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

PubMed

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.

Radical Transparency: Open Access as a Key Concept in Wiki Pedagogy

ERIC Educational Resources Information Center

Baltzersen, Rolf K.

2010-01-01

Educators have just started to use wikis and most of the educational research to date has focused primarily on the use of local wikis with access limitations. There seems to be little research related to how students can contribute in global, transparent wiki communities such as "Wikipedia" and "Wikibooks". The purpose of this…

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

PubMed

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.

Using Wiki to Create a Learning Community for Chemistry Teacher Leaders

ERIC Educational Resources Information Center

Shwartz, Y.; Katchevitch, D.

2013-01-01

This study focuses on using wikis as a learning environment, as part of a professional development program for chemistry teacher leaders. The study was performed in Israel and involved 20 chemistry teachers. One goal was to investigate how using wiki may promote effective science teacher professional development. Various aspects of the teachers'…

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

PubMed Central

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

2016-01-01

Background 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. Objective 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. Methods 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. Results 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

Engaging With a Wiki Related to Knowledge Translation: A Survey of WhatisKT Wiki Users

PubMed Central

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

2014-01-01

Background 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. Objective 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. Methods 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. Results 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. Conclusions 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

Wikis, Blogs, & More, Oh My!

ERIC Educational Resources Information Center

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…

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

PubMed

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.

The Executive Wiki: Wikis Can Be a Multitasking Administrators' Best Friend

ERIC Educational Resources Information Center

Warlick, David

2007-01-01

The poster child for the Web 2.0 movement, the wiki, demonstrates the spirit of open content more clearly than any other application. Wikipedia, the most famous wiki and the world's largest encyclopedia, defines a wiki as a Web site that "allows visitors to add, remove, edit, and change content." Even though it is a controversial information…

NASA Human Research Wiki - An Online Collaboration Tool

NASA Technical Reports Server (NTRS)

Barr, Y. R.; Rasbury, J.; Johnson, J.; Barsten, K.; Saile, L.; Watkins, S. D.

2011-01-01

In preparation for exploration-class missions, the Exploration Medical Capability (ExMC) element of NASA's Human Research Program (HRP) has compiled a large evidence base, which previously was available only to persons within the NASA community. The evidence base is comprised of several types of data, for example: information on more than 80 medical conditions which could occur during space flight, derived from several sources (including data on incidence and potential outcomes of these medical conditions, as captured in the Integrated Medical Model's Clinical Finding Forms). In addition, approximately 35 gap reports are included in the evidence base, identifying current understanding of the medical challenges for exploration, as well as any gaps in knowledge and/or technology that would need to be addressed in order to provide adequate medical support for these novel missions. In an effort to make the ExMC information available to the general public and increase collaboration with subject matter experts within and outside of NASA, ExMC has developed an online collaboration tool, very similar to a wiki, titled the NASA Human Research Wiki. The platform chosen for this data sharing, and the potential collaboration it could generate, is a MediaWiki-based application that would house the evidence, allow "read only" access to all visitors to the website, and editorial access to credentialed subject matter experts who have been approved by the Wiki's editorial board. Although traditional wikis allow users to edit information in real time, the NASA Human Research Wiki includes a peer review process to ensure quality and validity of information. The wiki is also intended to be a pathfinder project for other HRP elements that may want to use this type of web-based tool. The wiki website will be released with a subset of the data described and will continue to be populated throughout the year.

Using Wikis in Academic Libraries

ERIC Educational Resources Information Center

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…

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

NASA Technical Reports Server (NTRS)

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 the 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.

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

NASA Technical Reports Server (NTRS)

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.

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

NASA Technical Reports Server (NTRS)

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.

Wiki Writers: Students and Teachers Making Connections across Communities

ERIC Educational Resources Information Center

Andes, Laurie; Claggett, Elizabeth

2011-01-01

Expressions of delight and anticipation are a direct result of a schoolwide writing program designed by teachers to develop language skills in special education students. These second graders participated in a writing project that made use of wikis to facilitate collaboration among the students, parents, teachers, and university members of their…

Wikis in Collaborative Educational Scenarios: Integrated in LMS or Standalone Wikis?

ERIC Educational Resources Information Center

Forment, Marc Alier; De Pedro, Xavier; Casan, Maria Jose; Piguillem, Jordi; Galanis, Nikolas

2012-01-01

This article outlines a set of features that wiki engines require to successfully host collaborative educational scenarios. The authors explore multiple issues that deal with the use wikis with learning activities. One of the first issues to solve is software support for assessment methodologies. The second is choosing between using an integrated…

Designing Collaborative E-Learning Environments Based upon Semantic Wiki: From Design Models to Application Scenarios

ERIC Educational Resources Information Center

Li, Yanyan; Dong, Mingkai; Huang, Ronghuai

2011-01-01

The knowledge society requires life-long learning and flexible learning environment that enables fast, just-in-time and relevant learning, aiding the development of communities of knowledge, linking learners and practitioners with experts. Based upon semantic wiki, a combination of wiki and Semantic Web technology, this paper designs and develops…

VuWiki: An Ontology-Based Semantic Wiki for Vulnerability Assessments

NASA Astrophysics Data System (ADS)

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

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

ERIC Educational Resources Information Center

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…

A Longitudinal Study to Determine If Wiki Work Builds Community among Agricultural Adult Education Students

ERIC Educational Resources Information Center

Kelsey, Kathleen D.; Lin, Hong; Franke-Dvorak, Tanya C.

2011-01-01

Wiki has been lauded as a tool that enhances collaborative writing in educational settings and moves learners toward a state of communal constructivism (Holmes, Tangney, FitzGibbon, Savage, & Mehan., 2001). Many pedagogical claims exist regarding the benefits of using wiki. However, these claims have rarely been challenged. This study used a…

Promoting pedagogical experimentation: using a wiki in graduate level education.

PubMed

Martin, Carolyn Thompson

2012-12-01

Learning to write in a scholarly manner is often a challenge for graduate students. This study describes nursing students' use of a wiki to encourage writing collaboration among students by allowing them to cocreate, review, and edit each other's material as it is created. Students are introduced to the online wiki site the first week of the course. A technology representative assists students with a short introduction and class visits. All students participate in making decisions related to the overall character of the site. They create pages on topics related to their clinical placements. Student pages are peer and content expert reviewed for accuracy and comprehensiveness. Students include pictures, YouTube links, attachments, videos, and Web site links into their pages. Evidence-based content includes pharmacology, diagnostic criteria, pathophysiology, history, genetics, and references. Students present their pages, and feedback questionnaires are collected at the end of the semester. The wiki writing assignment introduces students, faculty, and the community to graduate student projects while exposing students to new technology. Areas explored include issues and best practices regarding classroom pedagogy, as well as student support and technical challenges in the use of a wiki. Suggestions for improvement are discussed.

Techtalk: Wikis and Collaborative Knowledge Construction

ERIC Educational Resources Information Center

Caverly, David C.; Ward, Anne

2008-01-01

In the last column, we began discussing Web 2.0 applications. In this column, we'll review participatory, social networking software called "wikis." We'll define wikis, discuss their use in college classrooms, explore benefits provided for collaborative knowledge construction, and explain five types of wikis with applications to developmental…

Wiki use in mental health practice: recognizing potential use of collaborative technology.

PubMed

Bastida, Richard; McGrath, Ian; Maude, Phil

2010-04-01

Web 2.0, the second-generation of the World Wide Web, differs to earlier versions of Web development and design in that it facilitates more user-friendly, interactive information sharing and mechanisms for greater collaboration between users. Examples of Web 2.0 include Web-based communities, hosted services, social networking sites, video sharing sites, blogs, mashups, and wikis. Users are able to interact with others across the world or to add to or change website content. This paper examines examples of wiki use in the Australian mental health sector. A wiki can be described as an online collaborative and interactive database that can be easily edited by users. They are accessed via a standard Web browser which has an interface similar to traditional Web pages, thus do not require special application or software for the user. Although there is a paucity of literature describing wiki use in mental health, other industries have developed uses, including a repository of knowledge, a platform for collaborative writing, a project management tool, and an alternative to traditional Web pages or Intranets. This paper discusses the application of wikis in other industries and offers suggestions by way of examples of how this technology could be used in the mental health sector.

TissueWikiMobile: an Integrative Protein Expression Image Browser for Pathological Knowledge Sharing and Annotation on a Mobile Device

PubMed Central

Cheng, Chihwen; Stokes, Todd H.; Hang, Sovandy; Wang, May D.

2016-01-01

Doctors need fast and convenient access to medical data. This motivates the use of mobile devices for knowledge retrieval and sharing. We have developed TissueWikiMobile on the Apple iPhone and iPad to seamlessly access TissueWiki, an enormous repository of medical histology images. TissueWiki is a three terabyte database of antibody information and histology images from the Human Protein Atlas (HPA). Using TissueWikiMobile, users are capable of extracting knowledge from protein expression, adding annotations to highlight regions of interest on images, and sharing their professional insight. By providing an intuitive human computer interface, users can efficiently operate TissueWikiMobile to access important biomedical data without losing mobility. TissueWikiMobile furnishes the health community a ubiquitous way to collaborate and share their expert opinions not only on the performance of various antibodies stains but also on histology image annotation. PMID:27532057

The application of wiki technology in medical education.

PubMed

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.

Add Java extensions to your wiki: Java applets can bring dynamic functionality to your wiki pages

DOE Office of Scientific and Technical Information (OSTI.GOV)

Scarberry, Randall E.

Virtually everyone familiar with today’s world wide web has encountered the free online encyclopedia Wikipedia many times. What you may not know is that Wikipedia is driven by an excellent open-source product called MediaWiki which is available to anyone for free. This has led to a proliferation of wiki sites devoted to just about any topic one can imagine. Users of a wiki can add content -- all that is required of them is that they type in their additions into their web browsers using the simple markup language called wikitext. Even better, the developers of wikitext made it extensible.more » With a little server-side development of your own, you can add your own custom syntax. Users aware of your extensions can then utilize them on their wiki pages with a few simple keystrokes. These extensions can be custom decorations, formatting, web applications, and even instances of the venerable old Java applet. One example of a Java applet extension is the Jmol extension (REF), used to embed a 3-D molecular viewer. This article will walk you through the deployment of a fairly elaborate applet via a MediaWiki extension. By no means exhaustive -- an entire book would be required for that -- it will demonstrate how to give the applet resize handles using using a little Javascript and CSS coding and some popular Javascript libraries. It even describes how a user may customize the extension somewhat using a wiki template. Finally, it explains a rudimentary persistence mechanism which allows applets to save data directly to the wiki pages on which they reside.« less

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

PubMed Central

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

Building a biomedical semantic network in Wikipedia with Semantic Wiki Links

PubMed Central

Good, Benjamin M.; Clarke, Erik L.; Loguercio, Salvatore; Su, Andrew I.

2012-01-01

Wikipedia is increasingly used as a platform for collaborative data curation, but its current technical implementation has significant limitations that hinder its use in biocuration applications. Specifically, while editors can easily link between two articles in Wikipedia to indicate a relationship, there is no way to indicate the nature of that relationship in a way that is computationally accessible to the system or to external developers. For example, in addition to noting a relationship between a gene and a disease, it would be useful to differentiate the cases where genetic mutation or altered expression causes the disease. Here, we introduce a straightforward method that allows Wikipedia editors to embed computable semantic relations directly in the context of current Wikipedia articles. In addition, we demonstrate two novel applications enabled by the presence of these new relationships. The first is a dynamically generated information box that can be rendered on all semantically enhanced Wikipedia articles. The second is a prototype gene annotation system that draws its content from the gene-centric articles on Wikipedia and exposes the new semantic relationships to enable previously impossible, user-defined queries. Database URL: http://en.wikipedia.org/wiki/Portal:Gene_Wiki PMID:22434829

Building a biomedical semantic network in Wikipedia with Semantic Wiki Links.

PubMed

Good, Benjamin M; Clarke, Erik L; Loguercio, Salvatore; Su, Andrew I

2012-01-01

Wikipedia is increasingly used as a platform for collaborative data curation, but its current technical implementation has significant limitations that hinder its use in biocuration applications. Specifically, while editors can easily link between two articles in Wikipedia to indicate a relationship, there is no way to indicate the nature of that relationship in a way that is computationally accessible to the system or to external developers. For example, in addition to noting a relationship between a gene and a disease, it would be useful to differentiate the cases where genetic mutation or altered expression causes the disease. Here, we introduce a straightforward method that allows Wikipedia editors to embed computable semantic relations directly in the context of current Wikipedia articles. In addition, we demonstrate two novel applications enabled by the presence of these new relationships. The first is a dynamically generated information box that can be rendered on all semantically enhanced Wikipedia articles. The second is a prototype gene annotation system that draws its content from the gene-centric articles on Wikipedia and exposes the new semantic relationships to enable previously impossible, user-defined queries. DATABASE URL: http://en.wikipedia.org/wiki/Portal:Gene_Wiki.

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

PubMed

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.

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

PubMed

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.

Eight Ways to Use School Wikis

ERIC Educational Resources Information Center

Nielsen, Lisa

2009-01-01

Wikis are great tools to help a school enrich instruction, and increase communication and collaboration among staff. They are also free (for educators using wikispaces) and provide unlimited storage for digital materials including video, screencasts, presentations, PDFs, etc. This article presents eight ways to use wikis in class.

Wiki Behavior in the Workplace: Emotional Aspects of Content Development

ERIC Educational Resources Information Center

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…

The Wiki as a Virtual Space for Qualitative Data Collection

ERIC Educational Resources Information Center

Castanos, Carolina; Piercy, Fred P.

2010-01-01

The authors make a case for using wiki technology in qualitative research. A wiki is an online database that allows users to create, edit, and/or reflect on the content of a web page. Thus, wiki technology can support qualitative research that attempts to understand the shared thinking of participants. To illustrate the use of the wiki for this…

A Neutral Control Condition for Hypnosis Experiments: "Wiki" Text.

PubMed

Varga, Katalin; Kekecs, Zoltán; Myhre, P S; Józsa, Emese

2017-01-01

A new control condition called Wiki is introduced. Key themes of each test suggestion of the Stanford Hypnotic Susceptibility Scale, Form C, were matched by a corresponding extract from Wikipedia.org. The authors compared phenomenological reports of participants across 4 conditions: hypnosis split into high and low hypnotizable subgroups, music, and Wiki condition, using the Phenomenology of Consciousness Inventory. High hypnotizables undergoing hypnosis reported higher altered experience and altered states of awareness than individuals in the Wiki condition, supporting the authors' hypothesis that the Wiki condition does not evoke an altered state of consciousness (internal dialogue, volitional control, and self-awareness did not differ). Wiki might be a viable control condition in hypnosis research given further examination.

Investigating Pedagogical Value of Wiki Technology

ERIC Educational Resources Information Center

Hazari, Sunil; North, Alexa; Moreland, Deborah

2009-01-01

This exploratory study investigates the potential of Wiki technology as a tool for teaching and learning. Wikis are a component of Web 2.0 technology tools that provide collaborative features and active learning opportunities in a web-based environment. This research study sought to empirically determine the pedagogical value of using Wiki…

Wiki surveys: open and quantifiable social data collection.

