH showed an aneuploid karyotype with t(12;16)(q13;p11) and several other rearrangements; RT-PCR demonstrated a FUS-DDIT3 fusion transcript type 1. Both the cell line and the original tumor harbored a TP53 compound heterozygous mutation in exon 4 and 7 and were wild type for PIK3CA. Moreover, among the 1254 variants called by whole exome sequencing, there was 77% concordance between the cell line and parent tumor. The recently described hotspot mutation in the TERT promoter region in myxoid liposarcomas was also found at C228T in DL-221. Xenografts suitable for additional pre-clinical studies were successfully established in mice after subcutaneous injection. The established DL-221 cell line is the only published available myxoid liposarcoma cell line that underwent spontaneous immortalization, without requiring SV40 transformation. The cell line and its xenograft model are unique and helpful tools to study the biology and novel potential targeted treatment approaches for myxoid liposarcoma. PMID:27270875

  10. Orbiter door closure tools

    NASA Technical Reports Server (NTRS)

    Acres, W. R.

    1980-01-01

    Safe reentry of the shuttle orbiter requires that the payload bay doors be closed and securely latched. Since a malfunction in the door drive or bulkhead latch systems could make safe reentry impossible, the requirement to provide tools to manually close and secure the doors was implemented. The tools would disconnect a disabled door or latch closure system and close and secure the doors if the normal system failed. The tools required to perform these tasks have evolved into a set that consists of a tubing cutter, a winch, a latching tool, and a bolt extractor. The design, fabrication, and performance tests of each tool are described.

  11. Systems biology: a new tool for farm animal science.

    PubMed

    Hollung, Kristin; Timperio, Anna M; Olivan, Mamen; Kemp, Caroline; Coto-Montes, Ana; Sierra, Veronica; Zolla, Lello

    2014-03-01

    It is rapidly emerging that the tender meat phenotype is affected by an enormous amount of variables, not only tied to genetics (livestock breeding selection), but also to extrinsic factors, such as feeding conditions, physical activity, rearing environment, administration of hormonal growth promotants, pre-slaughter handling and stress. Proteomics has been widely accepted by meat scientists over the last years and is now commonly used to shed light on the postmortem processes involved in meat tenderization. This review discusses the latest findings with the use of proteomics and systems biology to study the different biochemical pathways postmortem aiming at understanding the concerted action of different molecular mechanisms responsible for meat quality. The conversion of muscle to meat postmortem can be described as a sequence of events involving molecular pathways controlled by a complex interplay of many factors. Among the different pathways emerging are the influence of apoptosis and lately also the role of autophagy in muscle postmortem development. This review thus, focus on how systems-wide integrated investigations (metabolomics, transcriptomics, interactomics, phosphoproteomics, mathematical modeling), which have emerged as complementary tools to proteomics, have helped establishing a few milestones in our understanding of the events leading from muscle to meat conversion.

  12. Molecular pharmacognosy.

    PubMed

    Huang, LuQi; Xiao, PeiGen; Guo, LanPing; Gao, WenYuan

    2010-06-01

    This article analyzes the background and significance of molecular pharmacognosy, including the molecular identification of medicinal raw materials, phylogenetic evolution of medicinal plants and animals, evaluation and preservation of germplasm resources for medicinal plants and animals, etiology of endangerment and protection of endangered medicinal plants and animals, biosynthesis and bioregulation of active components in medicinal plants, and characteristics and the molecular bases of top-geoherbs.

  13. Implantation and Establishment of Pregnancy in Human and Nonhuman Primates

    PubMed Central

    Fazleabas, Asgerally T.

    2016-01-01

    Implantation and the establishment of pregnancy are critical for the propagation of the species, but yet remain the limiting steps in human and primate reproduction. Successful implantation requires a competent blastocyst and a receptive endometrium during a specific window of time during the menstrual cycle to initiate the bilateral communication required for the establishment of a successful pregnancy. This chapter provides an overview of these processes and discusses the molecular mechanisms associated with implantation of the blastocyst and decidualization of the uterus in primates. PMID:26450500

  14. The need for a standard nomenclature for gene classification (a Nucleotide Function Code) and an automated data-based tool to assist in understanding the molecular associations in cell signalling in plant-pathogen interactions.

