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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

    USDA-ARS?s Scientific Manuscript database

    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. Establishing Molecular Tools for Genetic Manipulation of the Pleuromutilin-Producing Fungus Clitopilus passeckerianus▿

    PubMed Central

    Kilaru, Sreedhar; Collins, Catherine M.; Hartley, Amanda J.; Bailey, Andy M.; Foster, Gary D.

    2009-01-01

    We describe efficient polyethylene glycol (PEG)-mediated and Agrobacterium-mediated transformation systems for a pharmaceutically important basidiomycete fungus, Clitopilus passeckerianus, which produces pleuromutilin, a diterpene antibiotic. Three dominant selectable marker systems based on hygromycin, phleomycin, and carboxin selection were used to study the feasibility of PEG-mediated transformation of C. passeckerianus. The PEG-mediated transformation of C. passeckerianus protoplasts was successful and generated hygromycin-resistant transformants more efficiently than either phleomycin or carboxin resistance. Agrobacterium-mediated transformation with plasmid pBGgHg containing hph gene under the control of the Agaricus bisporus gpdII promoter led to hygromycin-resistant colonies and was successful when homogenized mycelium and fruiting body gill tissue were used as starting material. Southern blot analysis of transformants revealed the apparently random integration of the transforming DNA to be predominantly multiple copies for the PEG-mediated system and a single copy for the Agrobacterium-mediated system within the genome. C. passeckerianus actin and tubulin promoters were amplified from genomic DNA and proved successful in driving green fluorescent protein and DsRed expression in C. passeckerianus, but only when constructs contained a 5′ intron, demonstrating that the presence of an intron is prerequisite for efficient transgene expression. The feasibility of RNA interference-mediated gene silencing was investigated using gfp as a target gene easily scored in C. passeckerianus. Upon transformation of gfp antisense constructs into a highly fluorescent strain, transformants were recovered that exhibited either reduced or undetectable fluorescence. This was confirmed by Northern blotting showing depletion of the target mRNA levels. This demonstrated that gene silencing is a suitable tool for modulating gene expression in C. passeckerianus. The molecular tools

  3. Establishing molecular tools for genetic manipulation of the pleuromutilin-producing fungus Clitopilus passeckerianus.

    PubMed

    Kilaru, Sreedhar; Collins, Catherine M; Hartley, Amanda J; Bailey, Andy M; Foster, Gary D

    2009-11-01

    We describe efficient polyethylene glycol (PEG)-mediated and Agrobacterium-mediated transformation systems for a pharmaceutically important basidiomycete fungus, Clitopilus passeckerianus, which produces pleuromutilin, a diterpene antibiotic. Three dominant selectable marker systems based on hygromycin, phleomycin, and carboxin selection were used to study the feasibility of PEG-mediated transformation of C. passeckerianus. The PEG-mediated transformation of C. passeckerianus protoplasts was successful and generated hygromycin-resistant transformants more efficiently than either phleomycin or carboxin resistance. Agrobacterium-mediated transformation with plasmid pBGgHg containing hph gene under the control of the Agaricus bisporus gpdII promoter led to hygromycin-resistant colonies and was successful when homogenized mycelium and fruiting body gill tissue were used as starting material. Southern blot analysis of transformants revealed the apparently random integration of the transforming DNA to be predominantly multiple copies for the PEG-mediated system and a single copy for the Agrobacterium-mediated system within the genome. C. passeckerianus actin and tubulin promoters were amplified from genomic DNA and proved successful in driving green fluorescent protein and DsRed expression in C. passeckerianus, but only when constructs contained a 5' intron, demonstrating that the presence of an intron is prerequisite for efficient transgene expression. The feasibility of RNA interference-mediated gene silencing was investigated using gfp as a target gene easily scored in C. passeckerianus. Upon transformation of gfp antisense constructs into a highly fluorescent strain, transformants were recovered that exhibited either reduced or undetectable fluorescence. This was confirmed by Northern blotting showing depletion of the target mRNA levels. This demonstrated that gene silencing is a suitable tool for modulating gene expression in C. passeckerianus. The molecular tools

  4. 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.

  5. 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

  6. Molecular tools used in agriculture

    USDA-ARS?s Scientific Manuscript database

    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....

  7. 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.

  8. Molecular tools for breeding basidiomycetes.

    PubMed

    Ramírez, L; Larraya, L M; Pisabarro, A G

    2000-09-01

    The industrial production of edible basidiomycetes is increasing every year as a response to the increasing public demand of them because of their nutritional properties. About a dozen of fungal species can be currently produced for food with sound industrial and economic bases. Notwithstanding, this production is threatened by biotic and abiotic factors that make it necessary to improve the fungal strains currently used in industry. Breeding of edible basidiomycetes, however, has been mainly empirical and slow since the genetic tools useful in the selection of the new genetic material to be introduced in the commercial strains have not been developed for these fungi as it was for other organisms. In this review we will discuss the main genetic factors that should be considered to develop breeding approaches and tools for higher basidiomycetes. These factors are (i) the genetic system controlling fungal mating; (ii) the genomic structure and organisation of these fungi; and (iii) the identification of genes involved in the control of quantitative traits. We will discuss the weight of these factors using the oyster mushroom Pleurotus ostreatus as a model organism for most of the edible fungi cultivated industrially.

  9. 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.

  10. 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

  11. 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.

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

    DTIC Science & Technology

    2003-06-01

    to steer me in the right directions, clarify my understanding of complex material, and offer suggestions of how to improve the dissertation were...tools developed at the Naval Postgraduate School. Evolved from CAPS and Distributed CAPS ( DCAPS ). Software Engineering Body of Knowledge (SWEBOK

  13. Application of molecular genetic tools for forest pathology

    Treesearch

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

    2012-01-01

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

  14. 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…

  15. The integration of molecular tools into veterinary and spatial epidemiology.

    PubMed

    Muellner, Petra; Zadoks, Ruth N; Perez, Andres M; Spencer, Simon E F; Schukken, Ynte H; French, Nigel P

    2011-09-01

    At the interface of molecular biology and epidemiology, the emerging discipline of molecular epidemiology offers unique opportunities to advance the study of diseases through the investigation of infectious agents at the molecular level. Molecular tools can increase our understanding of the factors that shape the spatial and temporal distribution of pathogens and disease. Both spatial and molecular aspects have always been important to the field of infectious disease epidemiology, but recently news tools have been developed which increase our ability to consider both elements within a common framework. This enables the epidemiologist to make inferences about disease patterns in space and time. This paper introduces some basic concepts of molecular epidemiology in a veterinary context and illustrates the application of molecular tools at a range of spatio-temporal scales. Case studies - a multi-state outbreak of Serratia mastitis, a national control program for campylobacteriosis, and evolution of foot-and-mouth-disease viruses - are used to demonstrate the importance of considering molecular aspects in modern epidemiological studies. The discipline of molecular epidemiology is in its infancy and our contribution aims to promote awareness, understanding and uptake of molecular epidemiology in veterinary science. Copyright © 2011 Elsevier Ltd. All rights reserved.

  16. Biorefinery: a design tool for molecular gelators.

    PubMed

    John, George; Shankar, Balachandran Vijai; Jadhav, Swapnil R; Vemula, Praveen Kumar

    2010-12-07

    Molecular gels, the macroscopic products of a nanoscale bottom-up strategy, have emerged as a promising functional soft material. The prospects of tailoring the architecture of gelator molecules have led to the formation of unique, highly tunable gels for a wide spectrum of applications from medicine to electronics. Biorefinery is a concept that integrates the processes of converting biomass/renewable feedstock and the associated infrastructure used to produce chemicals and materials, which is analogous to petroleum-based refinery. The current review assimilates the successful efforts to demonstrate the prospects of the biorefinery concept for developing new amphiphiles as molecular gelators. Amphiphiles based on naturally available raw materials such as amygdalin, vitamin C, cardanol, arjunolic acid, and trehalose that possess specific functionality were synthesized using biocatalysis and/or chemical synthesis. The hydrogels and organogels obtained from such amphiphiles were conceptually demonstrated for diverse applications including drug-delivery systems and the templated synthesis of hybrid materials.

  17. Aptamers as Valuable Molecular Tools in Neurosciences.

    PubMed

    Wolter, Olga; Mayer, Günter

    2017-03-08

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

  18. Molecular chaperones: toward new therapeutic tools.

    PubMed

    Almeida, Mauro B; do Nascimento, José Luiz Martins; Herculano, Anderson Manoel; Crespo-López, Maria Elena

    2011-07-01

    Molecular chaperones (or heat shock proteins) are evolutionarily conserved and essential proteins that play a key role in cell survival through cytoprotective mechanisms. Despite their possible clinical applications, the understanding of these structures is still quite limited. The aim of the present study is to review the literature to understand the physiological importance, implication in various diseases (especially in cancer and neurodegenerative diseases), possible applicability, and future prospects of heat shock proteins. The cytoprotective mechanisms of molecular chaperones can be co-opted by oncogenic processes favoring tumor growth, invasion, evasion of apoptosis, and metastasis, thus making inhibitors to these molecules possible therapeutic options for cancer patients. However, there is also evidence showing that upregulation of heat shock proteins can have an antineoplastic effect through immunomodulatory activity. This is why chaperones have already been investigated for conventional chemotherapy under specific conditions, yielding interesting results. The induction of heat shock protein activity is also of potential benefit in many other diseases where structural and functional preservation of proteins may enhance cell survival, including neurodegeneration, trauma, stroke, and cardiovascular disease. In addition, the immune properties of chaperones can potentially be exploited for such diseases as diabetes, atherosclerosis, and other chronic inflammatory conditions. Thus, continuing efforts to clarify the role of chaperones may guide the development of new therapeutic modalities capable of minimizing the impact of diseases such as cancer, heart disease, and diabetes as well as obtaining better results in neurological conditions currently lacking alternative treatments. Copyright © 2011 Elsevier Masson SAS. All rights reserved.

  19. GPU-powered tools boost molecular visualization.

    PubMed

    Chavent, Matthieu; Lévy, Bruno; Krone, Michael; Bidmon, Katrin; Nominé, Jean-Philippe; Ertl, Thomas; Baaden, Marc

    2011-11-01

    Recent advances in experimental structure determination provide a wealth of structural data on huge macromolecular assemblies such as the ribosome or viral capsids, available in public databases. Further structural models arise from reconstructions using symmetry orders or fitting crystal structures into low-resolution maps obtained by electron-microscopy or small angle X-ray scattering experiments. Visual inspection of these huge structures remains an important way of unravelling some of their secrets. However, such visualization cannot conveniently be carried out using conventional rendering approaches, either due to performance limitations or due to lack of realism. Recent developments, in particular drawing benefit from the capabilities of Graphics Processing Units (GPUs), herald the next generation of molecular visualization solutions addressing these issues. In this article, we present advances in computer science and visualization that help biologists visualize, understand and manipulate large and complex molecular systems, introducing concepts that remain little-known in the bioinformatics field. Furthermore, we compile currently available software and methods enhancing the shape perception of such macromolecular assemblies, for example based on surface simplification or lighting ameliorations.

  20. 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.

  1. 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.

  2. BALLView: a tool for research and education in molecular modeling.

    PubMed

    Moll, Andreas; Hildebrandt, Andreas; Lenhof, Hans-Peter; Kohlbacher, Oliver

    2006-02-01

    We present BALLView, a molecular viewer and modeling tool. It combines state-of-the-art visualization capabilities with powerful modeling functionality including implementations of force field methods and continuum electrostatics models. BALLView is a versatile and extensible tool for research in structural bioinformatics and molecular modeling. Furthermore, the convenient and intuitive graphical user interface offers novice users direct access to the full functionality, rendering it ideal for teaching. Through an interface to the object-oriented scripting language Python it is easily extensible.

  3. 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.

  4. 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

  5. [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…

  6. 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.

  7. 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

  8. Establishment of a molecular embryonic stem cell developmental toxicity assay.

    PubMed

    Panzica-Kelly, Julieta M; Brannen, Kimberly C; Ma, Yan; Zhang, Cindy X; Flint, Oliver P; Lehman-McKeeman, Lois D; Augustine-Rauch, Karen A

    2013-02-01

    The mouse embryonic stem cell test (EST) is a 10-day screen for teratogenic potential developed to reduce animal use for embryotoxicity testing of chemicals (Spielmann, 2005; Spielmann et al., 1997). In this study, we used the cytotoxicity IC(50) values and transcriptional expression changes as primary endpoints in a shorter 4-day version of the EST, the molecular embryonic stem cell assay. Mouse D3 embryonic stem cells were used for cytotoxicity assessment (monolayers) or grown as embryoid bodies in low attachment plates for transcriptional profiling. Sixty-five compounds with known in vivo teratogenicity (33 teratogens and 32 nonteratogens) were evaluated to develop a model for classifying compounds with teratogenic potential. The expression of 12 developmentally regulated gene targets (nanog, fgf5, gsc, cd34, axin2, apln, chst7, lhx1, fgf8, sox17, foxa2, and cxcr4) was measured following exposure of embryoid bodies to a single compound concentration (0.1 × the cytotoxicity IC(20)) for 4 days. In the decision-tree model, compounds with IC(50) values < 22 µM were categorized as teratogens, whereas compounds in the two groups with IC(50) values between 22-200 µM and > 200 µM were categorized as teratogens if ≥ 8 and 12 genes, respectively, were deregulated by at least 10%. Forty-seven of 65 compounds of the training set were correctly identified (72% total concordance). In a test set of 12 additional compounds (5 teratogens, 7 nonteratogens), 10 were correctly classified by this approach (83% concordance). The false positive rate in the training and test sets was 24 and 0%, respectively, indicating that this assay has potential to identify teratogens.

  9. 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/.

  10. 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

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

    NASA Astrophysics Data System (ADS)

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

    2017-03-01

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

  12. 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.

  13. The molecular epidemiology of parasite infections: tools and applications.

    PubMed

    Lymbery, A J; Thompson, R C A

    2012-02-01

    Molecular epidemiology, broadly defined, is the application of molecular genetic techniques to the dynamics of disease in a population. In this review, we briefly describe molecular and analytical tools available for molecular epidemiological studies and then provide an overview of how they can be applied to better understand parasitic disease. A range of new molecular tools have been developed in recent years, allowing for the direct examination of parasites from clinical or environmental samples, and providing access to relatively cheap, rapid, high throughput molecular assays. At the same time, new analytical approaches, in particular those derived from coalescent theory, have been developed to provide more robust estimates of evolutionary processes and demographic parameters from multilocus, genotypic data. To date, the primary application of molecular epidemiology has been to provide specific and sensitive identification of parasites and to resolve taxonomic issues, particularly at the species level and below. Population genetic studies have also been used to determine the extent of genetic diversity among populations of parasites and the degree to which this diversity is associated with different host cycles or epidemiologically important phenotypes. Many of these studies have also shed new light on transmission cycles of parasites, particularly the extent to which zoonotic transmission occurs, and on the prevalence and importance of mixed infections with different parasite species or intraspecific variants (polyparasitism). A major challenge, and one which is now being addressed by an increasing number of studies, is to find and utilize genetic markers for complex traits of epidemiological significance, such as drug resistance, zoonotic potential and virulence. Copyright © 2011 Elsevier B.V. All rights reserved.

  14. 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

  15. [The reaction report, a new tool of management in health establishments?].

    PubMed

    Stoerkel, Nadine

    2007-12-01

    Following technological developments and the overall economic situation, companies fall within a logic of innovation to survive in a competitive environment. So, these industries have become aware of their own wealth: human potential. They have been using, for some years, a tool of participative management: the reaction report. In fact, they use the reaction of new agents to favor the improvement of techniques. Just like companies, hospitals undergo constraints: accreditation, control of expenses, optimization of human and material resources, as many factors which require from health professionals to adapt to improve the services offered to the patients. So, these developments with which health establishments are confronted oblige them to show initiative, creativity, and to fall within a dynamics of change. They are more and more looking for the involvement and the participation of the agents to ensure their primary mission: to meet the population's needs as regard care. As a consequence, so as to favor the participation of their personnel, why wouldn't health establishments get inspired by this tool of management? But it is not easy to get a new method into people's habits. The reaction report can, however, be an efficient and relevant tool in the world of health. It can reveal itself as an essential asset in another approach of participative management and in a quality approach which has become a legal and statutory requirement.

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

    PubMed

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

    2017-06-20

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

  17. Management structure: establishing a laboratory utilization program and tools for utilization management.

    PubMed

    Snozek, Christine; Kaleta, Erin; Hernandez, James S

    2014-01-01

    As laboratories are challenged to do more with fewer resources, the pathologist and laboratory director will play a greater role in improving the effectiveness of the laboratory, as well as addressing the overuse, misuse and underuse of laboratory testing. We describe the necessary characteristics for pathologists and laboratory directors to successfully lead utilization efforts, as well as key leadership tools and essential steps in creating a utilization management program. When we established a laboratory test utilization program de novo, it became clear how important the laboratory director was in guiding those initiatives by working with stakeholders outside of the laboratory, particularly clinicians, nurses and administrators. © 2013.

  18. 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.

  19. 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

  20. 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 .

  1. 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.

  2. 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.

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

    PubMed

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

    2014-04-21

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

  4. 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.

  5. 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.

  6. 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.

  7. 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. Copyright © 2015 Elsevier B.V. All rights reserved.

  8. Personalized Dosimetry for Radionuclide Therapy Using Molecular Imaging Tools

    PubMed Central

    Ljungberg, Michael; Sjögreen Gleisner, Katarina

    2016-01-01

    For treatment of systemic malignancies, when external radiation therapy is not applicable, radionuclide therapy can be an alternative. In this form of therapy, radionuclides are administered to the patient, often in a form where the radionuclide is labelled to a molecule that plays the active part in the localization of the tumor. Since the aim is to impart lethal damage to tumor cells while maintaining possible side-effects to normal tissues at tolerable levels, a proper and accurate personalized dosimetry should be a pre-requisite. In radionuclide therapy, there is a need to measure the distribution of the radiopharmaceutical in vivo, as well as its re-distribution over time, in order estimate the total energy released in radioactive decays and subsequent charged-particle interactions, governing the absorbed dose to different organs and tumors. Measurements are usually performed by molecular imaging, more specifically planar and SPECT (Single-Photon Emission Computed Tomography) imaging, combined with CT. This review describes the different parts in the dosimetry chain of radionuclide therapy. Emphasis is given to molecular imaging tools and the requirements for determining absorbed doses from quantitative planar and SPECT images. As example solutions to the different problems that need to be addressed in such a dosimetric chain, we describe our tool, Lundadose, which is a set of methods that we have developed for personalized dosimetry. PMID:28536392

  9. 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

  10. 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.

  11. 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

  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

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

    2009-01-01

    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.

  14. 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

  15. Establishment of Tools for Neurogenetic Analysis of Sexual Behavior in the Silkmoth, Bombyx mori

    PubMed Central

    Kiya, Taketoshi; Morishita, Koudai; Uchino, Keiro; Iwami, Masafumi; Sezutsu, Hideki

    2014-01-01

    Background Silkmoth, Bombyx mori, is an ideal model insect for investigating the neural mechanisms underlying sex pheromone-induced innate behavior. Although transgenic techniques and the GAL4/UAS system are well established in the silkmoth, genetic tools useful for investigating brain function at the neural circuit level have been lacking. Results In the present study, we established silkmoth strains in which we could visualize neural projections (UAS-mCD8GFP) and cell nucleus positions (UAS-GFP.nls), and manipulate neural excitability by thermal stimulation (UAS-dTrpA1). In these strains, neural projections and nucleus position were reliably labeled with green fluorescent protein in a GAL4-dependent manner. Further, the behavior of silkworm larvae and adults could be controlled by GAL4-dependent misexpression of dTrpA1. Ubiquitous dTrpA1 misexpression led both silkmoth larvae and adults to exhibit seizure-like phenotypes in a heat stimulation-dependent manner. Furthermore, dTrpA1 misexpression in the sex pheromone receptor neurons of male silkmoths allowed us to control male sexual behavior by changing the temperature. Thermally stimulated male silkmoths exhibited full sexual behavior, including wing-flapping, orientation, and attempted copulation, and precisely approached a thermal source in a manner similar to male silkmoths stimulated with the sex pheromone. Conclusion These findings indicate that a thermogenetic approach using dTrpA1 is feasible in Lepidopteran insects and thermogenetic analysis of innate behavior is applicable in the silkmoth. These tools are essential for elucidating the relationships between neural circuits and function using neurogenetic methods. PMID:25396742

  16. Establishment of tools for neurogenetic analysis of sexual behavior in the silkmoth, Bombyx mori.

    PubMed

    Kiya, Taketoshi; Morishita, Koudai; Uchino, Keiro; Iwami, Masafumi; Sezutsu, Hideki

    2014-01-01

    Silkmoth, Bombyx mori, is an ideal model insect for investigating the neural mechanisms underlying sex pheromone-induced innate behavior. Although transgenic techniques and the GAL4/UAS system are well established in the silkmoth, genetic tools useful for investigating brain function at the neural circuit level have been lacking. In the present study, we established silkmoth strains in which we could visualize neural projections (UAS-mCD8GFP) and cell nucleus positions (UAS-GFP.nls), and manipulate neural excitability by thermal stimulation (UAS-dTrpA1). In these strains, neural projections and nucleus position were reliably labeled with green fluorescent protein in a GAL4-dependent manner. Further, the behavior of silkworm larvae and adults could be controlled by GAL4-dependent misexpression of dTrpA1. Ubiquitous dTrpA1 misexpression led both silkmoth larvae and adults to exhibit seizure-like phenotypes in a heat stimulation-dependent manner. Furthermore, dTrpA1 misexpression in the sex pheromone receptor neurons of male silkmoths allowed us to control male sexual behavior by changing the temperature. Thermally stimulated male silkmoths exhibited full sexual behavior, including wing-flapping, orientation, and attempted copulation, and precisely approached a thermal source in a manner similar to male silkmoths stimulated with the sex pheromone. These findings indicate that a thermogenetic approach using dTrpA1 is feasible in Lepidopteran insects and thermogenetic analysis of innate behavior is applicable in the silkmoth. These tools are essential for elucidating the relationships between neural circuits and function using neurogenetic methods.