PubMed

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.

Wiki Surveys: Open and Quantifiable Social Data Collection

PubMed Central

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

Choosing a Wiki Platform for Student Projects--Lessons Learned

ERIC Educational Resources Information Center

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…

Investment and Return: Wiki Engagement in a "Remedial" ESL Writing Course

ERIC Educational Resources Information Center

Nakamaru, Sarah

2012-01-01

This study explores the extent to which students in a community college remedial English as a second language (ESL) course engaged with a class wiki and the relationship between their pattern of engagement over time and success in exiting remediation. Participants included 47 students in two sections of ESL writing during the spring 2009 semester.…

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

ERIC Educational Resources Information Center

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…

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

NASA Astrophysics Data System (ADS)

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.

Using Wikis to Promote Collaborative EFL Writing

ERIC Educational Resources Information Center

Aydin, Zelilha; Yildiz, Senem

2014-01-01

This study focuses on the use of wikis in collaborative writing projects in foreign language learning classrooms. A total of 34 intermediate level university students learning English as a foreign language (EFL) were asked to accomplish three different wiki-based collaborative writing tasks, (argumentative, informative and decision-making) working…

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

PubMed Central

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

2010-01-01

Background: 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). Methods and Results: 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. Conclusions: 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. PMID:20805963

Using Wikis and Collaborative Learning for Science Teachers' Professional Development

ERIC Educational Resources Information Center

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,…

Supporting community annotation and user collaboration in the integrated microbial genomes (IMG) system

DOE PAGES

Chen, I-Min A.; Markowitz, Victor M.; Palaniappan, Krishna; ...

2016-04-26

Background: The exponential growth of genomic data from next generation technologies renders traditional manual expert curation effort unsustainable. Many genomic systems have included community annotation tools to address the problem. Most of these systems adopted a "Wiki-based" approach to take advantage of existing wiki technologies, but encountered obstacles in issues such as usability, authorship recognition, information reliability and incentive for community participation. Results: Here, we present a different approach, relying on tightly integrated method rather than "Wiki-based" method, to support community annotation and user collaboration in the Integrated Microbial Genomes (IMG) system. The IMG approach allows users to use existingmore » IMG data warehouse and analysis tools to add gene, pathway and biosynthetic cluster annotations, to analyze/reorganize contigs, genes and functions using workspace datasets, and to share private user annotations and workspace datasets with collaborators. We show that the annotation effort using IMG can be part of the research process to overcome the user incentive and authorship recognition problems thus fostering collaboration among domain experts. The usability and reliability issues are addressed by the integration of curated information and analysis tools in IMG, together with DOE Joint Genome Institute (JGI) expert review. Conclusion: By incorporating annotation operations into IMG, we provide an integrated environment for users to perform deeper and extended data analysis and annotation in a single system that can lead to publications and community knowledge sharing as shown in the case studies.« less

Supporting community annotation and user collaboration in the integrated microbial genomes (IMG) system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, I-Min A.; Markowitz, Victor M.; Palaniappan, Krishna

Background: The exponential growth of genomic data from next generation technologies renders traditional manual expert curation effort unsustainable. Many genomic systems have included community annotation tools to address the problem. Most of these systems adopted a "Wiki-based" approach to take advantage of existing wiki technologies, but encountered obstacles in issues such as usability, authorship recognition, information reliability and incentive for community participation. Results: Here, we present a different approach, relying on tightly integrated method rather than "Wiki-based" method, to support community annotation and user collaboration in the Integrated Microbial Genomes (IMG) system. The IMG approach allows users to use existingmore » IMG data warehouse and analysis tools to add gene, pathway and biosynthetic cluster annotations, to analyze/reorganize contigs, genes and functions using workspace datasets, and to share private user annotations and workspace datasets with collaborators. We show that the annotation effort using IMG can be part of the research process to overcome the user incentive and authorship recognition problems thus fostering collaboration among domain experts. The usability and reliability issues are addressed by the integration of curated information and analysis tools in IMG, together with DOE Joint Genome Institute (JGI) expert review. Conclusion: By incorporating annotation operations into IMG, we provide an integrated environment for users to perform deeper and extended data analysis and annotation in a single system that can lead to publications and community knowledge sharing as shown in the case studies.« less

Supporting community annotation and user collaboration in the integrated microbial genomes (IMG) system.

PubMed

Chen, I-Min A; Markowitz, Victor M; Palaniappan, Krishna; Szeto, Ernest; Chu, Ken; Huang, Jinghua; Ratner, Anna; Pillay, Manoj; Hadjithomas, Michalis; Huntemann, Marcel; Mikhailova, Natalia; Ovchinnikova, Galina; Ivanova, Natalia N; Kyrpides, Nikos C

2016-04-26

The exponential growth of genomic data from next generation technologies renders traditional manual expert curation effort unsustainable. Many genomic systems have included community annotation tools to address the problem. Most of these systems adopted a "Wiki-based" approach to take advantage of existing wiki technologies, but encountered obstacles in issues such as usability, authorship recognition, information reliability and incentive for community participation. Here, we present a different approach, relying on tightly integrated method rather than "Wiki-based" method, to support community annotation and user collaboration in the Integrated Microbial Genomes (IMG) system. The IMG approach allows users to use existing IMG data warehouse and analysis tools to add gene, pathway and biosynthetic cluster annotations, to analyze/reorganize contigs, genes and functions using workspace datasets, and to share private user annotations and workspace datasets with collaborators. We show that the annotation effort using IMG can be part of the research process to overcome the user incentive and authorship recognition problems thus fostering collaboration among domain experts. The usability and reliability issues are addressed by the integration of curated information and analysis tools in IMG, together with DOE Joint Genome Institute (JGI) expert review. By incorporating annotation operations into IMG, we provide an integrated environment for users to perform deeper and extended data analysis and annotation in a single system that can lead to publications and community knowledge sharing as shown in the case studies.

WhatisKT wiki: a case study of a platform for knowledge translation terms and definitions — descriptive analysis

PubMed Central

2013-01-01

Background More than a hundred terms, often with unclear definitions and varying emphases, are used by health research and practice communities across the world who are interested in getting the best possible evidence applied (e.g., knowledge translation, implementation science, diffusion of innovations, and technology transfer). This makes finding published evidence difficult and can result in reduced, misinterpreted, or challenging interactions among professionals. Open dialogue and interaction among various professionals is needed to achieve consolidation of vocabulary. We use case report methods to describe how we sought to build an online tool to present the range of terms and facilitate the dialogue process across groups and disciplines interested in harnessing research evidence for healthcare. Methods We used a wiki platform from Wikispaces to present the problem of terminology and make a case and opportunity for collaboration on usage. Wikis are web sites where communities of users can collaborate online to build content and discuss progress. We gathered terms related to getting research into practice, sought published definitions, and posted these on the wiki (WhatisKT http://whatiskt.wikispaces.com/). We built the wiki in mid-2008 and promoted it through various groups and publications. This report describes the content of the site, our promotion efforts, use of the site, and how the site was used for collaboration up to the end of 2011. Results The WhatisKT wiki site now includes more than 120 pages. Traffic to the site has increased substantially from an average of 200 monthly visits in 2008 to 1700 in 2011. Visitors from 143 countries viewed the wiki in 2011, compared with 12 countries in 2008. However, most use has been limited to short term accesses of about 40 seconds per visit, and discussion of consolidation and solidifying terminology is conspicuously absent. Conclusions Although considerable interest exists in the terms and definitions related

Wiki Effect on English as a Foreign Language Writing Achievement

ERIC Educational Resources Information Center

Savran Çelik, Seyd; Aydin, Selami

2016-01-01

The number of the studies conducted on the use of wikis on the English as a foreign language (EFL) learning process has remained fairly limited. More specifically, in the Turkish EFL context, little attention has been paid to the effects of wikis on EFL writing achievement. Thus, this study aims to examine the effects of a wiki-based writing…

WikiTextbooks: Designing Your Course around a Collaborative Writing Project

ERIC Educational Resources Information Center

Katz, Brian P.; Thoren, Elizabeth

2014-01-01

We have used wiki technology to support large-scale, collaborative writing projects in which the students build reference texts (called WikiTextbooks). The goal of this paper is to prepare readers to adapt this idea for their own courses. We give examples of the implementation of WikiTextbooks in a variety of courses, including lecture and…

Extending inter-professional learning through the use of a multi-disciplinary Wiki.

PubMed

Stephens, Melanie; Robinson, Leslie; McGrath, Denis

2013-11-01

This paper reports our experiences of a student learning activity which employed a Wiki for student radiographers and nurses to build on an inter-professional learning event. The aim of the Wiki was to facilitate inter-professional learning for students who, having met face-to-face once for a classroom based activity, would not be timetabled to meet again. It was designed to allow students from differing disciplines to: construct knowledge together, learn from and about one another, and collaboratively produce a textual learning resource. 150 nursing and radiography undergraduates were provided with a PBL trigger related to the acute presentation of stroke. The students met once (5 mixed-discipline groups) to discuss the role of the professions and the outcomes for the trigger scenario. Further learning was enabled through the provision of a Wiki for each group. At week 4, all Wikis were made visible for group peer assessment. Wiki editing skills were provided by student 'Wiki champions', who cascaded training to their peers. We report and reflect on the students' evaluations of both the Wiki as process and outcome and discuss the value of Wikis for inter-professional learning. Findings show that, in addition to being an enjoyable and flexible learning experience, the Wiki satisfied its intended aims. There was a variation in the level and quality of student participation the causes of which are discussed. Ground rules for effective Wiki use are proposed. Copyright © 2013 Elsevier Ltd. All rights reserved.

Use and acceptance of Wiki systems for students of veterinary medicine

PubMed Central

Kolski, Darius; Arlt, Sebastian; Birk, Stephan; Heuwieser, Wolfgang

2013-01-01

Objective: Wiki systems are gaining importance concerning the use in education, especially among young users. The aim of our study was to examine, how students of veterinary medicine commonly use wiki systems, whether they consider a veterinary wiki system useful and if they would participate in writing content. Methodology: For data collection a questionnaire was provided to students (n=210) of the faculty of Veterinary Medicine at the Freie Universität Berlin, Germany. It contained questions regarding the use of Wikipedia in general and concerning educational issues. Results: Most respondents, especially students in the first years, had comprehensive experience in the use of Wikipedia and veterinary wiki systems. In contrast, the experience in writing or editing of information was low (8.6% Wikipedia, 15.3% veterinary wiki systems). Male students had significantly more writing experience than females (p=0,008). In addition, students of the higher years were more experienced in writing and editing than students of the first year (7.4% in the 4th year). The familiarity with wiki systems offered by universities was low. The majority of students (96.2%) are willing to use veterinary wiki systems as an information tool in the future. Nevertheless, only a low percentage is willing to write or edit content. Many students, however, expect a better learning success when writing own texts. In general, students consider the quality of information in a wiki system as correct. Conclusion: In conclusion, wiki systems are considered a useful tool to gain information. This will lead to a successful implementation of wiki systems in veterinary education. A main challenge will be to develop concepts to activate students to participate not only in reading but in the writing and editing process. PMID:23467415

Social Negotiations in a Wiki Environment: A Case Study with Pre-Service Teachers

ERIC Educational Resources Information Center

Vratulis, Vetta; Dobson, Teresa M.

2008-01-01

Understanding of the nature of social negotiations in social software spaces used in support of formal, face-to-face education remains limited. In this paper, we consider how a community of learners working collaboratively in a wiki environment established social hierarchies and negotiated power. Described is a study with 36 pre-service teachers…

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

PubMed Central

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

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

PubMed

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.

The impact of group membership on collaborative learning with wikis.

PubMed

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.

The Impact of Group Membership on Collaborative Learning with Wikis

PubMed Central

Matschke, Christina; Moskaliuk, Johannes

2013-01-01

Abstract 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. PMID:23113690

Creating an open access cal/val repository via the LACO-Wiki online validation platform

NASA Astrophysics Data System (ADS)

Perger, Christoph; See, Linda; Dresel, Christopher; Weichselbaum, Juergen; Fritz, Steffen

2017-04-01

There is a major gap in the amount of in-situ data available on land cover and land use, either as field-based ground truth information or from image interpretation, both of which are used for the calibration and validation (cal/val) of products derived from Earth Observation. Although map producers generally publish their confusion matrices and the accuracy measures associated with their land cover and land use products, the cal/val data (also referred to as reference data) are rarely shared in an open manner. Although there have been efforts in compiling existing reference datasets and making them openly available, e.g. through the GOFC/GOLD (Global Observation for Forest Cover and Land Dynamics) portal or the European Commission's Copernicus Reference Data Access (CORDA), this represents a tiny fraction of the reference data collected and stored locally around the world. Moreover, the validation of land cover and land use maps is usually undertaken with tools and procedures specific to a particular institute or organization due to the lack of standardized validation procedures; thus, there are currently no incentives to share the reference data more broadly with the land cover and land use community. In an effort to provide a set of standardized, online validation tools and to build an open repository of cal/val data, the LACO-Wiki online validation portal has been developed, which will be presented in this paper. The portal contains transparent, documented and reproducible validation procedures that can be applied to local as well as global products. LACO-Wiki was developed through a user consultation process that resulted in a 4-step wizard-based workflow, which supports the user from uploading the map product for validation, through to the sampling process and the validation of these samples, until the results are processed and a final report is created that includes a range of commonly reported accuracy measures. One of the design goals of LACO-Wiki has been

What Does Wiki Reveal about the Knowledge Processing Strategies of School Pupils? Seventh-Graders as Users of Wiki and Processors of Knowledge in a Collaborative Writing Project

ERIC Educational Resources Information Center

Ahlholm, Maria; Grünthal, Satu; Harjunen, Elina

2017-01-01

On the basis of one teaching project carried out in a school, this article discusses collaborative writing in wiki platforms. It aims to find out what wiki reveals about pupils' knowledge construction, creation, and division and their collaborative writing skills. In this project, wiki is treated as a useful tool for analyzing these processes…

Wiki: Using the Web Connections to Connect Students

ERIC Educational Resources Information Center

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…

Wiki Use that Increases Communication and Collaboration Motivation

ERIC Educational Resources Information Center

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…

Using Wikis to Foster Collaborative Writing: Exploring Influencing Factors to Successful Implementation

ERIC Educational Resources Information Center

Hadjerrouit, Said

2012-01-01

Wiki technology provides new opportunities to foster collaborative learning in various educational settings. To empirically examine the impact of wikis on learning, this article explores students' collaborative writing activities performed on MediaWiki. The activities were analyzed using a taxonomy with ten categories (clarify content, add…

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

ERIC Educational Resources Information Center

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…

Cooperative Learning at a Distance: An Experiment with Wikis

ERIC Educational Resources Information Center

Campbell, Katherine; Ellingson, Dee Ann

2010-01-01

The merits of incorporating group work into learning environments are well established. Online classes and other distance learning settings, however, can make it challenging to introduce traditional group projects. Wikis use technology to facilitate group work in distance learning settings. Wikis allow individuals in different locations to…

Wikis as Discussion Forums: Exploring Students' Contribution and Their Attention to Form

ERIC Educational Resources Information Center

Nami, Fatemeh; Marandi, S. Susan

2014-01-01

The potential of wikis for learning has recently begun to capture the attention of English as a second/foreign language (ESL/EFL) research. While students' collaboration, attention to form, and perceptions of wikis in document mode have been widely addressed in previous research, the educational value of wikis used in thread mode, as discussion…

A Global Learning Wiki Project for Pre-Service Teachers

ERIC Educational Resources Information Center

Kuo, Chia-Ling

2015-01-01

In this study the author investigated 228 pre-service teachers' experiences with a global learning wiki project in an undergraduate educational technology course. The project connected pre-service teachers with students in 11 different countries on wiki sites, participants and their overseas partners posting questions about topics of interest to…

Wiki Mass Authoring for Experiential Learning: A Case Study

ERIC Educational Resources Information Center

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…

Application of Wikis with Scaffolding Structure in Laboratory Reporting

ERIC Educational Resources Information Center

Ge, Changfeng

2012-01-01

This work demonstrates how a Wiki can be mapped into different learning stages during group-based lab reporting via an adequate scaffolding structure. The scaffolding structure of the Wiki-based group report is comprised of six constructs in sequence: Appendix, Methods, Results, Analysis, Introduction and Conclusion. The scaffolding structure was…

Using a Wiki to Enhance Cooperative Learning in a Real Analysis Course

ERIC Educational Resources Information Center

Peterson, Elisha

2009-01-01

This article describes how the author used a wiki-based website in a real analysis course, and assesses its effectiveness. The wiki was used to post course materials, maintain a forum, enable students to write collaborative projects, and enable students to develop a glossary of important terms. The wiki proved to be very successful; it facilitated…

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

ERIC Educational Resources Information Center

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…

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

ERIC Educational Resources Information Center

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.…

Using wikis to investigate communication, collaboration and engagement in Capstone engineering design projects

NASA Astrophysics Data System (ADS)

Berthoud, L.; Gliddon, J.