    PubMed

    Lyon, Gary D; Newton, Adrian C; Marshall, Bruce

    2002-03-01

    summary Despite the adoption of Arabidopsis thaliana as a model plant system and the plethora of molecular information being obtained from its use, it is disappointing that the scientific community has not devised a cell signalling model integrating and visualizing these data. Lack of common systems of nomenclature and the sheer size and complexity of the task inhibit any individual from bringing together the knowledge into a unified structure. There are clearly many aspects of cell biology that are similar, even between plants and animals, that could facilitate development of a generic model. A gene-coding or nucleotide classification system which is 'user-friendly' would be beneficial to building such a model and enable rapid identification of orthologues of genes from different organisms. Whilst some international projects seek to address the problem of assigning unique numbers to genes, none suggest a nucleotide classification system that provides biological information that is transparent within the code. This paper discusses these issues and identifies the need for a more formal, semi-automated approach to modelling signal transduction utilizing the strengths of the proposed classification approach. By way of illustration, an example of a possible nucleotide function code is suggested, to demonstrate more clearly the benefits of such a system. Further discussion of this topic will be encouraged on websites ( and ).

  15. Tool setting device

    DOEpatents

    Brown, Raymond J.

    1977-01-01

    The present invention relates to a tool setting device for use with numerically controlled machine tools, such as lathes and milling machines. A reference position of the machine tool relative to the workpiece along both the X and Y axes is utilized by the control circuit for driving the tool through its program. This reference position is determined for both axes by displacing a single linear variable displacement transducer (LVDT) with the machine tool through a T-shaped pivotal bar. The use of the T-shaped bar allows the cutting tool to be moved sequentially in the X or Y direction for indicating the actual position of the machine tool relative to the predetermined desired position in the numerical control circuit by using a single LVDT.

  16. Formal Methods Tool Qualification

    NASA Technical Reports Server (NTRS)

    Wagner, Lucas G.; Cofer, Darren; Slind, Konrad; Tinelli, Cesare; Mebsout, Alain

    2017-01-01

    Formal methods tools have been shown to be effective at finding defects in safety-critical digital systems including avionics systems. The publication of DO-178C and the accompanying formal methods supplement DO-333 allows applicants to obtain certification credit for the use of formal methods without providing justification for them as an alternative method. This project conducted an extensive study of existing formal methods tools, identifying obstacles to their qualification and proposing mitigations for those obstacles. Further, it interprets the qualification guidance for existing formal methods tools and provides case study examples for open source tools. This project also investigates the feasibility of verifying formal methods tools by generating proof certificates which capture proof of the formal methods tool's claim, which can be checked by an independent, proof certificate checking tool. Finally, the project investigates the feasibility of qualifying this proof certificate checker, in the DO-330 framework, in lieu of qualifying the model checker itself.

  17. NASA establishes office of exploration

    NASA Astrophysics Data System (ADS)

    The National Aeronautics and Space Administration (NASA) has a new Office of Exploration that will coordinate agency activities that would “expand the human presence beyond Earth,” particularly to the moon and Mars.Sally K. Ride is serving as the office's acting assistant administrator until mid August. Ride, the first U.S. woman in space, has been in charge of a NASA study to determine a possible new major space goal for the United States. Her study group recently identified four major areas for concentrated examination as possible initiatives for a new national space objective: intensive study of Earth systems for better understanding of how to protect Earth's environment,a stepped-up robotic program to explore the planets, moons, and other solar system bodies,the establishment of a scientific base and a permanent human presence on the moon, andintensive exploration of Mars by robot, followed by human exploration of the planet.

