WorldWideScience

Sample records for gene wiki community

  1. Wikidata as a semantic framework for the Gene Wiki initiative.

    Science.gov (United States)

    Burgstaller-Muehlbacher, Sebastian; Waagmeester, Andra; Mitraka, Elvira; Turner, Julia; Putman, Tim; Leong, Justin; Naik, Chinmay; Pavlidis, Paul; Schriml, Lynn; Good, Benjamin M; Su, Andrew I

    2016-01-01

    Open biological data are distributed over many resources making them challenging to integrate, to update and to disseminate quickly. Wikidata is a growing, open community database which can serve this purpose and also provides tight integration with Wikipedia. In order to improve the state of biological data, facilitate data management and dissemination, we imported all human and mouse genes, and all human and mouse proteins into Wikidata. In total, 59,721 human genes and 73,355 mouse genes have been imported from NCBI and 27,306 human proteins and 16,728 mouse proteins have been imported from the Swissprot subset of UniProt. As Wikidata is open and can be edited by anybody, our corpus of imported data serves as the starting point for integration of further data by scientists, the Wikidata community and citizen scientists alike. The first use case for these data is to populate Wikipedia Gene Wiki infoboxes directly from Wikidata with the data integrated above. This enables immediate updates of the Gene Wiki infoboxes as soon as the data in Wikidata are modified. Although Gene Wiki pages are currently only on the English language version of Wikipedia, the multilingual nature of Wikidata allows for usage of the data we imported in all 280 different language Wikipedias. Apart from the Gene Wiki infobox use case, a SPARQL endpoint and exporting functionality to several standard formats (e.g. JSON, XML) enable use of the data by scientists. In summary, we created a fully open and extensible data resource for human and mouse molecular biology and biochemistry data. This resource enriches all the Wikipedias with structured information and serves as a new linking hub for the biological semantic web. Database URL: https://www.wikidata.org/. © The Author(s) 2016. Published by Oxford University Press.

  2. Using Wikis to Develop Collaborative Communities in an Environmental Chemistry Course

    Science.gov (United States)

    Pence, Laura E.; Pence, Harry E.

    2015-01-01

    Group construction of wikis in an environmental chemistry course provided an effective framework for students to develop and to manage collaborative communities, characterized by interactive projects designed to deepen learning. A sequence of assignments facilitated improvement of the students' wiki construction and editing skills and these…

  3. ICG: a wiki-driven knowledgebase of internal control genes for RT-qPCR normalization.

    Science.gov (United States)

    Sang, Jian; Wang, Zhennan; Li, Man; Cao, Jiabao; Niu, Guangyi; Xia, Lin; Zou, Dong; Wang, Fan; Xu, Xingjian; Han, Xiaojiao; Fan, Jinqi; Yang, Ye; Zuo, Wanzhu; Zhang, Yang; Zhao, Wenming; Bao, Yiming; Xiao, Jingfa; Hu, Songnian; Hao, Lili; Zhang, Zhang

    2018-01-04

    Real-time quantitative PCR (RT-qPCR) has become a widely used method for accurate expression profiling of targeted mRNA and ncRNA. Selection of appropriate internal control genes for RT-qPCR normalization is an elementary prerequisite for reliable expression measurement. Here, we present ICG (http://icg.big.ac.cn), a wiki-driven knowledgebase for community curation of experimentally validated internal control genes as well as their associated experimental conditions. Unlike extant related databases that focus on qPCR primers in model organisms (mainly human and mouse), ICG features harnessing collective intelligence in community integration of internal control genes for a variety of species. Specifically, it integrates a comprehensive collection of more than 750 internal control genes for 73 animals, 115 plants, 12 fungi and 9 bacteria, and incorporates detailed information on recommended application scenarios corresponding to specific experimental conditions, which, collectively, are of great help for researchers to adopt appropriate internal control genes for their own experiments. Taken together, ICG serves as a publicly editable and open-content encyclopaedia of internal control genes and accordingly bears broad utility for reliable RT-qPCR normalization and gene expression characterization in both model and non-model organisms. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  4. Community-based Ontology Development, Annotation and Discussion with MediaWiki extension Ontokiwi and Ontokiwi-based Ontobedia

    Science.gov (United States)

    Ong, Edison; He, Yongqun

    2016-01-01

    Hundreds of biological and biomedical ontologies have been developed to support data standardization, integration and analysis. Although ontologies are typically developed for community usage, community efforts in ontology development are limited. To support ontology visualization, distribution, and community-based annotation and development, we have developed Ontokiwi, an ontology extension to the MediaWiki software. Ontokiwi displays hierarchical classes and ontological axioms. Ontology classes and axioms can be edited and added using Ontokiwi form or MediaWiki source editor. Ontokiwi also inherits MediaWiki features such as Wikitext editing and version control. Based on the Ontokiwi/MediaWiki software package, we have developed Ontobedia, which targets to support community-based development and annotations of biological and biomedical ontologies. As demonstrations, we have loaded the Ontology of Adverse Events (OAE) and the Cell Line Ontology (CLO) into Ontobedia. Our studies showed that Ontobedia was able to achieve expected Ontokiwi features. PMID:27570653

  5. Technical Evaluation Report 27: Educational Wikis: Features and selection criteria

    Directory of Open Access Journals (Sweden)

    Jim Rudolph

    2004-04-01

    Full Text Available This report discusses the educational uses of the ‘wiki,’ an increasingly popular approach to online community development. Wikis are defined and compared with ‘blogging’ methods; characteristics of major wiki engines are described; and wiki features and selection criteria are examined.

  6. RTI Wiki

    Data.gov (United States)

    National Aeronautics and Space Administration — Under files is the link to the RTI wiki. Research Test and Integration (RTI) focuses on the development of long term plans for test and integration opportunities for...

  7. Integrating Wikis as Educational Tools for the Development of a Community of Inquiry

    Science.gov (United States)

    Eteokleous, Nikleia; Ktoridou, Despo; Orphanou, Maria

    2014-01-01

    This article describes a study that attempted to evaluate the integration of wikis as an educational tool in successfully achieving the learning objectives of a fifth-grade linguistics and literature course. A mixed-method approach was employed--data were collected via questionnaires, reflective journals, observations, and interviews. The results…

  8. "The Isle Is Full of Noises": Using Wiki Software to Establish a Discourse Community in a Shakespeare Classroom

    Science.gov (United States)

    Farabaugh, Robin

    2007-01-01

    For the last four semesters my courses in Shakespeare have used QwikiWiki and MediaWiki, two versions of the wiki software, for writing exercises and directed reflection on language--including both by the students about Shakespeare's language, and by the teacher/researcher regarding the students' performance in "Writing to Learn". In experimenting…

  9. Wikis, Blogs, & More, Oh My!

    Science.gov (United States)

    Villano, Matt

    2008-01-01

    Everyone seems to have a different definition for "Web 2.0," but most people agree the phrase describes a second generation of web-based communities and hosted services that aim to facilitate creativity, collaboration, and sharing between users. Technically speaking, these new technologies include blogs, wikis, folksonomies…

  10. Wikis in Libraries

    Directory of Open Access Journals (Sweden)

    Matthew Bejune

    2007-09-01

    Full Text Available Wikis have recently been adopted to support a variety of collaborative activities within libraries. This article and its companion wiki, LibraryWikis (http://librarywikis.pbwiki.com/, seek to document the phenomenon of wikis in libraries. This subject is considered within the framework of computer-supported cooperative work (CSCW. The author identified thirty-three library wikis and developed a classification schema with four categories: (1 collaboration among libraries (45.7 percent; (2 collaboration among library staff (31.4 percent; (3 collaboration among library staff and patrons (14.3 percent; and (4 collaboration among patrons (8.6 percent. Examples of library wikis are presented within the article, as is a discussion for why wikis are primarily utilized within categories I and II and not within categories III and IV. It is clear that wikis have great utility within libraries, and the author urges further application of wikis in libraries.

  11. WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research.

    Science.gov (United States)

    Slenter, Denise N; Kutmon, Martina; Hanspers, Kristina; Riutta, Anders; Windsor, Jacob; Nunes, Nuno; Mélius, Jonathan; Cirillo, Elisa; Coort, Susan L; Digles, Daniela; Ehrhart, Friederike; Giesbertz, Pieter; Kalafati, Marianthi; Martens, Marvin; Miller, Ryan; Nishida, Kozo; Rieswijk, Linda; Waagmeester, Andra; Eijssen, Lars M T; Evelo, Chris T; Pico, Alexander R; Willighagen, Egon L

    2018-01-04

    WikiPathways (wikipathways.org) captures the collective knowledge represented in biological pathways. By providing a database in a curated, machine readable way, omics data analysis and visualization is enabled. WikiPathways and other pathway databases are used to analyze experimental data by research groups in many fields. Due to the open and collaborative nature of the WikiPathways platform, our content keeps growing and is getting more accurate, making WikiPathways a reliable and rich pathway database. Previously, however, the focus was primarily on genes and proteins, leaving many metabolites with only limited annotation. Recent curation efforts focused on improving the annotation of metabolism and metabolic pathways by associating unmapped metabolites with database identifiers and providing more detailed interaction knowledge. Here, we report the outcomes of the continued growth and curation efforts, such as a doubling of the number of annotated metabolite nodes in WikiPathways. Furthermore, we introduce an OpenAPI documentation of our web services and the FAIR (Findable, Accessible, Interoperable and Reusable) annotation of resources to increase the interoperability of the knowledge encoded in these pathways and experimental omics data. New search options, monthly downloads, more links to metabolite databases, and new portals make pathway knowledge more effortlessly accessible to individual researchers and research communities. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  12. Using Wikis in Academic Libraries

    Science.gov (United States)

    Kai-Wah Chu, Samuel

    2009-01-01

    This is an exploratory study investigating the use of wikis in academic libraries. Reasons for using and not using wikis, level of control exerted on wikis users and perceived benefits and costs of using wikis are the major areas examined. Sixty universities were selected to complete either survey 1 or survey 2, depending on their usage of wikis…

  13. The Zebrafish GenomeWiki: a crowdsourcing approach to connect the long tail for zebrafish gene annotation

    OpenAIRE

    Singh, Meghna; Bhartiya, Deeksha; Maini, Jayant; Sharma, Meenakshi; Singh, Angom Ramcharan; Kadarkaraisamy, Subburaj; Rana, Rajiv; Sabharwal, Ankit; Nanda, Srishti; Ramachandran, Aravindhakshan; Mittal, Ashish; Kapoor, Shruti; Sehgal, Paras; Asad, Zainab; Kaushik, Kriti

    2014-01-01

    A large repertoire of gene-centric data has been generated in the field of zebrafish biology. Although the bulk of these data are available in the public domain, most of them are not readily accessible or available in nonstandard formats. One major challenge is to unify and integrate these widely scattered data sources. We tested the hypothesis that active community participation could be a viable option to address this challenge. We present here our approach to create standards for assimilat...

  14. Document and author promotion strategies in the secure wiki model

    DEFF Research Database (Denmark)

    Lindberg, Kasper; Jensen, Christian D.

    2012-01-01

    Wiki systems form a subclass of the more general Open Collaborative Authoring Systems, where content is created by a user community. The ability of anyone to edit the content is, at the same time, their strength and their weakness. Anyone can write documents that improve the value of the wiki-system......, but this also means that anyone can introduce errors into documents, either by accident or on purpose. A security model for wiki-style authoring systems, called the Secure Wiki Model, has previously been proposed to address this problem. This model is designed to prevent corruption of good quality documents......, by limiting updates, to such documents, to users who have demonstrated their ability to produce documents of similar or better quality. While this security model prevents all user from editing all documents, it does respect the wiki philosophy by allowing any author who has produced documents of a certain...

  15. Collaborative trust evaluation for wiki security

    DEFF Research Database (Denmark)

    Lindberg, Kasper; Jensen, Christian D.

    2012-01-01

    Wiki systems form a subclass of the more general Open Collaborative Authoring Systems, where content is created and maintained by a user community. The ability of anyone to edit the content is, at the same time, their strength and their weakness. Anyone can write documents that improve the value...... of the wiki-system, but at the same time, anyone can also introduce errors into these documents, by accident or on purpose. A security model for wiki-style authoring systems has previously been proposed. This model is based on both static and dynamic document access controls that enforce a simple integrity......, but this is true for all soft security systems. We show that the system parameters can be tuned so that the amount of work required by malicious and colluding users to reach this level is well beyond most attackers' capabilities....

  16. Wiki Web Collaboration

    CERN Document Server

    Ebersbach, Anja; Heigl, Richard

    2006-01-01

    A book about wikis! That's what people need. Because with wiki technology, lots of people can freely work - gether - they can even generate very large works in the intellectual realm. See for yourself: Today, we still marvel at our massive church buildings, each c- structed over a period of centuries, requiring an immense amount of labor and often bearing the cultural stamp of all of the epochs during which it was created. Someone just has to begin by placing stone upon stone and motivate the people nearby to help out a bit. In places where such enthusiastic fellow men and women lend a hand an

  17. Medical Wikis Dedicated to Clinical Practice: A Systematic Review

    Science.gov (United States)

    Llorca, Guy; Letrilliart, Laurent

    2015-01-01

    Background Wikis may give clinician communities the opportunity to build knowledge relevant to their practice. The only previous study reviewing a set of health-related wikis, without specification of purpose or audience, globally showed a poor reliability. Objective Our aim was to review medical wiki websites dedicated to clinical practices. Methods We used Google in ten languages, PubMed, Embase, Lilacs, and Web of Science to identify websites. The review included wiki sites, accessible and operating, having a topic relevant for clinical medicine, targeting physicians or medical students. Wikis were described according to their purposes, platform, management, information framework, contributions, content, and activity. Purposes were classified as “encyclopedic” or “non-encyclopedic”. The information framework quality was assessed based on the Health On the Net (HONcode) principles for collaborative websites, with additional criteria related to users’ transparency and editorial policy. From a sample of five articles per wikis, we assessed the readability using the Flesch test and compared articles according to the wikis’ main purpose. Annual editorial activities were estimated using the Google engine. Results Among 25 wikis included, 11 aimed at building an encyclopedia, five a textbook, three lessons, two oncology protocols, one a single article, and three at reporting clinical cases. Sixteen wikis were specialized with specific themes or disciplines. Fifteen wikis were using MediaWiki software as-is, three were hosted by online wiki farms, and seven were purpose-built. Except for one MediaWiki-based site, only purpose-built platforms managed detailed user disclosures. The owners were ten organizations, six individuals, four private companies, two universities, two scientific societies, and one unknown. Among 21 open communities, 10 required users’ credentials to give editing rights. The median information framework quality score was 6 out of 16

  18. A Runyakitara Culture Wiki

    African Journals Online (AJOL)

    Frederick Iraki

    wiki as a tool for Runyakitara culture documentation, collaboration, sharing, ... collaboration in education and research are augmented by technology [2, 10, 11]; ... Runyakitara culture; and section 5 concludes and discusses future work. ..... material which reflects the Runyakitara culture, perspective, and reality; as compared.

  19. Using wikis to stimulate collaborative learning in two online health sciences courses.

    Science.gov (United States)

    Zitzelsberger, Hilde; Campbell, Karen A; Service, Dorothea; Sanchez, Otto

    2015-06-01

    The use of wiki technology fits well in courses that encourage constructive knowledge building and social learning by a community of learners. Pedagogically, wikis have attracted interest in higher education environments because they facilitate the collaborative processes required for developing student group assignments. This article describes a pilot project to assess the implementation of wikis in two online small- and mid-sized elective courses comprising nursing students in third- or fourth-year undergraduate levels within interdisciplinary health sciences courses. The need exists to further develop the pedagogical use of wiki environments before they can be expected to support collaboration among undergraduate nursing students. Adapting wiki implementation to suitable well-matched courses will make adaptation of wikis into nursing curricula more effective and may increase the chances that nursing students will hone the collaborative abilities that are essential in their future professional roles in communities of practice. Copyright 2015, SLACK Incorporated.

  20. Reassessing the Gravity’s Rainbow Pynchon Wiki: a new research paradigm?

    Directory of Open Access Journals (Sweden)

    Simon Peter Rowberry

    2012-07-01

    Full Text Available Since the 'Against the Day 'Wiki launched in October 2006, the Pynchon Wiki collection has received over twenty thousand edits, making it one of the largest, dedicated literary reference Wikis. One can now view and add annotations to all seven of Pynchon’s novels – only 'Slow Learner 'and his non-fiction remain 'sans 'Wiki -, and a loose community of over four hundred contributors have done so. This paper will assess the importance of the 'Gravity’s Rainbow 'Wiki in transforming understanding and interpretation through asking four different questions: does the Wiki count as a disruptive force in the Pynchon interpretive industry, who contributes to the Wiki, what types of contribution they make, and how do they exploit the hypertextual features on offer through the MediaWiki package. I will suggest that the Pynchon Wiki does not fully depart from old media forms of interpretation and remains fragmented in both community, resembling a symphony of soloists, and potential connections. This is a version of Web 2.0 synthesizing both Darcy DiNucci’s original dystopian vision of fragmentation (DiNucci and Tim O’Reilly’s utopian idea of harnessing ‘collective intelligence’ (O’Reilly.

  1. WikiD : A WikiEngine Supporting Structured Data

    CERN Multimedia

    CERN. Geneva; Young, Jeffrey

    2005-01-01

    Ward Cunningham describes a wiki as "the simplest online database that could possibly work". The cost of this simplicity is that wikis are generally limited to a single collection containing a single kind of record (viz. WikiMarkupLanguage records). WikiD extends the Wiki model to support multiple collections containing arbitrary schemas of XML records with minimal additional complexity. WikiD is essentially a lightweight framework combining: * Open-source implementations of various loosely-coupled open-standard protocols (e.g. OpenURL, SRW/U, SRW Update, OAI-PMH, RSS) * An open-source version-controlled database. * A set of bootstrap collections. * XSL Stylesheets to render collection-level open-standard protocol responses into HTML for human consumption. Automated processes can ignore the stylesheet reference and use the open-standard protocol responses directly. Possible applications for WikiD include collaborative maintenance of registries, thesauri, taxonomies, reviews, and documentation. In addition to ...

  2. Untangling knowledge creation and knowledge integration in enterprise wikis

    DEFF Research Database (Denmark)

    Beck, Roman; Rai, Arun; Fischbach, Kai

    2015-01-01

    A central challenge organizations face is how to build, store, and maintain knowledge over time. Enterprise wikis are community-based knowledge systems situated in an organizational context. These systems have the potential to play an important role in managing knowledge within organizations......, but the motivating factors that drive individuals to contribute their knowledge to these systems is not very well understood. We theorize that enterprise wiki initiatives require two separate and distinct types of knowledge-sharing behaviors to succeed: knowledge creation (KC) and knowledge integration (KI). We...... examine a Wiki initiative at a major German bank to untangle the motivating factors behind KC and KI. Our results suggest KC and KI are indeed two distinct behaviors, reconcile inconsistent findings from past studies on the role of motivational factors for knowledge sharing to establish shared electronic...

  3. Sites of participation: Wiki fandom and the case of Lostpedia

    Directory of Open Access Journals (Sweden)

    Jason Mittell

    2009-11-01

    Full Text Available This essay explores the award-winning fan site Lostpedia to examine how the wiki platform enables fan engagement, structures participation, and distinguishes between various forms of content, including canon, fanon, and parody. I write as a participant-observer, with extensive experience as a Lostpedia reader and editor. The article uses the "digital breadcrumbs" of wikis to trace the history of fan creativity, participation, game play, and debates within a shared site of community fan engagement. Using the Lostpedia site as a case study of fan praxis, the article highlights how issues like competing fandoms, copyright, and modes of discourse become manifest via the user-generated content of a fan wiki.

  4. EVA Wiki - Transforming Knowledge Management for EVA Flight Controllers and Instructors

    Science.gov (United States)

    Johnston, Stephanie S.; Alpert, Brian K.; Montalvo, Edwin James; Welsh, Lawrence Daren; Wray, Scott; Mavridis, Costa

    2016-01-01

    The EVA Wiki was recently implemented as the primary knowledge database to retain critical knowledge and skills in the EVA Operations group at NASA's Johnson Space Center by ensuring that information is recorded in a common, easy to search repository. Prior to the EVA Wiki, information required for EVA flight controllers and instructors was scattered across different sources, including multiple file share directories, SharePoint, individual computers, and paper archives. Many documents were outdated, and data was often difficult to find and distribute. In 2011, a team recognized that these knowledge management problems could be solved by creating an EVA Wiki using MediaWiki, a free and open-source software developed by the Wikimedia Foundation. The EVA Wiki developed into an EVA-specific Wikipedia on an internal NASA server. While the technical implementation of the wiki had many challenges, one of the biggest hurdles came from a cultural shift. Like many enterprise organizations, the EVA Operations group was accustomed to hierarchical data structures and individually-owned documents. Instead of sorting files into various folders, the wiki searches content. Rather than having a single document owner, the wiki harmonized the efforts of many contributors and established an automated revision controlled system. As the group adapted to the wiki, the usefulness of this single portal for information became apparent. It transformed into a useful data mining tool for EVA flight controllers and instructors, as well as hundreds of others that support EVA. Program managers, engineers, astronauts, flight directors, and flight controllers in differing disciplines now have an easier-to-use, searchable system to find EVA data. This paper presents the benefits the EVA Wiki has brought to NASA's EVA community, as well as the cultural challenges it had to overcome.

  5. EVA Wiki - Transforming Knowledge Management for EVA Flight Controllers and Instructors

    Science.gov (United States)

    Johnston, Stephanie

    2016-01-01

    The EVA (Extravehicular Activity) Wiki was recently implemented as the primary knowledge database to retain critical knowledge and skills in the EVA Operations group at NASA's Johnson Space Center by ensuring that information is recorded in a common, searchable repository. Prior to the EVA Wiki, information required for EVA flight controllers and instructors was scattered across different sources, including multiple file share directories, SharePoint, individual computers, and paper archives. Many documents were outdated, and data was often difficult to find and distribute. In 2011, a team recognized that these knowledge management problems could be solved by creating an EVA Wiki using MediaWiki, a free and open-source software developed by the Wikimedia Foundation. The EVA Wiki developed into an EVA-specific Wikipedia on an internal NASA server. While the technical implementation of the wiki had many challenges, the one of the biggest hurdles came from a cultural shift. Like many enterprise organizations, the EVA Operations group was accustomed to hierarchical data structures and individually-owned documents. Instead of sorting files into various folders, the wiki searches content. Rather than having a single document owner, the wiki harmonized the efforts of many contributors and established an automated revision control system. As the group adapted to the wiki, the usefulness of this single portal for information became apparent. It transformed into a useful data mining tool for EVA flight controllers and instructors, and also for hundreds of other NASA and contract employees. Program managers, engineers, astronauts, flight directors, and flight controllers in differing disciplines now have an easier-to-use, searchable system to find EVA data. This paper presents the benefits the EVA Wiki has brought to NASA's EVA community, as well as the cultural challenges it had to overcome.

  6. Impact of Implementing a Wiki to Develop Structured Electronic Order Sets on Physicians' Intention to Use Wiki-Based Order Sets.

    Science.gov (United States)

    Archambault, Patrick Michel; Beaupré, Pierre; Bégin, Laura; Dupuis, Audrey; Côté, Mario; Légaré, France

    2016-05-17

    Wikis have the potential to promote best practices in health systems by sharing order sets with a broad community of stakeholders. However, little is known about the impact of using a wiki on clinicians' intention to use wiki-based order sets. The aims of this study were: (1) to describe the use of a wiki to create structured order sets for a single emergency department; (2) to evaluate whether the use of this wiki changed emergency physicians' future intention to use wiki-based order sets; and (3) to understand the impact of using the wiki on the behavioral determinants for using wiki-based order sets. This was a pre/post-intervention mixed-methods study conducted in one hospital in Lévis, Quebec. The intervention was comprised of receiving access to and being motivated by the department head to use a wiki for 6 months to create electronic order sets designed to be used in a computer physician order entry system. Before and after our intervention, we asked participants to complete a previously validated questionnaire based on the Theory of Planned Behavior. Our primary outcome was the intention to use wiki-based order sets in clinical practice. We also assessed participants' attitude, perceived behavioral control, and subjective norm to use wiki-based order sets. Paired pre- and post-Likert scores were compared using Wilcoxon signed-rank tests. The post-questionnaire also included open-ended questions concerning participants' comments about the wiki, which were then classified into themes using an existing taxonomy. Twenty-eight emergency physicians were enrolled in the study (response rate: 100%). Physicians' mean intention to use a wiki-based reminder was 5.42 (SD 1.04) before the intervention, and increased to 5.81 (SD 1.25) on a 7-point Likert scale (P =.03) after the intervention. Participants' attitude towards using a wiki-based order set also increased from 5.07 (SD 0.90) to 5.57 (SD 0.88) (P =.003). Perceived behavioral control and subjective norm did not

  7. Strata: typed semi-structured data in DokuWiki

    NARCIS (Netherlands)

    Wanders, B.; te Brinke, Steven

    2014-01-01

    A semantic wiki is a wiki that has a model of the knowledge contained in its pages. Currently, semantic wikis are not adopted by a large user base, because most implementations are research prototypes that implement their own wiki engine. To increase familiarity with semantic wikis and quick

  8. Engaging with a Wiki related to knowledge translation: a survey of WhatisKT Wiki users.

    Science.gov (United States)

    Mathew, Deepa; McKibbon, K Ann; Lokker, Cynthia; Colquhoun, Heather

    2014-01-21

    In 2008, WhatisKT wiki was launched as a collaborative platform for knowledge translation (KT) researchers and stakeholders to debate the use and definitions of KT-related terms. The wiki has definitions for over 110 terms from disciplines including health care, information technology, education, accounting, and business. WhatisKT wiki has over 115 registered users. Approximately 73,000 unique visitors have visited the wiki since 2008. Despite annual increases in visitors and regular maintenance of the wiki, no visitors have contributed content or started a discussion. We surveyed wiki users to gain an understanding of the perceived value of the website, reasons for not engaging in the wiki, and suggestions to facilitate collaboration and improve the usability of the wiki. We surveyed three cohorts: KT Canada members who were previously invited to join the wiki, registered wiki members, and unregistered visitors. The first two cohorts completed a Web-based survey that included the System Usability Scale (SUS) questionnaire to assess usability; additionally 3 participants were interviewed. Unregistered wiki visitors were surveyed with polls posted on the wiki. The study received ethics approval from the McMaster University Faculty of Health Sciences Research Ethics Board. Twenty-three participants completed the Web-based and SUS surveys; 15 participants indicated that they would collaborate on the wiki. The mean SUS score of 67 (95% CI 56-77) indicated that the wiki could be considered for design improvements. Study participants indicated that the wiki could be improved by email notification regarding new terms, better grouping of terms, user friendly interface, and training for users interested in editing content. The findings from this survey will be used to enhance the design and content of WhatisKT wiki. Further feedback from participants will be used to make the wiki an ideal collaboration platform for KT researchers interested in terminology.

  9. Wiki-Based Data and Information Integration (WikiDI2) System, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — The proposed innovation is: A data and information integration (DI2) system built from the methods and tools used to create Wiki websites. Wiki (Hawaiian for...

  10. Wiki Behavior in the Workplace: Emotional Aspects of Content Development

    Science.gov (United States)

    Gears, Deborah Ann

    2011-01-01

    Wikis have been found to be an easy-to-use, low-cost, and Internet-based technology useful in creating and mobilizing knowledge. Wikis hosted within firms (corporate wikis) have become a popular way for employees to share information and collaborate. Preliminary research suggested that as few as 6% of wiki consumers contributed to the…

  11. Biological knowledge bases using Wikis: combining the flexibility of Wikis with the structure of databases.

    Science.gov (United States)

    Brohée, Sylvain; Barriot, Roland; Moreau, Yves

    2010-09-01

    In recent years, the number of knowledge bases developed using Wiki technology has exploded. Unfortunately, next to their numerous advantages, classical Wikis present a critical limitation: the invaluable knowledge they gather is represented as free text, which hinders their computational exploitation. This is in sharp contrast with the current practice for biological databases where the data is made available in a structured way. Here, we present WikiOpener an extension for the classical MediaWiki engine that augments Wiki pages by allowing on-the-fly querying and formatting resources external to the Wiki. Those resources may provide data extracted from databases or DAS tracks, or even results returned by local or remote bioinformatics analysis tools. This also implies that structured data can be edited via dedicated forms. Hence, this generic resource combines the structure of biological databases with the flexibility of collaborative Wikis. The source code and its documentation are freely available on the MediaWiki website: http://www.mediawiki.org/wiki/Extension:WikiOpener.

  12. Technoeconomic analysis of biofuels: A wiki-based platform for lignocellulosic biorefineries

    DEFF Research Database (Denmark)

    Klein-Marcuschamer, Daniel; Oleskowicz-Popiel, Piotr; Simmons, Blake A.

    2010-01-01

    We present a process model for a lignocellulosic ethanol biorefinery that is open to the biofuels academic community. Beyond providing a series of static results, the wiki-based platform provides a dynamic and transparent tool for analyzing, exploring, and communicating the impact of process adva...

  13. Using Wikis and Collaborative Learning for Science Teachers' Professional Development

    Science.gov (United States)

    Chen, Y-H.; Jang, S-J.; Chen, P-J.

    2015-01-01

    Wiki bears great potential to transform learning and instruction by scaffolding personal and social constructivism. Past studies have shown that proper application of wiki benefits both students and teachers; however, few studies have integrated wiki and collaborative learning to examine the growth of science teachers' "Technological,…

  14. WikiScience: Wikipedia for science and technology

    OpenAIRE

    Aibar Puentes, Eduard

    2015-01-01

    Peer-reviewed Presentació de la conferència "WikiScience: Wikipedia for science and technology". Presentación de la conferencia "WikiScience: Wikipedia for science and technology". Presentation of the conference "Science Wiki: Wikipedia for science and technology".

  15. Choosing a Wiki Platform for Student Projects--Lessons Learned

    Science.gov (United States)

    Malaga, Ross A.

    2010-01-01

    Wikis offer many benefits, such as two-way flows of information, early and consistent feedback, and greater student group collaboration, in an educational setting. Some researchers have already reported on the use of Wikis in their classes. However, instructors must choose an appropriate Wiki platform in order to receive all of the benefits of…

  16. ArrayWiki: an enabling technology for sharing public microarray data repositories and meta-analyses

    Science.gov (United States)

    Stokes, Todd H; Torrance, JT; Li, Henry; Wang, May D

    2008-01-01

    Background A survey of microarray databases reveals that most of the repository contents and data models are heterogeneous (i.e., data obtained from different chip manufacturers), and that the repositories provide only basic biological keywords linking to PubMed. As a result, it is difficult to find datasets using research context or analysis parameters information beyond a few keywords. For example, to reduce the "curse-of-dimension" problem in microarray analysis, the number of samples is often increased by merging array data from different datasets. Knowing chip data parameters such as pre-processing steps (e.g., normalization, artefact removal, etc), and knowing any previous biological validation of the dataset is essential due to the heterogeneity of the data. However, most of the microarray repositories do not have meta-data information in the first place, and do not have a a mechanism to add or insert this information. Thus, there is a critical need to create "intelligent" microarray repositories that (1) enable update of meta-data with the raw array data, and (2) provide standardized archiving protocols to minimize bias from the raw data sources. Results To address the problems discussed, we have developed a community maintained system called ArrayWiki that unites disparate meta-data of microarray meta-experiments from multiple primary sources with four key features. First, ArrayWiki provides a user-friendly knowledge management interface in addition to a programmable interface using standards developed by Wikipedia. Second, ArrayWiki includes automated quality control processes (caCORRECT) and novel visualization methods (BioPNG, Gel Plots), which provide extra information about data quality unavailable in other microarray repositories. Third, it provides a user-curation capability through the familiar Wiki interface. Fourth, ArrayWiki provides users with simple text-based searches across all experiment meta-data, and exposes data to search engine crawlers

  17. The pathology informatics curriculum wiki: Harnessing the power of user-generated content.

    Science.gov (United States)

    Kim, Ji Yeon; Gudewicz, Thomas M; Dighe, Anand S; Gilbertson, John R

    2010-07-13

    The need for informatics training as part of pathology training has never been so critical, but pathology informatics is a wide and complex field and very few programs currently have the resources to provide comprehensive educational pathology informatics experiences to their residents. In this article, we present the "pathology informatics curriculum wiki", an open, on-line wiki that indexes the pathology informatics content in a larger public wiki, Wikipedia, (and other online content) and organizes it into educational modules based on the 2003 standard curriculum approved by the Association for Pathology Informatics (API). In addition to implementing the curriculum wiki at http://pathinformatics.wikispaces.com, we have evaluated pathology informatics content in Wikipedia. Of the 199 non-duplicate terms in the API curriculum, 90% have at least one associated Wikipedia article. Furthermore, evaluation of articles on a five-point Likert scale showed high scores for comprehensiveness (4.05), quality (4.08), currency (4.18), and utility for the beginner (3.85) and advanced (3.93) learners. These results are compelling and support the thesis that Wikipedia articles can be used as the foundation for a basic curriculum in pathology informatics. The pathology informatics community now has the infrastructure needed to collaboratively and openly create, maintain and distribute the pathology informatics content worldwide (Wikipedia) and also the environment (the curriculum wiki) to draw upon its own resources to index and organize this content as a sustainable basic pathology informatics educational resource. The remaining challenges are numerous, but largest by far will be to convince the pathologists to take the time and effort required to build pathology informatics content in Wikipedia and to index and organize this content for education in the curriculum wiki.

  18. A fielded wiki for personality genetics

    DEFF Research Database (Denmark)

    Nielsen, Finn Årup

    2010-01-01

    I describe a fielded wiki, where a Web form interface allows the entry, analysis and visualization of results from scientific papers in the personality genetics domain. Papers in this domain typically report the mean and standard deviation of multiple personality trait scores from statistics...... on human subjects grouped based on genotype. The wiki organizes the basic data in a single table with fixed columns, each row recording statistical values with respect to a specific personality trait reported in a specific paper with a specific genotype group. From this basic data hard-coded meta...

  19. Wikis and Collaborative Learning in Higher Education

    Science.gov (United States)

    Zheng, Binbin; Niiya, Melissa; Warschauer, Mark

    2015-01-01

    While collaborative learning and collaborative writing can be of great value to student learning, the implementation of a technology-supported collaborative learning environment is a challenge. With their built-in features for supporting collaborative writing and social communication, wikis are a promising platform for collaborative learning;…

  20. Social Media and Organizing – An Empirical Analysis of the Role of Wiki Affordances in Organizing Practices

    DEFF Research Database (Denmark)

    Mansour, Osama; Askenäs, Linda; Ghazawneh, Ahmad

    2013-01-01

    The evolution of social media has introduced novel possibilities for work and interaction in organizations. The wiki technology is one important kind of social media technologies that is increasingly used to facilitate the creation and sharing of organizational knowledge within communities. Given...... in that they extend the notion of affordance by theorizing new concepts that describe relational dynamics, situated and contextual conditions, and social factors involved in enacting, perceiving, and exploiting affordances.......The evolution of social media has introduced novel possibilities for work and interaction in organizations. The wiki technology is one important kind of social media technologies that is increasingly used to facilitate the creation and sharing of organizational knowledge within communities. Given...... the increasing use of social media in organizations and the lack of knowledge on their consequences for organizing, we use an affordance lens to explore the enactment of organizational wiki affordances. Using qualitative data obtained through interviews, field visits, and documents from two multinational...

  1. Implementation of a Multilevel Wiki for Cross-Domain Collaboration

    National Research Council Canada - National Science Library

    Ong, Kar Leong; Nguyen, Thuy; Irvine, Cynthia

    2008-01-01

    .... Wiki technology provides a hypertext content-based collaborative authoring and information sharing environment that includes the ability to create links to other web contents, relative stability...

  2. T-search : buscador con tesauro para wikis

    OpenAIRE

    Sagredo Olivenza, Ismael

    2009-01-01

    El auge de los entornos wiki, cada vez más extendidos, hace necesarias herramientas que permitan recuperar de forma eficiente la información de estos entornos. Hasta ahora los buscadores genéricos como Google son las mejores herramientas para encontrar en wikis como Wikipedia, pero no para wikis de menor difusión, donde Google y otros buscadores sólo tienen indizada una pequeña parte del sitio. Por otro lado, los buscadores que incorporan los entornos wiki son muy limitados, y sólo realizan b...

  3. Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources.

    Science.gov (United States)

    Waagmeester, Andra; Kutmon, Martina; Riutta, Anders; Miller, Ryan; Willighagen, Egon L; Evelo, Chris T; Pico, Alexander R

    2016-06-01

    The diversity of online resources storing biological data in different formats provides a challenge for bioinformaticians to integrate and analyse their biological data. The semantic web provides a standard to facilitate knowledge integration using statements built as triples describing a relation between two objects. WikiPathways, an online collaborative pathway resource, is now available in the semantic web through a SPARQL endpoint at http://sparql.wikipathways.org. Having biological pathways in the semantic web allows rapid integration with data from other resources that contain information about elements present in pathways using SPARQL queries. In order to convert WikiPathways content into meaningful triples we developed two new vocabularies that capture the graphical representation and the pathway logic, respectively. Each gene, protein, and metabolite in a given pathway is defined with a standard set of identifiers to support linking to several other biological resources in the semantic web. WikiPathways triples were loaded into the Open PHACTS discovery platform and are available through its Web API (https://dev.openphacts.org/docs) to be used in various tools for drug development. We combined various semantic web resources with the newly converted WikiPathways content using a variety of SPARQL query types and third-party resources, such as the Open PHACTS API. The ability to use pathway information to form new links across diverse biological data highlights the utility of integrating WikiPathways in the semantic web.

  4. Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources.

    Directory of Open Access Journals (Sweden)

    Andra Waagmeester

    2016-06-01

    Full Text Available The diversity of online resources storing biological data in different formats provides a challenge for bioinformaticians to integrate and analyse their biological data. The semantic web provides a standard to facilitate knowledge integration using statements built as triples describing a relation between two objects. WikiPathways, an online collaborative pathway resource, is now available in the semantic web through a SPARQL endpoint at http://sparql.wikipathways.org. Having biological pathways in the semantic web allows rapid integration with data from other resources that contain information about elements present in pathways using SPARQL queries. In order to convert WikiPathways content into meaningful triples we developed two new vocabularies that capture the graphical representation and the pathway logic, respectively. Each gene, protein, and metabolite in a given pathway is defined with a standard set of identifiers to support linking to several other biological resources in the semantic web. WikiPathways triples were loaded into the Open PHACTS discovery platform and are available through its Web API (https://dev.openphacts.org/docs to be used in various tools for drug development. We combined various semantic web resources with the newly converted WikiPathways content using a variety of SPARQL query types and third-party resources, such as the Open PHACTS API. The ability to use pathway information to form new links across diverse biological data highlights the utility of integrating WikiPathways in the semantic web.

  5. Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources

    Science.gov (United States)

    Waagmeester, Andra; Pico, Alexander R.

    2016-01-01

    The diversity of online resources storing biological data in different formats provides a challenge for bioinformaticians to integrate and analyse their biological data. The semantic web provides a standard to facilitate knowledge integration using statements built as triples describing a relation between two objects. WikiPathways, an online collaborative pathway resource, is now available in the semantic web through a SPARQL endpoint at http://sparql.wikipathways.org. Having biological pathways in the semantic web allows rapid integration with data from other resources that contain information about elements present in pathways using SPARQL queries. In order to convert WikiPathways content into meaningful triples we developed two new vocabularies that capture the graphical representation and the pathway logic, respectively. Each gene, protein, and metabolite in a given pathway is defined with a standard set of identifiers to support linking to several other biological resources in the semantic web. WikiPathways triples were loaded into the Open PHACTS discovery platform and are available through its Web API (https://dev.openphacts.org/docs) to be used in various tools for drug development. We combined various semantic web resources with the newly converted WikiPathways content using a variety of SPARQL query types and third-party resources, such as the Open PHACTS API. The ability to use pathway information to form new links across diverse biological data highlights the utility of integrating WikiPathways in the semantic web. PMID:27336457

  6. A Comparative Analysis of Wiki Discretionary Access Control in a CONOPS Environment

    National Research Council Canada - National Science Library

    Crawford, Frederick L

    2008-01-01

    This research conducts a comparative analysis of discretionary access controls of current wikis by experimenting with their discretionary access controls and functionality, comparing the wiki software...

  7. VuWiki: An Ontology-Based Semantic Wiki for Vulnerability Assessments

    Science.gov (United States)

    Khazai, Bijan; Kunz-Plapp, Tina; Büscher, Christian; Wegner, Antje

    2014-05-01

    The concept of vulnerability, as well as its implementation in vulnerability assessments, is used in various disciplines and contexts ranging from disaster management and reduction to ecology, public health or climate change and adaptation, and a corresponding multitude of ideas about how to conceptualize and measure vulnerability exists. Three decades of research in vulnerability have generated a complex and growing body of knowledge that challenges newcomers, practitioners and even experienced researchers. To provide a structured representation of the knowledge field "vulnerability assessment", we have set up an ontology-based semantic wiki for reviewing and representing vulnerability assessments: VuWiki, www.vuwiki.org. Based on a survey of 55 vulnerability assessment studies, we first developed an ontology as an explicit reference system for describing vulnerability assessments. We developed the ontology in a theoretically controlled manner based on general systems theory and guided by principles for ontology development in the field of earth and environment (Raskin and Pan 2005). Four key questions form the first level "branches" or categories of the developed ontology: (1) Vulnerability of what? (2) Vulnerability to what? (3) What reference framework was used in the vulnerability assessment?, and (4) What methodological approach was used in the vulnerability assessment? These questions correspond to the basic, abstract structure of the knowledge domain of vulnerability assessments and have been deduced from theories and concepts of various disciplines. The ontology was then implemented in a semantic wiki which allows for the classification and annotation of vulnerability assessments. As a semantic wiki, VuWiki does not aim at "synthesizing" a holistic and overarching model of vulnerability. Instead, it provides both scientists and practitioners with a uniform ontology as a reference system and offers easy and structured access to the knowledge field of

  8. Wiki Mass Authoring for Experiential Learning: A Case Study

    Science.gov (United States)

    Pardue, Harold; Landry, Jeffrey; Sweeney, Bob

    2013-01-01

    Web 2.0 services include sharing and collaborative technologies such as blogs, social networking sites, online office productivity tools, and wikis. Wikis are increasingly used for the design and implementation of pedagogy, for example to facilitate experiential learning. A U.S. government-funded project for system security risk assessment was…

  9. Wiki Use that Increases Communication and Collaboration Motivation

    Science.gov (United States)

    Davidson, Robyn

    2012-01-01

    Communication and collaboration can be readily enabled by the use of many ICT tools. A wiki, which is an easily accessible and editable website, is one such platform that provides the opportunity for students to work on group projects without the barriers that arise from traditional group work. Whilst wiki use is becoming more common, its use in…

  10. Wiki: Using the Web Connections to Connect Students

    Science.gov (United States)

    Donne, Vicki

    2012-01-01

    The present study reports on action research conducted using a resource wiki. Participants included 48 certified teachers and pre-service teachers enrolled in a face-to-face graduate course supplemented with online activities. Data collected include student reflections that indicate the use of a wiki at the university level is a feasible means of…

  11. Collaborative Tasks in Wiki-Based Environment in EFL Learning

    Science.gov (United States)

    Zou, Bin; Wang, Dongshuo; Xing, Minjie

    2016-01-01

    Wikis provide users with opportunities to post and edit messages to collaborate in the language learning process. Many studies have offered findings to show positive impact of Wiki-based language learning for learners. This paper explores the effect of collaborative task in error correction for English as a Foreign Language learning in an online…

  12. User Defined Structural Searches in MediaWiki

    DEFF Research Database (Denmark)

    Bouvin, Niels Olof; Albertsen, Johannes

    2008-01-01

    Wikipedia has been the poster child of user contributed content using the space of MediaWiki as the canvas on which to write. While well suited for authoring simple hypermedia documents, MediaWiki does not lend itself easily to let the author create dynamically assembled documents, or create pages...

  13. Gestión documental con plataformas wiki

    OpenAIRE

    Tramullas, Jesús

    2008-01-01

    This work revises the wiki concept and definition, a kind of collaboration management information tool. The work explains how the tool works and its technical features, and it proposes a planning and development built-in method for digital information services based on wiki.

  14. Horizontal gene transfer in an acid mine drainage microbial community.

    Science.gov (United States)

    Guo, Jiangtao; Wang, Qi; Wang, Xiaoqi; Wang, Fumeng; Yao, Jinxian; Zhu, Huaiqiu

    2015-07-04

    Horizontal gene transfer (HGT) has been widely identified in complete prokaryotic genomes. However, the roles of HGT among members of a microbial community and in evolution remain largely unknown. With the emergence of metagenomics, it is nontrivial to investigate such horizontal flow of genetic materials among members in a microbial community from the natural environment. Because of the lack of suitable methods for metagenomics gene transfer detection, microorganisms from a low-complexity community acid mine drainage (AMD) with near-complete genomes were used to detect possible gene transfer events and suggest the biological significance. Using the annotation of coding regions by the current tools, a phylogenetic approach, and an approximately unbiased test, we found that HGTs in AMD organisms are not rare, and we predicted 119 putative transferred genes. Among them, 14 HGT events were determined to be transfer events among the AMD members. Further analysis of the 14 transferred genes revealed that the HGT events affected the functional evolution of archaea or bacteria in AMD, and it probably shaped the community structure, such as the dominance of G-plasma in archaea in AMD through HGT. Our study provides a novel insight into HGT events among microorganisms in natural communities. The interconnectedness between HGT and community evolution is essential to understand microbial community formation and development.

  15. The impact of group membership on collaborative learning with wikis.

    Science.gov (United States)

    Matschke, Christina; Moskaliuk, Johannes; Kimmerle, Joachim

    2013-02-01

    The social web stimulates learning through collaboration. However, information in the social web is often associated with information about its author. Based on previous evidence that ingroup information is preferred to outgroup information, the current research investigates whether group memberships of wiki authors affect learning. In an experimental study, we manipulated the group memberships (ingroup vs. outgroup) of wiki authors by using nicknames. The designated group memberships (being fans of a soccer team or not) were completely irrelevant for the domain of the wiki (the medical disorder fibromyalgia). Nevertheless, wiki information from the ingroup led to more integration of information into prior knowledge as well as more increase of factual knowledge than information from the outgroup. The results demonstrate that individuals apply social selection strategies when considering information from wikis, which may foster, but also hinder, learning and collaboration. Practical implications for collaborative learning in the social web are discussed.

  16. Use of Semantic Wikis to support collaborative learning

    Directory of Open Access Journals (Sweden)

    Mauro Coccoli

    2012-08-01

    Full Text Available Semantic Wiki consentono, tramite un linguaggio comprensibile agli elaboratori e formalmente definito, l’annotazione semantica dei contenuti delle pagine Wiki e la rappresentazione esplicita delle relazioni di significato tra essi presenti. Essi offrono la possibilità di sfruttare sia i vantaggi delle tecnologie basate su ontologie sia i meccanismi collaborativi propri dei Wiki. L’articolo descrive un progetto, denominato Semantic WikiSUN, avviato per indagare le prospettive didattiche di tali sistemi. Esso è basato su un quadro teorico complesso che integra evidenze neurocognitive, teorie dell’apprendimento e modelli costruttivisti-sociali della conoscenza. Obiettivo del contributo è, sulla base della esperienza intrapresa, discutere potenzialità e criticità didattiche dei Semantic Wiki, estendendo talvolta la riflessione a considerazioni più generali sui processi di apprendimento mediati da tecnologie semantiche.

  17. Effective use of Wikis in College Mathematics Classes

    Directory of Open Access Journals (Sweden)

    Paul Martin

    2010-12-01

    Full Text Available Wikis are used in mathematics education in a variety of ways [3]. As with Wikipedia, mathematics related Wikis provide pages and links that describe many different branches of mathematics. Another common use is as a portal for distributing and collecting mathematics course materials [1]. This article describes the authors' use of course wikis for two different purposes in two undergraduate math courses. In Calculus-I, a wiki was utilized to share and present the outcome of an optimization problem that required small groups to collect information about student homes' attic insulation status and eventually to compute the optimal amount of new insulation to add that maximizes heating savings. The second wiki was for a small seminar-style course on Mathematical Mysteries where students collected and posted the results of their research relating to famous unsolved problems in mathematics. This wiki was also used as a platform for in-class presentations by the students and the instructors. In both cases, the bulk of the wiki contribution was by students.

  18. The application of wiki technology in medical education.

    Science.gov (United States)

    Rasmussen, Andrew; Lewis, Melanie; White, Jonathan

    2013-01-01

    BACKGROUND, AIMS AND METHODS: Recent years have seen the introduction of web-based technologies such as the 'wiki', which is a webpage whose content can be edited in real time using a web browser. This article reviews the current state of knowledge about the use of wikis in education, and considers whether wiki technology has features that might prove useful in medical education. Advantages and challenges of the technology are discussed, and recommendations for use are provided. We believe that wiki technology offers a number of potential benefits for administrators, students and instructors, including the ability to share information online, to construct knowledge together, to facilitate collaboration and to enable social learning and peer feedback. We believe that with proper planning and instructional design, wiki technology can be usefully employed in medical education. We intend to continue to study the impact of wiki technology in our own programme, and we encourage others to evaluate the application of wiki technology in other areas of medical education.

  19. Towards a Conceptual Framework for WikiGIS

    Directory of Open Access Journals (Sweden)

    Wided Batita

    2014-10-01

    Full Text Available As an emerging complex concept, GeoDesign requires an innovative theoretical basis, tools, supports and practices. For this reason, we propose a new concept, “WikiGIS”, designed to answer some dimensions of the GeoDesign process. WikiGIS focuses on the needs of GeoDesign, but we leave the door open for future improvement when tested in other areas that may have additional needs. WikiGIS is built on Web 2.0 technologies—and primarily on wiki—to manage the tracking of participants’ editing (i.e., managing the contributions history. It also offers GIS functions for geoprocessing and a design-based approach for sketching proposals. One of the main strengths of WikiGIS is its ability to manage the traceability of contributions with an easy and dynamical access, data quality and deltification. The core of this paper consists of presenting a conceptual framework for WikiGIS using UML diagrams. A user interface is presented later to show how our WikiGIS proposal works. This interface is simply a means to illustrate the concepts underlying WikiGIS.

  20. How Wikis can be Used to Manage Knowledge in SMEs

    DEFF Research Database (Denmark)

    Razmerita, Liana; Kirchner, Kathrin

    2011-01-01

    Companies are exploring new ways of knowledge sharing, collaboration and communication with employees, partners and customers, using social media tools like wikis, blogs or social networks. This article briefly reviews the literature concerning the introduction of social media into organizations...... and reports a small case study in an IT consulting company following the introduction of a wiki-based solution into its daily practices. The usage of the wiki and its impact on knowledge work are explored. The authors then compare the findings from the literature review with those from the case study...

  1. Using blogs and wikis in a graduate public health course.

    Science.gov (United States)

    Cobus, Laura

    2009-01-01

    Blogs and wikis are examples of Web 2.0 technology that facilitate collaboration in the online world. In the health sciences, the emergence of these social tools potentially increases the risk of generating harmful or biased information. Therefore, it is the health professional's responsibility to have the skills to critically appraise Web content that has not undergone traditional peer review. This was the focus in a three-credit graduate Urban Public Health course taught by a librarian and was addressed with assignments using blog and wiki technology within the course management tool Blackboard. The assignments fostered comprehension of the issues surrounding blogs and wikis as they relate to public health.

  2. A Semantic Wiki on Cooperation in Public Administration in Europe

    OpenAIRE

    Bernhard Krabina

    2010-01-01

    Authorities cooperate in various ways. The Web portal www.verwaltungskooperation.eu aims to share knowledge on collaboration projects. A semantic wiki approach was used to facilitate best practice documentation with Semantic Web and Web 2.0 technology.

  3. Introduction of a Wiki in an Enterprise: Motives and Challenges

    Directory of Open Access Journals (Sweden)

    Fernando L. F. Almeida

    2011-10-01

    Full Text Available Among the tools available to implement the collaborative production of knowledge in organizations, the use of wikis has been gaining momentum and showing a low-cost and high efficiency. However, some difficulties still arise when attempting to introduce this kind of technology in an organization. In addition to technological limitations, the cultural issues inherent in companies can also origin problems and promising projects can be abandoned without achieving all the objectives planned. In this work, we study the motives, challenges as well as the more common problems that appear during the wiki implantation process in an organization and the purposed solutions on the literature. The main objective is to identify forms for the wiki to become a tool that everyone can use in the organization and identify the best practices related, so that the project of creating a functional wiki for an organization can aspire to befall a success and not simply abandoned.

  4. Functional Potential of Bacterial Communities using Gene Context Information

    Directory of Open Access Journals (Sweden)

    Anwesha Mohapatra

    2017-12-01

    Full Text Available Estimation of the functional potential of a bacterial genome can be determined by accurate annotation of its metabolic pathways. Existing homology based methods for pathway annotation fail to account for homologous genes that participate in multiple pathways, causing overestimation of gene copy number. Mere presence of constituent genes of a candidate pathway which are dispersed on a genome often results in incorrect annotation, thereby leading to erroneous gene abundance and pathway estimation. Clusters of evolutionarily conserved coregulated genes are characteristic features in bacterial genomes and their spatial arrangement in the genome is constrained by the pathway encoded by them. Thus, in order to improve the accuracy of pathway prediction, it is important to augment homology based annotation with gene organization information. In this communication, we present a methodology considering prioritization of gene context for improved pathway annotation. Extensive literature mining was performed to confirm conserved juxtaposed arrangement of gene components of various pathways. Our method was utilized to identify and analyse the functional potential of all available completely sequenced bacterial genomes. The accuracy of the predicted gene clusters and their importance in metabolic pathways will be demonstrated using a few case studies. One of such case study corresponds to butyrate production pathways in gut bacteria where it was observed that gut pathogens and commensals possess a distinct set of pathway components. In another example, we will demonstrate how our methodology improves the prediction accuracy of carbohydrate metabolic potential in human microbial communities. Applicability of our method for estimation of functional potential in bacterial communities present in diverse environments will also be illustrated.

  5. The NASA Human Research Wiki - An Online Collaboration Tool

    Science.gov (United States)

    Barr, Yael; Rasbury, Jack; Johnson, Jordan; Barstend, Kristina; Saile, Lynn; Watkins, Sharmi

    2012-01-01

    The Exploration Medical Capability (ExMC) element is one of six elements of the Human Research Program (HRP). ExMC is charged with decreasing the risk of: "Inability to adequately recognize or treat an ill or injured crew member" for exploration-class missions In preparation for exploration-class missions, ExMC has compiled a large evidence base, previously available only to persons within the NASA community. ExMC has developed the "NASA Human Research Wiki" in an effort to make the ExMC information available to the general public and increase collaboration within and outside of NASA. The ExMC evidence base is comprised of several types of data, including: (1)Information on more than 80 medical conditions which could occur during space flight (a)Derived from several sources (b)Including data on incidence and potential outcomes, as captured in the Integrated Medical Model s (IMM) Clinical Finding Forms (CliFFs). (2)Approximately 25 gap reports (a)Identify any "gaps" in knowledge and/or technology that would need to be addressed in order to provide adequate medical support for these novel missions.

  6. Refactoring affordances in corporate wikis: a case for the use of mind maps

    Science.gov (United States)

    Puente, Gorka; Díaz, Oscar; Azanza, Maider

    2015-11-01

    The organisation of corporate wikis tends to deteriorate as time goes by. Rearranging categories, structuring articles and even moving sections among articles are cumbersome tasks in current wiki engines. This discourages the layman. But, it is the layman who writes the articles, knows the wiki content and detects refactoring opportunities. Our goal is to improve the refactoring affordances of current wiki engines by providing an alternative front-end tuned to refactoring. This is achieved by (1) surfacing the structure of the wiki corpus as a mind map, and (2) conducting refactoring as mind map reshaping. To this end, we introduce WikiWhirl, a domain-specific language for wiki refactoring. WikiWhirl is supported as an extension of FreeMind, a popular mind mapping tool. In this way, refactoring operations are intuitively conducted as actions upon mind map nodes. In a refactoring session a user imports the wiki structure as a FreeMind map; next, conducts the refactoring operations on the map, and finally, the effects are saved in the wiki database. The operational semantics of the WikiWhirl operations follow refactoring good practices (e.g., authorship preservation). Results from a controlled experiment suggest that WikiWhirl outperforms MediaWiki in three main affordance enablers: understandability, productivity and fulfillment of refactoring good practices.

  7. Wiki Surveys: Open and Quantifiable Social Data Collection

    Science.gov (United States)

    Salganik, Matthew J.; Levy, Karen E. C.

    2015-01-01

    In the social sciences, there is a longstanding tension between data collection methods that facilitate quantification and those that are open to unanticipated information. Advances in technology now enable new, hybrid methods that combine some of the benefits of both approaches. Drawing inspiration from online information aggregation systems like Wikipedia and from traditional survey research, we propose a new class of research instruments called wiki surveys. Just as Wikipedia evolves over time based on contributions from participants, we envision an evolving survey driven by contributions from respondents. We develop three general principles that underlie wiki surveys: they should be greedy, collaborative, and adaptive. Building on these principles, we develop methods for data collection and data analysis for one type of wiki survey, a pairwise wiki survey. Using two proof-of-concept case studies involving our free and open-source website www.allourideas.org, we show that pairwise wiki surveys can yield insights that would be difficult to obtain with other methods. PMID:25992565

  8. Wiki surveys: open and quantifiable social data collection.

    Science.gov (United States)

    Salganik, Matthew J; Levy, Karen E C

    2015-01-01

    In the social sciences, there is a longstanding tension between data collection methods that facilitate quantification and those that are open to unanticipated information. Advances in technology now enable new, hybrid methods that combine some of the benefits of both approaches. Drawing inspiration from online information aggregation systems like Wikipedia and from traditional survey research, we propose a new class of research instruments called wiki surveys. Just as Wikipedia evolves over time based on contributions from participants, we envision an evolving survey driven by contributions from respondents. We develop three general principles that underlie wiki surveys: they should be greedy, collaborative, and adaptive. Building on these principles, we develop methods for data collection and data analysis for one type of wiki survey, a pairwise wiki survey. Using two proof-of-concept case studies involving our free and open-source website www.allourideas.org, we show that pairwise wiki surveys can yield insights that would be difficult to obtain with other methods.

  9. Analysis of Students' Participation Patterns and Learning Presence in a Wiki-Based Project

    Science.gov (United States)

    Roussinos, Dimitrios; Jimoyiannis, Athanassios

    2013-01-01

    The educational applications of wikis are becoming very popular among instructors and researchers and they have captured their attention and imagination. This paper reports on the investigation of a wiki project designed to support university students' collaborative authoring and learning. The design framework of the wiki-based project is outlined…

  10. It's Time to Use a Wiki as Part of Your Web Site

    Science.gov (United States)

    Ribaric, Tim

    2007-01-01

    Without a doubt, the term "wiki" has leaked into almost every discussion concerning Web 2.0. The real question becomes: Is there a place for a wiki on every library Web site? The answer should be an emphatic "yes." People often praise the wiki because it offers simple page creation and provides instant gratification for amateur Web developers.…

  11. More than Just Wikipedia: Creating a Collaborative Research Library Using a Wiki

    Science.gov (United States)

    Munoz, Caroline Lego

    2012-01-01

    Increasingly, wiki technology is being used in education and business settings. Although most students are aware of Wikipedia, many do not understand that a wiki is a malleable platform that has a multitude of uses. Wiki technology is one of many social media tools that students need to not only become familiar with but also be able to effectively…

  12. Evaluating Types of Students' Interactions in a Wiki-Based Collaborative Learning Project

    Science.gov (United States)

    Prokofieva, Maria

    2013-01-01

    Wiki technology has been promoted as a collaborative software platform. This study investigates interactions that occur in a wiki-based collaborative learning project. The study draws on interaction literature and investigates the types of interactions with which students are engaged in wiki-based group projects, clusters that reflect online…

  13. The Use of Wikis in a Science Inquiry-Based Project in a Primary School

    Science.gov (United States)

    Lau, Wilfred W. F.; Lui, Vicky; Chu, Samuel K. W.

    2017-01-01

    This study explored the use of wikis in a science inquiry-based project conducted with Primary 6 students (aged 11-12). It used an online wiki-based platform called PBworks and addressed the following research questions: (1) What are students' attitudes toward learning with wikis? (2) What are students' interactions in online group collaboration…

  14. Upgrading to Web 2.0: An Experiential Project to Build a Marketing Wiki

    Science.gov (United States)

    Cronin, John J.

    2009-01-01

    Wikis are one of the newest features of Web 2.0. This article describes the implementation of a project in a marketing course in which students created an interactive textbook using wiki software. Several surprises encountered along the way are described, and the unique problem of grading individual contributions to a wiki is discussed. The author…

  15. Wikis as the Knowledge Management Tools in Organizations

    Directory of Open Access Journals (Sweden)

    Hossein Pashaeizad

    2012-02-01

    Full Text Available In an attempt to enhance knowledge, firms and corporations have been overwhelmed with assorted methods for retaining employee wisdom. To pay attention to the benefits of a successful knowledge management program can help create competitive advantage. Therefore, numerous knowledge management solutions have been developed and implemented. Some of these knowledge management initiatives provide a means to accumulate, organize, and access the firm’s most essential asset. With the advent and spread of information and communication technologies, especially Internet, social software and communication tools has risen to the challenge of capturing knowledge with a variety of methods. One of these tools is wiki that provides a new way of collaboration and knowledge sharing. Wiki is a software that allows users to work collectively on a web-based knowledge base. This paper reviews the role of wikis in knowledge creation and management

  16. Wiki-Based Clinical Practice Guidelines for the Management of Adult Onset Sarcoma: A New Paradigm in Sarcoma Evidence

    Science.gov (United States)

    Neuhaus, S. J.; Thomas, D.; Desai, J.; Vuletich, C.; von Dincklage, J.; Olver, I.

    2015-01-01

    In 2013 Australia introduced Wiki-based Clinical Practice Guidelines for the Management of Adult Onset Sarcoma. These guidelines utilized a customized MediaWiki software application for guideline development and are the first evidence-based guidelines for clinical management of sarcoma. This paper presents our experience with developing and implementing web-based interactive guidelines and reviews some of the challenges and lessons from adopting an evidence-based (rather than consensus-based) approach to clinical sarcoma guidelines. Digital guidelines can be easily updated with new evidence, continuously reviewed and widely disseminated. They provide an accessible method of enabling clinicians and consumers to access evidence-based clinical practice recommendations and, as evidenced by over 2000 views in the first four months after release, with 49% of those visits being from countries outside of Australia. The lessons learned have relevance to other rare cancers in addition to the international sarcoma community. PMID:25784832

  17. Proposing a Wiki-Based Technique for Collaborative Essay Writing

    Directory of Open Access Journals (Sweden)

    Mabel Ortiz Navarrete

    2014-10-01

    Full Text Available This paper aims at proposing a technique for students learning English as a foreign language when they collaboratively write an argumentative essay in a wiki environment. A wiki environment and collaborative work play an important role within the academic writing task. Nevertheless, an appropriate and systematic work assignment is required in order to make use of both. In this paper the proposed technique when writing a collaborative essay mainly attempts to provide the most effective way to enhance equal participation among group members by taking as a base computer mediated collaboration. Within this context, the students’ role is clearly defined and individual and collaborative tasks are explained.

  18. A Simple Application Program Interface for Saving Java Program Data on a Wiki

    OpenAIRE

    Yamanoue, Takashi; Oda, Kentaro; Shimozono, Koichi

    2012-01-01

    A simple application program interface (API) for Java programs running on a wiki is implemented experimentally. A Java program with the API can be running on a wiki, and the Java program can save its data on the wiki. The Java program consists of PukiWiki, which is a popular wiki in Japan, and a plug-in, which starts up Java programs and classes of Java. A Java applet with default access privilege cannot save its data at a local host. We have constructed an API of applets for easy and unified...

  19. Assisting Instructional Assessment of Undergraduate Collaborative Wiki and SVN Activities

    Science.gov (United States)

    Kim, Jihie; Shaw, Erin; Xu, Hao; Adarsh, G. V.

    2012-01-01

    In this paper we examine the collaborative performance of undergraduate engineering students who used shared project documents (Wikis, Google documents) and a software version control system (SVN) to support project collaboration. We present an initial implementation of TeamAnalytics, an instructional tool that facilitates the analyses of the…

  20. A Semantic Wiki on Cooperation in Public Administration in Europe

    Directory of Open Access Journals (Sweden)

    Bernhard Krabina

    2010-06-01

    Full Text Available Authorities cooperate in various ways. The Web portal www.verwaltungskooperation.eu aims to share knowledge on collaboration projects. A semantic wiki approach was used to facilitate best practice documentation with Semantic Web and Web 2.0 technology.

  1. Rationalities of Collaboration for Language Learning in a Wiki

    Science.gov (United States)

    Bradley, Linda; Lindstrom, Berner; Rystedt, Hans

    2010-01-01

    For language learning, online environments allowing for user generated content are becoming increasingly important since they offer possibilities for learners to elaborate on assignments and projects. This study investigates what wikis can do as a means to enhance group interaction, when students are encouraged to participate in constructing text…

  2. Wikis for Group Work: Encouraging Transparency, Benchmarking, and Feedback

    Science.gov (United States)

    Abdekhodaee, Amir; Chase, Anne-Marie; Ross, Bella

    2017-01-01

    Technology is recognised as playing a part in the changing landscape in higher education; altering delivery modes and providing flexible opportunities for learning. Research into the use of wikis has shown that they provide many opportunities for student learning and the development of twenty-first century skills, however, there has been limited…

  3. Muscle Research and Gene Ontology: New standards for improved data integration.

    Science.gov (United States)

    Feltrin, Erika; Campanaro, Stefano; Diehl, Alexander D; Ehler, Elisabeth; Faulkner, Georgine; Fordham, Jennifer; Gardin, Chiara; Harris, Midori; Hill, David; Knoell, Ralph; Laveder, Paolo; Mittempergher, Lorenza; Nori, Alessandra; Reggiani, Carlo; Sorrentino, Vincenzo; Volpe, Pompeo; Zara, Ivano; Valle, Giorgio; Deegan, Jennifer

    2009-01-29

    The Gene Ontology Project provides structured controlled vocabularies for molecular biology that can be used for the functional annotation of genes and gene products. In a collaboration between the Gene Ontology (GO) Consortium and the muscle biology community, we have made large-scale additions to the GO biological process and cellular component ontologies. The main focus of this ontology development work concerns skeletal muscle, with specific consideration given to the processes of muscle contraction, plasticity, development, and regeneration, and to the sarcomere and membrane-delimited compartments. Our aims were to update the existing structure to reflect current knowledge, and to resolve, in an accommodating manner, the ambiguity in the language used by the community. The updated muscle terminologies have been incorporated into the GO. There are now 159 new terms covering critical research areas, and 57 existing terms have been improved and reorganized to follow their usage in muscle literature. The revised GO structure should improve the interpretation of data from high-throughput (e.g. microarray and proteomic) experiments in the area of muscle science and muscle disease. We actively encourage community feedback on, and gene product annotation with these new terms. Please visit the Muscle Community Annotation Wiki http://wiki.geneontology.org/index.php/Muscle_Biology.

  4. Muscle Research and Gene Ontology: New standards for improved data integration

    Directory of Open Access Journals (Sweden)

    Nori Alessandra

    2009-01-01

    Full Text Available Abstract Background The Gene Ontology Project provides structured controlled vocabularies for molecular biology that can be used for the functional annotation of genes and gene products. In a collaboration between the Gene Ontology (GO Consortium and the muscle biology community, we have made large-scale additions to the GO biological process and cellular component ontologies. The main focus of this ontology development work concerns skeletal muscle, with specific consideration given to the processes of muscle contraction, plasticity, development, and regeneration, and to the sarcomere and membrane-delimited compartments. Our aims were to update the existing structure to reflect current knowledge, and to resolve, in an accommodating manner, the ambiguity in the language used by the community. Results The updated muscle terminologies have been incorporated into the GO. There are now 159 new terms covering critical research areas, and 57 existing terms have been improved and reorganized to follow their usage in muscle literature. Conclusion The revised GO structure should improve the interpretation of data from high-throughput (e.g. microarray and proteomic experiments in the area of muscle science and muscle disease. We actively encourage community feedback on, and gene product annotation with these new terms. Please visit the Muscle Community Annotation Wiki http://wiki.geneontology.org/index.php/Muscle_Biology.