2018-03-01

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 of engineering students from different disciplinary backgrounds and years. The students' perception of the usefulness of the tool were surveyed and the user contribution statistics and content categorisation were analysed for a case study wiki. Recommendations and lessons learned for the deployment of wikis are provided for interested academic staff from other institutions. Wikis were found to be of limited use to investigate levels of communication and collaboration in this study, but may be of interest in other contexts. Wikis were considered a potentially useful tool to track engagement for Capstone design projects in engineering subjects.

"Wiki-Ed Poetry": Transforming Preservice Teachers' Preconceptions about Poetry and Poetry Teaching

ERIC Educational Resources Information Center

Hughes, Janette; Dymoke, Sue

2011-01-01

This article focuses specifically on teacher candidates' preconceptions about poetry and poetry teaching and how these preconceptions shift as they work through various tasks on a wiki. Through an analysis of their definitions of poetry and ideas about poetry pedagogy captured in online discussion, survey, and interview responses, the authors…

Collaborative Tasks in Wiki-Based Environment in EFL Learning

ERIC Educational Resources Information Center

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…

Discussing the Factors Contributing to Students' Involvement in an EFL Collaborative Wiki Project

ERIC Educational Resources Information Center

Lee, Hsiao-chien; Wang, Pei-ling

2013-01-01

A growing number of researchers have acknowledged the potential for using wikis in online collaborative language learning. While researchers appreciate the wikis platform for engaging students in virtual team work and authentic language learning, many also have recognized the limitations of using wikis to promote student collaboration (Alyousef…

Wiki as a tool for microbiology teaching, learning and assessment.

PubMed

Sampaio-Maia, B; Maia, J S; Leitão, S; Amaral, M; Vieira-Marques, P

2014-05-01

Evidence suggests that cooperative learning and peer-assessment fosters students' ability to work with others and may lead to better cognitive outcomes and higher achievement. This work aimed to assess the use of an online collaborative tool for the teaching/learning and assessment of Microbiology. A total of 144 students were grouped and assigned to create wiki entries as well as to peer review wikis created by colleagues (peer-assessment process) using the Wiki module from Moodle Virtual Learning Environment (MVLE). MVLE actions log was used for tracking students' activity. The number of student's actions within wiki did not present a strong correlation with wiki scores, so it should not be used as a heavy evaluation parameter. The amount of work developed between members of the same group differed significantly, suggesting that final scores should be attributed individually. When peer-assessment process was implemented, the number of editing actions increased, suggesting that the peer-assessment strategy encourages the development of a better work. The vast majority of students execute the work in the last 10% of the period assigned for task development, which can be counter-productive for a truly collaborative work. Wiki revealed to be a useful tool for Microbiology teaching/learning and assessment, promoting collaborative work, promoting virtual mobility and facilitating the real-time monitoring of the students' work. This pedagogical project promoted also the involvement of students in their assessment process, encouraging their critical sense and quest for Excellency. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Evaluating the Use of a Wiki for Collaborative Learning

ERIC Educational Resources Information Center

Su, Feng; Beaumont, Chris

2010-01-01

A wiki is able to provide a learning environment which is closely aligned with the social-constructivist approach and is more natural than many tools where open collaboration and the exchange of ideas are important. This case study analyses and evaluates essential aspects for the successful deployment of a wiki in a higher education setting using…

Pedagogical Aspects of Integrating Wikis in Pre-Service Teacher Education

ERIC Educational Resources Information Center

Goldstein, Olzan; Peled, Yehuda

2016-01-01

The study examines pedagogical approaches in using wikis in teaching and learning in teacher education colleges. It focuses on: instructors' motivation for wiki-based teaching; course types; teaching methods; evaluation; content structure; characteristics of student collaboration and learning outcomes; involvement of instructors in the learning…

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

ERIC Educational Resources Information Center

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…

Using Regulation Activities to Improve Undergraduate Collaborative Writing on Wikis

ERIC Educational Resources Information Center

Cho, Moon-Heum; Lim, Seongmi

2017-01-01

Although wikis have been widely adopted to support collaborative writing in undergraduate classrooms, educators remain concerned about the level of student participation. Using regulation theories to design interventions in the form of activities, we examined their effects on collaborative writing on wikis. Results demonstrate that with the…

Taking Constructivism One Step Further: Post Hoc Analysis of a Student-Created Wiki.

PubMed

Pascoe, Michael; Monroe, Forrest; Macfarlane, Helen

2018-06-14

Wiki platform use has potential to improve student learning by improving engagement with course material. A student-created wiki was established to serve as a repository of study tools for students in a medical school curriculum. There is a scarcity of information describing student-led creation of wikis in medical education. The aim is to characterize website traffic of a student-created wiki and evaluate student perceptions of usage via a short anonymous online survey. Website analytics were used to track visitation statistics to the wiki and a survey was distributed to assess ease of use, interest in contributing to the wiki, and suggestions for improvement. Site traffic data indicated high usage, with a mean of 315 (SD 241) pageviews per day from July 2011 to March 2013 and 74,317 total user sessions. The mean session duration was 1.94 (SD 1.39) minutes. Comparing Fall 2011 to Fall 2012 sessions revealed a large increase in returning visitors (from 12,397 to 20,544, 65.7%) and sessions via mobile devices (831 to 1560, 87.7%). The survey received 164 responses; 88.0% (162/184) were aware of the wiki at the time of the survey. On average, respondents felt that the wiki was more useful in the preclinical years (mean 2.73, SD 1.25) than in the clinical years (mean 1.88, SD 1.12; P<.001). Perceived usefulness correlated with the percent of studying for which the respondent used electronic resources (Spearman ρ=.414, P<.001). Overall, the wiki was a highly utilized, although informal, part of the curriculum with much room for improvement and future exploration. ©Michael Pascoe, Forrest Monroe, Helen Macfarlane. Originally published in JMIR Medical Education (http://mededu.jmir.org), 14.06.2018.

AN OPEN-SOURCE COMMUNITY WEB SITE TO SUPPORT GROUND-WATER MODEL TESTING

EPA Science Inventory

A community wiki wiki web site has been created as a resource to support ground-water model development and testing. The Groundwater Gourmet wiki is a repository for user supplied analytical and numerical recipes, how-to's, and examples. Members are encouraged to submit analyti...

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

ERIC Educational Resources Information Center

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…

Using blogs and wikis in a graduate public health course.

PubMed

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.

Wiki Laboratory Notebooks: Supporting Student Learning in Collaborative Inquiry-Based Laboratory Experiments

NASA Astrophysics Data System (ADS)

Lawrie, Gwendolyn Angela; Grøndahl, Lisbeth; Boman, Simon; Andrews, Trish

2016-06-01

Recent examples of high-impact teaching practices in the undergraduate chemistry laboratory that include course-based undergraduate research experiences and inquiry-based experiments require new approaches to assessing individual student learning outcomes. Instructors require tools and strategies that can provide them with insight into individual student contributions to collaborative group/teamwork throughout the processes of experimental design, data analysis, display and communication of their outcomes in relation to their research question(s). Traditional assessments in the form of laboratory notebooks or experimental reports provide limited insight into the processes of collaborative inquiry-based activities. A wiki environment offers a collaborative domain that can potentially support collaborative laboratory processes and scientific record keeping. In this study, the effectiveness of the wiki in supporting laboratory learning and assessment has been evaluated through analysis of the content and histories for three consenting, participating groups of students. The conversational framework has been applied to map the relationships between the instructor, tutor, students and laboratory activities. Analytics that have been applied to the wiki platform include: character counts, page views, edits, timelines and the extent and nature of the contribution by each student to the wiki. Student perceptions of both the role and the impact of the wiki on their experiences and processes have also been collected. Evidence has emerged from this study that the wiki environment has enhanced co-construction of understanding of both the experimental process and subsequent communication of outcomes and data. A number of features are identified to support success in the use of the wiki platform for laboratory notebooks.

Evaluation of a Teaching Tool--Wiki--in Online Graduate Education

ERIC Educational Resources Information Center

Park, Caroline L.; Crocker, Cheryl; Nussey, Janice; Springate, Joyce; Hutchings, Darlene

2010-01-01

This study provides information on ways to enhance learning for students using online educational programs. Technologies that foster and engage students in the learning process are necessary in the online learning environment. Wiki is an online teaching strategy used to promote student interaction. A Wiki was introduced into three sections of a…

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

PubMed

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

GONUTS: the Gene Ontology Normal Usage Tracking System

PubMed Central

Renfro, Daniel P.; McIntosh, Brenley K.; Venkatraman, Anand; Siegele, Deborah A.; Hu, James C.

2012-01-01

The Gene Ontology Normal Usage Tracking System (GONUTS) is a community-based browser and usage guide for Gene Ontology (GO) terms and a community system for general GO annotation of proteins. GONUTS uses wiki technology to allow registered users to share and edit notes on the use of each term in GO, and to contribute annotations for specific genes of interest. By providing a site for generation of third-party documentation at the granularity of individual terms, GONUTS complements the official documentation of the Gene Ontology Consortium. To provide examples for community users, GONUTS displays the complete GO annotations from seven model organisms: Saccharomyces cerevisiae, Dictyostelium discoideum, Caenorhabditis elegans, Drosophila melanogaster, Danio rerio, Mus musculus and Arabidopsis thaliana. To support community annotation, GONUTS allows automated creation of gene pages for gene products in UniProt. GONUTS will improve the consistency of annotation efforts across genome projects, and should be useful in training new annotators and consumers in the production of GO annotations and the use of GO terms. GONUTS can be accessed at http://gowiki.tamu.edu. The source code for generating the content of GONUTS is available upon request. PMID:22110029

Cooperative or Collaborative Literacy Practices: Mapping Metadiscourse in a Business Students' Wiki Group Project

ERIC Educational Resources Information Center

Alyousef, Hesham Suleiman; Picard, Michelle Yvette

2011-01-01

Although wikis have been used successfully in collaborative learning in higher education, there is a lack of research investigating wikis in business module assessment tasks. Little research to date has been conducted on how wikis formatively develop international English as a second language (ESL) in business students' academic discourse. In this…

Collaborative Learning with a Wiki: Differences in Perceived Usefulness in Two Contexts of Use

ERIC Educational Resources Information Center

Naismith, L.; Lee, B.-H.; Pilkington, R. M.

2011-01-01

This paper investigates the potential of a wiki (FlexWiki) to support collaborative authoring of web resources in authentic coursework by two different sets of education students at different stages of their professional development. Research questions included: (1) how the selected wiki could be blended with curriculum activities and existing…

Using Wikis for Online Group Projects: Student and Tutor Perspectives

ERIC Educational Resources Information Center

Kear, Karen; Donelan, Helen; Williams, Judith

2014-01-01

This paper presents a study of the use of wikis to support online group projects in two courses at the UK Open University. The research aimed to investigate the effectiveness of a wiki in supporting (i) student collaboration and (ii) tutors' marking of the students' collaborative work. The paper uses the main factors previously identified by the…

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

ERIC Educational Resources Information Center

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…

Assessing Acceptance toward Wiki Technology in the Context of Higher Education

ERIC Educational Resources Information Center

Altanopoulou, Panagiota; Tselios, Nikolaos

2017-01-01

This study investigated undergraduate students' intention to use wiki technology. An extension of the Technology Acceptance Model (TAM) has been used by taking into account not only students' wiki perceived utility and usability, but also Big Five personality characteristics and two other variables, social norms, and facilitating conditions, as…

Collaborative Creativity Processes in a Wiki: A Study in Secondary Education

ERIC Educational Resources Information Center

Pifarré, Manoli; Marti, Laura; Guijosa, Alex

2014-01-01

This paper explores how wiki may be used to support secondary education students' collaborative creativity processes and how such interaction can promote critical and creativity thinking. A science case-based project in which 81 secondary students participated was designed, implemented and evaluated. Students worked in the science wiki project…

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

PubMed

Hamm, Michele P; Klassen, Terry P; Scott, Shannon D; Moher, David; Hartling, Lisa

2013-01-01

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. 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. 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. 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.

Education in Health Research Methodology: Use of a Wiki for Knowledge Translation

PubMed Central

Hamm, Michele P.; Klassen, Terry P.; Scott, Shannon D.; Moher, David; Hartling, Lisa

2013-01-01

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. PMID:23741424

Improving Critical Skills Using Wikis and CGPS in a Physics Classroom

NASA Astrophysics Data System (ADS)

Mohottala, H. E.

2016-10-01

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 providing numerical final answers but only the steps. Each week students were further evaluated on problem solving skills, opening up more opportunity for peer interaction through CGPS. Students developed a set of skills in decision making, problem solving, communication, negotiation, critical and independent thinking, and teamwork through the combination of wikis and CGPS.