  18. 75 FR 8045 - National Environmental Policy Act (NEPA) Draft Guidance, Establishing, Applying, and Revising...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-02-23

    ... fundamental tool used to harmonize our economic, environmental, and social aspirations and is a cornerstone of... From the Federal Register Online via the Government Publishing Office COUNCIL ON ENVIRONMENTAL QUALITY National Environmental Policy Act (NEPA) Draft Guidance, Establishing, Applying, and...

  19. Molecular and Paleontological Evidence for a Post-Cretaceous Origin of Rodents

    PubMed Central

    Wu, Shaoyuan; Wu, Wenyu; Zhang, Fuchun; Ye, Jie; Ni, Xijun; Sun, Jimin; Edwards, Scott V.; Meng, Jin; Organ, Chris L.

    2012-01-01

    The timing of the origin and diversification of rodents remains controversial, due to conflicting results from molecular clocks and paleontological data. The fossil record tends to support an early Cenozoic origin of crown-group rodents. In contrast, most molecular studies place the origin and initial diversification of crown-Rodentia deep in the Cretaceous, although some molecular analyses have recovered estimated divergence times that are more compatible with the fossil record. Here we attempt to resolve this conflict by carrying out a molecular clock investigation based on a nine-gene sequence dataset and a novel set of seven fossil constraints, including two new rodent records (the earliest known representatives of Cardiocraniinae and Dipodinae). Our results indicate that rodents originated around 61.7–62.4 Ma, shortly after the Cretaceous/Paleogene (K/Pg) boundary, and diversified at the intraordinal level around 57.7–58.9 Ma. These estimates are broadly consistent with the paleontological record, but challenge previous molecular studies that place the origin and early diversification of rodents in the Cretaceous. This study demonstrates that, with reliable fossil constraints, the incompatibility between paleontological and molecular estimates of rodent divergence times can be eliminated using currently available tools and genetic markers. Similar conflicts between molecular and paleontological evidence bedevil attempts to establish the origination times of other placental groups. The example of the present study suggests that more reliable fossil calibration points may represent the key to resolving these controversies. PMID:23071573

  20. Molecular and paleontological evidence for a post-Cretaceous origin of rodents.

    PubMed

    Wu, Shaoyuan; Wu, Wenyu; Zhang, Fuchun; Ye, Jie; Ni, Xijun; Sun, Jimin; Edwards, Scott V; Meng, Jin; Organ, Chris L

    2012-01-01

    The timing of the origin and diversification of rodents remains controversial, due to conflicting results from molecular clocks and paleontological data. The fossil record tends to support an early Cenozoic origin of crown-group rodents. In contrast, most molecular studies place the origin and initial diversification of crown-Rodentia deep in the Cretaceous, although some molecular analyses have recovered estimated divergence times that are more compatible with the fossil record. Here we attempt to resolve this conflict by carrying out a molecular clock investigation based on a nine-gene sequence dataset and a novel set of seven fossil constraints, including two new rodent records (the earliest known representatives of Cardiocraniinae and Dipodinae). Our results indicate that rodents originated around 61.7-62.4 Ma, shortly after the Cretaceous/Paleogene (K/Pg) boundary, and diversified at the intraordinal level around 57.7-58.9 Ma. These estimates are broadly consistent with the paleontological record, but challenge previous molecular studies that place the origin and early diversification of rodents in the Cretaceous. This study demonstrates that, with reliable fossil constraints, the incompatibility between paleontological and molecular estimates of rodent divergence times can be eliminated using currently available tools and genetic markers. Similar conflicts between molecular and paleontological evidence bedevil attempts to establish the origination times of other placental groups. The example of the present study suggests that more reliable fossil calibration points may represent the key to resolving these controversies.