  5. Use of Wiki software for the knowledge management at the IEN

    Energy Technology Data Exchange (ETDEWEB)

    Augusto, Silas C.; Oliveira, Mauro V.; Almeida, Jose Carlos S.; Marques, Luana F.S.; Antunes, Joao Francisco O., E-mail: silas@ien.gov.br, E-mail: mvitor@ien.gov.br, E-mail: jcsa@ien.gov.br, E-mail: lsales@ien.gov.br, E-mail: jfantunes@ien.gov.br [Instituto de Engenharia Nuclear (IEN/CNEN-RJ), Rio de Janeiro, RJ (Brazil)

    2015-07-01

    Thanks to the broad availability of internet access and the development of browser-based web applications known as 'wikis' (Hawaiian word for 'quick, fast'), it became possible for internet users to participate on big collaborative encyclopedic projects. The best example is Wikipedia, an online encyclopedia based on MediaWiki that receives contributions from internet users around the world. In this context, the word 'wiki' usually refers to the wiki software itself, and/or the collection of hypertext documents managed by it. Wiki software allows creating, editing and managing online-shared documents, which become available immediately after they are created/edited. With such capabilities, wikis can also be used within organizations as tools to allow its employees to collaborate in the construction of a common knowledge base containing information relevant to the organization. In such context, the wiki becomes a tool for knowledge management. This article describes the implementation of the WikiIEN, which is based on MediaWiki, as a tool for knowledge management at the IEN - Instituto de Engenharia Nuclear. This tool aims to improve the sharing of information among institute researchers, thorough a dynamic common knowledge base that can be on-line updated. In the article are presented the logical and computational structure of the wiki created for deposit of the knowledge generated at the IEN. (author)

  6. Use of Wiki software for the knowledge management at the IEN

    International Nuclear Information System (INIS)

    Augusto, Silas C.; Oliveira, Mauro V.; Almeida, Jose Carlos S.; Marques, Luana F.S.; Antunes, Joao Francisco O.

    2015-01-01

    Thanks to the broad availability of internet access and the development of browser-based web applications known as 'wikis' (Hawaiian word for 'quick, fast'), it became possible for internet users to participate on big collaborative encyclopedic projects. The best example is Wikipedia, an online encyclopedia based on MediaWiki that receives contributions from internet users around the world. In this context, the word 'wiki' usually refers to the wiki software itself, and/or the collection of hypertext documents managed by it. Wiki software allows creating, editing and managing online-shared documents, which become available immediately after they are created/edited. With such capabilities, wikis can also be used within organizations as tools to allow its employees to collaborate in the construction of a common knowledge base containing information relevant to the organization. In such context, the wiki becomes a tool for knowledge management. This article describes the implementation of the WikiIEN, which is based on MediaWiki, as a tool for knowledge management at the IEN - Instituto de Engenharia Nuclear. This tool aims to improve the sharing of information among institute researchers, thorough a dynamic common knowledge base that can be on-line updated. In the article are presented the logical and computational structure of the wiki created for deposit of the knowledge generated at the IEN. (author)

  7. SOIL Geo-Wiki: A tool for improving soil information

    Science.gov (United States)

    Skalský, Rastislav; Balkovic, Juraj; Fritz, Steffen; See, Linda; van der Velde, Marijn; Obersteiner, Michael

    2014-05-01

    Crowdsourcing is increasingly being used as a way of collecting data for scientific research, e.g. species identification, classification of galaxies and unravelling of protein structures. The WorldSoilProfiles.org database at ISRIC is a global collection of soil profiles, which have been 'crowdsourced' from experts. This system, however, requires contributors to have a priori knowledge about soils. Yet many soil parameters can be observed in the field without specific knowledge or equipment such as stone content, soil depth or color. By crowdsourcing this information over thousands of locations, the uncertainty in current soil datasets could be radically reduced, particularly in areas currently without information or where multiple interpretations are possible from different existing soil maps. Improved information on soils could benefit many research fields and applications. Better soil data could enhance assessments of soil ecosystem services (e.g. soil carbon storage) and facilitate improved process-based ecosystem modeling from local to global scales. Geo-Wiki is a crowdsourcing tool that was developed at IIASA for land cover validation using satellite imagery. Several branches are now available focused on specific aspects of land cover validation, e.g. validating cropland extent or urbanized areas. Geo-Wiki Pictures is a smart phone application for collecting land cover related information on the ground. The extension of Geo-Wiki to a mobile environment provides a tool for experts in land cover validation but is also a way of reaching the general public in the validation of land cover. Here we propose a Soil Geo-Wiki tool that builds on the existing functionality of the Geo-Wiki application, which will be largely designed for the collection and sharing of soil information. Two distinct applications are envisaged: an expert-oriented application mainly for scientific purposes, which will use soil science related language (e.g. WRB or any other global reference

  8. Distributed scaffolding: Wiki collaboration among Latino high school chemistry students

    Science.gov (United States)

    O'Sullivan, Edwin Duncan, Jr.

    The primary purpose of this study was to evaluate if wiki collaboration among Latino high school chemistry students can help reduce the science achievement gap between Latino and White students. The study was a quasi-experimental pre/post control group mixed-methods design. It used three intact sections of a high school chemistry course. The first research question asked if there is a difference in academic achievement between a treatment and control group on selected concepts from the topics of bonding, physical changes, and chemical changes, when Latino high school chemistry students collaborate on a quasi-natural wiki project. Overall results for all three activities (Bonding, Physical Changes, and Chemical Changes) indicated no significant difference between the wiki and control group. However, students performing the chemical changes activity did significantly better than their respective control group. Furthermore, there was a significant association, with large effect size, between group membership and ability to overcome the misconception that aqueous ionic reactants in precipitation reactions exist as molecular pairs of ions. Qualitative analysis of classroom and computer lab dialogue, discussion board communication, student focus groups, teacher interviews, and wiki content attributes the better performance of the chemical changes wiki group to favorable differences in intersubjectivity and calibrated assistance, as well as learning about submicroscopic representations of precipitation reactions in multiple contexts. Furthermore, the nonsignificant result overall points to an aversion to peer editing as a possible cause. Drawing considerably on Vygotsky and Piaget, the results are discussed within the context of how distributed scaffolding facilitated medium levels of cognitive conflict. The second research question asked what the characteristics of distributed metacognitive scaffolding are when Latino high school chemistry students collaborate on a quasi

  9. Zwei Stunden und der Rest der Woche. Bemerkungen zur Wiki-Pädagogik

    OpenAIRE

    Hrachovec, Herbert

    2006-01-01

    Wiki Webs offer a distinctive style of collaboration on the WorldWideWeb. We discuss their application in university teaching in relating them to three different, more traditional preconceptions. (1) The time frame of academic instruction, (2) Wiki features as compared to Learning Managment Systems and (3) some general philosophical attitudes to authorship and the development of the self. We argue that Wikis are excellent tools for trying to achieve the 19th century German idea of Bildung., i...

  10. Kajian Pembelajaran Online Berbasis Wiki Di Lingkup Perguruan Tinggi

    Directory of Open Access Journals (Sweden)

    Soetam Rizky Wicaksono

    2012-01-01

    Full Text Available Scope of online learning in higher education now more widely assumed to be a repository of teaching materials for both teachers and students. Nevertheless there are still many things that can still be developed and studied with an experimental model for online learning can be more participatory in the learning context given that the scope of the college is more directed to andragogik. One innovation that leads to this is to make the application of model-based learning wiki adopting crowdsourcing. This paper explores theoretical study attempted as a first step in the research development of wiki-based online learning model. The results of this study should be the basis for experiments to be conducted in order to adapt contextually in real state.

  11. Online Open Neuroimaging Mass Meta-Analysis with a Wiki

    DEFF Research Database (Denmark)

    Nielsen, Finn Arup; Kempton, Matthew J.; Williams, Steven C. R.

    2015-01-01

    We describe a system for meta-analysis where a wiki stores numerical data in a simple comma-separated values format and a web service performs the numerical statistical computation. We initially apply the system on multiple meta-analyses of structural neuroimaging data results. The described system...... allows for mass meta-analysis, e.g., meta-analysis across multiple brain regions and multiple mental disorders providing an overview of important relationships and their uncertainties in a collaborative environment....

  12. Ensino-aprendizagem colaborativo mediado pelo Wiki do Moodle Collaborative learning-teaching mediated by Wiki Moodle

    Directory of Open Access Journals (Sweden)

    Ilse Abegg

    2010-12-01

    Full Text Available Mediados pela ferramenta Wiki do Moodle, desenvolvemos atividades a distância no Curso de Física da UFSM com o intuito de produzir um objeto escolar hipermídia tematizado pelo Tema Estruturador do Ensino de Física 2: Calor, Ambiente e usos de Energia (oriundo dos PCN+ , locando o diálogo-problematizador na transversalidade curricular "Meio Ambiente". Problematizamos esta atividade, caracterizada como uma produção colaborativa de hipermídia de divulgação científico-tecnológica, ao longo do período letivo da disciplina Didática I da Física da instância curricular integradora. O trabalho em grupo mediado pelo wiki do Moodle tem sido implementado através do PEA (Planejamento, Execução e Avaliação de forma cíclico-espiralada, estudando os casos. Os resultados indicam boa potencialidade da mediação tecnológica, no âmbito do diálogo-problematizador e empowerment, para este tipo de trabalho escolar colaborativo a distância.Through the wiki Moodle, we developed distance education activities in the Physics Course at UFSM, aiming at producing a hypermedia school subject related to the discipline Physics 2 structuring teaching theme: Heat, Environment and uses of Energy (coming from the PCN+, placing the problematic dialogue in the transversal theme "Environment". We designed this activity, described as a collaborative production of hypermedia for scientific-technological dissemination, over the period of school discipline Didactic I from the Physics Course. The working group mediated by the wiki Moodle has been implemented through the PEA (Planning, Execution, and Assessment. The results are positive on the use of technology mediation concerning problematic dialogue and empowerment, in this type of collaborative and distance education.

  13. Wiki-pi: a web-server of annotated human protein-protein interactions to aid in discovery of protein function.

    Directory of Open Access Journals (Sweden)

    Naoki Orii

    Full Text Available Protein-protein interactions (PPIs are the basis of biological functions. Knowledge of the interactions of a protein can help understand its molecular function and its association with different biological processes and pathways. Several publicly available databases provide comprehensive information about individual proteins, such as their sequence, structure, and function. There also exist databases that are built exclusively to provide PPIs by curating them from published literature. The information provided in these web resources is protein-centric, and not PPI-centric. The PPIs are typically provided as lists of interactions of a given gene with links to interacting partners; they do not present a comprehensive view of the nature of both the proteins involved in the interactions. A web database that allows search and retrieval based on biomedical characteristics of PPIs is lacking, and is needed. We present Wiki-Pi (read Wiki-π, a web-based interface to a database of human PPIs, which allows users to retrieve interactions by their biomedical attributes such as their association to diseases, pathways, drugs and biological functions. Each retrieved PPI is shown with annotations of both of the participant proteins side-by-side, creating a basis to hypothesize the biological function facilitated by the interaction. Conceptually, it is a search engine for PPIs analogous to PubMed for scientific literature. Its usefulness in generating novel scientific hypotheses is demonstrated through the study of IGSF21, a little-known gene that was recently identified to be associated with diabetic retinopathy. Using Wiki-Pi, we infer that its association to diabetic retinopathy may be mediated through its interactions with the genes HSPB1, KRAS, TMSB4X and DGKD, and that it may be involved in cellular response to external stimuli, cytoskeletal organization and regulation of molecular activity. The website also provides a wiki-like capability allowing users

  14. Students' Engagement with a Collaborative Wiki Tool Predicts Enhanced Written Exam Performance

    Science.gov (United States)

    Stafford, Tom; Elgueta, Herman; Cameron, Harriet

    2014-01-01

    We introduced voluntary wiki-based exercises to a long-running cognitive psychology course, part of the core curriculum for an undergraduate degree in psychology. Over 2 yearly cohorts, students who used the wiki more also scored higher on the final written exam. Using regression analysis, it is possible to account for students' tendency to score…

  15. Investigating Technical and Pedagogical Usability Issues of Collaborative Learning with Wikis

    Science.gov (United States)

    Hadjerrouit, Said

    2012-01-01

    Wikis have been recently promoted as tools that foster collaborative learning. However, there has been little research devoted to the criteria that are suitable to address issues pertinent to collaborative learning. This paper proposes a set of criteria to explore technical and pedagogical usability issues of collaborative learning with wikis. The…

  16. Instructional Theory for Using a Class Wiki to Support Collaborative Learning in Higher Education

    Science.gov (United States)

    Lin, Chun-Yi

    2013-01-01

    The purpose of this study was to develop an instructional theory for using a class wiki to support collaborative learning in higher education. Although wikis have been identified in theory as one of the most powerful emerging technologies to support collaborative learning, challenges have been revealed in a number of studies regarding student…

  17. The Ecosystem Factor in Supporting Wiki Initiative for Knowledge Sharing in Malaysian Public Organisation

    Science.gov (United States)

    Khuzaimah, Khairil Hizar Md; Affandi, Haryanti Mohd; Hassan, Fadzil

    2015-01-01

    The purpose of this paper is to highlight the significance of considering the organizational ecosystem in implementing wikis for knowledge sharing.The findings suggest that a prerequisite of an effective wiki is the appreciation of the factors that make up the organizational ecosystem; technical and organizational factors are variable elements of…

  18. Wiki as a Corporate Learning Tool: Case Study for Software Development Company

    Science.gov (United States)

    Milovanovic, Milos; Minovic, Miroslav; Stavljanin, Velimir; Savkovic, Marko; Starcevic, Dusan

    2012-01-01

    In our study, we attempted to further investigate how Web 2.0 technologies influence workplace learning. Our particular interest was on using Wiki as a tool for corporate exchange of knowledge with the focus on informal learning. In this study, we collaborated with a multinational software development company that uses Wiki as a corporate tool…

  19. Improving Critical Skills Using Wikis and CGPS in a Physics Classroom

    Science.gov (United States)

    Mohottala, H. E.

    2016-01-01

    We report the combined use of Wikispaces (wikis) and collaborative group problem solving (CGPS) sessions conducted in introductory-level calculus-based physics classes. As a part of this new teaching tool, some essay-type problems were posted on the wiki page on a weekly basis and students were encouraged to participate in problem solving without…

  20. Using Wikis to Investigate Communication, Collaboration and Engagement in Capstone Engineering Design Projects

    Science.gov (United States)

    Berthoud, L.; Gliddon, J.

    2018-01-01

    In today's global Aerospace industry, virtual workspaces are commonly used for collaboration between geographically distributed multidisciplinary teams. This study investigated the use of wikis to look at communication, collaboration and engagement in 'Capstone' team design projects at the end of an engineering degree. Wikis were set up for teams…

  1. Plant interactions with multiple insect herbivores: from community to genes

    NARCIS (Netherlands)

    Stam, J.M.; Kroes, A.; Li, Y.; Gols, R.; Loon, van J.J.A.; Poelman, E.H.; Dicke, M.

    2014-01-01

    Every plant is a member of a complex insect community that consists of tens to hundreds of species that belong to different trophic levels. The dynamics of this community are critically influenced by the plant, which mediates interactions between community members that can occur on the plant

  2. USING WIKIS AS A SUPPORT AND ASSESSMENT TOOL IN COLLABORATIVE DIGITAL GAME-BASED LEARNING ENVIRONMENTS

    Directory of Open Access Journals (Sweden)

    Yavuz SAMUR

    2011-04-01

    Full Text Available In computer-supported collaborative learning (CSCL environments, there are many researches done on collaborative learning activities; however, in game-based learning environments, more research and literature on collaborative learning activities are required. Actually, both game-based learning environments and wikis enable us to use new chances for learning, especially in collaborative learning activities. Therefore, in this paper, related literature on wikis and how game & instructional designers can leverage from wikis in game-based learning settings for enhancing students’ collaborative learning activities are examined. Based on the reviewed literature, two main suggestions are given in this paper with their underlying reasons. First, using wikis as a support tool for enhancing collaboration in digital game-based learning (DGBL environments, and second using wikis as an assessment tool in DGBL are suggested.

  3. Wikis y el nuevo estudiante de lenguas extranjeras

    Directory of Open Access Journals (Sweden)

    Ana Gimeno Sanz

    2010-01-01

    Full Text Available Los entornos digitales cada vez son más comunes en la enseñanza de lenguas extranjeras, además de jugar un papel muy importante como organizadores de tareas, proveedores de input y como gestores de recursos para la enseñanza de idiomas. Permiten, asimismo, a los profesores organizar la interacción de los estudiantes y, al mismo tiempo, proporcionar un magnífico entorno para presentar distintos géneros informativos. Las wikis son hoy en día una de las redes sociales que cada vez se utilizan más para dar apoyo al aprendizaje cooperativo y para fomentar el aprendizaje autónomo. Están estrechamente relacionadas con las metodologías docentes que se basan en el desarrollo de un proyecto o en la resolución de problemas, prácticas docentes éstas en las que tanto alumnos como profesores contribuyen a la construcción del conocimiento y comparten experiencias. Las wikis también han contribuido a crear las llamadas "comunidades de práctica", a las que pueden acudir los estudiantes en contextos de autoaprendizaje o en aquellas situaciones donde se carece del apoyo de un tutor o profesor para encontrar apoyo y consejo. Añadido a esto, la proliferación de herramientas que fomentan la comunicación mediatizada por ordenador han multiplicado los métodos docentes que se aplican en el aula y fuera de ella y han tenido una influencia muy significativa en el surgimiento de un nuevo perfil de estudiante; es decir, aquél que está plenamente acostumbrado a utilizar estas herramientas para relacionarse socialmente con otras personas aunque no sea con fines educativos. Por último, mediante el uso de las wikis se ha desarrollado el concepto de "enseñanza entre pares" y "tutorización entre pares", especialmente en contextos de creación de textos escritos mediante la cooperación colectiva. Este hecho ha contribuido, asimismo, a que el estudiante tenga mayor conciencia de los procesos implícitos en la construcción y edición textual. Este cap

  4. [Radiological knowledge management with the help of departmental wikis].

    Science.gov (United States)

    Schuster, A; Brachthäuser, D; Mansour, M; Alfke, H

    2016-09-01

    In times of RIS (radiology information system) and KIS (hospital information system) systems, patient-related data are at the radiologist's disposal at the push of a button. However, this is not the case for other important data. The increasing complexity of modern medicine demands that up-to-date information like protocols, SOPs (Standards of Practice), news and modifications are constantly accessible to all employees. This aspect of quality assurance becomes increasingly important in the context of certification. For such knowledge management purposes we have built a wiki in our department. Here we report our positive experiences with this technology.

  5. WikiLeaks under fire: Is it electronic civil disobedience?

    Directory of Open Access Journals (Sweden)

    Miquel Comas Oliver

    2017-05-01

    Full Text Available This paper evaluates the usefulness of the civil disobedience theory to legitimate the e-leaking of secrets, i.e. ethical and electronic disclosure of confidential information. First, the main definitions of offline civil disobedience are reviewed. Liberalism established the dominant set of validity conditions: symbolic, peaceful, responsible, public, constitutionally loyal, etc. We criticize this standpoint thanks to the discursive approach, but also highlighting its prejudices. Second, we analyse whether WikiLeaks meets those classical requirements. Encrypted anonymity, partial decriminalization and limited irresponsibility become acceptable. Regarding publicity, the disobedient visualization of a political conflict can be satisfied without revealing the identity of its participants.

  6. Center for Fetal Monkey Gene Transfer for Heart, Lung, and Blood Diseases: An NHLBI Resource for the Gene Therapy Community

    Science.gov (United States)

    Skarlatos, Sonia I.

    2012-01-01

    Abstract The goals of the National Heart, Lung, and Blood Institute (NHLBI) Center for Fetal Monkey Gene Transfer for Heart, Lung, and Blood Diseases are to conduct gene transfer studies in monkeys to evaluate safety and efficiency; and to provide NHLBI-supported investigators with expertise, resources, and services to actively pursue gene transfer approaches in monkeys in their research programs. NHLBI-supported projects span investigators throughout the United States and have addressed novel approaches to gene delivery; “proof-of-principle”; assessed whether findings in small-animal models could be demonstrated in a primate species; or were conducted to enable new grant or IND submissions. The Center for Fetal Monkey Gene Transfer for Heart, Lung, and Blood Diseases successfully aids the gene therapy community in addressing regulatory barriers, and serves as an effective vehicle for advancing the field. PMID:22974119

  7. More than 9,000,000 unique genes in human gut bacterial community: estimating gene numbers inside a human body.

    Science.gov (United States)

    Yang, Xing; Xie, Lu; Li, Yixue; Wei, Chaochun

    2009-06-29

    Estimating the number of genes in human genome has been long an important problem in computational biology. With the new conception of considering human as a super-organism, it is also interesting to estimate the number of genes in this human super-organism. We presented our estimation of gene numbers in the human gut bacterial community, the largest microbial community inside the human super-organism. We got 552,700 unique genes from 202 complete human gut bacteria genomes. Then, a novel gene counting model was built to check the total number of genes by combining culture-independent sequence data and those complete genomes. 16S rRNAs were used to construct a three-level tree and different counting methods were introduced for the three levels: strain-to-species, species-to-genus, and genus-and-up. The model estimates that the total number of genes is about 9,000,000 after those with identity percentage of 97% or up were merged. By combining completed genomes currently available and culture-independent sequencing data, we built a model to estimate the number of genes in human gut bacterial community. The total number of genes is estimated to be about 9 million. Although this number is huge, we believe it is underestimated. This is an initial step to tackle this gene counting problem for the human super-organism. It will still be an open problem in the near future. The list of genomes used in this paper can be found in the supplementary table.

  8. Language-Agnostic Relation Extraction from Abstracts in Wikis

    Directory of Open Access Journals (Sweden)

    Nicolas Heist

    2018-03-01

    Full Text Available Large-scale knowledge graphs, such as DBpedia, Wikidata, or YAGO, can be enhanced by relation extraction from text, using the data in the knowledge graph as training data, i.e., using distant supervision. While most existing approaches use language-specific methods (usually for English, we present a language-agnostic approach that exploits background knowledge from the graph instead of language-specific techniques and builds machine learning models only from language-independent features. We demonstrate the extraction of relations from Wikipedia abstracts, using the twelve largest language editions of Wikipedia. From those, we can extract 1.6 M new relations in DBpedia at a level of precision of 95%, using a RandomForest classifier trained only on language-independent features. We furthermore investigate the similarity of models for different languages and show an exemplary geographical breakdown of the information extracted. In a second series of experiments, we show how the approach can be transferred to DBkWik, a knowledge graph extracted from thousands of Wikis. We discuss the challenges and first results of extracting relations from a larger set of Wikis, using a less formalized knowledge graph.

  9. Early community context, genes, and youth body mass index trajectories: an investigation of gene-community interplay over early life course.

    Science.gov (United States)

    Wickrama, Kandauda K A S; O'Neal, Catherine Walker; Lee, Tae Kyoung

    2013-09-01

    To investigate additive and interactive influences of community adversity and cumulative genetic sensitivity on youth body mass index (BMI) trajectories over adolescence and young adulthood. We used latent growth curve modeling to examine BMI trajectories over three waves (1995, 2001, and 2008) of the National Longitudinal Study of Adolescent Health (n = 14,563). We measured genetic sensitivity by a cumulative index of genes associated with serotonin and dopamine functions. Community adversity was positively associated with the initial level and rate of change in BMI trajectories over time. Adolescents experiencing community adversity had a higher BMI at Wave 1 and gained weight more quickly than those who did not live in adverse communities. Community adversity interacted with cumulative genetic sensitivity to explain variation in the rate of change in BMI trajectories. The influence of community adversity was greater for those with more sensitivity alleles than those with fewer sensitivity alleles. Gender, race/ethnicity, and family contexts were also associated with youth BMI trajectories. Community adversity in early adolescence, and its interaction with genes, has far-reaching consequences, including the rate of change in BMI trajectories extending into adulthood. This work has practical implications for future intervention/prevention programs. Published by Elsevier Inc.

  10. Analysis of tag-based Recommendation Performance for a Semantic Wiki

    DEFF Research Database (Denmark)

    Durao, Frederico; Dolog, Peter

    2009-01-01

    Recommendations play a very important role for revealing related topics addressed in the wikis beyond the currently viewed page. In this paper, we extend KiWi, a semantic wiki with three different recommendation approaches. The first approach is implemented as a traditional tag-based retrieval......, the second takes into account external factors such as tag popularity, tag representativeness and the affinity between user and tag and the third approach recommends pages in grouped by tag. The experiment evaluates the wiki performance in different scenarios regarding the amount of pages, tags and users...

  11. BOWiki: an ontology-based wiki for annotation of data and integration of knowledge in biology

    Directory of Open Access Journals (Sweden)

    Gregorio Sergio E

    2009-05-01

    Full Text Available Abstract Motivation Ontology development and the annotation of biological data using ontologies are time-consuming exercises that currently require input from expert curators. Open, collaborative platforms for biological data annotation enable the wider scientific community to become involved in developing and maintaining such resources. However, this openness raises concerns regarding the quality and correctness of the information added to these knowledge bases. The combination of a collaborative web-based platform with logic-based approaches and Semantic Web technology can be used to address some of these challenges and concerns. Results We have developed the BOWiki, a web-based system that includes a biological core ontology. The core ontology provides background knowledge about biological types and relations. Against this background, an automated reasoner assesses the consistency of new information added to the knowledge base. The system provides a platform for research communities to integrate information and annotate data collaboratively. Availability The BOWiki and supplementary material is available at http://www.bowiki.net/. The source code is available under the GNU GPL from http://onto.eva.mpg.de/trac/BoWiki.

  12. Co-development of a Wiki for Tracking the Environmental Footprint of Small Business Activities

    Directory of Open Access Journals (Sweden)

    Helen Hasan

    2017-10-01

    Full Text Available Aim/Purpose: Climate change mitigation is a global challenge, in which academia and business have a role to play. This research explores ways to develop a freely-available information system that would enable small businesses to identify and reduce their environmental footprint. Background: While large organizations have the resources to track emissions and other pertinent data, small businesses may not, despite intentions to be more environmentally responsible. Freely available applications to track emissions focus on the carbon footprint of things, whereas activities are a more meaningful unit of analysis for business managers. Methodology: Using a design science research approach, we conducted a study of a collaborative project that investigated how a low-cost, freely-available online wiki could be developed by group of students, under the guidance of university scholars and business owners. In the project, different student groups were tasked to create the wiki, input content and design a dashboard interface for managers to find data relevant to their business. The research takes an information systems view of the project, relying on the holistic notion of activity from activity theory and taking a design science approach to the study. Contribution: The paper contributes to the practices of green information systems, climate change, and small business. Theoretically it provides new insights into the linear view of design science in resource poor, collaborative projects. Findings: The research demonstrates the viability of an online system to track the envi-ronmental footprint of business activities. It reveals the challenges from a design science perspective of attempts to create online systems using freely available products and labor. Recommendations for Practitioners: Meaningful information systems to assist small businesses to manage their environmental footprint should focus on activities not things, be low cost and easy to use

  13. Denitrification gene expression in clay-soil bacterial community

    Science.gov (United States)

    Pastorelli, R.; Landi, S.

    2009-04-01

    Our contribution in the Italian research project SOILSINK was focused on microbial denitrification gene expression in Mediterranean agricultural soils. In ecosystems with high inputs of nitrogen, such as agricultural soils, denitrification causes a net loss of nitrogen since nitrate is reduced to gaseous forms, which are released into the atmosphere. Moreover, incomplete denitrification can lead to emission of nitrous oxide, a potent greenhouse gas which contributes to global warming and destruction of ozone layer. A critical role in denitrification is played by microorganisms and the ability to denitrify is widespread among a variety of phylogenetically unrelated organisms. Data reported here are referred to wheat cultivation in a clay-rich soil under different environmental impact management (Agugliano, AN, Italy). We analysed the RNA directly extracted from soil to provide information on in situ activities of specific populations. The expression of genes coding for two nitrate reductases (narG and napA), two nitrite reductases (nirS and nirK), two nitric oxide reductases (cnorB and qnorB) and nitrous oxide reductase (nosZ) was analyzed by reverse transcription (RT)-nested PCR. Only napA, nirS, nirK, qnorB and nosZ were detected and fragments sequenced showed high similarity with the corresponding gene sequences deposited in GenBank database. These results suggest the suitability of the method for the qualitative detection of denitrifying bacteria in environmental samples and they offered us the possibility to perform the denaturing gradient gel electrophoresis (DGGE) analyzes for denitrification genes.. Earlier conclusions showed nirK gene is more widely distributed in soil environment than nirS gene. The results concerning the nosZ expression indicated that microbial activity was clearly present only in no-tilled and no-fertilized soils.

  14. On the Application of WIKI technology as a Web application 2 in the ...

    African Journals Online (AJOL)

    pc

    2018-03-05

    Mar 5, 2018 ... development and continuous change in all aspects of life. Educational .... programs and applications which provide an ideal environment to integrate the ..... We can say that the wiki technology is a joint effort and an outcome ...

  15. Students’ engagement with a collaborative wiki tool predicts enhanced written exam performance

    Directory of Open Access Journals (Sweden)

    Tom Stafford

    2014-08-01

    Full Text Available We introduced voluntary wiki-based exercises to a long-running cognitive psychology course, part of the core curriculum for an undergraduate degree in psychology. Over 2 yearly cohorts, students who used the wiki more also scored higher on the final written exam. Using regression analysis, it is possible to account for students’ tendency to score well on other psychology exams, thus statistically removing some obvious candidate third factors, such as general talent or enthusiasm for psychology, which might drive this correlation. Such an analysis shows that both high- and low-grading students who used the wiki got higher scores on the final exam, with engaged wiki users scoring an average of an extra 5 percentage points. We offer an interpretation of the mechanisms of action in terms of the psychological literature on learning and memory.

  16. Development of generic and strategic skills through a wiki platform in industrial engineering programs

    Directory of Open Access Journals (Sweden)

    L. Celorrio-Barragué

    2016-03-01

    Full Text Available This paper describes the collaborative learning task carried out in the framework of a Strength of Materials course in an undergraduate degree program in Industrial Engineering using a wiki platform as a support tool. Stages of the teaching/learning process are described. These are: organization of the wiki to host the work of student groups, creation of working groups and assignation of projects, delivery of guidance material and model, editing the project and publishing pages on the wiki, assessments performed using rubrics, and the results obtained. The wiki platform provides interesting statistics for evaluating cooperation between students and time variation of students’ effort. The final quality of the projects is very high because a midterm evaluation in the form of a “peer review rubric” is carried out. Then, students improve their projects. The paper concludes by gathering the opinions made by students; the benefits provided by this teaching experience are then analyzed.

  17. Design and Implementation of Wiki Services in a Multilevel Secure Environment

    National Research Council Canada - National Science Library

    Ong, Kar L

    2007-01-01

    .... This thesis extends the existing collaboration capability in MYSEA to include hypertext content-based collaborative authoring and information sharing through the use of the increasingly popular wiki technology...

  18. Paper-pen peer-correction versus wiki-based peer-correction

    Directory of Open Access Journals (Sweden)

    Froldova Vladimira

    2016-01-01

    Full Text Available This study reports on the comparison of the students’ achievement and their attitudes towards the use of paper-pen peer-correction and wiki-based peer-correction within English language lessons and CLIL Social Science lessons at the higher secondary school in Prague. Questionnaires and semi-structured interviews were utilized to gather information. The data suggests that students made considerable use of wikis and showed higher degrees of motivation in wiki-based peer-correction during English language lessons than in CLIL Social Science lessons. In both cases wikis not only contributed to developing students’ writing skills, but also helped students recognize the importance of collaboration.

  19. Impact of a dermatology wiki website on dermatology education.

    Science.gov (United States)

    Karimkhani, Chante; Boyers, Lindsay N; Ellis, Lixia Z; Brice, Sylvia; Chen, David L; Dunnick, Cory A; Dellavalle, Robert P

    2015-01-15

    The Dermatology Education Wiki (dermwiki) website serves as a resource platform for medical students and residents. The readily accessible interface provides dermatology articles, survival guides, didactic lectures, and links to faculty talks as well as research opportunities. To assess medical student and resident satisfaction with the dermwiki website. Fourth-year medical students taking a dermatology elective were provided with a temporary password to access relevant dermwiki information. A satisfaction survey was created to assess whether medical students found the website helpful. Second- and third-year dermatology residents were also surveyed to compare satisfaction scores prior to and after the introduction of the dermwiki website. End-of-rotation medical student exam scores were tabulated and compared to the average scores from years prior to the development of the dermwiki website. Medical students rated the dermatology elective with the dermwiki website higher than rotations without a wiki (8.12 vs 7.31). Students planning to go into dermatology were more satisfied with the dermwiki website, reported accessing the website more frequently (11 times vs 9.5 times), and reported more time spent studying (12.2 hours vs 6.7 hours) than students not going into dermatology. End-of-rotation medical student exam scores did not differ from those prior to the development of the demwiki website. Ten second- and third-year dermatology residents unanimously stated that they were more satisfied with the program after the institution of the dermwiki website. Overall, addition of the dermwiki website to the dermatology elective curriculum has improved medical student and resident satisfaction scores. The improvement is greater among students planning to enter the field of dermatology. This study serves as a model for the incorporation of internet-based interactive tools to transform and supplement the learning environment.

  20. Wiki-based Collaborative Learning Experience in a Foreign Language Blended Course

    OpenAIRE

    Krasnova, Tatiana Ivanovna; Gorbatova, Tatiana Nikolaevna; Kudryashova, Aleksandra Vladimirovna; Popova, Anna Nikolaevna

    2016-01-01

    The article emphasizes the educational potential of wikis for learning foreign languages. It focuses on students’ collaboration based on integration of different types of activities within a highly motivating blended learning environment where learners can interact and share their ideas. The study aims to understand if wikis could enhance online collaboration and positively affect students’ attitudes to group work. It tries to explore the level of participation and contribution of students in...

  1. Developing Student Science and Information Literacy through Contributions to the Society of Exploration Geophysicists (SEG) Wiki

    Science.gov (United States)

    Guertin, L. A.; Farley, I.; Geary, A.

    2016-12-01

    Introductory-level Earth science courses provide the opportunity for science and non-science majors to expand discipline-specific content knowledge while enhancing skill sets applicable to all disciplines. The outcomes of the student work can then benefit the education and outreach efforts of an international organization - in this case, a wiki devoted exclusively to the geosciences, managed by the Society of Exploration Geophysicists (SEG). The course Environment Earth at Penn State Brandywine is a general education science course with the overarching course goal for students to understand, communicate examples, and make informed decisions relating to big ideas and fundamental concepts of Earth science. To help accomplish this goal, students carry out a semester-long digital engaged scholarship project that benefits the users of the SEG Wiki (http://wiki.seg.org/). To begin with developing the literacy of students and their ability to read, interpret, and evaluate sources of scientific news, the first assignment requires students to write an annotated bibliography on a specific topic that serves as the foundation for a new SEG Wiki article. Once students have collected and summarized information from reliable sources, students learn how writing for a wiki is different than writing a term paper and begin drafting their wiki page. Students peer review each other's work for content and clarity before publishing their work on the SEG wiki. Students respond positively to this project, reporting a better understanding of and respect towards the authors of online wiki pages, as well as an overall satisfaction of knowing their work will benefit others. Links to student-generated pages and instructional materials can be found at: http://sites.psu.edu/segwiki/.

  2. Connected Gene Communities Underlie Transcriptional Changes in Cornelia de Lange Syndrome.

    Science.gov (United States)

    Boudaoud, Imène; Fournier, Éric; Baguette, Audrey; Vallée, Maxime; Lamaze, Fabien C; Droit, Arnaud; Bilodeau, Steve

    2017-09-01

    Cornelia de Lange syndrome (CdLS) is a complex multisystem developmental disorder caused by mutations in cohesin subunits and regulators. While its precise molecular mechanisms are not well defined, they point toward a global deregulation of the transcriptional gene expression program. Cohesin is associated with the boundaries of chromosome domains and with enhancer and promoter regions connecting the three-dimensional genome organization with transcriptional regulation. Here, we show that connected gene communities, structures emerging from the interactions of noncoding regulatory elements and genes in the three-dimensional chromosomal space, provide a molecular explanation for the pathoetiology of CdLS associated with mutations in the cohesin-loading factor NIPBL and the cohesin subunit SMC1A NIPBL and cohesin are important constituents of connected gene communities that are centrally positioned at noncoding regulatory elements. Accordingly, genes deregulated in CdLS are positioned within reach of NIPBL- and cohesin-occupied regions through promoter-promoter interactions. Our findings suggest a dynamic model where NIPBL loads cohesin to connect genes in communities, offering an explanation for the gene expression deregulation in the CdLS. Copyright © 2017 by the Genetics Society of America.

  3. The Use of a Wiki to Facilitate Collaborative Learning in a South African Physiotherapy Department

    Directory of Open Access Journals (Sweden)

    M. Rowe

    2012-12-01

    Full Text Available The dominant form of teaching in higher education remains the lecture,even though evidence suggests that it alone is inadequate to facilitate the development ofthe higher order thinking skills required in clinical practice. The use of wikis may have a roleto play in facilitating collaborative learning practices that are important for professionaldevelopment. This descriptive survey evaluated the use of a wiki for a collaborative learningactivity within small groups of undergraduate physiotherapy students in a South Africanuniversity. Students participated in a wiki-based assignment and were then surveyedusing open- and closed-ended questions to determine their perceptions and experiences of the process. The results indicate thatalthough a wiki can be used to develop relevant content, there were significant challenges in its implementation. These included apoor understanding by students of how to work effectively in groups, a lack of physical and epistemological access to the internet,and the need for adequate preparation and support. Some features of the wiki were found to have an impact on the quality ofthe work produced, including the use of Discussion pages, peer review, and the public nature of the wiki. The conclusion is thatwikis may have a role to play in collaborative groupwork, but that that students need to be adequately prepared and supportedthroughout the process.

  4. Crowdsourcing the nodulation gene network discovery environment.

    Science.gov (United States)

    Li, Yupeng; Jackson, Scott A

    2016-05-26

    The Legumes (Fabaceae) are an economically and ecologically important group of plant species with the conspicuous capacity for symbiotic nitrogen fixation in root nodules, specialized plant organs containing symbiotic microbes. With the aim of understanding the underlying molecular mechanisms leading to nodulation, many efforts are underway to identify nodulation-related genes and determine how these genes interact with each other. In order to accurately and efficiently reconstruct nodulation gene network, a crowdsourcing platform, CrowdNodNet, was created. The platform implements the jQuery and vis.js JavaScript libraries, so that users are able to interactively visualize and edit the gene network, and easily access the information about the network, e.g. gene lists, gene interactions and gene functional annotations. In addition, all the gene information is written on MediaWiki pages, enabling users to edit and contribute to the network curation. Utilizing the continuously updated, collaboratively written, and community-reviewed Wikipedia model, the platform could, in a short time, become a comprehensive knowledge base of nodulation-related pathways. The platform could also be used for other biological processes, and thus has great potential for integrating and advancing our understanding of the functional genomics and systems biology of any process for any species. The platform is available at http://crowd.bioops.info/ , and the source code can be openly accessed at https://github.com/bioops/crowdnodnet under MIT License.

  5. Dynamic changes in functional gene copy numbers and microbial communities during degradation of pyrene in soils

    International Nuclear Information System (INIS)

    Peng Jingjing; Cai Chao; Qiao Min; Li Hong; Zhu Yongguan

    2010-01-01

    This study investigates the dynamics of pyrene degradation rates, microbial communities, and functional gene copy numbers during the incubation of pyrene-spiked soils. Spiking pyrene to the soil was found to have negligible effects on the bacterial community present. Our results demonstrated that there was a significant difference in nidA gene copy numbers between sampling dates in QZ soil. Mycobacterium 16S rDNA clone libraries showed that more than 90% mycobacteria detected were closely related to fast-growing PAH-degrading Mycobacterium in pyrene-spiked soil, while other sequences related to slow-growing Mycobacterium were only detected in the control soil. It is suggested that nidA gene copy number and fast-growing PAH-degrading Mycobacterium could be used as indicators to predict pyrene contamination and its degradation activity in soils. - nidA gene and fast-growing PAH-degrading Mycobacterium can serve as indicators for pyrene contamination.

  6. Health Care Professionals’ Beliefs About Using Wiki-Based Reminders to Promote Best Practices in Trauma Care

    OpenAIRE

    Archambault, Patrick Michel; Bilodeau, Andrea; Gagnon, Marie-Pierre; Aubin, Karine; Lavoie, André; Lapointe, Jean; Poitras, Julien; Croteau, Sylvain; Pham-Dinh, Martin; Légaré, France

    2012-01-01

    Background Wikis are knowledge translation tools that could help health professionals implement best practices in acute care. Little is known about the factors influencing professionals’ use of wikis. Objectives To identify and compare the beliefs of emergency physicians (EPs) and allied health professionals (AHPs) about using a wiki-based reminder that promotes evidence-based care for traumatic brain injuries. Methods Drawing on the theory of planned behavior, we conducted semistructured int...

  7. Functional Gene Diversity and Metabolic Potential of the Microbial Community in an Estuary-Shelf Environment

    Directory of Open Access Journals (Sweden)

    Yu Wang

    2017-06-01

    Full Text Available Microbes play crucial roles in various biogeochemical processes in the ocean, including carbon (C, nitrogen (N, and phosphorus (P cycling. Functional gene diversity and the structure of the microbial community determines its metabolic potential and therefore its ecological function in the marine ecosystem. However, little is known about the functional gene composition and metabolic potential of bacterioplankton in estuary areas. The East China Sea (ECS is a dynamic marginal ecosystem in the western Pacific Ocean that is mainly affected by input from the Changjiang River and the Kuroshio Current. Here, using a high-throughput functional gene microarray (GeoChip, we analyzed the functional gene diversity, composition, structure, and metabolic potential of microbial assemblages in different ECS water masses. Four water masses determined by temperature and salinity relationship showed different patterns of functional gene diversity and composition. Generally, functional gene diversity [Shannon–Weaner’s H and reciprocal of Simpson’s 1/(1-D] in the surface water masses was higher than that in the bottom water masses. The different presence and proportion of functional genes involved in C, N, and P cycling among the bacteria of the different water masses showed different metabolic preferences of the microbial populations in the ECS. Genes involved in starch metabolism (amyA and nplT showed higher proportion in microbial communities of the surface water masses than of the bottom water masses. In contrast, a higher proportion of genes involved in chitin degradation was observed in microorganisms of the bottom water masses. Moreover, we found a higher proportion of nitrogen fixation (nifH, transformation of hydroxylamine to nitrite (hao and ammonification (gdh genes in the microbial communities of the bottom water masses compared with those of the surface water masses. The spatial variation of microbial functional genes was significantly correlated

  8. Analyses of soil microbial community compositions and functional genes reveal potential consequences of natural forest succession.

    Science.gov (United States)

    Cong, Jing; Yang, Yunfeng; Liu, Xueduan; Lu, Hui; Liu, Xiao; Zhou, Jizhong; Li, Diqiang; Yin, Huaqun; Ding, Junjun; Zhang, Yuguang

    2015-05-06

    The succession of microbial community structure and function is a central ecological topic, as microbes drive the Earth's biogeochemical cycles. To elucidate the response and mechanistic underpinnings of soil microbial community structure and metabolic potential relevant to natural forest succession, we compared soil microbial communities from three adjacent natural forests: a coniferous forest (CF), a mixed broadleaf forest (MBF) and a deciduous broadleaf forest (DBF) on Shennongjia Mountain in central China. In contrary to plant communities, the microbial taxonomic diversity of the DBF was significantly (P the DBF. Furthermore, a network analysis of microbial carbon and nitrogen cycling genes showed the network for the DBF samples was relatively large and tight, revealing strong couplings between microbes. Soil temperature, reflective of climate regimes, was important in shaping microbial communities at both taxonomic and functional gene levels. As a first glimpse of both the taxonomic and functional compositions of soil microbial communities, our results suggest that microbial community structure and function potentials will be altered by future environmental changes, which have implications for forest succession.

  9. Abundances of Clinically Relevant Antibiotic Resistance Genes and Bacterial Community Diversity in the Weihe River, China

    Directory of Open Access Journals (Sweden)

    Xiaojuan Wang

    2018-04-01

    Full Text Available The spread of antibiotic resistance genes in river systems is an emerging environmental issue due to their potential threat to aquatic ecosystems and public health. In this study, we used droplet digital polymerase chain reaction (ddPCR to evaluate pollution with clinically relevant antibiotic resistance genes (ARGs at 13 monitoring sites along the main stream of the Weihe River in China. Six clinically relevant ARGs and a class I integron-integrase (intI1 gene were analyzed using ddPCR, and the bacterial community was evaluated based on the bacterial 16S rRNA V3–V4 regions using MiSeq sequencing. The results indicated Proteobacteria, Actinobacteria, Cyanobacteria, and Bacteroidetes as the dominant phyla in the water samples from the Weihe River. Higher abundances of blaTEM, strB, aadA, and intI1 genes (103 to 105 copies/mL were detected in the surface water samples compared with the relatively low abundances of strA, mecA, and vanA genes (0–1.94 copies/mL. Eight bacterial genera were identified as possible hosts of the intI1 gene and three ARGs (strA, strB, and aadA based on network analysis. The results suggested that the bacterial community structure and horizontal gene transfer were associated with the variations in ARGs.

  10. Development and usage of wiki-based software for point-of-care emergency medical information.

    Science.gov (United States)

    Donaldson, Ross I; Ostermayer, Daniel G; Banuelos, Rosa; Singh, Manpreet

    2016-11-01

    To describe the creation and evaluate the usage of the first medical wiki linked to dedicated mobile applications. With the support of multiple current and past contributors, we developed an emergency medicine wiki linked to offline mobile applications (WikEM) in 2009. First deployment was at the Harbor-UCLA Medical Center emergency medicine residency program, with the wiki later opened to public use. To evaluate the project, we performed a post hoc analysis of system use and surveyed 8 years of current and past residents. Outcomes included website and application analytics, as well as survey analysis by composite response categories. Over the 6-year period of this project, the wiki grew to over 7250 pages and 45 500 edits. The website receives more than 85 000 user sessions per month, with over 150 million page views to date. There have been over 200 000 installs of the mobile applications, progressing to produce over 5000 mobile sessions daily. Of potential survey respondents, 87.7% (107) completed the Internet-based survey. Among those who contributed to the wiki, 74.6% reported that it benefited their understanding of core emergency medicine content. Of program graduates, the vast majority reported use of the wiki as a resource after residency (93.8%) along with improvement in clinical efficiency (89.7%). Residents reported higher use and a more favorable opinion of wiki usefulness compared to graduates (P mobile applications is beneficial for resident education and useful in post-residency clinical practice. © The Author 2016. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  11. Education in health research methodology: use of a wiki for knowledge translation.

    Directory of Open Access Journals (Sweden)

    Michele P Hamm

    Full Text Available INTRODUCTION: A research-practice gap exists between what is known about conducting methodologically rigorous randomized controlled trials (RCTs and what is done. Evidence consistently shows that pediatric RCTs are susceptible to high risk of bias; therefore novel methods of influencing the design and conduct of trials are required. The objective of this study was to develop and pilot test a wiki designed to educate pediatric trialists and trainees in the principles involved in minimizing risk of bias in RCTs. The focus was on preliminary usability testing of the wiki. METHODS: The wiki was developed through adaptation of existing knowledge translation strategies and through tailoring the site to the identified needs of the end-users. The wiki was evaluated for usability and user preferences regarding the content and formatting. Semi-structured interviews were conducted with 15 trialists and systematic reviewers, representing varying levels of experience with risk of bias or the conduct of trials. Data were analyzed using content analysis. RESULTS: Participants found the wiki to be well organized, easy to use, and straightforward to navigate. Suggestions for improvement tended to focus on clarification of the text or on esthetics, rather than on the content or format. Participants liked the additional features of the site that were supplementary to the text, such as the interactive examples, and the components that focused on practical applications, adding relevance to the theory presented. While the site could be used by both trialists and systematic reviewers, the lack of a clearly defined target audience caused some confusion among participants. CONCLUSIONS: Participants were supportive of using a wiki as a novel educational tool. The results of this pilot test will be used to refine the risk of bias wiki, which holds promise as a knowledge translation intervention for education in medical research methodology.

  12. Community-Level Analysis of psbA Gene Sequences and Irgarol Tolerance in Marine Periphyton▿

    Science.gov (United States)

    Eriksson, K. M.; Clarke, A. K.; Franzen, L.-G.; Kuylenstierna, M.; Martinez, K.; Blanck, H.

    2009-01-01

    This study analyzes psbA gene sequences, predicted D1 protein sequences, species relative abundance, and pollution-induced community tolerance in marine periphyton communities exposed to the antifouling compound Irgarol 1051. The mechanism of action of Irgarol is the inhibition of photosynthetic electron transport at photosystem II by binding to the D1 protein. The metagenome of the communities was used to produce clone libraries containing fragments of the psbA gene encoding the D1 protein. Community tolerance was quantified with a short-term test for the inhibition of photosynthesis. The communities were established in a continuous flow of natural seawater through microcosms with or without added Irgarol. The selection pressure from Irgarol resulted in an altered species composition and an inducted community tolerance to Irgarol. Moreover, there was a very high diversity in the psbA gene sequences in the periphyton, and the composition of psbA and D1 fragments within the communities was dramatically altered by increased Irgarol exposure. Even though tolerance to this type of compound in land plants often depends on a single amino acid substitution (Ser264→Gly) in the D1 protein, this was not the case for marine periphyton species. Instead, the tolerance mechanism likely involves increased degradation of D1. When we compared sequences from low and high Irgarol exposure, differences in nonconserved amino acids were found only in the so-called PEST region of D1, which is involved in regulating its degradation. Our results suggest that environmental contamination with Irgarol has led to selection for high-turnover D1 proteins in marine periphyton communities at the west coast of Sweden. PMID:19088321

  13. Microbial Community and Functional Gene Changes in Arctic Tundra Soils in a Microcosm Warming Experiment

    Directory of Open Access Journals (Sweden)

    Ziming Yang

    2017-09-01

    Full Text Available Microbial decomposition of soil organic carbon (SOC in thawing Arctic permafrost is important in determining greenhouse gas feedbacks of tundra ecosystems to climate. However, the changes in microbial community structure during SOC decomposition are poorly known. Here we examine these changes using frozen soils from Barrow, Alaska, USA, in anoxic microcosm incubation at −2 and 8°C for 122 days. The functional gene array GeoChip was used to determine microbial community structure and the functional genes associated with SOC degradation, methanogenesis, and Fe(III reduction. Results show that soil incubation after 122 days at 8°C significantly decreased functional gene abundance (P < 0.05 associated with SOC degradation, fermentation, methanogenesis, and iron cycling, particularly in organic-rich soil. These observations correspond well with decreases in labile SOC content (e.g., reducing sugar and ethanol, methane and CO2 production, and Fe(III reduction. In contrast, the community functional structure was largely unchanged in the −2°C incubation. Soil type (i.e., organic vs. mineral and the availability of labile SOC were among the most significant factors impacting microbial community structure. These results demonstrate the important roles of microbial community in SOC degradation and support previous findings that SOC in organic-rich Arctic tundra is highly vulnerable to microbial degradation under warming.

  14. Analysis of the functional gene structure and metabolic potential of microbial community in high arsenic groundwater.

    Science.gov (United States)

    Li, Ping; Jiang, Zhou; Wang, Yanhong; Deng, Ye; Van Nostrand, Joy D; Yuan, Tong; Liu, Han; Wei, Dazhun; Zhou, Jizhong

    2017-10-15

    Microbial functional potential in high arsenic (As) groundwater ecosystems remains largely unknown. In this study, the microbial community functional composition of nineteen groundwater samples was investigated using a functional gene array (GeoChip 5.0). Samples were divided into low and high As groups based on the clustering analysis of geochemical parameters and microbial functional structures. The results showed that As related genes (arsC, arrA), sulfate related genes (dsrA and dsrB), nitrogen cycling related genes (ureC, amoA, and hzo) and methanogen genes (mcrA, hdrB) in groundwater samples were correlated with As, SO 4 2- , NH 4 + or CH 4 concentrations, respectively. Canonical correspondence analysis (CCA) results indicated that some geochemical parameters including As, total organic content, SO 4 2- , NH 4 + , oxidation-reduction potential (ORP) and pH were important factors shaping the functional microbial community structures. Alkaline and reducing conditions with relatively low SO 4 2- , ORP, and high NH 4 + , as well as SO 4 2- and Fe reduction and ammonification involved in microbially-mediated geochemical processes could be associated with As enrichment in groundwater. This study provides an overall picture of functional microbial communities in high As groundwater aquifers, and also provides insights into the critical role of microorganisms in As biogeochemical cycling. Copyright © 2017 Elsevier Ltd. All rights reserved.

  15. Community Structure Analysis of Gene Interaction Networks in Duchenne Muscular Dystrophy.

    Directory of Open Access Journals (Sweden)

    Tejaswini Narayanan

    Full Text Available Duchenne Muscular Dystrophy (DMD is an important pathology associated with the human skeletal muscle and has been studied extensively. Gene expression measurements on skeletal muscle of patients afflicted with DMD provides the opportunity to understand the underlying mechanisms that lead to the pathology. Community structure analysis is a useful computational technique for understanding and modeling genetic interaction networks. In this paper, we leverage this technique in combination with gene expression measurements from normal and DMD patient skeletal muscle tissue to study the structure of genetic interactions in the context of DMD. We define a novel framework for transforming a raw dataset of gene expression measurements into an interaction network, and subsequently apply algorithms for community structure analysis for the extraction of topological communities. The emergent communities are analyzed from a biological standpoint in terms of their constituent biological pathways, and an interpretation that draws correlations between functional and structural organization of the genetic interactions is presented. We also compare these communities and associated functions in pathology against those in normal human skeletal muscle. In particular, differential enhancements are observed in the following pathways between pathological and normal cases: Metabolic, Focal adhesion, Regulation of actin cytoskeleton and Cell adhesion, and implication of these mechanisms are supported by prior work. Furthermore, our study also includes a gene-level analysis to identify genes that are involved in the coupling between the pathways of interest. We believe that our results serve to highlight important distinguishing features in the structural/functional organization of constituent biological pathways, as it relates to normal and DMD cases, and provide the mechanistic basis for further biological investigations into specific pathways differently regulated

  16. BCD: a wiki-based decommissioning knowledge management tool

    International Nuclear Information System (INIS)

    Fontaine, V.; Coudouneau, L.; Goursaud, V.

    2008-01-01

    Knowledge management allows decommissioning stakeholders to take advantage of past experience (in terms of efficiency, quality, safety, cost, etc.), avoid repeating previous errors, and identify good ideas and practices. It is usually broken down into three processes: collecting information, supplementing and enriching it, and making it available to all decommissioning stakeholders. The CEA has been collecting and centralizing data for many years: the first qualitative assessment of operational experience began in 1991. However, the documents collected were not always relevant for this assessment and, for lack of enrichment and distribution, were generally not used to a significant extent. In order to take advantage of the existing and future body of knowledge and to share this knowledge among decommissioning stakeholders, the CEA decommissioning review unit decided to develop an intranet site known as BCD (from the French acronym for Central Decommissioning Database) using the same wiki technology as the collaborative web encyclopedia, Wikipedia. The objective of BCD is to develop a decommissioning encyclopedia comprising definitions and terminology, the regulatory framework, the lessons of experience with technical or contractual projects, guidelines, statements of results, etc. This article describes BCD and its potential, together with the results observed to date and its prospects for future development. (authors)

  17. Beyond Wiki to Judgewiki for Transparent Climate Change Decisions

    Science.gov (United States)

    Capron, M. E.

    2008-12-01

    Climate Change is like the prisoner's dilemma, a zero-sum game, or cheating in sports. Everyone and every country is tempted to selfishly maintain or advance their standard of living. The tremendous difference between standards of living amplifies the desire to opt out of Climate Change solutions adverse to economic competitiveness. Climate Change is also exceedingly complex. No one person, one organization, one country, or partial collection of countries has the capacity and the global support needed to make decisions on Climate Change solutions. There are thousands of potential actions, tens of thousands of known and unknown environmental and economic impacts. Some actions are belatedly found to be unsustainable beyond token volumes, corn ethanol or soy-biodiesel for example. Mankind can address human nature and complexity with a globally transparent information and decision process available to all 7 billion of us. We need a process that builds trust and simplifies complexity. Fortunately, we have the Internet for trust building communication and computers to simplify complexity. Mankind can produce new software tailored to the challenge. We would combine group information collection software (a wiki) with a decision-matrix (a judge), market forecasting, and video games to produce the tool mankind needs for trust building transparent decisions on Climate Change actions. The resulting software would be a judgewiki.

  18. Proposing a Wiki-Based Technique for Collaborative Essay Writing (Propuesta de un modelo pedagógico para la escritura colaborativa de ensayos en un entorno virtual wiki)

    Science.gov (United States)

    Ortiz Navarrete, Mabel; Ferreira Cabrera, Anita

    2014-01-01

    This paper aims at proposing a technique for students learning English as a foreign language when they collaboratively write an argumentative essay in a wiki environment. A wiki environment and collaborative work play an important role within the academic writing task. Nevertheless, an appropriate and systematic work assignment is required in…

  19. Search extension transforms Wiki into a relational system: a case for flavonoid metabolite database.

    Science.gov (United States)

    Arita, Masanori; Suwa, Kazuhiro

    2008-09-17

    In computer science, database systems are based on the relational model founded by Edgar Codd in 1970. On the other hand, in the area of biology the word 'database' often refers to loosely formatted, very large text files. Although such bio-databases may describe conflicts or ambiguities (e.g. a protein pair do and do not interact, or unknown parameters) in a positive sense, the flexibility of the data format sacrifices a systematic query mechanism equivalent to the widely used SQL. To overcome this disadvantage, we propose embeddable string-search commands on a Wiki-based system and designed a half-formatted database. As proof of principle, a database of flavonoid with 6902 molecular structures from over 1687 plant species was implemented on MediaWiki, the background system of Wikipedia. Registered users can describe any information in an arbitrary format. Structured part is subject to text-string searches to realize relational operations. The system was written in PHP language as the extension of MediaWiki. All modifications are open-source and publicly available. This scheme benefits from both the free-formatted Wiki style and the concise and structured relational-database style. MediaWiki supports multi-user environments for document management, and the cost for database maintenance is alleviated.

  20. The State of Wiki Usage in U.S. K-12 Schools: Leveraging Web 2.0 Data Warehouses to Study Quality and Equality in Online Learning Environments

    Science.gov (United States)

    Reich, Blair Justin Fire

    2012-01-01

    In the first part of this dissertation, I document wiki usage in U.S. K-12 settings by analyzing data on a representative sample drawn from a population of nearly 180,000 wikis. My research group, which I lead and managed, measured the opportunities wikis provide for students to develop 21st century skills such as expert thinking, complex…

  1. The State of Wiki Usage in U.S. K-12 Schools: Leveraging Web 2.0 Data Warehouses to Assess Quality and Equity in Online Learning Environments

    Science.gov (United States)

    Reich, Justin; Murnane, Richard; Willett, John

    2012-01-01

    To document wiki usage in U.S. K-12 settings, this study examined a representative sample drawn from a population of nearly 180,000 wikis. The authors measured the opportunities wikis provide for students to develop 21st-century skills such as expert thinking, complex communication, and new media literacy. The authors found four types of wiki…

  2. The Role of the Constructivist Learning Theory and Collaborative Learning Environment on Wiki Classroom, and the Relationship between Them

    Science.gov (United States)

    Alzahrani, Ibraheem; Woollard, John

    2013-01-01

    This paper seeks to discover the relationship between both the social constructivist learning theory and the collaborative learning environment. This relationship can be identified by giving an example of the learning environment. Due to wiki characteristics, Wiki technology is one of the most famous learning environments that can show the…

  3. The Effects of Using a Wiki on Student Engagement and Learning of Report Writing Skills in a University Statistics Course

    Science.gov (United States)

    Neumann, David L.; Hood, Michelle

    2009-01-01

    A wiki was used as part of a blended learning approach to promote collaborative learning among students in a first year university statistics class. One group of students analysed a data set and communicated the results by jointly writing a practice report using a wiki. A second group analysed the same data but communicated the results in a…

  4. Scaffolding Wiki-Supported Collaborative Learning for Small-Group Projects and Whole-Class Collaborative Knowledge Building

    Science.gov (United States)

    Lin, C-Y.; Reigeluth, C. M.

    2016-01-01

    While educators value wikis' potential, wikis may fail to support collaborative constructive learning without careful scaffolding. This article proposes literature-based instructional methods, revised based on two expert instructors' input, presents the collected empirical evidence on the effects of these methods and proposes directions for future…

  5. The Making of a History Standards Wiki: "Covering", "Uncovering", and "Discovering" Curriculum Frameworks Using a Highly Interactive Technology

    Science.gov (United States)

    Maloy, Robert W.; Poirier, Michelle; Smith, Hilary K.; Edwards, Sharon A.

    2010-01-01

    This article explores using a wiki, one of the newest forms of interactive computer-based technology, as a resource for teaching the Massachusetts K-12 History and Social Science Curriculum Framework, a set of state-mandated learning standards. Wikis are web pages that can be easily edited by multiple authors. They invite active involvement by…

  6. Enhancing Successful Outcomes of Wiki-Based Collaborative Writing: A State-of-the-Art Review of Facilitation Frameworks

    Science.gov (United States)

    Stoddart, Andrew; Chan, Joe Yong-Yi; Liu, Gi-Zen

    2016-01-01

    This state-of-the-art review research undertook a survey of a variety of studies regarding wiki-based collaborative writing projects and from this body of work extracted the best practices tenets of facilitation. Wiki-based collaborative writing projects are becoming more common in second language (L2) pedagogy. Such projects have multiple aims.…

  7. Empirical Testing of a Theoretical Extension of the Technology Acceptance Model: An Exploratory Study of Educational Wikis

    Science.gov (United States)

    Liu, Xun

    2010-01-01

    This study extended the technology acceptance model and empirically tested the new model with wikis, a new type of educational technology. Based on social cognitive theory and the theory of planned behavior, three new variables, wiki self-efficacy, online posting anxiety, and perceived behavioral control, were added to the original technology…

  8. Organic micropollutants in aerobic and anaerobic membrane bioreactors: Changes in microbial communities and gene expression

    KAUST Repository

    Harb, Moustapha; Wei, Chunhai; Wang, Nan; Amy, Gary L.; Hong, Pei-Ying

    2016-01-01

    Organic micro-pollutants (OMPs) are contaminants of emerging concern in wastewater treatment due to the risk of their proliferation into the environment, but their impact on the biological treatment process is not well understood. The purpose of this study is to examine the effects of the presence of OMPs on the core microbial populations of wastewater treatment. Two nanofiltration-coupled membrane bioreactors (aerobic and anaerobic) were subjected to the same operating conditions while treating synthetic municipal wastewater spiked with OMPs. Microbial community dynamics, gene expression levels, and antibiotic resistance genes were analyzed using molecular-based approaches. Results showed that presence of OMPs in the wastewater feed had a clear effect on keystone bacterial populations in both the aerobic and anaerobic sludge while also significantly impacting biodegradation-associated gene expression levels. Finally, multiple antibiotic-type OMPs were found to have higher removal rates in the anaerobic MBR, while associated antibiotic resistance genes were lower.

  9. Organic micropollutants in aerobic and anaerobic membrane bioreactors: Changes in microbial communities and gene expression

    KAUST Repository

    Harb, Moustapha

    2016-07-09

    Organic micro-pollutants (OMPs) are contaminants of emerging concern in wastewater treatment due to the risk of their proliferation into the environment, but their impact on the biological treatment process is not well understood. The purpose of this study is to examine the effects of the presence of OMPs on the core microbial populations of wastewater treatment. Two nanofiltration-coupled membrane bioreactors (aerobic and anaerobic) were subjected to the same operating conditions while treating synthetic municipal wastewater spiked with OMPs. Microbial community dynamics, gene expression levels, and antibiotic resistance genes were analyzed using molecular-based approaches. Results showed that presence of OMPs in the wastewater feed had a clear effect on keystone bacterial populations in both the aerobic and anaerobic sludge while also significantly impacting biodegradation-associated gene expression levels. Finally, multiple antibiotic-type OMPs were found to have higher removal rates in the anaerobic MBR, while associated antibiotic resistance genes were lower.

  10. Genetic Diversity of Bacterial Communities and Gene Transfer Agents in Northern South China Sea

    Science.gov (United States)

    Sun, Fu-Lin; Wang, You-Shao; Wu, Mei-Lin; Jiang, Zhao-Yu; Sun, Cui-Ci; Cheng, Hao

    2014-01-01

    Pyrosequencing of the 16S ribosomal RNA gene (rDNA) amplicons was performed to investigate the unique distribution of bacterial communities in northern South China Sea (nSCS) and evaluate community structure and spatial differences of bacterial diversity. Cyanobacteria, Proteobacteria, Actinobacteria, and Bacteroidetes constitute the majority of bacteria. The taxonomic description of bacterial communities revealed that more Chroococcales, SAR11 clade, Acidimicrobiales, Rhodobacterales, and Flavobacteriales are present in the nSCS waters than other bacterial groups. Rhodobacterales were less abundant in tropical water (nSCS) than in temperate and cold waters. Furthermore, the diversity of Rhodobacterales based on the gene transfer agent (GTA) major capsid gene (g5) was investigated. Four g5 gene clone libraries were constructed from samples representing different regions and yielded diverse sequences. Fourteen g5 clusters could be identified among 197 nSCS clones. These clusters were also related to known g5 sequences derived from genome-sequenced Rhodobacterales. The composition of g5 sequences in surface water varied with the g5 sequences in the sampling sites; this result indicated that the Rhodobacterales population could be highly diverse in nSCS. Phylogenetic tree analysis result indicated distinguishable diversity patterns among tropical (nSCS), temperate, and cold waters, thereby supporting the niche adaptation of specific Rhodobacterales members in unique environments. PMID:25364820

  11. Functional gene diversity of soil microbial communities from five oil-contaminated fields in China.

    Science.gov (United States)

    Liang, Yuting; Van Nostrand, Joy D; Deng, Ye; He, Zhili; Wu, Liyou; Zhang, Xu; Li, Guanghe; Zhou, Jizhong

    2011-03-01

    To compare microbial functional diversity in different oil-contaminated fields and to know the effects of oil contaminant and environmental factors, soil samples were taken from typical oil-contaminated fields located in five geographic regions of China. GeoChip, a high-throughput functional gene array, was used to evaluate the microbial functional genes involved in contaminant degradation and in other major biogeochemical/metabolic processes. Our results indicated that the overall microbial community structures were distinct in each oil-contaminated field, and samples were clustered by geographic locations. The organic contaminant degradation genes were most abundant in all samples and presented a similar pattern under oil contaminant stress among the five fields. In addition, alkane and aromatic hydrocarbon degradation genes such as monooxygenase and dioxygenase were detected in high abundance in the oil-contaminated fields. Canonical correspondence analysis indicated that the microbial functional patterns were highly correlated to the local environmental variables, such as oil contaminant concentration, nitrogen and phosphorus contents, salt and pH. Finally, a total of 59% of microbial community variation from GeoChip data can be explained by oil contamination, geographic location and soil geochemical parameters. This study provided insights into the in situ microbial functional structures in oil-contaminated fields and discerned the linkages between microbial communities and environmental variables, which is important to the application of bioremediation in oil-contaminated sites.

  12. Toward an ultra-high resolution community climate system model for the BlueGene platform

    International Nuclear Information System (INIS)

    Dennis, John M; Jacob, Robert; Vertenstein, Mariana; Craig, Tony; Loy, Raymond

    2007-01-01

    Global climate models need to simulate several small, regional-scale processes which affect the global circulation in order to accurately simulate the climate. This is particularly important in the ocean where small scale features such as oceanic eddies are currently represented with adhoc parameterizations. There is also a need for higher resolution to provide climate predictions at small, regional scales. New high-performance computing platforms such as the IBM BlueGene can provide the necessary computational power to perform ultra-high resolution climate model integrations. We have begun to investigate the scaling of the individual components of the Community Climate System Model to prepare it for integrations on BlueGene and similar platforms. Our investigations show that it is possible to successfully utilize O(32K) processors. We describe the scalability of five models: the Parallel Ocean Program (POP), the Community Ice CodE (CICE), the Community Land Model (CLM), and the new CCSM sequential coupler (CPL7) which are components of the next generation Community Climate System Model (CCSM); as well as the High-Order Method Modeling Environment (HOMME) which is a dynamical core currently being evaluated within the Community Atmospheric Model. For our studies we concentrate on 1/10 0 resolution for CICE, POP, and CLM models and 1/4 0 resolution for HOMME. The ability to simulate high resolutions on the massively parallel petascale systems that will dominate high-performance computing for the foreseeable future is essential to the advancement of climate science

  13. PyPedia: using the wiki paradigm as crowd sourcing environment for bioinformatics protocols.

    Science.gov (United States)

    Kanterakis, Alexandros; Kuiper, Joël; Potamias, George; Swertz, Morris A

    2015-01-01

    Today researchers can choose from many bioinformatics protocols for all types of life sciences research, computational environments and coding languages. Although the majority of these are open source, few of them possess all virtues to maximize reuse and promote reproducible science. Wikipedia has proven a great tool to disseminate information and enhance collaboration between users with varying expertise and background to author qualitative content via crowdsourcing. However, it remains an open question whether the wiki paradigm can be applied to bioinformatics protocols. We piloted PyPedia, a wiki where each article is both implementation and documentation of a bioinformatics computational protocol in the python language. Hyperlinks within the wiki can be used to compose complex workflows and induce reuse. A RESTful API enables code execution outside the wiki. Initial content of PyPedia contains articles for population statistics, bioinformatics format conversions and genotype imputation. Use of the easy to learn wiki syntax effectively lowers the barriers to bring expert programmers and less computer savvy researchers on the same page. PyPedia demonstrates how wiki can provide a collaborative development, sharing and even execution environment for biologists and bioinformaticians that complement existing resources, useful for local and multi-center research teams. PyPedia is available online at: http://www.pypedia.com. The source code and installation instructions are available at: https://github.com/kantale/PyPedia_server. The PyPedia python library is available at: https://github.com/kantale/pypedia. PyPedia is open-source, available under the BSD 2-Clause License.