Using Wiki Technology to Support Student Engagement: Lessons from the Trenches

ERIC Educational Resources Information Center

Cole, Melissa

2009-01-01

This paper reports on a failed experiment to use Wiki technology to support student engagement with the subject matter of a third year undergraduate module. Using qualitative data, the findings reveal that in an educational context, social technologies such as Wiki's, are perceived differently compared with ordinary personal use and this…

Wiki Acceptance by University Students to Improve Collaboration in Higher Education

ERIC Educational Resources Information Center

Cilliers, Liezel

2017-01-01

Web 2.0 technologies, such as wikis, can play a key role in promoting interaction, delivering education and providing communication between students. However, most of the existing literature does not seem to consider relationships between designing wiki-based learning activities and the student acceptance of this technology. The purpose of the…

Investigating Technical and Pedagogical Usability Issues of Collaborative Learning with Wikis

ERIC Educational Resources Information Center

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…

AOP Wiki Version 2.0

EPA Science Inventory

Version 2.0 of the AOP-Wiki was released on December 4, 2016. This was a major upgrade and should provide a better user experience. It fixes a number of bugs with the previous version, provides a more streamlined user interface, and sets the stage for providing more programmatic...

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)

ERIC Educational Resources Information Center

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…

A Student Authored Online Medical Education Textbook: Editing Patterns and Content Evaluation of a Medical Student Wiki

PubMed Central

Thompson, CL; Schulz1, Wade L.; Terrence, Adam

2011-01-01

The University of Minnesota medical student wiki (UMMedWiki) allows students to collaboratively edit classroom notes to support medical education. Since 2007, UMMedWiki has grown to include 1,591 articles that have collectively received 1.2 million pageviews. Although small-scale wikis have become increasingly important, little is known about their dynamics compared to large wikis, such as Wikipedia. To better understand UMMedWiki’s management and its potential reproducibility at other medical schools, we used an edit log with 28,000 entries to evaluate the behavior of its student editors. The development of tools to survey UMMedwiki allows for quality comparisons that improve both the wiki and the curriculum itself. We completed a content survey by comparing the UMMedWiki with two types of rubric data: TIME, a medical education taxonomy consisting of 1500 terms and national epidemiological data on 2,100 diseases. PMID:22195202

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

PubMed

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 < .001). A wiki paired with 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.

Integrating Wikis in the Support and Practice of Historical Analysis Skills

ERIC Educational Resources Information Center

Cabiness, Catherine; Donovan, Loretta; Green, Tim D.

2013-01-01

This case study examines the benefits of integrating wikis into the World History curriculum. Six middle school students chosen because of their designation in relevant subgroups--GATE, AVID, and RSP--participated in this 20-week study. Abstract historical concepts can be difficult to grasp; therefore, students collaborated via a wiki on topics…

Wikis for School Leaders: Using Technology to Improve Communication and Collaboration

ERIC Educational Resources Information Center

Sandifer, Stephanie D.

2011-01-01

Maximize the effectiveness of your professional activities through the use of wikis, and raise student achievement in turn! With strategies from online educator and technology expert Stephanie Sandifer, this book provides how-to advice on the way in which wikis result in a more efficient use of time, better communication, and increased adult…

Use of a Wiki-Based Software to Manage Research Group Activities

ERIC Educational Resources Information Center

Wang, Ting; Vezenov, Dmitri V.; Simboli, Brian

2014-01-01

This paper discusses use of the wiki software Confluence to organize research group activities and lab resources. Confluence can serve as an electronic lab notebook (ELN), as well as an information management and collaboration tool. The article provides a case study in how researchers can use wiki software in "home-grown" fashion to…

Implementation and Evaluation of a Wiki Involving Multiple Stakeholders Including Patients in the Promotion of Best Practices in Trauma Care: The WikiTrauma Interrupted Time Series Protocol

PubMed Central

Turgeon, Alexis F; Witteman, Holly O; Lauzier, François; Moore, Lynne; Lamontagne, François; Horsley, Tanya; Gagnon, Marie-Pierre; Droit, Arnaud; Weiss, Matthew; Tremblay, Sébastien; Lachaine, Jean; Le Sage, Natalie; Émond, Marcel; Berthelot, Simon; Plaisance, Ariane; Lapointe, Jean; Razek, Tarek; van de Belt, Tom H; Brand, Kevin; Bérubé, Mélanie; Clément, Julien; Grajales III, Francisco Jose; Eysenbach, Gunther; Kuziemsky, Craig; Friedman, Debbie; Lang, Eddy; Muscedere, John; Rizoli, Sandro; Roberts, Derek J; Scales, Damon C; Sinuff, Tasnim; Stelfox, Henry T; Gagnon, Isabelle; Chabot, Christian; Grenier, Richard; Légaré, France

2015-01-01

Background Trauma is the most common cause of mortality among people between the ages of 1 and 45 years, costing Canadians 19.8 billion dollars a year (2004 data), yet half of all patients with major traumatic injuries do not receive evidence-based care, and significant regional variation in the quality of care across Canada exists. Accordingly, our goal is to lead a research project in which stakeholders themselves will adapt evidence-based trauma care knowledge tools to their own varied institutional contexts and cultures. We will do this by developing and assessing the combined impact of WikiTrauma, a free collaborative database of clinical decision support tools, and Wiki101, a training course teaching participants how to use WikiTrauma. WikiTrauma has the potential to ensure that all stakeholders (eg, patients, clinicians, and decision makers) can all contribute to, and benefit from, evidence-based clinical knowledge about trauma care that is tailored to their own needs and clinical setting. Objective Our main objective will be to study the combined effect of WikiTrauma and Wiki101 on the quality of care in four trauma centers in Quebec. Methods First, we will pilot-test the wiki with potential users to create a version ready to test in practice. A rapid, iterative prototyping process with 15 health professionals from nonparticipating centers will allow us to identify and resolve usability issues prior to finalizing the definitive version for the interrupted time series. Second, we will conduct an interrupted time series to measure the impact of our combined intervention on the quality of care in four trauma centers that will be selected—one level I, one level II, and two level III centers. Participants will be health care professionals working in the selected trauma centers. Also, five patient representatives will be recruited to participate in the creation of knowledge tools destined for their use (eg, handouts). All participants will be invited to

Improving Critical Skills Using Wikis and CGPS in a Physics Classroom

ERIC Educational Resources Information Center

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…

Collaborative Knowledge Building with Wikis: The Impact of Redundancy and Polarity

ERIC Educational Resources Information Center

Moskaliuk, Johannes; Kimmerle, Joachim; Cress, Ulrike

2012-01-01

Wikis as shared digital artifacts may enable users to participate in processes of knowledge building. To what extent and with which quality knowledge building can take place is assumed to depend on the interrelation between people's prior knowledge and the information available in a wiki. In two experimental studies we examined the impact on…

News Writing Using Wiki: Impacts on Learning Experience of Student Journalists

ERIC Educational Resources Information Center

Ma, Will W. K.; Yuen, Allan H. K.

2008-01-01

Wiki empowers users in generating, revising, and organizing their own content. In this study, we review literature to gain theoretical support for wikis that impact learning. In a context of student journalists learning news writing, we design a two-phase field study: (1) Phase I--to examine learners' reflections on learning news writing in wiki…

What is a wiki, and how can it be used in resident education?

PubMed

Kohli, Marc D; Bradshaw, John K

2011-02-01

Training as a radiology resident is a complex task. Residents frequently encounter multiple hospital systems, each with unique workflow patterns and heterogenous information systems. We identified an opportunity to ease some of the resulting anxiety and frustration by centralizing high-quality resources using a wiki. In this manuscript, we describe our choice of wiki software, give basic information about hardware requirements, detail steps for configuration, outline information included on the wiki, and present the results of a resident acceptance survey.

Wiki Tools in the Preparation and Support of e-Learning Courses

ERIC Educational Resources Information Center

Jancarik, Antonin; Jancarikova, Katerina

2010-01-01

Wiki tools, which became known mainly thanks to the Wikipedia encyclopedia, represent quite a new phenomenon on the Internet. The work presented here deals with three areas connected to a possible use of wiki tools for the preparation of an e-learning course. To what extent does Wikipedia.com contain terms necessary for scientific lectures at the…

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

PubMed

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.

Active Wiki Knowledge Repository

DTIC Science & Technology

2012-10-01

data using SPARQL queries or RESTful web-services; ‘gardening’ tools for examining the semantically tagged content in the wiki; high-level language tool...Tagging & RDF triple-store Fusion and inferences for collaboration Tools for Consuming Data SPARQL queries or RESTful WS Inference & Gardening tools...other stores using AW SPARQL queries and rendering templates; and 4) Interactively share maps and other content using annotation tools to post notes

Linking NCBI to Wikipedia: a wiki-based approach.

PubMed

Page, Roderic D M

2011-03-31

The NCBI Taxonomy underpins many bioinformatics and phyloinformatics databases, but by itself provides limited information on the taxa it contains. One readily available source of information on many taxa is Wikipedia. This paper describes iPhylo Linkout, a Semantic wiki that maps taxa in NCBI's taxonomy database onto corresponding pages in Wikipedia. Storing the mapping in a wiki makes it easy to edit, correct, or otherwise annotate the links between NCBI and Wikipedia. The mapping currently comprises some 53,000 taxa, and is available at http://iphylo.org/linkout. The links between NCBI and Wikipedia are also made available to NCBI users through the NCBI LinkOut service.

Distributed scaffolding: Wiki collaboration among Latino high school chemistry students

NASA Astrophysics Data System (ADS)

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

Grades Five and Six Students' Representation of Meaning in Collaborative Wiki Writing

ERIC Educational Resources Information Center

Peterson, Shelley Stagg; Portier, Christine

2014-01-01

This paper examined grades 5 and 6 students' participation in wikis while writing reports on social studies topics. An analysis of eight wikis showed that students represented meanings they had constructed about their topics by engaging in knowledge telling practices (e.g., introducing, stating, or repeating information or an idea and developing…

Interlinking journal and wiki publications through joint citation: Working examples from ZooKeys and Plazi on Species-ID

PubMed Central

Penev, Lyubomir; Hagedorn, Gregor; Mietchen, Daniel; Georgiev, Teodor; Stoev, Pavel; Sautter, Guido; Agosti, Donat; Plank, Andreas; Balke, Michael; Hendrich, Lars; Erwin, Terry

2011-01-01

Abstract Scholarly publishing and citation practices have developed largely in the absence of versioned documents. The digital age requires new practices to combine the old and the new. We describe how the original published source and a versioned wiki page based on it can be reconciled and combined into a single citation reference. We illustrate the citation mechanism by way of practical examples focusing on journal and wiki publishing of taxon treatments. Specifically, we discuss mechanisms for permanent cross-linking between the static original publication and the dynamic, versioned wiki, as well as for automated export of journal content to the wiki, to reduce the workload on authors, for combining the journal and the wiki citation and for integrating it with the attribution of wiki contributors. PMID:21594104

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

PubMed

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.

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

ERIC Educational Resources Information Center

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…

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

ERIC Educational Resources Information Center

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…

The Use of a Wiki as an Instructional Tool: A Qualitative Investigation

ERIC Educational Resources Information Center

Aharony, Noa

2009-01-01

The current research aims to explore and analyze the application and use of a wiki in a knowledge management academic course. The research will focus on the level of collaboration among students and on the kind of interaction that takes place during the learning process. The population of this study was composed of wiki pages gathered from a…

SOIL Geo-Wiki: A tool for improving soil information

NASA Astrophysics Data System (ADS)

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

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

ERIC Educational Resources Information Center

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…

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

NASA Astrophysics Data System (ADS)

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/.

The Use of a Wiki at a College in Hungary as a Tool to Enhance Personal Learning

ERIC Educational Resources Information Center

Asztalos, Réka

2014-01-01

Wikis have been extensively used in language teaching for collaborative writing. However, there are very few studies about wikis as holistic learning environments. To fill this niche, the present research project aimed to explore the potential of the wiki as a platform for knowledge building and personalized learning that may enhance lifelong…

A Case Study of Wikis and Student-Designed Games in Physical Education

ERIC Educational Resources Information Center

Hastie, Peter A.; Casey, Ashley; Tarter, Anne-Marie

2010-01-01

This paper reports on the incorporation of wiki technology within physical education. Boys from two classes at a school in the United Kingdom were divided into small teams and given the task of creating a new game in a same genre as football, hockey, netball or rugby. Each team had a wiki on which were recorded all the plans and developments of…

A cloud-based semantic wiki for user training in healthcare process management.

PubMed

Papakonstantinou, D; Poulymenopoulou, M; Malamateniou, F; Vassilacopoulos, G

2011-01-01

Successful healthcare process design requires active participation of users who are familiar with the cooperative and collaborative nature of healthcare delivery, expressed in terms of healthcare processes. Hence, a reusable, flexible, agile and adaptable training material is needed with the objective to enable users instill their knowledge and expertise in healthcare process management and (re)configuration activities. To this end, social software, such as a wiki, could be used as it supports cooperation and collaboration anytime, anywhere and combined with semantic web technology that enables structuring pieces of information for easy retrieval, reuse and exchange between different systems and tools. In this paper a semantic wiki is presented as a means for developing training material for healthcare providers regarding healthcare process management. The semantic wiki should act as a collective online memory containing training material that is accessible to authorized users, thus enhancing the training process with collaboration and cooperation capabilities. It is proposed that the wiki is stored in a secure virtual private cloud that is accessible from anywhere, be it an excessively open environment, while meeting the requirements of redundancy, high performance and autoscaling.

Wiki Use That Increases Communication and Collaboration Motivation: A Reflection Several Semesters Later

ERIC Educational Resources Information Center

Davidson, Robyn

2015-01-01

The article "Wiki use that increases communication and collaboration motivation" (Davidson, 2012) appeared in the "Journal of Learning Design," Volume 5, Issue 2 in 2012. Three years on, Robyn Davidson reflects upon her original article. This article gave an account of how wikis were used as a platform to provide an opportunity…

Action Research as a Congruent Methodology for Understanding Wikis: The Case of Wikiversity

ERIC Educational Resources Information Center

Lawler, Cormac

2008-01-01

It is proposed that action research is an appropriate methodology for studying wikis, and is akin to research "the wiki way". This proposal is contextualised within the case of Wikiversity, a project of the Wikimedia Foundation. A framework for a participative research project is outlined, and challenges and implications of such a…

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

PubMed

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.

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

PubMed Central

Arita, Masanori; Suwa, Kazuhiro

2008-01-01

Background 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. Results 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. Conclusion 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. PMID:18822113

Improving Writing with Wiki Discussion Forums

ERIC Educational Resources Information Center

Corrigan, John

2010-01-01

Wikis are open-source sites, meaning that users may add, remove, or edit most content quickly. Because they are a public venue, students became more engaged and invested in what they wrote, wrote more frequently, edited their work more carefully, collaborated, and became accustomed to frequent peer and adult feedback. Writing practice and in-depth…

An Open-source Community Web Site To Support Ground-Water Model Testing

NASA Astrophysics Data System (ADS)

Kraemer, S. R.; Bakker, M.; Craig, J. R.