  17. Establishing a Measurement Tool for a Nursing Work Environment in Taiwan.

    PubMed

    Lin, Li-Chiu; Lee, Huan-Fang; Yen, Miaofen

    2017-02-01

    The nursing work environment is a critical global health care problem. Many health care providers are concerned about the associations between the nursing work environment and the outcomes of organizations, nurses, and patients. Nursing work environment instruments have been assessed in the West but have not been considered in Asia. However, different cultures will affect the factorial structure of the tool. Using a stratified nationwide random sample, we created a measurement tool for the nursing work environment in Taiwan. The Nursing Work Environment Index-Revised Scale and the Essentials of Magnetism scale were used to examine the factorial structure. Item analysis, exploratory factor analysis, and confirmatory factor analysis were used to examine the hypothesis model and generate a new factorial structure. The Taiwan Nursing Work Environment Index (TNWEI) was established to evaluate the nursing work environment in Taiwan. The four factors were labeled "Organizational Support" (7 items), "Nurse Staffing and Resources" (4 items), "Nurse-Physician Collaboration" (4 items), and "Support for Continuing Education" (4 items). The 19 items explained 58.5% of the variance. Confirmatory factor analysis showed a good fit to the model (x2/df = 5.99; p < .05, goodness of fit index [GFI] = .90; RMSEA = .07). The TNWEI provides a comprehensive and efficient method for measuring the nurses' work environment in Taiwan.

  18. Functional viral metagenomics and the next generation of molecular tools.

    PubMed

    Schoenfeld, Thomas; Liles, Mark; Wommack, K Eric; Polson, Shawn W; Godiska, Ronald; Mead, David

    2010-01-01

    The enzymes of bacteriophages and other viruses have been essential research tools since the first days of molecular biology. However, the current repertoire of viral enzymes only hints at their overall potential. The most commonly used enzymes are derived from a surprisingly small number of cultivated viruses, which is remarkable considering the extreme abundance and diversity of viruses revealed over the past decade by metagenomic analysis. To access the treasure trove of enzymes hidden in the global virosphere and develop them for research, therapeutic and diagnostic uses, improvements are needed in our ability to rapidly and efficiently discover, express and characterize viral genes to produce useful proteins. In this paper, we discuss improvements to sampling and cloning methods, functional and genomics-based screens, and expression systems, which should accelerate discovery of new enzymes and other viral proteins for use in research and medicine.

  19. 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

  20. 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

  1. 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

  2. [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)

  3. Establishing user needs for a stability assessment tool to guide wheelchair prescription.

    PubMed

    Moody, Louise; Evans, Jill; Fielden, Simon; Heelis, Mike; Dryer, Paul; Shapcott, Nigel; Magee, Paul; Stefanov, Dimitar

    2017-01-01

    The WheelSense project aims to develop a system for assessing the stability and performance of wheelchairs through a user-centred design process. This study sought to capture user needs and define the specification for the system. A mixed methods approach was adopted. An online survey was completed by 98 participants working in wheelchair provision. The results were built upon through 10 semi-structured interviews and one focus group (n = 5) with professionals working in wheelchair provision in three NHS Trusts in the UK. The results provided a picture of the current UK practice in stability testing. Issues with the reliability and usefulness of the existing methods used to assess the stability and performance of wheelchairs were highlighted. Requirements for a new system were ascertained. These included improved accuracy of tipping angles, features to support record keeping, improved client/carer education support and ability to model or predict client-wheelchair system performance in different configurations. The paper concludes that there is a need for improved tools to determine the stability of the client-wheelchair system and support the prescription process, to ensure client safety and optimum equipment performance. A list of requirements has been produced to guide the future development of WheelSense. Implications for Rehabilitation The results of this survey and interview-based study present a picture of wheelchair stability testing practices in the UK, and highlight the need for new, more informative methods for guiding wheelchair prescription. The requirements for the design of a new system, or further development of existing tools to support the stability testing and prescription of wheelchairs have been established.

  4. 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. © 2015 John Wiley & Sons Ltd.

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

    PubMed

    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.

  6. 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.

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

    PubMed

    Dallakian, Pavel; Haider, Norbert

    2011-02-01

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

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

    PubMed Central

    2011-01-01

    Background So far, there have been no Flash-based web tools available for chemical structure input. The authors herein present a feasibility study, aiming at the development of a compact and easy-to-use 2D structure editor, using Adobe's Flash technology and its programming language, ActionScript. As a reference model application from the Java world, we selected the Java Molecular Editor (JME). In this feasibility study, we made an attempt to realize a subset of JME's functionality in the Flash Molecular Editor (FlaME) utility. These basic capabilities are: structure input, editing and depiction of single molecules, data import and export in molfile format. Implementation The result of molecular diagram sketching in FlaME is accessible in V2000 molfile format. By integrating the molecular editor into a web page, its communication with the HTML elements on this page is established using the two JavaScript functions, getMol() and setMol(). In addition, structures can be copied to the system clipboard. Conclusion A first attempt was made to create a compact single-file application for 2D molecular structure input/editing on the web, based on Flash technology. With the application examples presented in this article, it could be demonstrated that the Flash methods are principally well-suited to provide the requisite communication between the Flash object (application) and the HTML elements on a web page, using JavaScript functions. PMID:21284863

  9. 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

  10. 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.

  11. 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.

  12. 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.

  13. 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.

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

    PubMed

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

    2013-09-01

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

  15. Molecular-signature analyses support the establishment of the actinobacterial genus Sphaerimonospora (Mingma et al. 2016).

    PubMed

    Meyers, Paul R

    2017-08-18

    The genera Microbispora and Sphaerimonospora were examined for GyrB and RecA amino-acid signatures to determine whether molecular-signature analyses support the recent establishment of the genus Sphaerimonospora. The creation of Sphaerimonospora was based mainly upon morphological differences between Microbispora and Sphaerimonospora and the clustering of the type strains of the two genera in phylogenetic trees based on a multilocus sequence analysis. The molecular-signature analyses showed that all members of Sphaerimonospora can be distinguished from all members of Microbispora at 14 amino acid positions in the GyrB protein and at four positions in the shorter RecA protein. These amino acid differences can be used as signatures to differentiate the members of these genera from each other and thus provide support for the establishment of the genus Sphaerimonospora. This is the first demonstration of the use of molecular signatures to support the establishment of a new genus in the family Streptosporangiaceae. Following the transfer of Microbispora mesophila and Microbispora thailandensis from Microbispora to Sphaerimonospora, all species in the genus Microbispora are characterised by the insertion of a small, hydrophobic amino acid after position 208 in the GyrB protein. This insertion is absent from the GyrB protein of members of the genus Sphaerimonospora. Copyright © 2017 Elsevier GmbH. All rights reserved.

  16. 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

  17. 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.

  18. Establishment of markerless gene deletion tools in thermophilic Bacillus smithii and construction of multiple mutant strains.

    PubMed

    Bosma, Elleke F; van de Weijer, Antonius H P; van der Vlist, Laurens; de Vos, Willem M; van der Oost, John; van Kranenburg, Richard

    2015-07-07

    Microbial conversion of biomass to fuels or chemicals is an attractive alternative for fossil-based fuels and chemicals. Thermophilic microorganisms have several operational advantages as a production host over mesophilic organisms, such as low cooling costs, reduced contamination risks and a process temperature matching that of commercial hydrolytic enzymes, enabling simultaneous saccharification and fermentation at higher efficiencies and with less enzymes. However, genetic tools for biotechnologically relevant thermophiles are still in their infancy. In this study we developed a markerless gene deletion method for the thermophile Bacillus smithii and we report the first metabolic engineering of this species as a potential platform organism. Clean deletions of the ldhL gene were made in two B. smithii strains (DSM 4216(T) and compost isolate ET 138) by homologous recombination. Whereas both wild-type strains produced mainly L-lactate, deletion of the ldhL gene blocked L-lactate production and caused impaired anaerobic growth and acid production. To facilitate the mutagenesis process, we established a counter-selection system for efficient plasmid removal based on lacZ-mediated X-gal toxicity. This counter-selection system was applied to construct a sporulation-deficient B. smithii ΔldhL ΔsigF mutant strain. Next, we demonstrated that the system can be used repetitively by creating B. smithii triple mutant strain ET 138 ΔldhL ΔsigF ΔpdhA, from which also the gene encoding the α-subunit of the E1 component of the pyruvate dehydrogenase complex is deleted. This triple mutant strain produced no acetate and is auxotrophic for acetate, indicating that pyruvate dehydrogenase is the major route from pyruvate to acetyl-CoA. In this study, we developed a markerless gene deletion method including a counter-selection system for thermophilic B. smithii, constituting the first report of metabolic engineering in this species. The described markerless gene deletion system

  19. 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.

  20. 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

  1. Establishing the Minimal Clinical Important Difference and Minimal Detectable Change for the Cumberland Ankle Instability Tool.

    PubMed

    Wright, Cynthia J; Linens, Shelley W; Cain, M Spencer

    2017-09-01

    To establish the minimal detectable change (MDC) and minimal clinically important difference (MCID) for the Cumberland Ankle Instability Tool (CAIT) in a population with chronic ankle instability (CAI). Experimental cohort. Laboratory. A convenience sample of individuals with CAI (N=50; 12 men; 38 women; episodes of giving way, 5.84±12.54mo). CAI inclusion criteria included a history of an ankle sprain, recurrent episodes of giving way, and a CAIT score ≤25. Participants completed demographic information, an injury history questionnaire, and the CAIT. Participants then either participated in 4 weeks of wobble board balance training, resistance tubing strength training, or no intervention. After 4 weeks, participants recompleted the CAIT and recorded their global rating of change (GRC). Dependent variables were pre- and postintervention scores on the CAIT and postintervention GRC. The MDC with 95% confidence interval was calculated. A receiver operating characteristic (ROC) curve identified the optimal CAIT cut point (MCID) between improved and unimproved individuals on the basis of their GRC. The area under the curve was used to identify a significant ROC curve (α=.05). The average CAIT score preintervention was 16.8±5.6, and postintervention, it was 20.0±5.2. Thirty-one participants (62%) rated themselves as improved on the GRC scale, whereas 19 (38%) were not improved. The ROC curve was significant (area under the curve, .797; P=.001), indicating that the CAIT change score significantly predicted clinical status. The MDC was 3.08, and the MCID was ≥3 points. The CAIT has an MDC and MCID of ≥3 points. When CAIT scores are used to assess patient change over time, these scores should be used as a minimum threshold to indicate detectable and clinically meaningful improvement. Copyright © 2017 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

  2. 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…

  3. 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…

  4. 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…

  5. 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…

  6. Synergistic dual positive feedback loops established by molecular sequestration generate robust bimodal response.

    PubMed

    Venturelli, Ophelia S; El-Samad, Hana; Murray, Richard M

    2012-11-27

    Feedback loops are ubiquitous features of biological networks and can produce significant phenotypic heterogeneity, including a bimodal distribution of gene expression across an isogenic cell population. In this work, a combination of experiments and computational modeling was used to explore the roles of multiple feedback loops in the bimodal, switch-like response of the Saccharomyces cerevisiae galactose regulatory network. Here, we show that bistability underlies the observed bimodality, as opposed to stochastic effects, and that two unique positive feedback loops established by Gal1p and Gal3p, which both regulate network activity by molecular sequestration of Gal80p, induce this bimodality. Indeed, systematically scanning through different single and multiple feedback loop knockouts, we demonstrate that there is always a concentration regime that preserves the system's bimodality, except for the double deletion of GAL1 and the GAL3 feedback loop, which exhibits a graded response for all conditions tested. The constitutive production rates of Gal1p and Gal3p operate as bifurcation parameters because variations in these rates can also abolish the system's bimodal response. Our model indicates that this second loss of bistability ensues from the inactivation of the remaining feedback loop by the overexpressed regulatory component. More broadly, we show that the sequestration binding affinity is a critical parameter that can tune the range of conditions for bistability in a circuit with positive feedback established by molecular sequestration. In this system, two positive feedback loops can significantly enhance the region of bistability and the dynamic response time.

  7. 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

  8. The growing contributions of molecular biology and immunology to protistan ecology: molecular signatures as ecological tools.

    PubMed

    Caron, David A; Countway, Peter D; Brown, Mark V

    2004-01-01

    Modern genetic and immunological techniques have become important tools for assessing protistan species diversity for both the identification and quantification of specific taxa in natural microbial communities. Although these methods are still gaining use among ecologists, the new approaches have already had a significant impact on our understanding of protistan diversity and biogeography. For example, genetic studies of environmental samples have uncovered many protistan phylotypes that do not match the DNA sequences of any cultured organisms, and whose morphological identities are unknown at the present time. Additionally, rapid and sensitive methods for detecting and enumerating taxa of special importance (e.g. bloom-forming algae, parasitic protists) have enabled much more detailed distributional and experimental studies than have been possible using traditional methods. Nevertheless, while the application of molecular approaches has advanced some aspects of aquatic protistan ecology, significant issues still thwart the widespread adoption of these approaches. These issues include the highly technical nature of some of the molecular methods, the reconciliation of morphology-based and sequence-based species identifications, and the species concept itself.

  9. Molecular imaging as a tool for translating breast cancer science

    PubMed Central

    Mankoff, David A

    2008-01-01

    The ability to measure biochemical and molecular processes underlies progress in breast cancer biology and treatment. These assays have traditionally been performed by analysis of cell culture or tissue samples. More recently, functional and molecular imaging has allowed the in vivo assay of biochemistry and molecular biology, which is highly complementary to tissue-based assays. This review briefly describes different imaging modalities used in molecular imaging and then reviews applications of molecular imaging to breast cancer, with a focus on translational work. It includes sections describing work in functional and physiological tumor imaging, imaging gene product expression, imaging the tumor microenvironment, reporter gene imaging, and cell labeling. Work in both animal models and human is discussed with an eye towards studies that have relevance to breast cancer treatment in patients. PMID:19091007

  10. Establishment gaps as an innovative tool to restore landscape-scale grassland biodiversity

    NASA Astrophysics Data System (ADS)

    Tóthmérész, Béla; Deák, Balázs; Török, Péter; Tischew, Sabine; Kirmer, Anita; Kelemen, András; Miglécz, Tamás; Tóth, Katalin; Radócz, Szilvia; Sonkoly, Judit; Valkó, Orsolya

    2017-04-01

    The large-scale abandonment of croplands resulted in landscape-scale changes in biodiversity, ecosystem services and agricultural production in Central Europe. Grasslands are vital landscape elements, and sustaining their biodiversity is crucial for biodiversity conservation. Thus, grassland restoration on former croplands offers a vital opportunity to restore grassland biodiversity. We studied vegetation changes in former croplands sown by grass seed mixtures in Hungary. We evaluated the usefulness of sowing grass seed mixtures, a frequently used restoration technique. We also developed a novel method (so-called establishment gaps) to increase the diversity of species-poor sown grasslands. We compiled a multi-species seed mixture containing 35 species. We established altogether 32 establishment gaps (size: 1×1-m, 2×2-m and 4×4-m) in 8-year-old restored grasslands. We evaluated the success and cost-effectiveness of spontaneous grassland recovery and active grassland restoration by seed sowing. We focused on the restoration of ecosystem services, like weed control, biomass production, and recovery of biodiversity. Using establishment gaps we could successfully introduce target species to the species-poor recovered grasslands. All sown species established in the establishment gaps and many of them maintained or even increased their first-year cover to the second year. Larger establishment gaps were characterised by higher cover of sown species and more homogeneous species composition compared to the smaller ones. Thus, we recommend using large establishment gaps in restoration practice. Our findings suggest that grassland restoration on croplands offer a viable solution for restoring biodiversity and ecosystem services. We found that both spontaneous grassland recovery and seed sowing can be cost-effective methods, and can be successful even during a relatively short period of a nature conservation project.

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

    PubMed

    Murakami, Masaaki

    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.

  12. 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.

  13. 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

  14. 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).

  15. 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,…

  16. 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.

  17. 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.

  18. 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

  19. Doppler spectroscopy, a powerful tool for studying molecular collision dynamics

    SciTech Connect

    Mestdagh, J.M.; Visticot, J.P.

    1994-12-31

    The present review describes the application of Doppler spectroscopy to studies in collision dynamics. The method was originally introduced by Kinsey (J. Chem. Phys. 66, 2560 (1976)). The authors used it to obtain angular and velocity distributions of Ba(6s6p{sup 1}P{sub 1}) atoms scattered in the 6s6p{sup 3}P{sub 2} level by collisions with argon and simple molecules. After a short review of their recent work, the authors outline those areas where Doppler spectroscopy is a valuable tool (sometimes the only tool) for exploring gas phase collision dynamics. In particular they make clear that Doppler spectroscopy should not be considered as alternative but rather as complementary to the standard way of measuring differential cross sections where a rotating mass spectrometer rather than laser induced fluorescence is used to detect the scattered particles.

  20. Application of molecular genetic tools to studies of forest pathosystems [Chapter 2

    Treesearch

    Mee-Sook Kim; Ned B. Klopfenstein; Richard C. Hamelin

    2005-01-01

    The use of molecular genetics in forest pathology has greatly increased over the past 10 years. For the most part, molecular genetic tools were initially developed to focus on individual components (e.g., pathogen, host) of forest pathosystems. As part of broader forest ecosystem complexes, forest pathosystems involve dynamic interactions among living components (e.g...

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

    PubMed Central

    2017-01-01

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

  2. 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

  3. 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

  4. 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

  5. Biomarkers for Intracellular Pathogens: Establishing tools as Vaccine and Therapeutic Endpoints for Visceral Leishmaniasis

    PubMed Central

    Vallur, Aarthy C.; Duthie, Malcolm S.; Reinhart, Caroline; Tutterrow, Yeung; Hamano, Shinjiro; Bhaskar, Khondaker Rifat Hasan; Coler, Rhea N.; Mondal, Dinesh; Reed, Steven G.

    2013-01-01

    Visceral leishmaniasis (VL) in South Asia is a serious disease affecting children and adults. Acute VL develops in only a fraction of those infected individuals, the majority being asymptomatic with the potential to transmit infection and develop disease. We followed 56 individuals characterized as being asymptomatic by sero-positivity with rk39 RDT in a hyper endemic district of Bangladesh to define the utility of Leishmania-specific antibodies and DNA in identifying infection. At baseline, 54 of the individuals were sero-positive with one or more quantitative antibody assays and antibody levels persisted at follow-up. Most sero-positive individuals (47/54) tested positive by qPCR at baseline, but only 16 tested positive at follow-up. The discrepancies among the different tests may shed light on the dynamics of asymptomatic infections of L. donovani, as well as underscore the need for standard diagnostic tools for active surveillance as well as assessing the effectiveness of prophylactic and therapeutic interventions. PMID:24237596

  6. Biomarkers for intracellular pathogens: establishing tools as vaccine and therapeutic endpoints for visceral leishmaniasis.

    PubMed

    Vallur, A C; Duthie, M S; Reinhart, C; Tutterrow, Y; Hamano, S; Bhaskar, K R H; Coler, R N; Mondal, D; Reed, S G

    2014-06-01

    Visceral leishmaniasis in South Asia is a serious disease affecting children and adults. Acute visceral leishmaniasis develops in only a fraction of those infected individuals, the majority being asymptomatic with the potential to transmit infection and develop disease. We followed 56 individuals characterized as being asymptomatic by seropositivity with rk39 rapid diagnostic test in a hyperendemic district of Bangladesh to define the utility of Leishmania-specific antibodies and DNA in identifying infection. At baseline, 54 of the individuals were seropositive with one or more quantitative antibody assays and antibody levels persisted at follow up. Most seropositive individuals (47/54) tested positive by quantitative PCR at baseline, but only 16 tested positive at follow up. The discrepancies among the different tests may shed light on the dynamics of asymptomatic infections of Leishmania donovani, as well as underscore the need for standard diagnostic tools for active surveillance as well as assessing the effectiveness of prophylactic and therapeutic interventions. ©2013 Infectious Disease Research Institute Clinical Microbiology and Infection © 2013 European Society of Clinical Microbiology and Infectious Diseases.

  7. Molecular tools and triatomine systematics: a public health perspective.

    PubMed

    Monteiro, F A; Escalante, A A; Beard, C B

    2001-07-01

    Triatomines, or kissing bugs, are vectors of Chagas disease to humans. This disease is a substantial public health problem affecting up to 12 million people throughout the Americas, and its control relies mainly on the insecticide treatment of triatomine-infested houses within villages. In this article, Fernando Monteiro, Ananias Escalante and Ben Beard review how molecular markers have been used to clarify triatomine systematics, and give examples of how our understanding of triatomine population structure and accurate vector identification can be used to optimize vector control.

  8. 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.

  9. 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.

  10. Establishing Baseline Normative Values for the Child Sport Concussion Assessment Tool.

    PubMed

    Brooks, M Alison; Snedden, Traci R; Mixis, Benjamin; Hetzel, Scott; McGuine, Timothy A

    2017-07-01

    The Child Sport Concussion Assessment Tool (SCAT3) is a postconcussion sideline assessment tool measuring symptoms, cognition, and balance in preadolescent children. Minimal normative baseline data exist to aid decision making in clinical and athletic settings. To collect normative baseline data for the Child SCAT3 in a large cohort of young athletes. A cross-sectional study was conducted from May 31 to August 12, 2014, at various sporting events (basketball, soccer, baseball, and swimming) in Central Wisconsin among children 5 to 13 years of age who were English-speaking and did not report a lower leg injury within the past 2 months or a concussion within the past month. Data were analyzed between October 8, 2014, and September 12, 2016. All Child SCAT3 components were assessed: child and parent report of symptom number and severity, cognition (Standardized Assessment of Concussion-child version [SAC-C]), and balance (modified Balance Error Scoring System [mBESS] and tandem gait). Summary statistics, mean differences, and effect sizes were calculated for each test component. Participants included 478 children (234 girls and 241 boys; mean [SD] age, 9.9 [1.9] years]) and their parents. Age had the largest effect on all Child SCAT3 components, with children 5 to 7 years of age reporting higher mean (SD) symptom severity scores compared with those 11 to 13 years of age (18.2 [10.0] vs 11.3 [9.0]; mean difference, 6.86 [95% CI, 4.22-9.50]; effect size, 0.74) and performing more poorly on the total SAC-C (mean [SD] score, 19.5 [5.1] vs 26.1 [2.1]; mean difference, -6.59 [95% CI, -7.49 to -5.68]; effect size, -2.1), mBESS (mean [SD] score, 1.67 [1.8] vs 0.76 [1.2]; mean difference, 0.91 [95% CI, 0.53-1.29]; effect size, 0.68), and tandem gait (mean [SD] time, 22.2 [8.3] vs 14.0 [3.7] seconds; mean difference, 8.23 seconds [95% CI, 6.63-9.82]; effect size, 1.55). Sex had a small effect on the mean (SD) number and severity of symptoms reported by the child (severity: boys

  11. 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

  12. 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

  13. 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

  14. 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.