  14. El proyecto Wiki Learning: Wikipedia como entorno de aprendizaje abierto

    Directory of Open Access Journals (Sweden)

    2016-10-01

    Full Text Available Los enfoques predominantes en el sistema educativo tradicional circunscriben las posibilidades de aprendizaje a entornos formales y cerrados. Sin embargo, las tecnologías móviles y plataformas digitales están transformando este paradigma, expandiendo las posibilidades de aprendizaje. A partir de esta condición y en el marco de la producción del conocimiento entre pares, sostenemos que Wikipedia puede ser utilizada como un entorno de aprendizaje abierto que cumple varios propósitos: a permite adquirir competencias básicas; b contribuye a la inteligencia colectiva; c acorta la brecha global de conocimiento; y, d facilita la construcción de redes globales de aprendizaje. Este estudio de caso tiene como objetivo presentar el proceso, estrategias y resultados del proyecto Wiki Learning, como modelo de aprendizaje abierto a través del uso de Wikipedia en una universidad mexicana. El proyecto abarcó desde la producción de artículos hasta talleres para el desarrollo de capacidades de profesores y estudiantes. Se realizaron encuestas a 57 docentes y 115 alumnos para identificar la percepción acerca de Wikipedia, su uso y posibilidades como herramienta educativa. Los resultados demostraron que a pesar de que todos son usuarios de Wikipedia, existe un desconocimiento general sobre su funcionamiento, estructura y comunidades, además de cierta desconfianza. Se presenta un desafío para romper el estigma y recuperar el valor de la gestión compartida del conocimiento, el propósito de la enciclopedia y su lugar como producto de la inteligencia colectiva.

  15. Wiki management a revolutionary new model for a rapidly changing and collaborative world

    CERN Document Server

    Collins, Rod

    2013-01-01

    We now live in a "wiki" world where mass collaboration is not only possible-it's often the best solution. Conventional management thought assumes that command-and-control is the most effective way to organize the efforts of large numbers of people, but rapid change and increasing complexity have rendered that model obsolete. As a result, most managers today lack the skills and knowledge needed to succeed in an age when networks are proving smarter and faster than hierarchies. Designing organizations for mass collaboration demands a new and very different model-wiki management.

  16. WikiHyperGlossary (WHG): an information literacy technology for chemistry documents.

    Science.gov (United States)

    Bauer, Michael A; Berleant, Daniel; Cornell, Andrew P; Belford, Robert E

    2015-01-01

    The WikiHyperGlossary is an information literacy technology that was created to enhance reading comprehension of documents by connecting them to socially generated multimedia definitions as well as semantically relevant data. The WikiHyperGlossary enhances reading comprehension by using the lexicon of a discipline to generate dynamic links in a document to external resources that can provide implicit information the document did not explicitly provide. Currently, the most common method to acquire additional information when reading a document is to access a search engine and browse the web. This may lead to skimming of multiple documents with the novice actually never returning to the original document of interest. The WikiHyperGlossary automatically brings information to the user within the current document they are reading, enhancing the potential for deeper document understanding. The WikiHyperGlossary allows users to submit a web URL or text to be processed against a chosen lexicon, returning the document with tagged terms. The selection of a tagged term results in the appearance of the WikiHyperGlossary Portlet containing a definition, and depending on the type of word, tabs to additional information and resources. Current types of content include multimedia enhanced definitions, ChemSpider query results, 3D molecular structures, and 2D editable structures connected to ChemSpider queries. Existing glossaries can be bulk uploaded, locked for editing and associated with multiple social generated definitions. The WikiHyperGlossary leverages both social and semantic web technologies to bring relevant information to a document. This can not only aid reading comprehension, but increases the users' ability to obtain additional information within the document. We have demonstrated a molecular editor enabled knowledge framework that can result in a semantic web inductive reasoning process, and integration of the WikiHyperGlossary into other software technologies, like

  17. Community Composition of Nitrous Oxide-Related Genes in Salt Marsh Sediments Exposed to Nitrogen Enrichment.

    Science.gov (United States)

    Angell, John H; Peng, Xuefeng; Ji, Qixing; Craick, Ian; Jayakumar, Amal; Kearns, Patrick J; Ward, Bess B; Bowen, Jennifer L

    2018-01-01

    Salt marshes provide many key ecosystem services that have tremendous ecological and economic value. One critical service is the removal of fixed nitrogen from coastal waters, which limits the negative effects of eutrophication resulting from increased nutrient supply. Nutrient enrichment of salt marsh sediments results in higher rates of nitrogen cycling and, commonly, a concurrent increase in the flux of nitrous oxide, an important greenhouse gas. Little is known, however, regarding controls on the microbial communities that contribute to nitrous oxide fluxes in marsh sediments. To address this disconnect, we generated profiles of microbial communities and communities of micro-organisms containing specific nitrogen cycling genes that encode several enzymes ( amoA, norB, nosZ) related to nitrous oxide flux from salt marsh sediments. We hypothesized that communities of microbes responsible for nitrogen transformations will be structured by nitrogen availability. Taxa that respond positively to high nitrogen inputs may be responsible for the elevated rates of nitrogen cycling processes measured in fertilized sediments. Our data show that, with the exception of ammonia-oxidizing archaea, the community composition of organisms involved in the production and consumption of nitrous oxide was altered under nutrient enrichment. These results suggest that previously measured rates of nitrous oxide production and consumption are likely the result of changes in community structure, not simply changes in microbial activity.

  18. Soil DNA extraction procedure influences protist 18S rRNA gene community profiling outcome

    DEFF Research Database (Denmark)

    Santos, Susana S.; Nunes, Ines Marques; Nielsen, Tue K.

    2017-01-01

    Advances in sequencing technologies allow deeper studies of the soil protist diversity and function. However, little attention has been given to the impact of the chosen soil DNA extraction procedure to the overall results. We examined the effect of three acknowledged DNA recovery methods, two...... manual methods (ISOm-11063, GnS-GII) and one commercial kit (MoBio), on soil protist community structures obtained from different sites with different land uses. Results from 18S rRNA gene amplicon sequencing suggest that DNA extraction method significantly affect the replicate homogeneity, the total...... number of operational taxonomic units (OTUs) recovered and the overall taxonomic structure and diversity of soil protist communities. However, DNA extraction effects did not overwhelm the natural variation among samples, as the community data still strongly grouped by geographical location...

  19. Patterns in wetland microbial community composition and functional gene repertoire associated with methane emissions.

    Science.gov (United States)

    He, Shaomei; Malfatti, Stephanie A; McFarland, Jack W; Anderson, Frank E; Pati, Amrita; Huntemann, Marcel; Tremblay, Julien; Glavina del Rio, Tijana; Waldrop, Mark P; Windham-Myers, Lisamarie; Tringe, Susannah G

    2015-05-19

    Wetland restoration on peat islands previously drained for agriculture has potential to reverse land subsidence and sequester atmospheric carbon dioxide as peat accretes. However, the emission of methane could potentially offset the greenhouse gas benefits of captured carbon. As microbial communities play a key role in governing wetland greenhouse gas fluxes, we are interested in how microbial community composition and functions are associated with wetland hydrology, biogeochemistry, and methane emission, which is critical to modeling the microbial component in wetland methane fluxes and to managing restoration projects for maximal carbon sequestration. Here, we couple sequence-based methods with biogeochemical and greenhouse gas measurements to interrogate microbial communities from a pilot-scale restored wetland in the Sacramento-San Joaquin Delta of California, revealing considerable spatial heterogeneity even within this relatively small site. A number of microbial populations and functions showed strong correlations with electron acceptor availability and methane production; some also showed a preference for association with plant roots. Marker gene phylogenies revealed a diversity of major methane-producing and -consuming populations and suggested novel diversity within methanotrophs. Methanogenic archaea were observed in all samples, as were nitrate-, sulfate-, and metal-reducing bacteria, indicating that no single terminal electron acceptor was preferred despite differences in energetic favorability and suggesting spatial microheterogeneity and microniches. Notably, methanogens were negatively correlated with nitrate-, sulfate-, and metal-reducing bacteria and were most abundant at sampling sites with high peat accretion and low electron acceptor availability, where methane production was highest. Wetlands are the largest nonanthropogenic source of atmospheric methane but also a key global carbon reservoir. Characterizing belowground microbial communities

  20. Experimental attempts of using the Wiki-based knowledge sharing system at Syowa Station by 47th JARE

    Directory of Open Access Journals (Sweden)

    Takanobu Sawagaki

    2007-11-01

    Full Text Available A web-based knowledge sharing system was experimentally developed on the LAN using the INTERSAT communication system, at Syowa Station during the wintering period of the 47th Japanese Antarctic Research Expedition (JARE47, 2005-2007. The system works on "wiki", which is a collaborative technology for organizing information on web sites. Wiki allows users to catch up on information produced by various activities at the station to date, linking and tracing among a large number of pages. A number of wiki systems have been developed under the GNU General Public License. JARE47 experimentally introduced a "PukiWiki" system in which all data are stored in hypertext format, and binary files can be attached to any pages. PukiWiki is able to extend its functions by using plug-ins, which allow users to modify the system. The wiki at Syowa Station was started on a small scale and expanded to permit storage of data entered by individual members, and to permit sharing of information up to date among all members, becoming a portal site for wintering members. During the complicated operations in summer season when many groups pursued the individual field activities, wiki played an important role for reconfirming and modifying procedures among members, as the key station around the Syowa area.

  1. Empathy 2.0 and the Wonderful World of Wiki Collaboration

    Science.gov (United States)

    Tarrant, Cindy; Godwin, Kathryn; Daniel, Stacey; Bolton, Dawn

    2013-01-01

    In a perfect world, diversity would abound in people's daily lives, promoting friendships across racial, ethnic, and religious lines. When that is not possible and students learn in a more segregated setting, wikis provide a tool to reach beyond the school walls, find a diverse audience, and create meaningful discourse. This article narrates an…

  2. A Novel Wiki-Based Remote Laboratory Platform for Engineering Education

    Science.gov (United States)

    Wang, Ning; Chen, Xuemin; Lan, Qianlong; Song, Gangbing; Parsaei, Hamid R.; Ho, Siu-Chun

    2017-01-01

    With the unprecedented growth of e-learning, more and more new IT technologies are used to develop e-learning tools. As one of the most common forms of social computing, Wiki technology has been used to develop the collaborative and cooperative learning platform to support multiple users learning online effectively. In this paper, we propose a new…

  3. Toward a Better Understanding of Culture: Wikis in the Beginning German Classroom

    Science.gov (United States)

    Ducate, Lara; Steckenbiller, Christiane

    2017-01-01

    The questions of how to teach culture, which culture(s) to teach and how to lead students to intercultural competence and understanding are common questions for language teachers. The current project employed wikis to systematically integrate culture and authentic texts into beginning German courses at a large south-eastern university in the…

  4. Attacks by “Anonymous‿ WikiLeaks Proponents not Anonymous

    NARCIS (Netherlands)

    Pras, Aiko; Sperotto, Anna; Moreira Moura, Giovane; Drago, Idilio; Barbosa, R.R.R.; Sadre, R.; de Oliveira Schmidt, R.; Hofstede, R.J.; Hofstede, Rick

    2010-01-01

    On November 28, 2010, the world started watching the whistle blower website WikiLeaks to begin publishing part of the 250,000 US Embassy Diplomatic cables. These confidential cables provide an insight on U.S. international affairs from 274 different embassies, covering topics such as analysis of

  5. Wikis and collaborative writing applications in health care: a scoping review

    NARCIS (Netherlands)

    Archambault, P.M.; Belt, T.H. van de; Grajales, F.J., 3rd; Faber, M.J.; Kuziemsky, C.E.; Gagnon, S.; Bilodeau, A.; Rioux, S.; Nelen, W.L.D.M.; Gagnon, M.P.; Turgeon, A.F.; Aubin, K.; Gold, I.; Poitras, J.; Eysenbach, G.; Kremer, J.A.M.; Legare, F.

    2013-01-01

    BACKGROUND: Collaborative writing applications (eg, wikis and Google Documents) hold the potential to improve the use of evidence in both public health and health care. The rapid rise in their use has created the need for a systematic synthesis of the evidence of their impact as knowledge

  6. Using Blackboard Wiki Pages as a Shared Space for Simulating the Professional Translation Work Environment

    Science.gov (United States)

    Vine, Juliet

    2015-01-01

    The Work-Integrated Simulation for Translators module is part of a three year undergraduate degree in translation. The semester long module aims to simulate several aspects of the translation process using the Blackboard virtual learning environment's Wikis as the interface for completing translation tasks. For each translation task, one of the…

  7. Use of wikis as a collaborative ICT tool for extending the frontiers of ...

    African Journals Online (AJOL)

    When Web 2.0 technologies are used in the classroom, learners and teachers are given the opportunity to extend the frontiers of knowledge by collaborating and contributing to knowledge. This paper explores the possibility of using Wikis – a Web 2.0 technology – to extend the frontiers of knowledge. It also discusses how ...

  8. Wiki and Digital Video Use in Strategic Interaction-Based Experiential EFL Learning

    Science.gov (United States)

    Dehaan, Jonathan; Johnson, Neil H.; Yoshimura, Noriko; Kondo, Takako

    2012-01-01

    This paper details the use of a free and access-controlled wiki as the learning management system for a four-week teaching module designed to improve the oral communication skills of Japanese university EFL students. Students engaged in repeated experiential learning cycles of planning, doing, observing, and evaluating their performance of a role…

  9. Developing Business Writing Skills and Reducing Writing Anxiety of EFL Learners through Wikis

    Science.gov (United States)

    Kassem, Mohamed Ali Mohamed

    2017-01-01

    The present study aimed at investigating the effect of using wikis on developing business writing skills and reducing writing anxiety of Business Administration students at Prince Sattam bin Abdul Aziz University, KSA. Sixty students, who were randomly chosen and divided into two equivalent groups: control and experimental, participated in the…

  10. Wikis to facilitate patient participation in developing information leaflets: first experiences

    NARCIS (Netherlands)

    Belt, T.H. van de; Faber, M.J.; Knijnenburg, J.M.; Duijnhoven, N.T.L. van; Nelen, W.L.D.M.; Kremer, J.A.M.

    2014-01-01

    OBJECTIVE: Although patients have gained a wealth of experienced based knowledge they are usually not involved in the development of patient information. We sought to determine the technical feasibility of wikis in generating dynamic patient information leaflets with participation from patients and

  11. Wikis: Developing Pre-Service Teachers' Leadership Skills and Knowledge of Content Standards

    Science.gov (United States)

    Reid-Griffin, Angelia; Slaten, Kelli M.

    2016-01-01

    In this initial phase of our multi-year research study we set out to explore the development of leadership skills in our pre-service secondary teachers after using an online wiki, Wikispaces. This paper presents our methods for preparing a group of 13 mathematics and 3 science secondary pre-service teachers to demonstrate the essential knowledge,…

  12. A global reference database of crowdsourced cropland data collected using the Geo-Wiki platform

    NARCIS (Netherlands)

    Laso Bayas, JC; Lesiv, M; Waldner, F; Schucknecht, A; Duerauer, M; See, L; Fritz, S.; Fraisl, D; Moorthy, I; McCallum, I.; Perger, C; Danylo, O; Defourny, P; Gallego, J; Gilliams, S; Akhtar, I.H.; Baishya, S. J.; Baruah, M; Bungnamei, K; Campos, A; Changkakati, T; Cipriani, A; Das, Krishna; Das, Keemee; Das, I; Davis, K.F.; Hazarika, P; Johnson, B.A.; Malek, Ziga; Molinari, M.E.; Panging, K; Pawe, C.K.; Pérez-Hoyos, A; Sahariah, P.K.; Sahariah, D; Saikia, A; Saikia, M; Schlesinger, Peter; Seidacaru, E; Singha, K; Wilson, John W

    2017-01-01

    A global reference data set on cropland was collected through a crowdsourcing campaign using the Geo-Wiki crowdsourcing tool. The campaign lasted three weeks, with over 80 participants from around the world reviewing almost 36,000 sample units, focussing on cropland identification. For quality

  13. Interdisciplinary Project-Based Learning: An Online Wiki Experience in Teacher Education

    Science.gov (United States)

    Biasutti, Michele; EL-Deghaidy, Heba

    2015-01-01

    In the current research study the use of Wikis as an online didactic tool to apply project-based learning in higher education was reported. The study was conducted in university teacher education programmes. During the online activities, participants developed interdisciplinary projects for the primary school working collaboratively in small…

  14. Evaluating the Impact of Wikis on Student Learning Outcomes: An Integrative Review.

    Science.gov (United States)

    Trocky, Nina M; Buckley, Kathleen M

    2016-01-01

    Although wikis appear to have been reported as effective tools for educators, uncertainty exists as to their effectiveness in achieving student learning outcomes. The aim of this integrative review was to examine the current evidence on the impact of wikis on student learning in courses requiring collaborative or co-developed assignments or activities. The authors searched several electronic databases for relevant articles and used R. Whittemore and K. Knafl's (2005) integrative review method to analyze and synthesize the evidence. Twenty-five articles met the selection criteria for this review, and four major themes for wiki use were identified: (a) writing skills, (b) collaboration, (c) knowledge acquisition, and (d) centralized repository. Although wikis have been found useful in improving student learning outcomes and hold great potential as an instructional strategy to aid students in learning various skills and gaining new knowledge, more research is needed on their effectiveness, especially in the area of nursing education. Copyright © 2016 Elsevier Inc. All rights reserved.

  15. Using Wiki in Teacher Education: Impact on Knowledge Management Processes and Student Satisfaction

    Science.gov (United States)

    Biasutti, Michele; EL-Deghaidy, Heba

    2012-01-01

    The current study reports on the use of Wiki as an online didactic tool to develop knowledge management (KM) processes in higher education. This study integrates social constructivist principles to learning where learners are pro-active and collaborative through higher order cognitive processes. The study was administered in two countries, namely…

  16. Data Collaborative: A Practical Exploration of Big Data in Course Wikis

    Science.gov (United States)

    Percell, Jay C.

    2016-01-01

    Wikis continue to be used within technology environments of K-12 and higher education because they offer a collaborative environment for students to produce and receive content in concert with each other or on an individual basis (Kirkham, 2014). These online spaces are typically used as a course management system where students can both receive…

  17. The Zones of Proximal and Distal Development in Chinese Language Studies with the Use of Wikis

    Science.gov (United States)

    Chew, Esyin; Ding, Seong Lin

    2014-01-01

    Educational practitioners in the higher education institutions of the UK have increasingly promoted the use of wikis. The technology enhanced learning experience of the UK was transferred to a local higher educational agency in Malaysia through a collaborative research project called WiLearn. By examining a student cohort enrolled in Chinese…

  18. The Effect of Google Earth and Wiki Models on Oral Presentation Skills of University EFL Learners

    Science.gov (United States)

    Awada, Ghada; Diab, Hassan B.

    2018-01-01

    This article reports the results of an experimental study that investigated the effectiveness of Google Earth and Wiki tools in improving the oral presentation skills of English as a Foreign Language (EFL) learners and boosting their motivation for learning. The participants (n =81) are enrolled in writing classes at two English-medium…

  19. Wiki, a New Wave of Innovation for Teaching and Collaborative Learning

    Directory of Open Access Journals (Sweden)

    Hassan Mirzajani

    2015-10-01

    Full Text Available Educational technology is a dynamic major which is ever developing. In the past, educational technology was one dimensional, but nowadays it has become multi-dimensional, flexible and learner-centered. A revolution has happened in teaching methods from the perspective of web. Novel technologies in web and new role of users’ have led to the appearance of application programs on the basis of collaborative and social intelligence. Users have active participation, exploit their own beliefs, make the target concept, edit it and participate there. The most important feature of this kind of media is users’ ability to participate in its content production. Users can exploit wikis in the process of educational technology. A wiki is a social medium which enables users to produce and edit constantly in an HTML environment. The aim of this article is to introduce wikis as educational and training tools. The degree to which these obstacles affect ICT users and institutes can support decision-making on how to equip them is discussed. Keywords: educational technology, wiki, collaborative learning, innovation

  20. Using Wikis as a Support and Assessment Tool in Collaborative Digital Game-Based Learning Environments

    Science.gov (United States)

    Samur, Yavuz

    2011-01-01

    In computer-supported collaborative learning (CSCL) environments, there are many researches done on collaborative learning activities; however, in game-based learning environments, more research and literature on collaborative learning activities are required. Actually, both game-based learning environments and wikis enable us to use new chances…

  1. Toward an ultra-high resolution community climate system model for the BlueGene platform

    Energy Technology Data Exchange (ETDEWEB)

    Dennis, John M [Computer Science Section, National Center for Atmospheric Research, Boulder, CO (United States); Jacob, Robert [Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL (United States); Vertenstein, Mariana [Climate and Global Dynamics Division, National Center for Atmospheric Research, Boulder, CO (United States); Craig, Tony [Climate and Global Dynamics Division, National Center for Atmospheric Research, Boulder, CO (United States); Loy, Raymond [Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL (United States)

    2007-07-15

    Global climate models need to simulate several small, regional-scale processes which affect the global circulation in order to accurately simulate the climate. This is particularly important in the ocean where small scale features such as oceanic eddies are currently represented with adhoc parameterizations. There is also a need for higher resolution to provide climate predictions at small, regional scales. New high-performance computing platforms such as the IBM BlueGene can provide the necessary computational power to perform ultra-high resolution climate model integrations. We have begun to investigate the scaling of the individual components of the Community Climate System Model to prepare it for integrations on BlueGene and similar platforms. Our investigations show that it is possible to successfully utilize O(32K) processors. We describe the scalability of five models: the Parallel Ocean Program (POP), the Community Ice CodE (CICE), the Community Land Model (CLM), and the new CCSM sequential coupler (CPL7) which are components of the next generation Community Climate System Model (CCSM); as well as the High-Order Method Modeling Environment (HOMME) which is a dynamical core currently being evaluated within the Community Atmospheric Model. For our studies we concentrate on 1/10{sup 0} resolution for CICE, POP, and CLM models and 1/4{sup 0} resolution for HOMME. The ability to simulate high resolutions on the massively parallel petascale systems that will dominate high-performance computing for the foreseeable future is essential to the advancement of climate science.

  2. Activities Based on Wiki Platform for Engineering Higher Education: Students' Point of View

    Directory of Open Access Journals (Sweden)

    Gláucia Nolasco de Almeida Mello

    2017-08-01

    Full Text Available The fast evolution of Information and Communication Technology (ICT introduced a new generation of learners that have been adopted mobile devices and Web 2.0 technologies to get information and communicate. The Web 2.0-based tools, such as blogs, wikis, Facebook, Instagram, etc, offer huge possibilities for collaboration. In this way, the main purpose of this research was plan an activity on wiki platform for Reinforced Concrete discipline in Civil Engineering course and answer the questions: (1 How should collaboration be effectively measured on wiki platform? (2 What is the students' point of view about using wiki platform for a collaboration activity? Wikispaces Classroom platform was chosen for the project because it is a free social writing platform, suitable for collaborative learning. Furthermore it works on modern browsers, tablets, and smart phone. A total of 167 students of Civil Engineering course were monitored on Wikispaces® platform. All students’ actions were analyzed and classified as low, medium or high level of collaboration. At the end of the project 111 students answered a questionnaire and 10 students participated of an informal interview where they expressed their opinion about the platform, the activities and the relationship with online peers. A descriptive statistical analysis of the data collected from the platform and the questionnaires answered by the students was performed. The results indicated that wiki platform is an important way to develop innovative activities and tasks for the purpose of to improve skills of engineering students such as: writing communication, organization, collaboration and critical thinking.

  3. Characterization of microbial community and the alkylscccinate synthase genes in petroleum reservoir fluids of China

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Lei; Mu, Bo-Zhong [University of Science and Technology (China)], email: bzmu@ecust.edu.cn; Gu, Ji-Dong [The University of Hong Kong (China)], email: jdgu@hkucc.hku.hk

    2011-07-01

    Petroleum reservoirs represent a special ecosystem consisting of specific temperature, pressure, salt concentration, oil, gas, water, microorganisms and, enzymes among others. This paper presents the characterization of microbial community and the alkyl succinate synthase genes in petroleum reservoir fluids in China. A few samples were analyzed and the physical and chemical characteristics are given in a tabular form. A flow chart shows the methods and procedures for microbial activities. Six petroleum reservoirs were studied using an archaeal 16S rRNA gene-based approach to establish the presence of archaea and the results are given. The correlation of archaeal and bacterial communities with reservoir conditions and diversity of the arachaeal community in water-flooding petroleum reservoirs at different temperatures is also shown. From the study, it can be summarized that, among methane producers, CO2-reducing methanogens are mostly found in oil reservoir ecosystems and as more assA sequences are revealed, more comprehensive molecular probes can be designed to track the activity of anaerobic alkane-degrading organisms in the environment.

  4. Wikis and Collaborative Writing Applications in Health Care: A Scoping Review Protocol

    Science.gov (United States)

    van de Belt, Tom H; Grajales III, Francisco J; Eysenbach, Gunther; Aubin, Karine; Gold, Irving; Gagnon, Marie-Pierre; Kuziemsky, Craig E; Turgeon, Alexis F; Poitras, Julien; Faber, Marjan J; Kremer, Jan A.M; Heldoorn, Marcel; Bilodeau, Andrea; Légaré, France

    2012-01-01

    The rapid rise in the use of collaborative writing applications (eg, wikis, Google Documents, and Google Knol) has created the need for a systematic synthesis of the evidence of their impact as knowledge translation (KT) tools in the health care sector and for an inventory of the factors that affect their use. While researchers have conducted systematic reviews on a range of software-based information and communication technologies as well as other social media (eg, virtual communities of practice, virtual peer-to-peer communities, and electronic support groups), none have reviewed collaborative writing applications in the medical sector. The overarching goal of this project is to explore the depth and breadth of evidence for the use of collaborative writing applications in health care. Thus, the purposes of this scoping review will be to (1) map the literature on collaborative writing applications; (2) compare the applications’ features; (3) describe the evidence of each application’s positive and negative effects as a KT intervention in health care; (4) inventory and describe the barriers and facilitators that affect the applications’ use; and (5) produce an action plan and a research agenda. A six-stage framework for scoping reviews will be used: (1) identifying the research question; (2) identifying relevant studies within the selected databases (using the EPPI-Reviewer software to classify the studies); (3) selecting studies (an iterative process in which two reviewers search the literature, refine the search strategy, and review articles for inclusion); (4) charting the data (using EPPI-Reviewer’s data-charting form); (5) collating, summarizing, and reporting the results (performing a descriptive, numerical, and interpretive synthesis); and (6) consulting knowledge users during three planned meetings. Since this scoping review concerns the use of collaborative writing applications as KT interventions in health care, we will use the Knowledge to Action

  5. Empirical phylogenies and species abundance distributions are consistent with pre-equilibrium dynamics of neutral community models with gene flow

    KAUST Repository

    Bonnet-Lebrun, Anne-Sophie

    2017-03-17

    Community characteristics reflect past ecological and evolutionary dynamics. Here, we investigate whether it is possible to obtain realistically shaped modelled communities - i.e., with phylogenetic trees and species abundance distributions shaped similarly to typical empirical bird and mammal communities - from neutral community models. To test the effect of gene flow, we contrasted two spatially explicit individual-based neutral models: one with protracted speciation, delayed by gene flow, and one with point mutation speciation, unaffected by gene flow. The former produced more realistic communities (shape of phylogenetic tree and species-abundance distribution), consistent with gene flow being a key process in macro-evolutionary dynamics. Earlier models struggled to capture the empirically observed branching tempo in phylogenetic trees, as measured by the gamma statistic. We show that the low gamma values typical of empirical trees can be obtained in models with protracted speciation, in pre-equilibrium communities developing from an initially abundant and widespread species. This was even more so in communities sampled incompletely, particularly if the unknown species are the youngest. Overall, our results demonstrate that the characteristics of empirical communities that we have studied can, to a large extent, be explained through a purely neutral model under pre-equilibrium conditions. This article is protected by copyright. All rights reserved.

  6. Empirical phylogenies and species abundance distributions are consistent with pre-equilibrium dynamics of neutral community models with gene flow

    KAUST Repository

    Bonnet-Lebrun, Anne-Sophie; Manica, Andrea; Eriksson, Anders; Rodrigues, Ana S.L.

    2017-01-01

    Community characteristics reflect past ecological and evolutionary dynamics. Here, we investigate whether it is possible to obtain realistically shaped modelled communities - i.e., with phylogenetic trees and species abundance distributions shaped similarly to typical empirical bird and mammal communities - from neutral community models. To test the effect of gene flow, we contrasted two spatially explicit individual-based neutral models: one with protracted speciation, delayed by gene flow, and one with point mutation speciation, unaffected by gene flow. The former produced more realistic communities (shape of phylogenetic tree and species-abundance distribution), consistent with gene flow being a key process in macro-evolutionary dynamics. Earlier models struggled to capture the empirically observed branching tempo in phylogenetic trees, as measured by the gamma statistic. We show that the low gamma values typical of empirical trees can be obtained in models with protracted speciation, in pre-equilibrium communities developing from an initially abundant and widespread species. This was even more so in communities sampled incompletely, particularly if the unknown species are the youngest. Overall, our results demonstrate that the characteristics of empirical communities that we have studied can, to a large extent, be explained through a purely neutral model under pre-equilibrium conditions. This article is protected by copyright. All rights reserved.

  7. Incorporating Wiki Technology in a Traditional Biostatistics Course: Effects on University Students’ Collaborative Learning, Approaches to Learning and Course Performance

    Directory of Open Access Journals (Sweden)

    Shirley S.M. Fong

    2017-08-01

    Full Text Available Aim/Purpose: To investigate the effectiveness of incorporating wiki technology in an under-graduate biostatistics course for improving university students’ collaborative learning, approaches to learning, and course performance. Methodology: During a three year longitudinal study, twenty-one and twenty-four undergraduate students were recruited by convenience sampling and assigned to a wiki group (2014-2015 and a control group (2013-2014 and 2015-2016, respectively. The students in the wiki group attended face-to-face lectures and used a wiki (PBworks weekly for online- group discussion, and the students in the control group had no access to the wiki and interacted face-to-face only. The students’ collaborative learning, approaches to learning, and course performance were evaluated using the Group Process Questionnaire (GPQ, Revised Study Process Questionnaire (R-SPQ-2F and course results, respectively, after testing. Findings: Multivariate analysis of variance results revealed that the R-SPQ-2F surface approach score, surface motive and strategy subscores were lower in the wiki group than in the control group (p < 0.05. The GPQ individual accountability and equal opportunity scores (components of collaboration were higher in the wiki group than in the control group (p < 0.001. No significant between-groups differences were found in any of the other outcome variables (i.e., overall course result, R-SPQ-2F deep approach score and subscores, GPQ positive interdependence score, social skills score, and composite score. Looking at the Wiki Questionnaire results, the subscale and composite scores we obtained were 31.5% to 37.7% lower than the norm. The wiki was used at a frequency of about 0.7 times per week per student. Recommendations for Practitioners: Using wiki technology in conjunction with the traditional face-to-face teaching method in a biostatistics course can enhance some aspects of undergraduate students’ collaborative learning

  8. Influence of secondary water supply systems on microbial community structure and opportunistic pathogen gene markers.

    Science.gov (United States)

    Li, Huan; Li, Shang; Tang, Wei; Yang, Yang; Zhao, Jianfu; Xia, Siqing; Zhang, Weixian; Wang, Hong

    2018-06-01

    Secondary water supply systems (SWSSs) refer to the in-building infrastructures (e.g., water storage tanks) used to supply water pressure beyond the main distribution systems. The purpose of this study was to investigate the influence of SWSSs on microbial community structure and the occurrence of opportunistic pathogens, the latter of which are an emerging public health concern. Higher numbers of bacterial 16S rRNA genes, Legionella and mycobacterial gene markers were found in public building taps served by SWSSs relative to the mains, regardless of the flushing practice (P water retention time, warm temperature and loss of disinfectant residuals promoted microbial growth and colonization of potential pathogens in SWSSs. Varied levels of microbial community shifts were found in different types of SWSSs during water transportation from the distribution main to taps, highlighting the critical role of SWSSs in shaping the drinking water microbiota. Overall, the results provided insight to factors that might aid in controlling pathogen proliferation in real-world water systems using SWSSs. Copyright © 2018 Elsevier Ltd. All rights reserved.

  9. EdWiki. El wiki como plataforma para la creación y publicación de contenidos educativos multiformato

    OpenAIRE

    Santanach Delisau, Francesc; Mor, Enric; Duran Cals, Jordi; Juhé Brogué, Albert

    2012-01-01

    El proceso de elaboración y distribución de materiales didácticos es de gran importancia en las instituciones educativas. Las plataformas para editar y publicar contenidos educativos en la red cobran cada día más importancia en la medida que permitan seguir procesos de calidad y que como herramientas sean fiables. En este trabajo se presenta EdWiki, una herramienta para la creación y edición de contenidos educativos en línea. Esta herramienta da respuesta a la necesidad de profesores y docent...

  10. The Impact of a Collaborative Wiki Assignment on Teaching and Learning in a Teacher Education Program

    Directory of Open Access Journals (Sweden)

    Vanessa Joy Bravo

    2011-10-01

    Full Text Available This study explored students’ perceptions and behaviors of public wiki use during a collaborative Wikipedia assignment in a graduate technology and literacy education course. Results confirmed that the majority of students had an overall positive experience posting content on Wikipedia. Students learned how to use Wikipedia through collaborative practice, including, how to adhere to its standards and cite work properly, the importance of critically evaluating online information, and the value of publishing work to an authentic audience. Students (prospective and current teachers reported numerous ways in which collaboration on Wikipedia could be integrated into their K-12 classrooms in order to promote higher order thinking and foster meaningful knowledge construction. Pedagogical practices for the effective integration of public wiki assignments in higher education and K-12 settings are recommended.

  11. Sulfamethoxazole and COD increase abundance of sulfonamide resistance genes and change bacterial community structures within sequencing batch reactors.

    Science.gov (United States)

    Guo, Xueping; Pang, Weihai; Dou, Chunling; Yin, Daqiang

    2017-05-01

    The abundant microbial community in biological treatment processes in wastewater treatment plants (WWTPs) may potentially enhance the horizontal gene transfer of antibiotic resistance genes with the presence of antibiotics. A lab-scale sequencing batch reactor was designed to investigate response of sulfonamide resistance genes (sulI, sulII) and bacterial communities to various concentrations of sulfamethoxazole (SMX) and chemical oxygen demand (COD) of wastewater. The SMX concentrations (0.001 mg/L, 0.1 mg/L and 10 mg/L) decreased with treatment time and higher SMX level was more difficult to remove. The presence of SMX also significantly reduced the removal efficiency of ammonia nitrogen, affecting the normal function of WWTPs. All three concentrations of SMX raised both sulI and sulII genes with higher concentrations exhibiting greater increases. The abundance of sul genes was positive correlated with treatment time and followed the second-order reaction kinetic model. Interestingly, these two genes have rather similar activity. SulI and sulII gene abundance also performed similar response to COD. Simpson index and Shannon-Weiner index did not show changes in the microbial community diversity. However, the 16S rRNA gene cloning and sequencing results showed the bacterial community structures varied during different stages. The results demonstrated that influent antibiotics into WWTPs may facilitate selection of ARGs and affect the wastewater conventional treatment as well as the bacteria community structures. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. INTERVIEW: Quick, Social and Collaborative - wiki-based user documentation at APC by Schneider Electric

    DEFF Research Database (Denmark)

    Møller, Margrethe H.; Pernille Bagger Nielsen, Pernille; Kalianov, Stanislav

    2013-01-01

    In the software documentation department at APC by Schneider Electric in Kolding, Denmark, Technical Writer Pernille Bagger Nielsen writes user documentation for the software developed by the company. In cooperation with Localization Manager Stanislav Kalianov she reorganised the user documentation...... for publication as wiki-based documentation on the internet. The new platform supports their strategy of using agile and iterative, topic-based, collaborative writing when developing user documentation. Their experience will interest readers who consider introducing a similar new strategy....

  13. The Leaky Pipe: Lead Pipers Weigh in on WikiLeaks

    Directory of Open Access Journals (Sweden)

    Editorial Board

    2010-12-01

    Full Text Available Introduction Let’s start off with a little background and context, just in case you haven’t been glued to the news to catch every nuance of the WikiLeaks story. The Guardian has a helpful timeline of the saga to get you (at least partially up to speed, and if you don’t like theirs, there are plenty [...

  14. Health care professionals' beliefs about using wiki-based reminders to promote best practices in trauma care.

    Science.gov (United States)

    Archambault, Patrick Michel; Bilodeau, Andrea; Gagnon, Marie-Pierre; Aubin, Karine; Lavoie, André; Lapointe, Jean; Poitras, Julien; Croteau, Sylvain; Pham-Dinh, Martin; Légaré, France

    2012-04-19

    Wikis are knowledge translation tools that could help health professionals implement best practices in acute care. Little is known about the factors influencing professionals' use of wikis. To identify and compare the beliefs of emergency physicians (EPs) and allied health professionals (AHPs) about using a wiki-based reminder that promotes evidence-based care for traumatic brain injuries. Drawing on the theory of planned behavior, we conducted semistructured interviews to elicit EPs' and AHPs' beliefs about using a wiki-based reminder. Previous studies suggested a sample of 25 EPs and 25 AHPs. We purposefully selected participants from three trauma centers in Quebec, Canada, to obtain a representative sample. Using univariate analyses, we assessed whether our participants' gender, age, and level of experience were similar to those of all eligible individuals. Participants viewed a video showing a clinician using a wiki-based reminder, and we interviewed participants about their behavioral, control, and normative beliefs-that is, what they saw as advantages, disadvantages, barriers, and facilitators to their use of a reminder, and how they felt important referents would perceive their use of a reminder. Two reviewers independently analyzed the content of the interview transcripts. We considered the 75% most frequently mentioned beliefs as salient. We retained some less frequently mentioned beliefs as well. Of 66 eligible EPs and 444 eligible AHPs, we invited 55 EPs and 39 AHPs to participate, and 25 EPs and 25 AHPs (15 nurses, 7 respiratory therapists, and 3 pharmacists) accepted. Participating AHPs had more experience than eligible AHPs (mean 14 vs 11 years; P = .04). We noted no other significant differences. Among EPs, the most frequently reported advantage of using a wiki-based reminder was that it refreshes the memory (n = 14); among AHPs, it was that it provides rapid access to protocols (n = 16). Only 2 EPs mentioned a disadvantage (the wiki added stress

  15. Polybacterial community analysis in human conjunctiva through 16S rRNA gene libraries.

    Science.gov (United States)

    Deepthi, KrishnanNair Geetha; Jayasudha, Rajagopalaboopathi; Girish, Rameshan Nair; Manikandan, Palanisamy; Ram, Rammohan; Narendran, Venkatapathy; Prabagaran, Solai Ramatchandirane

    2018-05-14

    The conjunctival sac of healthy human harbours a variety of microorganisms. When the eye is compromised, an occasional inadvertent spread happens to the adjacent tissue, resulting in bacterial ocular infections. Microbiological investigation of the conjunctival swab is one of the broadly used modality to study the aetiological agent of conjunctiva. However, most of the time such methods yield unsatisfactory results. Hence, the present study intends to identify the bacterial community in human conjunctiva of pre-operative subjects through 16S rRNA gene libraries. Out of 45 samples collected from preoperative patients undergoing cataract surgery, 36 libraries were constructed with bacterial nested-PCR-positive samples. The representative clones with unique restriction pattern were generated through Amplified Ribosomal DNA Restriction Analysis (ARDRA) which were sequenced for phylogenetic affiliation. A total of 211 representative clones were obtained which were distributed in phyla Actinobacteria, Firmicutes, α-Proteobacteria, β-Proteobacteria, γ-Proteobacteria, Bacteroidetes, and Deinococcus-Thermus. Findings revealed the presence of polybacterial community, especially in some cases even though no bacterium or a single bacterium alone was identified through cultivable method. Remarkably, we identified 17 species which have never been reported in any ocular infections. The sequencing data reported 6 unidentified bacteria suggesting the possibility of novel organisms in the sample. Since, polybacterial community has been identified consisting of both gram positive and gram negative bacteria, a broad spectrum antibiotic therapy is advisable to the patients who are undergoing cataract surgery. Consolidated effort would significantly improve a clear understanding of the nature of microbial community in the human conjunctiva which will promote administration of appropriate antibiotic regimen and also help in the development of oligonucleotide probes to screen the

  16. Use of a wiki as a radiology departmental knowledge management system.

    Science.gov (United States)

    Meenan, Christopher; King, Antoinette; Toland, Christopher; Daly, Mark; Nagy, Paul

    2010-04-01

    Information technology teams in health care are tasked with maintaining a variety of information systems with complex support requirements. In radiology, this includes picture archive and communication systems, radiology information systems, speech recognition systems, and other ancillary systems. Hospital information technology (IT) departments are required to provide 24 x 7 support for these mission-critical systems that directly support patient care in emergency and other critical care departments. The practical know-how to keep these systems operational and diagnose problems promptly is difficult to maintain around the clock. Specific details on infrequent failure modes or advanced troubleshooting strategies may reside with only a few senior staff members. Our goal was to reduce diagnosis and recovery times for issues with our mission-critical systems. We created a knowledge base for building and quickly disseminating technical expertise to our entire support staff. We used an open source, wiki-based, collaborative authoring system internally within our IT department to improve our ability to deliver a high level of service to our customers. In this paper, we describe our evaluation of the wiki and the ways in which we used it to organize our support knowledge. We found the wiki to be an effective tool for knowledge management and for improving our ability to provide mission-critical support for health care IT systems.

  17. Wiki en la Universitat Autònoma de Barcelona. Alcance y perspectivas

    Directory of Open Access Journals (Sweden)

    Sergi Robles

    2010-01-01

    Full Text Available Desde mayo del año 2004, un grupo de profesores de la Universitat Autònoma de Barcelona ha llevado a cabo distintas experiencias docentes en educación superior enfocadas a los nuevos planes piloto definidos en el marco del Espacio Europeo de Educación Superior (EEES basadas en la utilización del wiki, con el fin de mejorar el proceso de enseñanza-aprendizaje de los estudiantes. Se han desarrollado distintos materiales docentes para el aprendizaje autónomo y semi-presencial, diseñados para potenciar el trabajo colaborativo y a distancia. El análisis de los resultados obtenidos con la aplicación del wiki a la docencia ha permitido identificar las ventajas y las carencias del sistema de trabajo inicial y ampliar sus posibilidades con herramientas que aseguran una mejor adaptación de esta plataforma al EEES. La labor desarrollada por el grupo y el interés despertado en la comunidad universitaria son el punto de partida de la integración del wiki en el Campus Virtual (la plataforma institucional de soporte virtual del aprendizaje de la Universitat Autònoma de Barcelona que se está llevando a cabo actualmente.

  18. Peracetic acid disinfection kinetics for combined sewer overflows: indicator organisms, antibiotic resistance genes, and microbial community.

    Science.gov (United States)

    Eramo, Alessia; Medina, William Morales; Fahrenfeld, Nicole L

    2017-01-01

    Combined sewer overflows (CSOs) degrade water quality and end-of-pipe treatment is one potential solution for retrofitting this outdated infrastructure. The goal of this research was to evaluate peracetic acid (PAA) as a disinfectant for CSOs using viability based molecular methods for antibiotic resistance genes (ARGs), indicator organism marker gene BacHum, and 16S rRNA genes. Simulated CSO effluent was prepared using 23-40% wastewater, representing the higher end of the range of wastewater concentrations reported in CSO effluent. PAA residual following disinfection was greatest for samples with the lowest initial COD. Treatment of simulated CSO effluent (23% wastewater) with 100 mg∙min/L PAA (5 mg/L PAA, 20 min) was needed to reduce viable cell sul 1, tet (G), and BacHum (1.0±0.63-3.2±0.25-log) while 25 to 50 mg•min/L PAA (5 mg/L PAA, 5-10 min) was needed to reduce viable cell loads (0.62±0.56-1.6±0.08-log) in 40% wastewater from a different municipal treatment plant. Increasing contact time after the initial decrease in viable cell gene copies did not significantly improve treatment. A much greater applied Ct of 1200 mg∙min/L PAA (20 mg/L PAA, 60 min) was required for significant log reduction of 16S rRNA genes (3.29±0.13-log). No significant losses of mex B were observed during the study. Data were fitted to a Chick-Watson model and resulting inactivation constants for sul 1 and tet (G) > BacHum > 16S rRNA. Amplicon sequencing of the 16S rRNA gene indicated the initial viable and total microbial communities were distinct and that treatment with PAA resulted in marked increases of the relative abundance of select phyla, particularly Clostridia which increased by 1-1.5 orders of magnitude. Results confirm that membrane disruption is a mechanism for PAA disinfection and further treatment is needed to reduce total ARGs in CSO effluent.

  19. The use of virtual microscopy and a wiki in pathology education: Tracking student use, involvement, and response.

    Science.gov (United States)

    Leifer, Zev

    2015-01-01

    The pathology laboratory course at the New York College of Podiatric Medicine involves the use of Virtual Microscopy. The students can scan the whole slide, section by section, and zoom in or out. Using the advantages of digital pathology, the students can, in addition, access the slide collections from other medical schools and put up normal histology (control) slides side-by-side with the pathology. They can cut and paste and preserve the region of interest that they find. They can edit and annotate their slides. A wiki was created (http://pathlab2014.wikifoundry.com)for the Class of 2014. The students saved, edited and uploaded their slides. In the wiki format, other students could comment, further edit, and even delete the slides. The students studied Basic Mechanisms and System Pathology. During this time, they saved, edited, shared, and uploaded their slides to the wiki. These were available in one full presentation and were also grouped into 16 albums. They were available to all. Student access was followed by Google analytics. At the end of the course, a questionnaire was distributed, assessing their impression of the wiki format and soliciting strengths and weaknesses. The use of a wiki has a number of important advantages in pathology education. It trains the students in the more sophisticated skills that they will use as professional pathologists or as clinicians: (1) Telepathology-it enables them to share slides and discuss observations. (2) Archiving and retrieval - It models the challenge faced by hospitals, diagnostic labs and physicians in maintaining a collection of slides in a form that is easily accessible. (3) Image analysis-familiarity with the wiki format allows them to jump easily to capturing and storing images found in the literature or in a pathologist's report. Experience with the use of a wiki in pathology education has been quite satisfactory from both the faculty and the student's point of view.

  20. Physical Factors Correlate to Microbial Community Structure and Nitrogen Cycling Gene Abundance in a Nitrate Fed Eutrophic Lagoon.

    Science.gov (United States)

    Highton, Matthew P; Roosa, Stéphanie; Crawshaw, Josie; Schallenberg, Marc; Morales, Sergio E

    2016-01-01

    Nitrogenous run-off from farmed pastures contributes to the eutrophication of Lake Ellesmere, a large shallow lagoon/lake on the east coast of New Zealand. Tributaries periodically deliver high loads of nitrate to the lake which likely affect microbial communities therein. We hypothesized that a nutrient gradient would form from the potential sources (tributaries) creating a disturbance resulting in changes in microbial community structure. To test this we first determined the existence of such a gradient but found only a weak nitrogen (TN) and phosphorous gradient (DRP). Changes in microbial communities were determined by measuring functional potential (quantification of nitrogen cycling genes via nifH , nirS , nosZI , and nosZII using qPCR), potential activity (via denitrification enzyme activity), as well as using changes in total community (via 16S rRNA gene amplicon sequencing). Our results demonstrated that changes in microbial communities at a phylogenetic (relative abundance) and functional level (proportion of the microbial community carrying nifH and nosZI genes) were most strongly associated with physical gradients (e.g., lake depth, sediment grain size, sediment porosity) and not nutrient concentrations. Low nitrate influx at the time of sampling is proposed as a factor contributing to the observed patterns.

  1. Physical factors correlate to microbial community structure and nitrogen cycling gene abundance in a nitrate fed eutrophic lagoon

    Directory of Open Access Journals (Sweden)

    Matthew Paul Highton

    2016-10-01

    Full Text Available Nitrogenous run-off from farmed pastures contributes to the eutrophication of Lake Ellesmere, a large shallow lagoon/lake on the east coast of New Zealand. Tributaries periodically deliver high loads of nitrate to the lake which likely affect microbial communities therein. We hypothesized that a nutrient gradient would form from the potential sources (tributaries creating a disturbance resulting in changes in microbial community structure. To test this we first determined the existence of such a gradient but found only a weak nitrogen (TN and phosphorous gradient (DRP. Changes in microbial communities were determined by measuring functional potential (quantification of nitrogen cycling genes via nifH, nirS, nosZI and nosZII using qPCR, potential activity (via denitrification enzyme activity, as well as using changes in total community (via 16S rRNA gene amplicon sequencing. Our results demonstrated that changes in microbial communities at a phylogenetic (relative abundance and functional level (proportion of the microbial community carrying nifH and nosZI genes were most strongly associated with physical gradients (e.g. lake depth, sediment grain size, sediment porosity and not nutrient concentrations. Low nitrate influx at the time of sampling is proposed as a factor contributing to the observed patterns.

  2. Microbial community in persistent apical periodontitis: a 16S rRNA gene clone library analysis.

    Science.gov (United States)

    Zakaria, M N; Takeshita, T; Shibata, Y; Maeda, H; Wada, N; Akamine, A; Yamashita, Y

    2015-08-01

    To characterize the microbial composition of persistent periapical lesions of root filled teeth using a molecular genetics approach. Apical lesion samples were collected from 12 patients (23-80 years old) who visited the Kyushu University Hospital for apicectomy with persistent periapical lesions associated with root filled teeth. DNA was directly extracted from each sample and the microbial composition was comprehensively analysed using clone library analysis of the 16S rRNA gene. Enterococcus faecalis, Candida albicans and specific fimA genotypes of Porphyromonas gingivalis were confirmed using polymerase chain reaction (PCR) analysis with specific primers. Bacteria were detected in all samples, and the dominant findings were P. gingivalis (19.9%), Fusobacterium nucleatum (11.2%) and Propionibacterium acnes (9%). Bacterial diversity was greater in symptomatic lesions than in asymptomatic ones. In addition, the following bacteria or bacterial combinations were characteristic to symptomatic lesions: Prevotella spp., Treponema spp., Peptostreptococcaceae sp. HOT-113, Olsenella uli, Slackia exigua, Selemonas infelix, P. gingivalis with type IV fimA, and a combination of P. gingivalis, F. nucleatum, and Peptostreptococcaceae sp. HOT-113 and predominance of Streptococcus spp. On the other hand, neither Enterococcus faecalis nor C. albicans were detected in any of the samples. Whilst a diverse bacterial species were observed in the persistent apical lesions, some characteristic patterns of bacterial community were found in the symptomatic lesions. The diverse variation of community indicates that bacterial combinations as a community may cause persistent inflammation in periapical tissues rather than specific bacterial species. © 2014 International Endodontic Journal. Published by John Wiley & Sons Ltd.

  3. Microbial community structure of Arctic multiyear sea ice and surface seawater by 454 sequencing of the 16S RNA gene

    DEFF Research Database (Denmark)

    Bowman, Jeff S.; Rasmussen, Simon; Blom, Nikolaj

    2011-01-01

    community in MYI at two sites near the geographic North Pole using parallel tag sequencing of the 16S rRNA gene. Although the composition of the MYI microbial community has been characterized by previous studies, microbial community structure has not been. Although richness was lower in MYI than....... In addition, several low-abundance clades not previously reported in sea ice were present, including the phylum TM7 and the classes Spartobacteria and Opitutae. Members of Coraliomargarita, a recently described genus of the class Opitutae, were present in sufficient numbers to suggest niche occupation within...

  4. Pseudomonas community structure and antagonistic potential in the rhizosphere : insights gained by combining phylogenetic and functional gene-based analyses

    NARCIS (Netherlands)

    Costa, Rodrigo; Gomes, Newton C. M.; Kroegerrecklenfort, Ellen; Opelt, Katja; Berg, Gabriele; Smalla, Kornelia

    The Pseudomonas community structure and antagonistic potential in the rhizospheres of strawberry and oilseed rape (host plants of the fungal phytopathogen Verticillium dahliae) were assessed. The use of a new PCR-DGGE system, designed to target Pseudomonas-specific gacA gene fragments in

  5. Functional gene array-based analysis of microbial community structure in groundwaters with a gradient of contaminant levels

    Energy Technology Data Exchange (ETDEWEB)

    Waldron, P.J.; Wu, L.; Van Nostrand, J.D.; Schadt, C.W.; Watson, D.B.; Jardine, P.M.; Palumbo, A.V.; Hazen, T.C.; Zhou, J.

    2009-06-15

    To understand how contaminants affect microbial community diversity, heterogeneity, and functional structure, six groundwater monitoring wells from the Field Research Center of the U.S. Department of Energy Environmental Remediation Science Program (ERSP; Oak Ridge, TN), with a wide range of pH, nitrate, and heavy metal contamination were investigated. DNA from the groundwater community was analyzed with a functional gene array containing 2006 probes to detect genes involved in metal resistance, sulfate reduction, organic contaminant degradation, and carbon and nitrogen cycling. Microbial diversity decreased in relation to the contamination levels of the wells. Highly contaminated wells had lower gene diversity but greater signal intensity than the pristine well. The microbial composition was heterogeneous, with 17-70% overlap between different wells. Metal-resistant and metal-reducing microorganisms were detected in both contaminated and pristine wells, suggesting the potential for successful bioremediation of metal-contaminated groundwaters. In addition, results of Mantel tests and canonical correspondence analysis indicate that nitrate, sulfate, pH, uranium, and technetium have a significant (p < 0.05) effect on microbial community structure. This study provides an overall picture of microbial community structure in contaminated environments with functional gene arrays by showing that diversity and heterogeneity can vary greatly in relation to contamination.

  6. The diversity and abundance of phytase genes (beta-propeller phytases) in bacterial communities of the maize rhizosphere

    NARCIS (Netherlands)

    Cotta, S.R.; Cavalcante Franco Dias, A.; Seldin, L.; Andreote, F. D.; van Elsas, J. D.

    The ecology of microbial communities associated with organic phosphorus (P) mineralization in soils is still understudied. Here, we assessed the abundance and diversity of bacteria harbouring genes encoding beta-propeller phytases (BPP) in the rhizosphere of traditional and transgenic maize

  7. A Capstone Wiki Knowledge Base: A Case Study of an Online Tool Designed to Promote Life-Long Learning through Engineering Literature Research

    Science.gov (United States)

    Clarke, James B.; Coyle, James R.

    2011-01-01

    This article reports the results of a case study in which an experimental wiki knowledge base was designed, developed, and tested by the Brill Science Library at Miami University for an undergraduate engineering senior capstone project. The wiki knowledge base was created to determine if the science library could enhance the engineering literature…

  8. Ensino na comunidade e inteligência coletiva: partilhando saberes com o WIKI

    Directory of Open Access Journals (Sweden)

    Antonio Pithon Cyrino

    Full Text Available As novas tecnologias de informação e comunicação têm permitido a produção de inovações no processo de ensino-aprendizagem no ensino superior. Neste estudo de intervenção e pesquisa em disciplina de ensino em comunidade da Faculdade de Medicina de Botucatu - Unesp (FMB-Unesp, procura-se explorar tais possibilidades mediante o envolvimento de alunos, professores e membros da própria comunidade. Para tanto, desenvolveu-se uma página Wiki, com informações produzidas pelos alunos a respeito de um bairro da cidade de Botucatu, com o objetivo de criar um ambiente de troca, interação, cooperação e produção compartilhada de conhecimentos entre esses sujeitos. Um grupo de jovens dessa comunidade recebeu treinamento no uso do Wiki, o que lhes permitiu incluir na página informações novas sobre o território. A análise mostra que na produção textual desses jovens ganhou destaque alguns elementos significativos de seu cotidiano. A presença de um professor tutor na comunidade foi essencial para o êxito do processo. Os resultados alcançados apontam a viabilidade e potencialidade do uso do Wiki como ferramenta de inteligência coletiva, por permitir a troca de saberes entre alunos e comunidade, valorizando toda forma de conhecimento e a expressão das singularidades.

  9. Virtual strategies to improve transversal competences, using wikis in a collaborative work

    Science.gov (United States)

    Guinau, Marta; Playa, Elisabet

    2016-04-01

    A major educational aim in university degrees since the implementation of the European Credit Transfer System (ECTS) on the European universities is the work based on transversal competences. However, the first course students arrive at the Spanish universities with important deficiencies on some of these competences, especially regarding on oral and written expression, time management and collaborative work. The experience of the teachers involved in this work has revealed the coordination difficulty between the students to work in group, important deficiencies on information management and the stress caused by the oral presentations. The results presented here correspond to a teaching innovation project. It is based on: a) the development of works in groups of 3 or 4 students, proposed as flipped classrooms strategy and b) the implementation of a virtual tool (a wiki). This tool helps the students with scientific information management and facilitates the access of all the students belonging to the work group at the information provided by colleagues. The wiki also improves the monitoring and evaluation of the work and contributions of each student by teachers. Each group must develop a topic related to the subject - General Geology and Geochemistry - that the group chose from a list of earth sciences topics proposed by teachers. The resulting works are presented in poster and oral presentations (10 min. per group and 5 min. for questions). Each work is evaluated by teachers using the evidences provided on the wiki and by means of evaluation guides. Moreover, the students must self and co-evaluate the presented works. The implementation of this project has provided information to analyze the impact of these strategies and to quantify it in terms of 'Learning Analytics'.

  10. Antibiotic Resistance Genes and Correlations with Microbial Community and Metal Resistance Genes in Full-Scale Biogas Reactors As Revealed by Metagenomic Analysis

    DEFF Research Database (Denmark)

    Luo, Gang; Li, Bing; Li, Li-Guan

    2017-01-01

    resistance genes (MRGs). The total abundance of ARGs in all the samples varied from 7 × 10-3 to 1.08 × 10-1 copy of ARG/copy of 16S-rRNA gene, and the samples obtained from thermophilic biogas reactors had a lower total abundance of ARGs, indicating the superiority of thermophilic anaerobic digestion......Digested residues from biogas plants are often used as biofertilizers for agricultural crops cultivation. The antibiotic resistance genes (ARGs) in digested residues pose a high risk to public health due to their potential spread to the disease-causing microorganisms and thus reduce...... the susceptibility of disease-causing microorganisms to antibiotics in medical treatment. A high-throughput sequencing (HTS)-based metagenomic approach was used in the present study to investigate the variations of ARGs in full-scale biogas reactors and the correlations of ARGs with microbial communities and metal...

  11. Metatranscriptome Sequencing of a Reef-building Coral Elucidates Holobiont Community Gene Functions in Health and Disease

    Science.gov (United States)

    Timberlake, S.; Helbig, T.; Fernando, S.; Penn, K.; Alm, E.; Thompson, F.; Thompson, J. R.

    2012-12-01

    The coral reefs of the Abrolhos Bank of Brazil play a vital ecological role in the health of the Southern Atlantic Ocean, but accelerating rates of disease, particularly white plague, threaten this ecosystem. Thus, an understanding of white plague disease and diagnostic tests for it are urgently needed. The coral animal is associated with a distinct microbiome, a diverse assemblage of eukaryotes, bacteria, and viruses. That these microbes have a great influence on the health of the coral has been long known, however, most of their functions are still mysterious. While recent studies have contrasted healthy and white-plague-associated communities, the causative agents and mechanisms of the disease remain unknown. We collected fragments of healthy and diseased corals, as well as post-disease skeleton, from 12 colonies of the genus Mussismilia, the major component of the reef structure in the Abrolhos bank, and increasingly, a victim of white-plague disease. Fragments were flash-frozen in situ, and prepped for culture-free high throughput sequencing of gene transcripts with the Illumina II-G. While the membership of the microbial communities associated with coral has been previously described, the a coral holobiont community's gene function has, to date, never been assayed by this powerful approach. We designed a bioinformatics pipeline to analyze the short-read data from this complex sample: identifying the functions of genes expressed in the holobiont, and describing the active community's taxonomic composition. We show that gene functions expressed by the coral's bacterial assemblage are distinct from those of the underlying skeleton, and we highlight differences in the disease samples. We find that gene markers for the dissimilatory sulfate reduction pathway more abundant in the disease state, and we further quantify this difference with qPCR. Finally, we report the abundant expression of highly repetitive transcripts in the diseased coral samples, and highlight

  12. Prevalence of quinolone resistance genes, copper resistance genes, and the bacterial communities in a soil-ryegrass system co-polluted with copper and ciprofloxacin.

    Science.gov (United States)

    Tuo, Xiaxia; Gu, Jie; Wang, Xiaojuan; Sun, YiXin; Duan, Manli; Sun, Wei; Yin, Yanan; Guo, Aiyun; Zhang, Li

    2018-04-01

    The presence of high concentrations of residual antibiotics and antibiotic resistance genes (ARGs) in soil may pose potential health and environmental risks. This study investigated the prevalence of plasmid-mediated quinolone resistance (PMQR) genes, copper resistance genes (CRGs), and the bacterial communities in a soil-ryegrass pot system co-polluted with copper and ciprofloxacin (CIP; 0, 20, or 80 mg kg -1 dry soil). Compared with the samples on day 0, the total relative abundances of the PMQR genes and mobile genetic elements (MGEs) were reduced significantly by 80-89% in the ryegrass and soil by the cutting stage (after 75 days). The abundances of PMQR genes and MGEs were reduced by 63-81% in soil treated with 20 mg kg -1 CIP compared with the other treatments, but the abundances of CRGs increased by 18-42%. The presence of 80 mg kg -1 CIP affected the microbial community structure in the soil by increasing the abundances of Acidobacteria and Thaumarchaeota, but decreasing those of Firmicutes. Redundancy analysis indicated that the pH and microbial composition were the main factors that affected the variations in PMQR genes, MGEs, and CRGs, where they could explain 42.2% and 33.3% of the variation, respectively. Furthermore, intI2 may play an important role in the transfer of ARGs. We found that 80 mg kg -1 CIP could increase the abundances of ARGs and CRGs in a soil-ryegrass pot system. Copyright © 2018 Elsevier Ltd. All rights reserved.

  13. El wiki : espacio de comunicación y aprendizaje en ELE

    OpenAIRE

    Mendes, Laura Manuela Domingues

    2014-01-01

    Projeto de mestrado em Espanhol Língua Segunda e Língua Estrangeira En este trabajo se debate la pertinencia de la utilización de una aplicación de software social, el wiki, en el contexto de la enseñanza del Español como Lengua Extranjera, para fomentar el proceso de la lectoescritura en trabajo colaborativo en esta lengua. La propuesta es construir un entorno virtual dentro del espacio del aula para estimular el aprendizaje y comunicación real en español, producto de un conju...

  14. Wiki como herramienta de aprendizaje en grupo y evaluación al alumno

    Directory of Open Access Journals (Sweden)

    María Jesús Miró Obradors

    2013-11-01

    Full Text Available “Estimular el aprendizaje autónomo, incentivar el estudio individual y colectivo y reducir las formas pasivas de enseñanza" es uno de los objetivos de los nuevos planes de estudios. Siendo una Wiki aquél espacio de trabajo en línea que posibilita la creación colectiva de documentos utilizando un navegador web, consideramos ésta, una buena herramienta para el desarrollo del trabajo en grupo de los alumnos, así como para realizar una evaluación continuada de los mismos. Metodología: 1 Establecer grupos de estudiantes, 2 Crear wikis en las asignaturas abiertas en Moodle del Campus Virtual UCM (CV, 2 Introducción por el profesor de las actividades, 3 Abrir un foro, 4 Envío de las tareas (CV, 5 Calificación. Resultados y conclusiones: Alumnos de asignaturas en el Área de Bioquímica y Biología Molecular y Celular del Grado en Farmacia (UCM, han trabajado en wikis: a Una tabla, en la cual cada grupo de estudiantes introduce dos palabras clave (sin repetir de cada tema impartido y a su vez, redacta el enunciado de dos preguntas relativas a palabras clave que han incluido previamente otro grupo de alumnos. La lista resultante y revisada de unas 75 cuestiones, se utilizó para elaborar exámenes, realizados en clase tras la finalización de cada bloque de contenidos. b Cuestiones relativas a seminarios y películas de cine proyectadas previamente. El módulo Wiki de Moodle ha permitido a cada estudiante trabajar en páginas web on line con sus compañeros, habiendo podido añadir, expandir o modificar su contenido en ellas. Las versiones antiguas nunca se eliminan y pueden restaurarse. Esto ha permitido, además de calificar el trabajo de grupo, hacer un seguimiento del trabajo individual de cada estudiante, para su mejor evaluación. PIMCD 2013 nº 3 (UCM.

  15. Prokaryotic community profiling of local algae wastewaters using advanced 16S rRNA gene sequencing.

    Science.gov (United States)

    Limayem, Alya; Micciche, Andrew; Nayak, Bina; Mohapatra, Shyam

    2018-01-01

    Algae biomass-fed wastewaters are a promising source of lipid and bioenergy manufacture, revealing substantial end-product investment returns. However, wastewaters would contain lytic pathogens carrying drug resistance detrimental to algae yield and environmental safety. This study was conducted to simultaneously decipher through high-throughput advanced Illumina 16S ribosomal RNA (rRNA) gene sequencing, the cultivable and uncultivable bacterial community profile found in a single sample that was directly recovered from the local wastewater systems. Samples were collected from two previously documented sources including anaerobically digested (AD) municipal wastewater and swine wastewater with algae namely Chlorella spp. in addition to control samples, swine wastewater, and municipal wastewater without algae. Results indicated the presence of a significant level of Bacteria in all samples with an average of approximately 95.49% followed by Archaea 2.34%, in local wastewaters designed for algae cultivation. Taxonomic genus identification indicated the presence of Calothrix, Pseudomonas, and Clostridium as the most prevalent strains in both local municipal and swine wastewater samples containing algae with an average of 17.37, 12.19, and 7.84%, respectively. Interestingly, swine wastewater without algae displayed the lowest level of Pseudomonas strains algae indicates potential coexistence between these strains and algae microenvironment, suggesting further investigations. This finding was particularly relevant for the earlier documented adverse effects of some nosocomial Pseudomonas strains on algae growth and their multidrug resistance potential, requiring the development of targeted bioremediation with regard to the beneficial flora.

  16. Response of microbial community and catabolic genes to simulated petroleum hydrocarbon spills in soils/sediments from different geographic locations.

    Science.gov (United States)

    Liu, Q; Tang, J; Liu, X; Song, B; Zhen, M; Ashbolt, N J

    2017-10-01

    Study the response of microbial communities and selected petroleum hydrocarbon (PH)-degrading genes on simulated PH spills in soils/sediments from different geographic locations. A microcosm experiment was conducted by spiking mixtures of petroleum hydrocarbons (PHs) to soils/sediments collected from four different regions of China, including the Dagang Oilfield (DG), Sand of Bohai Sea (SS), Northeast China (NE) and Xiamen (XM). Changes in bacterial community and the abundance of PH-degrading genes (alkB, nah and phe) were analysed by denaturing gradient electrophoresis (DGGE) and qPCR, respectively. Degradation of alkanes and PAHs in SS and NE materials were greater (P < 0·05) than those in DG and XM. Clay content was negatively correlated with the degradation of total alkanes by 112 days and PAHs by 56 days, while total organic carbon content was negatively correlated with initial degradation of total alkanes as well as PAHs. Abundances of alkB, nah and phe genes increased 10- to 100-fold and varied by soil type over the incubation period. DGGE fingerprints identified the dominance of α-, β- and γ-Proteobacteria (Gram -ve) and Actinobacteria (Gram +ve) bacteria associated with degradation of PHs in the materials studied. The geographic divergence resulting from the heterogeneity of physicochemical properties of soils/sediments appeared to influence the abundance of metabolic genes and community structure of microbes capable of degrading PHs. When developing practical in-situ bioremediation approaches for PHs contamination of soils/sediment, appropriate microbial community structures and the abundance of PH-degrading genes appear to be influenced by geographic location. © 2017 The Society for Applied Microbiology.

  17. Effects of polycyclic aromatic hydrocarbons on microbial community structure and PAH ring hydroxylating dioxygenase gene abundance in soil.