2007-12-01

A community wiki wiki web site has been created as a resource to support ground-water model development and testing. The Groundwater Gourmet wiki is a repository for user supplied analytical and numerical recipes, howtos, and examples. Members are encouraged to submit analytical solutions, including source code and documentation. A diversity of code snippets are sought in a variety of languages, including Fortran, C, C++, Matlab, Python. In the spirit of a wiki, all contributions may be edited and altered by other users, and open source licensing is promoted. Community accepted contributions are graduated into the library of analytic solutions and organized into either a Strack (Groundwater Mechanics, 1989) or Bruggeman (Analytical Solutions of Geohydrological Problems, 1999) classification. The examples section of the wiki are meant to include laboratory experiments (e.g., Hele Shaw), classical benchmark problems (e.g., Henry Problem), and controlled field experiments (e.g., Borden landfill and Cape Cod tracer tests). Although this work was reviewed by EPA and approved for publication, it may not necessarily reflect official Agency policy. Mention of trade names or commercial products does not constitute endorsement or recommendation for use.

Scaffolding Strategies for Wiki-Based Collaboration: Action Research in a Multicultural Japanese Language Program

ERIC Educational Resources Information Center

Jung, Insung; Suzuki, Yoko

2015-01-01

Wikis can be used to encourage and support collaborative constructivist learning. However, their effectiveness depends upon the use of scaffolding strategies to guide the students in their use. This action research investigated three scaffolding strategies for wiki-based multicultural Japanese language learning: worked examples, grouping and peer…

Does Collaboration Occur when Children Are Learning with the Support of a Wiki?

ERIC Educational Resources Information Center

Allsop, Yasemin

2011-01-01

This paper reports on the outcomes of a mini-research project about visible forms of collaboration when children are learning with the support of Wikis-online editable websites. The findings were based on observing the children using the Wiki, analysis of the video recording of the task and the survey that was completed by the children using the…

The Effectiveness of Using Teacher-Teacher Wikis in Collaborative Lesson Planning and Its Impact on Teacher's Classroom Performance

ERIC Educational Resources Information Center

Al-Shareef, Samar Yahya; Al-Qarni, Reem Ali

2016-01-01

The paper highlights the main aspects and characteristic features of teacher-teacher Wikis, which are considered to be the most effective teaching and learning tools. The research studies the effectiveness of using Wikis by teachers during collaborative lesson planning. It also traces the impact of teacher-teacher Wikis on the teachers'…

Wikis and Collaborative Learning in Higher Education

ERIC Educational Resources Information Center

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;…

Wiki-based Data Management System for Toxicogenomics

EPA Science Inventory

We are developing a data management system to enable systems-based toxicology at the US EPA. This is built upon the WikiLIMS platform and is capabale of housing not just genomics data but also a wide variety of toxicology data and associated experimental design information. Thi...

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

ERIC Educational Resources Information Center

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…

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

PubMed Central

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 née Clark, Jennifer

2009-01-01

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 . PMID:19178689

Exploring Students' Perceptions of Integrating Wiki Technology and Peer Feedback into English Writing Courses

ERIC Educational Resources Information Center

Lin, Wen-Chuan; Yang, Shu Ching

2011-01-01

This study applied Wiki technology and peer review to an English as a foreign language writing class. The objective was to investigate whether this system, as a collaborative platform, would improve students' writing skills. The study gauged students' perceptions about integrating a Wiki writing course and peer feedback. The participants were 32…

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

ERIC Educational Resources Information Center

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…

Genome re-annotation: a wiki solution?

PubMed Central

Salzberg, Steven L

2007-01-01

The annotation of most genomes becomes outdated over time, owing in part to our ever-improving knowledge of genomes and in part to improvements in bioinformatics software. Unfortunately, annotation is rarely if ever updated and resources to support routine reannotation are scarce. Wiki software, which would allow many scientists to edit each genome's annotation, offers one possible solution. PMID:17274839

Collaboratively charting the gene-to-phenotype network of human congenital heart defects

PubMed Central

2010-01-01

Background How to efficiently integrate the daily practice of molecular biologists, geneticists, and clinicians with the emerging computational strategies from systems biology is still much of an open question. Description We built on the recent advances in Wiki-based technologies to develop a collaborative knowledge base and gene prioritization portal aimed at mapping genes and genomic regions, and untangling their relations with corresponding human phenotypes, congenital heart defects (CHDs). This portal is not only an evolving community repository of current knowledge on the genetic basis of CHDs, but also a collaborative environment for the study of candidate genes potentially implicated in CHDs - in particular by integrating recent strategies for the statistical prioritization of candidate genes. It thus serves and connects the broad community that is facing CHDs, ranging from the pediatric cardiologist and clinical geneticist to the basic investigator of cardiogenesis. Conclusions This study describes the first specialized portal to collaboratively annotate and analyze gene-phenotype networks. Of broad interest to the biological community, we argue that such portals will play a significant role in systems biology studies of numerous complex biological processes. CHDWiki is accessible at http://www.esat.kuleuven.be/~bioiuser/chdwiki PMID:20193066

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

ERIC Educational Resources Information Center

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…

Learning from a Wiki Way of Learning

ERIC Educational Resources Information Center

Page, Kelly L.; Reynolds, Nina

2015-01-01

There is a growing need to design learning experiences in higher education that develop collaborative and mediated social writing practices. A wiki way of learning addresses these needs. This paper reports findings from a case study involving 58 postgraduate students who in small groups participated over eight weeks in a mediated collaborative…

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

PubMed

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

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

PubMed Central

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

Wiki-Mediated Activities in Higher Education: Evidence-Based Analysis of Learning Effectiveness across Three Studies

ERIC Educational Resources Information Center

Altanopoulou, Panagiota; Tselios, Nikolaos; Katsanos, Christos; Georgoutsou, Maria; Panagiotaki, Maria-Antonia

2015-01-01

A considerable interest in using Web 2.0 technologies such as wikis in education has been observed recently. Despite the advantages of the wiki technology, a number of questions concerning design of appropriate activities and their learning effectiveness remain open. In this paper, we present the results of three activities involving first-year…

WikiSensing: An Online Collaborative Approach for Sensor Data Management

PubMed Central

Silva, Dilshan; Ghanem, Moustafa; Guo, Yike

2012-01-01

This paper presents a new methodology for collaborative sensor data management known as WikiSensing. It is a novel approach that incorporates online collaboration with sensor data management. We introduce the work on this research by describing the motivation and challenges of designing and developing an online collaborative sensor data management system. This is followed by a brief survey on popular sensor data management and online collaborative systems. We then present the architecture for WikiSensing highlighting its main components and features. Several example scenarios are described to present the functionality of the system. We evaluate the approach by investigating the performance of aggregate queries and the scalability of the system. PMID:23201997

Using Document Design to Create and Maintain Wikis

ERIC Educational Resources Information Center

Clark, Thomas; Stewart, Jeffrey

2010-01-01

As organizations strive to succeed in an increasingly competitive international environment, they are recognizing the importance of maximizing intellectual capital, the collective knowledge that resides within their companies. More and more businesses are turning to wikis, sites where content is collectively edited by users, to maximize the…

The GermOnline cross-species systems browser provides comprehensive information on genes and gene products relevant for sexual reproduction.

PubMed

Gattiker, Alexandre; Niederhauser-Wiederkehr, Christa; Moore, James; Hermida, Leandro; Primig, Michael

2007-01-01

We report a novel release of the GermOnline knowledgebase covering genes relevant for the cell cycle, gametogenesis and fertility. GermOnline was extended into a cross-species systems browser including information on DNA sequence annotation, gene expression and the function of gene products. The database covers eight model organisms and Homo sapiens, for which complete genome annotation data are available. The database is now built around a sophisticated genome browser (Ensembl), our own microarray information management and annotation system (MIMAS) used to extensively describe experimental data obtained with high-density oligonucleotide microarrays (GeneChips) and a comprehensive system for online editing of database entries (MediaWiki). The RNA data include results from classical microarrays as well as tiling arrays that yield information on RNA expression levels, transcript start sites and lengths as well as exon composition. Members of the research community are solicited to help GermOnline curators keep database entries on genes and gene products complete and accurate. The database is accessible at http://www.germonline.org/.

Keyword Extraction from Multiple Words for Report Recommendations in Media Wiki

NASA Astrophysics Data System (ADS)

Elakiya, K.; Sahayadhas, Arun

2017-03-01

This paper addresses the problem of multiple words search, with the goal of using these multiple word search to retrieve, relevant wiki page which will be recommended to end user. However, the existing system provides a link to wiki page for only a single keyword only which is available in Wikipedia. Therefore it is difficult to get the correct result when search input has multiple keywords or a sentence. We have introduced a ‘FastStringSearch’ technique which will provide option for efficient search with multiple key words and which will increase the flexibility for the end user to get his expected content easily.

Identifying Collaborative Behaviours Online: Training Teachers in Wikis

ERIC Educational Resources Information Center

Vinagre Laranjeira, Margarita

2016-01-01

In this paper we explore the data gathered from a group of nine in-service teachers who were trained online to become future telecollaborative teachers. Participants from different countries worked in two small groups in a wiki designed specially to facilitate discussion and collaboration. Tasks included reading and reviewing articles on…

Blended Learning Using Role-Plays, Wikis and Blogs

ERIC Educational Resources Information Center

Ruyters, Michele; Douglas, Kathy; Law, Siew Fang

2011-01-01

Student learning about legal skills in legal education is increasingly seen as important. These legal skills include advocacy and negotiation. These skills are often taught through role-play. This article discusses the combination of role-plays with online tools, including wikis and blogs, to assist students to master legal skills. The article…

Copyright and Collaborative Spaces: Open Licensing and Wikis

ERIC Educational Resources Information Center

Botterbusch, Hope R.; Parker, Preston

2008-01-01

As recently as ten years ago, it may have seemed like science fiction to imagine collaborative spaces on the Internet. Today, collaborative websites have proliferated: (1) blogs; (2) social networking; (3) image sharing; (4) video sharing; (5) open educational resources; and (6) popularity websites. Another type is called a wiki, an online…

The Wiki as a Time-Saving Mentoring Tool

ERIC Educational Resources Information Center

Kinsey, Joanne; Carleo, Jenny; O'Neill, Barbara; Polanin, Nicholas

2010-01-01

An important step in the acculturation of new Extension professionals is a mentoring process that includes the input of experienced Extension colleagues. The wiki is a technology tool that can be useful by providing an online venue for Mentor Team communication and a place to share articles, curricula, and other critical tenure documents. This…

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

ERIC Educational Resources Information Center

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…

Explaining Dynamic Interactions in Wiki-Based Collaborative Writing

ERIC Educational Resources Information Center

Li, Mimi; Zhu, Wei

2017-01-01

This article reports a case study that examined dynamic patterns of interaction that two small groups (Group A and Group B) of ESL students exemplified when they performed two writing tasks: a research proposal (Task 1) and an annotated bibliography (Task 2) in a wiki site. Group A demonstrated a collective pattern in Task 1, but switched to an…

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

PubMed Central

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

Rationalities of Collaboration for Language Learning in a Wiki

ERIC Educational Resources Information Center

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…

Exploring Teachers' Perceptions of Wikis for Learning Classroom Cases

ERIC Educational Resources Information Center

Quek, Choon Lang; Wang, Qiyun

2014-01-01

This paper explores three potential affordances (social, technical and pedagogical) of wikis in the context of designing 32 teachers' learning of classroom management cases. Two learning environments were designed and two groups of the teacher-participants posted their own written and audio cases, identified problems, discussed and proposed…

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

ERIC Educational Resources Information Center

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.…

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

PubMed

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.

The NASA Human Research Wiki - An Online Collaboration Tool

NASA Technical Reports Server (NTRS)

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.

Pedagogical Significance of Wikis: Towards Gaining Effective Learning Outcomes

ERIC Educational Resources Information Center

Hewege, Chandana Rathnasiri; Perera, Liyanage Chamila Roshani

2013-01-01

Purpose: The purpose of this paper is to explore the effectiveness and pedagogical implications of integrating wikis into the curriculum and the subsequent learning outcomes of a group of Net-Gens who enrolled in an International Marketing course. The research problem of the study is: "What are the learning outcomes and pedagogical…

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

ERIC Educational Resources Information Center

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…

Wikis and Academic Writing: Changing the Writer-Reader Relationship

ERIC Educational Resources Information Center

Kuteeva, Maria

2011-01-01

The development of information and communication technologies has resulted in the emergence of new kinds of academic genres and literacies. The more recent social web applications empower learners to create online content in a collaborative way. This paper focuses on the use of wikis in the course of Effective Communication in English. It aims to…

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

ERIC Educational Resources Information Center

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…

Using the Integrated Vehicle Health Management Research Test and Integration Plan Wiki to Identify Synergistic Test Opportunities

NASA Technical Reports Server (NTRS)

Koelfgen, Syri J.; Faber, James J.

2010-01-01

The National Aeronautics and Space Administration (NASA) and the aviation industry have recognized a need for developing a method to identify and combine resources to carry out research and testing more efficiently. The Integrated Vehicle Health Management (IVHM) Research Test and Integration Plan (RTIP) Wiki is a tool that is used to visualize, plan, and accomplish collaborative research and testing. Synergistic test opportunities are developed using the RTIP Wiki, and include potential common resource testing that combines assets and personnel from NASA, industry, academia, and other government agencies. A research scenario is linked to the appropriate IVHM milestones and resources detailed in the wiki, reviewed by the research team members, and integrated into a collaborative test strategy. The scenario is then implemented by creating a test plan when appropriate and the research is performed. The benefits of performing collaborative research and testing are achieving higher Technology Readiness Level (TRL) test opportunities with little or no additional cost, improved quality of research, and increased communication among researchers. In addition to a description of the method of creating these joint research scenarios, examples of the successful development and implementation of cooperative research using the IVHM RTIP Wiki are given.

Power to the people: a wiki-governance model for biobanks

PubMed Central

2012-01-01

Biobanks are adopting various modes of public engagement to close the agency gap between participants and biobank builders. We propose a wiki-governance model for biobanks that harnesses Web 2.0, and which gives citizens the ability to collaborate in biobank governance and policymaking. PMID:22647613

Developing Collaborative Autonomous Learning Abilities in Computer Mediated Language Learning: Attention to Meaning among Students in Wiki Space

ERIC Educational Resources Information Center

Kessler, Greg; Bikowski, Dawn

2010-01-01

This study reports on attention to meaning among 40 NNS pre-service EFL teachers as they collaboratively constructed a wiki in a 16-week online course. Focus is placed upon the nature of individual and group behavior when attending to meaning in a long-term wiki-based collaborative activity as well as the students' collaborative autonomous…

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

PubMed

Park, Seung; Parwani, Anil; Macpherson, Trevor; Pantanowitz, Liron

2012-01-01

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. 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. 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). 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 is an effective mechanism for mastery of content. Future residents

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

PubMed Central

Park, Seung; Parwani, Anil; MacPherson, Trevor; Pantanowitz, Liron

2012-01-01

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 is an

Improving Students' Summary Writing Ability through Collaboration: A Comparison between Online Wiki Group and Conventional Face-To-Face Group

ERIC Educational Resources Information Center

Wichadee, Saovapa

2013-01-01

Wikis, as one of the Web 2.0 social networking tools, have been increasingly integrated into second language (L2) instruction to promote collaborative writing. The current study examined and compared summary writing abilities between students learning by wiki-based collaboration and students learning by traditional face-to-face collaboration.…

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

ERIC Educational Resources Information Center

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…

Wikis for Building Content Knowledge in the Foreign Language Classroom

ERIC Educational Resources Information Center

Pellet, Stephanie H.