  15. 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

  16. 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

  17. 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.

  18. Lanthanides in molecular magnetism: old tools in a new field.

    PubMed

    Sorace, Lorenzo; Benelli, Cristiano; Gatteschi, Dante

    2011-06-01

    In this tutorial review we discuss some basic aspects concerning the magnetic properties of rare-earth ions, which are currently the subject of a renovated interest in the field of molecular magnetism, after the discovery that slow relaxation of the magnetization at liquid nitrogen temperature can occur in mononuclear complexes of these ions. Focusing on Dy(III) derivatives a tutorial discussion is given of the relation of the crystal field parameters, which determine the anisotropy of these systems and consequently their interesting magnetic properties, with the geometry of the coordination sphere around the lanthanide centre and with the pattern of f orbitals. The problem of systems of low point symmetry is also addressed by showing how detailed single crystal investigation, coupled to more sophisticated calculation procedures, is an absolute necessity to obtain meaningful structure-property relationships in these systems.

  19. 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

  20. 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.

  1. 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

  2. Bio++: efficient extensible libraries and tools for computational molecular evolution.

    PubMed

    Guéguen, Laurent; Gaillard, Sylvain; Boussau, Bastien; Gouy, Manolo; Groussin, Mathieu; Rochette, Nicolas C; Bigot, Thomas; Fournier, David; Pouyet, Fanny; Cahais, Vincent; Bernard, Aurélien; Scornavacca, Céline; Nabholz, Benoît; Haudry, Annabelle; Dachary, Loïc; Galtier, Nicolas; Belkhir, Khalid; Dutheil, Julien Y

    2013-08-01

    Efficient algorithms and programs for the analysis of the ever-growing amount of biological sequence data are strongly needed in the genomics era. The pace at which new data and methodologies are generated calls for the use of pre-existing, optimized-yet extensible-code, typically distributed as libraries or packages. This motivated the Bio++ project, aiming at developing a set of C++ libraries for sequence analysis, phylogenetics, population genetics, and molecular evolution. The main attractiveness of Bio++ is the extensibility and reusability of its components through its object-oriented design, without compromising the computer-efficiency of the underlying methods. We present here the second major release of the libraries, which provides an extended set of classes and methods. These extensions notably provide built-in access to sequence databases and new data structures for handling and manipulating sequences from the omics era, such as multiple genome alignments and sequencing reads libraries. More complex models of sequence evolution, such as mixture models and generic n-tuples alphabets, are also included.

  3. Thinking outside the box: using metastasis suppressors as molecular tools.

    PubMed

    Thiolloy, Sophie; Rinker-Schaeffer, Carrie W

    2011-04-01

    Metastasis, the process in which tumor cells move from a primary tumor through the circulation, lodge, and grow in distant locations, is a significant contributor to cancer patient morbidity and mortality, yet remains poorly understood. The molecular processes regulating tumorigenicity and metastasis are distinguishable, suggesting that it is possible to design therapeutic interventions to specifically control metastasis formation. Metastasis suppressors, which specifically regulate metastasis, are being used in "reverse genetics" approaches to discover the phenotypic alterations caused by modulating their levels and/or activity. This strategy is allowing the identification of tumor-host interactions that are crucial for efficient colonization and their disruption can be targeted to suppress metastases formation. In this review we discuss studies addressing invasion and migration, key functions for both early and late in the metastatic process. Metastasis suppressor functions, which modulate lodging and subsequent colonization of the secondary site, are also described. In sum this review focuses on metastasis suppressors that have yielded insight into mechanisms controlling metastasis formation. These serve as platform for out of the box thinking which will enable the discovery of new paradigms in metastasis research. Copyright © 2011. Published by Elsevier Ltd.

  4. 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.

  5. Ribosome-inactivating proteins: potent poisons and molecular tools.

    PubMed

    Walsh, Matthew J; Dodd, Jennifer E; Hautbergue, Guillaume M

    2013-11-15

    Ribosome-inactivating proteins (RIPs) were first isolated over a century ago and have been shown to be catalytic toxins that irreversibly inactivate protein synthesis. Elucidation of atomic structures and molecular mechanism has revealed these proteins to be a diverse group subdivided into two classes. RIPs have been shown to exhibit RNA N-glycosidase activity and depurinate the 28S rRNA of the eukaryotic 60S ribosomal subunit. In this review, we compare archetypal RIP family members with other potent toxins that abolish protein synthesis: the fungal ribotoxins which directly cleave the 28S rRNA and the newly discovered Burkholderia lethal factor 1 (BLF1). BLF1 presents additional challenges to the current classification system since, like the ribotoxins, it does not possess RNA N-glycosidase activity but does irreversibly inactivate ribosomes. We further discuss whether the RIP classification should be broadened to include toxins achieving irreversible ribosome inactivation with similar turnovers to RIPs, but through different enzymatic mechanisms.

  6. 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

  7. 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.

  8. 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.

  9. [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. Copyright © 2015 the American Physiological Society.

  10. 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

  11. 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.

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

    PubMed

    Li, Aiguo; Bozdag, Serdar; Kotliarov, Yuri; Fine, Howard A

    2010-07-15

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

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

    PubMed

    Gangadaran, Prakash; Ahn, Byeong-Cheol

    2017-01-01

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

  14. 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.

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

    PubMed

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

    2014-01-01

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

  16. 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

  17. 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.

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

    DOE PAGES

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

    2016-03-07

    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 ofmore » 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

  19. 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

  20. PS1-48: A Patient-centered Electronic Education Tool for Establishing Weight Loss Expectations after Bariatric Surgery

    PubMed Central

    Wood, G. Craig; Benotti, Peter; Gerhard, Glenn; Zaccone, Richard; Zhang, Yushan; Miller, Elaina; Still, Christopher

    2014-01-01

    Background/Aims Bariatric surgery candidates often struggle when deciding between intensive lifestyle therapy, pharmacological therapy, and/or bariatric surgery for achieving their long-term weight loss (WL) goals. Moreover, they often have unrealistic WL expectations prior to surgery. Despite huge individual variation in surgically induced WL, patient education is currently based on average WL results derived from program experience or published literature. Improved patient education tools are needed to provide realistic individual expectations for surgical WL. The purpose of this study was to develop an electronic application for patient education that can aid in surgical decisions, establishing realistic WL goals, and monitoring WL success. Methods Post-operative weight measurements from 2608 Roux-en-Y gastric bypass patients at Geisinger Clinic were collected over an eight year period. While accounting for surgical BMI and age, quantile regression was used to create expected WL curves (10th, 25th, 50th, 75th, and 90th %tile) for the 36 month post-operative period. Results A mobile application (Get-2-Goal) was designed to provide a simple, personalized interface that allows patients to track their WL and compare their WL results to their expected WL curves. Get-2-Goal was made publicly available at no cost on a popular Apps store and is compatible with current smartphone and tablet technology (>1000 downloads to date). Get-2-Goal allows patients to input their personal profile (e.g. age, BMI), review their expected WL, and track their WL post-operatively. Patients have the option of saving a graphic containing their personalized WL curves and e-mailing a tabular form of their WL results to family, friends, and/or care providers. Conclusions Get-2-Goal is a simple tool that may be used by Bariatric Surgery Programs to facilitate electronic patient education. This tool may assist patients in deciding to proceed to WL surgery, and will facilitate early

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

    PubMed

    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 two

  2. 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…

  3. 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…

  4. 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.

  5. 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

  6. Establishment and operation of a biorepository for molecular epidemiologic studies in Costa Rica.

    PubMed

    Cortés, Bernal; Schiffman, Mark; Herrero, Rolando; Hildesheim, Allan; Jiménez, Silvia; Shea, Katheryn; González, Paula; Porras, Carolina; Fallas, Greivin; Rodríguez, Ana Cecilia

    2010-04-01

    The Proyecto Epidemiológico Guanacaste (PEG) has conducted several large studies related to human papillomavirus (HPV) and cervical cancer in Guanacaste, Costa Rica in a long-standing collaboration with the U.S. National Cancer Institute. To improve molecular epidemiology efforts and save costs, we have gradually transferred technology to Costa Rica, culminating in state-of-the-art laboratories and a biorepository to support a phase III clinical trial investigating the efficacy of HPV 16/18 vaccine. Here, we describe the rationale and lessons learned in transferring molecular epidemiologic and biorepository technology to a developing country. At the outset of the PEG in the early 1990s, we shipped all specimens to repositories and laboratories in the United States, which created multiple problems. Since then, by intensive personal interactions between experts from the United States and Costa Rica, we have successfully transferred liquid-based cytology, HPV DNA testing and serology, chlamydia and gonorrhea testing, PCR-safe tissue processing, and viable cryopreservation. To accommodate the vaccine trial, a state-of-the-art repository opened in mid-2004. Approximately 15,000 to 50,000 samples are housed in the repository on any given day, and >500,000 specimens have been shipped, many using a custom-made dry shipper that permits exporting >20,000 specimens at a time. Quality control of shipments received by the NCI biorepository has revealed an error rate of <0.2%. Recently, the PEG repository has incorporated other activities; for example, large-scale aliquotting and long-term, cost-efficient storage of frozen specimens returned from the United States. Using Internet-based specimen tracking software has proven to be efficient even across borders. For long-standing collaborations, it makes sense to transfer the molecular epidemiology expertise toward the source of specimens. The successes of the PEG molecular epidemiology laboratories and biorepository prove that

  7. What to expect from molecular tools for non-documented pediatric infectious diseases.

    PubMed

    Filleron, Anne; Michon, Anne-Laure; Jumas-Bilak, Estelle; Jeziorski, Eric; Zorgniotti, Isabelle; Tran, Tu Anh; Filleron, Thomas; Rodière, Michel; Marchandin, Hélène

    2015-01-01

    Evaluation of the contribution of molecular tools to the overall diagnosis of infectious diseases in children. Results of 16S rDNA analysis (179 children; 228 specimens), combined to specific amplification of Kingella kingae (126 children; 166 osteoarticular specimens), were retrospectively analyzed for samples with inconclusive cultures. The overall positive yield in diagnosis was 12.8% of the patients for 16S rDNA PCR, 40.5% for K. kingae PCR and 45.2% for combined use of both methods. Results were related to clinical and biological data (direct examination, certainty/uncertainty of clinical diagnosis, fever, biological markers, previous antibiotics), and to the number of samples analyzed per patient, allowing the identification of specific situations with significant contribution of PCR methods. Molecular techniques constitute valuable tools to improve the bacterial infection diagnosis in children; however, specific indications, dedicated samples, and number of analyzed samples per patient are key points to optimize their contribution.

  8. 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.

  9. Molecular Basis for Cohesin Acetylation by Establishment of Sister Chromatid Cohesion N-Acetyltransferase ESCO1.

    PubMed

    Rivera-Colón, Yadilette; Maguire, Andrew; Liszczak, Glen P; Olia, Adam S; Marmorstein, Ronen

    2016-12-16

    Protein acetylation is a prevalent posttranslational modification that is regulated by diverse acetyltransferase enzymes. Although histone acetyltransferases (HATs) have been well characterized both structurally and mechanistically, far less is known about non-histone acetyltransferase enzymes. The human ESCO1 and ESCO2 paralogs acetylate the cohesin complex subunit SMC3 to regulate the separation of sister chromatids during mitosis and meiosis. Missense mutations within the acetyltransferase domain of these proteins correlate with diseases, including endometrial cancers and Roberts syndrome. Despite their biological importance, the mechanisms underlying acetylation by the ESCO proteins are not understood. Here, we report the X-ray crystal structure of the highly conserved zinc finger-acetyltransferase moiety of ESCO1 with accompanying structure-based mutagenesis and biochemical characterization. We find that the ESCO1 acetyltransferase core is structurally homologous to the Gcn5 HAT, but contains unique additional features including a zinc finger and an ∼40-residue loop region that appear to play roles in protein stability and SMC3 substrate binding. We identify key residues that play roles in substrate binding and catalysis, and rationalize the functional consequences of disease-associated mutations. Together, these studies reveal the molecular basis for SMC3 acetylation by ESCO1 and have broader implications for understanding the structure/function of non-histone acetyltransferases. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  10. 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. Copyright © 2011 Elsevier Ltd. All rights reserved.

  11. 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

  12. 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.

  13. Genetics and molecular profiling of multiple myeloma: novel tools for clinical management?

    PubMed

    Tassone, Pierfrancesco; Tagliaferri, Pierosandro; Rossi, Marco; Gaspari, Marco; Terracciano, Rosa; Venuta, Salvatore

    2006-07-01

    The understanding of molecular events involved in multiple myeloma (MM) development as well as of mechanisms underlying sensitivity/resistance to anticancer drugs has been dramatically increased by the wide-spread use of modern technologies for genetic analysis, global gene expression and proteomic profiling. Such analytical approaches, which are presently supported by reliable bioinformatic tools, have depicted a new scenario for the development of molecular-based anti-MM agents and for predicting clinical outcome. IgH translocations or a hyperdiploid state are emerging as early genetic signatures of MM which lead to deregulated expression of cyclin D. At present however, the major challenge remains the definition of the potential role of cytogenetic techniques and molecular profiling technologies in individual patient management. Here we will describe the prospective potential and current achievements of such technologies which might produce major advancements in the treatment of this still incurable disease.

  14. ANLIZE: A molecular mechanics force field visualization tool and its application to 18-crown-6

    NASA Astrophysics Data System (ADS)

    Stolworthy, Lloyd D.; Shirts, Randall B.

    1997-03-01

    We describe a software tool that allows one to visualize and analyze the importance of each individual steric interaction in a molecular mechanics force field. ANLIZE is presently implemented for the Dreiding force field for use with the Cerius2 software package, but could be implemented in any molecular mechanics package with a graphical user interface. ANLIZE calculates individual interactions in the force field, sorts them by size, and displays them in several ways from a menu of choices. This allows the user to scan through selected interactions to visualize which interactions are the primary determinants of preferred conformations. The features of ANLIZE are illustrated using 18-crown-6 as an example, and the factors governing conformational preference in 18-crown-6 are demonstrated. Users of molecular mechanics packages are encouraged to demand this functionality from commercial software producers.

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

    PubMed

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

    2015-01-01

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

  16. Establishing the Cardiothoracic Ratio Using Chest Radiographs in an Indigenous Ghanaian Population: A Simple Tool for Cardiomegaly Screening.

    PubMed

    Mensah, Y B; Mensah, K; Asiamah, S; Gbadamosi, H; Idun, E A; Brakohiapa, W; Oddoye, A

    2015-09-01

    Cardiothoracic ratio is a simple and cheap tool in the estimation of heart size. It is a useful index of cardiac size evaluation, and a value of 50% is generally considered to indicate the upper limit of normal. This study is to ascertain the normal mean value in cardiothoracic ratio of Ghanaians using chest radiography to serve as baseline for screening for cardiomegaly. Standard postero-anterior radiographs of the -clients/patients were used in the study. The cardiothoracic ratio (CTR) was obtained by dividing the transverse cardiac diameter [sum of the horizontal distances from the right and left lateral-most margins of the heart to the midline (spinous processes of the vertebral bodies)] by the maximum internal thoracic diameter. Systematic sampling with appropriate inclusion and exclusion criteria were used to obtain a sample size of 1989. The mean transverse cardiac diameter and cardiothoracic ratio increased with age. The transverse thoracic diameter increased with age until the sixth decade when it reduced with age. The mean CTR increased gradually with age with females having greater values than males. The mean CTR of the study population were 0.459, 0.467 and 0.452 for the general population, females and males respectively. This study has been able to establish 0.459 as the mean CTR values for Ghanaians. It has also shown the relationship between age and clients/patient's cardiothoracic ratio which compares favourably with findings of a similar study in Nigeria, a neighbouring country in the West African sub region with similar ethnic and social structure.

  17. 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.

  18. 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

  19. 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.

  20. 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

  1. 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

  2. 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.

  3. Molecular Dynamics as a tool for in silico screening of skin permeability.

    PubMed

    Rocco, Paolo; Cilurzo, Francesco; Minghetti, Paola; Vistoli, Giulio; Pedretti, Alessandro

    2017-08-30

    Prediction of skin permeability can have manifold applications ranging from drug delivery to toxicity prediction. Along with the semi-empirical or mechanistic models proposed in the last decades, Molecular Dynamics simulations have recently become a fruitful tool for investigating membrane permeability, in particular as they allow the involved mechanisms to be modelled at a molecular level. Despite their significant structural complexity, Molecular Dynamics simulations can also be utilized to study permeation through the lipid matrix that characterizes the stratum corneum. In this work, Steered Molecular Dynamics simulations are performed on a suitably developed stratum corneum lipid matrix model. Regardless of their actual tortuous path within the stratum corneum, the permeants, taken from a Fully Validated dataset of 80 compounds of known permeability coefficient, are moved through the bilayer along its normal. This allows the exploration of all the possible conformational and physicochemical constraints the molecule experiences when moving through the bilayer. The so performed Steered Molecular Dynamics simulations are then utilized to extract the corresponding lipophilicity and diffusion parameters as computed by subdividing the entire path in 18 regions of different polarity and composition. Correlative analyses showed that the water-lipids interface is the best performing region and that significant enhancements can be gained by including parameters accounting for the temperature effect. Taken together, the developed models possess an enhanced predictive power compared to the existing equations and statistics are approaching the best possible results, given the uncertainty in the utilized permeability data. Copyright © 2017. Published by Elsevier B.V.

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

    PubMed

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

    2013-01-01

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

  5. 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.

  6. 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.

  7. [Molecular and pathological analyses of newly established transgenic rats carrying human endogenous retrovirus gene, ERV3].

    PubMed

    Tanaka, S

    2000-03-01

    Endogeneous retroviruses are known to be integrated in eukaryotic genome as proviral DNA similarly to infectious retroviruses. They are present in many kinds of living things, but their functions, especially those in humans, are unclear. To investigate the function of human endogeneous retroviruses, we chose endogeneous retrovirus type 3 (ERV3) which is a single copy type of human endogeneous retrovirus with mRNA expression in organ tissues in vivo. The full provirus genome of ERV3 was subcloned as a transgene and two lines of transgenic rats carrying ERV3 gene (ERV3 rats) were established. One line of ERV3 rats, ETR5, showed tandem insertion of multiple copies of the transgene and expressed ERV3 mRNA in various organs. High levels of the mRNA expression were detected in both lacrimal and salivary glands. In placentas, where ERV3 is expected to express at high levels in humans, the mRNA expression was evident from 12 days gestation in ETR5 rats. Another line, ETR16, showed a single copy insertion and expressed ERV3 mRNAs only in the lacrimal and salivary glands. By Northern analysis, the expected size (3.5 kb) of ERV3 env transcription as was already shown in human tissues was confirmed in ETR16, but high expression of an additional large transcript (4.0 kb) was detected in ETR5. The result of RT-PCR analysis of the transcript in ETR5 indicated that the tandem insertion in ETR5 genome probably caused mis-promoting and mis-terminal poly(A) splicing in the 3'LTR, resulting in the extension of ERV3 env transcript to 4.0 kb mRNA with an addition of nontranslated LTR sequence. By Western blot using an antiserum against oligopeptides synthesized from ERV3 env sequences, protein product of the transgene was shown to be an 85 kDa band in the lacrimal gland of ETR5. Although no pathological significance was evident in these transgenic rats under conditions without any treatment, ERV3 rats may be a suitable model for analysis of the ERV3 function in vivo.

  8. 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.

  9. 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.

  10. 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).

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

    PubMed

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

    2009-06-01

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

  12. 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

  13. 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.

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

    PubMed

    Raja, Huzefa A; Miller, Andrew N; Pearce, Cedric J; Oberlies, Nicholas H

    2017-03-24

    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.

  15. 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/.

  16. [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.

  17. 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.

  18. 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.

  19. 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

  20. 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

  1. 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.

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

    PubMed

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

    2016-09-21

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

  3. 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

  4. 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

  5. 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.

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

    PubMed

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

    2015-09-01

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

  7. 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.

  8. 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.

  9. 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

  10. 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.

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

    PubMed Central

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

    2009-01-01

    Summary: The Biopython project is a mature open source international collaboration of volunteer developers, providing Python libraries for a wide range of bioinformatics problems. Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments, dealing with 3D macro molecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning. Availability: Biopython is freely available, with documentation and source code at www.biopython.org under the Biopython license. Contact: All queries should be directed to the Biopython mailing lists, see www.biopython.org/wiki/_Mailing_listspeter.cock@scri.ac.uk. PMID:19304878

  12. The Utilities of Chemical Reactions and Molecular Tools for O-GlcNAc Proteomic Studies.

    PubMed

    Kim, Eun Ju

    2015-07-06

    The post-translational modification of nuclear and cytoplasmic proteins with O-linked β-N-acetylglucosamine (O-GlcNAc) is involved in a wide variety of cellular processes and is associated with the pathological progression of chronic diseases. Considering its emerging biological significance, systematic identification, site mapping, and quantification of O-GlcNAc proteins are essential and have led to the development of several approaches for O-GlcNAc protein profiling. This minireview mainly focuses on the various useful chemical reactions and molecular tools with detailed reaction mechanisms widely adopted for O-GlcNAc protein/peptide enrichment and its quantification for comprehensive O-GlcNAc protein profiling. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. 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.

  14. Advances in the development of molecular tools for the control of bovine babesiosis in Mexico.

    PubMed

    Mosqueda, J; Figueroa, J V; Alvarez, A; Bautista, R; Falcon, A; Ramos, A; Canto, G; Vega, C A

    2007-05-01

    The severe negative impact that bovine babesiosis has in the Mexican cattle industry has not been ameliorated basically due to the lack of safe and effective commercially available vaccines and sensitive and reliable diagnostic tests. In recent years, the Bovine Babesiosis Laboratory at the National Center for Disciplinary Research in Veterinary Parasitology-INIFAP in Morelos State, Mexico has been directing efforts towards three main research areas: (1) The development of in vitro culture-derived, improved and safer live vaccines. This has been done in two ways: using gamma-irradiated bovine serum and erythrocytes for the in vitro culture of vaccine strains, which reduces the risk of contaminating pathogens, and improving the immune response, by the addition of L. casei, a strong stimulant of the innate immune system. (2) The study of antigens considered as vaccine candidates with the goal of developing a recombinant vaccine that suits the country's needs. Knowing their degree of conservation or variation in Mexican isolates, their phylogenetic relationship and their protective, immuno-stimulatory properties, are first steps towards that goal. (3) The development of new tools for diagnosis, detection and discrimination of bovine babesiosis is the third area. Developing variants of ELISA, which are more reliable than the currently used IFAT, are a priority, and finally, taking advantage of the genomes of Babesia bigemina, and B. bovis, we are identifying genes than allow us to discriminate isolates using molecular tools.