    Science.gov (United States)

    Sawulski, Przemyslaw; Clipson, Nicholas; Doyle, Evelyn

    2014-11-01

    Development of successful bioremediation strategies for environments contaminated with recalcitrant pollutants requires in-depth knowledge of the microorganisms and microbial processes involved in degradation. The response of soil microbial communities to three polycyclic aromatic hydrocarbons, phenanthrene (3-ring), fluoranthene (4-ring) and benzo(a)pyrene (5-ring), was examined. Profiles of bacterial, archaeal and fungal communities were generated using molecular fingerprinting techniques (TRFLP, ARISA) and multivariate statistical tools were employed to interpret the effect of PAHs on community dynamics and composition. The extent and rate of PAH removal was directly related to the chemical structure, with the 5-ring PAH benzo(a)pyrene degraded more slowly than phenathrene or fluoranthene. Bacterial, archaeal and fungal communities were all significantly affected by PAH amendment, time and their interaction. Based on analysis of clone libraries, Actinobacteria appeared to dominate in fluoranthene amended soil, although they also represented a significant portion of the diversity in phenanthrene amended and unamended soils. In addition there appeared to be more γ-Proteobacteria and less Bacteroidetes in soil amended with either PAH compared to the control. The soil bacterial community clearly possessed the potential to degrade PAHs as evidenced by the abundance of PAH ring hydroxylating (PAH-RHDα) genes from both gram negative (GN) and gram positive (GP) bacteria in PAH-amended and control soils. Although the dioxygenase gene from GP bacteria was less abundant in soil than the gene associated with GN bacteria, significant (p PAH-RHDα gene were observed during phenanthrene and fluoranthene degradation, whereas there was no significant difference in the abundance of the GN PAH-RHDα gene during the course of the experiment. Few studies to-date have examined the effect of pollutants on more than one microbial community in soil. The current study provides

  18. Community

    Science.gov (United States)

    stability Science & Innovation Collaboration Careers Community Environment Science & Innovation Recruitment Events Community Commitment Giving Campaigns, Drives Economic Development Employee Funded neighbor pledge: contribute to quality of life in Northern New Mexico through economic development

  19. Diversity of pufM genes, involved in aerobic anoxygenic photosynthesis, in the bacterial communities associated with colonial ascidians.

    Science.gov (United States)

    Martínez-García, Manuel; Díaz-Valdés, Marta; Antón, Josefa

    2010-03-01

    Ascidians are invertebrate filter feeders widely distributed in benthic marine environments. A total of 14 different ascidian species were collected from the Western Mediterranean and their bacterial communities were analyzed by denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene. Results showed that ascidian tissues harbored Bacteria belonging to Gamma- and Alphaproteobacteria classes, some of them phylogenetically related to known aerobic anoxygenic phototrophs (AAPs), such as Roseobacter sp. In addition, hierarchical cluster analysis of DGGE patterns showed a large variability in the bacterial diversity among the different ascidians analyzed, which indicates that they would harbor different bacterial communities. Furthermore, pufM genes, involved in aerobic anoxygenic photosynthesis in marine and freshwater systems, were widely detected within the ascidians analyzed, because nine out of 14 species had pufM genes inside their tissues. The pufM gene was only detected in those specimens that inhabited shallow waters (<77 m of depth). Most pufM gene sequences were very closely related to that of uncultured marine bacteria. Thus, our results suggest that the association of ascidians with bacteria related to AAPs could be a general phenomenon and that ascidian-associated microbiota could use the light that penetrates through the tunic tissue as an energy source.

  20. Audio Wiki for mobile communities: information system for the rest of Us

    CSIR Research Space (South Africa)

    Leinonen, T

    2006-09-01

    Full Text Available Music Stands MD-1 (speaker for the Nokia 3230). The pilot showed that the students learned to use mobile phones very fast in the small groups. During the first lesson, we only gave the student groups the mobile phones and the speakers and let them... to figure out how they worked. One group found that there was a radio applications and they started to play on the music with the speakers. Other group needed less than five minutes to figure out the radio in their own phone. Students basically learned...

  1. FoodWiki: a Mobile App Examines Side Effects of Food Additives Via Semantic Web.

    Science.gov (United States)

    Çelik Ertuğrul, Duygu

    2016-02-01

    In this article, a research project on mobile safe food consumption system (FoodWiki) is discussed that performs its own inferencing rules in its own knowledge base. Currently, the developed rules examines the side effects that are causing some health risks: heart disease, diabetes, allergy, and asthma as initial. There are thousands compounds added to the processed food by food producers with numerous effects on the food: to add color, stabilize, texturize, preserve, sweeten, thicken, add flavor, soften, emulsify, and so forth. Those commonly used ingredients or compounds in manufactured foods may have many side effects that cause several health risks such as heart disease, hypertension, cholesterol, asthma, diabetes, allergies, alzheimer etc. according to World Health Organization. Safety in food consumption, especially by patients in these risk groups, has become crucial, given that such health problems are ranked in the top ten health risks around the world. It is needed personal e-health knowledge base systems to help patients take control of their safe food consumption. The systems with advanced semantic knowledge base can provide recommendations of appropriate foods before consumption by individuals. The proposed FoodWiki system is using a concept based search mechanism that performs on thousands food compounds to provide more relevant information.

  2. Arquitectura en territorios informados y transparentes Una wiki en la escuela de arquitectura

    Directory of Open Access Journals (Sweden)

    Javier Fernández García

    2010-01-01

    Full Text Available El marco general de nuestra investigación en la universidad son los espacios de convivencia, información y formación que configuran los habitantes en un territorio online. La Web 2.0 nos ha dotado de nuevas herramientas con la que construir espacios. Desde la fundación en agosto de 2006 de CityWiki, indagamos en la arquitectura de estos lugares que se articulan en un espacio común en el que, a falta de jerarquía y policía, la acción en él la define el empoderamiento y la libertad del ciudadano responsable. A modo de laboratorio, desde entonces, embarcamos la actividad investigadora y docente en la actitud 2.0 incluida en la WWW. En la primera parte de este artículo se expone el pensamiento actualizado que empíricamente evoluciona emparejado a la actualidad de nuestras investigaciones. El objetivo es hacer entender el territorio wiki como informado y transparente llamado a añadir capas de información a la realidad para de esta forma no sustituirla sino ampliarla. Seguidamente, en la segunda parte, se describe y analiza la experiencia de innovación llevada a cabo durante el curso 2007/2008 en la que se ensayó un modelo docente instrumentados en los modos y paisajes previamente descritos.

  3. Wikis and Collaborative Writing Applications in Health Care: A Scoping Review

    Science.gov (United States)

    Grajales III, Francisco J; Faber, Marjan J; Kuziemsky, Craig E; Gagnon, Susie; Bilodeau, Andrea; Rioux, Simon; Nelen, Willianne LDM; Gagnon, Marie-Pierre; Turgeon, Alexis F; Aubin, Karine; Gold, Irving; Poitras, Julien; Eysenbach, Gunther; Kremer, Jan AM; Légaré, France

    2013-01-01

    Background Collaborative writing applications (eg, wikis and Google Documents) hold the potential to improve the use of evidence in both public health and health care. The rapid rise in their use has created the need for a systematic synthesis of the evidence of their impact as knowledge translation (KT) tools in the health care sector and for an inventory of the factors that affect their use. Objective Through the Levac six-stage methodology, a scoping review was undertaken to explore the depth and breadth of evidence about the effective, safe, and ethical use of wikis and collaborative writing applications (CWAs) in health care. Methods Multiple strategies were used to locate studies. Seven scientific databases and 6 grey literature sources were queried for articles on wikis and CWAs published between 2001 and September 16, 2011. In total, 4436 citations and 1921 grey literature items were screened. Two reviewers independently reviewed citations, selected eligible studies, and extracted data using a standardized form. We included any paper presenting qualitative or quantitative empirical evidence concerning health care and CWAs. We defined a CWA as any technology that enables the joint and simultaneous editing of a webpage or an online document by many end users. We performed qualitative content analysis to identify the factors that affect the use of CWAs using the Gagnon framework and their effects on health care using the Donabedian framework. Results Of the 111 studies included, 4 were experimental, 5 quasi-experimental, 5 observational, 52 case studies, 23 surveys about wiki use, and 22 descriptive studies about the quality of information in wikis. We classified them by theme: patterns of use of CWAs (n=26), quality of information in existing CWAs (n=25), and CWAs as KT tools (n=73). A high prevalence of CWA use (ie, more than 50%) is reported in 58% (7/12) of surveys conducted with health care professionals and students. However, we found only one

  4. A community resource for high-throughput quantitative RT-PCR analysis of transcription factor gene expression in Medicago truncatula

    Directory of Open Access Journals (Sweden)

    Redman Julia C

    2008-07-01

    Full Text Available Abstract Background Medicago truncatula is a model legume species that is currently the focus of an international genome sequencing effort. Although several different oligonucleotide and cDNA arrays have been produced for genome-wide transcript analysis of this species, intrinsic limitations in the sensitivity of hybridization-based technologies mean that transcripts of genes expressed at low-levels cannot be measured accurately with these tools. Amongst such genes are many encoding transcription factors (TFs, which are arguably the most important class of regulatory proteins. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR is the most sensitive method currently available for transcript quantification, and one that can be scaled up to analyze transcripts of thousands of genes in parallel. Thus, qRT-PCR is an ideal method to tackle the problem of TF transcript quantification in Medicago and other plants. Results We established a bioinformatics pipeline to identify putative TF genes in Medicago truncatula and to design gene-specific oligonucleotide primers for qRT-PCR analysis of TF transcripts. We validated the efficacy and gene-specificity of over 1000 TF primer pairs and utilized these to identify sets of organ-enhanced TF genes that may play important roles in organ development or differentiation in this species. This community resource will be developed further as more genome sequence becomes available, with the ultimate goal of producing validated, gene-specific primers for all Medicago TF genes. Conclusion High-throughput qRT-PCR using a 384-well plate format enables rapid, flexible, and sensitive quantification of all predicted Medicago transcription factor mRNAs. This resource has been utilized recently by several groups in Europe, Australia, and the USA, and we expect that it will become the 'gold-standard' for TF transcript profiling in Medicago truncatula.

  5. A Course Wiki: Challenges in Facilitating and Assessing Student-Generated Learning Content for the Humanities Classroom

    Science.gov (United States)

    Lazda-Cazers, Rasma

    2010-01-01

    New Web technology allows for the design of traditionally lecture-centered humanities courses by fostering active learning and engaging students as producers of learning content. The article presents the experiences with a student-generated wiki for a Germanic Mythology course. Evaluations indicated an overwhelmingly positive student experience…

  6. Social Media and Peer Feedback: What Do Students Really Think about Using Wiki and Facebook as Platforms for Peer Feedback?

    Science.gov (United States)

    Demirbilek, Muhammet

    2015-01-01

    Web 2.0 tools are becoming increasingly pervasive in higher education, and as a result, there is increasing interest in the use of online feedback activities. This study investigated students' actual experiences and perceptions using social media, Wiki and Facebook, tools to provide peer feedback on students' instructional material projects and to…

  7. Research and Teaching: WikiED--Using Web 2.0 Tools to Teach Content and Critical Thinking

    Science.gov (United States)

    Frisch, Jennifer K.; Jackson, Paula C.; Murray, Meg C.

    2013-01-01

    WIKIed Biology is a National Science Foundation Transforming Undergraduate Education in Science, Technology, Engineering, and Mathematics interdisciplinary project in which the authors developed and implemented a model for student centered, inquiry-driven instruction using Web 2.0 technologies to increase inquiry and conceptual understanding in…

  8. Challenges of the Administrative Consultation Wiki Research Project as a Learning and Competences Development Method for MPA Students

    Science.gov (United States)

    Kovac, Polonca; Stare, Janez

    2015-01-01

    Administrative Consultation Wiki (ACW) is a project run under the auspices of the Faculty of Administration and the Ministry of Public Administration in Slovenia since 2009. A crucial component thereof is the involvement of students of Master of Public Administration (MPA) degree programs to offer them an opportunity to develop competences in…

  9. Effect of phenylurea herbicides on soil microbial communities estimated by analysis of 16S rRNA gene fingerprints and community-level physiological profiles.

    Science.gov (United States)

    el Fantroussi, S; Verschuere, L; Verstraete, W; Top, E M

    1999-03-01

    The effect of three phenyl urea herbicides (diuron, linuron, and chlorotoluron) on soil microbial communities was studied by using soil samples with a 10-year history of treatment. Denaturing gradient gel electrophoresis (DGGE) was used for the analysis of 16S rRNA genes (16S rDNA). The degree of similarity between the 16S rDNA profiles of the communities was quantified by numerically analysing the DGGE band patterns. Similarity dendrograms showed that the microbial community structures of the herbicide-treated and nontreated soils were significantly different. Moreover, the bacterial diversity seemed to decrease in soils treated with urea herbicides, and sequence determination of several DGGE fragments showed that the most affected species in the soils treated with diuron and linuron belonged to an uncultivated bacterial group. As well as the 16S rDNA fingerprints, the substrate utilization patterns of the microbial communities were compared. Principal-component analysis performed on BIOLOG data showed that the functional abilities of the soil microbial communities were altered by the application of the herbicides. In addition, enrichment cultures of the different soils in medium with the urea herbicides as the sole carbon and nitrogen source showed that there was no difference between treated and nontreated soil in the rate of transformation of diuron and chlorotoluron but that there was a strong difference in the case of linuron. In the enrichment cultures with linuron-treated soil, linuron disappeared completely after 1 week whereas no significant transformation was observed in cultures inoculated with nontreated soil even after 4 weeks. In conclusion, this study showed that both the structure and metabolic potential of soil microbial communities were clearly affected by a long-term application of urea herbicides.

  10. Methods for the Isolation of Genes Encoding Novel PHA Metabolism Enzymes from Complex Microbial Communities.

    Science.gov (United States)

    Cheng, Jiujun; Nordeste, Ricardo; Trainer, Maria A; Charles, Trevor C

    2017-01-01

    Development of different PHAs as alternatives to petrochemically derived plastics can be facilitated by mining metagenomic libraries for diverse PHA cycle genes that might be useful for synthesis of bio-plastics. The specific phenotypes associated with mutations of the PHA synthesis pathway genes in Sinorhizobium meliloti and Pseudomonas putida, allows the use of powerful selection and screening tools to identify complementing novel PHA synthesis genes. Identification of novel genes through their function rather than sequence facilitates the functional proteins that may otherwise have been excluded through sequence-only screening methodology. We present here methods that we have developed for the isolation of clones expressing novel PHA metabolism genes from metagenomic libraries.

  11. Methods for the isolation of genes encoding novel PHB cycle enzymes from complex microbial communities.

    Science.gov (United States)

    Nordeste, Ricardo F; Trainer, Maria A; Charles, Trevor C

    2010-01-01

    Development of different PHAs as alternatives to petrochemically derived plastics can be facilitated by mining metagenomic libraries for diverse PHA cycle genes that might be useful for synthesis of bioplastics. The specific phenotypes associated with mutations of the PHA synthesis pathway genes in Sinorhizobium meliloti allows for the use of powerful selection and screening tools to identify complementing novel PHA synthesis genes. Identification of novel genes through their function rather than sequence facilitates finding functional proteins that may otherwise have been excluded through sequence-only screening methodology. We present here methods that we have developed for the isolation of clones expressing novel PHA metabolism genes from metagenomic libraries.

  12. Prevalence of antibiotic resistance genes and bacterial community composition in a river influenced by a wastewater treatment plant.

    Directory of Open Access Journals (Sweden)

    Elisabet Marti

    Full Text Available Antibiotic resistance represents a global health problem, requiring better understanding of the ecology of antibiotic resistance genes (ARGs, their selection and their spread in the environment. Antibiotics are constantly released to the environment through wastewater treatment plant (WWTP effluents. We investigated, therefore, the effect of these discharges on the prevalence of ARGs and bacterial community composition in biofilm and sediment samples of a receiving river. We used culture-independent approaches such as quantitative PCR to determine the prevalence of eleven ARGs and 16S rRNA gene-based pyrosequencing to examine the composition of bacterial communities. Concentration of antibiotics in WWTP influent and effluent were also determined. ARGs such as qnrS, bla TEM, bla CTX-M, bla SHV, erm(B, sul(I, sul(II, tet(O and tet(W were detected in all biofilm and sediment samples analyzed. Moreover, we observed a significant increase in the relative abundance of ARGs in biofilm samples collected downstream of the WWTP discharge. We also found significant differences with respect to community structure and composition between upstream and downstream samples. Therefore, our results indicate that WWTP discharges may contribute to the spread of ARGs into the environment and may also impact on the bacterial communities of the receiving river.

  13. Health Care Professionals’ Beliefs About Using Wiki-Based Reminders to Promote Best Practices in Trauma Care

    Science.gov (United States)

    Bilodeau, Andrea; Gagnon, Marie-Pierre; Aubin, Karine; Lavoie, André; Lapointe, Jean; Poitras, Julien; Croteau, Sylvain; Pham-Dinh, Martin; Légaré, France

    2012-01-01

    Background Wikis are knowledge translation tools that could help health professionals implement best practices in acute care. Little is known about the factors influencing professionals’ use of wikis. Objectives To identify and compare the beliefs of emergency physicians (EPs) and allied health professionals (AHPs) about using a wiki-based reminder that promotes evidence-based care for traumatic brain injuries. Methods Drawing on the theory of planned behavior, we conducted semistructured interviews to elicit EPs’ and AHPs’ beliefs about using a wiki-based reminder. Previous studies suggested a sample of 25 EPs and 25 AHPs. We purposefully selected participants from three trauma centers in Quebec, Canada, to obtain a representative sample. Using univariate analyses, we assessed whether our participants’ gender, age, and level of experience were similar to those of all eligible individuals. Participants viewed a video showing a clinician using a wiki-based reminder, and we interviewed participants about their behavioral, control, and normative beliefs—that is, what they saw as advantages, disadvantages, barriers, and facilitators to their use of a reminder, and how they felt important referents would perceive their use of a reminder. Two reviewers independently analyzed the content of the interview transcripts. We considered the 75% most frequently mentioned beliefs as salient. We retained some less frequently mentioned beliefs as well. Results Of 66 eligible EPs and 444 eligible AHPs, we invited 55 EPs and 39 AHPs to participate, and 25 EPs and 25 AHPs (15 nurses, 7 respiratory therapists, and 3 pharmacists) accepted. Participating AHPs had more experience than eligible AHPs (mean 14 vs 11 years; P = .04). We noted no other significant differences. Among EPs, the most frequently reported advantage of using a wiki-based reminder was that it refreshes the memory (n = 14); among AHPs, it was that it provides rapid access to protocols (n = 16). Only 2 EPs

  14. Investigation of energy gene expressions and community structures of free and attached acidophilic bacteria in chalcopyrite bioleaching.

    Science.gov (United States)

    Zhu, Jianyu; Jiao, Weifeng; Li, Qian; Liu, Xueduan; Qin, Wenqing; Qiu, Guanzhou; Hu, Yuehua; Chai, Liyuan

    2012-12-01

    In order to better understand the bioleaching mechanism, expression of genes involved in energy conservation and community structure of free and attached acidophilic bacteria in chalcopyrite bioleaching were investigated. Using quantitative real-time PCR, we studied the expression of genes involved in energy conservation in free and attached Acidithiobacillus ferrooxidans during bioleaching of chalcopyrite. Sulfur oxidation genes of attached A. ferrooxidans were up-regulated while ferrous iron oxidation genes were down-regulated compared with free A. ferrooxidans in the solution. The up-regulation may be induced by elemental sulfur on the mineral surface. This conclusion was supported by the results of HPLC analysis. Sulfur-oxidizing Acidithiobacillus thiooxidans and ferrous-oxidizing Leptospirillum ferrooxidans were the members of the mixed culture in chalcopyrite bioleaching. Study of the community structure of free and attached bacteria showed that A. thiooxidans dominated the attached bacteria while L. ferrooxidans dominated the free bacteria. With respect to available energy sources during bioleaching of chalcopyrite, sulfur-oxidizers tend to be on the mineral surfaces whereas ferrous iron-oxidizers tend to be suspended in the aqueous phase. Taken together, these results indicate that the main role of attached acidophilic bacteria was to oxidize elemental sulfur and dissolution of chalcopyrite involved chiefly an indirect bioleaching mechanism.

  15. Nested PCR Biases in Interpreting Microbial Community Structure in 16S rRNA Gene Sequence Datasets.

    Science.gov (United States)

    Yu, Guoqin; Fadrosh, Doug; Goedert, James J; Ravel, Jacques; Goldstein, Alisa M

    2015-01-01

    Sequencing of the PCR-amplified 16S rRNA gene has become a common approach to microbial community investigations in the fields of human health and environmental sciences. This approach, however, is difficult when the amount of DNA is too low to be amplified by standard PCR. Nested PCR can be employed as it can amplify samples with DNA concentration several-fold lower than standard PCR. However, potential biases with nested PCRs that could affect measurement of community structure have received little attention. In this study, we used 17 DNAs extracted from vaginal swabs and 12 DNAs extracted from stool samples to study the influence of nested PCR amplification of the 16S rRNA gene on the estimation of microbial community structure using Illumina MiSeq sequencing. Nested and standard PCR methods were compared on alpha- and beta-diversity metrics and relative abundances of bacterial genera. The effects of number of cycles in the first round of PCR (10 vs. 20) and microbial diversity (relatively low in vagina vs. high in stool) were also investigated. Vaginal swab samples showed no significant difference in alpha diversity or community structure between nested PCR and standard PCR (one round of 40 cycles). Stool samples showed significant differences in alpha diversity (except Shannon's index) and relative abundance of 13 genera between nested PCR with 20 cycles in the first round and standard PCR (Pnested PCR with 10 cycles in the first round and standard PCR. Operational taxonomic units (OTUs) that had low relative abundance (sum of relative abundance 27% of total OTUs in stool). Nested PCR introduced bias in estimated diversity and community structure. The bias was more significant for communities with relatively higher diversity and when more cycles were applied in the first round of PCR. We conclude that nested PCR could be used when standard PCR does not work. However, rare taxa detected by nested PCR should be validated by other technologies.

  16. Community.

    Science.gov (United States)

    Grauer, Kit, Ed.

    1995-01-01

    Art in context of community is the theme of this newsletter. The theme is introduced in an editorial "Community-Enlarging the Definition" (Kit Grauer). Related articles include: (1) "The Children's Bridge is not Destroyed: Heart in the Middle of the World" (Emil Robert Tanay); (2) "Making Bridges: The Sock Doll…

  17. Chronic exposure to triclosan sustains microbial community shifts and alters antibiotic resistance gene levels in anaerobic digesters.

    Science.gov (United States)

    Carey, Daniel E; Zitomer, Daniel H; Kappell, Anthony D; Choi, Melinda J; Hristova, Krassimira R; McNamara, Patrick J

    2016-08-10

    Triclosan, an antimicrobial chemical found in consumer personal care products, has been shown to stimulate antibiotic resistance in pathogenic bacteria. Although many studies focus on antibiotic resistance pertinent to medical scenarios, resistance developed in natural and engineered environments is less studied and has become an emerging concern for human health. In this study, the impacts of chronic triclosan (TCS) exposure on antibiotic resistance genes (ARGs) and microbial community structure were assessed in lab-scale anaerobic digesters. TCS concentrations from below detection to 2500 mg kg(-1) dry solids were amended into anaerobic digesters over 110 days and acclimated for >3 solid retention time values. Four steady state TCS concentrations were chosen (30-2500 mg kg(-1)). Relative abundance of mexB, a gene coding for a component of a multidrug efflux pump, was significantly higher in all TCS-amended digesters (30 mg kg(-1) or higher) relative to the control. TCS selected for bacteria carrying tet(L) and against those carrying erm(F) at concentrations which inhibited digester function; the pH decrease associated with digester failure was suspected to cause this selection. Little to no impact of TCS was observed on intI1 relative abundance. Microbial communities were also surveyed by high-throughput 16S rRNA gene sequencing. Compared to the control digesters, significant shifts in community structure towards clades containing commensal and pathogenic bacteria were observed in digesters containing TCS. Based on these results, TCS should be included in studies and risk assessments that attempt to elucidate relationships between chemical stressors (e.g. antibiotics), antibiotic resistance genes, and public health.

  18. Effect of Flooding and the nosZ Gene in Bradyrhizobia on Bradyrhizobial Community Structure in the Soil.

    Science.gov (United States)

    Saeki, Yuichi; Nakamura, Misato; Mason, Maria Luisa T; Yano, Tsubasa; Shiro, Sokichi; Sameshima-Saito, Reiko; Itakura, Manabu; Minamisawa, Kiwamu; Yamamoto, Akihiro

    2017-06-24

    We investigated the effects of the water status (flooded or non-flooded) and presence of the nosZ gene in bradyrhizobia on the bradyrhizobial community structure in a factorial experiment that examined three temperature levels (20°C, 25°C, and 30°C) and two soil types (andosol and gray lowland soil) using microcosm incubations. All microcosms were inoculated with Bradyrhizobium japonicum USDA6 T , B. japonicum USDA123, and B. elkanii USDA76 T , which do not possess the nosZ gene, and then half received B. diazoefficiens USDA110 T wt (wt for the wild-type) and the other half received B. diazoefficiens USDA110ΔnosZ. USDA110 T wt possesses the nosZ gene, which encodes N 2 O reductase; 110ΔnosZ, a mutant variant, does not. Changes in the community structure after 30- and 60-d incubations were investigated by denaturing-gradient gel electrophoresis and an image analysis. USDA6 T and 76 T strains slightly increased in non-flooded soil regardless of which USDA110 T strain was present. In flooded microcosms with the USDA110 T wt strain, USDA110 T wt became dominant, whereas in microcosms with the USDA110ΔnosZ, a similar change in the community structure occurred to that in non-flooded microcosms. These results suggest that possession of the nosZ gene confers a competitive advantage to B. diazoefficiens USDA110 T in flooded soil. We herein demonstrated that the dominance of B. diazoefficiens USDA110 T wt within the soil bradyrhizobial population may be enhanced by periods of flooding or waterlogging systems such as paddy-soybean rotations because it appears to have the ability to thrive in moderately anaerobic soil.

  19. Amoxicillin effects on functional microbial community and spread of antibiotic resistance genes in amoxicillin manufacture wastewater treatment system.

    Science.gov (United States)

    Meng, Lingwei; Li, Xiangkun; Wang, Xinran; Ma, Kaili; Liu, Gaige; Zhang, Jie

    2017-11-01

    This study aimed to reveal how amoxicillin (AMX) affected the microbial community and the spread mechanism of antibiotic resistance genes (ARGs) in the AMX manufacture wastewater treatment system. For this purpose, a 1.47 L expanded granular sludge bed (EGSB) reactor was designed and run for 241days treating artificial AMX manufacture wastewater. 454 pyrosequencing was applied to analyze functional microorganisms in the system. The antibiotic genes OXA- 1 , OXA -2 , OXA -10 , TEM -1 , CTX-M -1 , class I integrons (intI1) and 16S rRNA genes were also examined in sludge samples. The results showed that the genera Ignavibacterium, Phocoenobacter, Spirochaeta, Aminobacterium and Cloacibacillus contributed to the degradation of different organic compounds (such as various sugars and amines). And the relative quantification of each β-lactam resistance gene in the study was changed with the increasing of AMX concentration. Furthermore the vertical gene transfer was the main driver for the spread of ARGs rather than horizontal transfer pathways in the system. Copyright © 2017. Published by Elsevier B.V.

  20. Estimating the Prevalence of Potential Enteropathogenic Escherichia coli and Intimin Gene Diversity in a Human Community by Monitoring Sanitary Sewage

    Science.gov (United States)

    Yang, Kun; Pagaling, Eulyn

    2014-01-01

    Presently, the understanding of bacterial enteric diseases in the community and their virulence factors relies almost exclusively on clinical disease reporting and examination of clinical pathogen isolates. This study aimed to investigate the feasibility of an alternative approach that monitors potential enteropathogenic Escherichia coli (EPEC) and enterohemorrhagic E. coli (EHEC) prevalence and intimin gene (eae) diversity in a community by directly quantifying and characterizing target virulence genes in the sanitary sewage. The quantitative PCR (qPCR) quantification of the eae, stx1, and stx2 genes in sanitary sewage samples collected over a 13-month period detected eae in all 13 monthly sewage samples at significantly higher abundance (93 to 7,240 calibrator cell equivalents [CCE]/100 ml) than stx1 and stx2, which were detected sporadically. The prevalence level of potential EPEC in the sanitary sewage was estimated by calculating the ratio of eae to uidA, which averaged 1.0% (σ = 0.4%) over the 13-month period. Cloning and sequencing of the eae gene directly from the sewage samples covered the majority of the eae diversity in the sewage and detected 17 unique eae alleles belonging to 14 subtypes. Among them, eae-β2 was identified to be the most prevalent subtype in the sewage, with the highest detection frequency in the clone libraries (41.2%) and within the different sampling months (85.7%). Additionally, sewage and environmental E. coli isolates were also obtained and used to determine the detection frequencies of the virulence genes as well as eae genetic diversity for comparison. PMID:24141131

  1. Genes homologous to glycopeptide resistance vanA are widespread in soil microbial communities

    DEFF Research Database (Denmark)

    Guardabassi, L.; Agersø, Yvonne

    2006-01-01

    -Ala : D-Ala ligase genes unrelated to vanA. In order to enhance detection of vanA-homologous genes, a third PCR step was added using primers targeting vanA in soil Paenibacillus. Sequencing of 25 clones obtained by this method allowed recovery of 23 novel sequences having 86-100% identity with van...

  2. Experiencia del uso conjunto de WebQuests y Wikis en una asignatura universitaria no presencial

    Directory of Open Access Journals (Sweden)

    Torrico González, Ängel

    2007-01-01

    Full Text Available Desde hace unos años se viene investigando el uso de WebQuests para hacer posible una enseñanza de calidad en aulas no universitarias. El uso de estas técnicas en recintos universitarios es pequeño y habitualmente en asignaturas presenciales.Nosotros hemos realizado una experiencia en una asignatura de libre configuración no presencial dentro del Campus Andaluz Virtual, que nos ha servido para configurar una metodología propia, en la que destacamos el uso obligado de una herramienta con la que los alumnos puedan realizar una puesta en común de los resultados obtenidos: el Wiki, que unido al uso de la WebQuest nos ha proporcionado unos resultados muy positivos para el alumnado, tanto a nivel de enseñanza como de aprendizaje.

  3. Harnessing the web information ecosystem with wiki-based visualization dashboards.

    Science.gov (United States)

    McKeon, Matt

    2009-01-01

    We describe the design and deployment of Dashiki, a public website where users may collaboratively build visualization dashboards through a combination of a wiki-like syntax and interactive editors. Our goals are to extend existing research on social data analysis into presentation and organization of data from multiple sources, explore new metaphors for these activities, and participate more fully in the web!s information ecology by providing tighter integration with real-time data. To support these goals, our design includes novel and low-barrier mechanisms for editing and layout of dashboard pages and visualizations, connection to data sources, and coordinating interaction between visualizations. In addition to describing these technologies, we provide a preliminary report on the public launch of a prototype based on this design, including a description of the activities of our users derived from observation and interviews.

  4. Wikis: Developing pre-service teachers’ leadership skills and knowledge of content standards

    Directory of Open Access Journals (Sweden)

    Angelia Reid-Griffin

    2016-03-01

    Full Text Available In this initial phase of our multi-year research study we set out to explore the development of leadership skills in our pre-service secondary teachers after using an online wiki, Wikispaces. This paper presents our methods for preparing a group of 13 mathematics and 3 science secondary pre-service teachers to demonstrate the essential knowledge, skills and dispositions of beginning teacher leaders. Our findings indicate the pre-service teachers' overall satisfaction with demonstrating leadership through collaborative practices. They were successful in these new roles as teacher/collaborator within the context of communication about content standards. Though the candidates participated in other collaborative tasks, this effort was noted for bringing together technology, content standards and leadership qualities that are critical for beginning teachers. Implications for addressing the preservice teachers' development of leadership skills, as they become professional teachers will be shared.

  5. Ciberativismo: a guerra da WikiLeaks contra os segredos de Estado

    Directory of Open Access Journals (Sweden)

    Carole Ferreira da Cruz

    2012-07-01

    Full Text Available http://dx.doi.org/10.5007/1806-5023.2012v9n1p90 Resenha do livro WikiLeaks: a guerra de Julian Assange contra os Segredos de Estado (Editora Verus, 2011, 336 p., no qual os repórteres investigativos do The Guardian, David Leigh e Luke Harding, contam os bastidores do maior vazamento da história, que revelou ao mundo detalhes obscuros da diplomacia mundial e das guerras do Afeganistão e do Iraque. A partir da análise do livro-reportagem sobre a organização WikliLeaks, pretendemos refletir sobre os mecanismos de resistência e atuação contra-hegemônica no contexto das redes abertas pelas tecnologias digitais.

  6. Embassy cinema: what WikiLeaks reveals about US state support for Hollywood.

    Science.gov (United States)

    Moody, Paul

    2017-10-01

    In an article for Foreign Affairs at the outbreak of the World War II, film producer Walter Wanger referred to Hollywood movies as '120,000 American ambassadors'. The preeminence of Hollywood in presenting US ideology to the world has been asserted ever since. Yet the relationship between Hollywood and America's actual ambassadors, employed by the global network of American embassies, has rarely been investigated, despite the key role that this often overlooked aspect of the state apparatus plays in the maintenance of Hollywood's commercial interests and American cultural hegemony. The release by WikiLeaks in November 2010 of over 250,000 diplomatic cables has provided an opportunity to address this gap, by offering researchers an unparalleled insight into the worldwide network of American embassies. This article employs these documents to explain how these embassies have influenced global film policies since early 2003, and the implications they have for conceptions of American power in the wake of the 'War on Terror'.

  7. Design and Evaluation of Illumina MiSeq-Compatible, 18S rRNA Gene-Specific Primers for Improved Characterization of Mixed Phototrophic Communities.

    Science.gov (United States)

    Bradley, Ian M; Pinto, Ameet J; Guest, Jeremy S

    2016-10-01

    The use of high-throughput sequencing technologies with the 16S rRNA gene for characterization of bacterial and archaeal communities has become routine. However, the adoption of sequencing methods for eukaryotes has been slow, despite their significance to natural and engineered systems. There are large variations among the target genes used for amplicon sequencing, and for the 18S rRNA gene, there is no consensus on which hypervariable region provides the most suitable representation of diversity. Additionally, it is unclear how much PCR/sequencing bias affects the depiction of community structure using current primers. The present study amplified the V4 and V8-V9 regions from seven microalgal mock communities as well as eukaryotic communities from freshwater, coastal, and wastewater samples to examine the effect of PCR/sequencing bias on community structure and membership. We found that degeneracies on the 3' end of the current V4-specific primers impact read length and mean relative abundance. Furthermore, the PCR/sequencing error is markedly higher for GC-rich members than for communities with balanced GC content. Importantly, the V4 region failed to reliably capture 2 of the 12 mock community members, and the V8-V9 hypervariable region more accurately represents mean relative abundance and alpha and beta diversity. Overall, the V4 and V8-V9 regions show similar community representations over freshwater, coastal, and wastewater environments, but specific samples show markedly different communities. These results indicate that multiple primer sets may be advantageous for gaining a more complete understanding of community structure and highlight the importance of including mock communities composed of species of interest. The quantification of error associated with community representation by amplicon sequencing is a critical challenge that is often ignored. When target genes are amplified using currently available primers, differential amplification efficiencies

  8. Prevalence of antibiotic resistance genes in bacterial communities associated with Cladophora glomerata mats along the nearshore of Lake Ontario.

    Science.gov (United States)

    Ibsen, Michael; Fernando, Dinesh M; Kumar, Ayush; Kirkwood, Andrea E

    2017-05-01

    The alga Cladophora glomerata can erupt in nuisance blooms throughout the lower Great Lakes. Since bacterial abundance increases with the emergence and decay of Cladophora, we investigated the prevalence of antibiotic resistance (ABR) in Cladophora-associated bacterial communities up-gradient and down-gradient from a large sewage treatment plant (STP) on Lake Ontario. Although STPs are well-known sources of ABR, we also expected detectable ABR from up-gradient wetland communities, since they receive surface run-off from urban and agricultural sources. Statistically significant differences in aquatic bacterial abundance and ABR were found between down-gradient beach samples and up-gradient coastal wetland samples (ANOVA, Holm-Sidak test, p Cladophora sampled near the STP had the highest bacterial densities overall, including on ampicillin- and vancomycin-treated plates. However, quantitative polymerase chain reaction analysis of the ABR genes ampC, tetA, tetB, and vanA from environmental communities showed a different pattern. Some of the highest ABR gene levels occurred at the 2 coastal wetland sites (vanA). Overall, bacterial ABR profiles from environmental samples were distinguishable between living and decaying Cladophora, inferring that Cladophora may control bacterial ABR depending on its life-cycle stage. Our results also show how spatially and temporally dynamic ABR is in nearshore aquatic bacteria, which warrants further research.

  9. Wiki協作系統應用於數位典藏之內容加值與知識匯集 Application of Wiki Collaboration System for Value Adding and Knowledge Aggregation in a Digital Archive Project

    Directory of Open Access Journals (Sweden)

    Sinn-Cheng Lin

    2006-03-01

    Full Text Available 本文提出一個由「系統」、「內容」與「社群」三要素所構成的「維基協作金三角模型」,並應用於數位典藏計畫中,作為內容加值與知識匯集平台。基於此一模型,我們首先對眾多維基引擎進行比較分析,以選擇最適合的系統;接著,以台灣棒球新聞數位典藏庫為基礎,以維基協作系統為平台,運用知識組織技術,如分類、索引、索引典與控制詞彙等,進行內容加值與知識匯集,以提升數位內容品質;最後,隨著資料量及社群規模日益成長,則探討如何提高社群成員的互動與參與,使社群之運作與經營更上軌道。This paper proposes a model called “The Golden Triangle for Wiki Collaboration”, composed of three elements: system, content, and community. The proposed model is used in a Digital Archives Project as a means of value adding and knowledge aggregation. We first compared and analyzed multiple wiki engines to select the best system for our research purpose. We chose Taiwanese Baseball News Digital Archive as the base of the research project and the wiki collaboration system as the platform. In order to improve and enhance the quality of digital content, we took the approach of applying techniques of knowledge organization, such as classification, indexing, thesaurus, and controlled vocabularies, so that value and knowledge can be added and aggregated. As the data and community grow, interaction of community members becomes crucial. Therefore, we discussed ways to encourage group interaction and participation from the operational and managerial point of view.

  10. Wikis en lenguas para fines específicos y su traducción

    Directory of Open Access Journals (Sweden)

    Raquel Lázaro Gutiérrez

    2010-01-01

    Full Text Available Las herramientas Wiki pueden llegar a ser muy útiles tanto en la enseñanza de lenguas en general como en la traducción, sobre todo si se tiene en cuenta que, hoy en día, dentro del nuevo marco del Espacio Europeo de Educación Superior, los docentes tienen que enfrentarse a dificultades como grupos numerosos de alumnos, pocas clases presenciales y competencias transversales añadidas al contenido de las materias. Por este motivo, que una herramienta como las wikis, que permita trabajar fuera del aula y con la cual el estudiante puede realizar trabajos individuales y en grupo, conectado y en contacto con el resto de sus compañeros y profesores, resulta especialmente útil. Mientras que la sencillez de estas herramientas permite al docente diseñar actividades atractivas y útiles con un esfuerzo y conocimientos tecnológicos relativamente mínimos, para los estudiantes supone una gran oportunidad para aprender a trabajar con las TIC y de manera grupal y colaborativa. En este capítulo se describen las tareas y actividades que se diseñaron y pusieron en práctica para las asignaturas del Máster Oficial en Comunicación Intercultural, Interpretación y Traducción en los Servicios Públicos y para las asignaturas de inglés para fines específicos del postgrado y grado de la Facultad de Derecho de la Universidad de Alcalá, centrándonos de manera especial en su diseño, las dificultades y ventajas que plantearon y la respuesta que se obtuvo por parte del alumnado.

  11. Uso de wikis para la realización de trabajos colaborativos en el aula

    Directory of Open Access Journals (Sweden)

    Galache Laza, T.

    2006-01-01

    Full Text Available Habitualmente, la evaluación del alumnado que realizamos en la Universidad se basa únicamente en uno o varios exámenes individuales. Este hecho contrasta con su vida laboral posterior, donde se potenciará el trabajo en equipo, obteniendo la mayoría de los resultados a través de trabajos colaborativos. Con esta idea hemos realizado una experiencia docente en una asignatura optativa de la Diplomatura en Ciencias Empresariales, Investigación Operativa. Los alumnos de esta asignatura están distribuidos en tres grupos homogéneos de unos 20 alumnos. En cada uno de ellos hemos dedicado una parte importante de la calificación final a la realización de trabajos programados por los profesores, consistentes en realizar dentro de una plataforma Moodle, Wikis en los que cada grupo desarrolla un material predeterminado y conocido desde la programación del curso. Para cada grupo, cada uno de sus alumnos, deberá evaluar los Wikis realizados por los alumnos de los otros grupos, evaluación que ha de ser justificada y razonada, pudiendo cada profesor a su vez evaluarla de forma negativa o positiva. Con todo ello, los alumnos deben formar equipos para trabajar con sus compañeros en una tarea común a todos ellos y a su vez deben evaluar, de forma razonada, los trabajos realizados por sus compañeros de los otros grupos. Los resultados que hemos obtenido en cuanto a participación de los alumnos y rendimiento académico de los mismos son muy interesantes y nos llevan a la realización de importantes consideraciones de tipo práctico en trabajos colaborativos.

  12. Improved Vote Aggregation Techniques for the Geo-Wiki Cropland Capture Crowdsourcing Game

    Science.gov (United States)

    Baklanov, Artem; Fritz, Steffen; Khachay, Michael; Nurmukhametov, Oleg; Salk, Carl; See, Linda; Shchepashchenko, Dmitry

    2016-04-01

    Crowdsourcing is a new approach for solving data processing problems for which conventional methods appear to be inaccurate, expensive, or time-consuming. Nowadays, the development of new crowdsourcing techniques is mostly motivated by so called Big Data problems, including problems of assessment and clustering for large datasets obtained in aerospace imaging, remote sensing, and even in social network analysis. By involving volunteers from all over the world, the Geo-Wiki project tackles problems of environmental monitoring with applications to flood resilience, biomass data analysis and classification of land cover. For example, the Cropland Capture Game, which is a gamified version of Geo-Wiki, was developed to aid in the mapping of cultivated land, and was used to gather 4.5 million image classifications from the Earth's surface. More recently, the Picture Pile game, which is a more generalized version of Cropland Capture, aims to identify tree loss over time from pairs of very high resolution satellite images. Despite recent progress in image analysis, the solution to these problems is hard to automate since human experts still outperform the majority of machine learning algorithms and artificial systems in this field on certain image recognition tasks. The replacement of rare and expensive experts by a team of distributed volunteers seems to be promising, but this approach leads to challenging questions such as: how can individual opinions be aggregated optimally, how can confidence bounds be obtained, and how can the unreliability of volunteers be dealt with? In this paper, on the basis of several known machine learning techniques, we propose a technical approach to improve the overall performance of the majority voting decision rule used in the Cropland Capture Game. The proposed approach increases the estimated consistency with expert opinion from 77% to 86%.

  13. Antimicrobial susceptibility, risk factors and prevalence of bla cefotaximase, temoneira, and sulfhydryl variable genes among Escherichia coli in community-acquired pediatric urinary tract infection

    Directory of Open Access Journals (Sweden)

    Kallyadan V Nisha

    2017-01-01

    Conclusion: ESBL-producing E. coli from community-acquired pediatric UTI carries more than one type of beta-lactamase coding genes correlating their increased antibiotic resistance. Aggressive infection control policy, routine screening for detecting ESBL isolates in clinical samples, and antimicrobial stewardship are the keys to prevent their dissemination in community settings.

  14. Redox-Active Antibiotics Control Gene Expression and Community Behavior in Divergent Bacteria

    OpenAIRE

    Dietrich, Lars E. P.; Teal, Tracy K.; Price-Whelan, Alexa; Newman, Dianne K.

    2008-01-01

    It is thought that bacteria excrete redox-active pigments as antibiotics to inhibit competitors. In Pseudomonas aeruginosa, the endogenous antibiotic pyocyanin activates SoxR, a transcription factor conserved in Proteo- and Actinobacteria. In Escherichia coli, SoxR regulates the superoxide stress response. Bioinformatic analysis coupled with gene expression studies in P. aeruginosa and Streptomyces coelicolor revealed that the majority of SoxR regulons in bacteria lack the genes required for ...

  15. Bacterial community composition of South China Sea sediments through pyrosequencing-based analysis of 16S rRNA genes.

    Science.gov (United States)

    Zhu, Daochen; Tanabe, Shoko-Hosoi; Yang, Chong; Zhang, Weimin; Sun, Jianzhong

    2013-01-01

    Subseafloor sediments accumulate large amounts of organic and inorganic materials that contain a highly diverse microbial ecosystem. The aim of this study was to survey the bacterial community of subseafloor sediments from the South China Sea. Pyrosequencing of over 265,000 amplicons of the V3 hypervariable region of the 16S ribosomal RNA gene was performed on 16 sediment samples collected from multiple locations in the northern region of the South China Sea from depths ranging from 35 to 4000 m. A total of 9,726 operational taxonomic units (OTUs; between 695 and 2819 unique OTUs per sample) at 97% sequence similarity level were generated. In total, 40 bacterial phyla including 22 formally described phyla and 18 candidate phyla, with Proteobacteria, Firmicutes, Planctomycetes, Actinobacteria and Chloroflexi being most diverse, were identified. The most abundant phylotype, accounting for 42.6% of all sequences, belonged to Gammaproteobacteria, which possessed absolute predominance in the samples analyzed. Among the 18 candidate phyla, 12 were found for the first time in the South China Sea. This study provided a novel insight into the composition of bacterial communities of the South China Sea subseafloor. Furthermore, abundances and community similarity analysis showed that the compositions of the bacterial communities are very similar at phylum level at different depths from 35-4000 m.

  16. Variable effects of oxytetracycline on antibiotic resistance gene abundance and the bacterial community during aerobic composting of cow manure.

    Science.gov (United States)

    Qian, Xun; Sun, Wei; Gu, Jie; Wang, Xiao-Juan; Sun, Jia-Jun; Yin, Ya-Nan; Duan, Man-Li

    2016-09-05

    Livestock manure is often subjected to aerobic composting but little is known about the variation in antibiotic resistance genes (ARGs) during the composting process under different concentrations of antibiotics. This study compared the effects of three concentrations of oxytetracycline (OTC; 10, 60, and 200mg/kg) on ARGs and the succession of the bacterial community during composting. Very similar trends were observed in the relative abundances (RAs) of each ARG among the OTC treatments and the control during composting. After composting, the RAs of tetC, tetX, sul1, sul2, and intI1 increased 2-43 times, whereas those of tetQ, tetM, and tetW declined by 44-99%. OTC addition significantly increased the absolute abundances and RAs of tetC and intI1, while 200mg/kg OTC also enhanced those of tetM, tetQ, and drfA7. The bacterial community could be grouped according to the composting time under different treatments. The highest concentration of OTC had a more persistent effect on the bacterial community. In the present study, the succession of the bacterial community appeared to have a greater influence on the variation of ARGs during composting than the presence of antibiotics. Aerobic composting was not effective in reducing most of the ARGs, and thus the compost product should be considered as an important reservoir for ARGs. Copyright © 2016 Elsevier B.V. All rights reserved.

  17. Bacterial community composition of South China Sea sediments through pyrosequencing-based analysis of 16S rRNA genes.

    Directory of Open Access Journals (Sweden)

    Daochen Zhu

    Full Text Available BACKGROUND: Subseafloor sediments accumulate large amounts of organic and inorganic materials that contain a highly diverse microbial ecosystem. The aim of this study was to survey the bacterial community of subseafloor sediments from the South China Sea. METHODOLOGY/PRINCIPAL FINDINGS: Pyrosequencing of over 265,000 amplicons of the V3 hypervariable region of the 16S ribosomal RNA gene was performed on 16 sediment samples collected from multiple locations in the northern region of the South China Sea from depths ranging from 35 to 4000 m. A total of 9,726 operational taxonomic units (OTUs; between 695 and 2819 unique OTUs per sample at 97% sequence similarity level were generated. In total, 40 bacterial phyla including 22 formally described phyla and 18 candidate phyla, with Proteobacteria, Firmicutes, Planctomycetes, Actinobacteria and Chloroflexi being most diverse, were identified. The most abundant phylotype, accounting for 42.6% of all sequences, belonged to Gammaproteobacteria, which possessed absolute predominance in the samples analyzed. Among the 18 candidate phyla, 12 were found for the first time in the South China Sea. CONCLUSIONS: This study provided a novel insight into the composition of bacterial communities of the South China Sea subseafloor. Furthermore, abundances and community similarity analysis showed that the compositions of the bacterial communities are very similar at phylum level at different depths from 35-4000 m.

  18. Metagenomic analysis of bacterial community composition and antibiotic resistance genes in a wastewater treatment plant and its receiving surface water.

    Science.gov (United States)

    Tang, Junying; Bu, Yuanqing; Zhang, Xu-Xiang; Huang, Kailong; He, Xiwei; Ye, Lin; Shan, Zhengjun; Ren, Hongqiang

    2016-10-01

    The presence of pathogenic bacteria and the dissemination of antibiotic resistance genes (ARGs) may pose big risks to the rivers that receive the effluent from municipal wastewater treatment plants (WWTPs). In this study, we investigated the changes of bacterial community and ARGs along treatment processes of one WWTP, and examined the effects of the effluent discharge on the bacterial community and ARGs in the receiving river. Pyrosequencing was applied to reveal bacterial community composition including potential bacterial pathogen, and Illumina high-throughput sequencing was used for profiling ARGs. The results showed that the WWTP had good removal efficiency on potential pathogenic bacteria (especially Arcobacter butzleri) and ARGs. Moreover, the bacterial communities of downstream and upstream of the river showed no significant difference. However, the increase in the abundance of potential pathogens and ARGs at effluent outfall was observed, indicating that WWTP effluent might contribute to the dissemination of potential pathogenic bacteria and ARGs in the receiving river. Copyright © 2016 Elsevier Inc. All rights reserved.

  19. Time Course-Dependent Methanogenic Crude Oil Biodegradation: Dynamics of Fumarate Addition Metabolites, Biodegradative Genes, and Microbial Community Composition

    Directory of Open Access Journals (Sweden)

    Courtney R. A. Toth

    2018-01-01

    Full Text Available Biodegradation of crude oil in subsurface petroleum reservoirs has adversely impacted most of the world's oil, converting this resource to heavier forms that are of lower quality and more challenging to recover. Oil degradation in deep reservoir environments has been attributed to methanogenesis over geological time, yet our understanding of the processes and organisms mediating oil transformation in the absence of electron acceptors remains incomplete. Here, we sought to identify hydrocarbon activation mechanisms and reservoir-associated microorganisms that may have helped shape the formation of biodegraded oil by incubating oilfield produced water in the presence of light (°API = 32 or heavy crude oil (°API = 16. Over the course of 17 months, we conducted routine analytical (GC, GC-MS and molecular (PCR/qPCR of assA and bssA genes, 16S rRNA gene sequencing surveys to assess microbial community composition and activity changes over time. Over the incubation period, we detected the formation of transient hydrocarbon metabolites indicative of alkane and alkylbenzene addition to fumarate, corresponding with increases in methane production and fumarate addition gene abundance. Chemical and gene-based evidence of hydrocarbon biodegradation under methanogenic conditions was supported by the enrichment of hydrocarbon fermenters known to catalyze fumarate addition reactions (e.g., Desulfotomaculum, Smithella, along with syntrophic bacteria (Syntrophus, methanogenic archaea, and several candidate phyla (e.g., “Atribacteria”, “Cloacimonetes”. Our results reveal that fumarate addition is a possible mechanism for catalyzing the methanogenic biodegradation of susceptible saturates and aromatic hydrocarbons in crude oil, and we propose the roles of community members and candidate phyla in our cultures that may be involved in hydrocarbon transformation to methane in crude oil systems.

  20. Uso de wikis como herramienta de trabajo colaborativo en un proceso de formación inicial docente

    Directory of Open Access Journals (Sweden)

    Ilich Silva-Peña

    2013-01-01

    Full Text Available A través del presente artículo queremos compartir el desarrollo de una experiencia de utilización de wikis como estrategia de trabajo colaborativo en un curso de formación inicial docente. La experiencia se enmarcó en el contexto de un proyecto de Investigación+Desarrollo donde se exploraron mejoras tecnológicas a incorporar en la formación docente. Se utilizó el software Moodle ®, con características Open source. Para sistematizar los resultados desde la mirada de los/as estudiantes se aplicaron cuestionarios con respuestas abiertas, que fueron codificadas utilizando una metodología cualitativa. Los resultados muestran una alta valoración de los wikis como herramienta de aprendizaje, especialmente por el apoyo que otorga al trabajo pedagógico no presencial y asincrónico.

  1. Gene

    Data.gov (United States)

    U.S. Department of Health & Human Services — Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes,...

  2. Genes, communities & invasive species: understanding the ecological and evolutionary dynamics of host-pathogen interactions.

    Science.gov (United States)

    Burdon, J J; Thrall, P H; Ericson, L

    2013-08-01

    Reciprocal interactions between hosts and pathogens drive ecological, epidemiological and co-evolutionary trajectories, resulting in complex patterns of diversity at population, species and community levels. Recent results confirm the importance of negative frequency-dependent rather than 'arms-race' processes in the evolution of individual host-pathogen associations. At the community level, complex relationships between species abundance and diversity dampen or alter pathogen impacts. Invasive pathogens challenge these controls reflecting the earliest stages of evolutionary associations (akin to arms-race) where disease effects may be so great that they overwhelm the host's and community's ability to respond. Viewing these different stabilization/destabilization phases as a continuum provides a valuable perspective to assessment of the role of genetics and ecology in the dynamics of both natural and invasive host-pathogen associations. Copyright © 2013 Elsevier Ltd. All rights reserved.

  3. Redox-active antibiotics control gene expression and community behavior in divergent bacteria.

    Science.gov (United States)

    Dietrich, Lars E P; Teal, Tracy K; Price-Whelan, Alexa; Newman, Dianne K

    2008-08-29

    It is thought that bacteria excrete redox-active pigments as antibiotics to inhibit competitors. In Pseudomonas aeruginosa, the endogenous antibiotic pyocyanin activates SoxR, a transcription factor conserved in Proteo- and Actinobacteria. In Escherichia coli, SoxR regulates the superoxide stress response. Bioinformatic analysis coupled with gene expression studies in P. aeruginosa and Streptomyces coelicolor revealed that the majority of SoxR regulons in bacteria lack the genes required for stress responses, despite the fact that many of these organisms still produce redox-active small molecules, which indicates that redox-active pigments play a role independent of oxidative stress. These compounds had profound effects on the structural organization of colony biofilms in both P. aeruginosa and S. coelicolor, which shows that "secondary metabolites" play important conserved roles in gene expression and development.

  4. Effects of chlortetracycline and copper on tetracyclines and copper resistance genes and microbial community during swine manure anaerobic digestion.

    Science.gov (United States)

    Wang, Rui; Chen, Meixue; Feng, Feng; Zhang, Junya; Sui, Qianwen; Tong, Juan; Wei, Yuansong; Wei, Dongbin

    2017-08-01

    As antibiotic and heavy metals are over used in the livestock industry, animal manure is a reservoir of antibiotic resistance genes (ARGs). Anaerobic digestion has been reported to have the potential to reduce ARGs. However, few studies investigated whether reduction of ARGs would be affected by different external pressures including antibiotics and heavy metals during anaerobic digestion. The purpose of this study was thus to investigate effects of both chlortetracycline (CTC) and Cu on reduction of ARGs, heavy metal resistance genes (HMRGs) and mobile genetic elements (MGEs) during the swine manure anaerobic digestion. The results showed that the predominant ARGs (tetO, tetW, tetX, tetL) could be effectively reduced (approximately 1.00 log copies/g TS) through mesophilic anaerobic digestion. Microbial community evolution was the main driver. It was interesting that Treponema might indicate the termination of anaerobic digestion and compete with ARGs host bacteria. Addition of CTC, Cu and CTC+Cu affected microbial community change and hindered removal of ARGs, especially, CTC+Cu seriously affected Treponema and ARGs during anaerobic digestion. Copyright © 2017 Elsevier Ltd. All rights reserved.

  5. Bacterial community variations in an alfalfa-rice rotation system revealed by 16S rRNA gene 454-pyrosequencing.

    Science.gov (United States)

    Lopes, Ana R; Manaia, Célia M; Nunes, Olga C

    2014-03-01

    Crop rotation is a practice harmonized with the sustainable rice production. Nevertheless, the implications of this empirical practice are not well characterized, mainly in relation to the bacterial community composition and structure. In this study, the bacterial communities of two adjacent paddy fields in the 3rd and 4th year of the crop rotation cycle and of a nonseeded subplot were characterized before rice seeding and after harvesting, using 454-pyrosequencing of the 16S rRNA gene. Although the phyla Acidobacteria, Proteobacteria, Chloroflexi, Actinobacteria and Bacteroidetes predominated in all the samples, there were variations in relative abundance of these groups. Samples from the 3rd and 4th years of the crop rotation differed on the higher abundance of groups of presumable aerobic bacteria and of presumable anaerobic and acidobacterial groups, respectively. Members of the phylum Nitrospira were more abundant after rice harvest than in the previously sampled period. Rice cropping was positively correlated with the abundance of members of the orders Acidobacteriales and 'Solibacterales' and negatively with lineages such as Chloroflexi 'Ellin6529'. Studies like this contribute to understand variations occurring in the microbial communities in soils under sustainable rice production, based on real-world data. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  6. Bacterial community composition in the gut content of Lampetra japonica revealed by 16S rRNA gene pyrosequencing.

    Science.gov (United States)

    Zuo, Yu; Xie, Wenfang; Pang, Yue; Li, Tiesong; Li, Qingwei; Li, Yingying

    2017-01-01

    The composition of the bacterial communities in the hindgut contents of Lampetrs japonica was surveyed by Illumina MiSeq of the 16S rRNA gene. An average of 32385 optimized reads was obtained from three samples. The rarefaction curve based on the operational taxonomic units tended to approach the asymptote. The rank abundance curve representing the species richness and evenness was calculated. The composition of microbe in six classification levels was also analyzed. Top 20 members in genera level were displayed as the classification tree. The abundance of microorganisms in different individuals was displayed as the pie charts at the branch nodes in the classification tree. The differences of top 50 genera in abundance between individuals of lamprey are displayed as a heatmap. The pairwise comparison of bacterial taxa abundance revealed that there are no significant differences of gut microbiota between three individuals of lamprey at a given rarefied depth. Also, the gut microbiota derived from L. japonica displays little similarity with other aquatic organism of Vertebrata after UPGMA analysis. The metabolic function of the bacterial communities was predicted through KEGG analysis. This study represents the first analysis of the bacterial community composition in the gut content of L. japonica. The investigation of the gut microbiota associated with L. japonica will broaden our understanding of this unique organism.

  7. Bacterial community composition in the gut content of Lampetra japonica revealed by 16S rRNA gene pyrosequencing.

    Directory of Open Access Journals (Sweden)

    Yu Zuo

    Full Text Available The composition of the bacterial communities in the hindgut contents of Lampetrs japonica was surveyed by Illumina MiSeq of the 16S rRNA gene. An average of 32385 optimized reads was obtained from three samples. The rarefaction curve based on the operational taxonomic units tended to approach the asymptote. The rank abundance curve representing the species richness and evenness was calculated. The composition of microbe in six classification levels was also analyzed. Top 20 members in genera level were displayed as the classification tree. The abundance of microorganisms in different individuals was displayed as the pie charts at the branch nodes in the classification tree. The differences of top 50 genera in abundance between individuals of lamprey are displayed as a heatmap. The pairwise comparison of bacterial taxa abundance revealed that there are no significant differences of gut microbiota between three individuals of lamprey at a given rarefied depth. Also, the gut microbiota derived from L. japonica displays little similarity with other aquatic organism of Vertebrata after UPGMA analysis. The metabolic function of the bacterial communities was predicted through KEGG analysis. This study represents the first analysis of the bacterial community composition in the gut content of L. japonica. The investigation of the gut microbiota associated with L. japonica will broaden our understanding of this unique organism.

  8. Bacterial Community Diversity of Oil-Contaminated Soils Assessed by High Throughput Sequencing of 16S rRNA Genes

    Directory of Open Access Journals (Sweden)

    Mu Peng

    2015-09-01

    Full Text Available Soil bacteria play a major role in ecological and biodegradable function processes in oil-contaminated soils. Here, we assessed the bacterial diversity and changes therein in oil-contaminated soils exposed to different periods of oil pollution using 454 pyrosequencing of 16S rRNA genes. No less than 24,953 valid reads and 6246 operational taxonomic units (OTUs were obtained from all five studied samples. OTU richness was relatively higher in contaminated soils than clean samples. Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Planctomycetes and Proteobacteria were the dominant phyla among all the soil samples. The heatmap plot depicted the relative percentage of each bacterial family within each sample and clustered five samples into two groups. For the samples, bacteria in the soils varied at different periods of oil exposure. The oil pollution exerted strong selective pressure to propagate many potentially petroleum degrading bacteria. Redundancy analysis (RDA indicated that organic matter was the highest determinant factor for explaining the variations in community compositions. This suggests that compared to clean soils, oil-polluted soils support more diverse bacterial communities and soil bacterial community shifts were mainly controlled by organic matter and exposure time. These results provide some useful information for bioremediation of petroleum contaminated soil in the future.

  9. Bacterial Community Diversity of Oil-Contaminated Soils Assessed by High Throughput Sequencing of 16S rRNA Genes.

    Science.gov (United States)

    Peng, Mu; Zi, Xiaoxue; Wang, Qiuyu

    2015-09-24

    Soil bacteria play a major role in ecological and biodegradable function processes in oil-contaminated soils. Here, we assessed the bacterial diversity and changes therein in oil-contaminated soils exposed to different periods of oil pollution using 454 pyrosequencing of 16S rRNA genes. No less than 24,953 valid reads and 6246 operational taxonomic units (OTUs) were obtained from all five studied samples. OTU richness was relatively higher in contaminated soils than clean samples. Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Planctomycetes and Proteobacteria were the dominant phyla among all the soil samples. The heatmap plot depicted the relative percentage of each bacterial family within each sample and clustered five samples into two groups. For the samples, bacteria in the soils varied at different periods of oil exposure. The oil pollution exerted strong selective pressure to propagate many potentially petroleum degrading bacteria. Redundancy analysis (RDA) indicated that organic matter was the highest determinant factor for explaining the variations in community compositions. This suggests that compared to clean soils, oil-polluted soils support more diverse bacterial communities and soil bacterial community shifts were mainly controlled by organic matter and exposure time. These results provide some useful information for bioremediation of petroleum contaminated soil in the future.

  10. Identification of Carbohydrate Metabolism Genes in the Metagenome of a Marine Biofilm Community Shown to Be Dominated by Gammaproteobacteria and Bacteroidetes

    Directory of Open Access Journals (Sweden)

    Jennifer L. Edwards

    2010-10-01

    Full Text Available Polysaccharides are an important source of organic carbon in the marine environment and degradation of the insoluble and globally abundant cellulose is a major component of the marine carbon cycle. Although a number of species of cultured bacteria are known to degrade crystalline cellulose, little is known of the polysaccharide hydrolases expressed by cellulose-degrading microbial communities, particularly in the marine environment. Next generation 454 Pyrosequencing was applied to analyze the microbial community that colonizes and degrades insoluble polysaccharides in situ in the Irish Sea. The bioinformatics tool MG-RAST was used to examine the randomly sampled data for taxonomic markers and functional genes, and showed that the community was dominated by members of the Gammaproteobacteria and Bacteroidetes. Furthermore, the identification of 211 gene sequences matched to a custom-made database comprising the members of nine glycoside hydrolase families revealed an extensive repertoire of functional genes predicted to be involved in cellulose utilization. This demonstrates that the use of an in situ cellulose baiting method yielded a marine microbial metagenome considerably enriched in functional genes involved in polysaccharide degradation. The research reported here is the first designed to specifically address the bacterial communities that colonize and degrade cellulose in the marine environment and to evaluate the glycoside hydrolase (cellulase and chitinase gene repertoire of that community, in the absence of the biases associated with PCR-based molecular techniques.

  11. Evaluación de la wiki como herramienta de trabajo colaborativo en la docencia universitaria

    Directory of Open Access Journals (Sweden)

    Marisela Montenegro

    2010-01-01

    Full Text Available La herramienta wiki se está consolidando como una herramienta de trabajo colaborativo y colectivo que tiene su máxima expresión en el desarrollo de la wikipedia. La herramienta wiki consiste en una página virtual para la escritura colaborativa, en la cual cada una de las personas que participa puede ir añadiendo y cambiando los contenidos de la página. Esta herramienta permite recoger el proceso de construcción del texto, visualizando las formas de trabajo de los estudiantes, guardando un historial de las diferentes versiones y las aportaciones realizadas por cada participante. El uso de esta herramienta pone de manifiesto que la interacción e interdependencia en la creación colectiva necesita de diferentes elementos de soporte a fin de que la deseada interacción se produzca. Entre los aspectos a incidir resaltan la necesidad de reconocer y dar valor al trabajo del otro, al mismo tiempo que se desarrolla una concepción compartida de la autoría que ofrece la suficiente seguridad para modificar el trabajo que otra persona ha realizado. Esta herramienta virtual ha sido implementada en varias asignaturas de la Licenciatura de Psicología de la UAB -como por ejemplo "Psicología Social de la Comunicación", "Prácticum interno" o "Prácticas de Psicología Social: Cultura y conocimiento", mediante una plataforma virtual de trabajo hecha con Moodle. Los docentes diseñaron los espacios virtuales a partir de los objetivos del programa de las asignaturas y cada uno de los grupos de trabajo tuvo su propia página para el desarrollo del trabajo a lo largo del semestre. Además, se han implementado espacios presenciales de seguimiento de las tareas de los estudiantes. En este capítulo se describe el proceso seguido, poniendo como ejemplo algunas de estas asignaturas. Se describen las diferentes opciones implementadas, se muestran los hitos conseguidos en el uso de esta herramienta y se reflexiona sobre las implicaciones de su uso para los

  12. Expression of Critical Sulfur- and Iron-Oxidation Genes and the Community Dynamics During Bioleaching of Chalcopyrite Concentrate by Moderate Thermophiles.

    Science.gov (United States)

    Zhou, Dan; Peng, Tangjian; Zhou, Hongbo; Liu, Xueduan; Gu, Guohua; Chen, Miao; Qiu, Guanzhou; Zeng, Weimin

    2015-07-01

    Sulfate adenylyltransferase gene and 4Fe-4S ferredoxin gene are the key genes related to sulfur and iron oxidations during bioleaching system, respectively. In order to better understand the bioleaching and microorganism synergistic mechanism in chalcopyrite bioleaching by mixed culture of moderate thermophiles, expressions of the two energy metabolism genes and community dynamics of free and attached microorganisms were investigated. Specific primers were designed for real-time quantitative PCR to study the expression of these genes. Real-time PCR results showed that sulfate adenylyltransferase gene was more highly expressed in Sulfobacillus thermosulfidooxidans than that in Acidithiobacillus caldus, and expression of 4Fe-4S ferredoxin gene was higher in Ferroplasma thermophilum than that in S. thermosulfidooxidans and Leptospirillum ferriphilum. The results indicated that in the bioleaching system of chalcopyrite concentrate, sulfur and iron oxidations were mainly performed by S. thermosulfidooxidans and F. thermophilum, respectively. The community dynamics results revealed that S. thermosulfidooxidans took up the largest proportion during the whole period, followed by F. thermophilum, A. caldus, and L. ferriphilum. The CCA analysis showed that 4Fe-4S ferredoxin gene expression was mainly affected (positively correlated) by high pH and elevated concentration of ferrous ion, while no factor was observed to prominently influence the expression of sulfate adenylyltransferase gene.

  13. Imported anthropogenic bacteria may survive the Antarctic winter and introduce new genes into local bacterial communities

    OpenAIRE

    Brat Kristian; Sedlacek Ivo; Sevcikova Alena; Merta Zdenek; Laska Kamil; Sevcik Pavel

    2016-01-01

    We studied dynamic changes in anthropogenic bacterial communities at a summer-operated Czech research base (the Mendel Research Station) in the Antarctic during 2012 and 2013. We observed an increase in total numbers of detected bacteria between the beginning and the end of each stay in the Antarctic. In the first series of samples, bacteria of Bacillus sp. predominated. Surprisingly, high numbers of Gram-positive cocci and coliforms were found (including opportunistic human pathogens), altho...

  14. Fate of antibiotic resistance genes within the microbial communities of three waste water treatment plants

    OpenAIRE

    Di Cesare, Andrea; Eckert, Ester; D'Urso, Silvia; Doppelbauer, Julia; Corno, Gianluca

    2016-01-01

    Although Waste Water Treatment Plant (WWTP) are designed to reduce the biological pollution of urban waters, they lack a specific action against antibiotic resistance bacteria (ARB) or antibiotic resistance genes (ARGs). Nowadays, it is well documented that WWTPs constitute a reservoir of antibiotic resistances and, in some cases, they can be a favorable environment for the selection of ARB. This represent a serious concern for the public health, because the effluents of the WWTPs can be reus...