2012-01-01

Most pedagogical applications of wikis in foreign language education draw on this collaborative tool to improve (formal) writing skills or to develop target language cultural sensitivity, missing largely on the opportunity to support student-developed L2 content knowledge. Seeking an alternative to traditional teacher-centered approaches, this…

Assisting Instructional Assessment of Undergraduate Collaborative Wiki and SVN Activities

ERIC Educational Resources Information Center

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…

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

PubMed

Archambault, Patrick M; van de Belt, Tom H; Grajales, Francisco J; Faber, Marjan J; Kuziemsky, Craig E; Gagnon, Susie; Bilodeau, Andrea; Rioux, Simon; Nelen, Willianne L D M; Gagnon, Marie-Pierre; Turgeon, Alexis F; Aubin, Karine; Gold, Irving; Poitras, Julien; Eysenbach, Gunther; Kremer, Jan A M; Légaré, France

2013-10-08

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. 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. 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. 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 longitudinal study showing that CWA use is

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

PubMed Central

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

Stop Reinventing the Wheel: Using Wikis for Professional Knowledge Sharing

ERIC Educational Resources Information Center

Deitering, Anne-Marie; Bridgewater, Rachel

2007-01-01

This article details the development of the Library Instruction Wiki (http://instructionwiki.org): an effort to develop a web-based, knowledge-sharing resource. Though some library instruction is specific to a given institution or class, much of what instruction librarians teach is similar. Library instructors have repeatedly expressed the desire…

Exploring Collaborative Writing in Wikis: A Genre-Based Approach

ERIC Educational Resources Information Center

Coccetta, Francesca

2015-01-01

While CALL research into collaborative writing in the L2 using wikis has mainly focused on the texts written by learners in terms of their grammatical accuracy (e.g. Mak & Coniam, 2008; Lee, 2010), the purpose of the present study is to draw attention to these texts as instances of a given genre. It reports on a small-scale experiment…

Community Intelligence in Knowledge Curation: An Application to Managing Scientific Nomenclature

PubMed Central

Zou, Dong; Li, Ang; Liu, Guocheng; Chen, Fei; Wu, Jiayan; Xiao, Jingfa; Wang, Xumin; Yu, Jun; Zhang, Zhang

2013-01-01

Harnessing community intelligence in knowledge curation bears significant promise in dealing with communication and education in the flood of scientific knowledge. As knowledge is accumulated at ever-faster rates, scientific nomenclature, a particular kind of knowledge, is concurrently generated in all kinds of fields. Since nomenclature is a system of terms used to name things in a particular discipline, accurate translation of scientific nomenclature in different languages is of critical importance, not only for communications and collaborations with English-speaking people, but also for knowledge dissemination among people in the non-English-speaking world, particularly young students and researchers. However, it lacks of accuracy and standardization when translating scientific nomenclature from English to other languages, especially for those languages that do not belong to the same language family as English. To address this issue, here we propose for the first time the application of community intelligence in scientific nomenclature management, namely, harnessing collective intelligence for translation of scientific nomenclature from English to other languages. As community intelligence applied to knowledge curation is primarily aided by wiki and Chinese is the native language for about one-fifth of the world’s population, we put the proposed application into practice, by developing a wiki-based English-to-Chinese Scientific Nomenclature Dictionary (ESND; http://esnd.big.ac.cn). ESND is a wiki-based, publicly editable and open-content platform, exploiting the whole power of the scientific community in collectively and collaboratively managing scientific nomenclature. Based on community curation, ESND is capable of achieving accurate, standard, and comprehensive scientific nomenclature, demonstrating a valuable application of community intelligence in knowledge curation. PMID:23451119

Community intelligence in knowledge curation: an application to managing scientific nomenclature.

PubMed

Dai, Lin; Xu, Chao; Tian, Ming; Sang, Jian; Zou, Dong; Li, Ang; Liu, Guocheng; Chen, Fei; Wu, Jiayan; Xiao, Jingfa; Wang, Xumin; Yu, Jun; Zhang, Zhang

2013-01-01

Harnessing community intelligence in knowledge curation bears significant promise in dealing with communication and education in the flood of scientific knowledge. As knowledge is accumulated at ever-faster rates, scientific nomenclature, a particular kind of knowledge, is concurrently generated in all kinds of fields. Since nomenclature is a system of terms used to name things in a particular discipline, accurate translation of scientific nomenclature in different languages is of critical importance, not only for communications and collaborations with English-speaking people, but also for knowledge dissemination among people in the non-English-speaking world, particularly young students and researchers. However, it lacks of accuracy and standardization when translating scientific nomenclature from English to other languages, especially for those languages that do not belong to the same language family as English. To address this issue, here we propose for the first time the application of community intelligence in scientific nomenclature management, namely, harnessing collective intelligence for translation of scientific nomenclature from English to other languages. As community intelligence applied to knowledge curation is primarily aided by wiki and Chinese is the native language for about one-fifth of the world's population, we put the proposed application into practice, by developing a wiki-based English-to-Chinese Scientific Nomenclature Dictionary (ESND; http://esnd.big.ac.cn). ESND is a wiki-based, publicly editable and open-content platform, exploiting the whole power of the scientific community in collectively and collaboratively managing scientific nomenclature. Based on community curation, ESND is capable of achieving accurate, standard, and comprehensive scientific nomenclature, demonstrating a valuable application of community intelligence in knowledge curation.

Student-Initiated Attention to Form in Wiki-Based Collaborative Writing

ERIC Educational Resources Information Center

Kessler, Greg

2009-01-01

This study reports on student initiated attention to form within the collaborative construction of a wiki among pre-service Non-Native Speaker (NNS) English teachers. Forty NNS pre-service teachers from a large Mexican university were observed over a period of a sixteen week semester in an online content-based course aimed at improving their…

Empathy 2.0 and the Wonderful World of Wiki Collaboration

ERIC Educational Resources Information Center

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…

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

ERIC Educational Resources Information Center

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…

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

ERIC Educational Resources Information Center

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…

Assessment of Collaborative Learning Experiences by Graphical Analysis of Wiki Contributions

ERIC Educational Resources Information Center

Palomo-Duarte, Manuel; Dodero, Juan Manuel; Medina-Bulo, Inmaculada; Rodríguez-Posada, Emilio J.; Ruiz-Rube, Iván

2014-01-01

The widespread adoption of computers and Internet in our life has reached the classrooms, where computer-supported collaborative learning (CSCL) based on wikis offers new ways of collaboration and encourages student participation. When the number of contributions from students increases, traditional assessment procedures of e-learning settings…

Patterns of Computer-Mediated Interaction in Small Writing Groups Using Wikis

ERIC Educational Resources Information Center

Li, Mimi; Zhu, Wei

2013-01-01

Informed by sociocultural theory and guided especially by "collective scaffolding", this study investigated the nature of computer-mediated interaction of three groups of English as a Foreign Language students when they performed collaborative writing tasks using wikis. Nine college students from a Chinese university participated in the…

Can Facebook or Wikis Hook Learners Instead of the Schoolbook?

ERIC Educational Resources Information Center

Brahmi, Fakhreddine

2016-01-01

In this paper I will report on a personal experimentation with Facebook and wikis as collaborative learning tools. The aims of implementing these strategies were to develop students' writing skills and to change their attitudes towards learning in the digital age. I delved into this research because I do believe that learning in the new millennium…

Distributed Scaffolding: Wiki Collaboration among Latino High School Chemistry Students

ERIC Educational Resources Information Center

O'Sullivan, Edwin Duncan, Jr.

2013-01-01

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…

A Novel Wiki-Based Remote Laboratory Platform for Engineering Education

ERIC Educational Resources Information Center

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…

Using Wikis and Blogs for Assessment in First-Year Engineering

ERIC Educational Resources Information Center

Smith, Elizabeth Joy; Mills, Julie Evelyn; Myers, Baden

2009-01-01

Purpose: This paper aims to examine some of the strengths and weaknesses of the use of online tools such as wikis and blogs for assessment purposes, with the aim of proposing future developments and improvements. Design/methodology/approach: The paper utilises a case study approach by examining the outcomes of a new first-year course for all…

There and Back Again: From Research Methods to Principles of Learning, and Everything in Between: Consolidated Knowledge Using the Course Wiki

ERIC Educational Resources Information Center

Hogendoorn, Adrian

2017-01-01

A course wiki is an active environment in which students not only solve problems, but also find their own problems (Bransford, Brown, & Cocking, 1999). Wikis are novel, immersive environments requiring active participation, which enable students to build knowledge within a secure online setting (Hadjerrouit, 2011). This contribution traces a…

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

ERIC Educational Resources Information Center

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…

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

ERIC Educational Resources Information Center

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…

Wiki technology enhanced group project to promote active learning in a neuroscience course for first-year medical students: an exploratory study.

PubMed

Mi, Misa; Gould, Douglas

2014-01-01

A Wiki group project was integrated into a neuroscience course for first-year medical students. The project was developed as a self-directed, collaborative learning task to help medical students review course content and make clinically important connections. The goals of the project were to enhance students' understanding of key concepts in neuroscience, promote active learning, and reinforce their information literacy skills. The objective of the exploratory study was to provide a formative evaluation of the Wiki group project and to examine how Wiki technology was utilized to enhance active and collaborative learning of first-year medical students in the course and to reinforce information literacy skills.

WikiBuild: a new online collaboration process for multistakeholder tool development and consensus building.

PubMed

Gupta, Samir; Wan, Flora T; Newton, David; Bhattacharyya, Onil K; Chignell, Mark H; Straus, Sharon E

2011-12-08

Production of media such as patient education tools requires methods that can integrate multiple stakeholder perspectives. Existing consensus techniques are poorly suited to design of visual media, can be expensive and logistically demanding, and are subject to caveats arising from group dynamics such as participant hierarchies. Our objective was to develop a method that enables multistakeholder tool building while averting these difficulties. We developed a wiki-inspired method and tested this through the collaborative design of an asthma action plan (AAP). In the development stage, we developed the Web-based tool by (1) establishing AAP content and format options, (2) building a Web-based application capable of representing each content and format permutation, (3) testing this tool among stakeholders, and (4) revising this tool based on stakeholder feedback. In the wiki stage, groups of participants used the revised tool in three separate 1-week "wiki" periods during which each group collaboratively authored an AAP by making multiple online selections. In the development stage, we recruited 16 participants (9/16 male) (4 pulmonologists, 4 primary care physicians, 3 certified asthma educators, and 5 patients) for system testing. The mean System Usability Scale (SUS) score for the tool used in testing was 72.2 (SD 10.2). In the wiki stage, we recruited 41 participants (15/41 male) (9 pulmonologists, 6 primary care physicians, 5 certified asthma educators, and 21 patients) from diverse locations. The mean SUS score for the revised tool was 75.9 (SD 19.6). Users made 872, 466, and 599 successful changes to the AAP in weeks 1, 2, and 3, respectively. The site was used actively for a mean of 32.0 hours per week, of which 3.1 hours per week (9.7%) constituted synchronous multiuser use (2-4 users at the same time). Participants averaged 23 (SD 33) minutes of login time and made 7.7 (SD 15) changes to the AAP per day. Among participants, 28/35 (80%) were satisfied with

A Wiki-Based Group Project in an Inorganic Chemistry Foundation Course

ERIC Educational Resources Information Center

Kristian, Kathleen E.

2015-01-01

A semester-long group project that utilizes wiki sites to enhance collaboration was developed for a foundation course in inorganic chemistry. Through structured assignments, student groups use metal-based or metal-combating therapeutic agents as a model for applying and understanding course concepts; they also gain proficiency with scientific- and…

Collaboration or Cooperation? Analyzing Group Dynamics and Revision Processes in Wikis

ERIC Educational Resources Information Center

Arnold, Nike; Ducate, Lara; Kost, Claudia

2012-01-01

This study examines the online writing and revision behaviors of university language learners. In small groups, 53 intermediate German students from three classes at three different universities created wiki pages with background information about a novel read in class. All meaning- and language-related revisions were analyzed to determine whether…

Collaborative authoring: a case study of the use of a wiki as a tool to keep systematic reviews up to date

PubMed Central

Bender, Jacqueline L; O’Grady, Laura A; Deshpande, Amol; Cortinois, Andrea A; Saffie, Luis; Husereau, Don; Jadad, Alejandro R

2011-01-01

Background Systematic reviews are recognized as the most effective means of summarizing research evidence. However, they are limited by the time and effort required to keep them up to date. Wikis present a unique opportunity to facilitate collaboration among many authors. The purpose of this study was to examine the use of a wiki as an online collaborative tool for the updating of a type of systematic review known as a scoping review. Methods An existing peer-reviewed scoping review on asynchronous telehealth was previously published on an open, publicly available wiki. Log file analysis, user questionnaires and content analysis were used to collect descriptive and evaluative data on the use of the site from 9 June 2009 to 10 April 2010. Blog postings from referring sites were also analyzed. Results During the 10-month study period, there were a total of 1222 visits to the site, 3996 page views and 875 unique visitors from around the globe. Five unique visitors (0.6% of the total number of visitors) submitted a total of 6 contributions to the site: 3 contributions were made to the article itself, and 3 to the discussion pages. None of the contributions enhanced the evidence base of the scoping review. The commentary about the project in the blogosphere was positive, tempered with some skepticism. Interpretations Despite the fact that wikis provide an easy-to-use, free and powerful means to edit information, fewer than 1% of visitors contributed content to the wiki. These results may be a function of limited interest in the topic area, the review methodology itself, lack of familiarity with the wiki, and the incentive structure of academic publishing. Controversial and timely topics in addition to incentives and organizational support for Web 2.0 impact metrics might motivate greater participation in online collaborative efforts to keep scientific knowledge up to date. PMID:22567076

Online Wiki Collaboration by Teachers of Students with Autism Spectrum Disorders

ERIC Educational Resources Information Center

Kilham, Chris

2009-01-01

A shared understanding of autism spectrum disorders (ASD) and a coordinated approach to teaching diagnosed students is essential because of the complex learning needs of this cohort. This research examines the ways in which special educators used wiki technology to create a working document and to share and develop their perspectives about…

Content Creators and Language Learners: Exploring Web 2.0 and Wikis

ERIC Educational Resources Information Center

Craig, Dorothy Valcarcel

2013-01-01

This qualitative study examined the use of Wikis and blogs among graduate students in an online class that was part of a teacher preparation program in English as a Second Language. Participants included practicing teachers and graduate assistants who represented a variety of learning environments and experiences. The study was framed by a set of…

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

ERIC Educational Resources Information Center

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…

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

ERIC Educational Resources Information Center

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…

"I DON'T CARE DO UR OWN PAGE!!" A Case Study of Using Wikis for Collaborative Work in a UK Secondary School

ERIC Educational Resources Information Center

Grant, Lyndsay

2009-01-01

Alongside other forms of social software, wikis have been heralded as supporting more collaborative and democratic teaching and learning practices. This paper explores, through a case study approach, the use of wikis to support a collaborative research project undertaken in a UK secondary school. Findings are analysed in the context of research on…

Interactions in the microbiome: communities of organisms and communities of genes

PubMed Central

Boon, Eva; Meehan, Conor J; Whidden, Chris; Wong, Dennis H-J; Langille, Morgan GI; Beiko, Robert G

2014-01-01

A central challenge in microbial community ecology is the delineation of appropriate units of biodiversity, which can be taxonomic, phylogenetic, or functional in nature. The term ‘community’ is applied ambiguously; in some cases, the term refers simply to a set of observed entities, while in other cases, it requires that these entities interact with one another. Microorganisms can rapidly gain and lose genes, potentially decoupling community roles from taxonomic and phylogenetic groupings. Trait-based approaches offer a useful alternative, but many traits can be defined based on gene functions, metabolic modules, and genomic properties, and the optimal set of traits to choose is often not obvious. An analysis that considers taxon assignment and traits in concert may be ideal, with the strengths of each approach offsetting the weaknesses of the other. Individual genes also merit consideration as entities in an ecological analysis, with characteristics such as diversity, turnover, and interactions modeled using genes rather than organisms as entities. We identify some promising avenues of research that are likely to yield a deeper understanding of microbial communities that shift from observation-based questions of ‘Who is there?’ and ‘What are they doing?’ to the mechanistically driven question of ‘How will they respond?’ PMID:23909933

Wiki Technology: A Virtual, Cooperative Learning Tool Used to Enhance Student Learning

ERIC Educational Resources Information Center

Barrera, Alessandra L.