  15. Evaluation of Ribotyping as a Tool for Molecular Typing of Yersinia pseudotuberculosis Strains of Worldwide Origin

    PubMed Central

    Voskressenskaya, Ekaterina; Leclercq, Alexandre; Tseneva, Galina; Carniel, Elisabeth

    2005-01-01

    Yersinia pseudotuberculosis is a gram-negative bacterium that infects a wide range of animals, including humans, and is transmitted by the fecal-oral route. This species is found globally and is responsible for human outbreaks, mainly in cold countries. The aim of this study was to evaluate the potential of ribotyping for the molecular typing of worldwide isolates. For this purpose, 80 strains of Y. pseudotuberculosis belonging to the six classical serotypes and nine subserotypes and isolated from various countries and different hosts were analyzed. Combination of the EcoRI and EcoRV ribopatterns allowed the delineation of 27 ribotypes. In most instances, ribotypes were associated with specific subserotypes and allowed their subdivision. No association between the ribotype and the geographical origin of the strains was observed, arguing for a global spread of this organism. Similarly, no marked association between the ribotype and the type of host was noted, confirming the circulation of this pathogen in the environment, different animal species, and human hosts. Y. pseudotuberculosis exhibited ribopatterns very close to those of Y. pestis, although not completely identical. Altogether, the present study demonstrates that ribotyping may be a useful tool for molecular typing of global isolates of Y. pseudotuberculosis but that it has some limitations due to the small number of hybridizing bands that generate the diversity of the profiles. PMID:16333119

  16. Standardised molecular diagnostic tool for the identification of cryptic species within the Bemisia tabaci complex.

    PubMed

    Elfekih, S; Tay, W T; Gordon, K; Court, L; De Barro, P

    2017-07-23

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

  17. [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.

  18. Evaluation of molecular contaminants in the micro-environment between photomask and pellicle using analysis tool

    NASA Astrophysics Data System (ADS)

    Douzono, Mina; Shimada, Itsuka; Ueda, Tatsuji; Nonaka, Tatsuo; Kawano, Yukihiro; Murakami, Masashi

    2012-06-01

    The problem of haze and related defects become more serious as the dimension of lithography becomes smaller. It has been reported that the causes of haze defects are organic and inorganic molecular contamination deposited on mask surface. These haze problems influence the productivity of lithography process, but the formation mechanism of haze has not been clear. So it is important to understand chemical composition and formation mechanism of haze to prevent it. To analyze the chemical composition, several analytical techniques are useful, that is, ion chromatography (IC) or gas chromatography mass spectrometer (GC/MS) after liquid extraction of mask surface, surface analysis such as time-of-flight secondary ionization mass spectrometry (TOF-SIMS), X-ray photon spectrometry (XPS) and so on. However, these techniques are all destructive methods and are difficult to evaluate the airborne molecular contaminants (AMCs) with high sensitivity between mask and pellicle. We have successfully developed new and sensitive analysis tool consists of two parts and applied it for the evaluation of micro-environment between photomask and pellicle. One is the equipment to collect AMCs effectively, that provides diagonal two holes with needles on the pellicle to collect the gas while ventilating the high-purity nitrogen gas. The other is sampler which is named BremS™ to collect and measure exhausted AMCs in the space with high sensitivity. We applied this method to masks with different exposure dosage rate and introduce the usefulness of our method.

  19. 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.

  20. 210Pb as a tool for establishing sediment chronologies: examples of potentials and limitations of conventional dating models.

    PubMed

    Kirchner, Gerald

    2011-05-01

    For aquatic sediments, the use of (210)Pb originating from the decay of atmospheric (222)Rn is a well-established methodology to estimate sediment ages and sedimentation rates. Traditionally, the measurement of (210)Pb in soils and sediments involved laborious and time-consuming radiochemical separation procedures. Due to the recent development of advanced planar ('n-type') semi-conductors with high efficiencies in the low-energy range which enable the gamma-spectrometric analysis of the 46.5 keV decay line of (210)Pb, sediment dating using this radionuclide has gained renewed interest. In this contribution, potentials and limitations of the (210)Pb methodology and of the models used for estimating sediment ages and sedimentation rates are discussed and illustrated by examples of freshwater and marine sediments. Comparison with the use of (137)Cs shows that the information which may be gained by these two tracers is complementary. As a consequence, both radionuclides should be used in combination for dating of recent sediments. It is shown that for various sedimentation regimes additional information from other sources (e.g. sediment lithology) may be needed to establish a reliable chronology. A strategy for sediment dating using (210)Pb is recommended. Copyright © 2010 Elsevier Ltd. All rights reserved.

  1. Establishment of Bioprocess for Synthesis of Nicotinamide by Recombinant Escherichia coli Expressing High-Molecular-Mass Nitrile Hydratase.

    PubMed

    Wang, Zhe; Liu, Zhongmei; Cui, Wenjing; Zhou, Zhemin

    2017-08-01

    Application of engineered bacteria expressing nitrile hydratase for the production of amide is getting tremendous attention due to the rapid development of recombinant DNA technique. This study evaluated the effect of 3-cyanopyridine concentrations on nicotinamide production using recombinant Escherichia coli strain (BAG) expressing high-molecular-mass nitrile hydratase from Rhodococcus rhodochrous J1, and established proper process of whole-cell catalysis of 3-cyanopyridine and high cell-density cultivation. The process of substrate fed-batch was applied in the production of nicotinamide, and the concentration of product reached 390 g/L under the condition of low cell-density. After the high cell-density cultivation of BAG in 5 L bioreactor, the OD600 of cell attained 200 and the total activity reached 2813 U/mL. Different high density of BAG after fermentation in the tank was used to catalyze 3-cyanopyridine, and the concentration of nicotinamide reached to 508 g/L in just 60 min. The productivity of BAG was 212% higher than that of R. rhodochrous J1, and it is possible that BAG is able to achieve industrial production of nicotinamide.

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

    PubMed

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

    2016-11-08

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

  3. 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

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

    PubMed Central

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

    2013-01-01

    The molecular diagnosis of retinal dystrophies is difficult because of the very important number of genes implicated and is rarely helped by genotype-phenotype correlations. This prompted us to develop IROme, a custom designed in solution-based targeted exon capture assay (SeqCap EZ Choice library, Roche NimbleGen) for 60 retinitis pigmentosa-linked genes and three candidate genes (942 exons). Pyrosequencing was performed on a Roche 454 GS Junior benchtop high-throughput sequencing platform. In total, 23 patients affected by retinitis pigmentosa were analyzed. Per patient, 39.6 Mb were generated, and 1111 sequence variants were detected on average, at a median coverage of 17-fold. After data filtering and sequence variant prioritization, disease-causing mutations were identified in ABCA4, CNGB1, GUCY2D, PROM1, PRPF8, PRPF31, PRPH2, RHO, RP2, and TULP1 for twelve patients (55%), ten mutations having never been reported previously. Potential mutations were identified in 5 additional patients, and in only 6 patients no molecular diagnosis could be established (26%). In conclusion, targeted exon capture and next-generation sequencing are a valuable and efficient approach to identify disease-causing sequence variants in retinal dystrophies. PMID:23484092

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

    PubMed Central

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

    2015-01-01

    The evidence that two molecules interact in a living cell is often inferred from multiple different experiments. Experimental data is captured in multiple repositories, but there is no simple way to assess the evidence of an interaction occurring in a cellular environment. Merging and scoring of data are commonly required operations after querying for the details of specific molecular interactions, to remove redundancy and assess the strength of accompanying experimental evidence. We have developed both a merging algorithm and a scoring system for molecular interactions based on the proteomics standard initiative–molecular interaction standards. In this manuscript, we introduce these two algorithms and provide community access to the tool suite, describe examples of how these tools are useful to selectively present molecular interaction data and demonstrate a case where the algorithms were successfully used to identify a systematic error in an existing dataset. PMID:25652942

  6. From total suspended solids to molecular biology tools--a personal view of biological wastewater treatment process population dynamics.

    PubMed

    Jenkins, David

    2008-08-01

    The development of the tools needed to study the population dynamics of biological wastewater treatment processes is traced from its beginnings in the early 1900s to today's use of molecular biology tools (Oerther and Love, 2003). Examples of the benefits of population dynamics research in improving the performance and aiding the design and operation of biological wastewater treatment processes are given. Some thoughts on future areas of study are presented.

  7. Fifteen years of cell-penetrating, guanidinium-rich molecular transporters: basic science, research tools, and clinical applications.

    PubMed

    Stanzl, Erika Geihe; Trantow, Brian M; Vargas, Jessica R; Wender, Paul A

    2013-12-17

    All living systems require biochemical barriers. As a consequence, all drugs, imaging agents, and probes have targets that are either on, in, or inside of these barriers. Fifteen years ago, we initiated research directed at more fully understanding these barriers and at developing tools and strategies for breaching them that could be of use in basic research, imaging, diagnostics, and medicine. At the outset of this research and now to a lesser extent, the "rules" for drug design biased the selection of drug candidates mainly to those with an intermediate and narrow log P. At the same time, it was becoming increasingly apparent that Nature had long ago developed clever strategies to circumvent these "rules." In 1988, for example, independent reports documented the otherwise uncommon passage of a protein (HIV-Tat) across a membrane. A subsequent study implicated a highly basic domain in this protein (Tat49-57) in its cellular entry. This conspicuously contradictory behavior of a polar, highly charged peptide passing through a nonpolar membrane set the stage for learning how Nature had gotten around the current "rules" of transport. As elaborated in our studies and discussed in this Account, the key strategy used in Nature rests in part on the ability of a molecule to change its properties as a function of microenvironment; such molecules need to be polarity chameleons, polar in a polar milieu and relatively nonpolar in a nonpolar environment. Because this research originated in part with the protein Tat and its basic peptide domain, Tat49-57, the field focused heavily on peptides, even limiting its nomenclature to names such as "cell-penetrating peptides," "cell-permeating peptides," "protein transduction domains," and "membrane translocating peptides." Starting in 1997, through a systematic reverse engineering approach, we established that the ability of Tat49-57 to enter cells is not a function of its peptide backbone, but rather a function of the number and

  8. Cambrian archaeocyathan metazoans: revision of morphological characters and standardization of genus descriptions to establish an online identification tool.

    PubMed Central

    Kerner, Adeline; Debrenne, Françoise; Vignes-Lebbe, Régine

    2011-01-01

    Abstract Archaeocyatha represent the oldest calcified sponges and the first metazoans to build bioconstructions in association with calcimicrobes. They are a key group in biology, evolutionary studies, biostratigraphy, paleoecology and paleogeography of the early Cambrian times. The establishing of a new standardized terminology for archaeocyathans description has permitted the creation of the first knowledge base in English including descriptions of all archaeocyathan genera. This base, using the XPER² software package, is an integral part of the -Archaeocyatha- a knowledge base website, freely available at url http://www.infosyslab.fr/archaeocyatha. The website is composed of common information about Archaeocyatha, general remarks about the knowledge base, the description of the 307 genera recognized with images of type-specimens of type-species for each genus, as well as additional morphological data, an interactive free access key and its user guide. The automatic analysis and comparison of the digitized descriptions have identified some genera with highly similar morphology. These results are a great help for future taxonomic revisions and suggest a number of possible synonymies that require further study. PMID:22207818

  9. Cambrian archaeocyathan metazoans: revision of morphological characters and standardization of genus descriptions to establish an online identification tool.

    PubMed

    Kerner, Adeline; Debrenne, Françoise; Vignes-Lebbe, Régine

    2011-01-01

    Archaeocyatha represent the oldest calcified sponges and the first metazoans to build bioconstructions in association with calcimicrobes. They are a key group in biology, evolutionary studies, biostratigraphy, paleoecology and paleogeography of the early Cambrian times. The establishing of a new standardized terminology for archaeocyathans description has permitted the creation of the first knowledge base in English including descriptions of all archaeocyathan genera. This base, using the XPER² software package, is an integral part of the -Archaeocyatha- a knowledge base website, freely available at url http://www.infosyslab.fr/archaeocyatha. The website is composed of common information about Archaeocyatha, general remarks about the knowledge base, the description of the 307 genera recognized with images of type-specimens of type-species for each genus, as well as additional morphological data, an interactive free access key and its user guide.The automatic analysis and comparison of the digitized descriptions have identified some genera with highly similar morphology. These results are a great help for future taxonomic revisions and suggest a number of possible synonymies that require further study.

  10. 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.

  11. Initial validation of a proxy indicator of functioning as a potential tool for establishing a clinically meaningful cocaine use outcome.

    PubMed

    Kiluk, Brian D; Babuscio, Theresa A; Nich, Charla; Carroll, Kathleen M

    2017-10-01

    Establishing a non-abstinence cocaine use outcome as clinically meaningful has been elusive, in part due to the lack of association between cocaine use outcomes and meaningful indicators of long-term functioning. Using data pooled across 7 clinical trials evaluating treatments for cocaine (N=718), a dichotomous indicator of functioning was created to represent a meaningful outcome ('problem-free functioning' - PFF), defined as the absence of problems across non-substance-related domains on the Addiction Severity Index. Its validity was evaluated at multiple time points (baseline, end-of-treatment, terminal follow-up) and used to explore associations with cocaine use. The percentage of participants meeting PFF criteria increased over time (baseline=18%; end-of-treatment=32%; terminal follow-up=37%). At each time point, ANOVAs indicated those who met PFF criteria reported significantly less distress on the Brief Symptom Inventory and less perceived stress on the Perceived Stress Scale. Generalized linear models indicated categorical indices of self-reported cocaine use at the end of treatment were predictive of the probability of meeting PFF criteria during follow-up (β=-0.01, p<0.01; 95% CI: -0.008 to -0.003), with those reporting 0days or 1-4days ('occasional' use) in the final month of treatment showing an increased likelihood of achieving PFF. Initial validation of a proxy indicator of problem-free functioning demonstrated criterion validity and sensitivity to change over time. Frequency of cocaine use in the final month of treatment was associated with PFF during follow-up, with strongest associations between PFF and abstinence or 'occasional' use. Copyright © 2017 Elsevier B.V. All rights reserved.

  12. 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.

  13. 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. (c) 2010 Australian Society for Parasitology Inc. Published by Elsevier Ltd. All rights reserved.

  14. Establishing and implementing Demographic Surveillance System as a tool for monitoring health interventions in Korogwe District, northastern Tanzania.

    PubMed

    Kamugisha, Mathias L; Mmbando, Bruno P; Francis, Filbert; Ishengoma, Deus S; Challe, Daniel P; Lemnge, Martha M

    2011-10-01

    In the Korogwe demographic surveillance system (DSS) site in north-eastern Tanzania, information on vital events such as births, deaths and migration has been collected since its establishment in 2005. The aim was to obthin demographic and epidemiological indices to be used in the evaluation of health related interventions which have been undertaken in the area. Period covered is up to December 2010. Baseline survey was conducted in 14 villages of Korogwe district in October 2005 and DSS was launched in January 2006 years. Demographic, social economic status, immunisation coverage and birth history data was collected during the follow-up and each household was visited every 4 months. Estimates of mortality levels were derived from deaths that were collected during household visits. Birth history data were used to estimate the lifetime and period fertility of women aged 15-49 years. Estimates of crude migration and age specific migration rates were derived from the number of people moving in or out of the DSS site and the person-years lived. The population at baseline survey was 25,264 individuals in 5,853 households. The percentage of deaths was higher among adult aged 15-60 years compared to other age groups. The probability of dying among males (376/1000) aged 15-60 years was higher than females (339/1000) in the same age group. The lifetime and period fertility estimates were 5.6 and 5.1 children per woman respectively. Women aged 30-34 years are expected to have 3-4 children at the end of their childbearing age. Migration were higher at the youngest ages, lower rates at the 10-14 years age groups, a peak at the 20-24 ages, and a gradual decline up to the oldest ages. Majority of households in rural areas 51.8% were 1 in low socioeconomic status compared to 40.3% in urban areas which were in high socio-economic status. About 74% and 55.5% of the children received BCG and measles vaccination, respectively. In conclusion, Korogwe DSS has provided useful data which

  15. 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

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

    PubMed

    Sellers, Graham S; Griffin, Larry R; Hänfling, Bernd; Gómez, Africa

    2017-01-01

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

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

    PubMed Central

    Griffin, Larry R.; Hänfling, Bernd; Gómez, Africa

    2017-01-01

    The tadpole shrimp, Triops cancriformis, is a freshwater crustacean listed as endangered in the UK and Europe living in ephemeral pools. Populations are threatened by habitat destruction due to land development for agriculture and increased urbanisation. Despite this, there is a lack of efficient methods for discovering and monitoring populations. Established macroinvertebrate monitoring methods, such as net sampling, are unsuitable given the organism’s life history, that include long lived diapausing eggs, benthic habits and ephemerally active populations. Conventional hatching methods, such as sediment incubation, are both time consuming and potentially confounded by bet-hedging hatching strategies of diapausing eggs. Here we develop a new molecular diagnostic method to detect viable egg banks of T. cancriformis, and compare its performance to two conventional monitoring methods involving diapausing egg hatching. We apply this method to a collection of pond sediments from the Wildfowl & Wetlands Trust Caerlaverock National Nature Reserve, which holds one of the two remaining British populations of T. cancriformis. DNA barcoding of isolated eggs, using newly designed species-specific primers for a large region of mtDNA, was used to estimate egg viability. These estimates were compared to those obtained by the conventional methods of sediment and isolation hatching. Our method outperformed the conventional methods, revealing six ponds holding viable T. cancriformis diapausing egg banks in Caerlaverock. Additionally, designed species-specific primers for a short region of mtDNA identified degraded, inviable eggs and were used to ascertain the levels of recent mortality within an egg bank. Together with efficient sugar flotation techniques to extract eggs from sediment samples, our molecular method proved to be a faster and more powerful alternative for assessing the viability and condition of T. cancriformis diapausing egg banks. PMID:28507815

  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 Central

    Chung, E. J.; Nord, K.; Sugimoto, M. J.; Wonder, E.; Tirrell, M.; Mlinar, L. B.; Alenghat, F. J.; Fang, Y.

    2014-01-01

    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. PMID:25156590

  20. 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.

  1. 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

  2. Candidate gene molecular markers as tools for analyzing genetic susceptibility to Morbillivirus infection in stranded Cetaceans.

    PubMed

    Stejskalova, Karla; Bayerova, Zuzana; Futas, Jan; Hrazdilova, Kristyna; Klumplerova, Marie; Oppelt, Jan; Splichalova, Petra; Di Guardo, Giovanni; Mazzariol, Sandro; Di Francesco, Cristina Esmeralda; Di Francesco, Gabriella; Terracciano, Giuliana; Paiu, Romulus-Marian; Ursache, Teodor Dan; Modry, David; Horin, Petr

    2017-09-11

    Morbilliviruses, such as Cetacean morbillivirus (CeMV) or Phocine distemper virus (PDV), represent a growing threat for marine mammals on both hemispheres. Since free-ranging animal populations strongly rely on natural resistance mechanisms, innate immunity related genes and virus cell entry receptor genes may represent key factors involved in susceptibility to CeMV in Cetaceans. Using the next generation sequencing technology, we have sequenced eleven candidate genes in two model species, Stenella coeruleoalba and Phocoena phocoena. Suitable single nucleotide polymorphism markers of potential functional importance, located in genes coding for basigin (BSG, CD147), the signaling lymphocyte activating molecule (SLAMF1), the poliovirus related receptor-4 (NECTIN4, PVRL4), toll-like receptors 3,7,8 (TLR3, TLR7, TLR8), natural resistance-associated macrophage protein (SLC11A1) and natural cytotoxicity triggering receptor 1 (NCR1), were identified in each model species, along with MHC-DQB haplotypes unique for each species. This set of molecular markers represents a potentially useful tool for studying host genetic variation and susceptibility to Morbillivirus infection in Cetaceans as well as for studying functionally important genetic diversity of selected Cetacean populations. This article is protected by copyright. All rights reserved.

  3. 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

  4. 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

  5. [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.

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

    PubMed

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

    2014-11-11

    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.

  7. Tracking picosecond molecular dynamics in solution using a suite of synchrotron-x-ray spectroscopic tools

    NASA Astrophysics Data System (ADS)

    March, Anne Marie; Doumy, Gilles; Kanter, Elliot P.; Lehmann, Stefan; Moonshiram, Dooshaye; Southworth, Stephen H.; Young, Linda; Assefa, Tadesse A.; Bressler, Christian; Gawelda, Wojciech; Németh, Zoltán; Vankó, György

    2015-03-01

    Laser-pump, X-ray-probe techniques are powerful tools for exploring molecular structural changes that occur in complex environments such as solutions, during a photo-initiated reaction. We are developing such methods using hard x-rays from the Advanced Photon Source, combining x-ray emission spectroscopy and x-ray absorption spectroscopy as probes of electronic and geometric structure and using high-power, MHz lasers as pumps. The high-duty-cycle pump-probe measurements efficiently utilize the synchrotron x-ray flux and enable high-fidelity measurements of the structures of transient intermediates. We present measurements on the model system [Fe(II)(CN)6]4- (ferrocyanide) in an aqueous solution after excitation with 355 nm and 266 nm laser light. The system undergoes two wavelength dependent reactions: photooxidation and photoaquation. Iron K-edge absorption spectra were obtained along with iron emission spectra. Our data support the presence of a previously unobserved pentacoordinated intermediate species in the photoaquation reaction. Its lifetime has been measured to be 4.6 ns and details of its structure will be discussed. The work was supported by the U.S. Department of Energy, Office of Science, Chemical Sciences, Geosciences, and Biosciences Division.

  8. 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.