  15. Global analysis of gene expression dynamics within the marine microbial community during the VAHINE mesocosm experiment in the southwest Pacific

    Science.gov (United States)

    Pfreundt, Ulrike; Spungin, Dina; Bonnet, Sophie; Berman-Frank, Ilana; Hess, Wolfgang R.

    2016-07-01

    Microbial gene expression was followed for 23 days within a mesocosm (M1) isolating 50 m3 of seawater and in the surrounding waters in the Nouméa lagoon, New Caledonia, in the southwest Pacific as part of the VAriability of vertical and tropHIc transfer of diazotroph derived N in the south wEst Pacific (VAHINE) experiment. The aim of VAHINE was to examine the fate of diazotroph-derived nitrogen (DDN) in a low-nutrient, low-chlorophyll ecosystem. On day 4 of the experiment, the mesocosm was fertilized with phosphate. In the lagoon, gene expression was dominated by the cyanobacterium Synechococcus, closely followed by Alphaproteobacteria. In contrast, drastic changes in the microbial community composition and transcriptional activity were triggered within the mesocosm within the first 4 days, with transcription bursts from different heterotrophic bacteria in rapid succession. The microbial composition and activity of the surrounding lagoon ecosystem appeared more stable, although following similar temporal trends as in M1. We detected significant gene expression from Chromerida in M1, as well as the Nouméa lagoon, suggesting these photoautotrophic alveolates were present in substantial numbers in the open water. Other groups contributing substantially to the metatranscriptome were affiliated with marine Euryarchaeota Candidatus Thalassoarchaea (inside and outside) and Myoviridae bacteriophages likely infecting Synechococcus, specifically inside M1. High transcript abundances for ammonium transporters and glutamine synthetase in many different taxa (e.g., Pelagibacteraceae, Synechococcus, Prochlorococcus, and Rhodobacteraceae) was consistent with the known preference of most bacteria for this nitrogen source. In contrast, Alteromonadaceae highly expressed urease genes; Rhodobacteraceae and Prochlorococcus showed some urease expression, too. Nitrate reductase transcripts were detected on day 10 very prominently in Synechococcus and in Halomonadaceae. Alkaline

  16. The Diplomatic Asylum: From Haya De La Torre to The "WikiLeaks" Case

    Directory of Open Access Journals (Sweden)

    Agustina Vázquez

    2018-03-01

    Full Text Available The WikiLeaks’ founder represents not only a challenge to freedom of information, but also to International Law related to the diplomatic asylum. Julian Assange has been living in the Ecuadorian embassy in London for five years. In the last weeks, news surfaced that Sweden has ceased to request his extradition, the fact that caused much of the case under study. Assange’s situation seems to be diametrically different from Edward Snowden’s; however, both are labeled as "refugees for political reasons". While Assange looks forward to an improvement in his situation in the Ecuadorian embassy in London, Snowden still lives in Russia. Is the diplomatic asylum a usual practice? How to understand the diplomatic asylum in Latin America? What about England? In this paper, the analysis will assume that the concept of asylum is not recognized as a universal practice of International Law. However, in Latin America, it seems to be a usual practice since the judgment of the International Court of Justice on Haya de la Torre’s case.

  17. FoodWiki: Ontology-Driven Mobile Safe Food Consumption System

    Directory of Open Access Journals (Sweden)

    Duygu Çelik

    2015-01-01

    Full Text Available An ontology-driven safe food consumption mobile system is considered. Over 3,000 compounds are being added to processed food, with numerous effects on the food: to add color, stabilize, texturize, preserve, sweeten, thicken, add flavor, soften, emulsify, and so forth. According to World Health Organization, governments have lately focused on legislation to reduce such ingredients or compounds in manufactured foods as they may have side effects causing health risks such as heart disease, cancer, diabetes, allergens, and obesity. By supervising what and how much to eat as well as what not to eat, we can maximize a patient’s life quality through avoidance of unhealthy ingredients. Smart e-health systems with powerful knowledge bases can provide suggestions of appropriate foods to individuals. Next-generation smart knowledgebase systems will not only include traditional syntactic-based search, which limits the utility of the search results, but will also provide semantics for rich searching. In this paper, performance of concept matching of food ingredients is semantic-based, meaning that it runs its own semantic based rule set to infer meaningful results through the proposed Ontology-Driven Mobile Safe Food Consumption System (FoodWiki.

  18. Use of a wiki as an interactive teaching tool in pathology residency education: Experience with a genomics, research, and informatics in pathology course

    Directory of Open Access Journals (Sweden)

    Seung Park

    2012-01-01

    Full Text Available Background: The need for informatics and genomics training in pathology is critical, yet limited resources for such training are available. In this study we sought to critically test the hypothesis that the incorporation of a wiki (a collaborative writing and publication tool with roots in "Web 2.0" in a combined informatics and genomics course could both (1 serve as an interactive, collaborative educational resource and reference and (2 actively engage trainees by requiring the creation and sharing of educational materials. Materials and Methods: A 2-week full-time course at our institution covering genomics, research, and pathology informatics (GRIP was taught by 36 faculty to 18 second- and third-year pathology residents. The course content included didactic lectures and hands-on demonstrations of technology (e.g., whole-slide scanning, telepathology, and statistics software. Attendees were given pre- and posttests. Residents were trained to use wiki technology (MediaWiki and requested to construct a wiki about the GRIP course by writing comprehensive online review articles on assigned lectures. To gauge effectiveness, pretest and posttest scores for our course were compared with scores from the previous 7 years from the predecessor course (limited to informatics given at our institution that did not utilize wikis. Results: Residents constructed 59 peer-reviewed collaborative wiki articles. This group showed a 25% improvement (standard deviation 12% in test scores, which was greater than the 16% delta recorded in the prior 7 years of our predecessor course (P = 0.006. Conclusions: Our use of wiki technology provided a wiki containing high-quality content that will form the basis of future pathology informatics and genomics courses and proved to be an effective teaching tool, as evidenced by the significant rise in our resident posttest scores. Data from this project provide support for the notion that active participation in content creation

  19. Characterization of microbial community and antibiotic resistance genes in activated sludge under tetracycline and sulfamethoxazole selection pressure

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Yingying; Geng, Jinju, E-mail: jjgeng@nju.edu.cn; Ma, Haijun; Ren, Hongqiang; Xu, Ke; Ding, Lili

    2016-11-15

    To investigate the microbial community characteristics, antibiotic resistance genes (ARGs), and bioreactor effluent quality change under tetracycline (TC) and sulfamethoxazole (SMX) selection pressure, sequencing batch reactors (SBRs) were used with environmentally relevant concentration and high-level of TC and SMX concentrations (0, 5 ppb, 50 ppb and 10 ppm). Chemical oxygen demand (COD) and ammonia nitrogen (NH{sub 4}{sup +}−N) removals appeared unchanged (p > 0.05) with 5 and 50 ppb, but decreased significantly with 10 ppm (p < 0.05). Extracellular polymeric substances (EPS) concentrations increased significantly with increasing TC or SMX concentrations (p < 0.05). High-throughput 16S rRNA gene sequencing results suggested that Proteobacteria, Actinobacteria and Bacteroidetes were the three most abundant phyla in sludge samples. The Actinobacteria percentages increased with increasing TC or SMX concentration, while Proteobacteria and Bacteroidetes decreased. The microbial diversity achieved its maximum at 5 ppb and decreased with higher concentrations. The total ARGs abundances in sludge increased with addition of TC or SMX, and the higher relative abundances were in the order of sul1 > tetG > sul2 > tetA > intI1 > tetS > tetC. Pearson correlation analysis showed most ARGs (tetA, tetC, tetG, tetK, tetM, sul1) were significantly correlated with intI1 (p < 0.01). - Highlights: • COD and NH{sub 4}{sup +}−N removals significantly decrease under 10 ppm TC or SMX. • Activated sludge EPS concentrations increase with increasing TC or SMX concentrations. • TC and SMX affect the microbial community diversity of activated sludge. • Actinobacteria abundances increase with increase of TC or SMX concentration. • ARGs abundance increases with addition of TC or SMX.

  20. Abundance of Pathogenic Escherichia coli Virulence-Associated Genes in Well and Borehole Water Used for Domestic Purposes in a Peri-Urban Community of South Africa.

    Science.gov (United States)

    Abia, Akebe Luther King; Schaefer, Lisa; Ubomba-Jaswa, Eunice; Le Roux, Wouter

    2017-03-20

    In the absence of pipe-borne water, many people in Africa, especially in rural communities, depend on alternative water sources such as wells, boreholes and rivers for household and personal hygiene. Poor maintenance and nearby pit latrines, however, lead to microbial pollution of these sources. We evaluated the abundance of Escherichia coli and the prevalence of pathogenic E. coli virulence genes in water from wells, boreholes and a river in a South African peri-urban community. Monthly samples were collected between August 2015 and November 2016. In all, 144 water samples were analysed for E. coli using the Colilert 18 system. Virulence genes ( eagg , eaeA , stx1 , stx2 , flichH7 , ST , ipaH , ibeA ) were investigated using real-time polymerase chain reaction. Mean E. coli counts ranged between 0 and 443.1 Most Probable Number (MPN)/100 mL of water sample. Overall, 99.3% of samples were positive for at least one virulence gene studied, with flicH7 being the most detected gene (81/140; 57.6%) and the stx2 gene the least detected gene (8/140; 5.7%). Both intestinal and extraintestinal pathogenic E. coli genes were detected. The detection of virulence genes in these water sources suggests the presence of potentially pathogenic E. coli strains and is a public health concern.

  1. Abundance of Pathogenic Escherichia coli Virulence-Associated Genes in Well and Borehole Water Used for Domestic Purposes in a Peri-Urban Community of South Africa

    Directory of Open Access Journals (Sweden)

    Akebe Luther King Abia

    2017-03-01

    Full Text Available In the absence of pipe-borne water, many people in Africa, especially in rural communities, depend on alternative water sources such as wells, boreholes and rivers for household and personal hygiene. Poor maintenance and nearby pit latrines, however, lead to microbial pollution of these sources. We evaluated the abundance of Escherichia coli and the prevalence of pathogenic E. coli virulence genes in water from wells, boreholes and a river in a South African peri-urban community. Monthly samples were collected between August 2015 and November 2016. In all, 144 water samples were analysed for E. coli using the Colilert 18 system. Virulence genes (eagg, eaeA, stx1, stx2, flichH7, ST, ipaH, ibeA were investigated using real-time polymerase chain reaction. Mean E. coli counts ranged between 0 and 443.1 Most Probable Number (MPN/100 mL of water sample. Overall, 99.3% of samples were positive for at least one virulence gene studied, with flicH7 being the most detected gene (81/140; 57.6% and the stx2 gene the least detected gene (8/140; 5.7%. Both intestinal and extraintestinal pathogenic E. coli genes were detected. The detection of virulence genes in these water sources suggests the presence of potentially pathogenic E. coli strains and is a public health concern.

  2. Imported anthropogenic bacteria may survive the Antarctic winter and introduce new genes into local bacterial communities

    Directory of Open Access Journals (Sweden)

    Brat Kristian

    2016-03-01

    Full Text Available We studied dynamic changes in anthropogenic bacterial communities at a summer-operated Czech research base (the Mendel Research Station in the Antarctic during 2012 and 2013. We observed an increase in total numbers of detected bacteria between the beginning and the end of each stay in the Antarctic. In the first series of samples, bacteria of Bacillus sp. predominated. Surprisingly, high numbers of Gram-positive cocci and coliforms were found (including opportunistic human pathogens, although the conditions for bacterial life were unfavourable (Antarctic winter. In the second series of samples, coliforms and Gram-positive cocci predominated. Dangerous human pathogens were also detected. Yersinia enterocolitica was identified as serotype O:9. Antibiotic susceptibility testing showed medium-to-high resistance rates to ampicillin, cefalotin, cefuroxime, amoxicillin-clavulanate and gentamicin in Enterobacteriaceae. 16S rRNA sequencing showed high rates of accordance between nucleotide sequences among the tested strains. Three conclusions were drawn: (1 Number of anthropogenic bacteria were able to survive the harsh conditions of the Antarctic winter (inside and outside the polar station. Under certain circumstances (e.g. impaired immunity, the surviving bacteria might pose a health risk to the participants of future expeditions or to other visitors to the base. (2 The bacteria released into the outer environment might have impacts on local ecosystems. (3 New characteristics (e.g. resistance to antibiotics may be introduced into local bacterial communities.

  3. Response of a diuron-degrading community to diuron exposure assessed by real-time quantitative PCR monitoring of phenylurea hydrolase A and B encoding genes

    OpenAIRE

    Pesce , S.; Beguet , J.; Rouard , N.; Devers Lamrani , M.; Martin Laurent , F.

    2013-01-01

    A real-time quantitative PCR method was developed to detect and quantify phenlylurea hydrolase genes' (puhA and puhB) sequences from environmental DNA samples to assess diuron-degrading genetic potential in some soil and sediment microbial communities. In the soil communities, mineralization rates (determined with [ring-14C]-labeled diuron) were linked to diuron-degrading genetic potentials estimated from puhB number copies, which increased following repeated diuron treatments. In the sedimen...

  4. High-throughput analysis of ammonia oxidiser community composition via a novel, amoA-based functional gene array.

    Directory of Open Access Journals (Sweden)

    Guy C J Abell

    Full Text Available Advances in microbial ecology research are more often than not limited by the capabilities of available methodologies. Aerobic autotrophic nitrification is one of the most important and well studied microbiological processes in terrestrial and aquatic ecosystems. We have developed and validated a microbial diagnostic microarray based on the ammonia-monooxygenase subunit A (amoA gene, enabling the in-depth analysis of the community structure of bacterial and archaeal ammonia oxidisers. The amoA microarray has been successfully applied to analyse nitrifier diversity in marine, estuarine, soil and wastewater treatment plant environments. The microarray has moderate costs for labour and consumables and enables the analysis of hundreds of environmental DNA or RNA samples per week per person. The array has been thoroughly validated with a range of individual and complex targets (amoA clones and environmental samples, respectively, combined with parallel analysis using traditional sequencing methods. The moderate cost and high throughput of the microarray makes it possible to adequately address broader questions of the ecology of microbial ammonia oxidation requiring high sample numbers and high resolution of the community composition.

  5. Characterization of microbial community and antibiotic resistance genes in activated sludge under tetracycline and sulfamethoxazole selection pressure

    International Nuclear Information System (INIS)

    Zhang, Yingying; Geng, Jinju; Ma, Haijun; Ren, Hongqiang; Xu, Ke; Ding, Lili

    2016-01-01

    To investigate the microbial community characteristics, antibiotic resistance genes (ARGs), and bioreactor effluent quality change under tetracycline (TC) and sulfamethoxazole (SMX) selection pressure, sequencing batch reactors (SBRs) were used with environmentally relevant concentration and high-level of TC and SMX concentrations (0, 5 ppb, 50 ppb and 10 ppm). Chemical oxygen demand (COD) and ammonia nitrogen (NH_4"+−N) removals appeared unchanged (p > 0.05) with 5 and 50 ppb, but decreased significantly with 10 ppm (p tetG > sul2 > tetA > intI1 > tetS > tetC. Pearson correlation analysis showed most ARGs (tetA, tetC, tetG, tetK, tetM, sul1) were significantly correlated with intI1 (p < 0.01). - Highlights: • COD and NH_4"+−N removals significantly decrease under 10 ppm TC or SMX. • Activated sludge EPS concentrations increase with increasing TC or SMX concentrations. • TC and SMX affect the microbial community diversity of activated sludge. • Actinobacteria abundances increase with increase of TC or SMX concentration. • ARGs abundance increases with addition of TC or SMX.

  6. Differential distribution and abundance of diazotrophic bacterial communities across different soil niches using a gene-targeted clone library approach.

    Science.gov (United States)

    Yousuf, Basit; Kumar, Raghawendra; Mishra, Avinash; Jha, Bhavanath

    2014-11-01

    Diazotrophs are key players of the globally important biogeochemical nitrogen cycle, having a significant role in maintaining ecosystem sustainability. Saline soils are pristine and unexplored habitats representing intriguing ecosystems expected to harbour potential diazotrophs capable of adapting in extreme conditions, and these implicated organisms are largely obscure. Differential occurrence of diazotrophs was studied by the nifH gene-targeted clone library approach. Four nifH gene clone libraries were constructed from different soil niches, that is saline soils (low and high salinity; EC 3.8 and 7.1 ds m(-1) ), and agricultural and rhizosphere soil. Additionally, the abundance of diazotrophic community members was assessed using quantitative PCR. Results showed environment-dependent metabolic versatility and the presence of nitrogen-fixing bacteria affiliated with a range of taxa, encompassing members of the Alphaproteobacteria, Betaproteobacteria, Deltaproteobacteria, Gammaproteobacteria, Cyanobacteria and Firmicutes. The analyses unveiled the dominance of Alphaproteobacteria and Gammaproteobacteria (Pseudomonas, Halorhodospira, Ectothiorhodospira, Bradyrhizobium, Agrobacterium, Amorphomonas) as nitrogen fixers in coastal-saline soil ecosystems, and Alphaproteobacteria and Betaproteobacteria (Bradyrhizobium, Azohydromonas, Azospirillum, Ideonella) in agricultural/rhizosphere ecosystems. The results revealed a repertoire of novel nitrogen-fixing bacterial guilds particularly in saline soil ecosystems. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  7. Nasal PCR assay for the detection of Mycobacterium leprae pra gene to study subclinical infection in a community.

    Science.gov (United States)

    Arunagiri, Kamalanathan; Sangeetha, Gopalakrishnan; Sugashini, Padmavathy Krishnan; Balaraman, Sekar; Showkath Ali, M K

    2017-03-01

    Leprosy is a chronic infectious disease caused by Mycobacterium leprae. Identification of Mycobacterium leprae is difficult in part due to the inability of the leprosy bacillus to grow in vitro. A number of diagnostic methods for leprosy diagnosis have been proposed. Both serological tests and molecular probes have shown certain potential for detection and identification of Mycobacterium leprae in patients. In this study, we have investigated whether Mycobacterium leprae DNA from the nasal secretion of healthy household contacts and the non contacts could be detected through PCR amplification as a method to study the sub clinical infection in a community. A total of 200 samples, 100 each from contacts and non contacts representing all age groups and sex were included in this study. The M. leprae specific primer (proline-rich region) of pra gene was selected and PCR was performed using extracted DNA from the sample. A total of 13 samples were found to be positive for nasal PCR for pra gene among the male and female contacts out of which 7% were males and 6% were females. Even though several diagnostic tools are available to detect the cases of leprosy, they lack the specificity and sensitivity. PCR technology has demonstrated the improved diagnostic accuracy for epidemiological studies and requires minimal time. Although nasal PCR studies have been reported from many countries it is not usually recommended due to the high percentage of negative results in the contact. Copyright © 2017 Elsevier Ltd. All rights reserved.

  8. Loss-of-function mutations in the thyrotropin receptor gene as a major determinant of hyperthyrotropinemia in a consanguineous community.

    Science.gov (United States)

    Tenenbaum-Rakover, Yardena; Grasberger, Helmut; Mamanasiri, Sunee; Ringkananont, Usanee; Montanelli, Lucia; Barkoff, Marla S; Dahood, Ahmad Mahameed-Hag; Refetoff, Samuel

    2009-05-01

    Resistance to TSH (RTSH) is a condition of impaired responsiveness of the thyroid gland to TSH, characterized by elevated serum TSH, low or normal thyroid hormone levels, and hypoplastic or normal-sized thyroid gland. The aim of the study was to evaluate the clinical course and the genotype-phenotype relationship of RTSH caused by two different TSH receptor (TSHR) gene mutations in a consanguineous population. We conducted a clinical and genetic investigation of 46 members of an extended family and 163 individuals living in the same town. In vitro functional studies of the mutant TSHRs were also performed. Two TSHR gene mutations (P68S and L653V) were identified in 33 subjects occurring as homozygous L653V (five subjects), heterozygous L653V (20 subjects), heterozygous P68S (four subjects), and compound heterozygous L653V/P68S (four subjects). With the exception of one individual with concomitant autoimmune thyroid disease, all homozygotes and compound heterozygotes presented with compensated RTSH (high TSH with free T(4) and T(3) in the normal range). Only nine of 24 heterozygotes had mild hyperthyrotropinemia. The L653V mutation resulted in a higher serum TSH concentration and showed a more severe in vitro abnormality than P68S. Haplotype analysis predicted a founder of the L653V six to seven generations earlier, whereas the P68S is older. Cross-sectional and prospective longitudinal studies indicate that TSH and T(4) concentrations remain stable over time. High frequency hyperthyrotropinemia in an Israeli Arab-Muslim consanguineous community is attributed to two inactivating TSHR gene mutations. Concordant genotype-phenotype was demonstrated clinically and by in vitro functional analysis. Retrospective and prospective studies indicate that in the absence of concomitant autoimmune thyroid disease, elevated TSH levels reflect stable compensated RTSH.

  9. Media Art Wiki. Uso de Wikis para la enseñanza interdisciplinar y multimedia del arte de los nuevos medios de comunicación en entornos virtuales de aprendizaje

    Directory of Open Access Journals (Sweden)

    Pau Alsina

    2010-01-01

    Full Text Available Este capítulo expone y analiza una experiencia piloto de uso de Wikis para la enseñanza de las prácticas artísticas vinculadas a los nuevos medios de comunicación digital. El denominado "Media Art Wiki" constituye un recurso para la enseñanza del Arte y la Estética de los nuevos medios en un contexto de enseñanza-aprendizaje virtual como es la Universitat Oberta de Catalunya (UOC. Los objetivos iniciales del proyecto consistieron en generar un entorno dinámico de documentación multimedia de las prácticas de Arte de los nuevos medios, y a su vez, que ese espacio de contenidos abiertos pudiera alimentarse de la acción participativa y colaborativa de los estudiantes de las diferentes asignaturas implicadas, contribuyendo de este modo a un enfoque interdisciplinar de la materia común. El Media Art Wiki pretende innovar dentro del aula virtual en cuatro aspectos diferentes: proceso, formato, estructura y contenidos tratando de responder asimismo a un planteamiento pedagógico, que vincule cada una de las actividades implicadas en el Wiki con varios programas y asignaturas. En este capítulo intentaremos dar cuenta de las implicaciones del uso de este tipo de herramientas en la enseñanza universitaria, estructurando el texto en diferentes apartados que, por un lado, trazan el contexto a partir del cual surgió el proyecto, sus necesidades, objetivos y motivaciones dentro del marco teórico del aprendizaje significativo- y el contexto -modelo de enseñanza-aprendizaje- de la UOC. Por otro lado procedemos a la descripción técnica y de contenido del proyecto, así como el diseño de la estrategia didáctica y de las actividades a desarrollar por los estudiantes a corto y medio plazo. Finalmente exponemos la evaluación de dicha experiencia desde la perspectiva de los docentes y los estudiantes para llegar a plantear nuestras conclusiones y posibilidades de desarrollos de futuro.

  10. WikiBuild: A New Application to Support Patient and Health Care Professional Involvement in the Development of Patient Support Tools

    Science.gov (United States)

    2011-01-01

    Active patient and public involvement as partners in their own health care and in the development of health services is key to achieving a health care system that is responsive to patients’ needs and values. It promotes better use of the health care system, and improves health outcomes, quality of life and patient satisfaction. By involving patients and health care professionals as partners in the creation and updating of patient health support tools, wikis—highly accessible, interactive vehicles of communication—have the potential to empower users to implement these support tools in daily life. Acknowledging the potential of wikis, and recognizing that they capitalize on the free and open access to information, scientists, opinion leaders and patient advocates have suggested that wikis could help decision-making constituencies improve the delivery of health care. They might also decrease its cost and improve access to knowledge within developing countries. However, little is known about the efficacy of wikis in helping to attain these goals. There is also a need to know more about the intention of patients and health care workers to use wikis, in what circumstances and what factors will influence their use of wikis. In this issue of the Journal of Medical Internet Research, Gupta et al describe how they developed and tested a new wiki-inspired application to improve asthma care. The researchers involved patients with asthma, primary care physicians, pulmonologists and certified asthma educators in the construction of an asthma action plan. Their paper—entitled “WikiBuild: a new online collaboration process for multistakeholder tool development and consensus building”—is the first description of a wiki-inspired technology built to involve patients and health care professionals in the development of a patient support tool. This innovative study has made important contributions toward how wikis could be generalized to involve multiple stakeholders in

  11. Collaborative data model and data base development for paleoenvironmental and archaeological domain using Semantic MediaWiki

    Science.gov (United States)

    Willmes, C.

    2017-12-01

    In the frame of the Collaborative Research Centre 806 (CRC 806) an interdisciplinary research project, that needs to manage data, information and knowledge from heterogeneous domains, such as archeology, cultural sciences, and the geosciences, a collaborative internal knowledge base system was developed. The system is based on the open source MediaWiki software, that is well known as the software that enables Wikipedia, for its facilitation of a web based collaborative knowledge and information management platform. This software is additionally enhanced with the Semantic MediaWiki (SMW) extension, that allows to store and manage structural data within the Wiki platform, as well as it facilitates complex query and API interfaces to the structured data stored in the SMW data base. Using an additional open source software called mobo, it is possible to improve the data model development process, as well as automated data imports, from small spreadsheets to large relational databases. Mobo is a command line tool that helps building and deploying SMW structure in an agile, Schema-Driven Development way, and allows to manage and collaboratively develop the data model formalizations, that are formalized in JSON-Schema format, using version control systems like git. The combination of a well equipped collaborative web platform facilitated by Mediawiki, the possibility to store and query structured data in this collaborative database provided by SMW, as well as the possibility for automated data import and data model development enabled by mobo, result in a powerful but flexible system to build and develop a collaborative knowledge base system. Furthermore, SMW allows the application of Semantic Web technology, the structured data can be exported into RDF, thus it is possible to set a triple-store including a SPARQL endpoint on top of the database. The JSON-Schema based data models, can be enhanced into JSON-LD, to facilitate and profit from the possibilities of Linked Data

  12. Idiopathic neonatal necrotising fasciitis caused by community-acquired MSSA encoding Panton Valentine Leukocidin genes.

    LENUS (Irish Health Repository)

    Dunlop, Rebecca L E

    2012-02-01

    Neonatal necrotising fasciitis is very rare in comparison to the adult presentation of the disease and a Plastic Surgeon may only encounter one such case during his or her career. Often this is initially misdiagnosed and managed as simple cellulitis. It generally affects previously healthy babies, the site is often the lower back area and a history of minor skin trauma may be elicited. The causative organism is usually Streptococcus or polymicrobial, as is the case in the adult population. We present the case of a previously healthy 11-day-old infant with idiopathic, rapidly progressive necrotising fasciitis of the back, cause by Methicillin sensitive Staphylococcus aureus (MSSA) infection. The strain was isolated and found to encode the Panton-Valentine Leukocidin genes, which have been associated with particularly severe necrotising infections in other sites, with high mortality. These strains are the subject of specific treatment and eradication guidance in the UK but awareness of this and the importance of obtaining detailed culture typing is likely to be low amongst Plastic Surgeons.

  13. Metabolonote: A wiki-based database for managing hierarchical metadata of metabolome analyses

    Directory of Open Access Journals (Sweden)

    Takeshi eAra

    2015-04-01

    Full Text Available Metabolomics—technology for comprehensive detection of small molecules in an organism—lags behind the other omics in terms of publication and dissemination of experimental data. Among the reasons for this are difficulty precisely recording information about complicated analytical experiments (metadata, existence of various databases with their own metadata descriptions, and low reusability of the published data, resulting in submitters (the researchers who generate the data being insufficiently motivated. To tackle these issues, we developed Metabolonote, a Semantic MediaWiki-based database designed specifically for managing metabolomic metadata. We also defined a metadata and data description format, called TogoMD, with an ID system that is required for unique access to each level of the tree-structured metadata such as study purpose, sample, analytical method, and data analysis. Separation of the management of metadata from that of data and permission to attach related information to the metadata provide advantages for submitters, readers, and database developers. The metadata are enriched with information such as links to comparable data, thereby functioning as a hub of related data resources. They also enhance not only readers' understanding and use of data, but also submitters' motivation to publish the data. The metadata are computationally shared among other systems via APIs, which facilitates the construction of novel databases by database developers. A permission system that allows publication of immature metadata and feedback from readers also helps submitters to improve their metadata. Hence, this aspect of Metabolonote, as a metadata preparation tool, is complementary to high-quality and persistent data repositories such as MetaboLights. A total of 808 metadata for analyzed data obtained from 35 biological species are published currently. Metabolonote and related tools are available free of cost at http://metabolonote.kazusa.or.jp/.

  14. Get the Diagnosis: an evidence-based medicine collaborative Wiki for diagnostic test accuracy.

    Science.gov (United States)

    Hammer, Mark M; Kohlberg, Gavriel D

    2017-04-01

    Despite widespread calls for its use, there are challenges to the implementation of evidence-based medicine (EBM) in clinical practice. In response to the challenges of finding timely, pertinent information on diagnostic test accuracy, we developed an online, crowd-sourced Wiki on diagnostic test accuracy called Get the Diagnosis (GTD, http://www.getthediagnosis.org). Since its launch in November 2008 till October 2015, GTD has accumulated information on 300 diagnoses, with 1617 total diagnostic entries. There are a total of 1097 unique diagnostic tests with a mean of 5.4 tests (range 0-38) per diagnosis. 73% of entries (1182 of 1617) have an associated sensitivity and specificity and 89% of entries (1432 of 1617) have associated peer-reviewed literature citations. Altogether, GTD contains 474 unique literature citations. For a sample of three diagnoses, the search precision (percentage of relevant results in the first 30 entries) in GTD was 100% as compared with a range of 13.3%-63.3% for PubMed and between 6.7% and 76.7% for Google Scholar. GTD offers a fast, precise and efficient way to look up diagnostic test accuracy. On three selected examples, GTD had a greater precision rate compared with PubMed and Google Scholar in identifying diagnostic test information. GTD is a free resource that complements other currently available resources. 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/.

  15. Wikis, blogs and podcasts: a new generation of Web-based tools for virtual collaborative clinical practice and education

    Directory of Open Access Journals (Sweden)

    Maramba Inocencio

    2006-08-01

    Full Text Available Abstract Background We have witnessed a rapid increase in the use of Web-based 'collaborationware' in recent years. These Web 2.0 applications, particularly wikis, blogs and podcasts, have been increasingly adopted by many online health-related professional and educational services. Because of their ease of use and rapidity of deployment, they offer the opportunity for powerful information sharing and ease of collaboration. Wikis are Web sites that can be edited by anyone who has access to them. The word 'blog' is a contraction of 'Web Log' – an online Web journal that can offer a resource rich multimedia environment. Podcasts are repositories of audio and video materials that can be "pushed" to subscribers, even without user intervention. These audio and video files can be downloaded to portable media players that can be taken anywhere, providing the potential for "anytime, anywhere" learning experiences (mobile learning. Discussion Wikis, blogs and podcasts are all relatively easy to use, which partly accounts for their proliferation. The fact that there are many free and Open Source versions of these tools may also be responsible for their explosive growth. Thus it would be relatively easy to implement any or all within a Health Professions' Educational Environment. Paradoxically, some of their disadvantages also relate to their openness and ease of use. With virtually anybody able to alter, edit or otherwise contribute to the collaborative Web pages, it can be problematic to gauge the reliability and accuracy of such resources. While arguably, the very process of collaboration leads to a Darwinian type 'survival of the fittest' content within a Web page, the veracity of these resources can be assured through careful monitoring, moderation, and operation of the collaborationware in a closed and secure digital environment. Empirical research is still needed to build our pedagogic evidence base about the different aspects of these tools in

  16. Wikis: Hacía un modelo comunitario de preservación y socialización del conocimiento

    OpenAIRE

    Bordignon, Fernando R. A.

    2007-01-01

    Spanish Abstract: El software social está compuesto por una serie de herramientas que ayudan a formar y gestionar comunidades de usuarios o pares. Hablar de términos como folksonomias, bitácoras o blogs, sistemas de recomendación y entornos colaborativos de desarrollo es enfocar la atención en una nueva generación de software que tiene por característica la ruptura de la asimetría que caracterizó la relación anterior entre usuarios y generadores de contenidos. Las wikis son una de las p...

  17. The Impact of ICT Training Through Wikis on In-Service EFL Teachers: Changes in Beliefs, Attitudes, and Competencies

    Directory of Open Access Journals (Sweden)

    Yamith José Fandiño Parra

    2012-12-01

    Full Text Available The development of information and communication technology (ICT invites teachers to abandon traditional roles and act more as mentors, exploring the new media themselves as learners and thus acting as role models for their students (Fitzpatrick & Davies, 2003. For turning students into producers of online content and creating a collaborative learning environment, wikis appear to help foreign language teachers to infuse ICT in their classrooms (Kovacic, Bubas & Zlatovic, 2007. Within this context, results from an action research project carried out in four public schools suggest that beliefs, attitudes, and competencies can be impacted positively when working on the use of new technologies with in-service English teachers.

  18. Characterization of microbial communities found in the human vagina by analysis of terminal restriction fragment length polymorphisms of 16S rRNA genes

    NARCIS (Netherlands)

    Coolen, MJL; Post, E; Davis, CC; Forney, LJ

    2005-01-01

    To define and monitor the structure of microbial communities found in the human vagina, a cultivation-independent approach based on analyses of terminal restriction fragment length polymorphisms (T-RFLP) of 16S rRNA genes was developed and validated. Sixteen bacterial strains commonly found in the

  19. Marine Microbial Gene Abundance and Community Composition in Response to Ocean Acidification and Elevated Temperature in Two Contrasting Coastal Marine Sediments

    Directory of Open Access Journals (Sweden)

    Ashleigh R. Currie

    2017-08-01

    Full Text Available Marine ecosystems are exposed to a range of human-induced climate stressors, in particular changing carbonate chemistry and elevated sea surface temperatures as a consequence of climate change. More research effort is needed to reduce uncertainties about the effects of global-scale warming and acidification for benthic microbial communities, which drive sedimentary biogeochemical cycles. In this research, mesocosm experiments were set up using muddy and sandy coastal sediments to investigate the independent and interactive effects of elevated carbon dioxide concentrations (750 ppm CO2 and elevated temperature (ambient +4°C on the abundance of taxonomic and functional microbial genes. Specific quantitative PCR primers were used to target archaeal, bacterial, and cyanobacterial/chloroplast 16S rRNA in both sediment types. Nitrogen cycling genes archaeal and bacterial ammonia monooxygenase (amoA and bacterial nitrite reductase (nirS were specifically targeted to identify changes in microbial gene abundance and potential impacts on nitrogen cycling. In muddy sediment, microbial gene abundance, including amoA and nirS genes, increased under elevated temperature and reduced under elevated CO2 after 28 days, accompanied by shifts in community composition. In contrast, the combined stressor treatment showed a non-additive effect with lower microbial gene abundance throughout the experiment. The response of microbial communities in the sandy sediment was less pronounced, with the most noticeable response seen in the archaeal gene abundances in response to environmental stressors over time. 16S rRNA genes (amoA and nirS were lower in abundance in the combined stressor treatments in sandy sediments. Our results indicated that marine benthic microorganisms, especially in muddy sediments, are susceptible to changes in ocean carbonate chemistry and seawater temperature, which ultimately may have an impact upon key benthic biogeochemical cycles.

  20. Occurrence and analysis of irp2 virulence gene in isolates of Klebsiella pneumoniae and Enterobacter spp. from microbiota and hospital and community-acquired infections.

    Science.gov (United States)

    Souza Lopes, Ana Catarina; Rodrigues, Juliana Falcão; Cabral, Adriane Borges; da Silva, Maíra Espíndola; Leal, Nilma Cintra; da Silveira, Vera Magalhães; de Morais Júnior, Marcos Antônio

    2016-07-01

    Eighty-five isolates of Klebsiella pneumoniae and Enterobacter spp., originating from hospital- and community-acquired infections and from oropharyngeal and faecal microbiota from patients in Recife-PE, Brazil, were analyzed regarding the presence of irp2 gene. This is a Yersinia typical gene involved in the synthesis of siderophore yersiniabactin. DNA sequencing confirmed the identity of irp2 gene in five K. pneumoniae, five Enterobacter aerogenes and one Enterobacter amnigenus isolates. To our knowledge in the current literature, this is the first report of the irp2 gene in E. amnigenus, a species considered an unusual human pathogen, and in K. pneumoniae and E. aerogenes isolates from the normal microbiota and from community infections, respectively. Additionally, the analyses of nucleotide and amino acid sequences suggest the irp2 genes derived from isolates used in this study are more closely related to that of Yersinia pestis P.CE882 than to that of Yersinia enterocolitica 8081. These data demonstrated that K. pneumoniae and Enterobacter spp. from normal microbiota and from community- and hospital-acquired infections possess virulence factors important for the establishment of extra-intestinal infections. Copyright © 2016 Elsevier Ltd. All rights reserved.

  1. Highlighting of quorum sensing lux genes and their expression in the hydrothermal vent shrimp Rimicaris exoculata ectosymbiontic community. Possible use as biogeographic markers.

    Directory of Open Access Journals (Sweden)

    Simon Le Bloa

    Full Text Available Rimicaris exoculata is a caridean shrimp that dominates the fauna at several hydrothermal vent sites of the Mid-Atlantic Ridge. It has two distinct and stable microbial communities. One of these epibiontic bacterial communities is located in the shrimp gut and has a distribution and role that are poorly understood. The second colonizes its enlarged gill chamber and is involved in host nutrition. It is eliminated after each molt, and has colonization processes reminiscent of those of a biofilm. The presence and expression of genes usually involved in quorum sensing (QS were then studied. At four sites, Rainbow, TAG, Snake Pit and Logatchev, two lux genes were identified in the R. exoculata epibiontic community at different shrimp molt stages and life stages. RT-PCR experiments highlighted lux gene expression activity at TAG, Snake Pit and Rainbow vent sites. Their potential QS activity and their possible roles in epibiont colonization processes are discussed. Moreover, phylogenetic analysis has shown the presence of three clades for luxS (Epsilonproteobacteria and four clades for luxR (Gammaproteobacteria genes, each clade being restricted to a single site. These genes are more divergent than the 16S rRNA one. They could therefore be used as biogeographical genetic markers.

  2. Variation of bacterial communities and expression of Toll-like receptor genes in the rumen of steers differing in susceptibility to subacute ruminal acidosis.

    Science.gov (United States)

    Chen, Yanhong; Oba, Masahito; Guan, Le Luo

    2012-10-12

    In order to determine differences in the ruminal bacterial community and host Toll-like receptor (TLR) gene expression of beef cattle with different susceptibility to acidosis, rumen papillae and content were collected from acidosis-susceptible (AS, n=3) and acidosis-resistant (AR, n=3) steers. The ruminal bacterial community was characterized using PCR-denaturing gradient gel electrophoresis (PCR-DGGE) and quantitative real time PCR (qRT-PCR) analysis. Global R analysis of bacterial profile similarity revealed that bacterial diversity was significantly different between AR and AS groups for both rumen content (P=0.001) and epithelial (P=0.002) communities. The copy number of total bacterial 16S rRNA genes in content of AS steers was 10-fold higher than that of AR steers, and the copy number of total 16S rRNA genes of epimural bacteria in AR steers was positively correlated with ruminal pH (r=0.59, P=0.04), and negatively correlated with total VFA concentration (r=-0.59, P=0.05). The expressions of host TLR2 and 4 genes were significantly higher in AR steers compared to those in AS steers. These findings enhance our understanding about the ruminal microbial ecology and host gene expression changes that may be useful in the prevention of ruminal acidosis. Copyright © 2012 Elsevier B.V. All rights reserved.

  3. Association of Panton Valentine Leukocidin (PVL) genes with methicillin resistant Staphylococcus aureus (MRSA) in Western Nepal: a matter of concern for community infections (a hospital based prospective study)

    DEFF Research Database (Denmark)

    Bhatta, Dharm R.; Cavaco, Lina; Nath, Gopal

    2016-01-01

    Methicillin resistant Staphylococcus aureus (MRSA) is a major human pathogen associated with nosocomial and community infections. Panton Valentine leukocidin (PVL) is considered one of the important virulence factors of S. aureus responsible for destruction of white blood cells, necrosis...... and apoptosis and as a marker of community acquired MRSA. This study was aimed to determine the prevalence of PVL genes among MRSA isolates and to check the reliability of PVL as marker of community acquired MRSA isolates from Western Nepal. A total of 400 strains of S. aureus were collected from clinical...... specimens and various units (Operation Theater, Intensive Care Units) of the hospital and 139 of these had been confirmed as MRSA by previous study. Multiplex PCR was used to detect mecA and PVL genes. Clinical data as well as antimicrobial susceptibility data was analyzed and compared among PVL positive...

  4. Emerging contaminants and nutrients synergistically affect the spread of class 1 integron-integrase (intI1) and sul1 genes within stable streambed bacterial communities.

    Science.gov (United States)

    Subirats, Jèssica; Timoner, Xisca; Sànchez-Melsió, Alexandre; Balcázar, José Luis; Acuña, Vicenç; Sabater, Sergi; Borrego, Carles M

    2018-07-01

    Wastewater effluents increase the nutrient load of receiving streams while introducing a myriad of anthropogenic chemical pollutants that challenge the resident aquatic (micro)biota. Disentangling the effects of both kind of stressors and their potential interaction on the dissemination of antibiotic resistance genes in bacterial communities requires highly controlled manipulative experiments. In this work, we investigated the effects of a combined regime of nutrients (at low, medium and high concentrations) and a mixture of emerging contaminants (ciprofloxacin, erythromycin, sulfamethoxazole, diclofenac, and methylparaben) on the bacterial composition, abundance and antibiotic resistance profile of biofilms grown in artificial streams. In particular, we investigated the effect of this combined stress on genes encoding resistance to ciprofloxacin (qnrS), erythromycin (ermB), sulfamethoxazole (sul1 and sul2) as well as the class 1 integron-integrase gene (intI1). Only genes conferring resistance to sulfonamides (sul1 and sul2) and intI1 gene were detected in all treatments during the study period. Besides, bacterial communities exposed to emerging contaminants showed higher copy numbers of sul1 and intI1 genes than those not exposed, whereas nutrient amendments did not affect their abundance. However, bacterial communities exposed to both emerging contaminants and a high nutrient concentration (1, 25 and 1 mg L -1 of phosphate, nitrate and ammonium, respectively) showed the highest increase on the abundance of sul1 and intI1 genes thus suggesting a factors synergistic effect of both stressors. Since none of the treatments caused a significant change on the composition of bacterial communities, the enrichment of sul1 and intI1 genes within the community was caused by their dissemination under the combined pressure exerted by nutrients and emerging contaminants. To the best of our knowledge, this is the first study demonstrating the contribution of nutrients on

  5. Community structures and activity of denitrifying microbes in a forested catchment in central Japan: survey using nitrite reductase genes

    Science.gov (United States)

    Ohte, N.; Aoki, M.; Katsuyama, C.; Suwa, Y.; Tange, T.

    2012-12-01

    To elucidate the mechanisms of denitrification processes in the forested catchment, microbial ecological approaches have been applied in an experimental watershed that has previously investigated its hydrological processes. The study catchment is located in the Chiba prefecture in central Japan under the temperate Asian monsoon climate. Potential activities of denitrification of soil samples were measured by incubation experiments under anoxic condition associated with Na15NO3 addition. Existence and variety of microbes having nitrite reductase genes were investigated by PCR amplification, cloning and sequencings of nirK and nirS fragments after DNA extraction. Contrary to our early expectation that the potential denitrification activity was higher at deeper soil horizon with consistent groundwater residence than that in the surface soil, denitrification potential was higher in shallower soil horizons than deeper soils. This suggested that the deficiency of NO3- as a respiratory substrate for denitrifier occurred in deeper soils especially in the summer. However, high denitrification activity and presence of microbes having nirK and nirS in surface soils usually under aerobic condition was explainable by the fact that the majority of denitrifying bacteria have been recognized as a facultative anaerobic bacterium. This also suggests the possibility of that denitrification occurs even in the surface soils if the wet condition is provided by rainwater during and after a storm event. Community structures of microbes having nirK were different between near surface and deeper soil horizons, and ones having nirS was different between saturated zone (under groundwater table) and unsaturated soil horizons. These imply that microbial communities with nisK are sensitive to the concentration of soil organic matters and ones with nirS is sensitive to soil moisture contents.

  6. Wikis y aprendizaje colaborativo: lecciones aprendidas (y por aprender en la facultad de educación

    Directory of Open Access Journals (Sweden)

    Rocío Anguita Martínez

    2010-01-01

    Full Text Available El Espacio Europeo de Educación Superior ha llevado a las Universidades de toda Europa, entre ellas las españolas, a cambios metodológicos para su adaptación al Proceso de Bolonia. Estos entornos educativos suponen una nueva conceptualización de la docencia, en la que las Nuevas Tecnologías de apoyo a los procesos de enseñanza-aprendizaje adquieren un papel fundamental. En este escenario, una comunidad de profesores procedentes de la Facultad de Educación y Trabajo Social de la Universidad de Valladolid (UVa, vienen desarrollando desde hace años diversas innovaciones educativas en la asignatura de Nuevas Tecnologías Aplicadas a la Educación (NNTT. Innovaciones que han desencadenado en la puesta en práctica durante el curso académico 2007-2008 de una plataforma Wiki como eje transversal para el desarrollo de aprendizaje colaborativo. Este artículo analiza cómo desde una asignatura soportada por tecnología Wiki y orientada sobre los principios del aprendizaje por indagación (IBL se puede ayudar a promover el trabajo colaborativo y el pensamiento crítico entre los estudiantes desde la apertura de posibilidades didácticas y docentes.

  7. LACO-Wiki: A land cover validation tool and a new, innovative teaching resource for remote sensing and the geosciences

    Science.gov (United States)

    See, Linda; Perger, Christoph; Dresel, Christopher; Hofer, Martin; Weichselbaum, Juergen; Mondel, Thomas; Steffen, Fritz

    2016-04-01

    The validation of land cover products is an important step in the workflow of generating a land cover map from remotely-sensed imagery. Many students of remote sensing will be given exercises on classifying a land cover map followed by the validation process. Many algorithms exist for classification, embedded within proprietary image processing software or increasingly as open source tools. However, there is little standardization for land cover validation, nor a set of open tools available for implementing this process. The LACO-Wiki tool was developed as a way of filling this gap, bringing together standardized land cover validation methods and workflows into a single portal. This includes the storage and management of land cover maps and validation data; step-by-step instructions to guide users through the validation process; sound sampling designs; an easy-to-use environment for validation sample interpretation; and the generation of accuracy reports based on the validation process. The tool was developed for a range of users including producers of land cover maps, researchers, teachers and students. The use of such a tool could be embedded within the curriculum of remote sensing courses at a university level but is simple enough for use by students aged 13-18. A beta version of the tool is available for testing at: http://www.laco-wiki.net.

  8. Characterization of the Fecal Microbial Communities of Duroc Pigs Using 16S rRNA Gene Pyrosequencing

    Directory of Open Access Journals (Sweden)

    Edward Alain B. Pajarillo

    2015-04-01

    Full Text Available This study characterized the fecal bacterial community structure and inter-individual variation in 30-week-old Duroc pigs, which are known for their excellent meat quality. Pyrosequencing of the V1–V3 hypervariable regions of the 16S rRNA genes generated 108,254 valid reads and 508 operational taxonomic units at a 95% identity cut-off (genus level. Bacterial diversity and species richness as measured by the Shannon diversity index were significantly greater than those reported previously using denaturation gradient gel electrophoresis; thus, this study provides substantial information related to both known bacteria and the untapped portion of unclassified bacteria in the population. The bacterial composition of Duroc pig fecal samples was investigated at the phylum, class, family, and genus levels. Firmicutes and Bacteroidetes predominated at the phylum level, while Clostridia and Bacteroidia were most abundant at the class level. This study also detected prominent inter-individual variation starting at the family level. Among the core microbiome, which was observed at the genus level, Prevotella was consistently dominant, as well as a bacterial phylotype related to Oscillibacter valericigenes, a valerate producer. This study found high bacterial diversity and compositional variation among individuals of the same breed line, as well as high abundance of unclassified bacterial phylotypes that may have important functions in the growth performance of Duroc pigs.

  9. Fitness and Recovery of Bacterial Communities and Antibiotic Resistance Genes in Urban Wastewaters Exposed to Classical Disinfection Treatments.

    Science.gov (United States)

    Di Cesare, Andrea; Fontaneto, Diego; Doppelbauer, Julia; Corno, Gianluca

    2016-09-20

    Antibiotic resistance genes (ARGs) are increasingly appreciated to be important as micropollutants. Indirectly produced by human activities, they are released into the environment, as they are untargeted by conventional wastewater treatments. In order to understand the fate of ARGs and of other resistant forms (e.g., phenotypical adaptations) in urban wastewater treatment plants (WWTPs), we monitored three WWTPs with different disinfection processes (chlorine, peracetic acid (PAA), and ultraviolet light (UV)). We monitored WWTPs influx and pre- and postdisinfection effluent over 24 h, followed by incubation experiments lasting for 96 h. We measured bacterial abundance, size distribution and aggregational behavior, the proportion of intact (active) cells, and the abundances of four ARGs and of the mobile element integron1. While all the predisinfection treatments of all WWTPs removed the majority of bacteria and of associated ARGs, of the disinfection processes only PAA efficiently removed bacterial cells. However, the stress imposed by PAA selected for bacterial aggregates and, similarly to chlorine, stimulated the selection of ARGs during the incubation experiment. This suggests disinfections based on chemically aggressive destruction of bacterial cell structures can promote a residual microbial community that is more resistant to antibiotics and, given the altered aggregational behavior, to competitive stress in nature.

  10. Response of a diuron-degrading community to diuron exposure assessed by real-time quantitative PCR monitoring of phenylurea hydrolase A and B encoding genes.

    Science.gov (United States)

    Pesce, Stéphane; Beguet, Jérémie; Rouard, Nadine; Devers-Lamrani, Marion; Martin-Laurent, Fabrice

    2013-02-01

    A real-time quantitative PCR method was developed to detect and quantify phenlylurea hydrolase genes' (puhA and puhB) sequences from environmental DNA samples to assess diuron-degrading genetic potential in some soil and sediment microbial communities. In the soil communities, mineralization rates (determined with [ring-¹⁴C]-labeled diuron) were linked to diuron-degrading genetic potentials estimated from puhB number copies, which increased following repeated diuron treatments. In the sediment communities, mineralization potential did not depend solely on the quantity of puhB copies, underlining the need to assess gene expression. In the sediment samples, both puhB copy numbers and mineralization capacities were highly conditioned by whether or not diuron-treated soil was added. This points to transfers of degradative potential from soils to sediments. No puhA gene was detected in soil and sediment DNA extracts. Moreover, some sediments exhibited high diuron mineralization potential even though puhB genes were not detected, suggesting the existence of alternative diuron degradation pathways.

  11. Occurrence of diarrhoeagenic Escherichia coli virulence genes in water and bed sediments of a river used by communities in Gauteng, South Africa.

    Science.gov (United States)

    Abia, Akebe Luther King; Ubomba-Jaswa, Eunice; Momba, Maggy Ndombo Benteke

    2016-08-01

    In most developing countries, especially in Southern Africa, little is known about the presence of diarrhoeagenic Escherichia coli (DEC) pathotypes in riverbed sediments. The present study sought to investigate the presence of DEC virulence genes in riverbed sediments of the Apies River, a river used by many communities in Gauteng, South Africa. Water and sediment samples were collected from the river between July and August 2013 (dry season) and also between January and February 2014 (wet season) following standard procedures. Isolation of E. coli was done using the Colilert®-18 Quanti-Tray® 2000 system. DNA was extracted from E. coli isolates using the InstaGene™ matrix from Bio-Rad and used as template DNA for real-time PCR. Water pH, temperature, dissolved oxygen, electrical conductivity and turbidity were measured in situ. Over 59 % of 180 samples analysed were positive for at least one of the seven DEC virulence genes investigated. The eaeA gene was the most isolated gene (29.44 %) while the ipaH gene the least isolated (8.33 %). The ipaH gene (p = 0.012) and the ST gene (stIa, p = 0.0001, and stIb, p = 0.019) were positively correlated with temperature. The detection of diarrhoeagenic E. coli virulence genes in the sediments of the Apies River shows that the sediments of this river might not only be a reservoir of faecal indicator bacteria like E. coli but also pathogenic strains of this bacterium. These organisms could represent a public health risk for poor communities relying on this water source for various purposes such as drinking and recreational use. There is therefore an urgent need to monitor these DEC pathotypes especially in areas without adequate water supplies.

  12. [Characterizing Beijing's Airborne Bacterial Communities in PM2.5 and PM1 Samples During Haze Pollution Episodes Using 16S rRNA Gene Analysis Method].

    Science.gov (United States)

    Wang, Bu-ying; Lang, Ji-dong; Zhang, Li-na; Fang, Jian-huo; Cao, Chen; Hao, Ji-ming; Zhu, Ting; Tian, Geng; Jiang, Jing-kun

    2015-08-01

    During 8th-14th Jan., 2013, severe particulate matter (PM) pollution episodes happened in Beijing. These air pollution events lead to high risks for public health. In addition to various PM chemical compositions, biological components in the air may also impose threaten. Little is known about airborne microbial community in such severe air pollution conditions. PM2.5 and PM10 samples were collected during that 7-day pollution period. The 16S rRNA gene V3 amplification and the MiSeq sequencing were performed for analyzing these samples. It is found that there is no significant difference at phylum level for PM2.5 bacterial communities during that 7-day pollution period both at phylum and at genus level. At genus level, Arthrobacter and Frankia are the major airborne microbes presented in Beijing winter.samples. At genus level, there are 39 common genera (combined by first 50 genera bacterial of the two analysis) between the 16S rRNA gene analysis and those are found by Metagenomic analysis on the same PM samples. Frankia and Paracoccus are relatively more abundant in 16S rRNA gene data, while Kocuria and Geodermatophilus are relatively more abundant in Meta-data. PM10 bacterial communities are similar to those of PM2.5 with some noticeable differences, i.e., at phylum level, more Firmicutes and less Actinobacteria present in PM10 samples than in PM2.5 samples, while at genus level, more Clostridium presents in PM10 samples. The findings in Beijing were compared with three 16S rRNA gene studies in other countries. Although the sampling locations and times are different from each other, compositions of bacterial community are similar for those sampled at the ground atmosphere. Airborne microbial communities near the ground surface are different from those sampled in the upper troposphere.

  13. Incorporation of Cross-Disciplinary Teaching and a Wiki Research Project to Engage Undergraduate Students' to Develop Information Literacy, Critical Thinking, and Communication Skills

    Science.gov (United States)

    Crist, Courtney A.; Duncan, Susan E.; Bianchi, Laurie M.

    2017-01-01

    A Wiki research project was created in the Functional Foods for Health (FST/HNFE 2544) as an instructional tool and assignment for improving undergraduate students' proficiency in evaluating appropriate information sources for rapidly evolving science and research. The project design targeted improving students' information literacy skills…

  14. The Effects of Wiki-Based Recursive Process Writing on Chinese Narrative Essays for Chinese as a Second Language (CSL) Students in Singapore

    Science.gov (United States)

    Chin, Chee Kuen; Gong, Cheng; Tay, Boon Pei

    2015-01-01

    This paper reports on the effects of using wiki-based process writing in Singapore's Chinese as a Second Language (CSL) scenarios. A group of 32 Secondary 1 (Seventh Grade) students ("Students") received various forms of online scaffolding at different steps of the writing process over two years. A whole set of teaching materials on 45…

  15. Co-creation of information leaflets to meet the support needs of people living with complex regional pain syndrome (CRPS) through innovative use of wiki technology.

    Science.gov (United States)

    Rodham, Karen; Gavin, Jeff; Coulson, Neil; Watts, Leon

    2016-01-01

    People living with complex regional pain syndrome (CRPS) experience frustration with the lack of knowledge and understanding of CRPS as a pain condition. We report on our attempt to address this issue. People living with CRPS taking part in a larger study were invited to co-construct a CRPS wiki page that addressed the areas in which they had experienced the most difficulty. A blank wiki page was set up for participants to populate with issues they felt needed to be raised and addressed. Participants failed to engage with the wiki technology. We modified our procedure and completed an inductive analysis of a sister-forum which participants were using as part of the larger study. Six issues of importance were identified. We used the discussion forum threads to populate the themes. Due to a continued lack of engagement with the wiki technology, the team decided to create a suite of leaflets which were piloted with delegates at a CRPS patient conference. Future work should be mindful of the extent to which patients are able and willing to share their experiences through such technology. Striking the balance between patient-endorsed and researcher-driven co-creation of such material is imperative.

  16. Studying the use of forest management decision support systems: An initial synthesis of lessons learned from case studies compiled using a semantic wiki

    NARCIS (Netherlands)

    Gordon, S.N.; Floris, A.; Boerboom, L.G.J.; Lamas, T.; Eriksson, L.O.; Nieuwenhuis, M.G.; Rodriguez, L.

    2014-01-01

    In order to share information on the development and use of forest management decision support systems (FMDSS), a European-initiated network has established a wiki website as part of its activities. Case studies and associated lessons learned were solicited from the network using semantic structures

  17. Mountain pine beetles colonizing historical and naive host trees are associated with a bacterial community highly enriched in genes contributing to terpene metabolism.

    Science.gov (United States)

    Adams, Aaron S; Aylward, Frank O; Adams, Sandye M; Erbilgin, Nadir; Aukema, Brian H; Currie, Cameron R; Suen, Garret; Raffa, Kenneth F

    2013-06-01

    The mountain pine beetle, Dendroctonus ponderosae, is a subcortical herbivore native to western North America that can kill healthy conifers by overcoming host tree defenses, which consist largely of high terpene concentrations. The mechanisms by which these beetles contend with toxic compounds are not well understood. Here, we explore a component of the hypothesis that beetle-associated bacterial symbionts contribute to the ability of D. ponderosae to overcome tree defenses by assisting with terpene detoxification. Such symbionts may facilitate host tree transitions during range expansions currently being driven by climate change. For example, this insect has recently breached the historical geophysical barrier of the Canadian Rocky Mountains, providing access to näive tree hosts and unprecedented connectivity to eastern forests. We use culture-independent techniques to describe the bacterial community associated with D. ponderosae beetles and their galleries from their historical host, Pinus contorta, and their more recent host, hybrid P. contorta-Pinus banksiana. We show that these communities are enriched with genes involved in terpene degradation compared with other plant biomass-processing microbial communities. These pine beetle microbial communities are dominated by members of the genera Pseudomonas, Rahnella, Serratia, and Burkholderia, and the majority of genes involved in terpene degradation belong to these genera. Our work provides the first metagenome of bacterial communities associated with a bark beetle and is consistent with a potential microbial contribution to detoxification of tree defenses needed to survive the subcortical environment.

  18. WEBQUEST AND WIKI: SEARCH OF INFORMATION IN INTERNET AND DEVELOPMENT OF COMPETENCES IN COLLABORATIVE WEBQUEST Y WIKIS: BÚSQUEDA DE INFORMACIÓN EN RED Y DESARROLLO DE COMPETENCIAS EN COLABORACIÓN

    Directory of Open Access Journals (Sweden)

    Lourdes Villalustre Martínez

    2011-03-01

    Full Text Available In university education is committed to strategies and resources, -that exploit the potential of digital tools-, such as Webquests as supported collaborative research methodologies in the search for information and the use of content on the Internet for conducting projects. Which can be articulated from 2.0 tools like wikis, for its versatility and capacity to generate knowledge collaboratively by creating online content.In the virtual subject of Education in the rural area was designed a collaborative learning activity based on the philosophy of webquests and supported by the use of wikis, - setting up what was called Gameproject - that facilitates access and management information to create a project of socio-educational intervention.After its implementation in several years, 161 students were asked about competences they considered to have developed and consolidated with the proposed collaborative work. The students stressed the skills to research, collection and processing of information, and other more specific competences relating to the future performance of their work. Noted that students without prior experience in virtual training, considered to have consolidated over the powers associated with the use of tools.En la formación universitaria se está apostando por estrategias y recursos didácticos, -que aprovechan las potencialidades de diferentes instrumentos digitales-, como las Webquests en tanto metodologías de investigación colaborativa apoyada en la búsqueda de información y en la utilización de contenidos alojados en Internet para la realización de proyectos. Los cuales pueden articularse a partir de herramientas 2.0 como las wikis, por su gran versatilidad y capacidad para generar conocimiento de forma colaborativa mediante la creación de contenidos on-line.   En la asignatura virtual de Educación en el ámbito rural1 se ha diseñado una actividad formativa en colaboración basada en la filosofía de las webquests y

  19. Effects of oxytetracycline on archaeal community, and tetracycline resistance genes in anaerobic co-digestion of pig manure and wheat straw.

    Science.gov (United States)

    Wang, Xiaojuan; Pan, Hongjia; Gu, Jie; Qian, Xun; Gao, Hua; Qin, Qingjun

    2016-12-01

    In this study, the effects of different concentrations of oxytetracycline (OTC) on biogas production, archaeal community structure, and the levels of tetracycline resistance genes (TRGs) were investigated in the anaerobic co-digestion products of pig manure and wheat straw. PCR denaturing gradient gel electrophoresis analysis and real-time quantitative polymerase chain reaction (RT-qPCR) (PCR) were used to detect the archaeal community structure and the levels of four TRGs: tet(M), tet(Q), tet(W), and tet(C). The results showed that anaerobic co-digestion with OTC at concentrations of 60, 100, and 140 mg/kg (dry weight of pig manure) reduced the cumulative biogas production levels by 9.9%, 10.4%, and 14.1%, respectively, compared with that produced by the control, which lacked the antibiotic. The addition of OTC substantially modified the structure of the archaeal community. Two orders were identified by phylogenetic analysis, that is, Pseudomonadales and Methanomicrobiales, and the methanogen present during anaerobic co-digestion with OTC may have been resistant to OTC. The abundances of tet(Q) and tet(W) genes increased as the OTC concentration increased, whereas the abundances of tet(M) and tet(C) genes decreased as the OTC concentration increased.

  20. Analysis of Microbial Communities in the Oil Reservoir Subjected to CO2-Flooding by Using Functional Genes as Molecular Biomarkers for Microbial CO2 Sequestration

    Directory of Open Access Journals (Sweden)

    Jin-Feng eLiu

    2015-03-01

    Full Text Available Sequestration of CO2 in oil reservoirs is considered to be one of the feasible options for mitigating atmospheric CO2 building up and also for the in situ potential bioconversion of stored CO2 to methane. However, the information on these functional microbial communities and the impact of CO2 storage on them is hardly available. In this paper a comprehensive molecular survey was performed on microbial communities in production water samples from oil reservoirs experienced CO2-flooding by analysis of functional genes involved in the process, including cbbM, cbbL, fthfs, [FeFe]-hydrogenase and mcrA. As a comparison, these functional genes in the production water samples from oil reservoir only experienced water-flooding in areas of the same oil bearing bed were also analyzed. It showed that these functional genes were all of rich diversity in these samples, and the functional microbial communities and their diversity were strongly affected by a long-term exposure to injected CO2. More interestingly, microorganisms affiliated with members of the genera Methanothemobacter, Acetobacterium and Halothiobacillus as well as hydrogen producers in CO2 injected area either increased or remained unchanged in relative abundance compared to that in water-flooded area, which implied that these microorganisms could adapt to CO2 injection and, if so, demonstrated the potential for microbial fixation and conversion of CO2 into methane in subsurface oil reservoirs.

  1. Making sense of the German Wikipedia community

    Directory of Open Access Journals (Sweden)

    Rikke Frank Jørgensen

    2012-08-01

    Full Text Available This article presents the findings from a qualitative study of the German Wikipedia community, focusing on how people engaged with Wikipedia make sense of norms, collaborative practices and means of regulation within the community. The study highlights the strong focus on the quality of the end-product (the encyclopedia in the German community, stressing that article quality is seen as more important than the wiki-process as such. As the community has grown, an increasing number of rules and mechanisms have been deployed to resolve various issues and conflicts, however the interviewees do not perceive Wikipedia as being bureaucratic, but rather describe it as a “rule-governed anarchy”. The findings suggest that people contribute for a variety of reasons, yet point to reactions from and interactions with fellow Wikipedians as one of the strongest motivational drivers for participation.

  2. Un modelo de implementación de una wiki para la formación jurídica

    Directory of Open Access Journals (Sweden)

    Ana Giménez Costa

    2010-01-01

    Full Text Available Desde la experiencia en el uso de la herramienta wiki en diversas asignaturas impartidas en la Facultad de Ciencias Jurídicas de la Universitat Rovira i Virgili de Tarragona se pueden extraer algunas conclusiones que permiten la elaboración de una estrategia para la implementación de actividades de trabajo colaborativo, utilizando dicha herramienta. Con carácter previo al diseño de la actividad es necesario contextualizarla, reflexionando sobre algunas cuestiones como los potenciales usuarios, los objetivos de la actividad, el plan de trabajo, los recursos técnicos y humanos necesarios, el sistema de seguimiento del aprendizaje, las vías de comunicación, el sistema y criterios de evaluación. Una vez contextualizada, se puede proceder al diseño de la actividad y de la documentación y a su presentación on line, adoptando decisiones y elaborando materiales sobre las competencias a desarrollar, el objeto del trabajo, los criterios de evaluación, el cronograma, las reglas de estilo, los criterios de formación de los grupos, la metodología, las vías de comunicación, y el diseño y formalización del espacio de trabajo en el campus virtual. Por último, es necesario alertar sobre diversos problemas que pueden aparecer durante la elaboración del trabajo en grupo mediante una wiki, tanto de carácter tecnológico como sociológicos.

  3. WEBQUEST Y WIKIS: BÚSQUEDA DE INFORMACIÓN EN RED Y DESARROLLO DE COMPETENCIAS EN COLABORACIÓN

    Directory of Open Access Journals (Sweden)

    Lourdes Villalustre Martínez

    2011-04-01

    Full Text Available En la formación universitaria se está apostando por estrategias y recursos didácticos, -que aprovechan las potencialidades de diferentes instrumentos digitales-, como las Webquests en tanto metodologías de investigación colaborativa apoyada en la búsqueda de información y en la utilización de contenidos alojados en Internet para la realización de proyectos. Los cuales pueden articularse a partir de herramientas 2.0 como las wikis, por su gran versatilidad y capacidad para generar conocimiento de forma colaborativa mediante la creación de contenidos on-line.   En la asignatura virtual de Educación en el ámbito rural1 se ha diseñado una actividad formativa en colaboración basada en la filosofía de las webquests y apoyada en el uso de las wikis, - configurando lo que se denominó Gameproject- Del Moral; Villalustre (2007b, que promueve el acceso y gestión de la información para elaborar un proyecto de intervención socio-educativo. Tras su implementación en varios años, se preguntó a 161 estudiantes sobre las competencias que consideraban haber desarrollado y/o consolidado con el trabajo colaborativo planteado. Éstos destacaron mayoritariamente las habilidades para la investigación, la recogida y tratamiento de la información, y otras más específicas vinculadas al futuro desempeño de su actividad profesional. Hay que destacar que los estudiantes sin experiencia previa en cursos de formación virtual consideraron haber consolidado más las competencias vinculadas al uso de herramientas informáticas.

  4. La investigación del discurso escrito en el aprendizaje de idiomas en entornos colaborativos y wikis

    Directory of Open Access Journals (Sweden)

    María Belén Díez-Bedmar

    2010-01-01

    Full Text Available Es bien sabido que el uso de las nuevas tecnologías ha sido instrumental en la promoción del conocimiento digital y del aprendizaje colaborativo del lenguaje. Sin embargo, Bax (2003 ha visto en la comunicación asistida por ordenador un gran potencial en las etapas abierta y de normalización. Aunque un número importante de investigaciones en los últimos años se han dedicado a la comunicación asíncrona por medio de web 1.0, los esfuerzos realizados en la actualidad han comenzado a analizar el uso de herramientas de video síncronas (Jáuregui y Bañados, 2008, blogs (Murray y Hourigan, 2008 y wikis (Lund, 2008. En este artículo presentamos una experiencia colaborativa en línea entre dos Instituciones de Educación Superior en Inglaterra y España (curso académico 2008/2009. Dicha experiencia ofreció a los alumnos la oportunidad de desarrollar su destreza escritora por medio de una serie de actividades de naturaleza digital en las que el wiki estaba integrado de forma natural. Los alumnos ingleses y españoles se embarcaron en la redacción de un folleto turístico de un monumento relevante desde el punto de vista histórico/artístico del otro país de forma colaborativa, ayudando al compañero en la redacción de su folleto y siendo ayudado de la misma manera.

  5. Who possesses drug resistance genes in the aquatic environment?: sulfamethoxazole (SMX) resistance genes among the bacterial community in water environment of Metro-Manila, Philippines.