  1. Using molecular biology to study mycorrhizal fungal community ecology: Limits and perspectives.

    PubMed

    Chagnon, Pierre-Luc; Bainard, Luke D

    2015-01-01

    Molecular tools have progressively replaced morphological approaches to characterize microbial communities in nature. Arbuscular mycorrhizal (AM) fungi are no exception to this rule. Yet, one challenge posed by these symbionts is that they colonize simultaneously both plant roots and soil, which complicates their detection and quantification. In most studies conducted to date, AM fungal communities have been characterized from roots only, soil only or spores only. Here, we discuss the pitfalls associated to drawing ecological inferences using such datasets. We also conclude by arguing that molecular biology will contribute most to advance knowledge in AM fungal ecology if it is integrated into broader perspectives taking into account the natural history of these organisms. This calls for a better merging of molecular and morphological approaches, and the establishment of intensive, long-term research programs.

  2. Knowledge Mapping: A Multipurpose Task Analysis Tool.

    ERIC Educational Resources Information Center

    Esque, Timm J.

    1988-01-01

    Describes knowledge mapping, a tool developed to increase the objectivity and accuracy of task difficulty ratings for job design. Application in a semiconductor manufacturing environment is discussed, including identifying prerequisite knowledge for a given task; establishing training development priorities; defining knowledge levels; identifying…

  3. Final Technical Report: PV Fault Detection Tool.

    SciTech Connect

    King, Bruce Hardison; Jones, Christian Birk

    2015-12-01

    The PV Fault Detection Tool project plans to demonstrate that the FDT can (a) detect catastrophic and degradation faults and (b) identify the type of fault. This will be accomplished by collecting fault signatures using different instruments and integrating this information to establish a logical controller for detecting, diagnosing and classifying each fault.

  4. Molecular motors

    NASA Astrophysics Data System (ADS)

    Allemand, Jean François Desbiolles, Pierre

    2015-10-01

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

  5. Establishing operations and reinforcement effects.

    PubMed

    Vollmer, T R; Iwata, B A

    1991-01-01

    Positive reinforcement procedures have had a major impact on educational programs for the developmentally disabled; nevertheless, variation in reinforcer effectiveness both within and across individuals is a common phenomenon. This study examined one class of variables--establishing operations--that might influence the effectiveness of reinforcers. Five developmentally disabled adult males participated. Responding on one of two motor tasks--switch closure or block placement--was assessed during baseline, satiation, and deprivation conditions with respect to three classes of consequences: small food items, music, and social praise. Deprivation and satiation conditions were constructed so as not to alter significantly the normal course of events in a subject's day. For example, food deprivation entailed scheduling sessions just prior to a subject's regular lunch, and social deprivation involved limiting a subject's access to social interaction for 15 minutes, during which time the subject had access to an assortment of other activities. Results showed that each stimulus class functioned as reinforcement with different degrees of effectiveness during satiation versus deprivation conditions. These results are discussed in light of previous research on enhancement of reinforcer efficacy as well as the assessment and identification of functional reinforcers, and implications are presented for future research and client habilitation.

  6. Institute for Rock Magnetism established

    NASA Astrophysics Data System (ADS)

    Banerjee, Subir K.

    There is a new focal point for cooperative research in advanced rock magnetism. The University of Minnesota in Minneapolis has established an Institute for Rock Magnetism (IRM) that will provide free access to modern equipment and encourage visiting fellows to focus on important topics in rock magnetism and related interdisciplinary research. Funding for the first three years has been secured from the National Science Foundation, the W.M. Keck Foundation, and the University of Minnesota.In the fall of 1986, the Geomagnetism and Paleomagnetism (GP) section of the AGU held a workshop at Asilomar, Calif., to pinpoint important and emerging research areas in paleomagnetism and rock magnetism, and the means by which to achieve them. In a report of this workshop published by the AGU in September 1987, two urgent needs were set forth. The first was for interdisciplinary research involving rock magnetism, and mineralogy, petrology, sedimentology, and the like. The second need was to ease the access of rock magnetists and paleomagnetists around the country to the latest equipment in modern magnetics technology, such as magneto-optics or electronoptics. Three years after the publication of the report, we announced the opening of these facilities at the GP section of the AGU Fall 1990 Meeting. A classified advertisement inviting applications for visiting fellowships was published in the January 22, 1991, issue of Eos.