  9. 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

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

    NASA Astrophysics Data System (ADS)

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

    2017-05-01

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

  11. Development of a web-based query tool for quality assurance of clinical molecular genetic test results.

    PubMed

    McGinniss, Matthew J; Chen, Rebecca; Pratt, Victoria M; Buller, Arlene; Quan, Franklin; Strom, Charles M; Sun, Weimin; Crossley, Beryl

    2007-02-01

    The College of American Pathologists molecular pathology checklist item (MOL.20550) calls for periodic review of molecular genetic statistics, including percentages of normal and abnormal findings and allele frequencies. A web-based query tool application for clinical molecular genetic test results was developed to plot dynamically and display genotype and/or allele frequencies for any time period. This tool is used to produce plots of all high-volume molecular genetic assays (>50 samples per month). A single web page contains pull-down menus, enabling the user to select the type of chart to be generated (genotype or allele frequency), the molecular genetic assays to chart (from one to all), the ending date for data in the chart (month and year), and the duration of the time period to plot (1 to 12 months). The rendered graphical and textual frequency data can then be viewed or printed. This tool can be used by any laboratory and interfaced with a standard laboratory information system. Monthly quality control charts and tables are now generated in minutes compared with the hours it took using manual charting applications. This simplified process enables timely compliance with a College of American Pathologists checklist item.

  12. 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

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  14. 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.

  15. 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.

  16. Molecular genetics as a tool to remove bottlenecks in the biosynthesis of β-lactam antibiotics.

    PubMed

    Fierro, F; Barredo, J L; Díez, B; Gutiérrez, S; Marcos, A T; Martín, J F

    1996-09-01

    Several strains of Penicillium chrysogenum with different productions of penicillin were characterized at the molecular level in order to establish the basis of the increased penicillin production rates. The cluster of penicillin biosynthetic genes was located in an amplified genomic region of 57.9 kb in a high-producing strain (E1) and 106.5 kb in two strains (AS-P-78 and P2) producing moderately high levels of penicillin. This region was shown to be present in multiple tandemly repeated copies with a different copy number depending on the strain. The sequence TTTACA appeared at the junction points between repeats and at the borders of the amplified region in strains AS-P-78 and P2, while its reverse complementary TGTAAA was found in strain E1. The tandem reiteration and deletion appear to arise by site-specific recombination induced by mutagenic treatments. Finally, the relationship between glucose repression and pH regulation was studied in strain AS-P-78.

  17. 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.

  18. 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

  19. Establishing Minimum Flow Requirements Based on Benthic Vegetation: What are Some Issues Related to Identifying Quantity of Inflow and Tools Used to Quantify Ecosystem Response?

    NASA Astrophysics Data System (ADS)

    Hunt, M. J.; Nuttle, W. K.; Cosby, B. J.; Marshall, F. E.

    2005-05-01

    Establishing minimum flow requirements in aquatic ecosystems is one way to stipulate controls on water withdrawals in a watershed. The basis of the determination is to identify the amount of flow needed to sustain a threshold ecological function. To develop minimum flow criteria an understanding of ecological response in relation to flow is essential. Several steps are needed including: (1) identification of important resources and ecological functions, (2) compilation of available information, (3) determination of historical conditions, (4) establishment of technical relationships between inflow and resources, and (5) identification of numeric criteria that reflect the threshold at which resources are harmed. The process is interdisciplinary requiring the integration of hydrologic and ecologic principles with quantitative assessments. The tools used quantify the ecological response and key questions related to how the quantity of flow influences the ecosystem are examined by comparing minimum flow determination in two different aquatic systems in South Florida. Each system is characterized by substantial hydrologic alteration. The first, the Caloosahatchee River is a riverine system, located on the southwest coast of Florida. The second, the Everglades- Florida Bay ecotone, is a wetland mangrove ecosystem, located on the southern tip of the Florida peninsula. In both cases freshwater submerged aquatic vegetation (Vallisneria americana or Ruppia maritima), located in areas of the saltwater- freshwater interface has been identified as a basis for minimum flow criteria. The integration of field studies, laboratory studies, and literature review was required. From this information we developed ecological modeling tools to quantify and predict plant growth in response to varying environmental variables. Coupled with hydrologic modeling tools questions relating to the quantity and timing of flow and ecological consequences in relation to normal variability are addressed.

  20. 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

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

    PubMed

    Kothavade, Rajendra J

    2012-08-01

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

  2. 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.

  3. 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

  4. 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.

  5. Torsion-Angle Molecular Dynamics as a New Efficient Tool for NMR Structure Calculation

    NASA Astrophysics Data System (ADS)

    Stein, Evan G.; Rice, Luke M.; Brünger, Axel T.

    1997-01-01

    Molecular dynamics in torsion-angle space was applied to nuclear magnetic resonance structure calculation using nuclear Overhauser effect-derived distances andJ-coupling-constant-derived dihedral angle restraints. Compared to two other commonly used algorithms, molecular dynamics in Cartesian space and metric-matrix distance geometry combined with Cartesian molecular dynamics, the method shows increased computational efficiency and success rate for large proteins, and it shows a dramatically increased radius of convergence for DNA. The torsion-angle molecular dynamics algorithm starts from an extended strand conformation and proceeds in four stages: high-temperature torsion-angle molecular dynamics, slow-cooling torsion-angle molecular dynamics, Cartesian molecular dynamics, and minimization. Tests were carried out using experimental NMR data for protein G, interleukin-8, villin 14T, and a 12 base-pair duplex of DNA, and simulated NMR data for bovine pancreatic trypsin inhibitor. For villin 14T, a monomer consisting of 126 residues, structure determination by torsion-angle molecular dynamics has a success rate of 85%, a more than twofold improvement over other methods. In the case of the 12 base-pair DNA duplex, torsion-angle molecular dynamics had a success rate of 52% while Cartesian molecular dynamics and metric-matrix distance geometry always failed.

  6. 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.

  7. 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.

  8. 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).

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

    PubMed Central

    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). PMID:24109552

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

    PubMed

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

    2003-07-01

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

  11. Molecular phylogenetics of the gomphoid-phalloid fungi with an establishment of the new subclass Phallomycetidae and two new orders

    Treesearch

    Kentaro Hosaka; Scott T. Bates; Ross E. Beever; Michael A. Castellano; Wesley Colgan; Laura S. Dominguez; Eduardo R. Nouhra; Jozsef Geml; Admir J. Giachini; S. Ray Kenney; Nicholas B. Simpson; Joseph W. Spatafora; James M. Trappe

    2006-01-01

    Molecular phylogenetic analyses for the gomphoid-phalloid fungi were conducted based on the five gene dataset with extensive taxon sampling. The monophyly of the gomphoid-phalloid clade was strongly supported, and four well supported major subclades were recognized. Three of the four subclades were represented entirely by gastroid taxa, and only Gomphales contained...

  12. 3DMolNavi: A web-based retrieval and navigation tool for flexible molecular shape comparison

    PubMed Central

    2012-01-01

    Background Many molecules of interest are flexible and undergo significant shape deformation as part of their function, but most existing methods of molecular shape comparison treat them as rigid shapes, which may lead to incorrect measure of the shape similarity of flexible molecules. Currently, there still is a limited effort in retrieval and navigation for flexible molecular shape comparison, which would improve data retrieval by helping users locate the desirable molecule in a convenient way. Results To address this issue, we develop a web-based retrieval and navigation tool, named 3DMolNavi, for flexible molecular shape comparison. This tool is based on the histogram of Inner Distance Shape Signature (IDSS) for fast retrieving molecules that are similar to a query molecule, and uses dimensionality reduction to navigate the retrieved results in 2D and 3D spaces. We tested 3DMolNavi in the Database of Macromolecular Movements (MolMovDB) and CATH. Compared to other shape descriptors, it achieves good performance and retrieval results for different classes of flexible molecules. Conclusions The advantages of 3DMolNavi, over other existing softwares, are to integrate retrieval for flexible molecular shape comparison and enhance navigation for user’s interaction. 3DMolNavi can be accessed via https://engineering.purdue.edu/PRECISE/3dmolnavi/index.html. PMID:22583488

  13. 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).

  14. 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.

  15. Molecular biology in breast cancer: should molecular classifiers be assessed by conventional tools or by gene expression arrays?

    PubMed

    Fumagalli, Debora; Andre, Fabrice; Piccart-Gebhart, Martine J; Sotiriou, Christos; Desmedt, Christine

    2012-12-01

    Breast cancer is a complex disease, with heterogeneous presentations and clinical courses. Standard clinico-pathological parameters, relying on single gene or protein characterization determined with sometimes poorly-reproducible technologies, have shown limitations in the classification of the disease and in the prediction of individual patient outcomes and responses to therapy. Gene-expression profiling has revealed great potential to accurately classify breast cancer and define patient prognosis and prediction to anti-cancer therapy. Nevertheless, the performance of molecular classifiers remains sub-optimal, and both technical and conceptual improvements are needed. It is likely that determining the ideal strategy for tailoring treatment of breast cancer will require a more systematic, structured and multi-dimensional approach than in the past. Besides implementing cutting-edge technologies to detect genetic and epigenetic cancer alterations, the future of breast cancer research will in all probability rely on the innovative and multilevel integration of molecular profiles with clinical parameters of the disease and patient-related factors. Copyright © 2012. Published by Elsevier Ireland Ltd.

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

    PubMed

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

    2017-03-01

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

  17. Establishment and Molecular Cytogenetic Characterization of a Cell Culture Model of Head and Neck Squamous Cell Carcinoma (HNSCC)

    PubMed Central

    Bauer, Verena L.; Hieber, Ludwig; Schaeffner, Quirin; Weber, Johannes; Braselmann, Herbert; Huber, Reinhard; Walch, Axel; Zitzelsberger, Horst

    2010-01-01

    Cytogenetic analysis of head and neck squamous cell carcinoma (HNSCC) established several biomarkers that have been correlated to clinical parameters during the past years. Adequate cell culture model systems are required for functional studies investigating those potential prognostic markers in HNSCC. We have used a cell line, CAL 33, for the establishment of a cell culture model in order to perform functional analyses of interesting candidate genes and proteins. The cell line was cytogenetically characterized using array CGH, spectral karyotyping (SKY) and fluorescence in situ hybridization (FISH). As a starting point for the investigation of genetic markers predicting radiosensitivity in tumor cells, irradiation experiments were carried out and radiation responses of CAL 33 have been determined. Radiosensitivity of CAL 33 cells was intermediate when compared to published data on tumor cell lines. PMID:24710094

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

    USDA-ARS?s Scientific Manuscript database

    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...

  19. 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.

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

    SciTech Connect

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

    2016-03-07

    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

  1. 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

    2017-08-01

    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. © 2017 Stichting International Foundation for Animal Genetics.

  2. 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.

  3. 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.

  4. Conservation and promotion of the geological heritage in the «Ile-de-France» region (France): Establishment of a decision support-tool based on inventory

    NASA Astrophysics Data System (ADS)

    Auberger, Elise; Gély, Jean-Pierre; De Wever, Patrick; Merle, Didier

    2017-04-01

    Based on an initiative by the "Regional Commission of Geological Patrimony" (CRPG), the French state and the regional government of Ile-de-France co-financed the setting up of an inventory with the aim of safeguarding geological sites of patrimonial interest. This project forms part of larger scale policies, at the national and European level. Geological studies in the Paris region began as early as the 18th century, in the fields of cartography and paleontology. Later on, prominent scientists like G. Cuvier, A. Brongniart and A. d'Orbigny established the first concepts in sedimentology and stratigraphy through the description of Cenozoic fossil sites that rank amongst the richest in the world and geological formations in the Paris Basin. Eventually, later on, five historical stratotypes were established in the Ile-de-France region. Yet, at present, this geological heritage is constantly threatened by expanding urbanisation. To conserve this diverse geological patrimony, we have set up a protocol composed of 4 main actions: i) The exhaustive and objective referencing of geological sites in Ile-de-France. This information is centralised in a database, which currently comprises 639 sites (mainly of anthropic nature such as quarries) ii) The pre-selection of sites (298 out of the initial 639) based on sufficient accessibility and potential geological interest. iii) The use of a method of description and hierarchisation - following the guidelines of the National Geological Heritage Inventory Program (INPG) - on the pre-selected sites. iv) Establishment of a schedule specifying actions of geo-conservation which will take into account the patrimonial value of the sites, but also their threats, their juridical status and the socio-economic context of the region. The purpose of this program is to conserve a collection of geological sites that reflect the totality of the regional geology in Ile-de-France. The results of this study will be released to the general public and

  5. Molecular tools for cryptic Candida species identification with applications in a clinical laboratory.

    PubMed

    Gamarra, Soledad; Dudiuk, Catiana; Mancilla, Estefanía; Vera Garate, María Verónica; Guerrero, Sergio; Garcia-Effron, Guillermo

    2013-01-01

    Candida spp. includes more than 160 species but only 20 species pose clinical problems. C. albicans and C. parapsilosis account for more than 75% of all the fungemias worldwide. In 1995 and 2005, one C. albicans and two C. parapsilosis-related species were described, respectively. Using phenotypic traits, the identification of these newly described species is inconclusive or impossible. Thus, molecular-based procedures are mandatory. In the proposed educational experiment we have adapted different basic molecular biology techniques designed to identify these species including PCR, multiplex PCR, PCR-based restriction endonuclease analysis and nuclear ribosomal RNA amplification. During the classes, students acquired the ability to search and align gene sequences, design primers, and use bioinformatics software. Also, in the performed experiments, fungal molecular taxonomy concepts were introduced and the obtained results demonstrated that classic identification (phenotypic) in some cases needs to be complemented with molecular-based techniques. As a conclusion we can state that we present an inexpensive and well accepted group of classes involving important concepts that can be recreated in any laboratory. Copyright © 2013 International Union of Biochemistry and Molecular Biology, Inc.

  6. Volarea - a bioinformatics tool to calculate the surface area and the volume of molecular systems.

    PubMed

    Ribeiro, João V; Tamames, Juan A C; Cerqueira, Nuno M F S A; Fernandes, Pedro A; Ramos, Maria J

    2013-12-01

    We have developed a computer program named 'VolArea' that allows for a rapid and fully automated analysis of molecular structures. The software calculates the surface area and the volume of molecular structures, as well as the volume of molecular cavities. The surface area facility can be used to calculate the solvent-exposed surface area of a molecule or the contact area between two molecules. The volume algorithm can be used to predict not only the space occupied by any molecular structure, but also the volume of cavities, such as tunnels or clefts. The software finds wide application in the characterization of systems, such as protein/ligand complexes, enzyme active sites, protein/protein interfaces, enzyme channels, membrane pores, solvent tunnels, among others. Some examples are given to illustrate its potential. VolArea is as a plug-in of the widely distributed software Visual Molecular Dynamics (VMD) and is freely available at http://www.fc.up.pt/PortoBioComp/Software/Volarea/Home.html. © 2013 John Wiley & Sons A/S.

  7. Establishment and molecular characterization of a sweet potato germplasm bank of the highlands of Paraná State, Brazil.

    PubMed

    Camargo, L K P; Mógor, A F; Resende, J T V; Da-Silva, P R

    2013-11-18

    The sweet potato (Ipomoea batatas L.) is a crop of great importance in developing countries, as a food staple, for animal feed, and potentially for biofuel. Development of cultivars adapted to specific regions within these countries would be useful. To start a breeding program, the first step is the establishment of a germplasm bank. We initiated a sweet potato germplasm bank with accessions collected from the highlands of Paraná State, Brazil. To establish this germplasm bank, we carried out numerous sweet potato-collecting expeditions in regions with an altitude above 700 meters in this region; 116 genotypes currently comprise this collection. The genetic diversity of this germplasm bank was estimated using inter simple sequence repeat (ISSR) markers. Polymorphic information content (PIC), marker index (MI), and resolving power (RP) were calculated to determine the viability of ISSR markers for use in sweet potato genetic studies. The correlation between PIC and MI (r(2) = 0.81) and between MI and RP (r(2) = 0.97) were positive and significant, indicating that ISSR markers are robust for sweet potato identification. Two ISSR primers, 807 and 808, gave the best results for all attributes, and thus could be used as representative ISSR primers for the genetic analysis of sweet potato. Cluster analysis and principal component analysis indicated high genetic variability (0.51 of similarity among all genotypes); genotypes collected from different counties grouped together.

  8. 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.

  9. 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

  10. 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

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

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

    USDA-ARS?s Scientific Manuscript database

    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...

  17. 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.

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

    USDA-ARS?s Scientific Manuscript database

    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...

  19. 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…

  20. 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…

  1. 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.

  2. 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…

  3. 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…

  4. 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…

  5. 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.

  6. 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.

  7. Making Molecular Imaging a Clinical Tool for Precision Oncology: A Review.

    PubMed

    Mankoff, David A; Farwell, Michael D; Clark, Amy S; Pryma, Daniel A

    2017-05-01

    Individualized cancer treatment, tailored to a particular patient and the tumor's biological features (precision oncology), requires a detailed knowledge of tumor biology. Biological characterization is typically performed on biopsy material, but this approach can present challenges for widespread and/or heterogeneous disease and for performing serial assays to infer changes in response to therapy. Molecular imaging is a complementary approach that provides noninvasive and quantitative measures of the in vivo biology of the full disease burden and is well suited to serial assay. Molecular imaging can provide unique information to guide precision oncology that includes measuring the regional expression of therapeutic targets, measuring drug pharmacokinetics, measuring therapy pharmacodynamics, and providing a marker of therapeutic efficacy that is highly indicative of outcome. Thus far, most trials of novel molecular imaging in oncology have been small, single-center trials. Only a few methods have progressed to multicenter trials and even fewer have become part of clinical practice. Molecular imaging holds great promise for precision oncology, complementing tissue-based markers to guide more effective, less toxic, and more cost-effective cancer treatments. Beyond logistical and technical challenges, moving new imaging tests from the laboratory to the clinic requires a compelling use case that will benefit patients and/or improve cost-effectiveness, and it requires the collaboration of imagers, oncologists, and industry to reach its true clinical potential.

  8. 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…

  9. Microarray-based gene expression analysis as a process characterization tool to establish comparability of complex biological products: scale-up of a whole-cell immunotherapy product.

    PubMed

    Wang, Min; Senger, Ryan S; Paredes, Carlos; Banik, Gautam G; Lin, Andy; Papoutsakis, Eleftherios T

    2009-11-01

    Whole-cell immunotherapies and other cellular therapies have shown promising results in clinical trials. Due to the complex nature of the whole cell product and of the sometimes limited correlation of clinical potency with the proposed mechanism of action, these cellular immunotherapy products are generally not considered well characterized. Therefore, one major challenge in the product development of whole cell therapies is the ability to demonstrate comparability of product after changes in the manufacturing process. Such changes are nearly inevitable with increase in manufacturing experience leading to improved and robust processes that may have higher commercial feasibility. In order to comprehensively assess the impact of the process changes on the final product, and thus establish comparability, a matrix of characterization assays (in addition to lot release assays) assessing the various aspects of the cellular product are required. In this study, we assessed the capability of DNA-microarray-based, gene-expression analysis as a characterization tool using GVAX cancer immunotherapy cells manufactured by Cell Genesys, Inc. The GVAX immunotherapy product consists two prostate cancer cell lines (CG1940 and CG8711) engineered to secrete human GM-CSF. To demonstrate the capability of the assay, we assessed the transcriptional changes in the product when produced in the presence or absence of fetal bovine serum, and under normal and hypoxic conditions, both changes intended to stress the cell lines. We then assessed the impact of an approximately 10-fold process scale-up on the final product at the transcriptional level. These data were used to develop comparisons and statistical analyses suitable for characterizing culture reproducibility and cellular product similarity. Use of gene-expression data for process characterization proved to be a reproducible and sensitive method for detecting differences due to small or large changes in culture conditions as might be

  10. Molecular cytogenetic anomalies and phenotype alterations in a newly established cell line from Wilms tumor with diffuse anaplasia.

    PubMed

    Faussillon, Marine; Murakami, Ichiro; Bichat, Magalie; Telvi, Louise; Jeanpierre, Cécile; Nezelof, Christian; Jaubert, Francis; Gogusev, Jean

    2008-07-01

    The novel continuous cell line WT-Pe.1 was established in vitro from Wilms tumor with histological features of diffuse anaplasia. The cultures grew as poorly differentiated epithelial-like cells with pleomorphic polygonal shapes and formation of typical monolayers. WT-Pe.1 cells were immunoreactive for cytokeratin, vimentin, laminin, villin, CD10, and CD24 proteins. Conventional cytogenetic analysis by RHG-banding revealed a hypotriploid karyotype with numerous abnormalities including ring chromosomes, double-minutes, homogeneous staining regions, radial structures, dicentrics, and several marker chromosomes. Comparative genomic hybridization analysis revealed DNA copy numbers losses on chromosome segments 1p, 3p, 6q, 9q34.1 approximately q34.3, 11q24 approximately q25, 14q12 approximately qter, 16q, 18q, and 22q11 approximately q13; gain of genomic material was localized on chromosome arms 1q, 4p, 6q, and 7p and the entire chromosome 12. With DNA from the original tumor, copy number losses were detected on chromosomes 1p, 14q, 16q, 17q, and 22q and gains were observed on 1q, 4p, 8q, 12p, 12q, and chromosome 14p. Copy number amplifications of distinct loci were found on 1q21.1 and 4p15.3, as well as an elevated copy number of cyclin D2 (CCND2) and cyclin D associated kinase (CDK4) genes on chromosome 12 (confirmed by fluorescence in situ hybridization).

  11. 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.

  12. Morphological and molecular characterization of new Drosophila cell lines established from a strain permissive for gypsy transposition.

    PubMed

    Chalvet, F; Debec, A; Marcaillou, C; Rougeau, C; Bucheton, A

    1998-01-01

    The gypsy element of Drosophila melanogaster is the first retrovirus identified in invertebrates. Its transposition is controlled by a host gene called flamenco (flam): restrictive alleles of this gene maintain the retrovirus in a repressed state while permissive alleles allow high levels of transposition. To develop a cell system to study the gypsy element, we established four independent cell lines derived from the Drosophila strain SS, which contains a permissive allele of flamenco, and which is devoid of transposing copies of gypsy. The ultrastructural analysis of three SS cell lines revealed some remarkable characteristics, such as many nuclear virus-like particles, cytoplasmic dense particles, and massive cisternae filled with a fibrous material of unknown origin. Gypsy intragenomic distribution has been compared between the three cell lines and the original SS fly strain, and revealed in two of the cell lines an increase in copy number of a restriction fragment usually present in active gypsy elements. This multiplication seems to have occurred during the passage to the cell culture. Availability of SS cell lines should assist studies of gypsy transposition and infectivity and might be useful to produce high amounts of gypsy viral particles. These new lines already allowed us to show that the Envelope-like products of gypsy can be expressed as membrane proteins.