2015-01-01

This study demonstrates the use of wiki technology (an editable webpage environment) to provide a virtual, asynchronous collaborative-learning environment for students for the purpose of working on course-content-focused study-guide questions. To analyze the effectiveness of this course tool, students' responses to various qualitative and…

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

DTIC Science & Technology

2008-12-01

always light at the end of the tunnel . Last but not less, the author would like to share the success of the completion of this thesis research...modern clients (e.g. Blackberries , iPhones, tactical digital assistants like the TACTICOMP), wikis do not require extensive user training or loading of

Investigating a Nigerian XXL-Cohort Wiki-Learning Experience: Observation, Feedback and Reflection

ERIC Educational Resources Information Center

Aborisade, Peter

2009-01-01

A regular feature of the Nigerian tertiary education context is large numbers of students crammed into small classrooms or lecture theatres. This context had long begged for the creation of innovative learning spaces and adoption of engaging pedagogies. Recourse to technology support and experimenting with the WIKI as a learning tool at the…

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

ERIC Educational Resources Information Center

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…

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

ERIC Educational Resources Information Center

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…

Horizontal gene transfer in an acid mine drainage microbial community.

PubMed

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.

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

NASA Astrophysics Data System (ADS)

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'.

Incorporating Current Research, Wikis, and Discussion Lists in a Mathematics Capstone Course

ERIC Educational Resources Information Center

Narasimhan, Revathi

2009-01-01

This article shows how current mathematical research and innovative internet technologies such as wikis and email discussion lists can enliven a senior seminar or capstone course. We give example of assignments as well as examples of how new technologies can enhance a course. This paper grew out of the author's experience of teaching a senior…

Guidelines for the functional annotation of microRNAs using the Gene Ontology

PubMed Central

D'Eustachio, Peter; Smith, Jennifer R.; Zampetaki, Anna

2016-01-01

MicroRNA regulation of developmental and cellular processes is a relatively new field of study, and the available research data have not been organized to enable its inclusion in pathway and network analysis tools. The association of gene products with terms from the Gene Ontology is an effective method to analyze functional data, but until recently there has been no substantial effort dedicated to applying Gene Ontology terms to microRNAs. Consequently, when performing functional analysis of microRNA data sets, researchers have had to rely instead on the functional annotations associated with the genes encoding microRNA targets. In consultation with experts in the field of microRNA research, we have created comprehensive recommendations for the Gene Ontology curation of microRNAs. This curation manual will enable provision of a high-quality, reliable set of functional annotations for the advancement of microRNA research. Here we describe the key aspects of the work, including development of the Gene Ontology to represent this data, standards for describing the data, and guidelines to support curators making these annotations. The full microRNA curation guidelines are available on the GO Consortium wiki (http://wiki.geneontology.org/index.php/MicroRNA_GO_annotation_manual). PMID:26917558

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

ERIC Educational Resources Information Center

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…

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

ERIC Educational Resources Information Center

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…

Improving Teacher Candidates' Lesson Planning Competencies through Peer Review in a Wiki Environment

ERIC Educational Resources Information Center

Salajan, Florin D.; Nyachwaya, James M.; Hoffman, Jeanette G.; Hill, Brent D.

2016-01-01

This article examines the implementation of a wiki-type platform for lesson planning for teacher candidates in an undergraduate general instructional methods course in the teacher education program of a Midwestern university in the United States. The study draws on the results of two separate sets of analysis involving 159 participants. Teacher…

Leveraging the power of Web 2.0 tools: a wiki platform as a multimedia teaching and learning environment in dental education.

PubMed

Salajan, Florin D; Mount, Greg J

2012-04-01

This article presents the development and implementation of a wiki-based application for the delivery of educational content in dentistry. The Dental Procedure Education System (DPES) is a new web application that uses SharePoint to combine online collaborative authoring characteristic of wiki spaces with instructional video documentaries. Harnessing the wiki's versatility, DPES offers faculty members an avenue to develop an authoritative source of information for both students, through DPES Pro, and the public at large, through DPES Public. Principles of cognitive theory of multimedia learning, constructivist theory, and collaborative writing were employed in the development of DPES. An authoring protocol, with a clearly defined sequence of steps, was established in order to keep the production of the DPES procedures consistent and predictable. Initial, anecdotal user reports indicate that DPES is well received among dental students and faculty members. Expected outcomes and benefits of DPES use are discussed, and directions for research are proposed.

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

PubMed

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.

The Logic of Wikis: The Possibilities of the Web 2.0 Classroom

ERIC Educational Resources Information Center

Glassman, Michael; Kang, Min Ju

2011-01-01

The emergence of Web 2.0 and some of its ascendant tools such as blogs and wikis have the potential to dramatically change education, both in how we conceptualize and operationalize processes and strategies. We argue in this paper that it is a change that has been over a century in coming. The promise of the Web 2.0 is similar to ideas proposed by…

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

ERIC Educational Resources Information Center

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,…

A Collaborative, Wiki-Based Organic Chemistry Project Incorporating Free Chemistry Software on the Web

ERIC Educational Resources Information Center

Evans, Michael J.; Moore, Jeffrey S.

2011-01-01

In recent years, postsecondary instructors have recognized the potential of wikis to transform the way students learn in a collaborative environment. However, few instructors have embraced in-depth student use of chemistry software for the creation of interactive chemistry content on the Web. Using currently available software, students are able…

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.

PubMed

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.

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

ERIC Educational Resources Information Center

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…

WikiPEATia - a web based platform for assembling peatland data through ‘crowd sourcing’

NASA Astrophysics Data System (ADS)

Wisser, D.; Glidden, S.; Fieseher, C.; Treat, C. C.; Routhier, M.; Frolking, S. E.

2009-12-01

The Earth System Science community is realizing that peatlands are an important and unique terrestrial ecosystem that has not yet been well-integrated into large-scale earth system analyses. A major hurdle is the lack of accessible, geospatial data of peatland distribution, coupled with data on peatland properties (e.g., vegetation composition, peat depth, basal dates, soil chemistry, peatland class) at the global scale. This data, however, is available at the local scale. Although a comprehensive global database on peatlands probably lags similar data on more economically important ecosystems such as forests, grasslands, croplands, a large amount of field data have been collected over the past several decades. A few efforts have been made to map peatlands at large scales but existing data have not been assembled into a single geospatial database that is publicly accessible or do not depict data with a level of detail that is needed in the Earth System Science Community. A global peatland database would contribute to advances in a number of research fields such as hydrology, vegetation and ecosystem modeling, permafrost modeling, and earth system modeling. We present a Web 2.0 approach that uses state-of-the-art webserver and innovative online mapping technologies and is designed to create such a global database through ‘crowd-sourcing’. Primary functions of the online system include form-driven textual user input of peatland research metadata, spatial data input of peatland areas via a mapping interface, database editing and querying editing capabilities, as well as advanced visualization and data analysis tools. WikiPEATia provides an integrated information technology platform for assembling, integrating, and posting peatland-related geospatial datasets facilitates and encourages research community involvement. A successful effort will make existing peatland data much more useful to the research community, and will help to identify significant data gaps.

A gene-targeted approach to investigate the intestinal butyrate-producing bacterial community

PubMed Central

2013-01-01

Background Butyrate, which is produced by the human microbiome, is essential for a well-functioning colon. Bacteria that produce butyrate are phylogenetically diverse, which hinders their accurate detection based on conventional phylogenetic markers. As a result, reliable information on this important bacterial group is often lacking in microbiome research. Results In this study we describe a gene-targeted approach for 454 pyrotag sequencing and quantitative polymerase chain reaction for the final genes in the two primary bacterial butyrate synthesis pathways, butyryl-CoA:acetate CoA-transferase (but) and butyrate kinase (buk). We monitored the establishment and early succession of butyrate-producing communities in four patients with ulcerative colitis who underwent a colectomy with ileal pouch anal anastomosis and compared it with three control samples from healthy colons. All patients established an abundant butyrate-producing community (approximately 5% to 26% of the total community) in the pouch within the 2-month study, but patterns were distinctive among individuals. Only one patient harbored a community profile similar to the healthy controls, in which there was a predominance of but genes that are similar to reference genes from Acidaminococcus sp., Eubacterium sp., Faecalibacterium prausnitzii and Roseburia sp., and an almost complete absence of buk genes. Two patients were greatly enriched in buk genes similar to those of Clostridium butyricum and C. perfringens, whereas a fourth patient displayed abundant communities containing both genes. Most butyrate producers identified in previous studies were detected and the general patterns of taxa found were supported by 16S rRNA gene pyrotag analysis, but the gene-targeted approach provided more detail about the potential butyrate-producing members of the community. Conclusions The presented approach provides quantitative and genotypic insights into butyrate-producing communities and facilitates a more specific

Mining Genotype-Phenotype Associations from Public Knowledge Sources via Semantic Web Querying

PubMed Central

Kiefer, Richard C.; Freimuth, Robert R.; Chute, Christopher G; Pathak, Jyotishman

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. PMID:24303249

Mining Genotype-Phenotype Associations from Public Knowledge Sources via Semantic Web Querying.

PubMed

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.

Online Intercultural Collaborations Using Wikis: An Analysis of Students' Comments and Factors Affecting Project Success

ERIC Educational Resources Information Center

Forsythe, Edo

2014-01-01

Online intercultural collaborations using wiki pages are becoming common in foreign language education. However, research into their effectiveness and the types of comments students make in their interactions remains scant. This study addresses this gap by exploring three years' worth of interactions among Japanese students of English and American…

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

PubMed

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.

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

ERIC Educational Resources Information Center

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…

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

ERIC Educational Resources Information Center

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…

WikiBuild: A New Online Collaboration Process For Multistakeholder Tool Development and Consensus Building

PubMed Central

Wan, Flora T; Newton, David; Bhattacharyya, Onil K; Chignell, Mark H; Straus, Sharon E

2011-01-01

Background Production of media such as patient education tools requires methods that can integrate multiple stakeholder perspectives. Existing consensus techniques are poorly suited to design of visual media, can be expensive and logistically demanding, and are subject to caveats arising from group dynamics such as participant hierarchies. Objective Our objective was to develop a method that enables multistakeholder tool building while averting these difficulties. Methods We developed a wiki-inspired method and tested this through the collaborative design of an asthma action plan (AAP). In the development stage, we developed the Web-based tool by (1) establishing AAP content and format options, (2) building a Web-based application capable of representing each content and format permutation, (3) testing this tool among stakeholders, and (4) revising this tool based on stakeholder feedback. In the wiki stage, groups of participants used the revised tool in three separate 1-week “wiki” periods during which each group collaboratively authored an AAP by making multiple online selections. Results In the development stage, we recruited 16 participants (9/16 male) (4 pulmonologists, 4 primary care physicians, 3 certified asthma educators, and 5 patients) for system testing. The mean System Usability Scale (SUS) score for the tool used in testing was 72.2 (SD 10.2). In the wiki stage, we recruited 41 participants (15/41 male) (9 pulmonologists, 6 primary care physicians, 5 certified asthma educators, and 21 patients) from diverse locations. The mean SUS score for the revised tool was 75.9 (SD 19.6). Users made 872, 466, and 599 successful changes to the AAP in weeks 1, 2, and 3, respectively. The site was used actively for a mean of 32.0 hours per week, of which 3.1 hours per week (9.7%) constituted synchronous multiuser use (2–4 users at the same time). Participants averaged 23 (SD 33) minutes of login time and made 7.7 (SD 15) changes to the AAP per day. Among

Impact of a dermatology wiki website on dermatology education.

PubMed

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.

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

ERIC Educational Resources Information Center

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…

Detection of gene communities in multi-networks reveals cancer drivers

NASA Astrophysics Data System (ADS)

Cantini, Laura; Medico, Enzo; Fortunato, Santo; Caselle, Michele

2015-12-01

We propose a new multi-network-based strategy to integrate different layers of genomic information and use them in a coordinate way to identify driving cancer genes. The multi-networks that we consider combine transcription factor co-targeting, microRNA co-targeting, protein-protein interaction and gene co-expression networks. The rationale behind this choice is that gene co-expression and protein-protein interactions require a tight coregulation of the partners and that such a fine tuned regulation can be obtained only combining both the transcriptional and post-transcriptional layers of regulation. To extract the relevant biological information from the multi-network we studied its partition into communities. To this end we applied a consensus clustering algorithm based on state of art community detection methods. Even if our procedure is valid in principle for any pathology in this work we concentrate on gastric, lung, pancreas and colorectal cancer and identified from the enrichment analysis of the multi-network communities a set of candidate driver cancer genes. Some of them were already known oncogenes while a few are new. The combination of the different layers of information allowed us to extract from the multi-network indications on the regulatory pattern and functional role of both the already known and the new candidate driver genes.