    Science.gov (United States)

    Suzuki, Satoru; Ogo, Mitsuko; Miller, Todd W; Shimizu, Akiko; Takada, Hideshige; Siringan, Maria Auxilia T

    2013-01-01

    Recent evidence has shown that antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) are ubiquitous in natural environments, including sites considered pristine. To understand the origin of ARGs and their dynamics, we must first define their actual presence in the natural bacterial assemblage. Here we found varying distribution profiles of sul genes in "colony forming bacterial assemblages" and "natural bacterial assemblages." Our monitoring for antibiotic contamination revealed that sulfamethoxazole (SMX) is a major contaminant in aquatic environments of Metro-Manila, which would have been derived from human and animal use, and subsequently decreased through the process of outflow from source to the sea. The SMX-resistant bacterial rate evaluated by the colony forming unit showed 10 to 86% of the total colony numbers showed higher rates from freshwater sites compared to marine sites. When sul genes were quantified by qPCR, colony-forming bacteria conveyed sul1 and sul2 genes in freshwater and seawater (10(-5)-10(-2) copy/16S) but not sul3. Among the natural bacterial assemblage, all sul1, sul2, and sul3 were detected (10(-5)-10(-3) copy/16S), whereas all sul genes were at an almost non-detectable level in the freshwater assemblage. This study suggests that sul1 and sul2 are main sul genes in culturable bacteria, whereas sul3 is conveyed by non-culturable bacteria in the sea. As a result marine bacteria possess sul1, sul2 and sul3 genes in the marine environment.

  6. Who Possesses Drug Resistance Genes in the Aquatic Environment? : Sulfamethoxazole (SMX Resistance Genes among the Bacterial Community in Water Environment of Metro-Manila, Philippines

    Directory of Open Access Journals (Sweden)

    Satoru eSuzuki

    2013-04-01

    Full Text Available Recent evidence has shown that antibiotic resistant bacteria (ARB and antibiotic resistance genes (ARG are ubiquitous in natural environments, including sites considered pristine. To understand the origin of ARGs and their dynamics, we must first define their actual presence in the natural bacterial assemblage. Here we found varying distribution profiles of sul genes in colony forming bacterial assemblages and natural bacterial assemblages. Our monitoring for antibiotic contamination revealed that sulfamethoxazole (SMX is a major contaminant in aquatic environments of Metro-Manila, which would have been derived from human and animal use, and subsequently decreased through the process of outflow from source to the sea. The SMX-resistant bacterial rate evaluated by the colony forming unit showed 10 to 86 % of the total colony numbers showed higher rates from freshwater sites compared to marine sites. When sul genes were quantified by qPCR, colony-forming bacteria conveyed sul1 and sul2 genes in freshwater and seawater (10-5-10-2 copy/16S but not sul3. Among the natural bacterial assemblage, all sul1, sul2 and sul3 were detected (10-5-10-3 copy/16S, whereas all sul genes were at an almost non-detectable level in the freshwater assemblage. This study suggests that sul1 and sul2 are main sul genes in culturable bacteria, whereas sul3 is conveyed by non-culturable bacteria in the sea. As a result marine bacteria possess sul1, sul2 and sul3 genes in the marine environment.

  7. Community analysis of chronic wound bacteria using 16S rRNA gene-based pyrosequencing: impact of diabetes and antibiotics on chronic wound microbiota.

    Directory of Open Access Journals (Sweden)

    Lance B Price

    Full Text Available BACKGROUND: Bacterial colonization is hypothesized to play a pathogenic role in the non-healing state of chronic wounds. We characterized wound bacteria from a cohort of chronic wound patients using a 16S rRNA gene-based pyrosequencing approach and assessed the impact of diabetes and antibiotics on chronic wound microbiota. METHODOLOGY/PRINCIPAL FINDINGS: We prospectively enrolled 24 patients at a referral wound center in Baltimore, MD; sampled patients' wounds by curette; cultured samples under aerobic and anaerobic conditions; and pyrosequenced the 16S rRNA V3 hypervariable region. The 16S rRNA gene-based analyses revealed an average of 10 different bacterial families in wounds--approximately 4 times more than estimated by culture-based analyses. Fastidious anaerobic bacteria belonging to the Clostridiales family XI were among the most prevalent bacteria identified exclusively by 16S rRNA gene-based analyses. Community-scale analyses showed that wound microbiota from antibiotic treated patients were significantly different from untreated patients (p = 0.007 and were characterized by increased Pseudomonadaceae abundance. These analyses also revealed that antibiotic use was associated with decreased Streptococcaceae among diabetics and that Streptococcaceae was more abundant among diabetics as compared to non-diabetics. CONCLUSIONS/SIGNIFICANCE: The 16S rRNA gene-based analyses revealed complex bacterial communities including anaerobic bacteria that may play causative roles in the non-healing state of some chronic wounds. Our data suggest that antimicrobial therapy alters community structure--reducing some bacteria while selecting for others.

  8. Towards Distributed Citizen Participation: Lessons from WikiLeaks and the Queensland Floods

    Directory of Open Access Journals (Sweden)

    Axel Bruns

    2012-12-01

    Full Text Available This paper examines the rapid and ad hoc development and interactions of participative citizen communities during acute events, using the examples of the 2011 floods in Queensland, Australia, and the global controversy surrounding Wikileaks and its spokesman, Julian Assange. The self-organising community responses to such events which can be observed in these cases bypass or leapfrog, at least temporarily, most organisational or administrative hurdles which may otherwise frustrate the establishment of online communities; they fast-track the processes of community development and structuration. By understanding them as a form of rapid prototyping, e-democracy initiatives can draw important lessons from observing the community activities around such acute events.

  9. An assessment of the hypervariable domains of the 16S rRNA genes for their value in determining microbial community diversity: the paradox of traditional ecological indices.

    Science.gov (United States)

    Mills, DeEtta K; Entry, James A; Voss, Joshua D; Gillevet, Patrick M; Mathee, Kalai

    2006-09-01

    Amplicon length heterogeneity PCR (LH-PCR) was investigated for its ability to distinguish between microbial community patterns from the same soil type under different land management practices. Natural sagebrush and irrigated mouldboard-ploughed soils from Idaho were queried as to which hypervariable domains, or combinations of 16S rRNA gene domains, were the best molecular markers. Using standard ecological indices to measure richness, diversity and evenness, the combination of three domains, V1, V3 and V1+V2, or the combined V1 and V3 domains were the markers that could best distinguish the undisturbed natural sagebrush communities from the mouldboard-ploughed microbial communities. Bray-Curtis similarity and multidimensional scaling were found to be better metrics to ordinate and cluster the LH-PCR community profiling data. The use/misuse of traditional ecological indices such as diversity and evenness to study microbial community profiles will remain a major point to consider when performing metagenomic studies.

  10. PCR detection of oxytetracycline resistance genes from diverse habitats in total community DNA and in streptomycete isolates.

    NARCIS (Netherlands)

    Nikolakopoulou, T.L.; Egan, S.; Overbeek, van L.S.; Guillaume, G.; Heuer, H.; Wellington, E.M.H.; Elsas, van J.D.; Collard, J.M.; Smalla, K.; Karagouni, A.D.

    2005-01-01

    A range of European habitats was screened by PCR for detection of the oxytetracycline resistance genes otr(A) and otr(B), found in the oxytetracycline-producing strain Streptomyces rimosus. Primers were developed to detect these otr genes in tetracycline-resistant (TcR) streptomycete isolates from

  11. The Songbird Neurogenomics (SoNG Initiative: Community-based tools and strategies for study of brain gene function and evolution

    Directory of Open Access Journals (Sweden)

    Lewin Harris A

    2008-03-01

    Full Text Available Abstract Background Songbirds hold great promise for biomedical, environmental and evolutionary research. A complete draft sequence of the zebra finch genome is imminent, yet a need remains for application of genomic resources within a research community traditionally focused on ethology and neurobiological methods. In response, we developed a core set of genomic tools and a novel collaborative strategy to probe gene expression in diverse songbird species and natural contexts. Results We end-sequenced cDNAs from zebra finch brain and incorporated additional sequences from community sources into a database of 86,784 high quality reads. These assembled into 31,658 non-redundant contigs and singletons, which we annotated via BLAST search of chicken and human databases. The results are publicly available in the ESTIMA:Songbird database. We produced a spotted cDNA microarray with 20,160 addresses representing 17,214 non-redundant products of an estimated 11,500–15,000 genes, validating it by analysis of immediate-early gene (zenk gene activation following song exposure and by demonstrating effective cross hybridization to genomic DNAs of other songbird species in the Passerida Parvorder. Our assembly was also used in the design of the "Lund-zfa" Affymetrix array representing ~22,000 non-redundant sequences. When the two arrays were hybridized to cDNAs from the same set of male and female zebra finch brain samples, both arrays detected a common set of regulated transcripts with a Pearson correlation coefficient of 0.895. To stimulate use of these resources by the songbird research community and to maintain consistent technical standards, we devised a "Community Collaboration" mechanism whereby individual birdsong researchers develop experiments and provide tissues, but a single individual in the community is responsible for all RNA extractions, labelling and microarray hybridizations. Conclusion Immediately, these results set the foundation for a

  12. Effect of red mud addition on tetracycline and copper resistance genes and microbial community during the full scale swine manure composting.

    Science.gov (United States)

    Wang, Rui; Zhang, Junya; Sui, Qianwen; Wan, Hefeng; Tong, Juan; Chen, Meixue; Wei, Yuansong; Wei, Dongbin

    2016-09-01

    Swine manure has been considered as the reservoir of antibiotic resistance genes (ARGs). Composting is one of the most suitable technologies for treating livestock manures, and red mud was proved to have a positive effect on nitrogen conservation during composting. This study investigated the abundance of eight tetracycline and three copper resistance genes, the bacterial community during the full scale swine manure composting with or without addition of red mud. The results showed that ARGs in swine manure could be effectively removed through composting (reduced by 2.4log copies/g TS), especially during the thermophilic phase (reduced by 1.5log copies/g TS), which the main contributor might be temperature. Additionally, evolution of bacterial community could also have a great influence on ARGs. Although addition of red mud could enhance nitrogen conservation, it obviously hindered removal of ARGs (reduced by 1.7log copies/g TS) and affected shaping of bacterial community during composting. Copyright © 2016 Elsevier Ltd. All rights reserved.

  13. Effects of graphene oxide on the performance, microbial community dynamics and antibiotic resistance genes reduction during anaerobic digestion of swine manure.

    Science.gov (United States)

    Zhang, Junya; Wang, Ziyue; Wang, Yawei; Zhong, Hui; Sui, Qianwen; Zhang, Changping; Wei, Yuansong

    2017-12-01

    The role of graphene oxide (GO) on anaerobic digestion (AD) of swine manure concerning the performance, microbial community and antibiotic resistance genes (ARGs) reduction was investigated. Results showed that methane production was reduced by 13.1%, 10.6%, 2.7% and 17.1% at GO concentration of 5mg/L, 50mg/L, 100mg/L and 500mg/L, respectively, but propionate degradation was enhanced along with GO addition. Both bacterial and archaeal community changed little after GO addition. AD could well reduce ARGs abundance, but it was deteriorated at the GO concentration of 50mg/L and 100mg/L and enhanced at 500mg/L, while no obvious changes at 5mg/L. Network and SEM analysis indicated that changes of each ARG was closely associated with variation of microbial community composition, environmental variables contributed most to the dynamics of ARGs indirectly, GO influenced the ARGs dynamics negatively and (heavy metal resistance genes (MRGs)) influenced the most directly. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. High Levels of Antibiotic Resistance Genes and Their Correlations with Bacterial Community and Mobile Genetic Elements in Pharmaceutical Wastewater Treatment Bioreactors.

    Directory of Open Access Journals (Sweden)

    Wenda Tao

    Full Text Available To understand the diversity and abundance of antibiotic resistance genes (ARGs in pharmaceutical wastewater treatment bioreactors, the ARGs in sludge from two full-scale pharmaceutical wastewater treatment plants (PWWTPs were investigated and compared with sludge samples from three sewage treatment plants (STPs using metagenomic approach. The results showed that the ARG abundances in PWWTP sludge ranged from 54.7 to 585.0 ppm, which were higher than those in STP sludge (27.2 to 86.4 ppm. Moreover, the diversity of ARGs in PWWTP aerobic sludge (153 subtypes was higher than that in STP aerobic sludge (118 subtypes. In addition, it was found that the profiles of ARGs in PWWTP aerobic sludge were similar to those in STP aerobic sludge but different from those in PWWTP anaerobic sludge, suggesting that dissolve oxygen (DO could be one of the important factors affecting the profiles of ARGs. In PWWTP aerobic sludge, aminoglycoside, sulfonamide and multidrug resistance genes were frequently detected. While, tetracycline, macrolide-lincosamide-streptogramin and polypeptide resistance genes were abundantly present in PWWTP anaerobic sludge. Furthermore, we investigated the microbial community and the correlation between microbial community and ARGs in PWWTP sludge. And, significant correlations between ARG types and seven bacterial genera were found. In addition, the mobile genetic elements (MGEs were also examined and correlations between the ARGs and MGEs in PWWTP sludge were observed. Collectively, our results suggested that the microbial community and MGEs, which could be affected by DO, might be the main factors shaping the profiles of ARGs in PWWTP sludge.

  15. El diseño de una Wiki sobre ecoturismo como herramienta para el aprendizaje universitario de turismo en entorno virtual

    Directory of Open Access Journals (Sweden)

    Francesc González Reverté

    2010-01-01

    Full Text Available La experiencia consiste en la creación de una wiki sobre Ecoturismo organizada en torno al trabajo colectivo como objeto de aprendizaje de la evaluación continua para la asignatura de (Ecoturismo. Tiene dos objetivos de innovación: 1 el desarrollo de metodologías docentes aptas para el trabajo colaborativo, y 2 habituar al uso de las herramientas del web 2.0 a estudiantes y a docentes. Las principales aportaciones del proyecto han sido el diseño de una metodología novedosa de trabajo en equipo en entorno de aprendizaje virtual; y la integración de las entradas de la wiki como recurso docente. Las encuestas de satisfacción realizadas entre los estudiantes muestran la excelente acogida del proyecto. Los principales problemas detectados tienen que ver con las dificultades técnicas en la implementación de la wiki así como el exceso de carga docente que ha supuesto.

  16. Antimicrobial susceptibility, risk factors and prevalence of bla cefotaximase, temoneira, and sulfhydryl variable genes among Escherichia coli in community-acquired pediatric urinary tract infection.

    Science.gov (United States)

    Nisha, Kallyadan V; Veena, Shetty A; Rathika, Shenoy D; Vijaya, Shenoy M; Avinash, Shetty K

    2017-01-01

    The emergence of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli has become an important challenge among pediatric patients with community-acquired urinary tract infection (UTI). The aim of this study was to assess the antimicrobial susceptibility patterns, associated risk factors and to survey the frequency of bla cefotaximase (CTX-M), bla temoneira (TEM), and bla sulfhydryl variable (SHV) genotypes in ESBL-producing E. coli isolated from children with community-acquired UTI. This was a prospective study conducted from November 2012 to March 2016 in a tertiary care center. E. coli isolated in urine cultures from children aged ≤18 years was identified and confirmed for ESBL production. ESBL-positive strains were screened for ESBL encoding genes. Chi-square test and Fisher's exact test were used to compare the difference in antibiotic susceptibility with respect to ESBL positive and negative, and binary logistic regression was used to identify the risk factors associated with ESBL production. Among 523 E. coli isolates, 196 (37.5%) were ESBL positive, >90% were resistant to cephalosporins, and 56% were resistant to fluoroquinolones. Least resistance was observed for imipenem, netilmicin, and nitrofurantoin (2%, 8.6%, 15.3%). Association between ESBL production and drug resistance was significant for ceftazidime ( P antibiotics were the common risk factors. ESBL-producing E. coli from community-acquired pediatric UTI carries more than one type of beta-lactamase coding genes correlating their increased antibiotic resistance. Aggressive infection control policy, routine screening for detecting ESBL isolates in clinical samples, and antimicrobial stewardship are the keys to prevent their dissemination in community settings.

  17. Bacterial community structure in High-Arctic snow and freshwater as revealed by pyrosequencing of 16S rRNA genes and cultivation

    Directory of Open Access Journals (Sweden)

    Annette K. Møller

    2013-04-01

    Full Text Available The bacterial community structures in High-Arctic snow over sea ice and an ice-covered freshwater lake were examined by pyrosequencing of 16S rRNA genes and 16S rRNA gene sequencing of cultivated isolates. Both the pyrosequence and cultivation data indicated that the phylogenetic composition of the microbial assemblages was different within the snow layers and between snow and freshwater. The highest diversity was seen in snow. In the middle and top snow layers, Proteobacteria, Bacteroidetes and Cyanobacteria dominated, although Actinobacteria and Firmicutes were relatively abundant also. High numbers of chloroplasts were also observed. In the deepest snow layer, large percentages of Firmicutes and Fusobacteria were seen. In freshwater, Bacteroidetes, Actinobacteria and Verrucomicrobia were the most abundant phyla while relatively few Proteobacteria and Cyanobacteria were present. Possibly, light intensity controlled the distribution of the Cyanobacteria and algae in the snow while carbon and nitrogen fixed by these autotrophs in turn fed the heterotrophic bacteria. In the lake, a probable lower light input relative to snow resulted in low numbers of Cyanobacteria and chloroplasts and, hence, limited input of organic carbon and nitrogen to the heterotrophic bacteria. Thus, differences in the physicochemical conditions may play an important role in the processes leading to distinctive bacterial community structures in High-Arctic snow and freshwater.

  18. Operating conditions influence microbial community structures, elimination of the antibiotic resistance genes and metabolites during anaerobic digestion of cow manure in the presence of oxytetracycline.

    Science.gov (United States)

    Turker, Gokhan; Akyol, Çağrı; Ince, Orhan; Aydin, Sevcan; Ince, Bahar

    2018-01-01

    The way that antibiotic residues in manure follow is one of the greatest concerns due to its potential negative impacts on microbial communities, the release of metabolites and antibiotic resistant genes (ARGs) into the nature and the loss of energy recovery in anaerobic digestion (AD) systems. This study evaluated the link between different operating conditions, the biodegradation of oxytetracycline (OTC) and the formation of its metabolites and ARGs in anaerobic digesters treating cow manure. Microbial communities and ARGs were determined through the use of quantitative real-time PCR. The biodegradation of OTC and occurrence of metabolites were determined using UV-HPLC and LC/MS/MS respectively. The maximum quantity of resistance genes was also examined at the beginning of AD tests and concentration was in the order of: tetM >tetO. The numbers of ARGs were always higher at high volatile solids (VS) content and high mixing rate. The results of the investigation revealed that relationship between mixing rate and VS content plays a crucial role for elimination of ARGs, OTC and metabolites. This can be attributed to high abundance of microorganisms due to high VS content and their increased contact with elevated mixing rate. An increased interaction between microorganisms triggers the promotion of ARGs. Copyright © 2017 Elsevier Inc. All rights reserved.

  19. Culture-Independent Identification of Manganese-Oxidizing Genes from Deep-Sea Hydrothermal Vent Chemoautotrophic Ferromanganese Microbial Communities Using a Metagenomic Approach

    Science.gov (United States)

    Davis, R.; Tebo, B. M.

    2013-12-01

    Microbial activity has long been recognized as being important to the fate of manganese (Mn) in hydrothermal systems, yet we know very little about the organisms that catalyze Mn oxidation, the mechanisms by which Mn is oxidized or the physiological function that Mn oxidation serves in these hydrothermal systems. Hydrothermal vents with thick ferromanganese microbial mats and Mn oxide-coated rocks observed throughout the Pacific Ring of Fire are ideal models to study the mechanisms of microbial Mn oxidation, as well as primary productivity in these metal-cycling ecosystems. We sampled ferromanganese microbial mats from Vai Lili Vent Field (Tmax=43°C) located on the Eastern Lau Spreading Center and Mn oxide-encrusted rhyolytic pumice (4°C) from Niua South Seamount on the Tonga Volcanic Arc. Metagenomic libraries were constructed and assembled from these samples and key genes known to be involved in Mn oxidation and carbon fixation pathways were identified in the reconstructed genomes. The Vai Lili metagenome assembled to form 121,157 contiguous sequences (contigs) greater than 1000bp in length, with an N50 of 8,261bp and a total metagenome size of 593 Mbp. Contigs were binned using an emergent self-organizing map of tetranucleotide frequencies. Putative homologs of the multicopper Mn-oxidase MnxG were found in the metagenome that were related to both the Pseudomonas-like and Bacillus-like forms of the enzyme. The bins containing the Pseudomonas-like mnxG genes are most closely related to uncultured Deltaproteobacteria and Chloroflexi. The Deltaproteobacteria bin appears to be an obligate anaerobe with possible chemoautotrophic metabolisms, while the Chloroflexi appears to be a heterotrophic organism. The metagenome from the Mn-stained pumice was assembled into 122,092 contigs greater than 1000bp in length with an N50 of 7635 and a metagenome size of 385 Mbp. Both forms of mnxG genes are present in this metagenome as well as the genes encoding the putative Mn

  20. The Variability of the 16S rRNA Gene in Bacterial Genomes and Its Consequences for Bacterial Community Analyses

    Czech Academy of Sciences Publication Activity Database

    Větrovský, Tomáš; Baldrian, Petr

    2013-01-01

    Roč. 8, č. 2 (2013) E-ISSN 1932-6203 R&D Projects: GA MŠk LD12048; GA MŠk LD12050 Institutional support: RVO:61388971 Keywords : OPERON COPY NUMBER * MICROBIAL COMMUNITIES * MOLECULAR MARKERS Subject RIV: EE - Microbiology, Virology Impact factor: 3.534, year: 2013

  1. Bacterial communities in chitin-amended soil as revealed by 16S rRNA gene based pyrosequencing

    NARCIS (Netherlands)

    Cretoiu, M.S.; Kielak, A.M.; Schluter, A.; van Elsas, J.D.

    2014-01-01

    Chitin and its derivatives are natural biopolymers that are often used as compounds for the control of soil-borne plant pathogens. In spite of recent advances in agricultural practices involving chitin amendments, the microbial communities in chitin-amended soils remain poorly known. The objectives

  2. Bacterial communities in chitin-amended soil as revealed by 16S rRNA gene based pyrosequencing

    NARCIS (Netherlands)

    Cretoiu, Mariana Silvia; Kielak, Anna Maria; Schluter, Andreas; van Elsas, Jan Dirk

    Chitin and its derivatives are natural biopolymers that are often used as compounds for the control of soilborne plant pathogens. In spite of recent advances in agricultural practices involving chitin amendments, the microbial communities in chitin-amended soils remain poorly known. The objectives

  3. Wiki, tekster og arbeidsmåter i morgendagens engelskfag: et eksempel fra lærerutdanninga

    Directory of Open Access Journals (Sweden)

    Hilde Brox

    2014-09-01

    Full Text Available Artikkelen diskuterer hvordan wiki kan brukes i engelskundervisning for å la nye og tradisjonelle tekster møtes i digital dialogisk interaksjon. Med utgangpunkt i begrepene multimodalitet, hypertekstualitet og prosessualitet, tre egenskaper som i følge Ture Schwebs (2006 skiller digitale tekster fra analoge, diskuterer artikkelen et eksempel fra et undervisningopplegg for lærerstudenter. Basert på et bilde skapte studentene et felles nettsted og en kollektiv, fiktiv, men realistisk historie. Historien dannet så i neste omgang en ramme for produksjon av tekster i ulike modaliteter og sjangre. Bildet etablerte en bestemt historisk og kulturell kontekst som studentene aktivt måtte utforske for å skape sine tekster. Wikiens funksjonaliteter åpnet opp for samskriving, utvikling av ferdigheter for å tolke og skape tekster med sammensatte modaliteter, utnyttelse av hypertekstens struktur og samarbeid om tekstskaping som prosess på tvers av tid og rom. Dette er kunnskaper og ferdigheter framtidige lærere vil trenge.

  4. Students’ perceptions about the use of wiki. analysis of an experience of collaborative learning at the University of Girona

    Directory of Open Access Journals (Sweden)

    Albert Ruda González

    2013-02-01

    Full Text Available 0 0 1 47 260 USAL 2 1 306 14.0 Normal 0 21 false false false ES JA X-NONE /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Tabla normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin-top:0cm; mso-para-margin-right:0cm; mso-para-margin-bottom:10.0pt; mso-para-margin-left:0cm; line-height:115%; mso-pagination:widow-orphan; font-size:11.0pt; font-family:Calibri; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-ansi-language:ES; mso-fareast-language:EN-US;} This paper focuses on frustration experienced by law students as a result of using wikis to carry out a group investigation assignment at an on-site university. The reasons which may have contributed to such a negative response by the students are explored and some proposals for improvement are presented.

  5. Challenges to Freedom of Expression in the Digital World: Lessons from WikiLeaks and the Arab Spring

    Directory of Open Access Journals (Sweden)

    Arne HINTZ

    2012-01-01

    Full Text Available Two recent developments – the WikiLeaks releases and the Arab Spring – have demonstrated the capacities of individuals and movements in advancing free expression, transparency and social change through the use of online and social media. However they have also highlighted new sets of challenges and threats that interfere with, and restrict, such media uses. In this article I will present an analytical framework for understanding and investigating these contemporary restrictions to freedom of expression, based on the dimensions of information control, access to infrastructure, critical resources and applications, surveillance, and physical repression. The model takes into account current trends such as the use of intermediaries in control regimes, and provides a global perspective that incorporates restrictions in both East and West. Further, I will outline how free expression advocates and civil society campaigns, such as the Icelandic Modern Media Initiative (IMMI, have contested these practices, and discuss whether their agendas confirm the issue areas highlighted above. The restrictions to, and the advocacy for, free online communication demonstrate some of the key struggles and contestations on freedom of expression in the current digital media environment, the strategic points of intervention by different actors (states, businesses, and civil society, and the requirements for “modern freedom of expression”.

  6. Effects of gene-augmentation on the formation, characteristics and microbial community of 2,4-dichlorophenoxyacetic acid degrading aerobic microbial granules

    International Nuclear Information System (INIS)

    Quan, Xiang-chun; Ma, Jing-yun; Xiong, Wei-cong; Yang, Zhi-feng

    2011-01-01

    Highlights: ► The first study to cultivate aerobic granules capable of utilizing 2,4-D as the sole carbon source. ► Granules cultivated through gene-augmentation were first compared systematically with the control on granule formation, degradation kinetics, morphology, and microbial community. ► The first report on the fate of transconjugats in the granules during long term operation after bioaugmentation. ► The first study to isolate in dominant bacteria in 2,4-D degrading microbial granules. - Abstract: Development of 2,4-dichlorophenoxyacetic acid (2,4-D) degrading aerobic granular sludge was conducted in two sequencing batch reactors (SBR) with one bioaugmented with a plasmid pJP4 donor strain Pseudomonas putida SM1443 and the other as a control. Half-matured aerobic granules pre-grown on glucose were used as the starting seeds and a two-stage operation strategy was applied. Granules capable of utilizing 2,4-D (about 500 mg/L) as the sole carbon source was successfully cultivated in both reactors. Gene-augmentation resulted in the enhancement of 2,4-D degradation rates by the percentage of 65–135% for the granules on Day 18, and 6–24% for the granules on Day 105. Transconjugants receiving plasmid pJP4 were established in the granule microbial community after bioaugmentation and persisted till the end of operation. Compared with the control granules, the granules in the bioaugmented reactor demonstrated a better settling ability, larger size, more abundant microbial diversity and stronger tolerance to 2,4-D. The finally obtained granules in the bioaugmented and control reactor had a granule size of around 600 μm and 500 μm, a Shannon–Weaver diversity index (H) of 0.96 and 0.55, respectively. A shift in microbial community was found during the granulation process.

  7. Influence of heterogeneous ammonium availability on bacterial community structure and the expression of nitrogen fixation and ammonium transporter genes during in situ bioremediation of uranium-contaminated groundwater

    Energy Technology Data Exchange (ETDEWEB)

    Mouser, P.J.; N' Guessan, A.L.; Elifantz, H.; Holmes, D.E.; Williams, K.H.; Wilkins, M.J.; Long, P.E.; Lovley, D.R.

    2009-04-01

    The impact of ammonium availability on microbial community structure and the physiological status and activity of Geobacter species during in situ bioremediation of uranium-contaminated groundwater was evaluated. Ammonium concentrations varied by as much as two orders of magnitude (<4 to 400 {micro}M) across the study site. Analysis of 16S rRNA gene sequences suggested that ammonium influenced the composition of the microbial community prior to acetate addition with Rhodoferax species predominating over Geobacter species at the site with the highest ammonium, and Dechloromonas species dominating at sites with lowest ammonium. However, once acetate was added, and dissimilatory metal reduction was stimulated, Geobacter species became the predominant organisms at all locations. Rates of U(VI) reduction appeared to be more related to the concentration of acetate that was delivered to each location rather than the amount of ammonium available in the groundwater. In situ mRNA transcript abundance of the nitrogen fixation gene, nifD, and the ammonium importer gene, amtB, in Geobacter species indicated that ammonium was the primary source of nitrogen during in situ uranium reduction, and that the abundance of amtB transcripts was inversely correlated to ammonium levels across all sites examined. These results suggest that nifD and amtB expression by subsurface Geobacter species are closely regulated in response to ammonium availability to ensure an adequate supply of nitrogen while conserving cell resources. Thus, quantifying nifD and amtB expression appears to be a useful approach for monitoring the nitrogen-related physiological status of Geobacter species in subsurface environments during bioremediation. This study also emphasizes the need for more detailed analysis of geochemical/physiological interactions at the field scale, in order to adequately model subsurface microbial processes.

  8. Bacterial community composition in the gut content and ambient sediment of sea cucumber Apostichopus japonicus revealed by 16S rRNA gene pyrosequencing.

    Directory of Open Access Journals (Sweden)

    Fei Gao

    Full Text Available The composition of the bacterial communities in the contents of the foregut and hindgut of the sea cucumber Apostichopus japonicus and in the ambient surface sediment was surveyed by 16S rRNA gene 454-pyrosequencing. A total of 188,623 optimized reads and 15,527 operational taxonomic units (OTUs were obtained from the ten gut contents samples and four surface sediment samples. The sequences in the sediments, foregut contents, and hindgut contents were assigned to 38.0±4.7, 31.2±6.2 and 27.8±6.5 phyla, respectively. The bacterial richness and Shannon diversity index were both higher in the ambient sediments than in the gut contents. Proteobacteria was the predominant phylum in both the gut contents and sediment samples. The predominant classes in the foregut, hindgut, and ambient sediment were Holophagae and Gammaproteobacteria, Deltaproteobacteria and Gammaproteobacteria, and Gammaproteobacteria and Deltaproteobacteria, respectively. The potential probiotics, including sequences related to Bacillus, lactic acid bacteria (Lactobacillus, Lactococcus, and Streptococcus and Pseudomonas were detected in the gut of A. japonicus. Principle component analysis and heatmap figure showed that the foregut, hindgut, and ambient sediment respectively harbored different characteristic bacterial communities. Selective feeding of A. japonicus may be the primary source of the different bacterial communities between the foregut contents and ambient sediments.

  9. A ribosomal RNA gene intergenic spacer based PCR and DGGE fingerprinting method for the analysis of specific rhizobial communities in soil.

    Science.gov (United States)

    de Oliveira, Valéria Maia; Manfio, Gilson Paulo; da Costa Coutinho, Heitor Luiz; Keijzer-Wolters, Anneke Christina; van Elsas, Jan Dirk

    2006-03-01

    A direct molecular method for assessing the diversity of specific populations of rhizobia in soil, based on nested PCR amplification of 16S-23S ribosomal RNA gene (rDNA) intergenic spacer (IGS) sequences, was developed. Initial generic amplification of bacterial rDNA IGS sequences from soil DNA was followed by specific amplification of (1) sequences affiliated with Rhizobium leguminosarum "sensu lato" and (2) R. tropici. Using analysis of the amplified sequences in clone libraries obtained on the basis of soil DNA, this two-sided method was shown to be very specific for rhizobial subpopulations in soil. It was then further validated as a direct fingerprinting tool of the target rhizobia based on denaturing gradient gel electrophoresis (DGGE). The PCR-DGGE approach was applied to soils from fields in Brazil cultivated with common bean (Phaseolus vulgaris) under conventional or no-tillage practices. The community fingerprints obtained allowed the direct analysis of the respective rhizobial community structures in soil samples from the two contrasting agricultural practices. Data obtained with both primer sets revealed clustering of the community structures of the target rhizobial types along treatment. Moreover, the DGGE profiles obtained with the R. tropici primer set indicated that the abundance and diversity of these organisms were favoured under NT practices. These results suggest that the R. leguminosarum-as well as R. tropici-targeted IGS-based nested PCR and DGGE are useful tools for monitoring the effect of agricultural practices on these and related rhizobial subpopulations in soils.

  10. Size Matters: Assessing Optimum Soil Sample Size for Fungal and Bacterial Community Structure Analyses Using High Throughput Sequencing of rRNA Gene Amplicons

    Directory of Open Access Journals (Sweden)

    Christopher Ryan Penton

    2016-06-01

    Full Text Available We examined the effect of different soil sample sizes obtained from an agricultural field, under a single cropping system uniform in soil properties and aboveground crop responses, on bacterial and fungal community structure and microbial diversity indices. DNA extracted from soil sample sizes of 0.25, 1, 5 and 10 g using MoBIO kits and from 10 and 100 g sizes using a bead-beating method (SARDI were used as templates for high-throughput sequencing of 16S and 28S rRNA gene amplicons for bacteria and fungi, respectively, on the Illumina MiSeq and Roche 454 platforms. Sample size significantly affected overall bacterial and fungal community structure, replicate dispersion and the number of operational taxonomic units (OTUs retrieved. Richness, evenness and diversity were also significantly affected. The largest diversity estimates were always associated with the 10 g MoBIO extractions with a corresponding reduction in replicate dispersion. For the fungal data, smaller MoBIO extractions identified more unclassified Eukaryota incertae sedis and unclassified glomeromycota while the SARDI method retrieved more abundant OTUs containing unclassified Pleosporales and the fungal genera Alternaria and Cercophora. Overall, these findings indicate that a 10 g soil DNA extraction is most suitable for both soil bacterial and fungal communities for retrieving optimal diversity while still capturing rarer taxa in concert with decreasing replicate variation.

  11. Distribution of virulence genes and genotyping of CTX-M-15-producing Klebsiella pneumoniae isolated from patients with community-acquired urinary tract infection (CA-UTI).

    Science.gov (United States)

    Ranjbar, Reza; Memariani, Hamed; Sorouri, Rahim; Memariani, Mojtaba

    2016-11-01

    Klebsiella pneumoniae is one of the most important agents of community-acquired urinary tract infection (CA-UTI). In addition to extended-spectrum β-lactamases (ESBLs), a number of virulence factors have been shown to play an important role in the pathogenesis of K. pneumoniae, including capsule, siderophores, and adhesins. Little is known about the genetic diversity and virulence content of the CTX-M-15-producing K. pneumoniae isolated from CA-UTI in Iran. A total of 152 K. pneumoniae isolates were collected from CA-UTI patients in Tehran from September 2015 through April 2016. Out of 152 isolates, 40 (26.3%) carried bla CTX-M-15 . PCR was performed for detection of virulence genes in CTX-M-15-producing isolates. Furthermore, all of these isolates were subjected to multiple-locus variable-number of tandem repeat (VNTR) analysis (MLVA). Using MLVA method, 36 types were identified. CTX-M-15-producing K. pneumoniae isolates were grouped into 5 clonal complexes (CCs). Of these isolates, mrkD was the most prevalent virulence gene (95%), followed by kpn (60%), rmpA (37.5%), irp (35%), and magA (2.5%). No correlation between MLVA types or CCs and virulence genes or antibiotic resistance patterns was observed. Overall, it is thought that CTX-M-15-producing K. pneumoniae strains isolated from CA-UTI have arisen from different clones. Copyright © 2016 Elsevier Ltd. All rights reserved.

  12. Metagenomic Analyses Reveal That Energy Transfer Gene Abundances Can Predict the Syntrophic Potential of Environmental Microbial Communities

    Directory of Open Access Journals (Sweden)

    Lisa Oberding

    2016-01-01

    Full Text Available Hydrocarbon compounds can be biodegraded by anaerobic microorganisms to form methane through an energetically interdependent metabolic process known as syntrophy. The microorganisms that perform this process as well as the energy transfer mechanisms involved are difficult to study and thus are still poorly understood, especially on an environmental scale. Here, metagenomic data was analyzed for specific clusters of orthologous groups (COGs related to key energy transfer genes thus far identified in syntrophic bacteria, and principal component analysis was used in order to determine whether potentially syntrophic environments could be distinguished using these syntroph related COGs as opposed to universally present COGs. We found that COGs related to hydrogenase and formate dehydrogenase genes were able to distinguish known syntrophic consortia and environments with the potential for syntrophy from non-syntrophic environments, indicating that these COGs could be used as a tool to identify syntrophic hydrocarbon biodegrading environments using metagenomic data.

  13. The rpb2 gene represents a viable alternative molecular marker for the analysis of environmental fungal communities

    Czech Academy of Sciences Publication Activity Database

    Větrovský, Tomáš; Kolařík, Miroslav; Žifčáková, Lucia; Zelenka, Tomáš; Baldrian, Petr

    2016-01-01

    Roč. 16, č. 2 (2016), s. 388-401 ISSN 1755-098X R&D Projects: GA ČR GA13-06763S; GA ČR GAP504/12/0709; GA MŠk LD12050 Institutional support: RVO:61388971 Keywords : community composition * diversity * fungi Subject RIV: EE - Microbiology, Virology Impact factor: 7.332, year: 2016

  14. Polynucleotide probes that target a hypervariable region of 16S rRNA genes to identify bacterial isolates corresponding to bands of community fingerprints.

    Science.gov (United States)

    Heuer, H; Hartung, K; Wieland, G; Kramer, I; Smalla, K

    1999-03-01

    Temperature gradient gel electrophoresis (TGGE) is well suited for fingerprinting bacterial communities by separating PCR-amplified fragments of 16S rRNA genes (16S ribosomal DNA [rDNA]). A strategy was developed and was generally applicable for linking 16S rDNA from community fingerprints to pure culture isolates from the same habitat. For this, digoxigenin-labeled polynucleotide probes were generated by PCR, using bands excised from TGGE community fingerprints as a template, and applied in hybridizations with dot blotted 16S rDNA amplified from bacterial isolates. Within 16S rDNA, the hypervariable V6 region, corresponding to positions 984 to 1047 (Escherichia coli 16S rDNA sequence), which is a subset of the region used for TGGE (positions 968 to 1401), best met the criteria of high phylogenetic variability, required for sufficient probe specificity, and closely flanking conserved priming sites for amplification. Removal of flanking conserved bases was necessary to enable the differentiation of closely related species. This was achieved by 5' exonuclease digestion, terminated by phosphorothioate bonds which were synthesized into the primers. The remaining complementary strand was removed by single-strand-specific digestion. Standard hybridization with truncated probes allowed differentiation of bacteria which differed by only two bases within the probe target site and 1.2% within the complete 16S rDNA. However, a truncated probe, derived from an excised TGGE band of a rhizosphere community, hybridized with three phylogenetically related isolates with identical V6 sequences. Only one of the isolates comigrated with the excised band in TGGE, which was shown to be due to identical sequences, demonstrating the utility of a combined TGGE and V6 probe approach.

  15. Barriers to prostate cancer prevention and community recommended health education strategies in an urban African American community in Jackson, Mississippi.

    Science.gov (United States)

    Ekúndayò, Olúgbémiga T; Tataw, David B

    2013-01-01

    This article describes the use of survey research in collaboration with the African American urban community of Georgetown, Jackson, Mississippi to identify and understand prostate cancer knowledge, resource utilization, and health education strategies considered most effective in reaching the community with prostate cancer prevention messages. The study revealed profound needs in disease identification and resources awareness and utilization. Barriers to utilization were identified by participants to include lack of self-efficacy, low self-esteem, lack of trust in the health care system, limited knowledge of prostate pathology, and limited ability to pay. Participants' recommended strategies for reaching the community with prostate cancer education include traditional and nontraditional strategies. The list of recommendations exclude modern-day outlets such as handheld devices, Twitter, Facebook, blogs, wikis, and other Internet-based outlets. The findings provide a road map for program development and an intervention research agenda custom-tailored to the Georgetown community of Jackson, Mississippi.

  16. La wiki-webquest: una actividad colaborativa en la asignatura de "Nuevas Tecnologías Aplicadas a la Educación"

    Directory of Open Access Journals (Sweden)

    Roberto Santos Fernández

    2010-01-01

    Full Text Available Las instituciones de educación superior están sufriendo un proceso de reconversión buscando su adaptación a las características del Espacio Europeo de Educación Superior. Uno de los cambios más importantes, a los que debe hacer frente su profesorado, consiste en una reorganización metodológica diferente de sus clases. Por ello, es necesario pensar en nuevas fórmulas en la formación del profesorado. Como resultado de esta necesidad, decidimos organizar la asignatura de Nuevas Tecnologías Aplicadas a la Educación, de la Facultad de Educación de Valladolid, empleando una metodología activa, el IBL, apoyada en una plataforma Wiki, proponiendo a nuestro alumnado una serie de actividades que debían realizar colaborativamente. En este trabajo, presentamos una de esas actividades, la elaboración de una Wiki- WebQuest. A partir de la descripción de esta actividad, pretendemos mostrar algunas luces y sombras sobre su puesta en práctica (la versatilidad y flexibilidad de la plataforma, la posibilidad de colaboración entre la universidad y la escuela, la falta de adaptación de algunos contenidos al nivel curricular del curso concreto, la falta de asesoramiento del profesorado al alumnado de primaria sobre el uso de estas nuevas herramientas, etc. Esta actividad fue desarrollada a partir de la colaboración con contextos educativos reales (dos centros de primaria, sirviendo de caso de estudio para diseñar una Wiki-WebQuest. Asimismo, también colaboraron dos asignaturas de la titulación de Magisterio (Didáctica General y Metodología del Idioma Extranjero, con el objetivo de enriquecer el proceso de aprendizaje.

  17. Wiki Loves Monuments 2011: experiència a Espanya i reflexions des de la difusió del patrimoni cultural

    Directory of Open Access Journals (Sweden)

    Emilio José Rodríguez Posada

    2012-05-01

    Full Text Available La Wikipedia va néixer al ciberespai. Els seus primers anys es van caracteritzar per una feina distribuïda i asíncrona entre usuaris de tot el planeta, que amb prou feines tenien relació personal fora de la xarxa. Amb el pas del temps, alguns dels seus voluntaris van fer les anomenades wikitrobades, però al començament les reunions de wikimedistes tenien la finalitat d'estrènyer llaços i no comportaven cap millora directa dels continguts dels projectes. Més endavant van sorgir iniciatives presencials en les quals es van involucrar, a més de voluntaris, algunes entitats culturals; la més recent i que ha tingut més impacte és Wiki Loves Monuments 2011, un concurs destinat a fotografiar monuments de divuit països europeus, entre els quals hi ha Espanya. Gràcies a l'alta participació, s'han pres en conjunt més de 160.000 fotografies de monuments. Espanya ha ocupat el tercer lloc en nombre d'imatges. En aquest article estudiem els orígens de Wiki Loves Monuments, com es va posar en marxa, com es va desenvolupar i els resultats obtinguts. L'èxit de l'edició 2011 i les peticions d'altres països han fet que ja es treballi en l'organització de Wiki Loves Monuments 2012, aquesta vegada a escala mundial.

  18. The Effects of Wiki-based Recursive Process Writing on Chinese Narrative Essays for Chinese as a Second Language (CSL Students in Singapore

    Directory of Open Access Journals (Sweden)

    Chee Kuen Chin

    2015-01-01

    Full Text Available This paper reports on the effects of using wiki-based process writing in Singapore’s Chinese as a Second Language (CSL scenarios. A group of 32 Secondary 1 (Seventh Grade students (“Students” received various forms of online scaffolding at different steps of the writing process over two years. A whole set of teaching materials on 45 writing skills was developed and uploaded to the Wiki platform through five recursive cycles. In each cycle, the students were encouraged to apply skills they learned via Wiki platform in their writing and afterwards work as a team in the platform to peer-review each other’s first draft. With feedback received from peer revision, students proceeded to edit their first draft, focusing on the content of narratives and the appropriateness on their use of micro writing skills. The scaffolding decreased as the project progressed. Students’ pre-, mid- and post-writing tests were marked and compared. The authors analyzed the impact that the feedback in the process had towards the students’ overall writing performance. It was discovered that students' quality of written products was improved in general. It was also discovered that students benefited the most from giving remarks to their peers’ writing. The revision patterns of high, medium and low language ability students were also compared. It was found that the higher the language ability of the students, the more concerned they were with macro level for their revisions. ICT-mediated process writing has not garnered much attention in the field of CSL. The study hopes to contribute to the literature of ICTmediated writing instruction in the field of CSL.

  19. Physics collaboration and communication through emerging media: *odcasts, blogs and wikis

    Science.gov (United States)

    Clark, Charles W.; Williams, Jamie

    2006-05-01

    The entertainment and news industries are being transformed by the emergence of innovative, internet-based media tools. Audio and video downloads are beginning to compete with traditional entertainment distribution channels, and the blogosphere has become an alternative press with demonstrated news-making power of its own. The scientific community, and physics in particular, is just beginning to experiment with these tools. We believe that they have great potential for enhancing the quality and effectiveness of collaboration and communication, and that the coming generation of physicists will expect them to be used creatively. We will report on our experience in producing seminar podcasts (google ``QIBEC'' or search ``quantum'' on Apple iTunes), and on operating a distributed research institute using a group-based blog.

  20. The `WikiGuidelines' smartphone application: Bridging the gaps in availability of evidence-based smartphone mental health applications.

    Science.gov (United States)

    Zhang, Melvyn W B; Ho, Roger C M; Mcintyre, Roger S

    2016-07-27

    Over the past decade, there have been massive advances in technology. These advances in technology have significantly transformed various aspects of healthcare. The advent of E-health and its influence on healthcare practice also implies that there is a paradigm shift in the way healthcare professionals work. Conventionally, healthcare professionals would have to refer to books and journals for updates in treatment algorithms, but with the advent of technology, they could access this information via the web or via various smartphone applications on the go. In the field of Psychiatry, one of the commonest mental health disorder to date, with significant morbidity and mortality is that of Major depressive disorder. Routinely, clinicians and healthcare professionals are advised to refer to standard guidelines in guiding them with regards to their treatment options. Given the high prevalence of conditions like Major Depressive Disorder, it is thus of importance that whatever guidelines that clinicians and healthcare professionals refer to are constantly kept up to date, so that patients could benefit from latest evidence based therapy and treatment. A review of the current literature highlights that whilst there are a multitude of smartphone applications designed for mental health care, previous systematic review has highlighted a paucity of evidence based applications. More importantly, current literature with regards to provision of treatment information to healthcare professionals and patients are limited to web-based interventions. It is the aim of this technical note to highlight a methodology to which the authors have conceptualized in the implementation of an evidence based mental health guideline applications, known as the `Wiki Guidelines' smartphone application. The authors hope to illustrate the algorithms behind the development of the application, and how it could be easily updated by the guidelines working group.

  1. Bulk soil and maize rhizosphere resistance genes, mobile genetic elements and microbial communities are differently impacted by organic and inorganic fertilization

    DEFF Research Database (Denmark)

    Wolters, Birgit; Jacquiod, Samuel Jehan Auguste; Sørensen, Søren Johannes

    2018-01-01

    Organic soil fertilizers, such as livestock manure and biogas digestate, frequently contain bacteria carrying resistance genes (RGs) to antimicrobial substances and mobile genetic elements (MGEs). The effects of different fertilizers (inorganic, manure, digestate) on RG and MGE abundance...... and microbial community composition were investigated in a field plot experiment. The relative abundances of RGs [sul1, sul2, tet(A), tet(M), tet(Q), tet(W), qacEΔ1/qacE] and MGEs [intI1, intI2, IncP-1, IncP-1ε and LowGC plasmids] in total community (TC)-DNA from organic fertilizers, bulk soil and maize......, integrons and few genera affiliated to Bacteroidetes and Firmicutes in bulk soil, while digestate increased sul2, tet(W) and intI2. At harvest, treatment effects vanished in bulk soil. However, organic fertilizer effects were still detectable in the rhizosphere for RGs [manure: intI1, sul1; digestate: tet...

  2. Effects of superabsorbent polymers on the abundances of antibiotic resistance genes, mobile genetic elements, and the bacterial community during swine manure composting.

    Science.gov (United States)

    Guo, Aiyun; Gu, Jie; Wang, Xiaojuan; Zhang, Ranran; Yin, Yanan; Sun, Wei; Tuo, Xiaxia; Zhang, Li

    2017-11-01

    Superabsorbent polymers (SAPs) are considered suitable amendments for reducing the selection pressure due to heavy metals and the abundances of antibiotic resistance genes (ARGs) during composting. In this study, three SAP (sodium polyacrylate) levels (0, 5, and 15mgkg -1 of compost) were applied and their effects on the abundances of ARGs, mobile genetic elements (MGEs), and the bacterial community were investigated. After composting, the abundances of ARGs and MGEs decreased to different extent, where the removal efficiencies for tetW, dfrA7, ermX, aac(6')-ib-cr and MGEs exceeded 90%. The high SAP concentration significantly reduced the abundances of ARGs and MGEs, and changed the microbial community. Redundancy analysis indicated that the moisture content mainly explained the changes in ARGs and MGEs. Network analysis determined the potential hosts of ARGs and MGEs, and their co-occurrence. The results suggested that applying 15mgkg -1 SAP is appropriate for reducing ARGs in compost. Copyright © 2017. Published by Elsevier Ltd.

  3. Effects of different swine manure to wheat straw ratios on antibiotic resistance genes and the microbial community structure during anaerobic digestion.

    Science.gov (United States)

    Song, Wen; Wang, Xiaojuan; Gu, Jie; Zhang, Sheqi; Yin, Yanan; Li, Yang; Qian, Xun; Sun, Wei

    2017-05-01

    This study explored the effects of different mass ratios of swine manure relative to wheat straw (3:7, 5:5, and 7:3, i.e., control reactors C1, C2, and C3, respectively) on variations in antibiotic resistance genes (ARGs) and the microbial community during anaerobic digestion (AD). The cumulative biogas production volumes were 1711, 3857, and 3226mL in C1, C2, and C3, respectively. After AD, the total relative abundance of ARGs decreased by 4.23 logs in C3, whereas the reductions were only 1.03 and 1.37 logs in C1 and C2, respectively. Network analysis showed that the genera Solibacillus, Enterococcus, Facklamia, Corynebacterium_1, and Acinetobacter were potential hosts of ermB, sul1, and dfrA7. Redundancy analysis showed that the bacterial communities and environmental factors played important roles in the variation in ARGs. Thus, reductions in ARGs should be considered before reusing animal manure treated by AD. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. Population Abundance of Potentially Pathogenic Organisms in Intestinal Microbiome of Jungle Crow (Corvus macrorhynchos Shown with 16S rRNA Gene-Based Microbial Community Analysis

    Directory of Open Access Journals (Sweden)

    Isamu Maeda

    2013-01-01

    Full Text Available Jungle Crows (Corvus macrorhynchos prefer human habitats because of their versatility in feeding accompanied with human food consumption. Therefore, it is important from a public health viewpoint to characterize their intestinal microbiota. However, no studies have been involved in molecular characterization of the microbiota based on huge and reliable number of data acquisition. In this study, 16S rRNA gene-based microbial community analysis coupled with the next-generation DNA sequencing techniques was applied to the taxonomic classification of intestinal microbiome for three jungle crows. Clustering of the reads into 130 operational taxonomic units showed that at least 70% of analyzed sequences for each crow were highly homologous to Eimeria sp., which belongs to the protozoan phylum Apicomplexa. The microbiotas of three crows also contained potentially pathogenic bacteria with significant percentages, such as the genera Campylobacter and Brachyspira. Thus, the profiling of a large number of 16S rRNA gene sequences in crow intestinal microbiomes revealed the high-frequency existence or vestige of potentially pathogenic microorganisms.

  5. MicroScope-an integrated resource for community expertise of gene functions and comparative analysis of microbial genomic and metabolic data.

    Science.gov (United States)

    Médigue, Claudine; Calteau, Alexandra; Cruveiller, Stéphane; Gachet, Mathieu; Gautreau, Guillaume; Josso, Adrien; Lajus, Aurélie; Langlois, Jordan; Pereira, Hugo; Planel, Rémi; Roche, David; Rollin, Johan; Rouy, Zoe; Vallenet, David

    2017-09-12

    The overwhelming list of new bacterial genomes becoming available on a daily basis makes accurate genome annotation an essential step that ultimately determines the relevance of thousands of genomes stored in public databanks. The MicroScope platform (http://www.genoscope.cns.fr/agc/microscope) is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis. Starting from the results of our syntactic, functional and relational annotation pipelines, MicroScope provides an integrated environment for the expert annotation and comparative analysis of prokaryotic genomes. It combines tools and graphical interfaces to analyze genomes and to perform the manual curation of gene function in a comparative genomics and metabolic context. In this article, we describe the free-of-charge MicroScope services for the annotation and analysis of microbial (meta)genomes, transcriptomic and re-sequencing data. Then, the functionalities of the platform are presented in a way providing practical guidance and help to the nonspecialists in bioinformatics. Newly integrated analysis tools (i.e. prediction of virulence and resistance genes in bacterial genomes) and original method recently developed (the pan-genome graph representation) are also described. Integrated environments such as MicroScope clearly contribute, through the user community, to help maintaining accurate resources. © The Author 2017. Published by Oxford University Press.

  6. Influence of heavy metals on rhizosphere microbial communities of Siam weed (Chromolaena odorata (L. using a 16S rRNA gene amplicon sequencing approach

    Directory of Open Access Journals (Sweden)

    Thanyaporn Ruangdech

    2017-06-01

    Full Text Available A 16S rRNA amplicon sequencing approach was used to assess the impacts of cadmium (Cd and zinc (Zn contamination on populations of rhizobacteria on Siam weed (Chromolaena odorata (L.. Bacterial communities were characterized using the Illumina MiSeq platform and the V6 hypervariable region of the 16S rRNA gene. Among the 54,026 unique operational taxonomic units (OTUs identified, 99.7% were classified as bacteria and the rest were classified as archaea. Several dominant bacterial phyla were observed in all samples—Proteobacteria, Actinobacteria, Acidobacteria, Firmicutes and Bacteroidetes. These five phyla accounted for 89.2% of all OTUs identified among all sites, and only two OTUs could not be classified to a phylum. Comparison among samples containing low and high levels of Cd contamination using nonparametric Shannon and Shannon diversity indices showed that soils with low levels of diversity had a higher level of Cd (p < 0.05. These results indicated that levels of Cd may significantly alter bacterial species selection. The Cd- and Zn-resistant bacteria from each sample were subjected to heavy-metal minimum inhibitory concentration (MIC analyses. The MIC values obtained from 1152 isolates were used to individually analyze the pattern of gene function using the BioNumerics software. The results of this analysis showed that 26.7% of the bacteria were resistant to Cd concentrations up to 320 mg/L and only 2.3% of bacteria were resistant to Zn at concentrations up to 3200 mg/L. The MIC analyses indicated that the number of resistant bacteria decreased with increasing metal concentrations and those bacteria resistant to Cd and Zn may contain more than one group of metal-resistance genes.

  7. Evaluating the microbial community and gene regulation involved in crystallization kinetics of ZnS formation in reduced environments

    Science.gov (United States)

    Falk, Nicholas; Chaganti, Subba Rao; Weisener, Christopher G.

    2018-01-01

    In anoxic environments, sulfate-reducing bacteria (SRB) may precipitate sparingly-soluble, fine-grained sulfides as by-products of dissimilatory sulfate reduction. This bio-mechanism lends importance to acid rock drainage (ARD) remediation efforts for its ability to immobilize harmful metals from contaminant pathways, including Zn. However, SRB often coexist alongside multiple bacterial guilds in these environments, and may be sustained or hindered by the activities and metabolic by-products of their cohorts, driven by the commonly available substrates. Thus, the effectiveness of onset sulfate reduction and resultant metal-sulfide generation in ARD treatment can be enhanced by unravelling the complexities associated with these interactions. This research used material sourced from a passive bioreactor system located at the Stockton Coal Mine, New Zealand to investigate SRB activity and associated community function. RNA sequencing showed spore-forming Desulfitobacterium and Desulfotomaculum as the dominant SRB enriched from the reduced zone of the bioreactor. Metatranscriptomic analysis revealed acetogenic bacteria as syntrophic partners in substrate availability and Pseudomonas as metal-resistant community members. ZnS precipitates were observed by scanning electron microscopy (SEM) in short-term batch enrichments as well as long-term raw bioreactor material, with observed differences in mineral arrangement indicative of different nucleation scenarios. Syntrophy, metal response mechanisms, and the capacity for sporulation were observed as key microbial functions in mine waste reclamation settings. Here, Zn and S mass balance calculations coupled with RNA sequence data and microscopy illuminated favourable physicochemical and biological conditions for early metal sulfide precipitation in passive treatment systems for ARD and highlight the advantages of linking both lab and field-scale studies.

  8. Long-term nutrient addition differentially alters community composition and diversity of genes that control nitrous oxide flux from salt marsh sediments

    Science.gov (United States)

    Kearns, Patrick J.; Angell, John H.; Feinman, Sarah G.; Bowen, Jennifer L.

    2015-03-01

    Enrichment of natural waters, soils, and sediments by inorganic nutrients, including nitrogen, is occurring at an increasing rate and has fundamentally altered global biogeochemical cycles. Salt marshes are critical for the removal of land-derived nitrogen before it enters coastal waters. This is accomplished via multiple microbially mediated pathways, including denitrification. Many of these pathways, however, are also a source of the greenhouse gas nitrous oxide (N2O). We used clone libraries and quantative PCR (qPCR) to examine the effect of fertilization on the diversity and abundance of two functional genes associated with denitrification and N2O production (norB and nosZ) in experimental plots at the Great Sippewissett Salt Marsh (Falmouth, MA, USA) that have been enriched with nutrients for over 40 years. Our data showed distinct nosZ and norB community structures at different nitrogen loads, especially at the highest level of fertilization. Furthermore, calculations of the Shannon Diversity Index and Chao1 Richness Estimator indicated that nosZ gene diversity and richness increased with increased nitrogen supply, however no such relationship existed with regard to richness and diversity of the norB gene. Results from qPCR demonstrated that nosZ gene abundance was an order of magnitude lower in the extra-highly fertilized plots compared to the other plots, but the abundance of norB was not affected by fertilization. The majority of sequences obtained from the marsh plots had no close cultured relatives and they were divergent from previously sequenced norB and nosZ fragments. Despite their divergence from any cultured representatives, most of the norB and nosZ sequences appeared to be from members of the Alpha- and Betaproteobacteria, suggesting that these classes are particularly important in salt marsh nitrogen cycling. Our results suggest that both norB and nosZ containing microbes are affected by fertilization and that the Great Sippewissett Marsh may

  9. Propuesta de utilización de wikis para el desarrollo de la expresión escrita mediante el trabajo colaborativo

    Directory of Open Access Journals (Sweden)

    Juan Carlos Araujo Portugal

    2017-06-01

    Full Text Available Escribir en la lengua materna como en una extranjera cada vez resulta más difícil. En este artículo se plantean unas actividades a realizar a través de un wiki que tienen como objetivo usar y fomentar la escritura colaborativa por parte de los alumnos en una lengua extranjera para el desarrollo de la expresión escrita en ese idioma. Todo ello se encuadra en el contexto de las enseñanzas de idiomas que imparten las Escuelas Oficiales de Idiomas en España, pero que podría adaptarse a cualquier centro de enseñanza de idiomas. Previamente se analizan diversas corrientes pedagógicas que se pueden utilizar para la consecución del objetivo didáctico señalado, seleccionando el constructivismo. También se intenta justificar por qué un wiki resulta más adecuado para dicho objetivo que el correo electrónico, el blogs o los foros de discusión.

  10. A simultaneous journal / wiki publication and dissemination of a new species description: Neobidessodes darwiniensis sp. n. from northern Australia (Coleoptera, Dytiscidae, Bidessini

    Directory of Open Access Journals (Sweden)

    Lars Hendrich

    2011-02-01

    Full Text Available Here, we describe a new Australian species in journal format and simultaneously open the description in a wiki format on the www.species-id.net. The wiki format will always link to the fixed original journal description of the taxon, however it permits future edits and additions to species'  taxonomy and biology. The diving beetle Neobidessodes darwiniensis sp. n. (Coleoptera, Dytiscidae, Bidessini is described based on a single female, collected in a rest pool of the Harriet Creek in the Darwin Area, Northern Territory. Within Neobidessodes the new species is well characterized by its elongate oval body with rounded sides, short and stout segments of antennae, length of body and dorsal surface coloration. In addition to external morphology, we used mitochondrial cox1 sequence data to support generic assignment and to delineate the new species from other Australian Bidessini including all other known Neobidessodes. Illustrations based on digital images are provided here and as online resources. A modified key is provided. Altogether ten species of the genus are now known worldwide, nine from Australia and one from New Guinea.

  11. Complex community of nitrite-dependent anaerobic methane oxidation bacteria in coastal sediments of the Mai Po wetland by PCR amplification of both 16S rRNA and pmoA genes.

    Science.gov (United States)

    Chen, Jing; Zhou, Zhichao; Gu, Ji-Dong

    2015-02-01

    In the present work, both 16S rRNA and pmoA gene-based PCR primers were employed successfully to study the diversity and distribution of n-damo bacteria in the surface and lower layer sediments at the coastal Mai Po wetland. The occurrence of n-damo bacteria in both the surface and subsurface sediments with high diversity was confirmed in this study. Unlike the two other known n-damo communities from coastal areas, the pmoA gene-amplified sequences in the present work clustered not only with some freshwater subclusters but also within three newly erected marine subclusters mostly, indicating the unique niche specificity of n-damo bacteria in this wetland. Results suggested vegetation affected the distribution and community structures of n-damo bacteria in the sediments and n-damo could coexist with sulfate-reducing methanotrophs in the coastal ecosystem. Community structures of the Mai Po n-damo bacteria based on 16S rRNA gene were different from those of either the freshwater or the marine. In contrast, structures of the Mai Po n-damo communities based on pmoA gene grouped with the marine ones and were clearly distinguished from the freshwater ones. The abundance of n-damo bacteria at this wetland was quantified using 16S rRNA gene PCR primers to be 2.65-6.71 × 10(5) copies/g dry sediment. Ammonium and nitrite strongly affected the community structures and distribution of n-damo bacteria in the coastal Mai Po wetland sediments.

  12. La Universidad de Extremadura y su compromiso pedagógico con la educación virtual: los wikis como expresión de la web 2.0

    Directory of Open Access Journals (Sweden)

    Miguel Ángel Martín Sánchez

    2010-01-01

    Full Text Available Las universidades actuales se enfrentan al reto de actualizar no sólo sus recursos tecnológicos, sino también, y quizá más profundamente, el conocimiento de los docentes y su práctica pedagógica. Creemos que sólo así se logrará una verdadera innovación en los procesos de enseñanza/aprendizaje en este nuevo Espacio Europeo de Educación Superior. Una de las innovaciones que la tecnología ofrece es la relacionada con herramientas de software social, donde podemos encontrar la tecnología Wiki como motor de diversas experiencias didácticas en el ámbito universitario. La implantación de herramientas como el Wiki está provocando en el profesorado un proceso de replanteamiento de su racionalidad pedagógica y de sus prácticas docentes. Mediante el presente artículo pretendemos ofrecer un acercamiento a distintas prácticas con Wikis que desde hace algunos años se vienen implantando en la Universidad de Extremadura, en ellas son protagonistas la formación del profesorado, la reflexión del alumnado sobre la propia actividad mediante portafolios y diarios personales y, finalmente, el uso de los Wikis como herramientas para desarrollar aprendizaje colaborativo.

  13. Evolution properties of the community members for dynamic networks

    Science.gov (United States)

    Yang, Kai; Guo, Qiang; Li, Sheng-Nan; Han, Jing-Ti; Liu, Jian-Guo

    2017-03-01

    The collective behaviors of community members for dynamic social networks are significant for understanding evolution features of communities. In this Letter, we empirically investigate the evolution properties of the new community members for dynamic networks. Firstly, we separate data sets into different slices, and analyze the statistical properties of new members as well as communities they joined in for these data sets. Then we introduce a parameter φ to describe community evolution between different slices and investigate the dynamic community properties of the new community members. The empirical analyses for the Facebook, APS, Enron and Wiki data sets indicate that both the number of new members and joint communities increase, the ratio declines rapidly and then becomes stable over time, and most of the new members will join in the small size communities that is s ≤ 10. Furthermore, the proportion of new members in existed communities decreases firstly and then becomes stable and relatively small for these data sets. Our work may be helpful for deeply understanding the evolution properties of community members for social networks.

  14. Profiling the Succession of Bacterial Communities throughout the Life Stages of a Higher Termite Nasutitermes arborum (Termitidae, Nasutitermitinae) Using 16S rRNA Gene Pyrosequencing

    Science.gov (United States)

    Diouf, Michel; Roy, Virginie; Mora, Philippe; Frechault, Sophie; Lefebvre, Thomas; Hervé, Vincent; Rouland-Lefèvre, Corinne; Miambi, Edouard

    2015-01-01

    Previous surveys of the gut microbiota of termites have been limited to the worker caste. Termite gut microbiota has been well documented over the last decades and consists mainly of lineages specific to the gut microbiome which are maintained across generations. Despite this intimate relationship, little is known of how symbionts are transmitted to each generation of the host, especially in higher termites where proctodeal feeding has never been reported. The bacterial succession across life stages of the wood-feeding higher termite Nasutitermes arborum was characterized by 16S rRNA gene deep sequencing. The microbial community in the eggs, mainly affiliated to Proteobacteria and Actinobacteria, was markedly different from the communities in the following developmental stages. In the first instar and last instar larvae and worker caste termites, Proteobacteria and Actinobacteria were less abundant than Firmicutes, Bacteroidetes, Spirochaetes, Fibrobacteres and the candidate phylum TG3 from the last instar larvae. Most of the representatives of these phyla (except Firmicutes) were identified as termite-gut specific lineages, although their relative abundances differed. The most salient difference between last instar larvae and worker caste termites was the very high proportion of Spirochaetes, most of which were affiliated to the Treponema Ic, Ia and If subclusters, in workers. The results suggest that termite symbionts are not transmitted from mother to offspring but become established by a gradual process allowing the offspring to have access to the bulk of the microbiota prior to the emergence of workers, and, therefore, presumably through social exchanges with nursing workers. PMID:26444989

  15. The abundance of functional genes, cbbL, nifH, amoA and apsA, and bacterial community structure of intertidal soil from Arabian Sea.

    Science.gov (United States)

    Keshri, Jitendra; Yousuf, Basit; Mishra, Avinash; Jha, Bhavanath

    2015-06-01

    The Gulf of Cambay is a trumpet-shaped inlet of the Arabian Sea, located along the west coast of India and confronts a high tidal range with strong water currents. The region belongs to a semi-arid zone and saline alkaline intertidal soils are considered biologically extreme. The selected four soil types (S1-S4) were affected by salinity, alkalinity and sodicity. Soil salinity ranged from 20 to 126 dS/m, soil pH 8.6-10.0 with high sodium adsorption ratio (SAR) and exchangeable sodium percentage (ESP). Abundance of the key functional genes like cbbL, nifH, amoA and apsA involved in biogeochemical cycling were targeted using qPCR, which varied from (2.36 ± 0.03) × 10(4) to (2.87 ± 0.26) × 10(8), (1.18 ± 0.28) × 10(6) to (1.01 ± 0.26) × 10(9), (1.41 ± 0.21) × 10(6) to (1.29 ± 0.05) × 10(8) and (8.47 ± 0.23) × 10(4) to (1.73 ± 0.01) × 10(6) per gram dry weight, respectively. The microbial community structure revealed that soils S1 and S3 were dominated by phylum Firmicutes whereas S4 and S2 showed an abundance of Proteobacterial clones. These soils also represented Bacteroidetes, Chloroflexi, Actinobacteria, Planctomycetes and Acidobacteria clones. Molecular phylogeny showed a significant variation in the bacterial community distribution among the intertidal soil types. A high number of novel taxonomic units were observed which makes the intertidal zone a unique reservoir of unidentified bacterial taxa that may be explored further. Copyright © 2015 Elsevier GmbH. All rights reserved.