  13. 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

  14. Metabolomics as a Powerful Tool for Molecular Quality Assessment of the Fish Sparus aurata

    PubMed Central

    Picone, Gianfranco; Engelsen, Søren Balling; Savorani, Francesco; Testi, Silvia; Badiani, Anna; Capozzi, Francesco

    2011-01-01

    The molecular profiles of perchloric acid solutions extracted from the flesh of Sparus aurata fish specimens, produced according to different aquaculture systems, have been investigated. The 1H-NMR spectra of aqueous extracts are indicative of differences in the metabolite content of fish reared under different conditions that are already distinguishable at their capture, and substantially maintain the same differences in their molecular profiles after sixteen days of storage under ice. The fish metabolic profiles are studied by top-down chemometric analysis. The results of this exploratory investigation show that the fish metabolome accurately reflects the rearing conditions. The level of many metabolites co-vary with the rearing conditions and a few metabolites are quantified including glycogen (stress indicator), histidine, alanine and glycine which all display significant changes dependent on the aquaculture system and on the storage times. PMID:22254093

  15. 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

  16. 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.

  17. Dextran-lipase conjugates as tools for low molecular weight ligand immobilization in microarray development.

    PubMed

    Herranz, Sonia; Marciello, Marzia; Olea, David; Hernández, Margarita; Domingo, Concepción; Vélez, Marisela; Gheber, Levi A; Guisán, Jose M; Moreno-Bondi, María Cruz

    2013-08-06

    The development of effective array biosensors relies heavily on careful control of the density of surface-immobilized ligands on the transducing platform. In this paper we describe the synthesis of new dextran-lipase conjugates for use in immobilizing low molecular weight haptens onto glass planar waveguides for immunosensor development. The conjugates were synthesized by immobilizing bacterial thermoalkalophilic lipases (Geobacillus thermocatenulatus lipase 2, BTL2) on agarose macroporous beads, followed by covalent coupling to dextran networks of variable molecular weight (1500-40000). The chimeras were immobilized via nonspecific hydrophobic interactions onto glass planar waveguides modified with 1,1,1,3,3,3-hexamethyldisilazane to obtain highly ordered and homogeneous molecular architectures as confirmed by atomic force microscopy. Microcystin LR (MCLR) was covalently bound to the dextran-BTL2 conjugates. The usefulness of this approach in immunosensor development was demonstrated by determining amounts of MCLR down to a few picograms per liter with an automated array biosensor and evanescent wave excitation for fluorescence measurements of attached DyLight649-labeled secondary antibody. Modifying BTL2 with dextrans of an increased molecular weight (>6000) provided surfaces with an increased loading capacity that was ascribed to the production of three-dimensional surfaces by the effect of analyte binding deep in the volume, leading to expanded dynamic ranges (0.09-136.56 ng L(-1)), lower limits of detection (0.007 ± 0.001 ng L(-1)), and lower IC50 values (4.4 ± 0.7 ng L(-1)). These results confirm the effectiveness of our approach for the development of high-performance biosensing platforms.

  18. 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

  19. 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

  20. 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. Copyright © 2015 Elsevier Inc. All rights reserved.

  1. Molecular paleoparasitological hybridization approach as effective tool for diagnosing human intestinal parasites from scarce archaeological remains.

    PubMed

    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.

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

    PubMed

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

    2015-10-01

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

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

    PubMed

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

    2015-10-01

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

  4. 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.

  5. 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.

  6. 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

  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. 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.

  9. Cell specific aptamer-photosensitizer conjugates as a molecular tool in photodynamic therapy

    PubMed Central

    Mallikaratchy, Prabodhika; Tang, Zhiwen

    2010-01-01

    This paper describes the application of a molecular construct of a photosensitizer and an aptamer for photo-therapeutically targeting tumor cells. The key step in increasing selectivity in chemotherapeutic drugs is to create effective molecular platforms that could target cancer cells but not normal cells. Recently, we have developed a strategy via cell-SELEX (Systematic Evolution of Ligands by Exponential Enrichment) to obtain cell specific aptamers using intact viable cells as targets to select aptamers that can recognize cell membrane proteins with high selectivity and excellent affinity. We have identified an aptamer TD05 that only recognizes Ramos cells, a Burkitt’s lymphoma cell line. Here, the high specificity of aptamers in target cell binding and an efficient phototherapy reagent, Ce6, are molecularly engineered to construct a highly selective Aptamer-photosensitizer conjugates (APS) to effectively destroy target cancer cells. Introduction of the APS conjugates followed by irradiation of light selectively destroyed target Ramos cells but not acute lymphoblastic leukemia and myeloid leukemia cell lines. This study demonstrates that the use of cancer specific aptamers conjugated to a photosensitizer will enhance the selectivity of photodynamic therapy. Coupled with the advantages of the cell-SELEX in generating multiple effective aptamers for diseased cell recognition, we will be able to develop highly efficient photosensitizer based therapeutical reagents for clinical applications. PMID:18058891

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

    PubMed Central

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

    2011-01-01

    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. PMID:22006909

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

    PubMed Central

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

    2002-01-01

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

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

    PubMed

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

    2015-02-07

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

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

    PubMed

    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 Ca(2+), flavoprotein and optical imaging.

  14. 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

  15. 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

  16. 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.

  17. 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.

  18. Molecular tools and analytical approaches for the characterization of farm animal genetic diversity.

    PubMed

    Lenstra, J A; Groeneveld, L F; Eding, H; Kantanen, J; Williams, J L; Taberlet, P; Nicolazzi, E L; Sölkner, J; Simianer, H; Ciani, E; Garcia, J F; Bruford, M W; Ajmone-Marsan, P; Weigend, S

    2012-10-01

    Genetic studies of livestock populations focus on questions of domestication, within- and among-breed diversity, breed history and adaptive variation. In this review, we describe the use of different molecular markers and methods for data analysis used to address these questions. There is a clear trend towards the use of single nucleotide polymorphisms and whole-genome sequence information, the application of Bayesian or Approximate Bayesian analysis and the use of adaptive next to neutral diversity to support decisions on conservation. © 2012 The Authors, Animal Genetics © 2012 Stichting International Foundation for Animal Genetics.

  19. 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.

  20. 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.

  1. 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

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

    PubMed

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

    2017-04-01

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

  3. 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. 2010 S. Karger AG, Basel.

  4. 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

  5. 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.

  6. GEOM: A new tool for molecular modelling based on distance geometry calculations with NMR data

    NASA Astrophysics Data System (ADS)

    Sanner, Michel; Widmer, Armin; Senn, Hans; Braun, Werner

    1989-09-01

    GEOM is a new graphics tool which allows the use of distance geometry to compute linear and cyclic structures typically arising in drug design situations. Modified amino acids or monomeric organic entities can be easily constructed in an interactive way and deposited in the library of the distance geometry program together with geometric information required for structure calculation in dihedral angle space. In addition, GEOM is able to produce all files needed to calculate a structure based on NMR data (NOE and J-coupling constraints) and it permits the graphic analysis and comparison of computed structures. The application of GEOM is demonstrated in three examples: modelling of cyclosporin A structures with and without a limited set of H-bond constraints and modelling of a cyclic hexapeptide with a full NMR data set.

  7. mDCC_tools: characterizing multi-modal atomic motions in molecular dynamics trajectories.

    PubMed

    Kasahara, Kota; Mohan, Neetha; Fukuda, Ikuo; Nakamura, Haruki

    2016-08-15

    We previously reported the multi-modal Dynamic Cross Correlation (mDCC) method for analyzing molecular dynamics trajectories. This method quantifies the correlation coefficients of atomic motions with complex multi-modal behaviors by using a Bayesian-based pattern recognition technique that can effectively capture transiently formed, unstable interactions. Here, we present an open source toolkit for performing the mDCC analysis, including pattern recognitions, complex network analyses and visualizations. We include a tutorial document that thoroughly explains how to apply this toolkit for an analysis, using the example trajectory of the 100 ns simulation of an engineered endothelin-1 peptide dimer. The source code is available for free at http://www.protein.osaka-u.ac.jp/rcsfp/pi/mdcctools/, implemented in C ++ and Python, and supported on Linux. kota.kasahara@protein.osaka-u.ac.jp Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

  8. 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

  9. 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.

  10. 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

  11. mDCC_tools: characterizing multi-modal atomic motions in molecular dynamics trajectories

    PubMed Central

    Kasahara, Kota; Mohan, Neetha; Fukuda, Ikuo; Nakamura, Haruki

    2016-01-01

    Summary: We previously reported the multi-modal Dynamic Cross Correlation (mDCC) method for analyzing molecular dynamics trajectories. This method quantifies the correlation coefficients of atomic motions with complex multi-modal behaviors by using a Bayesian-based pattern recognition technique that can effectively capture transiently formed, unstable interactions. Here, we present an open source toolkit for performing the mDCC analysis, including pattern recognitions, complex network analyses and visualizations. We include a tutorial document that thoroughly explains how to apply this toolkit for an analysis, using the example trajectory of the 100 ns simulation of an engineered endothelin-1 peptide dimer. Availability and implementation: The source code is available for free at http://www.protein.osaka-u.ac.jp/rcsfp/pi/mdcctools/, implemented in C ++ and Python, and supported on Linux. Contact: kota.kasahara@protein.osaka-u.ac.jp Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27153575

  12. 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.

  13. Molecular Line Emission as a Tool for Galaxy Observations (LEGO). I. HCN as a tracer of moderate gas densities in molecular clouds and galaxies

    NASA Astrophysics Data System (ADS)

    Kauffmann, Jens; Goldsmith, Paul F.; Melnick, Gary; Tolls, Volker; Guzman, Andres; Menten, Karl M.

    2017-09-01

    Trends observed in galaxies, such as the Gao & Solomon relation, suggest a linear relationship between the star formation rate and the mass of dense gas available for star formation. Validation of such trends requires the establishment of reliable methods to trace the dense gas in galaxies. One frequent assumption is that the HCN (J = 1-0) transition is unambiguously associated with gas at H2 densities ≫ 104 cm-3. If so, the mass of gas at densities ≫ 104 cm-3 could be inferred from the luminosity of this emission line, LHCN (1-0). Here we use observations of the Orion A molecular cloud to show that the HCN (J = 1-0) line traces much lower densities 103 cm-3 in cold sections of this molecular cloud, corresponding to visual extinctions AV ≈ 6 mag. We also find that cold and dense gas in a cloud like Orion produces too little HCN emission to explain LHCN (1-0) in star forming galaxies, suggesting that galaxies might contain a hitherto unknown source of HCN emission. In our sample of molecules observed at frequencies near 100 GHz (also including 12CO, 13CO, C18O, CN, and CCH), N2H+ is the only species clearly associated with relatively dense gas.

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. 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

  19. 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.

  20. The 2002 Chandigarh cholera outbreak revisited: utility of MALDI-TOF as a molecular epidemiology tool.

    PubMed

    Taneja, N; Sethuraman, N; Mishra, A; Mohan, B

    2016-06-01

    In July 2002, an outbreak of cholera occurred in north India with two separate geographical foci. Pulsed field gel electrophoresis (PFGE) was previously used in typing a representative sample of these isolates. This study evaluates the usefulness of MALDI-TOF as an epidemiological tool for typing Vibrio cholerae isolates in comparison with PFGE and Amplified fragment length polymorphisms (AFLP). Forty-six isolates of V. cholerae isolated from stool of patients affected in the July 2002 outbreak were typed using MALDI-TOF. To validate its utility, clinical and environmental isolates previously characterized by PFGE and AFLP were included for dendrogram analysis. All 46 isolates were correctly identified by MALDI-TOF to species level. Two distinct clades appeared on dendrogram using MALDI-TOF corresponding to the two geographical foci of the outbreak. For the study of evolution of organisms from environment, AFLP was superior as it clearly demarcated clinical and environmental isolates. The outbreak was not due to a single clone but due to multiple clones circulating simultaneously, as was seen with PFGE also. MALDI-TOF appears to be a highly discriminatory, cost-effective and rapid epidemiological typing technique that can be used in the investigation of cholera outbreaks. © 2016 The Society for Applied Microbiology.

  1. DAMBE6: New Tools for Microbial Genomics, Phylogenetics, and Molecular Evolution

    PubMed Central

    2017-01-01

    Abstract DAMBE is a comprehensive software workbench for data analysis in molecular biology, phylogenetics, and evolution. Several important new functions have been added since version 5 of DAMBE: 1) comprehensive genomic profiling of translation initiation efficiency of different genes in different prokaryotic species, 2) a new index of translation elongation (ITE) that takes into account both tRNA-mediated selection and background mutation on codon–anticodon adaptation, 3) a new and accurate phylogenetic approach based on pairwise alignment only, which is useful for highly divergent sequences from which a reliable multiple sequence alignment is difficult to obtain. Many other functions have been updated and improved including PWM for motif characterization, Gibbs sampler for de novo motif discovery, hidden Markov models for protein secondary structure prediction, self-organizing map for nonlinear clustering of transcriptomic data, comprehensive sequence alignment, and phylogenetic functions. DAMBE features a graphic, user-friendly and intuitive interface, and is freely available from http://dambe.bio.uottawa.ca. PMID:28379490

  2. 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

  3. 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. © 2015 John Wiley & Sons Ltd.

  4. 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.

  5. Assessment of Changes in Microbial Community Structure during Operation of an Ammonia Biofilter with Molecular Tools

    PubMed Central

    Sakano, Y.; Kerkhof, L.

    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. PMID:9835577

  6. 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.

  7. 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

  8. 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.

  9. 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

  10. 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.

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

    SciTech Connect

    Sakano, Y.; Kerkhof, L.

    1998-12-01

    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.

  12. 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.

  13. 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

  14. 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. Copyright © 2016. Published by Elsevier GmbH.

  15. 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.

  16. 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

  17. A powerful molecular engineering tool provided efficient Chlamydomonas mutants as bio-sensing elements for herbicides detection.

    PubMed

    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 I(50) 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.

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

    PubMed

    Abdel-Azeim, Safwat; Chermak, Edrisse; Vangone, Anna; Oliva, Romina; Cavallo, Luigi

    2014-01-01

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

  19. Molecular tools to track bacteria responsible for fuel deterioration and microbiologically influenced corrosion.

    PubMed

    Suflita, Joseph M; Aktas, Deniz F; Oldham, Athenia L; Perez-Ibarra, Beatriz Monica; Duncan, Kathleen

    2012-01-01

    Investigating the susceptibility of various fuels to anaerobic biodegradation has become complicated with the recognition that the fuels themselves are not sterile. Bacterial DNA could be obtained when various fuels were filtered through a hydrophobic teflon (0.22 μm) membrane filter. Bacterial 16S rRNA genes from these preparations were PCR amplified, cloned, and the resulting libraries sequenced to identify the fuel-borne bacterial communities. The most common sequence, found in algal- and camelina-based biofuels as well as in ultra-low sulfur diesel (ULSD) and F76 diesel, was similar to that of a Tumebacillus. The next most common sequence was similar to Methylobacterium and was found in the biofuels and ULSD. Higher level phylogenetic groups included representatives of the Firmicutes (Bacillus, Lactobacillus and Streptococcus), several Actinobacteria, Deinococcus-Thermus, Chloroflexi, Cyanobacteria, Bacteroidetes, Alphaproteobacteria (Methylobacterium and Sphingomonadales), Betaproteobacteria (Oxalobacteraceae and Burkholderiales) and Deltaproteobacteria. All of the fuel-associated bacterial sequences, except those obtained from a few facultative microorganisms, were from aerobes and only remotely affiliated with sequences that resulted from anaerobic successional events evident when ULSD was incubated with a coastal seawater and sediment inoculum. Thus, both traditional and alternate fuel formulations harbor a characteristic microflora, but these microorganisms contributed little to the successional patterns that ultimately resulted in fuel decomposition, sulfide formation and metal biocorrosion. The findings illustrate the value of molecular approaches to track the fate of bacteria that might come in contact with fuels and potentially contribute to corrosion problems throughout the energy value chain.

  20. Molecular ecological tools to decipher the role of our microbial mass in obesity.

    PubMed

    Hermes, G D A; Zoetendal, E G; Smidt, H

    2015-03-01

    After birth, our gastrointestinal (GI) tract is colonised by a highly complex assemblage of microbes, collectively termed the GI microbiota, that develops intimate interactions with our body. Recent evidence indicates that the GI microbiota and its products may contribute to the development of obesity and related diseases. This, coupled with the current worldwide epidemic of obesity, has moved microbiome research into the spotlight of attention. Although the main cause of obesity and its associated metabolic complications is excess caloric intake compared with expenditure, differences in GI tract microbial ecology between individuals might be an important biomarker, mediator or new therapeutic target. This can be investigated using a diverse set of complementary so called -omics technologies, such as 16S ribosomal RNA gene-targeted composition profiling, metabolomics, metagenomics, metatranscriptomics and metaproteomics. This review aims to describe the different molecular approaches and their contributions to our understanding of the role of the GI microbiota in host energy homeostasis. Correspondingly, we highlight their respective strengths, but also try to create awareness for their specific limitations. However, it is currently still unclear which bacterial groups play a role in the development of obesity in humans. This might partly be explained by the heterogeneity in genotype, lifestyle, diet and the complex ethology of obesity and its associated metabolic disorders (OAMD). Nevertheless, recent research on this matter has shown a conceptual shift by focusing on more homogenous subpopulations, through the use of both anthropometric (weight, total body fat) as well as biochemical variables (insulin resistance, hyperlipidaemia) to define categories. Combined with technological advances, recent data suggests that an OAMD associated microbiota can be characterised by a potential pro-inflammatory composition, with less potential for the production of short chain

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

    PubMed

    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/.

  2. 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

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

    NASA Astrophysics Data System (ADS)

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

    2010-12-01

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

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

    NASA Astrophysics Data System (ADS)

    Singh, R.; Olson, M. S.

    2007-12-01

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

  6. 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. © The American Genetic Association 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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

    PubMed

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

    2016-11-01

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

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

    NASA Astrophysics Data System (ADS)

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

    1996-10-01

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

  9. Molecular Phylogeny and Description of the Novel Katablepharid Roombia truncata gen. et sp. nov., and Establishment of the Hacrobia Taxon nov

    PubMed Central

    Okamoto, Noriko; Chantangsi, Chitchai; Horák, Aleš; Leander, Brian S.; Keeling, Patrick J.

    2009-01-01

    Background Photosynthetic eukaryotes with a secondary plastid of red algal origin (cryptophytes, haptophytes, stramenopiles, dinoflagellates, and apicomplexans) are hypothesized to share a single origin of plastid acquisition according to Chromalveolate hypothesis. Recent phylogenomic analyses suggest that photosynthetic “chromalveolates” form a large clade with inclusion of several non-photosynthetic protist lineages. Katablepharids are one such non-photosynthetic lineage closely related to cryptophytes. Despite their evolutionary and ecological importance, katablepharids are poorly investigated. Methodology/Principal Findings Here, we report a newly discovered flagellate, Roombia truncata gen. et sp. nov., that is related to katablepharids, but is morphologically distinct from othermembers of the group in the following ways: (1) two flagella emerge from a papilla-like subapical protrusion, (2) conspicuous ejectisomes are aligned in multiple (5–11) rows, (3) each ejectisome increases in size towards the posterior end of the rows, and (4) upon feeding, a part of cytoplasm elastically stretch to engulf whole prey cell. Molecular phylogenies inferred from Hsp90, SSU rDNA, and LSU rDNA sequences consistently and strongly show R. truncata as the sister lineage to all other katablepharids, including lineages known only from environmental sequence surveys. A close association between katablepharids and cryptophytes was also recovered in most analyses. Katablepharids and cryptophytes are together part of a larger, more inclusive, group that also contains haptophytes, telonemids, centrohelids and perhaps biliphytes. The monophyly of this group is supported by several different molecular phylogenetic datasets and one shared lateral gene transfer; therefore, we formally establish this diverse clade as the “Hacrobia.” Conclusions/Significance Our discovery of R. truncata not only expands our knowledge in the less studied flagellate group, but provide a better

  10. 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.

  11. 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

  12. Engineering OsBAK1 gene as a molecular tool to improve rice architecture for high yield.

    PubMed

    Li, Dan; Wang, Lei; Wang, Min; Xu, Yun-Yuan; Luo, Wei; Liu, Ya-Ju; Xu, Zhi-Hong; Li, Jia; Chong, Kang

    2009-10-01

    Generating a new variety of plant with erect-leaf is a critical strategy to improve rice grain yield, as plants with this trait can be dense-planted. The erect-leaf is a significant morphological trait partially regulated by Brassinosteroids (BRs) in rice plants. So far, only a few genes can be used for molecular breeding in rice. Here, we identified OsBAK1 as a potential gene to alter rice architecture. Based on rice genome sequences, four closely related homologs of Arabidopsis BAK1 (AtBAK1) gene were amplified. Phylogenetic analysis and suppression of a weak Arabidopsis mutant bri1-5 indicated that OsBAK1 (Os08g0174700) is the closest relative of AtBAK1. Genetic, physiological, and biochemical analyses all suggest that the function of OsBAK1 is conserved with AtBAK1. Overexpression of a truncated intracellular domain of OsBAK1, but not the extracellular domain of OsBAK1, resulted in a dwarfed phenotype, similar to the rice BR-insensitive mutant plants. The expression of OsBAK1 changed important agricultural traits of rice such as plant height, leaf erectness, grain morphologic features, and disease resistance responses. Our results suggested that a new rice variety with erect-leaf and normal reproduction can be generated simply by suppressing the expression level of OsBAK1. Therefore, OsBAK1 is a potential molecular breeding tool for improving rice grain yield by modifying rice architecture.

  13. 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.

  14. 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.

  15. 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

  16. 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

  17. 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

  18. 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.

  19. A Critical Appraisal of Molecular Xenomonitoring as a Tool for Assessing Progress toward Elimination of Lymphatic Filariasis

    PubMed Central

    Farid, Hoda A.; Morsy, Zakariya S.; Helmy, Hanan; Ramzy, Reda M. R.; Setouhy, Maged El; Weil, Gary J.