  7. Molecular force spectroscopy on cells.

    PubMed

    Liu, Baoyu; Chen, Wei; Zhu, Cheng

    2015-04-01

    Molecular force spectroscopy has become a powerful tool to study how mechanics regulates biology, especially the mechanical regulation of molecular interactions and its impact on cellular functions. This force-driven methodology has uncovered a wealth of new information of the physical chemistry of molecular bonds for various biological systems. The new concepts, qualitative and quantitative measures describing bond behavior under force, and structural bases underlying these phenomena have substantially advanced our fundamental understanding of the inner workings of biological systems from the nanoscale (molecule) to the microscale (cell), elucidated basic molecular mechanisms of a wide range of important biological processes, and provided opportunities for engineering applications. Here, we review major force spectroscopic assays, conceptual developments of mechanically regulated kinetics of molecular interactions, and their biological relevance. We also present current challenges and highlight future directions.

  8. Lunar hand tools

    NASA Technical Reports Server (NTRS)

    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.

  9. Machine tool locator

    DOEpatents

    Hanlon, John A.; Gill, Timothy J.

    2001-01-01

    Machine tools can be accurately measured and positioned on manufacturing machines within very small tolerances by use of an autocollimator on a 3-axis mount on a manufacturing machine and positioned so as to focus on a reference tooling ball or a machine tool, a digital camera connected to the viewing end of the autocollimator, and a marker and measure generator for receiving digital images from the camera, then displaying or measuring distances between the projection reticle and the reference reticle on the monitoring screen, and relating the distances to the actual position of the autocollimator relative to the reference tooling ball. The images and measurements are used to set the position of the machine tool and to measure the size and shape of the machine tool tip, and examine cutting edge wear. patent

  10. Health Care Management Courses in Greek Universities: A First Attempt to Establish Factors Affecting Satisfaction

    ERIC Educational Resources Information Center

    Kotsifos, Vangelis; Alegakis, Athanasios; Philalithis, Anastas

    2012-01-01

    Purpose: The object of this study is to formulate, establish and apply a suitable and reliable tool for measuring the course experience satisfaction of Master graduates. A questionnaire was formulated, based on similar tools, and adjusted to the reality of Hellenic Higher Education, in order to measure the satisfaction of graduates in three Master…

  11. OEXP Analysis Tools Workshop

    NASA Technical Reports Server (NTRS)

    Garrett, L. Bernard; Wright, Robert L.; Badi, Deborah; Findlay, John T.

    1988-01-01

    This publication summarizes the software needs and available analysis tools presented at the OEXP Analysis Tools Workshop held at the NASA Langley Research Center, Hampton, Virginia on June 21 to 22, 1988. The objective of the workshop was to identify available spacecraft system (and subsystem) analysis and engineering design tools, and mission planning and analysis software that could be used for various NASA Office of Exploration (code Z) studies, specifically lunar and Mars missions.

  12. Authoring tool evaluation

    SciTech Connect

    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.

  13. A GRB tool shed

    NASA Astrophysics Data System (ADS)

    Haglin, David J.; Roiger, Richard J.; Hakkila, Jon; Pendleton, Geoffrey; Mallozzi, Robert

    2000-09-01

    We describe the design of a suite of software tools to allow users to query Gamma Ray Burst (GRB) data and perform data mining expeditions. We call this suite of tools a shed (SHell for Expeditions using Datamining). Our schedule is to have a completed prototype (funded via the NASA AISRP) by February, 2002. Meanwhile, interested users will find a partially functioning tool shed at http:/grb.mankato.msus.edu. .