  16. The Response of a 16S Ribosomal RNA Gene Fragment Amplified Community to Lead, Zinc, and Copper Pollution in a Shanghai Field Trial

    Directory of Open Access Journals (Sweden)

    Shumeng Kou

    2018-03-01

    Full Text Available Industrial and agricultural activities have caused extensive metal contamination of land throughout China and across the globe. The pervasive nature of metal pollution can be harmful to human health and can potentially cause substantial negative impact to the biosphere. To investigate the impact of anthropogenic metal pollution found in high concentrations in industrial, agricultural, and urban environments, 16S ribosomal RNA gene amplicon sequencing was used to track change in the amplified microbial community after metal contamination in a large-scale field experiment in Shanghai. A total of 1,566 operational taxonomic units (OTUs identified from 448,108 sequences gathered from 20 plots treated as controls or with lead, zinc, copper, or all three metals. Constrained Analysis of Principal Coordinates ordination did not separate control and lead treatment but could separate control/lead, zinc, copper, and three metal treatment. DESeq2 was applied to identify 93 significantly differentially abundant OTUs varying in 211 pairwise instances between the treatments. Differentially abundant OTUs representing genera or species belonging to the phyla Chloroflexi, Cyanobacteria, Firmicutes, Latescibacteria, and Planctomycetes were almost universally reduced in abundance due to zinc, copper, or three metal treatment; with three metal treatment abolishing the detection of some OTUs, such as Leptolyngbya, Desmonostoc muscorum, and Microcoleus steenstrupii. The greatest increases due to metal treatment were observed in Bacteroidetes, Actinobacteria, Chlamydiae, Nitrospirae, and Proteobacteria (α, β, δ, and γ; the most (relative abundant being uncharacterized species within the genera Methylobacillus, Solirubrobacter, and Ohtaekwangia. Three metal treatment alone resulted in identification of 22 OTUs (genera or species which were not detected in control soil, notably including Yonghaparkia alkaliphila, Pedobacter steynii, Pseudolabrys taiwanensis

  17. The Response of a 16S Ribosomal RNA Gene Fragment Amplified Community to Lead, Zinc, and Copper Pollution in a Shanghai Field Trial.

    Science.gov (United States)

    Kou, Shumeng; Vincent, Gilles; Gonzalez, Emmanuel; Pitre, Frederic E; Labrecque, Michel; Brereton, Nicholas J B

    2018-01-01

    Industrial and agricultural activities have caused extensive metal contamination of land throughout China and across the globe. The pervasive nature of metal pollution can be harmful to human health and can potentially cause substantial negative impact to the biosphere. To investigate the impact of anthropogenic metal pollution found in high concentrations in industrial, agricultural, and urban environments, 16S ribosomal RNA gene amplicon sequencing was used to track change in the amplified microbial community after metal contamination in a large-scale field experiment in Shanghai. A total of 1,566 operational taxonomic units (OTUs) identified from 448,108 sequences gathered from 20 plots treated as controls or with lead, zinc, copper, or all three metals. Constrained Analysis of Principal Coordinates ordination did not separate control and lead treatment but could separate control/lead, zinc, copper, and three metal treatment. DESeq2 was applied to identify 93 significantly differentially abundant OTUs varying in 211 pairwise instances between the treatments. Differentially abundant OTUs representing genera or species belonging to the phyla Chloroflexi, Cyanobacteria, Firmicutes, Latescibacteria, and Planctomycetes were almost universally reduced in abundance due to zinc, copper, or three metal treatment; with three metal treatment abolishing the detection of some OTUs, such as Leptolyngbya , Desmonostoc muscorum , and Microcoleus steenstrupii . The greatest increases due to metal treatment were observed in Bacteroidetes, Actinobacteria, Chlamydiae, Nitrospirae, and Proteobacteria (α, β, δ, and γ); the most (relative) abundant being uncharacterized species within the genera Methylobacillus , Solirubrobacter , and Ohtaekwangia . Three metal treatment alone resulted in identification of 22 OTUs (genera or species) which were not detected in control soil, notably including Yonghaparkia alkaliphila , Pedobacter steynii , Pseudolabrys taiwanensis , Methylophilus

  18. Effects of manure and mineral fertilization strategies on soil antibiotic resistance gene levels and microbial community in a paddy–upland rotation system

    International Nuclear Information System (INIS)

    Lin, Hui; Sun, Wanchun; Zhang, Zulin; Chapman, Stephen J.; Freitag, Thomas E.; Fu, Jianrong; Zhang, Xin; Ma, Junwei

    2016-01-01

    This work investigated the responses of antibiotic resistance genes (ARGs) and the soil microbial community in a paddy–upland rotation system to mineral fertilizer (NPK) and different application dosages of manure combined with NPK. The occurrence of five tetracycline ARGs (tetA, tetB, tetC, tetG and tetW), two sulfonamide ARGs (sul1 and sul2) and one genetic element (IntI1) was quantified. NPK application showed only slight or no impact on soil ARGs abundances compared with the control without fertilizer. Soil ARGs abundances could be increased by manure-NPK application but was related to manure dosage (2250–9000 kg ha"−"1). Principal component analysis (PCA) showed that the soil ARG profile of the treatment with 9000 kg ha"−"1 manure separated clearly from the other treatments; the ARGs that contributed most to the discrimination of this treatment were tetA, tetG, tetW, sul1, sul2 and IntI1. Community level physiological profile (CLPP) analysis showed that increasing manure dosage from 4500 kg ha"−"1 to 9000 kg ha"−"1 induced a sharp increase in almost all of the detected ARGs but would not change the microbial community at large. However, 9000 kg ha"−"1 manure application produced a decline in soil microbial activity. Determination of antibiotics and heavy metals in soils suggested that the observed bloom of soil ARGs might associate closely with the accumulation of copper and zinc in soil. - Highlights: • The occurrence of ten ARGs in a manure and a paddy soil from China was tested. • The fate of ARGs in soil varied between ARG types and fertilization strategies. • The increase in soil ARG caused by manure-NPK fertilization was manure dosage-related. • Excessive manure greatly increased soil ARGs and inhibited soil microbial activity. • Cu and Zn levels in soils associated closely with the observed soil ARGs bloom. - The elevation of soil ARGs abundances in soil caused by manure application combined with NPK in a paddy

  19. Wikimedia as a platform for scientific information

    CERN Multimedia

    CERN. Geneva

    2012-01-01

    During this presentation the topics that will touched upon include various ways in which wikis are being used in scientific research and publishing, currently, as well as some that are more speculative. Many of the examples are drawn from the biological sciences, and the talk is intended to stimulate debate as to how the physics community - and CERN in particular - can enhance its interaction with the Wikimedia community, or via Wikimedia with the public at large. For instance: PLOS Computational Biology Topic Pages Wodak SJ, Mietchen D, Collings AM, Russell RB, Bourne PE (2012) "Topic Pages: PLoS Computational Biology Meets Wikipedia". PLoS Comput Biol 8(3): e1002446 Open Access Media Importer A proposed Wiki Journal, a peer-review journal to encourage academics to contribute Wikipedia articles Encyclopedia of Original Research and JATS-to-MediaWiki The Gene Wiki Wikigenes Wikis in Scholarly Publishing The Journal of the Future His talk is being draft...

  20. Development of a decision aid for cardiopulmonary resuscitation and invasive mechanical ventilation in the intensive care unit employing user-centered design and a wiki platform for rapid prototyping.

    Directory of Open Access Journals (Sweden)

    Ariane Plaisance

    Full Text Available Upon admission to an intensive care unit (ICU, all patients should discuss their goals of care and express their wishes concerning life-sustaining interventions (e.g., cardiopulmonary resuscitation (CPR. Without such discussions, interventions that prolong life at the cost of decreasing its quality may be used without appropriate guidance from patients.To adapt an existing decision aid about CPR to create a wiki-based decision aid individually adapted to each patient's risk factors; and to document the use of a wiki platform for this purpose.We conducted three weeks of ethnographic observation in our ICU to observe intensivists and patients discussing goals of care and to identify their needs regarding decision making. We interviewed intensivists individually. Then we conducted three rounds of rapid prototyping involving 15 patients and 11 health professionals. We recorded and analyzed all discussions, interviews and comments, and collected sociodemographic data. Using a wiki, a website that allows multiple users to contribute or edit content, we adapted the decision aid accordingly and added the Good Outcome Following Attempted Resuscitation (GO-FAR prediction rule calculator.We added discussion of invasive mechanical ventilation. The final decision aid comprises values clarification, risks and benefits of CPR and invasive mechanical ventilation, statistics about CPR, and a synthesis section. We added the GO-FAR prediction calculator as an online adjunct to the decision aid. Although three rounds of rapid prototyping simplified the information in the decision aid, 60% (n = 3/5 of the patients involved in the last cycle still did not understand its purpose.Wikis and user-centered design can be used to adapt decision aids to users' needs and local contexts. Our wiki platform allows other centers to adapt our tools, reducing duplication and accelerating scale-up. Physicians need training in shared decision making skills about goals of care and in

  1. Development of a decision aid for cardiopulmonary resuscitation and invasive mechanical ventilation in the intensive care unit employing user-centered design and a wiki platform for rapid prototyping.

    Science.gov (United States)

    Plaisance, Ariane; Witteman, Holly O; LeBlanc, Annie; Kryworuchko, Jennifer; Heyland, Daren Keith; Ebell, Mark H; Blair, Louisa; Tapp, Diane; Dupuis, Audrey; Lavoie-Bérard, Carole-Anne; McGinn, Carrie Anna; Légaré, France; Archambault, Patrick Michel

    2018-01-01

    Upon admission to an intensive care unit (ICU), all patients should discuss their goals of care and express their wishes concerning life-sustaining interventions (e.g., cardiopulmonary resuscitation (CPR)). Without such discussions, interventions that prolong life at the cost of decreasing its quality may be used without appropriate guidance from patients. To adapt an existing decision aid about CPR to create a wiki-based decision aid individually adapted to each patient's risk factors; and to document the use of a wiki platform for this purpose. We conducted three weeks of ethnographic observation in our ICU to observe intensivists and patients discussing goals of care and to identify their needs regarding decision making. We interviewed intensivists individually. Then we conducted three rounds of rapid prototyping involving 15 patients and 11 health professionals. We recorded and analyzed all discussions, interviews and comments, and collected sociodemographic data. Using a wiki, a website that allows multiple users to contribute or edit content, we adapted the decision aid accordingly and added the Good Outcome Following Attempted Resuscitation (GO-FAR) prediction rule calculator. We added discussion of invasive mechanical ventilation. The final decision aid comprises values clarification, risks and benefits of CPR and invasive mechanical ventilation, statistics about CPR, and a synthesis section. We added the GO-FAR prediction calculator as an online adjunct to the decision aid. Although three rounds of rapid prototyping simplified the information in the decision aid, 60% (n = 3/5) of the patients involved in the last cycle still did not understand its purpose. Wikis and user-centered design can be used to adapt decision aids to users' needs and local contexts. Our wiki platform allows other centers to adapt our tools, reducing duplication and accelerating scale-up. Physicians need training in shared decision making skills about goals of care and in using the

  2. Genetic structure of a natural oak community in central Italy: Evidence of gene flow between three sympatric white oak species (Quercus, Fagaceae

    Directory of Open Access Journals (Sweden)

    Gaby Antonecchia

    2015-12-01

    Full Text Available Incomplete reproductive barriers between species, especially in sympatric areas where several species coexist, may result in hybridization and an increase in genetic diversity. Here we assessed the amount of genetic diversity in a community of three interfertile and sympatric European oaks (Quercus frainetto Ten., Q. petraea Liebl. Matt. and Q. pubescens Willd. situated in central Italy. We used 11 microsatellite markers derived from Expressed Sequence Tag (EST-SSRs and we implemented a Bayesian clustering analysis to assign individuals to species or hybrids. All genotyped loci were polymorphic for all the species and three genetic clusters corresponding to each species were detected. Significant differences and a higher level of gene flow were observed between the three oak species. Occurrence of hybrids varied markedly within the studied area: hybrids between Q. petraea and Q, pubescens were the most frequent, while hybrids between Q. petraea and Q. frainetto were particularly rare. Q. pubescens and Q. petraea showed the highest number of alleles compared to Q. frainetto,which was characterized by a low number of private, but highly frequent, alleles. However, Q. frainetto showed a lower genetic diversity and a stronger reproductive isolation from the other two oak species.

  3. Persistence of antibiotic resistance genes and bacterial community changes in drinking water treatment system: From drinking water source to tap water.

    Science.gov (United States)

    Su, Hao-Chang; Liu, You-Sheng; Pan, Chang-Gui; Chen, Jun; He, Liang-Ying; Ying, Guang-Guo

    2018-03-01

    As emerging contaminants, antibiotic resistance genes (ARGs) have become a public concern. This study aimed to investigate the occurrence and diversity of ARGs, and variation in the composition of bacterial communities in source water, drinking water treatment plants, and tap water in the Pearl River Delta region, South China. Various ARGs were present in the different types of water. Among the 27 target ARGs, floR and sul1 dominated in source water from three large rivers in the region. Pearson correlation analysis suggested that sul1, sul2, floR, and cmlA could be potential indicators for ARGs in water samples. The total abundance of the detected ARGs in tap water was much lower than that in source water. Sand filtration and sedimentation in drinking water treatment plants could effectively remove ARGs; in contrast, granular activated carbon filtration increased the abundance of ARGs. It was found that Pseudomonas may be involved in the proliferation and dissemination of ARGs in the studied drinking water treatment system. Bacteria and ARGs were still present in tap water after treatment, though they were significantly reduced. More research is needed to optimize the water treatment process for ARG removal. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. 台灣棒球維基館網站推展成效探討 Evaluating the Effectiveness of TaiwanBaseballWiki

    Directory of Open Access Journals (Sweden)

    Sinn-Cheng Lin

    2007-12-01

    Full Text Available 本文旨在探討台灣棒球維基館成立兩年餘之發展成效。首先,本研究分析2005/4/14至2007/8/19期間之相關數據,發現:(一網站瀏覽量共3600多萬次,其中74%來自前20%的高流量頁面;瀏覽量月成長率平均值約15%;(二註冊使用者月成長率平均值約33%,雖已有880餘位,但編寫10次以上者僅163人,只佔18.43%,卻完成了高達91%的內容,而使用者中1.9%的17位核心使用者更貢獻了80.8%的主要內容;(三頁面月成長率平均值約6.06%,在一萬多個內容頁面中,每日平均被瀏覽10次以上的僅有915頁。其次,本研究針對使用者進行問卷調查,結果顯示:(一受訪者以年輕球迷居多,平均年齡24.8歲;(二受訪者有64%未註冊帳號,多數原因為只做短暫的查詢;(三受訪者僅有34%曾參與寫作,其動機以增進內容豐富性佔多數。此外,本文綜合多項指標,提出一個客觀的核心頁面評定準則,並建議台灣棒球維基館在進一步掌握使用者特性後,應加強內容品質之提升,並積極推展具歷史傳承、知識深化等價值之內容,以平衡目前較偏重於當代職棒明星之走向。This research study aims to evaluate the effectiveness of TaiwanBaseballWiki, established in 2005. First, the researchers collected data and analyzed the web logs from April 14, 2005 to August 19, 2007. A number of statistical measurements were used to analyze the data. The results show that 1. The number of page views has grown by almost 15% per month on average; 74% of page views came from 20% high browsing pages; 2. The registered users has grown by nearly 33% every month on average. It is also found that only 163 users have edited more than 10 times and were accounted for 91% of all the editing. Among them, the most active 1.9% of the users did 80.8% of all the editing; 3. The pages have grown by almost 6.06% per month on average, and only 8

  5. Temporal dynamics of in-situ fiber-adherent bacterial community under ruminal acidotic conditions determined by 16S rRNA gene profiling.

    Directory of Open Access Journals (Sweden)

    Renee M Petri

    Full Text Available Subacute rumen acidotic (SARA conditions are a consequence of high grain feeding. Recent work has shown that the pattern of grain feeding can significantly impact the rumen epimural microbiota. In a continuation of these works, the objective of this study was to determine the role of grain feeding patterns on the colonization and associated changes in predicted functional properties of the fiber-adherent microbial community over a 48 h period. Eight rumen-cannulated Holstein cows were randomly assigned to interrupted or continuous 60%-grain challenge model (n = 4 per model to induce SARA conditions. Cows in the continuous model were challenged for 4 weeks, whereas cows of interrupted model had a 1-wk break in between challenges. To determine dynamics of rumen fiber-adherent microbial community we incubated the same hay from the diet samples for 24 and 48 h in situ during the baseline (no grain fed, week 1 and 4 of the continuous grain feeding model as well as during the week 1 following the break in the interrupted model. Microbial DNA was extracted and 16SrRNA amplicon (V3-V5 region sequencing was done with the Illumina MiSeq platform. A significant decrease (P 0.1% relative abundance in the rumen, 18 of which were significantly impacted by the feeding challenge model. Correlation analysis of the significant OTUs to rumen pH as an indicator of SARA showed genus Succiniclasticum had a positive correlation to SARA conditions regardless of treatment. Predictive analysis of functional microbial properties suggested that the glyoxylate/dicarboxylate pathway was increased in response to SARA conditions, decreased between 24h to 48h of incubation, negatively correlated with propanoate metabolism and positively correlated to members of the Veillonellaceae family including Succiniclasticum spp. This may indicate an adaptive response in bacterial metabolism under SARA conditions. This research clearly indicates that changes to the colonizing fiber

  6. Genes and Gene Therapy

    Science.gov (United States)

    ... correctly, a child can have a genetic disorder. Gene therapy is an experimental technique that uses genes to ... or prevent disease. The most common form of gene therapy involves inserting a normal gene to replace an ...

  7. ANALYSIS OF BACTERIAL COMMUNITIES IN SEAGRASS BED SEDIMENTS BY DOUBLE-GRADIENT DENATURING GRADIENT GEL ELECTROPHORESIS OF PCR-AMPLIFIED 16SRRNA GENES

    Science.gov (United States)

    Bacterial communities associated with seagrass bed sediments are not well studied. The work presented here investigated several factors, including the presence or absence of vegetation, depth into sediment, and season, and their impact on bacterial community diversity. Double gra...

  8. VNTR polymorphisms of the IL-4 and IL-1RN genes and their relationship with frailty syndrome in Mexican community-dwelling elderly.

    Science.gov (United States)

    Pérez-Suárez, Thalía Gabriela; Gutiérrez-Robledo, Luis Miguel; Ávila-Funes, José Alberto; Acosta, José Luis; Escamilla-Tilch, Mónica; Padilla-Gutiérrez, Jorge Ramón; Torres-Carrillo, Norma; Torres-Castro, Sara; López-Ortega, Mariana; Muñoz-Valle, José Francisco; Torres-Carrillo, Nora Magdalena

    2016-10-01

    Inflammation is a key event that is closely associated with the pathophysiology of frailty. The relationship of genetic polymorphisms into inflammatory cytokines with frailty remains poorly understood. The aim of this study was to investigate the association between VNTR polymorphisms of the IL-4 and IL-1RN genes with the risk of frailty. We included a sample of 630 community-dwelling elderly aged 70 and older. Both IL-4 and IL-1RN VNTR polymorphisms were genotyped by the polymerase chain reaction (PCR) method. Mean age was 77.7 years (SD = 6.0) and 52.5 % were women. The participants classified as frail were more likely to be older, had lower MMSE score (p VNTR polymorphism did not show significant differences between study groups (p > 0.05). However, we just observed a significant difference in the allelic frequencies for the A2 allele of the IL-1RN VNTR polymorphism between frail and nonfrail groups (OR 1.84, 95 % CI 1.08-3.12, p = 0.02). In addition, we analyzed the combined effect of the IL-4 and IL-1RN VNTR polymorphisms and their possible association with frailty, where the combined IL-4 (low) -IL-1Ra (high) genotype was identified as a marker of risk to frailty syndrome (OR 7.86, 95 % CI 1.83-33.69, p = 0.006). Our results suggest that both A2 allele and the combined IL-4 (low) -IL-1Ra (high) genotype might be genetic markers of susceptibility to frailty in Mexican elderly.

  9. Discriminating activated sludge flocs from biofilm microbial communities in a novel pilot-scale reciprocation MBR using high-throughput 16S rRNA gene sequencing.

    Science.gov (United States)

    De Sotto, Ryan; Ho, Jaeho; Lee, Woonyoung; Bae, Sungwoo

    2018-03-29

    Membrane bioreactors (MBRs) are a well-established filtration technology that has become a popular solution for treating wastewater. One of the drawbacks of MBRs, however, is the formation of biofilm on the surface of membrane modules. The occurrence of biofilms leads to biofouling, which eventually compromises water quality and damages the membranes. To prevent this, it is vital to understand the mechanism of biofilm formation on membrane surfaces. In this pilot-scale study, a novel reciprocation membrane bioreactor was operated for a period of 8 months and fed with domestic wastewater from an aerobic tank of a local WWTP. Water quality parameters were monitored and the microbial composition of the attached biofilm and suspended aggregates was evaluated in this reciprocating MBR configuration. The abundance of nitrifiers and composition of microbial communities from biofilm and suspended solids samples were investigated using qPCR and high throughput 16S amplicon sequencing. Removal efficiencies of 29%, 16%, and 15% of chemical oxygen demand, total phosphorus and total nitrogen from the influent were observed after the MBR process with average effluent concentrations of 16 mg/L, 4.6 mg/L, and 5.8 mg/L respectively. This suggests that the energy-efficient MBR, apart from reducing the total energy consumption, was able to maintain effluent concentrations that are within regulatory standards for discharge. Molecular analysis showed the presence of amoA Bacteria and 16S Nitrospira genes with the occurrence of nitrification. Candidatus Accumulibacter, a genus with organisms that can accumulate phosphorus, was found to be present in both groups which explains why phosphorus removal was observed in the system. High-throughput 16S rRNA amplicon sequencing revealed the genus Saprospira to be the most abundant species from the total OTUs of both the membrane tank and biofilm samples. Copyright © 2018 Elsevier Ltd. All rights reserved.

  10. Signaling network of dendritic cells in response to pathogens: a community-input supported knowledgebase

    Directory of Open Access Journals (Sweden)

    Nudelman Irina

    2010-10-01

    Full Text Available Abstract Background Dendritic cells are antigen-presenting cells that play an essential role in linking the innate and adaptive immune systems. Much research has focused on the signaling pathways triggered upon infection of dendritic cells by various pathogens. The high level of activity in the field makes it desirable to have a pathway-based resource to access the information in the literature. Current pathway diagrams lack either comprehensiveness, or an open-access editorial interface. Hence, there is a need for a dependable, expertly curated knowledgebase that integrates this information into a map of signaling networks. Description We have built a detailed diagram of the dendritic cell signaling network, with the goal of providing researchers with a valuable resource and a facile method for community input. Network construction has relied on comprehensive review of the literature and regular updates. The diagram includes detailed depictions of pathways activated downstream of different pathogen recognition receptors such as Toll-like receptors, retinoic acid-inducible gene-I-like receptors, C-type lectin receptors and nucleotide-binding oligomerization domain-like receptors. Initially assembled using CellDesigner software, it provides an annotated graphical representation of interactions stored in Systems Biology Mark-up Language. The network, which comprises 249 nodes and 213 edges, has been web-published through the Biological Pathway Publisher software suite. Nodes are annotated with PubMed references and gene-related information, and linked to a public wiki, providing a discussion forum for updates and corrections. To gain more insight into regulatory patterns of dendritic cell signaling, we analyzed the network using graph-theory methods: bifan, feedforward and multi-input convergence motifs were enriched. This emphasis on activating control mechanisms is consonant with a network that subserves persistent and coordinated responses to

  11. Signaling network of dendritic cells in response to pathogens: a community-input supported knowledgebase.

    Science.gov (United States)

    Patil, Sonali; Pincas, Hanna; Seto, Jeremy; Nudelman, German; Nudelman, Irina; Sealfon, Stuart C

    2010-10-07

    Dendritic cells are antigen-presenting cells that play an essential role in linking the innate and adaptive immune systems. Much research has focused on the signaling pathways triggered upon infection of dendritic cells by various pathogens. The high level of activity in the field makes it desirable to have a pathway-based resource to access the information in the literature. Current pathway diagrams lack either comprehensiveness, or an open-access editorial interface. Hence, there is a need for a dependable, expertly curated knowledgebase that integrates this information into a map of signaling networks. We have built a detailed diagram of the dendritic cell signaling network, with the goal of providing researchers with a valuable resource and a facile method for community input. Network construction has relied on comprehensive review of the literature and regular updates. The diagram includes detailed depictions of pathways activated downstream of different pathogen recognition receptors such as Toll-like receptors, retinoic acid-inducible gene-I-like receptors, C-type lectin receptors and nucleotide-binding oligomerization domain-like receptors. Initially assembled using CellDesigner software, it provides an annotated graphical representation of interactions stored in Systems Biology Mark-up Language. The network, which comprises 249 nodes and 213 edges, has been web-published through the Biological Pathway Publisher software suite. Nodes are annotated with PubMed references and gene-related information, and linked to a public wiki, providing a discussion forum for updates and corrections. To gain more insight into regulatory patterns of dendritic cell signaling, we analyzed the network using graph-theory methods: bifan, feedforward and multi-input convergence motifs were enriched. This emphasis on activating control mechanisms is consonant with a network that subserves persistent and coordinated responses to pathogen detection. This map represents a navigable

  12. Characterization of Plasmid-Mediated Quinolone Resistance Determinants in High-Level Quinolone-Resistant Enterobacteriaceae Isolates from the Community: First Report of qnrD Gene in Algeria.

    Science.gov (United States)

    Yanat, Betitera; Machuca, Jesús; Díaz-De-Alba, Paula; Mezhoud, Halima; Touati, Abdelaziz; Pascual, Álvaro; Rodríguez-Martínez, José-Manuel

    2017-01-01

    The objective was to assess the prevalence of plasmid-mediated quinolone resistance (PMQR)-producing isolates in a collection of quinolone-resistant Enterobacteriaceae of community origin isolated in Bejaia, Algeria. A total of 141 nalidixic acid-resistant Enterobacteriaceae community isolates were collected in Bejaia (Northern Algeria) and screened for PMQR genes using polymerase chain reaction (PCR). For PMQR-positive strains, antimicrobial susceptibility testing was performed by broth microdilution and disk diffusion. Mutations in the quinolone resistance-determining regions of the target genes, gyrA and parC, were detected with a PCR-based method and sequencing. Southern blotting, conjugation and transformation assays and molecular typing by pulsed-field gel electrophoresis (PFGE), and multilocus sequence typing were also performed. The prevalence of PMQR-producing Enterobacteriaceae isolates was 13.5% (19/141); 11 of these isolates produced Aac(6')-Ib-cr and 8 were qnr-positive (4 qnrB1-like, 2 qnrS1-like, and 2 qnrD1-like), including the association with aac(6')-Ib-cr gene in three cases. PMQR gene transfer by conjugation was successful in 6 of 19 isolates tested. PFGE revealed that most of the PMQR-positive Escherichia coli isolates were unrelated, except for two groups comprising two and four isolates, respectively, including the virulent multidrug-resistant clone E. coli ST131 that were clonally related. Our findings indicate that PMQR determinants are prevalent in Enterobacteriaceae isolates from the community studied. We describe the first report of the qnrD gene in Algeria.

  13. Employment of Near Full-Length Ribosome Gene TA-Cloning and Primer-Blast to Detect Multiple Species in a Natural Complex Microbial Community Using Species-Specific Primers Designed with Their Genome Sequences.

    Science.gov (United States)

    Zhang, Huimin; He, Hongkui; Yu, Xiujuan; Xu, Zhaohui; Zhang, Zhizhou

    2016-11-01

    It remains an unsolved problem to quantify a natural microbial community by rapidly and conveniently measuring multiple species with functional significance. Most widely used high throughput next-generation sequencing methods can only generate information mainly for genus-level taxonomic identification and quantification, and detection of multiple species in a complex microbial community is still heavily dependent on approaches based on near full-length ribosome RNA gene or genome sequence information. In this study, we used near full-length rRNA gene library sequencing plus Primer-Blast to design species-specific primers based on whole microbial genome sequences. The primers were intended to be specific at the species level within relevant microbial communities, i.e., a defined genomics background. The primers were tested with samples collected from the Daqu (also called fermentation starters) and pit mud of a traditional Chinese liquor production plant. Sixteen pairs of primers were found to be suitable for identification of individual species. Among them, seven pairs were chosen to measure the abundance of microbial species through quantitative PCR. The combination of near full-length ribosome RNA gene library sequencing and Primer-Blast may represent a broadly useful protocol to quantify multiple species in complex microbial population samples with species-specific primers.

  14. Observation of high seasonal variation in community structure of denitrifying bacteria in arable soil receiving artificial fertilizer and cattle manure by determining T-RFLP of nir gene fragments

    DEFF Research Database (Denmark)

    Priemé, Anders; Wolsing, Martin

    2004-01-01

    Temporal and spatial variation of communities of soil denitrifying bacteria at sites receiving mineral fertilizer (60 and 120 kg N ha-1 year-1) and cattle manure (75 and 150 kg N ha-1 year-1) were explored using terminal restriction fragment length polymorphism (T-RFLP) analyses of PCR amplified...... nitrite reductase (nirK and nirS) gene fragments. The analyses were done three times during the year: in March, July and October. nirK gene fragments could be amplified in all three months, whereas nirS gene fragments could be amplified only in March. Analysis of similarities in T-RFLP patterns revealed...... a significant seasonal shift in the community structure of nirK-containing bacteria. Also, sites treated with mineral fertilizer or cattle manure showed different communities of nirK-containing denitrifying bacteria, since the T-RFLP patterns of soils treated with these fertilizers were significantly different...

  15. Broiler chickens, broiler chicken meat, pigs and pork as sources of ExPEC related virulence genes and resistance in Escherichia coli isolates from community-dwelling humans and UTI patients.

    Science.gov (United States)

    Jakobsen, Lotte; Spangholm, Daniel J; Pedersen, Karl; Jensen, Lars B; Emborg, Hanne-Dorthe; Agersø, Yvonne; Aarestrup, Frank M; Hammerum, Anette M; Frimodt-Møller, Niels

    2010-08-15

    Urinary tract infection (UTI) is one of the most common bacterial infections. UTI is primarily caused by extraintestinal pathogenic Escherichia coli (ExPEC) from the patients' own fecal flora. The ExPEC often belong to phylogroups B2 and D, the groups which include potent human ExPEC isolates causing UTI, bacteremia, and meningitis. The external sources of these ExPEC in the human intestine are unknown. The food supply may transmit ExPEC to humans. However, evidence of this hypothesis is limited. To assess this hypothesis, the objective of our study was to investigate the presence of ExPEC related virulence genes in E. coli isolates from UTI patients, community-dwelling humans, meat, and production animals. Accordingly, we included 964 geographically and temporally matched E. coli isolates from UTI patients (n=102), community-dwelling humans (n=109), fresh Danish (n=197) and imported broiler chicken meat (n=86), broiler chickens (n=138), fresh Danish (n=177) and imported pork (n=10), and pigs (n=145) in the study. All isolates were investigated for the presence of eight ExPEC related genes (kpsM II, papA, papC, iutA, sfaS, focG, afa, hlyD) using PCR. To investigate any similarities between isolates from the different origins, we performed a cluster analysis including antimicrobial resistance data previously published. We detected seven of the eight ExPEC related genes in isolates from broiler chicken meat, broiler chickens, pork and pigs. Our findings suggest that broiler chicken meat, broiler chickens, pork and pigs could be the source of strains with these ExPEC related virulence genes in community-dwelling humans and UTI patients. Especially detection of ExPEC related virulence genes in isolates belonging to phylogroups B2 and D is very concerning and may have a significant medical impact. The cluster analysis of virulence gene and antimicrobial resistance profiles showed strong similarities between UTI patient, community-dwelling human isolates, meat, and

  16. RAS Initiative - Community Outreach

    Science.gov (United States)

    Through community and technical collaborations, workshops and symposia, and the distribution of reference reagents, the RAS Initiative seeks to increase the sharing of knowledge and resources essential to defeating cancers caused by mutant RAS genes.

  17. Adaptação de um wiki para a informatização da documentação do sistema de gestão da qualidade

    Directory of Open Access Journals (Sweden)

    Graziele Cristina Silveira Zerbini Costal

    2013-01-01

    Full Text Available A documentação de um Sistema de Gestão da Qualidade padrão ISO 9001 é muitas vezes vista como uma fonte de burocracia nas organizações. Este artigo descreve o WikiQMS como uma alternativa para a informatização da documentação de tal sistema. O método científico foi aplicado para o desenvolvimento do sistema. O protótipo foi desenvolvido a partir de um software wiki, com base nos requisitos da ISO 9001 levantados na literatura e também pela avaliação de um painel de especialistas. O experimento de campo em uma empresa júnior permitiu validar o sistema em uma situação real de implantação da documentação do Sistema de Gestão da Qualidade. O protótipo atende adequadamente aos requisitos mínimos de implantação e gestão da documentação do Sistema de Gestão da Qualidade padrão ISO 9001. Além disso, o WikiQMS apresenta as vantagens de uma solução da Web 2.0 para a questão da edição colaborativa, autoria coletiva, acessibilidade e usabilidade.

  18. Community Structure of Denitrifiers, Bacteria, and Archaea along Redox Gradients in Pacific Northwest Marine Sediments by Terminal Restriction Fragment Length Polymorphism Analysis of Amplified Nitrite Reductase (nirS) and 16S rRNA Genes

    Science.gov (United States)

    Braker, Gesche; Ayala-del-Río, Héctor L.; Devol, Allan H.; Fesefeldt, Andreas; Tiedje, James M.

    2001-01-01

    Steep vertical gradients of oxidants (O2 and NO3−) in Puget Sound and Washington continental margin sediments indicate that aerobic respiration and denitrification occur within the top few millimeters to centimeters. To systematically explore the underlying communities of denitrifiers, Bacteria, and Archaea along redox gradients at distant geographic locations, nitrite reductase (nirS) genes and bacterial and archaeal 16S rRNA genes (rDNAs) were PCR amplified and analyzed by terminal restriction fragment length polymorphism (T-RFLP) analysis. The suitablility of T-RFLP analysis for investigating communities of nirS-containing denitrifiers was established by the correspondence of dominant terminal restriction fragments (T-RFs) of nirS to computer-simulated T-RFs of nirS clones. These clones belonged to clusters II, III, and IV from the same cores and were analyzed in a previous study (G. Braker, J. Zhou, L. Wu, A. H. Devol, and J. M. Tiedje, Appl. Environ. Microbiol. 66:2096–2104, 2000). T-RFLP analysis of nirS and bacterial rDNA revealed a high level of functional and phylogenetic diversity, whereas the level of diversity of Archaea was lower. A comparison of T-RFLPs based on the presence or absence of T-RFs and correspondence analysis based on the frequencies and heights of T-RFs allowed us to group sediment samples according to the sampling location and thus clearly distinguish Puget Sound and the Washington margin populations. However, changes in community structure within sediment core sections during the transition from aerobic to anaerobic conditions were minor. Thus, within the top layers of marine sediments, redox gradients seem to result from the differential metabolic activities of populations of similar communities, probably through mixing by marine invertebrates rather than from the development of distinct communities. PMID:11282647

  19. Broiler chickens, broiler chicken meat, pigs and pork as sources of ExPEC related virulence genes and resistance in Escherichia coli isolates from community-dwelling humans and UTI patients

    DEFF Research Database (Denmark)

    Jakobsen, L; Spangholm, D. J.; Pedersen, Karl

    2010-01-01

    Urinary tract infection (UTI) is one of the most common bacterial infections. UTI is primarily caused by extraintestinal pathogenic Escherichia coli (ExPEC) from the patients' own fecal flora. The ExPEC often belong to phylogroups B2 and D, the groups which include potent human ExPEC isolates...... causing UTI, bacteremia, and meningitis. The external sources of these ExPEC in the human intestine are unknown. The food supply may transmit ExPEC to humans. However, evidence of this hypothesis is limited. To assess this hypothesis, the objective of our study was to investigate the presence of Ex......PEC related virulence genes in E. coli isolates from UTI patients, community-dwelling humans, meat, and production animals. Accordingly, we included 964 geographically and temporally matched E. coli isolates from UTI patients (n=102), community-dwelling humans (n=109), fresh Danish (n=197) and imported...

  20. Community genetics reveal elevated levels of sympatric gene flow among morphologically similar but not among morphologically dissimilar species of Lake Victoria cichlid fish

    NARCIS (Netherlands)

    Konijnendijk, N.; Joyce, D.A.; Mrosso, H.D.J.; Egas, M.; Seehausen, O.

    2011-01-01

    We examined genetic structure among five species of Lake Victoria haplochromine cichlids in four island communities, using a full factorial sampling design that compared genetic differentiation between pairs of species and populations of varying morphological similarity and geographical proximity.

  1. Composition and Metabolic Activities of the Bacterial Community in Shrimp Sauce at the Flavor-Forming Stage of Fermentation As Revealed by Metatranscriptome and 16S rRNA Gene Sequencings.

    Science.gov (United States)

    Duan, Shan; Hu, Xiaoxi; Li, Mengru; Miao, Jianyin; Du, Jinghe; Wu, Rongli

    2016-03-30

    The bacterial community and the metabolic activities involved at the flavor-forming stage during the fermentation of shrimp sauce were investigated using metatranscriptome and 16S rRNA gene sequencings. Results showed that the abundance of Tetragenococcus was 95.1%. Tetragenococcus halophilus was identified in 520 of 588 transcripts annotated in the Nr database. Activation of the citrate cycle and oxidative phosphorylation, along with the absence of lactate dehydrogenase gene expression, in T. halophilus suggests that T. halophilus probably underwent aerobic metabolism during shrimp sauce fermentation. The metabolism of amino acids, production of peptidase, and degradation of limonene and pinene were very active in T. halophilus. Carnobacterium, Pseudomonas, Escherichia, Staphylococcus, Bacillus, and Clostridium were also metabolically active, although present in very small populations. Enterococcus, Abiotrophia, Streptococcus, and Lactobacillus were detected in metatranscriptome sequencing, but not in 16S rRNA gene sequencing. Many minor taxa showed no gene expression, suggesting that they were in dormant status.

  2. A horizontally gene transferred copper resistance locus confers hyper‐resistance to antibacterial copper toxicity and enables survival of community acquired methicillin resistant Staphylococcus aureus USA300 in macrophages

    Science.gov (United States)

    Purves, Joanne; Thomas, Jamie; Riboldi, Gustavo P.; Zapotoczna, Marta; Tarrant, Emma; Andrew, Peter W.; Londoño, Alejandra; Planet, Paul J.; Geoghegan, Joan A.; Waldron, Kevin J.

    2018-01-01

    Summary Excess copper is highly toxic and forms part of the host innate immune system's antibacterial arsenal, accumulating at sites of infection and acting within macrophages to kill engulfed pathogens. We show for the first time that a novel, horizontally gene transferred copper resistance locus (copXL), uniquely associated with the SCCmec elements of the highly virulent, epidemic, community acquired methicillin resistant Staphylococcus aureus (CA‐MRSA) USA300, confers copper hyper‐resistance. These genes are additional to existing core genome copper resistance mechanisms, and are not found in typical S. aureus lineages, but are increasingly identified in emerging pathogenic isolates. Our data show that CopX, a putative P1B‐3‐ATPase efflux transporter, and CopL, a novel lipoprotein, confer copper hyper‐resistance compared to typical S. aureus strains. The copXL genes form an operon that is tightly repressed in low copper environments by the copper regulator CsoR. Significantly, CopX and CopL are important for S. aureus USA300 intracellular survival within macrophages. Therefore, the emergence of new S. aureus clones with the copXL locus has significant implications for public health because these genes confer increased resistance to antibacterial copper toxicity, enhancing bacterial fitness by altering S. aureus interaction with innate immunity. PMID:29521441

  3. Eine studentische Wiki-Bibliothek für unterrichtsbegleitende Materialien: Konzeption, Implementierung und Evaluation für das Medizinische Curriculum München (MeCuM [A student-driven wiki-library for educational materials: Concept, implementation, and evaluation for the Medical Curriculum Munich (MeCuM

    Directory of Open Access Journals (Sweden)

    Berger, Michael

    2007-11-01

    Full Text Available [english] Problem: The new study regulation for medical licensing in Germany has caused significant reform of the medical curricula. At Munich University (LMU, the Medical Curriculum Munich (MeCuM was introduced in 2004. More individual responsibility of the students regarding their academic goals as well as a problem-oriented thought process are essential features of the new curriculum. Through our project, an open web based platform for the design of curriculum-specific teaching and study material has become accessible to students and faculty of the MeCuM. Methods: Students created an online library in harmony with the curricular structure of the MeCuM. The technical implementation was carried out with the MediaWiki-Open-Source software. Contents can be edited from all students or faculty of the MeCuM in an anonymous or personalized manner. An online questionnaire was carried out to evaluate the project. Results: Our online library as a wiki is the first solution of this kind in medical education in Germany. The concept was implemented without technical difficulties and is linked to the official websites of LMU Munich. The website’s contents were visited 417,808 times from December 2005 through June 2007. Online-based evaluation showed that the project is positively recognized, and students are motivated to contribute actively. Discussion: The project closely reflects the academic curriculum of the MeCuM and creates additional opportunities for interaction between students and teachers. The design as an open source project allows easy handling as well as frequent control and ability to update the contents, but integrity and accuracy of the data content require further effort. Additional evaluation will be essential for improvements. The integration of faculty as reviewers and tutors is planned. Sustainability of the project is dependent upon continued student leadership. The concept of the project has been transferred to another medical

  4. Different bacterial communities in heat and gamma irradiation treated replant disease soils revealed by 16S rRNA gene analysis – contribution to improved aboveground apple plant growth?

    Directory of Open Access Journals (Sweden)

    Bunlong eYim

    2015-11-01

    Full Text Available Replant disease (RD severely affects apple production in propagation tree nurseries and in fruit orchards worldwide. This study aimed to investigate the effects of soil disinfection treatments on plant growth and health in a biotest in two different RD soil types under greenhouse conditions and to link the plant growth status with the bacterial community composition at the time of plant sampling. In the biotest performed we observed that the aboveground growth of apple rootstock M26 plants after eight weeks was improved in the two RD soils either treated at 50 °C or with gamma irradiation compared to the untreated RD soils. Total community DNA was extracted from soil loosely adhering to the roots and quantitative real-time PCR revealed no pronounced differences in 16S rRNA gene copy numbers. 16S rRNA gene-based bacterial community analysis by denaturing gradient gel electrophoresis (DGGE and 454-pyrosequencing revealed significant differences in the bacterial community composition even after eight weeks of plant growth. In both soils, the treatments affected different phyla but only the relative abundance of Acidobacteria was reduced by both treatments. The genera Streptomyces, Bacillus, Paenibacillus and Sphingomonas had a higher relative abundance in both heat treated soils, whereas the relative abundance of Mucilaginibacter, Devosia and Rhodanobacter was increased in the gamma-irradiated soils and only the genus Phenylobacterium was increased in both treatments. The increased abundance of genera with potentially beneficial bacteria, i.e. potential degraders of phenolic compounds might have contributed to the improved plant growth in both treatments.

  5. A ribosomal RNA gene intergenic spacer based PCR and DGGE fingerprinting method for the analysis of specific rhizobial communities in soil

    NARCIS (Netherlands)

    de Oliveira, VM; Manfio, GP; Coutinho, HLD; Keijzer-Wolters, AC; van Elsas, JD

    A direct molecular method for assessing the diversity of specific populations of rhizobia in soil, based on nested PCR amplification of 16S-23S ribosomal RNA gene (rDNA) intergenic spacer (IGS) sequences, was developed. Initial generic amplification of bacterial rDNA IGS sequences from soil DNA was

  6. A ribosomal RNA gene intergenic spacer based PCR and DGGE fingerprinting method for the analysis of specific rhizobial communities in soil

    NARCIS (Netherlands)

    Oliveira, de V.M.; Manfio, G.P.; Coutinho, H.L.D.; Keijzer-Wolters, A.C.; Elsas, van J.D.

    2006-01-01

    A direct molecular method for assessing the diversity of specific populations of rhizobia in soil, based on nested PCR amplification of 16S-23S ribosomal RNA gene (rDNA) intergenic spacer (IGS) sequences, was developed. Initial generic amplification of bacterial rDNA IGS sequences from soil DNA was

  7. FunGene: the functional gene pipeline and repository.

    Science.gov (United States)

    Fish, Jordan A; Chai, Benli; Wang, Qiong; Sun, Yanni; Brown, C Titus; Tiedje, James M; Cole, James R

    2013-01-01

    Ribosomal RNA genes have become the standard molecular markers for microbial community analysis for good reasons, including universal occurrence in cellular organisms, availability of large databases, and ease of rRNA gene region amplification and analysis. As markers, however, rRNA genes have some significant limitations. The rRNA genes are often present in multiple copies, unlike most protein-coding genes. The slow rate of change in rRNA genes means that multiple species sometimes share identical 16S rRNA gene sequences, while many more species share identical sequences in the short 16S rRNA regions commonly analyzed. In addition, the genes involved in many important processes are not distributed in a phylogenetically coherent manner, potentially due to gene loss or horizontal gene transfer. While rRNA genes remain the most commonly used markers, key genes in ecologically important pathways, e.g., those involved in carbon and nitrogen cycling, can provide important insights into community composition and function not obtainable through rRNA analysis. However, working with ecofunctional gene data requires some tools beyond those required for rRNA analysis. To address this, our Functional Gene Pipeline and Repository (FunGene; http://fungene.cme.msu.edu/) offers databases of many common ecofunctional genes and proteins, as well as integrated tools that allow researchers to browse these collections and choose subsets for further analysis, build phylogenetic trees, test primers and probes for coverage, and download aligned sequences. Additional FunGene tools are specialized to process coding gene amplicon data. For example, FrameBot produces frameshift-corrected protein and DNA sequences from raw reads while finding the most closely related protein reference sequence. These tools can help provide better insight into microbial communities by directly studying key genes involved in important ecological processes.

  8. FunGene: the Functional Gene Pipeline and Repository

    Directory of Open Access Journals (Sweden)

    Jordan A. Fish

    2013-10-01

    Full Text Available Ribosomal RNA genes have become the standard molecular markers for microbial community analysis for good reasons, including universal occurrence in cellular organisms, availability of large databases, and ease of rRNA gene region amplification and analysis. As markers, however, rRNA genes have some significant limitations. The rRNA genes are often present in multiple copies, unlike most protein-coding genes. The slow rate of change in rRNA genes means that multiple species sometimes share identical 16S rRNA gene sequences, while many more species share identical sequences in the short 16S rRNA regions commonly analyzed. In addition, the genes involved in many important processes are not distributed in a phylogenetically coherent manner, potentially due to gene loss or horizontal gene transfer.While rRNA genes remain the most commonly used markers, key genes in ecologically important pathways, e.g., those involved in carbon and nitrogen cycling, can provide important insights into community composition and function not obtainable through rRNA analysis. However, working with ecofunctional gene data requires some tools beyond those required for rRNA analysis. To address this, our Functional Gene Pipeline and Repository (FunGene; http://fungene.cme.msu.edu/ offers databases of many common ecofunctional genes and proteins, as well as integrated tools that allow researchers to browse these collections and choose subsets for further analysis, build phylogenetic trees, test primers and probes for coverage, and download aligned sequences. Additional FunGene tools are specialized to process coding gene amplicon data. For example, FrameBot produces frameshift-corrected protein and DNA sequences from raw reads while finding the most closely related protein reference sequence. These tools can help provide better insight into microbial communities by directly studying key genes involved in important ecological processes.

  9. From documents to datasets: A MediaWiki-based method of annotating and extracting species observations in century-old field notebooks.

    Science.gov (United States)

    Thomer, Andrea; Vaidya, Gaurav; Guralnick, Robert; Bloom, David; Russell, Laura

    2012-01-01

    Part diary, part scientific record, biological field notebooks often contain details necessary to understanding the location and environmental conditions existent during collecting events. Despite their clear value for (and recent use in) global change studies, the text-mining outputs from field notebooks have been idiosyncratic to specific research projects, and impossible to discover or re-use. Best practices and workflows for digitization, transcription, extraction, and integration with other sources are nascent or non-existent. In this paper, we demonstrate a workflow to generate structured outputs while also maintaining links to the original texts. The first step in this workflow was to place already digitized and transcribed field notebooks from the University of Colorado Museum of Natural History founder, Junius Henderson, on Wikisource, an open text transcription platform. Next, we created Wikisource templates to document places, dates, and taxa to facilitate annotation and wiki-linking. We then requested help from the public, through social media tools, to take advantage of volunteer efforts and energy. After three notebooks were fully annotated, content was converted into XML and annotations were extracted and cross-walked into Darwin Core compliant record sets. Finally, these recordsets were vetted, to provide valid taxon names, via a process we call "taxonomic referencing." The result is identification and mobilization of 1,068 observations from three of Henderson's thirteen notebooks and a publishable Darwin Core record set for use in other analyses. Although challenges remain, this work demonstrates a feasible approach to unlock observations from field notebooks that enhances their discovery and interoperability without losing the narrative context from which those observations are drawn."Compose your notes as if you were writing a letter to someone a century in the future."Perrine and Patton (2011).

  10. An integrated study of photochemical function and expression of a key photochemical gene (psbA) in photosynthetic communities of Lake Bonney (McMurdo Dry Valleys, Antarctica)

    Czech Academy of Sciences Publication Activity Database

    Kong, W.; Wei, L.; Romancová, Ingrid; Prášil, Ondřej; Morgan-Kiss, R. M.

    2014-01-01

    Roč. 89, č. 6 (2014), s. 293-302 ISSN 0168-6496 R&D Projects: GA MŠk ED2.1.00/03.0110 Grant - others:NSF Office of Polar Programs(US) OPP-0631659, OPP-1056396 Institutional support: RVO:61388971 Keywords : photochemistry * lake Bonnney * communities Subject RIV: EE - Microbiology, Virology Impact factor: 3.568, year: 2014

  11. Diversity of Microbial Communities in Production and Injection Waters of Algerian Oilfields Revealed by 16S rRNA Gene Amplicon 454 Pyrosequencing

    Science.gov (United States)

    Lenchi, Nesrine; İnceoğlu, Özgül; Kebbouche-Gana, Salima; Gana, Mohamed Lamine; Llirós, Marc; Servais, Pierre; García-Armisen, Tamara

    2013-01-01

    The microorganisms inhabiting many petroleum reservoirs are multi-extremophiles capable of surviving in environments with high temperature, pressure and salinity. Their activity influences oil quality and they are an important reservoir of enzymes of industrial interest. To study these microbial assemblages and to assess any modifications that may be caused by industrial practices, the bacterial and archaeal communities in waters from four Algerian oilfields were described and compared. Three different types of samples were analyzed: production waters from flooded wells, production waters from non-flooded wells and injection waters used for flooding (water-bearing formations). Microbial communities of production and injection waters appeared to be significantly different. From a quantitative point of view, injection waters harbored roughly ten times more microbial cells than production waters. Bacteria dominated in injection waters, while Archaea dominated in production waters. Statistical analysis based on the relative abundance and bacterial community composition (BCC) revealed significant differences between production and injection waters at both OTUs0.03 and phylum level. However, no significant difference was found between production waters from flooded and non-flooded wells, suggesting that most of the microorganisms introduced by the injection waters were unable to survive in the production waters. Furthermore, a Venn diagram generated to compare the BCC of production and injection waters of one flooded well revealed only 4% of shared bacterial OTUs. Phylogenetic analysis of bacterial sequences indicated that Alpha-, Beta- and Gammaproteobacteria were the main classes in most of the water samples. Archaeal sequences were only obtained from production wells and each well had a unique archaeal community composition, mainly belonging to Methanobacteria, Methanomicrobia, Thermoprotei and Halobacteria classes. Many of the bacterial genera retrieved had already

  12. IntPath--an integrated pathway gene relationship database for model organisms and important pathogens.

    Science.gov (United States)

    Zhou, Hufeng; Jin, Jingjing; Zhang, Haojun; Yi, Bo; Wozniak, Michal; Wong, Limsoon

    2012-01-01

    Pathway data are important for understanding the relationship between genes, proteins and many other molecules in living organisms. Pathway gene relationships are crucial information for guidance, prediction, reference and assessment in biochemistry, computational biology, and medicine. Many well-established databases--e.g., KEGG, WikiPathways, and BioCyc--are dedicated to collecting pathway data for public access. However, the effectiveness of these databases is hindered by issues such as incompatible data formats, inconsistent molecular representations, inconsistent molecular relationship representations, inconsistent referrals to pathway names, and incomprehensive data from different databases. In this paper, we overcome these issues through extraction, normalization and integration of pathway data from several major public databases (KEGG, WikiPathways, BioCyc, etc). We build a database that not only hosts our integrated pathway gene relationship data for public access but also maintains the necessary updates in the long run. This public repository is named IntPath (Integrated Pathway gene relationship database for model organisms and important pathogens). Four organisms--S. cerevisiae, M. tuberculosis H37Rv, H. Sapiens and M. musculus--are included in this version (V2.0) of IntPath. IntPath uses the "full unification" approach to ensure no deletion and no introduced noise in this process. Therefore, IntPath contains much richer pathway-gene and pathway-gene pair relationships and much larger number of non-redundant genes and gene pairs than any of the single-source databases. The gene relationships of each gene (measured by average node degree) per pathway are significantly richer. The gene relationships in each pathway (measured by average number of gene pairs per pathway) are also considerably richer in the integrated pathways. Moderate manual curation are involved to get rid of errors and noises from source data (e.g., the gene ID errors in WikiPathways and

  13. Development of antibiotic resistance genes in microbial communities during long-term operation of anaerobic reactors in the treatment of pharmaceutical wastewater.

    Science.gov (United States)

    Aydin, Sevcan; Ince, Bahar; Ince, Orhan

    2015-10-15

    Biological treatment processes offer the ideal conditions in which a high diversity of microorganisms can grow and develop. The wastewater produced during these processes is contaminated with antibiotics and, as such, they provide the ideal setting for the acquisition and proliferation of antibiotic resistance genes (ARGs). This research investigated the occurrence and variation in the ARGs found during the one-year operation of the anaerobic sequencing batch reactors (SBRs) used to treat pharmaceutical wastewater that contained combinations of sulfamethoxazole-tetracycline-erythromycin (STE) and sulfamethoxazole-tetracycline (ST). The existence of eighteen ARGs encoding resistance to sulfamethoxazole (sul1, sul2, sul3), erythromycin (ermA, ermF, ermB, msrA, ereA), tetracycline (tetA, tetB, tetC, tetD, tetE, tetM, tetS, tetQ, tetW, tetX) and class Ι integron gene (intΙ 1) in the STE and ST reactors was investigated by quantitative real-time PCR. Due to the limited availability of primers to detect ARGs, Illumina sequencing was also performed on the sludge and effluent of the STE and ST reactors. Although there was good reactor performance in the SBRs, which corresponds to min 80% COD removal efficiency, tetA, tetB, sul1, sul2 and ermB genes were among those ARGs detected in the effluent from STE and ST reactors. A comparison of the ARGs acquired from the STE and ST reactors revealed that the effluent from the STE reactor had a higher number of ARGs than that from the ST reactor; this could be due to the synergistic effects of erythromycin. According to the expression of genes results, microorganisms achieve tetracycline and erythromycin resistance through a combination of three mechanisms: efflux pumping protein, modification of the antibiotic target and modifying enzymes. There was also a significant association between the presence of the class 1 integron and sulfamethoxazole resistance genes. Copyright © 2015 Elsevier Ltd. All rights reserved.

  14. Phylogenetic diversity and spatial distribution of the microbial community associated with the Caribbean deep-water sponge Polymastia cf. corticata by 16S rRNA, aprA, and amoA gene analysis.

    Science.gov (United States)

    Meyer, Birte; Kuever, Jan

    2008-08-01

    Denaturing gradient gel electrophoresis (DGGE)-based analyses of 16S rRNA, aprA, and amoA genes demonstrated that a phylogenetically diverse and complex microbial community was associated with the Caribbean deep-water sponge Polymastia cf. corticata Ridley and Dendy, 1887. From the 38 archaeal and bacterial 16S rRNA phylotypes identified, 53% branched into the sponge-specific, monophyletic sequence clusters determined by previous studies (considering predominantly shallow-water sponge species), whereas 26% appeared to be P. cf. corticata specifically associated microorganisms ("specialists"); 21% of the phylotypes were confirmed to represent seawater- and sediment-derived proteobacterial species ("contaminants") acquired by filtration processes from the host environment. Consistently, the aprA and amoA gene-based analyses indicated the presence of environmentally derived sulfur- and ammonia-oxidizers besides putative sponge-specific sulfur-oxidizing Gammaproteobacteria and Alphaproteobacteria and a sulfate-reducing archaeon. A sponge-specific, endosymbiotic sulfur cycle as described for marine oligochaetes is proposed to be also present in P. cf. corticata. Overall, the results of this work support the recent studies that demonstrated the sponge species specificity of the associated microbial community while the biogeography of the host collection site has only a minor influence on the composition. In P. cf. corticata, the specificity of the sponge-microbe associations is even extended to the spatial distribution of the microorganisms within the sponge body; distinct bacterial populations were associated with the different tissue sections, papillae, outer and inner cortex, and choanosome. The local distribution of a phylotype within P. cf. corticata correlated with its (1) phylogenetic affiliation, (2) classification as sponge-specific or nonspecifically associated microorganism, and (3) potential ecological role in the host sponge.

  15. Development of a Decision Aid for Cardiopulmonary Resuscitation Involving Intensive Care Unit Patients' and Health Professionals' Participation Using User-Centered Design and a Wiki Platform for Rapid Prototyping: A Research Protocol

    Science.gov (United States)

    Heyland, Daren Keith; Ebell, Mark H; Dupuis, Audrey; Lavoie-Bérard, Carole-Anne; Légaré, France; Archambault, Patrick Michel

    2016-01-01

    Background Cardiopulmonary resuscitation (CPR) is an intervention used in cases of cardiac arrest to revive patients whose heart has stopped. Because cardiac arrest can have potentially devastating outcomes such as severe neurological deficits even if CPR is performed, patients must be involved in determining in advance if they want CPR in the case of an unexpected arrest. Shared decision making (SDM) facilitates discussions about goals of care regarding CPR in intensive care units (ICUs). Patient decision aids (DAs) are proven to support the implementation of SDM. Many patient DAs about CPR exist, but they are not universally implemented in ICUs in part due to lack of context and cultural adaptation. Adaptation to local context is an important phase of implementing any type of knowledge tool such as patient DAs. User-centered design supported by a wiki platform to perform rapid prototyping has previously been successful in creating knowledge tools adapted to the needs of patients and health professionals (eg, asthma action plans). This project aims to explore how user-centered design and a wiki platform can support the adaptation of an existing DA for CPR to the local context. Objective The primary objective is to use an existing DA about CPR to create a wiki-based DA that is adapted to the context of a single ICU and tailorable to individual patient’s risk factors while employing user-centered design. The secondary objective is to document the use of a wiki platform for the adaptation of patient DAs. Methods This study will be conducted in a mixed surgical and medical ICU at Hôtel-Dieu de Lévis, Quebec, Canada. We plan to involve all 5 intensivists and recruit at least 20 alert and oriented patients admitted to the ICU and their family members if available. In the first phase of this study, we will observe 3 weeks of daily interactions between patients, families, intensivists, and other allied health professionals. We will specifically observe 5 dyads of

  16. OpenTox predictive toxicology framework: toxicological ontology and semantic media wiki-based OpenToxipedia.

    Science.gov (United States)

    Tcheremenskaia, Olga; Benigni, Romualdo; Nikolova, Ivelina; Jeliazkova, Nina; Escher, Sylvia E; Batke, Monika; Baier, Thomas; Poroikov, Vladimir; Lagunin, Alexey; Rautenberg, Micha; Hardy, Barry

    2012-04-24

    The OpenTox Framework, developed by the partners in the OpenTox project (http://www.opentox.org), aims at providing a unified access to toxicity data, predictive models and validation procedures. Interoperability of resources is achieved using a common information model, based on the OpenTox ontologies, describing predictive algorithms, models and toxicity data. As toxicological data may come from different, heterogeneous sources, a deployed ontology, unifying the terminology and the resources, is critical for the rational and reliable organization of the data, and its automatic processing. The following related ontologies have been developed for OpenTox: a) Toxicological ontology - listing the toxicological endpoints; b) Organs system and Effects ontology - addressing organs, targets/examinations and effects observed in in vivo studies; c) ToxML ontology - representing semi-automatic conversion of the ToxML schema; d) OpenTox ontology- representation of OpenTox framework components: chemical compounds, datasets, types of algorithms, models and validation web services; e) ToxLink-ToxCast assays ontology and f) OpenToxipedia community knowledge resource on toxicology terminology.OpenTox components are made available through standardized REST web services, where every compound, data set, and predictive method has a unique resolvable address (URI), used to retrieve its Resource Description Framework (RDF) representation, or to initiate the associated calculations and generate new RDF-based resources.The services support the integration of toxicity and chemical data from various sources, the generation and validation of computer models for toxic effects, seamless integration of new algorithms and scientifically sound validation routines and provide a flexible framework, which allows building arbitrary number of applications, tailored to solving different problems by end users (e.g. toxicologists). The OpenTox toxicological ontology projects may be accessed via the Open

  17. Gene Therapy

    Science.gov (United States)

    Gene therapy Overview Gene therapy involves altering the genes inside your body's cells in an effort to treat or stop disease. Genes contain your ... that don't work properly can cause disease. Gene therapy replaces a faulty gene or adds a new ...

  18. 應用 Google Analytics 於數位典藏網站計量分析 A Web Metrics Study on Taiwan Baseball Wiki Using Google Analytics

    Directory of Open Access Journals (Sweden)

    Sinn-Cheng Lin

    2010-04-01

    Full Text Available 數位典藏系統的最終目的是為了提供使用者使用,因此,必須從使用者角度評估系統的設計,以充分掌握使用者需求,發掘系統潛在問題,藉以改善系統、提升品質與增進使用者滿意度。本研究選擇以使用者到訪率極高的數位典藏網站-「台灣棒球維基館」為對象,利用著名的網站計量軟體GoogleAnalytics做為主要分析工具,再輔以問卷調查結果,希望能掌握使用者的多樣面貌,包括:誰在使用?何時使用?何地使用?使用何物?如何使用q工具,有效地分析網站營運成果,解析網站使用客群,據以調整網站未來經營方向。The ultimate purpose of digital archives is to provide users with an easy access to archived data. The assessment of the website with digital archives should be from the user’s perspectives so that users’ needs can be better understood, the potential design problems can be easily revealed, and the websites can be improved accordingly. This study analyzed Taiwan Baseball Wiki, a very popular website dedicated to baseball archives in Taiwan. Google Analytics, a well-known web metrics tool, was used as the primary research instrument. In addition, a questionnaire survey was conducted to collect the users’ profile. Questions such as the 5W1H (i.e., who, when, where, why, what, and how questions regarding the users and the use of the website, and the satisfaction level of the users are investigated. The results of the research provided valuable reference for future improvement of the website, especially for the areas of website management and administration. Furthermore, this study recommended web metrics tools to other websites which provide digital archives. The application of these tools can help with understanding and optimizing web usage.

  19. Identification of nitrogen-fixing genes and gene clusters from metagenomic library of acid mine drainage.

    Science.gov (United States)

    Dai, Zhimin; Guo, Xue; Yin, Huaqun; Liang, Yili; Cong, Jing; Liu, Xueduan

    2014-01-01

    Biological nitrogen fixation is an essential function of acid mine drainage (AMD) microbial communities. However, most acidophiles in AMD environments are uncultured microorganisms and little is known about the diversity of nitrogen-fixing genes and structure of nif gene cluster in AMD microbial communities. In this study, we used metagenomic sequencing to isolate nif genes in the AMD microbial community from Dexing Copper Mine, China. Meanwhile, a metagenome microarray containing 7,776 large-insertion fosmids was constructed to screen novel nif gene clusters. Metagenomic analyses revealed that 742 sequences were identified as nif genes including structural subunit genes nifH, nifD, nifK and various additional genes. The AMD community is massively dominated by the genus Acidithiobacillus. However, the phylogenetic diversity of nitrogen-fixing microorganisms is much higher than previously thought in the AMD community. Furthermore, a 32.5-kb genomic sequence harboring nif, fix and associated genes was screened by metagenome microarray. Comparative genome analysis indicated that most nif genes in this cluster are most similar to those of Herbaspirillum seropedicae, but the organization of the nif gene cluster had significant differences from H. seropedicae. Sequence analysis and reverse transcription PCR also suggested that distinct transcription units of nif genes exist in this gene cluster. nifQ gene falls into the same transcription unit with fixABCX genes, which have not been reported in other diazotrophs before. All of these results indicated that more novel diazotrophs survive in the AMD community.

  20. Identification of nitrogen-fixing genes and gene clusters from metagenomic library of acid mine drainage.

    Directory of Open Access Journals (Sweden)

    Zhimin Dai

    Full Text Available Biological nitrogen fixation is an essential function of acid mine drainage (AMD microbial communities. However, most acidophiles in AMD environments are uncultured microorganisms and little is known about the diversity of nitrogen-fixing genes and structure of nif gene cluster in AMD microbial communities. In this study, we used metagenomic sequencing to isolate nif genes in the AMD microbial community from Dexing Copper Mine, China. Meanwhile, a metagenome microarray containing 7,776 large-insertion fosmids was constructed to screen novel nif gene clusters. Metagenomic analyses revealed that 742 sequences were identified as nif genes including structural subunit genes nifH, nifD, nifK and various additional genes. The AMD community is massively dominated by the genus Acidithiobacillus. However, the phylogenetic diversity of nitrogen-fixing microorganisms is much higher than previously thought in the AMD community. Furthermore, a 32.5-kb genomic sequence harboring nif, fix and associated genes was screened by metagenome microarray. Comparative genome analysis indicated that most nif genes in this cluster are most similar to those of Herbaspirillum seropedicae, but the organization of the nif gene cluster had significant differences from H. seropedicae. Sequence analysis and reverse transcription PCR also suggested that distinct transcription units of nif genes exist in this gene cluster. nifQ gene falls into the same transcription unit with fixABCX genes, which have not been reported in other diazotrophs before. All of these results indicated that more novel diazotrophs survive in the AMD community.

  1. Identification of Nitrogen-Fixing Genes and Gene Clusters from Metagenomic Library of Acid Mine Drainage

    Science.gov (United States)

    Yin, Huaqun; Liang, Yili; Cong, Jing; Liu, Xueduan

    2014-01-01

    Biological nitrogen fixation is an essential function of acid mine drainage (AMD) microbial communities. However, most acidophiles in AMD environments are uncultured microorganisms and little is known about the diversity of nitrogen-fixing genes and structure of nif gene cluster in AMD microbial communities. In this study, we used metagenomic sequencing to isolate nif genes in the AMD microbial community from Dexing Copper Mine, China. Meanwhile, a metagenome microarray containing 7,776 large-insertion fosmids was constructed to screen novel nif gene clusters. Metagenomic analyses revealed that 742 sequences were identified as nif genes including structural subunit genes nifH, nifD, nifK and various additional genes. The AMD community is massively dominated by the genus Acidithiobacillus. However, the phylogenetic diversity of nitrogen-fixing microorganisms is much higher than previously thought in the AMD community. Furthermore, a 32.5-kb genomic sequence harboring nif, fix and associated genes was screened by metagenome microarray. Comparative genome analysis indicated that most nif genes in this cluster are most similar to those of Herbaspirillum seropedicae, but the organization of the nif gene cluster had significant differences from H. seropedicae. Sequence analysis and reverse transcription PCR also suggested that distinct transcription units of nif genes exist in this gene cluster. nifQ gene falls into the same transcription unit with fixABCX genes, which have not been reported in other diazotrophs before. All of these results indicated that more novel diazotrophs survive in the AMD community. PMID:24498417

  2. Interaction between the NOS3 gene and obesity as a determinant of risk of type 2 diabetes: the Atherosclerosis Risk in Communities study.

    Directory of Open Access Journals (Sweden)

    Jan Bressler

    Full Text Available Endothelial nitric oxide synthase 3 (NOS3 catalyzes the production of nitric oxide from L-arginine in endothelial cells. Obesity is a modifiable risk factor for diabetes, and obese individuals have been reported to have reduced nitric oxide availability compared to controls whose weight is in the normal range. Since homozygous carriers of the NOS3 G894T variant are predicted to have decreased enzyme activity, the association between NOS3 genotype and type 2 diabetes, and possible effect modification by body mass index (BMI were evaluated. The prevalence of diabetes and BMI was determined at baseline in 14,374 participants 45-66 years of age from the prospective biracial population-based Atherosclerosis Risk in Communities (ARIC Study of the development of atherosclerosis in four communities in the United States. Individuals with a BMI ≥30 kg/m(2 were considered obese. Those subjects not meeting the case definition were the comparison groups for the 728 African American and 980 white participants with diabetes. Multivariable logistic regression models adjusted for age, sex, and field center were used to test for main genetic effects and interaction with obesity. Although the NOS3 G894T variant was not independently associated with diabetes in either African Americans or whites, significant interaction between BMI and the NOS3 polymorphism indicated that obesity was an effect modifier of diabetes risk for white individuals with the TT genotype (odds ratio (OR for interaction = 1.65, p = 0.04. In stratified analyses, homozygosity for the NOS3 T allele in obese white participants but not in those whose BMI <30 kg/m(2 was associated with an elevated risk of diabetes (OR = 1.47, p = 0.02 when compared to the common GG genotype. These results suggest that interaction between obesity and NOS3 genotype may be a determinant of diabetes case status in whites in the ARIC cohort. Replication in other populations will be required to confirm

  3. Using web 2.0 tools in a community service program with spanish heritage speakers in the United States

    Directory of Open Access Journals (Sweden)

    Jennifer LEEMAN

    2011-12-01

    Full Text Available Normal 0 21 false false false ES X-NONE X-NONE /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Tabla normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:10.0pt; font-family:"Calibri","sans-serif"; mso-bidi-font-family:"Times New Roman";} This article analyzes the use of the Web 2.0 in a critical community service program in which students of Spanish from a large public institution in the United States were in charge of organizing, planning and delivering a Spanish course to young heritage speakers of Spanish. After a short description of the program and its context, the article analyzes how a class blog and a wiki were implemented as communication and collaboration tools, as well as their strengths and weaknesses in helping achieve the program’s goals. Through these technologies, it was possible to enhance participant interaction and to provide opportunities for self-reflection. In addition, the blog and the wiki helped students develop their Spanish written skills and played a role in the development of other literacies. Suggestions for future service learning programs are included at the end of the article.