    2008-01-01

    We used molecular xenomonitoring (MX, detection of filarial DNA in mosquitoes) to evaluate the impact of mass drug administration (MDA) in sentinel locations in Egypt with high (11.5%) and low (4.1%) baseline microfilaria prevalence rates. Blood-fed Culex pipiens were pooled by household and tested for Wuchereria bancrofti DNA by PCR. There was no significant relationship between the infection status of household residents and parasite DNA status of mosquitoes from the same houses. After 5 MDA rounds, parasite DNA rates in mosquitoes in high- and low-prevalence areas were reduced by 93.8% and 100% to 0.19% (95% CI: 0.076–0.382%) and 0% (95% CI: 0–0.045%), respectively. These changes were consistent with decreases in microfilaria prevalence rates in these sites; they provide insight regarding the minimal mosquito DNA rates necessary for sustained transmission of filariasis in Egypt. We conclude that MX is a powerful tool for monitoring the impact of MDA on filariasis endemicity and transmission. PMID:17978055

  20. 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.

  1. 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.

  2. 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

  3. The APHL/CDC Public Health Laboratory Interoperability Project Portal: A Web-based Collaborative Tool to Establish a National Harmonized Vocabulary for Public Health Data Exchange

    PubMed Central

    Lazo, Robert; Li, Wenkai; Meigs, Michelle; Abner, Sheila; Carroll, John; Miller, Charles; Zarcone, Patina; Hinrichs, Steven; Nordenberg, Dale

    2006-01-01

    Public health laboratories at all capacity levels are facing challenges in exchanging electronic data among themselves and with their partners. In response to this the Association of Public Health Laboratories working collaboratively with CDC launched an innovative portal development project in January 2006. This portal will enable public health laboratories to collaborate in a web-based environment to establish a standardized vocabulary for test identifications and test results, a cornerstone for creating interoperable information systems. PMID:17238618

  4. Molecular tools for diagnostics

    USDA-ARS?s Scientific Manuscript database

    About 25,000 species of nematodes have been described, among which more than 4,000 are parasites of plants. However, estimates of the total number of nematode species on the planet vary from 100,000 to several million, and thus the actual total number of plant-parasitic nematode (PPN) species is lik...

  5. 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.

  6. Tracking of Listeria monocytogenes in meat establishment using Whole Genome Sequencing as a food safety management tool: A proof of concept.

    PubMed

    Nastasijevic, Ivan; Milanov, Dubravka; Velebit, Branko; Djordjevic, Vesna; Swift, Craig; Painset, Anais; Lakicevic, Brankica

    2017-09-18

    Repeated Listeria outbreaks particularly associated with Ready-To-Eat (RTE) delicatessen meat products have been reported annually at global level. The most frequent scenario that led to foodborne outbreaks was the post-thermal treatment cross-contamination of deli meat products during slicing and modified atmosphere packaging (MAP). The precondition for such cross contamination is the previous introduction of Listeria into meat processing facilities and subsequent colonization of the production environment, associated with formation of biofilms resilient to common sanitation procedures regularly applied in meat establishments. The use of Whole Genome Sequencing (WGS) can facilitate the understanding of contamination and colonization routes of pathogens within the food production environment and enable efficient pathogen tracking among different departments. This study aimed to: a) provide a proof of concept on practical use of WGS in a meat establishment to define the entry routes and spread pattern of L. monocytogenes, and b) to consider the regular use of WGS in meat processing establishments as a strong support of food safety management system. The results revealed that Listeria spp. was present in slaughter line, chilling chambers, deboning, slicing, MAP, as well as in corridors and dispatch (53 positive samples, out of 240). Eight L. monocytogenes isolates (out of 53) were identified from the slaughterhouse, chilling chambers, deboning, MAP and dispatch. L. monocytogenes isolates were of three different serotypes (1/2a, 1/2c, 4b) and correspondingly of three MLST sequence types. Overall, two pairs of L. monocytogenes isolates were genetically identical, i.e. two serotype 4b isolates (ST1), isolated from water drain at dispatch unit and two isolates obtained from slaughterhouse (floorwall junction at the carcass wash point) and MAP (water drain). These findings indicated that L. monocytogenes isolates identified in meat processing units (MAP, chilling chamber

  7. 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

  8. 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

  9. 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.

  10. 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

  11. ESIprot: a universal tool for charge state determination and molecular weight calculation of proteins from electrospray ionization mass spectrometry data.

    PubMed

    Winkler, Robert

    2010-02-01

    Electrospray ionization (ESI) ion trap mass spectrometers with relatively low resolution are frequently used for the analysis of natural products and peptides. Although ESI spectra of multiply charged protein molecules also can be measured on this type of devices, only average spectra are produced for the majority of naturally occurring proteins. Evaluating such ESI protein spectra would provide valuable information about the native state of investigated proteins. However, no suitable and freely available software could be found which allows the charge state determination and molecular weight calculation of single proteins from average ESI-MS data. Therefore, an algorithm based on standard deviation optimization (scatter minimization) was implemented for the analysis of protein ESI-MS data. The resulting software ESIprot was tested with ESI-MS data of six intact reference proteins between 12.4 and 66.7 kDa. In all cases, the correct charge states could be determined. The obtained absolute mass errors were in a range between -0.2 and 1.2 Da, the relative errors below 30 ppm. The possible mass accuracy allows for valid conclusions about the actual condition of proteins. Moreover, the ESIprot algorithm demonstrates an extraordinary robustness and allows spectral interpretation from as little as two peaks, given sufficient quality of the provided m/z data, without the necessity for peak intensity data. ESIprot is independent from the raw data format and the computer platform, making it a versatile tool for mass spectrometrists. The program code was released under the open-source GPLv3 license to support future developments of mass spectrometry software. Copyright 2010 John Wiley & Sons, Ltd.

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

    PubMed

    Clark, Alex M; Sarker, Malabika; Ekins, Sean

    2014-01-01

    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. 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. 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.

  13. 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.

  14. 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

  15. Establishing tools for early diagnosis of congenital toxoplasmosis: Flow cytometric IgG avidity assay as a confirmatory test for neonatal screening.

    PubMed

    de Castro Zacche-Tonini, Aline; Fonseca, Giuliana Schmidt França; de Jesus, Laura Néspoli Nassar Pansini; Barros, Geisa Baptista; Coelho-Dos-Reis, Jordana Grazziela Alves; Béla, Samantha Ribeiro; Machado, Anderson Silva; Carneiro, Ana Carolina Aguiar Vasconcelos; Andrade, Gláucia Manzan Queiroz; Vasconcelos-Santos, Daniel Vitor; Januário, José Nélio; Teixeira-Carvalho, Andréa; Vitor, Ricardo Wagner Almeida; Ferro, Eloísa Amália Vieira; Mineo, José Roberto; Martins-Filho, Olindo Assis; Lemos, Elenice Moreira

    2017-08-18

    The aim of this study was to evaluate the performance of conventional serology (Q-Preven™ and ELFAVIDAS™) and flow cytometry-based serologic tools for early serologic diagnosis of congenital toxoplasmosis. The study groups included prospectively confirmed cases of congenital toxoplasmosis (TOXO=88) and age-matching non-infected controls (NI=15).The results demonstrated that all samples tested positive/indeterminate for anti-T. gondii IgM screening at birth using air-dried whole blood samples. Serum samples collected at 30-45days after birth tested positive for ELFAVIDAS™ IgG in both groups. While all NI tested negative for ELFAVIDAS™ IgM and IgA, only 78% and 36% of TOXO tested positive for IgM and IgA, respectively. Flow cytometry-based anti-T. gondii IgM, IgA and IgG reactivity displayed moderate performance with low sensitivity (47.6%, 72.6% and 75.0%, respectively). Regardless the remarkable specificity of IgG1, IgG2 and IgG3 subclasses for early diagnosis, weak or moderate specificity was observed (Se=73.9%, 60.2% and 83.0%, respectively). The analysis of IgG avidity indices (AI) demonstrated the highest performance among the flow cytometry-based methods (Se=96.6%; Sp=93.3%), underscoring the low avidity index (AI<60%) within TOXO (97.0%) in contrast with the high avidity index (AI>60%) in NI (93%). Analysis of anti-T. gondii IgG and IgG3 reactivity for mother:infant paired samples may represent a relevant complementary tests for early diagnosis. In conclusion, a feasible high-standard algorithm (Accuracy=97.1%) was proposed consisting of Q-Preven™ IgM screening at birth, followed by ELFAVIDAS™ IgM and flow cytometric IgG avidity analysis at 30-45days after birth as a high performance tool for early serological diagnosis of congenital toxoplasmosis. Copyright © 2017. Published by Elsevier B.V.

  16. Establishment of in vitro soybean aphids, Aphis glycines (Hemiptera: Aphididae): a tool to facilitate studies of aphid symbionts, plant-insect interactions and insecticide efficacy.

    PubMed

    Gunadi, Andika; Bansal, Raman; Finer, John J; Michel, Andy

    2017-06-01

    Studies on plant-insect interactions of the soybean aphid, Aphis glycines (Matsumura), can be influenced by environmental fluctuations, status of the host plant and variability in microbial populations. Maintenance of aphids on in vitro-grown plants minimizes environmental fluctuations, provides uniform host materials and permits the selective elimination of aphid-associated microbes for more standardized controls in aphid research. Aphids were reared on sterile, in vitro-grown soybean seedlings germinated on plant tissue culture media amended with a mixture of antimicrobials. For initiation and maintenance of in vitro aphid colonies, single aphids were inoculated onto single in vitro seedlings. After three rounds of transfer of 'clean' aphids to fresh in vitro seedlings, contamination was no longer observed, and aphids performed equally well when compared with those reared on detached leaves. The addition of the insecticides thiamethoxam and chlorantraniliprole to the culture medium confirmed uptake and caused significant mortality to the in vitro aphids. The use of the antimicrobial mixture removed the associated bacteria Arsenophonus but retained Buchnera and Wolbachia within the in vitro aphids. The in vitro aphid system is a novel and highly useful tool to understand insecticidal efficacy and expand our knowledge of tritrophic interactions among plants, insects and symbionts. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

  17. Essential veterinary education in modern molecular tools for the detection of disease: what veterinarians will need to know about genomics and molecular biology and diagnostics (including bioterrorist weapons) in 2025.

    PubMed

    de Lamballerie, X

    2009-08-01

    Future veterinary education programmes in microbiology will undoubtedly include an increasing emphasis on new and existing molecular tools. They should also, however, provide veterinarians with a comprehensive and clear understanding of the types of results that can be obtained using a particular approach (for example, specific diagnostic procedures as against open diagnostic procedures, phenotypic versus genotypic characterisation, etc.). Furthermore, students should gain a sound knowledge of which type of test is the most appropriate in a given clinical or epidemiological situation, and what conclusions can or cannot be drawn from the results. Consequently, each veterinary curriculum should focus on the following items: the principles of molecular biology and genomics; the detection of disease and characteristics of molecular tests; the principles of micro-organism taxonomy, sequence comparison and molecular epidemiology and their applications (such as: taxonomic identification, epidemiological survey, genetic evolution and the traceability of strains); and the role of the veterinarian in the field of zoonoses and human public health.

  18. 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.

  19. 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.

  20. Medicine authentication technology as a counterfeit medicine-detection tool: a Delphi method study to establish expert opinion on manual medicine authentication technology in secondary care.

    PubMed

    Naughton, Bernard; Roberts, Lindsey; Dopson, Sue; Brindley, David; Chapman, Stephen

    2017-05-06

    This study aims to establish expert opinion and potential improvements for the Falsified Medicines Directive mandated medicines authentication technology. A two-round Delphi method study using an online questionnaire. Large National Health Service (NHS) foundation trust teaching hospital. Secondary care pharmacists and accredited checking technicians. Seven-point rating scale answers which reached a consensus of 70-80% with a standard deviation (SD) of <1.0. Likert scale questions which reached a consensus of 70-80%, a SD of <1.0 and classified as important according to study criteria. Consensus expert opinion has described database cross-checking technology as quick and user friendly and suggested the inclusion of an audio signal to further support the detection of counterfeit medicines in secondary care (70% consensus, 0.9 SD); other important consensus with a SD of <1.0 included reviewing the colour and information in warning pop up screens to ensure they were not mistaken for the 'already dispensed here' pop up, encouraging the dispenser/checker to act on the warnings and making it mandatory to complete an 'action taken' documentation process to improve the quarantine of potentially counterfeit, expired or recalled medicines. This paper informs key opinion leaders and decision makers as to the positives and negatives of medicines authentication technology from an operator's perspective and suggests the adjustments which may be required to improve operator compliance and the detection of counterfeit medicines in the secondary care sector. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

  1. Headspace-solid phase microextraction-gas chromatography as a tool to define an index that establishes the retention capacity of the wine polymeric fraction towards ethyl esters.

    PubMed

    Rocha, Sílvia M; Coutinho, Paula; Delgadillo, Ivonne; Coimbra, Manuel A

    2007-05-25

    A headspace-solid phase microextraction followed by gas chromatographic analysis (HS-SPME-GC) was developed to be applied in the study of the interactions between the wine polymeric fraction and the ethyl esters: ethyl hexanoate, ethyl octanoate, and ethyl decanoate. Wine models (WM) were prepared with 10% (v/v) aqueous ethanol at pH 3.5 with distinct wine polymeric concentrations prepared from white wine of Vitis vinifera L. var. Fernão-Pires: 1.0 g L(-1) (PWM1), with a polymeric concentration approaching the real one in wine; 10.0 g L(-1) (PWM10); and 30.0 g L(-1) (PWM30), saturated with polymeric fraction. A reference wine model (RWM) was prepared without polymeric fraction. Each volatile compound (4.0 mg L(-1)) was added separately to the RWM and to the WM with the three levels of polymeric material (PWM). From the retention index (RI) calculated for each compound using the formula: [RI = 1 - (C(RWM) - C(PWM))/C(RWM)], where C(RWM) is the concentration of the compound in the RWM and C(PWM) is the concentration of the compound in the given PWM, the retention capacity of each wine polymeric fraction towards the three esters was established. The higher retention indexes were observed for ethyl decanoate, the more hydrophobic compound, and for the PWM with higher concentration. Furthermore, this study also suggested that the retained compounds are dosed to the headspace, which may promote the perception of their aroma for a longer period of time.

  2. A concept taxonomy and an instrument hierarchy: tools for establishing and evaluating the conceptual framework of a patient-reported outcome (PRO) instrument as applied to product labeling claims.

    PubMed

    Erickson, Pennifer; Willke, Richard; Burke, Laurie

    2009-01-01

    To facilitate development and evaluation of a PRO instrument conceptual framework, we propose two tools--a PRO concept taxonomy and a PRO instrument hierarchy. FDA's draft guidance on patient reported outcome (PRO) measures states that a clear description of the conceptual framework of an instrument is useful for evaluating its adequacy to support a treatment benefit claim for use in product labeling the draft guidance, however does not propose tools for establishing or evaluating a PRO instrument's conceptual framework. We draw from our review of PRO concepts and instruments that appear in prescription drug labeling approved in the United States from 1997 to 2007. We propose taxonomy terms that define relationships between PRO concepts, including "family,"compound concept," and "singular concept." Based on the range of complexity represented by the concepts, as defined by the taxonomy, we propose nine instrument orders for PRO measurement. The nine orders range from individual event counts to multi-item, multiscale instruments. This analysis of PRO concepts and instruments illustrates that the taxonomy and hierarchy are applicable to PRO concepts across a wide range of therapeutic areas and provide a basis for defining the instrument conceptual framework complexity. Although the utility of these tools in the drug development, review, and approval processes has not yet been demonstrated, these tools could be useful to improve communication and enhance efficiency in the instrument development and review process.

  3. 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.

  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 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

  5. 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

  6. 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.

  7. "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.

  8. Use of Molecular Tools to Identify Patients With Indolent Breast Cancers With Ultralow Risk Over 2 Decades.

    PubMed

    Esserman, Laura J; Yau, Christina; Thompson, Carlie K; van 't Veer, Laura J; Borowsky, Alexander D; Hoadley, Katherine A; Tobin, Nicholas P; Nordenskjöld, Bo; Fornander, Tommy; Stål, Olle; Benz, Christopher C; Lindström, Linda S

    2017-06-29

    The frequency of cancers with indolent behavior has increased with screening. Better tools to identify indolent tumors are needed to avoid overtreatment. To determine if a multigene classifier is associated with indolent behavior of invasive breast cancers in women followed for 2 decades. This is a secondary analysis of a randomized clinical trial of tamoxifen vs no systemic therapy, with more than 20-year follow-up. An indolent threshold (ultralow risk) of the US Food and Drug Administration-cleared MammaPrint 70-gene expression score was established above which no breast cancer deaths occurred after 15 years in the absence of systemic therapy. Immunohistochemical markers (n = 727 women) and Agilent microarrays, for MammaPrint risk scoring (n = 652 women), were performed from formalin-fixed paraffin-embedded primary tumor blocks. Participants were postmenopausal women with clinically detected node-negative breast cancers treated with mastectomy or lumpectomy and radiation enrolled in the Stockholm tamoxifen (STO-3) trial, 1976 to 1990. After 2 years of tamoxifen vs no systemic therapy, regardless of hormone receptor status, patients without relapse who reconsented were further randomized to 3 additional years or none. Breast cancer-specific survival assessed by Kaplan-Meier analyses and multivariate Cox proportional hazard modeling, adjusted for treatment, patient age, year of diagnosis, tumor size, grade, hormone receptors, and ERBB2/HER2 and Ki67 status. In this secondary analysis of node-negative postmenopausal women, conducted in the era before mammography screening, among the 652 women with MammaPrint scoring available (median age, 62.8 years of age), 377 (58%) and 275 (42%) were MammaPrint low and high risk, respectively, while 98 (15%) were ultralow risk. At 20 years, women with 70-gene high and low tumors but not ultralow tumors had a significantly higher risk of disease-specific death compared with ultralow-risk patients by Cox analysis (hazard

  9. 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

  10. 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

  11. 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...

  12. 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...

  13. 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

  14. 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.

  15. 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.

  16. Geochemical Tools and Paleoclimate Clues: Multi-Molecular and Isotopic Investigations of Tropical Marine Sediments and Alpine Ice

    DTIC Science & Technology

    2006-02-01

    circulation. Marine biomarkers, such as sterols and phytol, were used to reconstruct productivity in the Peru Margin upwelling zone, where...hydrogen isotopic information embedded in plant wax biomarkers represents a valuable for tool for reconstructing past climate states. In Chapter 3, SBSE...local or regional biomarker inputs of the sort useful for paleoclimate reconstruction . In particular, biomass burning indicators appeared to be

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

    USDA-ARS?s Scientific Manuscript database

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

    USDA-ARS?s Scientific Manuscript database

    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...

  19. 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.

  20. 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.

  1. 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.

  2. CRISPR/Cas9: molecular tool for gene therapy to target genome and epigenome in the treatment of lung cancer.

    PubMed

    Sachdeva, M; Sachdeva, N; Pal, M; Gupta, N; Khan, I A; Majumdar, M; Tiwari, A

    2015-11-01

    Although varied drugs and therapies have been developed for lung cancer treatment, in the past 5 years overall survival rates have not improved much. It has also been reported that lung cancer is diagnosed in most of the patients when it is already in the advanced stages with heterogeneous tumors where single therapy is mostly ineffective. A combination of therapies are being administered and specific genes in specific tissues are targeted while protecting normal cell, but most of the therapies face drawbacks for the development of resistance against them and tumor progression. Therefore, therapeutic implications for various therapies need to be complemented by divergent strategies. This review frames utilization of CRISPR/Cas9 for molecular targeted gene therapy leading to long-term repression and activation or inhibition of molecular targets linked to lung cancer, avoiding the cycles of therapy.

  3. MelanomaDB: A Web Tool for Integrative Analysis of Melanoma Genomic Information to Identify Disease-Associated Molecular Pathways

    PubMed Central

    Trevarton, Alexander J.; Mann, Michael B.; Knapp, Christoph; Araki, Hiromitsu; Wren, Jonathan D.; Stones-Havas, Steven; Black, Michael A.; Print, Cristin G.

    2013-01-01

    Despite on-going research, metastatic melanoma survival rates remain low and treatment options are limited. Researchers can now access a rapidly growing amount of molecular and clinical information about melanoma. This information is becoming difficult to assemble and interpret due to its dispersed nature, yet as it grows it becomes increasingly valuable for understanding melanoma. Integration of this information into a comprehensive resource to aid rational experimental design and patient stratification is needed. As an initial step in this direction, we have assembled a web-accessible melanoma database, MelanomaDB, which incorporates clinical and molecular data from publically available sources, which will be regularly updated as new information becomes available. This database allows complex links to be drawn between many different aspects of melanoma biology: genetic changes (e.g., mutations) in individual melanomas revealed by DNA sequencing, associations between gene expression and patient survival, data concerning drug targets, biomarkers, druggability, and clinical trials, as well as our own statistical analysis of relationships between molecular pathways and clinical parameters that have been produced using these data sets. The database is freely available at http://genesetdb.auckland.ac.nz/melanomadb/about.html. A subset of the information in the database can also be accessed through a freely available web application in the Illumina genomic cloud computing platform BaseSpace at http://www.biomatters.com/apps/melanoma-profiler-for-research. The MelanomaDB database illustrates dysregulation of specific signaling pathways across 310 exome-sequenced melanomas and in individual tumors and identifies the distribution of somatic variants in melanoma. We suggest that MelanomaDB can provide a context in which to interpret the tumor molecular profiles of individual melanoma patients relative to biological information and available drug therapies. PMID:23875173

  4. Novel calibration tools and validation concepts for microarray-based platforms used in molecular diagnostics and food safety control.

    PubMed

    Brunner, C; Hoffmann, K; Thiele, T; Schedler, U; Jehle, H; Resch-Genger, U

    2015-04-01

    Commercial platforms consisting of ready-to-use microarrays printed with target-specific DNA probes, a microarray scanner, and software for data analysis are available for different applications in medical diagnostics and food analysis, detecting, e.g., viral and bacteriological DNA sequences. The transfer of these tools from basic research to routine analysis, their broad acceptance in regulated areas, and their use in medical practice requires suitable calibration tools for regular control of instrument performance in addition to internal assay controls. Here, we present the development of a novel assay-adapted calibration slide for a commercialized DNA-based assay platform, consisting of precisely arranged fluorescent areas of various intensities obtained by incorporating different concentrations of a "green" dye and a "red" dye in a polymer matrix. These dyes present "Cy3" and "Cy5" analogues with improved photostability, chosen based upon their spectroscopic properties closely matching those of common labels for the green and red channel of microarray scanners. This simple tool allows to efficiently and regularly assess and control the performance of the microarray scanner provided with the biochip platform and to compare different scanners. It will be eventually used as fluorescence intensity scale for referencing of assays results and to enhance the overall comparability of diagnostic tests.