  14. Risk Assessment Tools

    DTIC Science & Technology

    1994-10-01

    2W0 ww) A number of computer-based risk assessment tools were enhanced or creaited to provide Increased access to risk assessment instruments and...produced an extensible authoring tool , SYNTAS, for test instruments that will simplify the data gathering phase of subsequent work. SYNTAS gives DNA...Ultimately it became a computer-assisted software engineerting (CASE) tool capable of producing a wide variety of assessment instruments . In addition, its

  15. Hand and Power Tools

    DTIC Science & Technology

    1998-01-01

    Hand and Power Tools U.S. Department of Labor Occupational Safety and Health Administration OSHA 3080 1998 (Revised) Report Documentation Page Report...Date 00001998 Report Type N/A Dates Covered (from... to) - Title and Subtitle Hand and Power Tools Contract Number Grant Number Program...basic safety procedures and safeguards associated with hand and portable power tools . Material in this booklet is based on the standards of the

  16. MISR ENVI Tool

    Atmospheric Science Data Center

    2013-03-20

    ...   The misr_envi tool imports MISR Level 1B2 Ellipsoid and Terrain stacked block data into ENVI. The data are ... tool reads and geolocates the Land BRF parameter from a MISR Level 2 Land Surface data file. The tool consists of a set of routines ... Sample ENVI menu file with added entry for MISR L1B2 to invoke this code: envi.men.4.0wMISR ...

  17. Double diameter boring tool

    DOEpatents

    Ashbaugh, Fred N.; Murry, Kenneth R.

    1988-12-27

    A boring tool and a method of operation are provided for boring two concentric holes of precision diameters and depths in a single operation. The boring tool includes an elongated tool body, a shank for attachment to a standard adjustable boring head which is used on a manual or numerical control milling machine and first and second diametrically opposed cutting edges formed for cutting in opposite directions. The diameter of the elongated tool body is substantially equal to the distance from the first cutting edge tip to the axis of rotation plus the distance from the second cutting edge tip to the axis of rotation. The axis of rotation of the tool is spaced from the tool centerline a distance substantially equal to one-half the distance from the second cutting edge tip to the axis of rotation minus one-half the distance from the first cutting edge tip to the axis of rotation. The method includes the step of inserting the boring tool into the boring head, adjusting the distance between the tool centerline and the tool axis of rotation as described above and boring the two concentric holes.

  18. Tool use as adaptation.

    PubMed

    Biro, Dora; Haslam, Michael; Rutz, Christian

    2013-11-19

    Tool use is a vital component of the human behavioural repertoire. The benefits of tool use have often been assumed to be self-evident: by extending control over our environment, we have increased energetic returns and buffered ourselves from potentially harmful influences. In recent decades, however, the study of tool use in both humans and non-human animals has expanded the way we think about the role of tools in the natural world. This Theme Issue is aimed at bringing together this developing body of knowledge, gathered across multiple species and from multiple research perspectives, to chart the wider evolutionary context of this phylogenetically rare behaviour.

  19. Demand Response Analysis Tool

    SciTech Connect

    2012-03-01

    Demand Response Analysis Tool is a software developed at the Lawrence Berkeley National Laboratory. It is initially funded by Southern California Edison. Our goal in developing this tool is to provide an online, useable, with standardized methods, an analysis tool to evaluate demand and demand response performance of commercial and industrial facilities. The tool provides load variability and weather sensitivity analysis capabilities as well as development of various types of baselines. It can be used by researchers, real estate management firms, utilities, or any individuals who are interested in analyzing their demand and demand response capabilities.

  20. Tool use as adaptation

    PubMed Central

    Biro, Dora; Haslam, Michael; Rutz, Christian

    2013-01-01

    Tool use is a vital component of the human behavioural repertoire. The benefits of tool use have often been assumed to be self-evident: by extending control over our environment, we have increased energetic returns and buffered ourselves from potentially harmful influences. In recent decades, however, the study of tool use in both humans and non-human animals has expanded the way we think about the role of tools in the natural world. This Theme Issue is aimed at bringing together this developing body of knowledge, gathered across multiple species and from multiple research perspectives, to chart the wider evolutionary context of this phylogenetically rare behaviour. PMID:24101619