  4. Insight into effects of antibiotics on reactor performance and evolutions of antibiotic resistance genes and microbial community in a membrane reactor.

    Science.gov (United States)

    Wen, Qinxue; Yang, Lian; Zhao, Yaqi; Huang, Long; Chen, Zhiqiang

    2018-04-01

    A lab-scale anoxic/oxic-membrane bioreactor was designed to treat antibiotics containing wastewater at different antibiotics concentrations (0.5 mg/L, 1 mg/L and 3 mg/L of each antibiotic). Overall COD and NH 4 + N removal (more than 90%) were not affected during the exposure to antibiotics and good TN removal was also achieved, while TP removal was significantly affected. The maximum removal efficiency of penicillin and chlorotetracycline reached 97.15% and 96.10% respectively due to strong hydrolysis, and sulfamethoxazole reached 90.07% by biodegradation. However, 63.87% of norfloxacin maximum removal efficiency was achieved mainly by sorption. The system had good ability to reduce ARGs, peaking to more than 4 orders of magnitude, which mainly depended on the biomass retaining of the membrane module. Antibiotics concentration influenced the evolution of ARGs and bacterial communities in the reactor. This research provides great implication to reduce ARGs and antibiotics in antibiotics containing wastewater using A/O-MBR. Copyright © 2018 Elsevier Ltd. All rights reserved.

  5. Bacterial community structure in Apis florea larvae analyzed by denaturing gradient gel electrophoresis and 16S rRNA gene sequencing.

    Science.gov (United States)

    Saraithong, Prakaimuk; Li, Yihong; Saenphet, Kanokporn; Chen, Zhou; Chantawannakul, Panuwan

    2015-10-01

    This study characterizes the colonization and composition of bacterial flora in dwarf Asian honeybee (Apis florea) larvae and compares bacterial diversity and distribution among different sampling locations. A. florea larvae were collected from 3 locations in Chiang Mai province, Thailand. Bacterial DNA was extracted from each larva using the phenol-chloroform method. Denaturing gradient gel electrophoresis was performed, and the dominant bands were excised from the gels, cloned, and sequenced for bacterial species identification. The result revealed similarities of bacterial community profiles in each individual colony, but differences between colonies from the same and different locations. A. florea larvae harbor bacteria belonging to 2 phyla (Firmicutes and Proteobacteria), 5 classes (Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Bacilli, and Clostridia), 6 genera (Clostridium, Gilliamella, Melissococcus, Lactobacillus, Saccharibacter, and Snodgrassella), and an unknown genus from uncultured bacterial species. The classes with the highest abundance of bacteria were Alphaproteobacteria (34%), Bacilli (25%), Betaproteobacteria (11%), Gammaproteobacteria (10%), and Clostridia (8%), respectively. Similarly, uncultured bacterial species were identified (12%). Environmental bacterial species, such as Saccharibacter floricola, were also found. This is the first study in which sequences closely related to Melissococcus plutonius, the causal pathogen responsible for European foulbrood, have been identified in Thai A. florea larvae. © 2014 Institute of Zoology, Chinese Academy of Sciences.

  6. Vitamin B-12, apolipoprotein E genotype, and cognitive performance in community-living older adults: evidence of a gene-micronutrient interaction.

    Science.gov (United States)

    Feng, Lei; Li, Jialiang; Yap, Keng-Bee; Kua, Ee-Heok; Ng, Tze-Pin

    2009-04-01

    The relation between vitamin B-12 and cognitive function in older adults is unclear. Limited evidence suggests that the relation is modulated by apolipoprotein E epsilon4. Hence, it is important to further examine this gene-nutrient interaction. The aim was to investigate the role of apolipoprotein E (APOE) epsilon4 as a genetic predisposing factor modulating the effect of vitamin B-12 on cognitive function. A battery of neuropsychological tests, including the Mini-Mental State Examination (MMSE) for global cognition, was administered at the baseline assessment to 539 Chinese adults aged > or =55 y. The MMSE was repeated at a median 18 mo (n = 376) and a median of 38 mo (n = 247) after baseline. The interaction of vitamin B-12 and APOE epsilon4 on cognitive function was examined in a linear mixed-effects model for MMSE and in a multiple linear regression model for neuropsychological test scores. APOE epsilon4 was associated with a lower MMSE score. Vitamin B-12 (natural log transformed) was positively related to MMSE score, and this association was much stronger in APOE epsilon4 carriers than in APOE epsilon4 noncarriers (P for interaction = 0.016). Significant interactions between natural log-transformed vitamin B-12 and APOE epsilon4 were also found for the Digit Span Backward Longest Sequence (P for interaction = 0.013) and Rey Auditory Verbal Learning Test immediate recall (P for interaction = 0.005). Better performance in these 2 tests was associated with vitamin B-12 in APOE epsilon4 carriers but not in APOE epsilon4 noncarriers. The association between vitamin B-12 and cognitive function was moderated by APOE epsilon4 status.

  7. Community Economics

    OpenAIRE

    武藤, 宣道; Nobumichi, MUTOH

    2000-01-01

    This paper examines the new field of community economics with respect to Japan. A number of studies in community economics have already been produced in OECD countries including the United States. Although these are of great interest, each country has its own historical, socioeconomic context and must therefore develop its own approach to community economics. Community-oriented economics is neither macro-nor micro-economics in the standard economics textbook sense. Most community economics st...

  8. LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs

    KAUST Repository

    Ma, L.

    2014-11-15

    Long non-coding RNAs (lncRNAs) perform a diversity of functions in numerous important biological processes and are implicated in many human diseases. In this report we present lncRNAWiki (http://lncrna.big.ac.cn), a wiki-based platform that is open-content and publicly editable and aimed at community-based curation and collection of information on human lncRNAs. Current related databases are dependent primarily on curation by experts, making it laborious to annotate the exponentially accumulated information on lncRNAs, which inevitably requires collective efforts in community-based curation of lncRNAs. Unlike existing databases, lncRNAWiki features comprehensive integration of information on human lncRNAs obtained from multiple different resources and allows not only existing lncRNAs to be edited, updated and curated by different users but also the addition of newly identified lncRNAs by any user. It harnesses community collective knowledge in collecting, editing and annotating human lncRNAs and rewards community-curated efforts by providing explicit authorship based on quantified contributions. LncRNAWiki relies on the underling knowledge of scientific community for collective and collaborative curation of human lncRNAs and thus has the potential to serve as an up-to-date and comprehensive knowledgebase for human lncRNAs.

  9. Developing leadership practices in hospital-based nurse educators in an online learning community.

    Science.gov (United States)

    Stutsky, Brenda J; Spence Laschinger, Heather K

    2014-01-01

    Hospital-based nurse educators are in a prime position to mentor future nurse leaders; however, they need to first develop their own leadership practices. The goal was to establish a learning community where hospital-based nurse educators could develop their own nursing leadership practices within an online environment that included teaching, cognitive, and social presence. Using a pretest/posttest-only nonexperimental design, 35 nurse educators from three Canadian provinces engaged in a 12-week online learning community via a wiki where they learned about exemplary leadership practices and then shared stories about their own leadership practices. Nurse educators significantly increased their own perceived leadership practices after participation in the online community, and teaching, cognitive, and social presence was determined to be present in the online community. It was concluded that leadership development can be enhanced in an online learning community using a structured curriculum, multimedia presentations, and the sharing and analysis of leadership stories. Educators who participated should now be better equipped to role model exemplary leadership practices and mentor our nurse leaders of the future.

  10. Serotonin transporter gene (SLC6A4) polymorphism and susceptibility to a home-visiting maternal-infant attachment intervention delivered by community health workers in South Africa: Reanalysis of a randomized controlled trial.

    Science.gov (United States)

    Morgan, Barak; Kumsta, Robert; Fearon, Pasco; Moser, Dirk; Skeen, Sarah; Cooper, Peter; Murray, Lynne; Moran, Greg; Tomlinson, Mark

    2017-02-01

    Clear recognition of the damaging effects of poverty on early childhood development has fueled an interest in interventions aimed at mitigating these harmful consequences. Psychosocial interventions aimed at alleviating the negative impacts of poverty on children are frequently shown to be of benefit, but effect sizes are typically small to moderate. However, averaging outcomes over an entire sample, as is typically done, could underestimate efficacy because weaker effects on less susceptible individuals would dilute estimation of effects on those more disposed to respond. This study investigates whether a genetic polymorphism of the serotonin transporter gene moderates susceptibility to a psychosocial intervention. We reanalyzed data from a randomized controlled trial of a home-visiting program delivered by community health workers in a black, isiXhosa-speaking population in Khayelitsha, South Africa. The intervention, designed to enhance maternal-infant attachment, began in the third trimester and continued until 6 mo postpartum. Implemented between April 1999 and February 2003, the intervention comprised 16 home visits delivered to 220 mother-infant dyads by specially trained community health workers. A control group of 229 mother-infant dyads did not receive the intervention. Security of maternal-infant attachment was the main outcome measured at infant age 18 mo. Compared to controls, infants in the intervention group were significantly more likely to be securely attached to their primary caregiver (odds ratio [OR] = 1.7, p = 0.029, 95% CI [1.06, 2.76], d = 0.29). After the trial, 162 intervention and 172 control group children were reenrolled in a follow-up study at 13 y of age (December 2012-June 2014). At this time, DNA collected from 279 children (134 intervention and 145 control) was genotyped for a common serotonin transporter polymorphism. There were both genetic data and attachment security data for 220 children (110 intervention and 110 control), of

  11. Serotonin transporter gene (SLC6A4 polymorphism and susceptibility to a home-visiting maternal-infant attachment intervention delivered by community health workers in South Africa: Reanalysis of a randomized controlled trial.

    Directory of Open Access Journals (Sweden)

    Barak Morgan

    2017-02-01

    Full Text Available Clear recognition of the damaging effects of poverty on early childhood development has fueled an interest in interventions aimed at mitigating these harmful consequences. Psychosocial interventions aimed at alleviating the negative impacts of poverty on children are frequently shown to be of benefit, but effect sizes are typically small to moderate. However, averaging outcomes over an entire sample, as is typically done, could underestimate efficacy because weaker effects on less susceptible individuals would dilute estimation of effects on those more disposed to respond. This study investigates whether a genetic polymorphism of the serotonin transporter gene moderates susceptibility to a psychosocial intervention.We reanalyzed data from a randomized controlled trial of a home-visiting program delivered by community health workers in a black, isiXhosa-speaking population in Khayelitsha, South Africa. The intervention, designed to enhance maternal-infant attachment, began in the third trimester and continued until 6 mo postpartum. Implemented between April 1999 and February 2003, the intervention comprised 16 home visits delivered to 220 mother-infant dyads by specially trained community health workers. A control group of 229 mother-infant dyads did not receive the intervention. Security of maternal-infant attachment was the main outcome measured at infant age 18 mo. Compared to controls, infants in the intervention group were significantly more likely to be securely attached to their primary caregiver (odds ratio [OR] = 1.7, p = 0.029, 95% CI [1.06, 2.76], d = 0.29. After the trial, 162 intervention and 172 control group children were reenrolled in a follow-up study at 13 y of age (December 2012-June 2014. At this time, DNA collected from 279 children (134 intervention and 145 control was genotyped for a common serotonin transporter polymorphism. There were both genetic data and attachment security data for 220 children (110 intervention and

  12. Beyond Social Media: A Cross-Sectional Survey of Other Internet and Mobile Phone Applications in a Community Psychiatry Population.

    Science.gov (United States)

    Colder Carras, Michelle; Mojtabai, Ramin; Cullen, Bernadette

    2018-03-01

    Popular media applications have been shown to benefit people with severe mental illness by facilitating communication and social support, helping patients cope with or manage symptoms, and providing a way to monitor or predict mental health states. Although many studies of technology use by individuals with severe mental illness have focused primarily on use of social media, this study provides additional information about use of Internet applications such as blogs, wikis (websites that allow collaborative editing of content and structure by users), video games, and Skype by a community psychiatry population. All English-speaking patients attending an outpatient program during a 4-week period in 2011 (N=274) were surveyed about their technology use and demographic information; 189 patients provided demographic data and comprised the sample. Among Internet users (n=112), rates of use of message boards, wikis, Skype, role-playing games, and blogs ranged from 26.8% to 34.8%. Among mobile phone users (n=162), 41.4% used their phones to access the Internet and 25.3% used Twitter on their phones. In multivariate analysis, patients who had attended or completed college had much greater odds of accessing the Internet on mobile phones. Older patients were much less likely to access the Internet or use Twitter. Our findings indicate that use of several popular forms of media is not uncommon in a community psychiatry population, but that rates of use differ on the basis of age and education. As the digital divide between people with severe mental illness and the general population is lessening, further research is needed to determine how to best leverage various types of media to support mental health recovery and complement clinical care.

  13. Community relations

    International Nuclear Information System (INIS)

    O'Neil, C.

    1997-01-01

    The interaction of the oil and gas companies with the Northern communities regarding drilling activities was an important aspect of oil and gas operations conducted in the Beaufort Sea. During the 1960s the industry and aboriginal people basically ignored each other. Later, the industry put more emphasis on community consultation until finally two-way communication was established. Respect for the land and the environment were very important to aboriginal people who depended on the land and its resources for their traditional way of life. Community relations policies by the various companies involved in the area, and the impact they have had on their respective communities were recounted. Not all efforts were successful, however, the companies and the communities learned from their experiences, and by the time operations ceased, the communities seemed to be more appreciative of the ways they were being treated by the oil companies. 22 figs

  14. Claiming Community

    DEFF Research Database (Denmark)

    Jensen, Steffen Bo

    As its point of departure this working paper takes the multitude of different uses and meanings of the concept of community in local politics in Cape Town. Instead of attempting to define it in substantive terms, the paper takes a social constructivist approach to the study of community...... is termed community work. First, the paper explores how community has become a governmental strategy, employed by the apartheid regime as well, although in different ways, as post-apartheid local government. Secondly, the paper explores the ways in which community becomes the means in which local residents...... lay claim on the state, as well as how it enters into local power struggles between different political groups within the township. In the third part, the paper explores how the meanings of community and the struggles to realise it have changed as South Africa, nationally and locally, has become...

  15. Gene expression

    International Nuclear Information System (INIS)

    Hildebrand, C.E.; Crawford, B.D.; Walters, R.A.; Enger, M.D.

    1983-01-01

    We prepared probes for isolating functional pieces of the metallothionein locus. The probes enabled a variety of experiments, eventually revealing two mechanisms for metallothionein gene expression, the order of the DNA coding units at the locus, and the location of the gene site in its chromosome. Once the switch regulating metallothionein synthesis was located, it could be joined by recombinant DNA methods to other, unrelated genes, then reintroduced into cells by gene-transfer techniques. The expression of these recombinant genes could then be induced by exposing the cells to Zn 2+ or Cd 2+ . We would thus take advantage of the clearly defined switching properties of the metallothionein gene to manipulate the expression of other, perhaps normally constitutive, genes. Already, despite an incomplete understanding of how the regulatory switch of the metallothionein locus operates, such experiments have been performed successfully

  16. Biclique communities

    DEFF Research Database (Denmark)

    Jørgensen, Sune Lehmann; Hansen-Schwartz, Martin; Hansen, Lars Kai

    2008-01-01

    We present a method for detecting communities in bipartite networks. Based on an extension of the k-clique community detection algorithm, we demonstrate how modular structure in bipartite networks presents itself as overlapping bicliques. If bipartite information is available, the biclique...... community detection algorithm retains all of the advantages of the k-clique algorithm, but avoids discarding important structural information when performing a one-mode projection of the network. Further, the biclique community detection algorithm provides a level of flexibility by incorporating independent...

  17. [Community Nutrition].

    Science.gov (United States)

    Aranceta, Javier

    2004-06-01

    In the last 20 years, Public Health Nutrition focused mainly on the qualitative aspects which may influence the onset of chronic diseases, quality of life, physical and mental performance and life expectancy. This applied knowledge organised as part of preventive and health promotion programs led to the development of Community Nutrition. The aim of Community Nutrition actions is to adequate lifestyles related to food consumption patterns in order to improve the quality of life and contribute to health promotion of the population in the community where programs and services are delivered. Key functions to develop in a Community Nutrition Unit consist in the identification and assessment of nutrition problems in the community as well as the design, implementation and evaluation of intervention programs by means of appropriate strategies. These should aim at different populations groups and settings, such as work places, schools, high risk groups or the general public. Nowadays, Community Nutrition work efforts should focus on three main aspects: nutrition education in schools and in the community; food safety and food security and the development and reinforcement of food preparation skills across all age groups. Social catering services, either in schools, the work place or at the community level, need to ensure adequate nutritional supply, provide foods contributing to healthy eating practices as well as to enhance culinary traditions and social learning. Food safety and food security have become a top priority in Public Health. The concepts referes to the availability of food safe and adequate as well as in sufficient amount in order to satisfy nutrition requirements of all individuals in the community. Social changes along new scientific developments will introduce new demands in Community Nutrition work and individual dietary counselling will become a key strategy. In order to face new challenges, community nutrition pactitioners require a high quality

  18. Community noise

    Science.gov (United States)

    Bragdon, C. R.

    Airport and community land use planning as they relate to airport noise reduction are discussed. Legislation, community relations, and the physiological effect of airport noise are considered. Noise at the Logan, Los Angeles, and Minneapolis/St. Paul airports is discussed.

  19. Community Drive

    DEFF Research Database (Denmark)

    Magnussen, Rikke

    2018-01-01

    Schools and educational institutions are challenged by not adequately educating students for independent knowledge collaboration and solving of complex societal challenges (Bundsgaard & Hansen, 2016; Slot et al., 2017). As an alternative strategy to formal learning has Community-driven research...... opportunity to break boundaries between research institutions and surrounding communities through the involvement of new types of actors, knowledge forms and institutions (OECD, 2011). This paper presents the project Community Drive a three year cross disciplinary community-driven game– and data-based project....... In the paper we present how the project Community Drive initiated in May 2018 is based on results from pilot projects conducted from 2014 – 2017. Overall these studies showed that it is a strong motivational factor for students to be given the task to change their living conditions through redesign...

  20. Community Ecology

    CERN Document Server

    1988-01-01

    This book presents the proceedings of a workshop on community ecology organized at Davis, in April, 1986, sponsored by the Sloan Foundation. There have been several recent symposia on community ecology (Strong et. al., 1984, Diamond and Case, 1987) which have covered a wide range of topics. The goal of the workshop at Davis was more narrow: to explore the role of scale in developing a theoretical approach to understanding communities. There are a number of aspects of scale that enter into attempts to understand ecological communities. One of the most basic is organizational scale. Should community ecology proceed by building up from population biology? This question and its ramifications are stressed throughout the book and explored in the first chapter by Simon Levin. Notions of scale have long been important in understanding physical systems. Thus, in understanding the interactions of organisms with their physical environment, questions of scale become paramount. These more physical questions illustrate the...

  1. Methopedia - Pedagogical Design Community for European Educators

    DEFF Research Database (Denmark)

    Ryberg, Thomas; Niemczik, Christian; Brenstein, Elke

    2009-01-01

    source Wiki and Social Networking technologies. We describe the issues, functionalities and needs that have emerged from the workshops, such as metadata (taxonomy & tags), localised versions (multi-lingual) and the need for visual descriptions. Furthermore, we discuss the templates trainers/educators can...

  2. Developing strategies for detection of gene doping.

    Science.gov (United States)

    Baoutina, Anna; Alexander, Ian E; Rasko, John E J; Emslie, Kerry R

    2008-01-01

    It is feared that the use of gene transfer technology to enhance athletic performance, the practice that has received the term 'gene doping', may soon become a real threat to the world of sport. As recognised by the anti-doping community, gene doping, like doping in any form, undermines principles of fair play in sport and most importantly, involves major health risks to athletes who partake in gene doping. One attraction of gene doping for such athletes and their entourage lies in the apparent difficulty of detecting its use. Since the realisation of the threat of gene doping to sport in 2001, the anti-doping community and scientists from different disciplines concerned with potential misuse of gene therapy technologies for performance enhancement have focused extensive efforts on developing robust methods for gene doping detection which could be used by the World Anti-Doping Agency to monitor athletes and would meet the requirements of a legally defensible test. Here we review the approaches and technologies which are being evaluated for the detection of gene doping, as well as for monitoring the efficacy of legitimate gene therapy, in relation to the detection target, the type of sample required for analysis and detection methods. We examine the accumulated knowledge on responses of the body, at both cellular and systemic levels, to gene transfer and evaluate strategies for gene doping detection based on current knowledge of gene technology, immunology, transcriptomics, proteomics, biochemistry and physiology. (c) 2008 John Wiley & Sons, Ltd.

  3. Mechanisms of pollution induced community tolerance in a soil microbial community exposed to Cu

    International Nuclear Information System (INIS)

    Wakelin, Steven; Gerard, Emily; Black, Amanda; Hamonts, Kelly; Condron, Leo; Yuan, Tong; Nostrand, Joy van; Zhou, Jizhong; O'Callaghan, Maureen

    2014-01-01

    Pollution induced community tolerance (PICT) to Cu 2+ , and co-tolerance to nanoparticulate Cu, ionic silver (Ag + ), and vancomycin were measured in field soils treated with Cu 2+ 15 years previously. EC 50 values were determined using substrate induced respiration and correlations made against soil physicochemical properties, microbial community structure, physiological status (qCO 2 ; metabolic quotient), and abundances of genes associated with metal and antibiotic resistance. Previous level of exposure to copper was directly (P  2+ , and also of nanoparticle Cu. However, Cu-exposed communities had no co-tolerance to Ag + and had increased susceptibly to vancomycin. Increased tolerance to both Cu correlated (P  + or vancomycin. • Tolerance not due to shifts in community composition or resistance genes. - Pollution induced community tolerance to Cu was linked with increased metabolic quotient but not changes in community composition or abundance of metal resistance genes in a field soil

  4. “Las intervenciones de enfermería” como patrón pedagógico de e-learning, wiki y aplicación móvil

    Directory of Open Access Journals (Sweden)

    Ma Elena García Puig

    2013-01-01

    Full Text Available Este artículo tiene el objetivo de enseñar las intervenciones de enfermería resolviendo las dificultades para relacionar los fundamentos conceptuales y profesionales de enfermería que sucede en algunos casos de la práctica del cuidado. Para ello se plantea utilizar la organización psicológica del conocimiento propuesta por Joseph Novak y el lenguaje de patrón. Además este contenido habitualmente se imparte mediante una metodología presencial y unos recursos didácticos que no incorporan las nuevas tecnologías demandadas por la Sociedad de la Información y del Conocimiento. Por tanto, objetos para el aprendizaje como las wiki y aplicaciones móviles deberían dar respuesta a estas demandas. Ambos son reusables en diferentes contextos de la formación en enfermería, como es, la universitaria, la continuada y la especializada.

  5. European Community.

    Science.gov (United States)

    1987-05-01

    The European Community was established in 1951 to reconcile France and Germany after World War II and to make possible the eventual federation of Europe. By 1986, there were 12 member countries: France, Italy, Belgium, the Federal Republic of Germany, Luxembourg, the Netherlands, Denmark, Ireland, the United Kingdom, Greece, Spain, and Portugal. Principal areas of concern are internal and external trade, agriculture, monetary coordination, fisheries, common industrial and commercial policies, assistance, science and research, and common social and regional policies. The European Community has a budget of US$34.035 billion/year, funded by customs duties and 1.4% of each member's value-added tax. The treaties establishing the European Community call for members to form a common market, a common customs tariff, and common agricultural, transport, economic, and nuclear policies. Major European Community institutions include the Commission, Council of Ministers, European Parliament, Court of Justice, and Economic and Social Committee. The Community is the world's largest trading unit, accounting for 15% of world trade. The 2 main goals of the Community's industrial policy are to create an open internal market and to promote technological innovation in order to improve international competitiveness. The European Community aims to contribute to the economic and social development of Third World countries as well.

  6. The hunt for gene dopers.

    Science.gov (United States)

    Mansour, Mai M H; Azzazy, Hassan M E

    2009-07-01

    Gene doping, the abuse of gene therapy for illicit athletic enhancement, is perceived as a coming threat and is a prime concern to the anti-doping community. This doping technique represents a significant ethical challenge and there are concerns regarding its safety for athletes. This article presents the basics of gene doping, potential strategies for its detection and the role of promising new technologies in aiding detection efforts. These include the use of lab-on-a-chip techniques as well as nanoparticles to enhance the performance of current analytical methods and to develop new doping detection strategies.

  7. Trichoderma genes

    Science.gov (United States)

    Foreman, Pamela [Los Altos, CA; Goedegebuur, Frits [Vlaardingen, NL; Van Solingen, Pieter [Naaldwijk, NL; Ward, Michael [San Francisco, CA

    2012-06-19

    Described herein are novel gene sequences isolated from Trichoderma reesei. Two genes encoding proteins comprising a cellulose binding domain, one encoding an arabionfuranosidase and one encoding an acetylxylanesterase are described. The sequences, CIP1 and CIP2, contain a cellulose binding domain. These proteins are especially useful in the textile and detergent industry and in pulp and paper industry.

  8. Natural Communities

    Data.gov (United States)

    Kansas Data Access and Support Center — This dataset shows the locations of known tracts of high quality natural communities in Kansas, generalized to the PLSS section. It is not a compehensive dataset of...

  9. COMMUNITY OPHTHALMOLOGY

    African Journals Online (AJOL)

    2016-11-04

    Nov 4, 2016 ... The Role of Research in Social Marketing: The Community Eye. Outreach Clinic .... Serious thought was given to the possibility of establishing static eye care .... Information obtained included vital statistics, work history, job.

  10. Community concepts.

    Science.gov (United States)

    Yeung, Thomas; Bates, Tony

    2004-03-01

    Since the publication of "Sustainable Communities--building for the future", Government attention has focused largely on high-density affordable housing in the four "growth areas": Thames Gateway; Ashford; Milton Keynes--South Midlands, and London--Stansted--Cambridge. In this article, Thomas Yeung and Tony Bates suggest that a greater and more sustainable impact would be achieved if architects, planners, and developers considered the potential for community-based water and waste management and on-site energy generation and distribution right from the start of the project. In particular, they consider that the communal nature of hospitals, universities, and public/community housing provides a great opportunity for on-site renewable CHP and/or distributed heating, which could combine global environmental benefits with improved local amenities. They describe a simple model for prioritising energy management in the built environment, and draw on lessons learnt at ETRCL in Dagenham and BedZED in Surrey to offer a few recommendations for Government and developers. Tony Bates is the business development manager for Scott Wilson in the South East and is responsible for the promotion of sustainable communities through relationships with architects, developers, land owners and local authorities. Thomas Yeung leads the Energy Infrastructure Technologies group in Scott Wilson. This team offers an integrated approach to clean community-based energy generation, energy management, waste and water management, sustainable transport, and sustainable buildings/communities.

  11. Community expectations

    International Nuclear Information System (INIS)

    Kraemer, L.

    2004-01-01

    Historically, the relationship between the nuclear generator and the local community has been one of stability and co-operation. However in more recent times (2000-2003) the nuclear landscape has had several major issues that directly effect the local nuclear host communities. - The associations mandate is to be supportive of the nuclear industry through ongoing dialogue, mutual cooperation and education, - To strengthen community representation with the nuclear industry and politically through networking with other nuclear host communities. As a result of these issues, the Mayors of a number of communities started having informal meetings to discuss the issues at hand and how they effect their constituents. These meetings led to the official formation of the CANHC with representation from: In Canada it is almost impossible to discuss decommissioning and dismantling of Nuclear Facilities without also discussing Nuclear Waste disposal for reasons that I will soon make clear. Also I would like to briefly touch on how and why expectation of communities may differ by geography and circumstance. (author)

  12. Gene Ontology Consortium: going forward.

    Science.gov (United States)

    2015-01-01

    The Gene Ontology (GO; http://www.geneontology.org) is a community-based bioinformatics resource that supplies information about gene product function using ontologies to represent biological knowledge. Here we describe improvements and expansions to several branches of the ontology, as well as updates that have allowed us to more efficiently disseminate the GO and capture feedback from the research community. The Gene Ontology Consortium (GOC) has expanded areas of the ontology such as cilia-related terms, cell-cycle terms and multicellular organism processes. We have also implemented new tools for generating ontology terms based on a set of logical rules making use of templates, and we have made efforts to increase our use of logical definitions. The GOC has a new and improved web site summarizing new developments and documentation, serving as a portal to GO data. Users can perform GO enrichment analysis, and search the GO for terms, annotations to gene products, and associated metadata across multiple species using the all-new AmiGO 2 browser. We encourage and welcome the input of the research community in all biological areas in our continued effort to improve the Gene Ontology. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  13. Perturbation metatranscriptomics for studying complex microbial communities

    DEFF Research Database (Denmark)

    Williams, Rohan B.H.; Kirkegaard, Rasmus Hansen; Arumugam, Krithika

    Studying the functional state of natural or engineered microbial communities presents substantial challenges due to both the complexities of field sampling, and, in the laboratory context, the inability of culture or reactor systems to maintain community composition ex situ over long periods. Here...... correlation between orthologous genes (Pearson r=0.4). We also used these data to annotate uncharacterized genes in the Ca. nitrospira defluvii genome: finding clear evidence for several previously unrecognized denitrification related genes, using a combination of expression profiles and protein domain data...... are associated with the transition from anoxic to aerobic conditions, and are observable at a whole community level and 3) these data provide a means of identifying unannotated genes in reference genomes that are likely to be associated with specific functional processes. More broadly, our approach permits...

  14. Ageing genes

    DEFF Research Database (Denmark)

    Rattan, Suresh

    2018-01-01

    The idea of gerontogenes is in line with the evolutionary explanation of ageing as being an emergent phenomenon as a result of the imperfect maintenance and repair systems. Although evolutionary processes did not select for any specific ageing genes that restrict and determine the lifespan...... of an individual, the term ‘gerontogenes’ primarily refers to any genes that may seem to influence ageing and longevity, without being specifically selected for that role. Such genes can also be called ‘virtual gerontogenes’ by virtue of their indirect influence on the rate and process of ageing. More than 1000...... virtual gerontogenes have been associated with ageing and longevity in model organisms and humans. The ‘real’ genes, which do influence the essential lifespan of a species, and have been selected for in accordance with the evolutionary life history of the species, are known as the longevity assurance...

  15. The duplicated genes database: identification and functional annotation of co-localised duplicated genes across genomes.

    Directory of Open Access Journals (Sweden)

    Marion Ouedraogo

    Full Text Available BACKGROUND: There has been a surge in studies linking genome structure and gene expression, with special focus on duplicated genes. Although initially duplicated from the same sequence, duplicated genes can diverge strongly over evolution and take on different functions or regulated expression. However, information on the function and expression of duplicated genes remains sparse. Identifying groups of duplicated genes in different genomes and characterizing their expression and function would therefore be of great interest to the research community. The 'Duplicated Genes Database' (DGD was developed for this purpose. METHODOLOGY: Nine species were included in the DGD. For each species, BLAST analyses were conducted on peptide sequences corresponding to the genes mapped on a same chromosome. Groups of duplicated genes were defined based on these pairwise BLAST comparisons and the genomic location of the genes. For each group, Pearson correlations between gene expression data and semantic similarities between functional GO annotations were also computed when the relevant information was available. CONCLUSIONS: The Duplicated Gene Database provides a list of co-localised and duplicated genes for several species with the available gene co-expression level and semantic similarity value of functional annotation. Adding these data to the groups of duplicated genes provides biological information that can prove useful to gene expression analyses. The Duplicated Gene Database can be freely accessed through the DGD website at http://dgd.genouest.org.

  16. Designed communities?

    DEFF Research Database (Denmark)

    Stender, Marie

    2013-01-01

    In current residential spaces there seem to be an increasing emphasis on small-scale communities. A number of new, high profiled residential complexes thus seek to promote new ways of social living by rethinking architectural design, typologies and concepts. In this paper I explore the emergence ...

  17. Walkable Communities

    Centers for Disease Control (CDC) Podcasts

    2008-04-18

    This podcast is for a general audience and discusses the benefits of walkable communities, as they relate to health, the environment, and social interaction.  Created: 4/18/2008 by National Center for Environmental Health (NCEH), ATSDR.   Date Released: 5/8/2008.

  18. Interfirm communities

    DEFF Research Database (Denmark)

    Bergenholtz, Carsten

    2012-01-01

    . These results yield a paradox which the present paper aims to address. Based on an in-depth case study of how a high-tech small firm organizes its interfirm activity, I show how a hybrid social relation, that is neither weak nor strong, is a useful conception for interfirm communities. Hereby, the study also...

  19. Invasion of nitrite oxidizer dominated communities: interactions between propagule pressure and community composition

    DEFF Research Database (Denmark)

    Kinnunen, Marta; Dechesne, Arnaud; Albrechtsen, Hans-Jørgen

    consider a broader community ecology framework. For example, the effect of propagule pressure, often studied in macro-ecology, has rarely been examined for microbial communities. Also, the interactions between processes governing community assembly and propagule pressure on invasion success have never been...... by nitrite oxidizer strain (Candidatus Nitrotoga sp. HW29) at 3 different propagule pressures. The reactors were then operated another 2 weeks before analyzing community composition by targeted qPCRs and 16S rRNA gene amplicon analysis. We successfully assembled resident communities with different ratios...

  20. Gene doping.

    Science.gov (United States)

    Haisma, H J; de Hon, O

    2006-04-01

    Together with the rapidly increasing knowledge on genetic therapies as a promising new branch of regular medicine, the issue has arisen whether these techniques might be abused in the field of sports. Previous experiences have shown that drugs that are still in the experimental phases of research may find their way into the athletic world. Both the World Anti-Doping Agency (WADA) and the International Olympic Committee (IOC) have expressed concerns about this possibility. As a result, the method of gene doping has been included in the list of prohibited classes of substances and prohibited methods. This review addresses the possible ways in which knowledge gained in the field of genetic therapies may be misused in elite sports. Many genes are readily available which may potentially have an effect on athletic performance. The sporting world will eventually be faced with the phenomena of gene doping to improve athletic performance. A combination of developing detection methods based on gene arrays or proteomics and a clear education program on the associated risks seems to be the most promising preventive method to counteract the possible application of gene doping.

  1. Gene Locater

    DEFF Research Database (Denmark)

    Anwar, Muhammad Zohaib; Sehar, Anoosha; Rehman, Inayat-Ur

    2012-01-01

    software's for calculating recombination frequency is mostly limited to the range and flexibility of this type of analysis. GENE LOCATER is a fully customizable program for calculating recombination frequency, written in JAVA. Through an easy-to-use interface, GENE LOCATOR allows users a high degree...... of flexibility in calculating genetic linkage and displaying linkage group. Among other features, this software enables user to identify linkage groups with output visualized graphically. The program calculates interference and coefficient of coincidence with elevated accuracy in sample datasets. AVAILABILITY...

  2. Community Evolution

    OpenAIRE

    Saganowski, Stanisław; Bródka, Piotr; Kazienko, Przemysław

    2016-01-01

    The continuous interest in the social network area contributes to the fast development of this field. The new possibilities of obtaining and storing data facilitate deeper analysis of the entire social network, extracted social groups and single individuals as well. One of the most interesting research topic is the network dynamics and dynamics of social groups in particular, it means analysis of group evolution over time. It is the natural step forward after social community extraction. Havi...

  3. In Silico Gene-Level Evolution Explains Microbial Population Diversity through Differential Gene Mobility

    NARCIS (Netherlands)

    van Dijk, Bram; Hogeweg, P.

    2016-01-01

    Microbial communities can show astonishing ecological and phylogenetic diversity. What is the role of pervasive horizontal gene transfer (HGT) in shaping this diversity in the presence of clonally expanding "killer strains"? Does HGT of antibiotic production and resistance genes erase phylogenetic

  4. Characterization of 16S rRNA genes from oil field microbial communities indicates the presence of a variety of sulfate-reducing, fermentative, and sulfide-oxidizing bacteria.

    OpenAIRE

    Voordouw, G; Armstrong, S M; Reimer, M F; Fouts, B; Telang, A J; Shen, Y; Gevertz, D

    1996-01-01

    Oil field bacteria were characterized by cloning and sequencing of PCR-amplified 16S rRNA genes. A variety of gram-negative, sulfate-reducing bacteria was detected (16 members of the family Desulfovibrionaceae and 8 members of the family Desulfobacteriaceae). In contrast, a much more limited number of anaerobic, fermentative, or acetogenic bacteria was found (one Clostridium sp., one Eubacterium sp., and one Synergistes sp.). Potential sulfide oxidizers and/or microaerophiles (Thiomicrospira,...

  5. Building a Community Infrastructure for Scalable On-Line Performance Analysis Tools around Open|SpeedShop

    Energy Technology Data Exchange (ETDEWEB)

    Galarowicz, James E. [Krell Institute, Ames, IA (United States); Miller, Barton P. [Univ. of Wisconsin, Madison, WI (United States). Computer Sciences Dept.; Hollingsworth, Jeffrey K. [Univ. of Maryland, College Park, MD (United States). Computer Sciences Dept.; Roth, Philip [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Future Technologies Group, Computer Science and Math Division; Schulz, Martin [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Center for Applied Scientific Computing (CASC)

    2013-12-19

    laboratories Los Alamos and Sandia leveraging co-funding for Krell by ASC’s Common Computing Environment (CCE) program as laid out in the original proposal. The ASC CCE co-funding, coordinated through LLNL, was for 50% of the total project funding, with the ASC CCE portion of the funding going entirely to Krell, while the ASCR funding itself was split between Krell and the funded partners. This report covers the entire project from both funding sources. Additionally, the team leveraged the expertise of software engineering researchers from Carnegie Mellon University, who specialize in software framework design, in order to achieve a broadly acceptable component framework. The Component Based Tool Framework (CBTF) software has been released to the community. Information related to the project and the released software can be found on the CBTF wiki page at: http://sourceforge.net/p/cbtf/wiki/Home.

  6. Online Communities

    DEFF Research Database (Denmark)

    Sørensen, Henrik; Lassen, Astrid Heidemann; Gorm Hansen, Katrine

    ”Online Communities” er et medie for brugere og fagfolk, hvor de kan mødes digitalt for at dele erfaringer, og dette kan anvendes som inspiration indenfor Brugerdreven Innovation. Via ”desk research” kan virksomheder opnå adgang til varierende mængder af brugere på en forholdsvist enkelt måde. I...... denne rapport beskrives eksperimentets opbygning, resultater og mulige værdi. Vi håber hermed på at kunne give praktisk indsigt i, hvorledes virksomheder fra byggematerialeindustrien kan agere i online communities....

  7. Acclimation of subsurface microbial communities to mercury

    DEFF Research Database (Denmark)

    de Lipthay, Julia R; Rasmussen, Lasse D; Øregaard, Gunnar

    2008-01-01

    of mercury tolerance and functional versatility of bacterial communities in contaminated soils initially were higher for surface soil, compared with the deeper soils. However, following new mercury exposure, no differences between bacterial communities were observed, which indicates a high adaptive potential......We studied the acclimation to mercury of bacterial communities of different depths from contaminated and noncontaminated floodplain soils. The level of mercury tolerance of the bacterial communities from the contaminated site was higher than those of the reference site. Furthermore, the level...... of the subsurface communities, possibly due to differences in the availability of mercury. IncP-1 trfA genes were detected in extracted community DNA from all soil depths of the contaminated site, and this finding was correlated to the isolation of four different mercury-resistance plasmids, all belonging...

  8. A comparative gene expression database for invertebrates

    Directory of Open Access Journals (Sweden)

    Ormestad Mattias

    2011-08-01

    Full Text Available Abstract Background As whole genome and transcriptome sequencing gets cheaper and faster, a great number of 'exotic' animal models are emerging, rapidly adding valuable data to the ever-expanding Evo-Devo field. All these new organisms serve as a fantastic resource for the research community, but the sheer amount of data, some published, some not, makes detailed comparison of gene expression patterns very difficult to summarize - a problem sometimes even noticeable within a single lab. The need to merge existing data with new information in an organized manner that is publicly available to the research community is now more necessary than ever. Description In order to offer a homogenous way of storing and handling gene expression patterns from a variety of organisms, we have developed the first web-based comparative gene expression database for invertebrates that allows species-specific as well as cross-species gene expression comparisons. The database can be queried by gene name, developmental stage and/or expression domains. Conclusions This database provides a unique tool for the Evo-Devo research community that allows the retrieval, analysis and comparison of gene expression patterns within or among species. In addition, this database enables a quick identification of putative syn-expression groups that can be used to initiate, among other things, gene regulatory network (GRN projects.

  9. Gene Ontology

    Directory of Open Access Journals (Sweden)

    Gaston K. Mazandu

    2012-01-01

    Full Text Available The wide coverage and biological relevance of the Gene Ontology (GO, confirmed through its successful use in protein function prediction, have led to the growth in its popularity. In order to exploit the extent of biological knowledge that GO offers in describing genes or groups of genes, there is a need for an efficient, scalable similarity measure for GO terms and GO-annotated proteins. While several GO similarity measures exist, none adequately addresses all issues surrounding the design and usage of the ontology. We introduce a new metric for measuring the distance between two GO terms using the intrinsic topology of the GO-DAG, thus enabling the measurement of functional similarities between proteins based on their GO annotations. We assess the performance of this metric using a ROC analysis on human protein-protein interaction datasets and correlation coefficient analysis on the selected set of protein pairs from the CESSM online tool. This metric achieves good performance compared to the existing annotation-based GO measures. We used this new metric to assess functional similarity between orthologues, and show that it is effective at determining whether orthologues are annotated with similar functions and identifying cases where annotation is inconsistent between orthologues.

  10. High-resolution phylogenetic microbial community profiling

    Energy Technology Data Exchange (ETDEWEB)

    Singer, Esther; Coleman-Derr, Devin; Bowman, Brett; Schwientek, Patrick; Clum, Alicia; Copeland, Alex; Ciobanu, Doina; Cheng, Jan-Fang; Gies, Esther; Hallam, Steve; Tringe, Susannah; Woyke, Tanja

    2014-03-17

    The representation of bacterial and archaeal genome sequences is strongly biased towards cultivated organisms, which belong to merely four phylogenetic groups. Functional information and inter-phylum level relationships are still largely underexplored for candidate phyla, which are often referred to as microbial dark matter. Furthermore, a large portion of the 16S rRNA gene records in the GenBank database are labeled as environmental samples and unclassified, which is in part due to low read accuracy, potential chimeric sequences produced during PCR amplifications and the low resolution of short amplicons. In order to improve the phylogenetic classification of novel species and advance our knowledge of the ecosystem function of uncultivated microorganisms, high-throughput full length 16S rRNA gene sequencing methodologies with reduced biases are needed. We evaluated the performance of PacBio single-molecule real-time (SMRT) sequencing in high-resolution phylogenetic microbial community profiling. For this purpose, we compared PacBio and Illumina metagenomic shotgun and 16S rRNA gene sequencing of a mock community as well as of an environmental sample from Sakinaw Lake, British Columbia. Sakinaw Lake is known to contain a large age of microbial species from candidate phyla. Sequencing results show that community structure based on PacBio shotgun and 16S rRNA gene sequences is highly similar in both the mock and the environmental communities. Resolution power and community representation accuracy from SMRT sequencing data appeared to be independent of GC content of microbial genomes and was higher when compared to Illumina-based metagenome shotgun and 16S rRNA gene (iTag) sequences, e.g. full-length sequencing resolved all 23 OTUs in the mock community, while iTags did not resolve closely related species. SMRT sequencing hence offers various potential benefits when characterizing uncharted microbial communities.

  11. Mining Genotype-Phenotype Associations from Public Knowledge Sources via Semantic Web Querying.

    Science.gov (United States)

    Kiefer, Richard C; Freimuth, Robert R; Chute, Christopher G; Pathak, Jyotishman

    2013-01-01

    Gene Wiki Plus (GeneWiki+) and the Online Mendelian Inheritance in Man (OMIM) are publicly available resources for sharing information about disease-gene and gene-SNP associations in humans. While immensely useful to the scientific community, both resources are manually curated, thereby making the data entry and publication process time-consuming, and to some degree, error-prone. To this end, this study investigates Semantic Web technologies to validate existing and potentially discover new genotype-phenotype associations in GWP and OMIM. In particular, we demonstrate the applicability of SPARQL queries for identifying associations not explicitly stated for commonly occurring chronic diseases in GWP and OMIM, and report our preliminary findings for coverage, completeness, and validity of the associations. Our results highlight the benefits of Semantic Web querying technology to validate existing disease-gene associations as well as identify novel associations although further evaluation and analysis is required before such information can be applied and used effectively.

  12. Gene doping: gene delivery for olympic victory

    OpenAIRE

    Gould, David

    2012-01-01

    With one recently recommended gene therapy in Europe and a number of other gene therapy treatments now proving effective in clinical trials it is feasible that the same technologies will soon be adopted in the world of sport by unscrupulous athletes and their trainers in so called ‘gene doping’. In this article an overview of the successful gene therapy clinical trials is provided and the potential targets for gene doping are highlighted. Depending on whether a doping gene product is secreted...

  13. Metagenomic analysis of microbial communities and beyond

    DEFF Research Database (Denmark)

    Schreiber, Lars

    2014-01-01

    From small clone libraries to large next-generation sequencing datasets – the field of community genomics or metagenomics has developed tremendously within the last years. This chapter will summarize some of these developments and will also highlight pitfalls of current metagenomic analyses...... heterologous expression of metagenomic DNA fragments to discover novel metabolic functions. Lastly, the chapter will shortly discuss the meta-analysis of gene expression of microbial communities, more precisely metatranscriptomics and metaproteomics....

  14. Community-managed Data Sharing, Curation, and Publication: SEN on SEAD

    Science.gov (United States)

    Martin, R. L.; Myers, J.; Hsu, L.

    2017-12-01

    While data publication in support of reuse and scientific reproducibility is increasingly being recognized as a key aspect of modern research practice, best practices are still to be developed at the level of scientific communities. Often, such practices are discussed in the abstract - as community standards for data plans or as requirements for yet-to-be-built software - with no clear path to community adoption. In contrast, the Sediment Experimentalist Network, supported through the National Science Foundation's (NSF) EarthCube initiative, has encouraged an iterative, practice-based approach within its community that has resulted in the publication of dozens of datasets, comprised of millions of files totaling more than 4 TB in size, and the documentation of more than 100 experimental procedures, instruments, and facilities, by multiple research teams. A key element of SEN's approach has been to leverage cloud-based data services that provide robust core capabilities with community-based management and customization capabilities. These services - data sharing, curation, and publication services developed through the NSF-supported Sustainable Environment - Actionable Data (SEAD) project and the wiki-based SEN Knowledge Base (KB) - have allowed the SEN team to ground discussions in reality and leverage the practical questions arising as researchers publish data to drive discussion and evolve towards better practices. In this presentation we summarize how SEN interacts with researchers, the best practices that have been developed, and the capabilities of SEAD and the SEN KB that support them. We also describe issues that have arisen in the community - related, for example, to recommended and required metadata, individual, project and community branding, and data version and derivation relationships - and describe how SEN's outreach activities, collaboration with the SEAD team, and the flexible design of the data services themselves have, in combination, been able to

  15. MIIB: A Metric to Identify Top Influential Bloggers in a Community.

    Science.gov (United States)

    Khan, Hikmat Ullah; Daud, Ali; Malik, Tahir Afzal

    2015-01-01

    Social networking has revolutionized the use of conventional web and has converted World Wide Web into the social web as users can generate their own content. This change has been possible due to social web platforms like forums, wikis, and blogs. Blogs are more commonly being used as a form of virtual communication to express an opinion about an event, product or experience and can reach a large audience. Users can influence others to buy a product, have certain political or social views, etc. Therefore, identifying the most influential bloggers has become very significant as this can help us in the fields of commerce, advertisement and product knowledge searching. Existing approaches consider some basic features, but lack to consider some other features like the importance of the blog on which the post has been created. This paper presents a new metric, MIIB (Metric for Identification of Influential Bloggers), based on various features of bloggers' productivity and popularity. Productivity refers to bloggers' blogging activity and popularity measures bloggers' influence in the blogging community. The novel module of BlogRank depicts the importance of blog sites where bloggers create their posts. The MIIB has been evaluated against the standard model and existing metrics for finding the influential bloggers using dataset from the real-world blogosphere. The obtained results confirm that the MIIB is able to find the most influential bloggers in a more effective manner.

  16. MIIB: A Metric to Identify Top Influential Bloggers in a Community.

    Directory of Open Access Journals (Sweden)

    Hikmat Ullah Khan

    Full Text Available Social networking has revolutionized the use of conventional web and has converted World Wide Web into the social web as users can generate their own content. This change has been possible due to social web platforms like forums, wikis, and blogs. Blogs are more commonly being used as a form of virtual communication to express an opinion about an event, product or experience and can reach a large audience. Users can influence others to buy a product, have certain political or social views, etc. Therefore, identifying the most influential bloggers has become very significant as this can help us in the fields of commerce, advertisement and product knowledge searching. Existing approaches consider some basic features, but lack to consider some other features like the importance of the blog on which the post has been created. This paper presents a new metric, MIIB (Metric for Identification of Influential Bloggers, based on various features of bloggers' productivity and popularity. Productivity refers to bloggers' blogging activity and popularity measures bloggers' influence in the blogging community. The novel module of BlogRank depicts the importance of blog sites where bloggers create their posts. The MIIB has been evaluated against the standard model and existing metrics for finding the influential bloggers using dataset from the real-world blogosphere. The obtained results confirm that the MIIB is able to find the most influential bloggers in a more effective manner.

  17. Genes and Hearing Loss

    Science.gov (United States)

    ... ENTCareers Marketplace Find an ENT Doctor Near You Genes and Hearing Loss Genes and Hearing Loss Patient ... mutation may only have dystopia canthorum. How Do Genes Work? Genes are a road map for the ...

  18. Developing Learning Communities: Using Communities of Practice within Community Psychology

    Science.gov (United States)

    Lawthom, Rebecca

    2011-01-01

    The idea that communities need to be inclusive is almost axiomatic. The process, whereby, community members engage in inclusive practices is far less understood. Similarly, UK universities are being encouraged to include the wider community and extent campus boundaries. Here, I suggest a particular theoretical lens which sheds light on engagement…

  19. Gene expression and gene therapy imaging

    International Nuclear Information System (INIS)

    Rome, Claire; Couillaud, Franck; Moonen, Chrit T.W.

    2007-01-01

    The fast growing field of molecular imaging has achieved major advances in imaging gene expression, an important element of gene therapy. Gene expression imaging is based on specific probes or contrast agents that allow either direct or indirect spatio-temporal evaluation of gene expression. Direct evaluation is possible with, for example, contrast agents that bind directly to a specific target (e.g., receptor). Indirect evaluation may be achieved by using specific substrate probes for a target enzyme. The use of marker genes, also called reporter genes, is an essential element of MI approaches for gene expression in gene therapy. The marker gene may not have a therapeutic role itself, but by coupling the marker gene to a therapeutic gene, expression of the marker gene reports on the expression of the therapeutic gene. Nuclear medicine and optical approaches are highly sensitive (detection of probes in the picomolar range), whereas MRI and ultrasound imaging are less sensitive and require amplification techniques and/or accumulation of contrast agents in enlarged contrast particles. Recently developed MI techniques are particularly relevant for gene therapy. Amongst these are the possibility to track gene therapy vectors such as stem cells, and the techniques that allow spatiotemporal control of gene expression by non-invasive heating (with MRI guided focused ultrasound) and the use of temperature sensitive promoters. (orig.)

  20. Imaging reporter gene for monitoring gene therapy

    International Nuclear Information System (INIS)

    Beco, V. de; Baillet, G.; Tamgac, F.; Tofighi, M.; Weinmann, P.; Vergote, J.; Moretti, J.L.; Tamgac, G.

    2002-01-01

    Scintigraphic images can be obtained to document gene function at cellular level. This approach is presented here and the use of a reporter gene to monitor gene therapy is described. Two main ways are presented: either the use of a reporter gene coding for an enzyme the action of which will be monitored by radiolabeled pro-drug, or a cellular receptor gene, the action of which is documented by a radio labeled cognate receptor ligand. (author)

  1. RaMP: A Comprehensive Relational Database of Metabolomics Pathways for Pathway Enrichment Analysis of Genes and Metabolites.

    Science.gov (United States)

    Zhang, Bofei; Hu, Senyang; Baskin, Elizabeth; Patt, Andrew; Siddiqui, Jalal K; Mathé, Ewy A

    2018-02-22

    The value of metabolomics in translational research is undeniable, and metabolomics data are increasingly generated in large cohorts. The functional interpretation of disease-associated metabolites though is difficult, and the biological mechanisms that underlie cell type or disease-specific metabolomics profiles are oftentimes unknown. To help fully exploit metabolomics data and to aid in its interpretation, analysis of metabolomics data with other complementary omics data, including transcriptomics, is helpful. To facilitate such analyses at a pathway level, we have developed RaMP (Relational database of Metabolomics Pathways), which combines biological pathways from the Kyoto Encyclopedia of Genes and Genomes (KEGG), Reactome, WikiPathways, and the Human Metabolome DataBase (HMDB). To the best of our knowledge, an off-the-shelf, public database that maps genes and metabolites to biochemical/disease pathways and can readily be integrated into other existing software is currently lacking. For consistent and comprehensive analysis, RaMP enables batch and complex queries (e.g., list all metabolites involved in glycolysis and lung cancer), can readily be integrated into pathway analysis tools, and supports pathway overrepresentation analysis given a list of genes and/or metabolites of interest. For usability, we have developed a RaMP R package (https://github.com/Mathelab/RaMP-DB), including a user-friendly RShiny web application, that supports basic simple and batch queries, pathway overrepresentation analysis given a list of genes or metabolites of interest, and network visualization of gene-metabolite relationships. The package also includes the raw database file (mysql dump), thereby providing a stand-alone downloadable framework for public use and integration with other tools. In addition, the Python code needed to recreate the database on another system is also publicly available (https://github.com/Mathelab/RaMP-BackEnd). Updates for databases in RaMP will be

  2. Identification of the Bacterial Community Responsible for ...

    African Journals Online (AJOL)

    Identification of bacteria community responsible for decontaminating Eleme petrochemical industrial effluent using 16S PCR denaturing gradient gel electrophoresis (DGGE) was determined. Gene profiles were determined by extracting DNA from bacterial isolates and amplified by polymerase chain reaction (PCR) using ...

  3. ESIP Federation: A Case Study on Enabling Collaboration Infrastructure to Support Earth Science Informatics Communities

    Science.gov (United States)

    Robinson, E.; Meyer, C. B.; Benedict, K. K.

    2013-12-01

    A critical part of effective Earth science data and information system interoperability involves collaboration across geographically and temporally distributed communities. The Federation of Earth Science Information Partners (ESIP) is a broad-based, distributed community of science, data and information technology practitioners from across science domains, economic sectors and the data lifecycle. ESIP's open, participatory structure provides a melting pot for coordinating around common areas of interest, experimenting on innovative ideas and capturing and finding best practices and lessons learned from across the network. Since much of ESIP's work is distributed, the Foundation for Earth Science was established as a non-profit home for its supportive collaboration infrastructure. The infrastructure leverages the Internet and recent advances in collaboration web services. ESIP provides neutral space for self-governed groups to emerge around common Earth science data and information issues, ebbing and flowing as the need for them arises. As a group emerges, the Foundation quickly equips the virtual workgroup with a set of ';commodity services'. These services include: web meeting technology (Webex), a wiki and an email listserv. WebEx allows the group to work synchronously, dynamically viewing and discussing shared information in real time. The wiki is the group's primary workspace and over time creates organizational memory. The listserv provides an inclusive way to email the group and archive all messages for future reference. These three services lower the startup barrier for collaboration and enable automatic content preservation to allow for future work. While many of ESIP's consensus-building activities are discussion-based, the Foundation supports an ESIP testbed environment for exploring and evaluating prototype standards, services, protocols, and best practices. After community review of testbed proposals, the Foundation provides small seed funding and a

  4. Characterization of 16S rRNA genes from oil field microbial communities indicates the presence of a variety of sulfate-reducing, fermentative, and sulfide-oxidizing bacteria.

    Science.gov (United States)

    Voordouw, G; Armstrong, S M; Reimer, M F; Fouts, B; Telang, A J; Shen, Y; Gevertz, D

    1996-05-01

    Oil field bacteria were characterized by cloning and sequencing of PCR-amplified 16S rRNA genes. A variety of gram-negative, sulfate-reducing bacteria was detected (16 members of the family Desulfovibrionaceae and 8 members of the family Desulfobacteriaceae). In contrast, a much more limited number of anaerobic, fermentative, or acetogenic bacteria was found (one Clostridium sp., one Eubacterium sp., and one Synergistes sp.). Potential sulfide oxidizers and/or microaerophiles (Thiomicrospira, Arcobacter, Campylobacter, and Oceanospirillum spp.) were also detected. The first two were prominently amplified from uncultured production water DNA and represented 28 and 47% of all clones, respectively. Growth on media containing sulfide as the electron donor and nitrate as the electron acceptor and designed for the isolation of Thiomicrospira spp. gave only significant enrichment of the Campylobacter sp., which was shown to be present in different western Canadian oil fields. This newly discovered sulfide oxidizer may provide a vital link in the oil field sulfur cycle by reoxidizing sulfide formed by microbial sulfate or sulfur reduction.

  5. Using Wiki Technology in the Classroom

    DEFF Research Database (Denmark)

    Majgaard, Gunver

    2013-01-01

    as a collaborative learning tool for encyclopaedia articles on learning and technology. There were several potential dilemmas in the students’ collaborative work: Inspiration versus imitation of others’ ideas and solutions; academic achievements versus friendships; varying work ethics and academic levels...

  6. Permissiveness of soil microbial communities towards broad host range plasmids

    DEFF Research Database (Denmark)

    Klümper, Uli

    . Plasmids are implicated in the rapid spread of antibiotic resistance and the emergence of multi-resistant pathogenic bacteria, making it crucial to be able to quantify, understand, and, ideally, control plasmid transfer in mixed microbial communities. The fate of plasmids in microbial communities...... of microbial communities may be directly interconnected through transfer of BHR plasmids at a so far unrecognized level. The developed method furthermore enabled me to explore how agronomic practices may affect gene transfer in soil microbial communities. I compared bacterial communities extracted from plots...

  7. Community Hospital Telehealth Consortium

    National Research Council Canada - National Science Library

    Williams, Elton

    2004-01-01

    The Community Hospital Telehealth Consortium is a unique, forward-thinking, community-based healthcare service project organized around 5 not-for-profit community hospitals located throughout Louisiana and Mississippi...

  8. Involving the Community

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

    Step 3: Identifying the different community groups and other stakeholders concerned .... How can two-way communication enhance community participation in ...... for maintenance and the rights of specific community groups to drinkable water.

  9. Community Hospital Telehealth Consortium

    National Research Council Canada - National Science Library

    Williams, Elton

    2003-01-01

    The Community Hospital Telehealth Consortium is a unique, forward-thinking, community-based healthcare service project organized around 5 not-for-profit community hospitals located throughout Louisiana and Mississippi...

  10. Community Hospital Telehealth Consortium

    National Research Council Canada - National Science Library

    Williams, Jr, Elton L

    2007-01-01

    The Community Hospital Telehealth Consortium is a unique, forward-thinking, community-based healthcare service project organized around 5 not-for-profit community hospitals located throughout Louisiana and Mississippi...

  11. Community Mentoring: A Tool for Successful Communities

    Science.gov (United States)

    Dodge, Kathryn E.

    2015-01-01

    Mentoring occurs in an ad hoc and largely invisible manner in communities. This mentoring happens through modeling, storytelling, and asking open-ended questions. If Extension specialists and agents were more conscious and intentional about teaching community members and leaders about community mentoring, they would be more successful in resolving…

  12. Keeping "Community" in a Community Land Trust

    Science.gov (United States)

    Gray, Karen A.; Galande, Mugdha

    2011-01-01

    This instrumental case study examined the role of grassroots community organizing in a community land trust (CLT) in a southern U.S. city. Twenty-nine homeowners, renters, board members, community members, and current and former CLT employees were interviewed. In addition, two focus groups of 11 and six participants composed of CLT residents and…

  13. Strong seasonality and interannual recurrence in marine myovirus communities.

    Science.gov (United States)

    Pagarete, A; Chow, C-E T; Johannessen, T; Fuhrman, J A; Thingstad, T F; Sandaa, R A

    2013-10-01

    The temporal community dynamics and persistence of different viral types in the marine environment are still mostly obscure. Polymorphism of the major capsid protein gene, g23, was used to investigate the community composition dynamics of T4-like myoviruses in a North Atlantic fjord for a period of 2 years. A total of 160 unique operational taxonomic units (OTUs) were identified by terminal restriction fragment length polymorphism (TRFLP) of the gene g23. Three major community profiles were identified (winter-spring, summer, and autumn), which resulted in a clear seasonal succession pattern. These seasonal transitions were recurrent over the 2 years and significantly correlated with progression of seawater temperature, Synechococcus abundance, and turbidity. The appearance of the autumn viral communities was concomitant with the occurrence of prominent Synechococcus blooms. As a whole, we found a highly dynamic T4-like viral community with strong seasonality and recurrence patterns. These communities were unexpectedly dominated by a group of persistently abundant viruses.

  14. Renal Gene Expression Database (RGED): a relational database of gene expression profiles in kidney disease.

    Science.gov (United States)

    Zhang, Qingzhou; Yang, Bo; Chen, Xujiao; Xu, Jing; Mei, Changlin; Mao, Zhiguo

    2014-01-01

    We present a bioinformatics database named Renal Gene Expression Database (RGED), which contains comprehensive gene expression data sets from renal disease research. The web-based interface of RGED allows users to query the gene expression profiles in various kidney-related samples, including renal cell lines, human kidney tissues and murine model kidneys. Researchers can explore certain gene profiles, the relationships between genes of interests and identify biomarkers or even drug targets in kidney diseases. The aim of this work is to provide a user-friendly utility for the renal disease research community to query expression profiles of genes of their own interest without the requirement of advanced computational skills. Website is implemented in PHP, R, MySQL and Nginx and freely available from http://rged.wall-eva.net. http://rged.wall-eva.net. © The Author(s) 2014. Published by Oxford University Press.

  15. Renal Gene Expression Database (RGED): a relational database of gene expression profiles in kidney disease

    Science.gov (United States)

    Zhang, Qingzhou; Yang, Bo; Chen, Xujiao; Xu, Jing; Mei, Changlin; Mao, Zhiguo

    2014-01-01

    We present a bioinformatics database named Renal Gene Expression Database (RGED), which contains comprehensive gene expression data sets from renal disease research. The web-based interface of RGED allows users to query the gene expression profiles in various kidney-related samples, including renal cell lines, human kidney tissues and murine model kidneys. Researchers can explore certain gene profiles, the relationships between genes of interests and identify biomarkers or even drug targets in kidney diseases. The aim of this work is to provide a user-friendly utility for the renal disease research community to query expression profiles of genes of their own interest without the requirement of advanced computational skills. Availability and implementation: Website is implemented in PHP, R, MySQL and Nginx and freely available from http://rged.wall-eva.net. Database URL: http://rged.wall-eva.net PMID:25252782

  16. Global gene expression in Escherichia coli biofilms

    DEFF Research Database (Denmark)

    Schembri, Mark; Kjærgaard, K.; Klemm, Per

    2003-01-01

    It is now apparent that microorganisms undergo significant changes during the transition from planktonic to biofilm growth. These changes result in phenotypic adaptations that allow the formation of highly organized and structured sessile communities, which possess enhanced resistance to antimicr......It is now apparent that microorganisms undergo significant changes during the transition from planktonic to biofilm growth. These changes result in phenotypic adaptations that allow the formation of highly organized and structured sessile communities, which possess enhanced resistance...... the transition to biofilm growth, and these included genes expressed under oxygen-limiting conditions, genes encoding (putative) transport proteins, putative oxidoreductases and genes associated with enhanced heavy metal resistance. Of particular interest was the observation that many of the genes altered...... in expression have no current defined function. These genes, as well as those induced by stresses relevant to biofilm growth such as oxygen and nutrient limitation, may be important factors that trigger enhanced resistance mechanisms of sessile communities to antibiotics and hydrodynamic shear forces....

  17. On Community Education and Community Development

    Directory of Open Access Journals (Sweden)

    Dušana Findeisen

    1996-12-01

    Full Text Available In this paper Dušana Findeisen introduces community education and development. She particularly insists upon the fact that in the future our life will not be organised around a paid full time job and that we will be forced into searching other ways of getting involved into society and to acquire our social identity. Community education is one of the ways we could eventually choose. Since community development education in Slovenia has not developed yet the author begins by describing some basic concepts like community and history of community education and community development movement. Further on, she introduces the Andragogical Summer School based in a small Slovenian town, its aim being to encourage Slovenian adult educators to encourage community development projects.

  18. Conjugative plasmids: Vessels of the communal gene pool

    DEFF Research Database (Denmark)

    Norman, Anders; Hansen, Lars H.; Sørensen, Søren Johannes

    2009-01-01

    to the hosts and, potentially, other resident prokaryotes within specific environmental niches. Insight into the evolution of plasmid modules therefore contributes to our knowledge of gene dissemination and evolution within prokaryotic communities. This communal pool provides the prokaryotes with an important...... mechanistic framework for obtaining adaptability and functional diversity that alleviates the need for large genomes of specialized ‘private genes'....

  19. A case of familial transmission of community-acquired methicillin-resistant Staphylococcus aureus carrying the lnu(A gene in Santa Fe city, Argentina Caso de transmisión familiar de Staphylococcus aureus resistente a la meticilina adquirido en la comunidad portador del gen lnu(A en la ciudad de Santa Fe, Argentina

    Directory of Open Access Journals (Sweden)

    Emilce de los A Méndez

    2012-12-01

    Full Text Available Community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA is increasingly recognized as an important pathogen causing skin and soft tissue infections as well as necrotizing pneumonia. We describe a case of familial transmission of CA-MRSA between a 6-month-old boy and his mother in Santa Fe City, Argentina. Both isolates showed an identical antimicrobial susceptibility profile, carried type IV SCCmec and harboured the pvl and the lnu(A genes. Isolates showed indistinguishable SmaI-PFGE patterns confirming their genetic relationship. These results corroborate the intrafamilial transmission of CA-MRSA and might associate this strain with the repetitive events of furunculosis within the family.Staphylococcus aureus resistente a la meticilina adquirido en la comunidad (SARM-AC es reconocido como un patógeno importante que causa infecciones de piel y partes blandas y neumonía necrotizante. Describimos un caso de transmisión familiar de SARM-AC entre un nino de 6 meses de edad y su madre en la ciudad de Santa Fe, Argentina. Ambos aislamientos mostraron idéntico perfil de sensibilidad a los antimicrobianos, tenían el SCCmec tipo IV, y contenían los genes pvl y lnu(A. Los aislamientos presentaron patrones de SmaI-PFGE indistinguibles entre sí, lo cual confirmó su relación genética. Estos resultados corroboran la transmisión intrafamiliar de SARM-AC; asimismo, este aislamiento podría asociarse con los eventos repetitivos de furunculosis en la familia.

  20. Quantitative phylogenetic assessment of microbial communities indiverse environments

    Energy Technology Data Exchange (ETDEWEB)

    von Mering, C.; Hugenholtz, P.; Raes, J.; Tringe, S.G.; Doerks,T.; Jensen, L.J.; Ward, N.; Bork, P.

    2007-01-01

    The taxonomic composition of environmental communities is an important indicator of their ecology and function. Here, we use a set of protein-coding marker genes, extracted from large-scale environmental shotgun sequencing data, to provide a more direct, quantitative and accurate picture of community composition than traditional rRNA-based approaches using polymerase chain reaction (PCR). By mapping marker genes from four diverse environmental data sets onto a reference species phylogeny, we show that certain communities evolve faster than others, determine preferred habitats for entire microbial clades, and provide evidence that such habitat preferences are often remarkably stable over time.