  5. Relations between lipoprotein(a) concentrations, LPA genetic variants, and the risk of mortality in patients with established coronary heart disease: a molecular and genetic association study.

    PubMed

    Zewinger, Stephen; Kleber, Marcus E; Tragante, Vinicius; McCubrey, Raymond O; Schmidt, Amand F; Direk, Kenan; Laufs, Ulrich; Werner, Christian; Koenig, Wolfgang; Rothenbacher, Dietrich; Mons, Ute; Breitling, Lutz P; Brenner, Herrmann; Jennings, Richard T; Petrakis, Ioannis; Triem, Sarah; Klug, Mira; Filips, Alexandra; Blankenberg, Stefan; Waldeyer, Christoph; Sinning, Christoph; Schnabel, Renate B; Lackner, Karl J; Vlachopoulou, Efthymia; Nygård, Ottar; Svingen, Gard Frodahl Tveitevåg; Pedersen, Eva Ringdal; Tell, Grethe S; Sinisalo, Juha; Nieminen, Markku S; Laaksonen, Reijo; Trompet, Stella; Smit, Roelof A J; Sattar, Naveed; Jukema, J Wouter; Groesdonk, Heinrich V; Delgado, Graciela; Stojakovic, Tatjana; Pilbrow, Anna P; Cameron, Vicky A; Richards, A Mark; Doughty, Robert N; Gong, Yan; Cooper-DeHoff, Rhonda; Johnson, Julie; Scholz, Markus; Beutner, Frank; Thiery, Joachim; Smith, J Gustav; Vilmundarson, Ragnar O; McPherson, Ruth; Stewart, Alexandre F R; Cresci, Sharon; Lenzini, Petra A; Spertus, John A; Olivieri, Oliviero; Girelli, Domenico; Martinelli, Nicola I; Leiherer, Andreas; Saely, Christoph H; Drexel, Heinz; Mündlein, Axel; Braund, Peter S; Nelson, Christopher P; Samani, Nilesh J; Kofink, Daniel; Hoefer, Imo E; Pasterkamp, Gerard; Quyyumi, Arshed A; Ko, Yi-An; Hartiala, Jaana A; Allayee, Hooman; Tang, W H Wilson; Hazen, Stanley L; Eriksson, Niclas; Held, Claes; Hagström, Emil; Wallentin, Lars; Åkerblom, Axel; Siegbahn, Agneta; Karp, Igor; Labos, Christopher; Pilote, Louise; Engert, James C; Brophy, James M; Thanassoulis, George; Bogaty, Peter; Szczeklik, Wojciech; Kaczor, Marcin; Sanak, Marek; Virani, Salim S; Ballantyne, Christie M; Lee, Vei-Vei; Boerwinkle, Eric; Holmes, Michael V; Horne, Benjamin D; Hingorani, Aroon; Asselbergs, Folkert W; Patel, Riyaz S; Krämer, Bernhard K; Scharnagl, Hubert; Fliser, Danilo; März, Winfried; Speer, Thimoteus

    2017-07-01

    Lipoprotein(a) concentrations in plasma are associated with cardiovascular risk in the general population. Whether lipoprotein(a) concentrations or LPA genetic variants predict long-term mortality in patients with established coronary heart disease remains less clear. We obtained data from 3313 patients with established coronary heart disease in the Ludwigshafen Risk and Cardiovascular Health (LURIC) study. We tested associations of tertiles of lipoprotein(a) concentration in plasma and two LPA single-nucleotide polymorphisms ([SNPs] rs10455872 and rs3798220) with all-cause mortality and cardiovascular mortality by Cox regression analysis and with severity of disease by generalised linear modelling, with and without adjustment for age, sex, diabetes diagnosis, systolic blood pressure, BMI, smoking status, estimated glomerular filtration rate, LDL-cholesterol concentration, and use of lipid-lowering therapy. Results for plasma lipoprotein(a) concentrations were validated in five independent studies involving 10 195 patients with established coronary heart disease. Results for genetic associations were replicated through large-scale collaborative analysis in the GENIUS-CHD consortium, comprising 106 353 patients with established coronary heart disease and 19 332 deaths in 22 studies or cohorts. The median follow-up was 9·9 years. Increased severity of coronary heart disease was associated with lipoprotein(a) concentrations in plasma in the highest tertile (adjusted hazard radio [HR] 1·44, 95% CI 1·14-1·83) and the presence of either LPA SNP (1·88, 1·40-2·53). No associations were found in LURIC with all-cause mortality (highest tertile of lipoprotein(a) concentration in plasma 0·95, 0·81-1·11 and either LPA SNP 1·10, 0·92-1·31) or cardiovascular mortality (0·99, 0·81-1·2 and 1·13, 0·90-1·40, respectively) or in the validation studies. In patients with prevalent coronary heart disease, lipoprotein(a) concentrations and genetic variants showed

  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. A method to compare the performance of two molecular diagnostic tools in the absence of a gold standard.

    PubMed

    Xue, Xiaonan; Oktay, Maja; Goswami, Sumanta; Kim, Mimi Y

    2017-01-01

    The paper is motivated by the problem of comparing the accuracy of two molecular tests in detecting genetic mutations in tumor samples when there is no gold standard test. Commonly used sequencing methods require a large number of tumor cells in the tumor sample and the proportion of tumor cells with mutation positivity to be above a threshold level whereas new tests aim to reduce the requirement for number of tumor cells and the threshold level. A new latent class model is proposed to compare these two tests in which a random variable is used to represent the unobserved proportion of mutation positivity so that these two tests are conditionally dependent; furthermore, an independent random variable is included to address measurement error associated with the reading from each test, while existing latent class models often assume conditional independence and do not allow measurement error. In addition, methods for calculating the sample size for a study that is sufficiently powered to compare the accuracy of two molecular tests are proposed and compared. The proposed methods are then applied to a study which aims to compare two molecular tests for detecting EGFR mutations in lung cancer patients.

  8. 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

  9. 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.

  10. Practical benefits of knowing the enemy: modern molecular tools for diagnosing the etiology of bacterial diseases and understanding the taxonomy and diversity of plant-pathogenic bacteria.

    PubMed

    Bull, Carolee T; Koike, Steven T

    2015-01-01

    Knowing the identity of bacterial plant pathogens is essential to strategic and sustainable disease management in agricultural systems. This knowledge is critical for growers, diagnosticians, extension agents, and others dealing with crops. However, such identifications are linked to bacterial taxonomy, a complicated and changing discipline that depends on methods and information that are often not used by those who are diagnosing field problems. Modern molecular tools for fingerprinting and sequencing allow for pathogen identification in the absence of distinguishing or conveniently tested phenotypic characteristics. These methods are also useful in studying the etiology and epidemiology of phytopathogenic bacteria from epidemics, as was done in numerous studies conducted in California's Salinas Valley. Multilocus and whole-genome sequence analyses are becoming the cornerstones of studies of microbial diversity and bacterial taxonomy. Whole-genome sequence analysis needs to become adequately accessible, automated, and affordable in order to be used routinely for identification and epidemiology. The power of molecular tools in accurately identifying bacterial pathogenesis is therefore of value to the farmer, diagnostician, phytobacteriologist, and taxonomist.

  11. 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.

  12. Recent progress and challenges in population genetics of polyploid organisms: an overview of current state-of-the-art molecular and statistical tools.

    PubMed

    Dufresne, France; Stift, Marc; Vergilino, Roland; Mable, Barbara K

    2014-01-01

    Despite the importance of polyploidy and the increasing availability of new genomic data, there remain important gaps in our knowledge of polyploid population genetics. These gaps arise from the complex nature of polyploid data (e.g. multiple alleles and loci, mixed inheritance patterns, association between ploidy and mating system variation). Furthermore, many of the standard tools for population genetics that have been developed for diploids are often not feasible for polyploids. This review aims to provide an overview of the state-of-the-art in polyploid population genetics and to identify the main areas where further development of molecular techniques and statistical theory is required. We review commonly used molecular tools (amplified fragment length polymorphism, microsatellites, Sanger sequencing, next-generation sequencing and derived technologies) and their challenges associated with their use in polyploid populations: that is, allele dosage determination, null alleles, difficulty of distinguishing orthologues from paralogues and copy number variation. In addition, we review the approaches that have been used for population genetic analysis in polyploids and their specific problems. These problems are in most cases directly associated with dosage uncertainty and the problem of inferring allele frequencies and assumptions regarding inheritance. This leads us to conclude that for advancing the field of polyploid population genetics, most priority should be given to development of new molecular approaches that allow efficient dosage determination, and to further development of analytical approaches to circumvent dosage uncertainty and to accommodate 'flexible' modes of inheritance. In addition, there is a need for more simulation-based studies that test what kinds of biases could result from both existing and novel approaches. © 2013 John Wiley & Sons Ltd.

  13. 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…

  14. 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…

  15. Evaluation of Whole Genome Mapping as a Fast and Automated Molecular Epidemiological Tool for the Study of Cronobacter spp. in Powdered Infant Formula Processing Facilities.

    PubMed

    Tang, Yanjie; Rasschaert, Geertrui; Yu, Liping; Chilton, Claire; Baert, Leen

    2017-09-01

    Cronobacter has been identified as the causative agent of outbreaks or sporadic cases of meningitis, necrotizing enterocolitis, and septicemia associated with powdered infant formula. Food processing environments may provide a possible contamination route. The purpose of this study was to evaluate whole genome mapping (WGM) as a fast and automated molecular epidemiological method for characterizing Cronobacter spp. in the processing environment. This is the first study indicating the applicability of WGM to Cronobacter. WGM was compared with ribotyping, which is often used as an automated typing tool, and with pulsed-field gel electrophoresis, which is a well-known and highly discriminating tool that is also based on restriction site analysis. The comparison of the three tools was carried out on a subset of Cronobacter isolates collected from 2011 to 2014 through a monitoring program. The performance characteristics of WGM have not yet been described; therefore, in the current study its performance was evaluated based on five criteria: typeability, reproducibility, stability, epidemiological concordance, and the discrimination power. WGM was shown to produce typeable, reproducible, and stable results. With a similar cut-off of 98%, WGM was shown to have a discriminatory power equivalent to pulsed-field gel electrophoresis and higher than ribotyping. Future studies are needed to confirm the indicated cut-off level of 98%.

  16. 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

  17. 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.

  18. 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.

  19. 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.

  20. 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

  1. 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.

  2. Pump-Probe Fragmentation Action Spectroscopy: A Powerful Tool to Unravel Light-Induced Processes in Molecular Photocatalysts.

    PubMed

    Imanbaew, Dimitri; Lang, Johannes; Gelin, Maxim F; Kaufhold, Simon; Pfeffer, Michael G; Rau, Sven; Riehn, Christoph

    2017-05-08

    We present a proof of concept that ultrafast dynamics combined with photochemical stability information of molecular photocatalysts can be acquired by electrospray ionization mass spectrometry combined with time-resolved femtosecond laser spectroscopy in an ion trap. This pump-probe "fragmentation action spectroscopy" gives straightforward access to information that usually requires high purity compounds and great experimental efforts. Results of gas-phase studies on the electronic dynamics of two supramolecular photocatalysts compare well to previous findings in solution and give further evidence for a directed electron transfer, a key process for photocatalytic hydrogen generation. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Molecular karyotyping as a relevant diagnostic tool in children with growth retardation with Silver-Russell features.

    PubMed

    Spengler, Sabrina; Begemann, Matthias; Ortiz Brüchle, Nadina; Baudis, Michael; Denecke, Bernd; Kroisel, Peter Michael; Oehl-Jaschkowitz, Barbara; Schulze, Bernd; Raabe-Meyer, Gisela; Spaich, Christiane; Blümel, Peter; Jauch, Anna; Moog, Ute; Zerres, Klaus; Eggermann, Thomas

    2012-11-01

    To determine the contribution of submicroscopic chromosomal imbalances to the etiology of Silver-Russell syndrome (SRS) and SRS-like phenotypes. We performed molecular karyotyping in 41 patients with SRS or SRS-like features without known chromosome 7 and 11 defects using the Affymetrix SNP Array 6.0 system (Affymetrix, High Wycombe, United Kingdom). In 8 patients, pathogenic copy number variations with sizes ranging from 672 kb to 9.158 Mb were identified. The deletions in 1q21, 15q26, 17p13, and 22q11 were associated with known microdeletion syndromes with overlapping features with SRS. The duplications in 22q13 and Xq25q27 represent unique novel copy number variations but have an obvious influence on the phenotype. In 5 additional patients, the pathogenetic relevance of the detected variants remained unclear. Pathogenic submicroscopic imbalances were detectable in a significant proportion of patients with short stature and features reminiscent of SRS. Therefore, molecular karyotyping should be implemented in routine diagnostics for growth-retarded patients with even slight dysmorphisms suggestive for SRS. Copyright © 2012 Mosby, Inc. All rights reserved.

  4. 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.

  5. Exploration of NVE classical trajectories as a tool for molecular crystal structure prediction, with tests on ice polymorphs.

    PubMed

    Buch, V; Martonák, R; Parrinello, M

    2006-05-28

    Following an initial Communication [Buch et al., J. Chem. Phys. 123, 051108 (2005)], a new molecular-dynamics-based approach is explored to search for candidate crystal structures of molecular solids corresponding to minima of the enthalpy. The approach is based on the observation of phase transitions in an artificial periodic system with a small unit cell and relies on the existence of an optimal energy range for observing freezing to low-lying minima in the course of classical trajectories. Tests are carried out for O structures of nine H2O-ice polymorphs. NVE trajectories for a range of preimposed box shapes display freezing to the different crystal polymorphs whenever the box dimensions approximate roughly the appropriate unit cell; the exception is ice II for which freezing requires unit cell dimensions close to the correct ones. In an alternate version of the algorithm, an initial box shape is picked at random and subsequently readjusted at short trajectory intervals by enthalpy minimization. Tests reveal the existence of ice forms which are "difficult" and "easy" to locate in this way. The former include ice IV, which is also difficult to crystallize experimentally from the liquid, and ice II, which does not interface with the liquid in the phase diagram. On the other hand, the latter crystal search procedure located successfully the remaining seven ice polymorphs, including ice V, which corresponds to the most complicated structure of all ice phases, with a monoclinic cell of 28 molecules.

  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 Central

    Hanna, Rachid; von Tiedemann, Andreas

    2010-01-01

    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. PMID:20838883

  7. 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.

  8. 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

  9. 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.

  10. 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.

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

    PubMed Central

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

    2011-01-01

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

  12. New tools for the investigations of Neuro-AIDS at a molecular level: The potential role of data-mining.

    PubMed

    Orlando, Bruno; Giacomelli, Luca; Chiappelli, Francesco; Barkhordarian, André

    2013-01-01

    Cognitive impairment represents the most significant and devastating neurological complication associated with HIV infection. Despite recent advances in our knowledge of the clinical features, pathogenesis, and molecular aspects of HIV-related dementia, current diagnostic strategies are associated with significant limitations. It has been suggested that the use of some biomarkers may assist researchers and clinicians in predicting the onset of the disease process and in evaluating the effects of new therapies. However, the large number of chemicals and metabolic pathways involved in the pathogenesis of neurodegeneration, warrants the development of novel approaches to integrate this huge amount of data. The contribution of theoretical disciplines, such as bioinformatics and data-mining, may be useful for testing new hypotheses in diagnosis and patient-centered treatment interventions.

  13. An FDA bioinformatics tool for microbial genomics research on molecular characterization of bacterial foodborne pathogens using microarrays.

    PubMed

    Fang, Hong; Xu, Joshua; Ding, Don; Jackson, Scott A; Patel, Isha R; Frye, Jonathan G; Zou, Wen; Nayak, Rajesh; Foley, Steven; Chen, James; Su, Zhenqiang; Ye, Yanbin; Turner, Steve; Harris, Steve; Zhou, Guangxu; Cerniglia, Carl; Tong, Weida

    2010-10-07

    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 a genomics tool, ArrayTrack™, which provides extensive functionalities to manage, analyze, and interpret genomic data for mammalian species. ArrayTrack™ has been widely adopted by the research community and used for pharmacogenomics data review in the FDA's Voluntary Genomics Data Submission program. ArrayTrack™ has been extended to manage and analyze genomics data from bacterial pathogens of human, animal, and food origin. It was populated with bioinformatics data from public databases such as NCBI, Swiss-Prot, KEGG Pathway, and Gene Ontology to facilitate pathogen detection and characterization. ArrayTrack™'s data processing and visualization tools were enhanced with analysis capabilities designed specifically for microbial genomics including flag-based hierarchical clustering analysis (HCA), flag concordance heat maps, and mixed scatter plots. These specific functionalities were evaluated on data generated from a custom Affymetrix array (FDA-ECSG) previously developed within the FDA. The FDA-ECSG array represents 32 complete genomes of Escherichia coli and Shigella. The new functions were also used to analyze microarray data focusing on antimicrobial resistance genes from Salmonella isolates in a poultry production environment using a universal antimicrobial resistance microarray developed by the United States Department of Agriculture (USDA). The application of ArrayTrack™ to different microarray platforms demonstrates its utility in microbial genomics research, and thus will improve the capabilities of the FDA to rapidly identify foodborne bacteria and their genetic traits (e.g., antimicrobial resistance, virulence, etc.) during outbreak investigations. ArrayTrack™ is free to use and available to public, private, and academic researchers at

  14. Molecular Phylogeny and Taxonomy of a New Freshwater Hymenostomatid from Northeastern China, with the Establishment of a New Genus Anteglaucoma gen. n. (Protista, Ciliophora, Oligohymenophorea).

    PubMed

    Pan, Xuming; Shi, Zihan; Wang, Chundi; Bourland, William A; Chen, Ying; Song, Weibo

    2017-09-01

    The morphology, infraciliature and SSU rDNA sequence of a new freshwater hymenostomatid ciliate, Anteglaucoma harbinensis gen. nov., spec. nov., collected from a farmland pond in Harbin, China, were investigated. The new genus Anteglaucoma is characterized as follows: small to medium-sized Glaucomidae with oral apparatus in anterior one-third of cell; paroral membrane composed of almost longitudinally arranged dikinetids; three adoral membranelles nearly equal in length and arranged almost longitudinally in parallel; silverline pattern tetrahymenid. The improved diagnosis of family Glaucomidae Corliss 1971 is provided based on the previous and present work. The type species Anteglaucoma harbinensis spec. nov. is defined by having 32-35 somatic kineties; four or five postoral kineties; membranelle 1 and membranelle 2 having five or six kinetosomal rows, membranelle 3 having three kinetosomal rows; single macronuclear nodule; contractile vacuole on average 15% from posterior body end; locomotion characterized by crawling with a rather hectic jerking motion; freshwater habitat. Phylogenetic analyses show that Anteglaucoma clusters in the family Glaucomidae and groups with the genera Glaucoma. The molecular and morphological data indicate that Glaucomidae is related to the family Bromeliophryidae in the phylogenetic trees. © 2016 The Author(s) Journal of Eukaryotic Microbiology © 2016 International Society of Protistologists.

  15. Molecular breeding

    USDA-ARS?s Scientific Manuscript database

    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...

  16. Establishing effective simulation protocols for beta- and alpha/beta-peptides. II. Molecular mechanical (MM) model for a cyclic beta-residue.

    PubMed

    Zhu, Xiao; Koenig, Peter; Gellman, Samuel H; Yethiraj, Arun; Cui, Qiang

    2008-05-01

    All-atom molecular mechanical (MM) force field parameters are developed for a cyclic beta-amino acid, amino-cyclo-pentane-carboxylic acid (ACPC), using a multi-objective evolutionary algorithm. The MM model is benchmarked using several short, ACPC-containing alpha/beta-peptides in water and methanol with SCC-DFTB (self consistent charge-density functional tight binding)/MM simulations as the reference. Satisfactory agreements are found between the MM and SCC-DFTB/MM results regarding the distribution of key dihedral angles for the tetra-alpha/beta-peptide in water. For the octa-alpha/beta-peptide in methanol, the MM and SCC-DFTB/MM simulations predict the 11- and 14/15-helical form as the more stable conformation, respectively; however, the two helical forms are very close in energy (2-4 kcal/mol) at both theoretical levels, which is also the conclusion from recent NMR experiments. As the first application, the MM model is applied to an alpha/beta-pentadeca-peptide in water with both explicit and implicit solvent models. The stability of the peptide is sensitive to the starting configuration in the explicit solvent simulations due to their limited length ( approximately 10-40 ns). Multiple ( approximately 20 x 20 ns) implicit solvent simulations consistently show that the 14/15-helix is the predominant conformation of this peptide, although substantially different conformations are also accessible. The calculated nuclear Overhauser effect (NOE) values averaged over different trajectories are consistent with experimental data, which emphasizes the importance of considering conformational heterogeneity in such comparisons for highly dynamical peptides.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  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. 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

  4. 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.

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

    PubMed

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

    2012-11-01

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

  6. Application of data science tools to quantify and distinguish between structures and models in molecular dynamics datasets.

    PubMed

    Kalidindi, Surya R; Gomberg, Joshua A; Trautt, Zachary T; Becker, Chandler A

    2015-08-28

    Structure quantification is key to successful mining and extraction of core materials knowledge from both multiscale simulations as well as multiscale experiments. The main challenge stems from the need to transform the inherently high dimensional representations demanded by the rich hierarchical material structure into useful, high value, low dimensional representations. In this paper, we develop and demonstrate the merits of a data-driven approach for addressing this challenge at the atomic scale. The approach presented here is built on prior successes demonstrated for mesoscale representations of material internal structure, and involves three main steps: (i) digital representation of the material structure, (ii) extraction of a comprehensive set of structure measures using the framework of n-point spatial correlations, and (iii) identification of data-driven low dimensional measures using principal component analyses. These novel protocols, applied on an ensemble of structure datasets output from molecular dynamics (MD) simulations, have successfully classified the datasets based on several model input parameters such as the interatomic potential and the temperature used in the MD simulations.

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

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

  8. 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

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

    PubMed

    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. 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.

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

    PubMed

    Dumonceaux, Tim J; Green, Margaret; Hammond, Christine; Perez, Edel; Olivier, Chrystel

    2014-01-01

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

  11. 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

  12. 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