The Use of Wiki in Teaching Programming: Effects upon Achievement, Attitudes, and Collaborative Programming Behaviors

ERIC Educational Resources Information Center

Lin, Yu-Tzu; Wu, Cheng-Chih; Chiu, Chiung-Fang

2018-01-01

This article explores the feasibility of employing cooperative program editing tools in teaching programming. A quasi-experimental study was conducted, in which the experimental group co-edited the programs with peers using the wiki. The control group co-edited the programs with peers using only the face-to-face approach. The findings show that…

Bacterial community and arsenic functional genes diversity in arsenic contaminated soils from different geographic locations

PubMed Central

Gu, Yunfu; D. Van Nostrand, Joy; Wu, Liyou; He, Zhili; Qin, Yujia; Zhao, Fang-Jie; Zhou, Jizhong

2017-01-01

To understand how soil microbial communities and arsenic (As) functional genes respond to soil arsenic (As) contamination, five soils contaminated with As at different levels were collected from diverse geographic locations, incubated for 54 days under flooded conditions, and examined by both MiSeq sequencing of 16S rRNA gene amplicons and functional gene microarray (GeoChip 4.0). The results showed that both bacterial community structure and As functional gene structure differed among geographical locations. The diversity of As functional genes correlated positively with the diversity of 16S rRNA genes (P< 0.05). Higher diversities of As functional genes and 16S rRNA genes were observed in the soils with higher available As. Soil pH, phosphate-extractable As, and amorphous Fe content were the most important factors in shaping the bacterial community structure and As transformation functional genes. Geographic location was also important in controlling both the bacterial community and As transformation functional potential. These findings provide insights into the variation of As transformation functional genes in soils contaminated with different levels of As at different geographic locations, and the impact of environmental As contamination on the soil bacterial community. PMID:28475654

A Collaborative Web-Based Approach to Planning Research, Integration, and Testing Using a Wiki

NASA Technical Reports Server (NTRS)

Delaney, Michael M.; Koshimoto, Edwin T.; Noble, Deleena; Duggan, Christopher

2010-01-01

The National Aeronautics and Space Administration Integrated Vehicle Health Management program touches on many different research areas while striving to enable the automated detection, diagnosis, prognosis, and mitigation of adverse events at the aircraft and system level. At the system level, the research focus is on the evaluation of multidisciplinary integrated methods, tools, and technologies for achieving the program goal. The participating program members form a diverse group of government, industry, and academic researchers. The program team developed the Research and Test Integration Plan in order to track significant test and evaluation activities, which are important for understanding, demonstrating, and communicating the overall project state and project direction. The Plan is a living document, which allows the project team the flexibility to construct conceptual test scenarios and to track project resources. The Plan also incorporates several desirable feature requirements for Plan users and maintainers. A wiki has proven to be the most efficient and effective means of implementing the feature requirements for the Plan. The wiki has proven very valuable as a research project management tool, and there are plans to expand its scope.

Community-wide plasmid gene mobilization and selection

PubMed Central

Sentchilo, Vladimir; Mayer, Antonia P; Guy, Lionel; Miyazaki, Ryo; Green Tringe, Susannah; Barry, Kerrie; Malfatti, Stephanie; Goessmann, Alexander; Robinson-Rechavi, Marc; van der Meer, Jan R

2013-01-01

Plasmids have long been recognized as an important driver of DNA exchange and genetic innovation in prokaryotes. The success of plasmids has been attributed to their independent replication from the host's chromosome and their frequent self-transfer. It is thought that plasmids accumulate, rearrange and distribute nonessential genes, which may provide an advantage for host proliferation under selective conditions. In order to test this hypothesis independently of biases from culture selection, we study the plasmid metagenome from microbial communities in two activated sludge systems, one of which receives mostly household and the other chemical industry wastewater. We find that plasmids from activated sludge microbial communities carry among the largest proportion of unknown gene pools so far detected in metagenomic DNA, confirming their presumed role of DNA innovators. At a system level both plasmid metagenomes were dominated by functions associated with replication and transposition, and contained a wide variety of antibiotic and heavy metal resistances. Plasmid families were very different in the two metagenomes and grouped in deep-branching new families compared with known plasmid replicons. A number of abundant plasmid replicons could be completely assembled directly from the metagenome, providing insight in plasmid composition without culturing bias. Functionally, the two metagenomes strongly differed in several ways, including a greater abundance of genes for carbohydrate metabolism in the industrial and of general defense factors in the household activated sludge plasmid metagenome. This suggests that plasmids not only contribute to the adaptation of single individual prokaryotic species, but of the prokaryotic community as a whole under local selective conditions. PMID:23407308

Evaluate Wiki Technology as e-Learning Tool from the Point View of Al-Baha University Students: A Pilot Study with Undergraduate Students in Both Faculties of Science and Education

ERIC Educational Resources Information Center

Alzahrani, Ibraheem

2012-01-01

Wikis technologies are one of Web 2.0 applications that can be used to improve the learning method and to engage students in learning with others in a collaborative environment. This paper investigates the potential use of wiki technology in Al-Baha University through students' perceptions; the study seeks to answer the main question. How to…

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

ERIC Educational Resources Information Center

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…

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

ERIC Educational Resources Information Center

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…

Using Wikis to Enhance Website Peer Evaluation in an Online Website Development Course: An Exploratory Study

ERIC Educational Resources Information Center

He, Wu

2011-01-01

Peer evaluations are often used to improve learning in educational settings. As more and more online courses are offered, it is becoming increasingly important to explore new techniques for conducting peer evaluation in online courses. In recent years, wikis have increasingly been used in higher education to support learning and group work.…

Exploring Factors Affecting Students' Continued Wiki Use for Individual and Collaborative Learning: An Extended UTAUT Perspective

ERIC Educational Resources Information Center

Yueh, Hsiu-Ping; Huang, Jo-Yi; Chang, Chueh

2015-01-01

The purpose of this study was to investigate what factors affect students' adaptation and continued use of a Wiki system for collaborative writing tasks through an extension of the Unified Theory of Acceptance and Use of Technology (UTAUT). This study was conducted in a general education course in a university in northern Taiwan. Data were…

Lateral Gene Transfer in a Heavy Metal-Contaminated-Groundwater Microbial Community

PubMed Central

Hemme, Christopher L.; Green, Stefan J.; Rishishwar, Lavanya; Prakash, Om; Pettenato, Angelica; Chakraborty, Romy; Deutschbauer, Adam M.; Van Nostrand, Joy D.; Wu, Liyou; He, Zhili; Jordan, I. King; Arkin, Adam P.; Kostka, Joel E.

2016-01-01

ABSTRACT Unraveling the drivers controlling the response and adaptation of biological communities to environmental change, especially anthropogenic activities, is a central but poorly understood issue in ecology and evolution. Comparative genomics studies suggest that lateral gene transfer (LGT) is a major force driving microbial genome evolution, but its role in the evolution of microbial communities remains elusive. To delineate the importance of LGT in mediating the response of a groundwater microbial community to heavy metal contamination, representative Rhodanobacter reference genomes were sequenced and compared to shotgun metagenome sequences. 16S rRNA gene-based amplicon sequence analysis indicated that Rhodanobacter populations were highly abundant in contaminated wells with low pHs and high levels of nitrate and heavy metals but remained rare in the uncontaminated wells. Sequence comparisons revealed that multiple geochemically important genes, including genes encoding Fe2+/Pb2+ permeases, most denitrification enzymes, and cytochrome c553, were native to Rhodanobacter and not subjected to LGT. In contrast, the Rhodanobacter pangenome contained a recombinational hot spot in which numerous metal resistance genes were subjected to LGT and/or duplication. In particular, Co2+/Zn2+/Cd2+ efflux and mercuric resistance operon genes appeared to be highly mobile within Rhodanobacter populations. Evidence of multiple duplications of a mercuric resistance operon common to most Rhodanobacter strains was also observed. Collectively, our analyses indicated the importance of LGT during the evolution of groundwater microbial communities in response to heavy metal contamination, and a conceptual model was developed to display such adaptive evolutionary processes for explaining the extreme dominance of Rhodanobacter populations in the contaminated groundwater microbiome. PMID:27048805

A Formative Evaluation of WIKI's as a Learning Tool in a Face to Face Juvenile Justice Course

ERIC Educational Resources Information Center

Bowman, Scott Wm.

2013-01-01

Current literature indicates an increased pedagogical value of technology integration in university coursework. One form of technology that encourages collaborative, online teaching and learning is a "wiki," an online application that allows participants to partner and direct a website. This article describes the design and formative evaluation of…

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

PubMed

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.

Enhancing Teaching and Learning of Home Economics in Secondary Schools with Wikis: An Action Research Study

ERIC Educational Resources Information Center

Lai, Yiu-Chi; Lum, Edmund Kit-Leung

2012-01-01

This article discusses an action research study using a wiki as a course platform for teaching and learning Home Economics in secondary schools. A secondary Home Economics teacher observed that dessert recipes were too wordy and that students generally felt bored and were not eager to read them in full. To improve his teaching effectiveness, the…

Utilizing semantic Wiki technology for intelligence analysis at the tactical edge

NASA Astrophysics Data System (ADS)

Little, Eric

2014-05-01

Challenges exist for intelligence analysts to efficiently and accurately process large amounts of data collected from a myriad of available data sources. These challenges are even more evident for analysts who must operate within small military units at the tactical edge. In such environments, decisions must be made quickly without guaranteed access to the kinds of large-scale data sources available to analysts working at intelligence agencies. Improved technologies must be provided to analysts at the tactical edge to make informed, reliable decisions, since this is often a critical collection point for important intelligence data. To aid tactical edge users, new types of intelligent, automated technology interfaces are required to allow them to rapidly explore information associated with the intersection of hard and soft data fusion, such as multi-INT signals, semantic models, social network data, and natural language processing of text. Abilities to fuse these types of data is paramount to providing decision superiority. For these types of applications, we have developed BLADE. BLADE allows users to dynamically add, delete and link data via a semantic wiki, allowing for improved interaction between different users. Analysts can see information updates in near-real-time due to a common underlying set of semantic models operating within a triple store that allows for updates on related data points from independent users tracking different items (persons, events, locations, organizations, etc.). The wiki can capture pictures, videos and related information. New information added directly to pages is automatically updated in the triple store and its provenance and pedigree is tracked over time, making that data more trustworthy and easily integrated with other users' pages.

Availability of drug information on community pharmacy websites in Tennessee.

PubMed

Borja-Hart, Nancy; Hohmeier, Kenneth C

2017-06-01

This study reports the availability and type of drug information resources on community pharmacy websites in Tennessee. A list of pharmacies was obtained from the Tennessee Board of Pharmacy. All community pharmacies located in Tennessee with a website were evaluated. Community pharmacy websites that listed a drug information resource were further analysed into pharmacy type and drug information provider. One hundred and sixty-nine websites were evaluated. Thirty-six websites listed a drug information resource. Fifty per cent of those sites used the drug information provider RxWiki. Other providers included drugs.com, First Data Bank, A.D.A.M., RxList, Gold Standard Multimedia and Express Scripts. Community pharmacy websites are underutilized as a provider for credible drug information for the public. © 2017 Royal Pharmaceutical Society.

IntPath--an integrated pathway gene relationship database for model organisms and important pathogens

PubMed Central

2012-01-01

Background 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. Results 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

IntPath--an integrated pathway gene relationship database for model organisms and important pathogens.

PubMed

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

Evaluating the Effectiveness of the Open-Access ChemWiki Resource as a Replacement for Traditional General Chemistry Textbooks

ERIC Educational Resources Information Center

Allen, Gregory; Guzman-Alvarez, Alberto; Smith, Amy; Gamage, Alan; Molinaro, Marco; Larsen, Delmar S.

2015-01-01

Open educational resources (OERs) provide a potential alternative to costly textbooks and can allow content to be edited and adapted to a variety of classroom environments. At the University of California, Davis, the OER "ChemWiki" project, as part of the greater STEMWiki Hyperlibrary, was developed to supplant traditional post-secondary…

Evolution properties of the community members for dynamic networks

NASA Astrophysics Data System (ADS)

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.

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

NASA Astrophysics Data System (ADS)

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

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

ERIC Educational Resources Information Center

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…

Gene expression of indoor fungal communities under damp building conditions: Implications for human health.

PubMed

Hegarty, B; Dannemiller, K C; Peccia, J

2018-03-03

Dampness and visible mold growth in homes are associated with negative human health outcomes, but causal relationships between fungal exposure and health are not well established. The purpose of this study was to determine whether dampness in buildings impacts fungal community gene expression and how, in turn, gene expression may modulate human health impacts. A metatranscriptomic study was performed on house dust fungal communities to investigate the expression of genes and metabolic processes in chamber experiments at water activity levels of 0.5, 0.85, and 1.0. Fungi at water activities as low as 0.5 were metabolically active, focusing their transcriptional resources on primary processes essential for cell maintenance. Metabolic complexity increased with water activity where communities at 1.0 displayed more diverse secondary metabolic processes. Greater gene expression at increasing water activity has important implications for human health: Fungal communities at 1.0 a w upregulated a greater number of allergen-, mycotoxin-, and pathogenicity-encoding genes versus communities at 0.85 and 0.5 a w . In damp buildings, fungi may display increases in secondary metabolic processes with the potential for greater per-cell production of allergens, toxins, and pathogenicity. Assessments in wet versus dry buildings that do not account for this elevated health impact may not accurately reflect exposure. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

The medical matters wiki: building a library Web site 2.0.

PubMed

Robertson, Justin; Burnham, Judy; Li, Jie; Sayed, Ellen

2008-01-01

New and innovative information technologies drive the ever-evolving library profession. From clay tablet to parchment scroll to manufactured paper to computer screen pixel, information storage, retrieval, and delivery methods continue to evolve, and each advance irrevocably affects the way libraries, and librarians, work. The Internet has forever altered information and library science, both in theory and practice, but even within this context the progression continues. Though ambiguously defined, Web 2.0 offers a new outlook and new software, presenting librarians with potentially invaluable new tools and methods. This paper discusses the creation, implementation, and maintenance of a Web 2.0 technology, the wiki, as a resource tool for an academic biomedical library.

Making your database available through Wikipedia: the pros and cons.

PubMed

Finn, Robert D; Gardner, Paul P; Bateman, Alex

2012-01-01

Wikipedia, the online encyclopedia, is the most famous wiki in use today. It contains over 3.7 million pages of content; with many pages written on scientific subject matters that include peer-reviewed citations, yet are written in an accessible manner and generally reflect the consensus opinion of the community. In this, the 19th Annual Database Issue of Nucleic Acids Research, there are 11 articles that describe the use of a wiki in relation to a biological database. In this commentary, we discuss how biological databases can be integrated with Wikipedia, thereby utilising the pre-existing infrastructure, tools and above all, large community of authors (or Wikipedians). The limitations to the content that can be included in Wikipedia are highlighted, with examples drawn from articles found in this issue and other wiki-based resources, indicating why other wiki solutions are necessary. We discuss the merits of using open wikis, like Wikipedia, versus other models, with particular reference to potential vandalism. Finally, we raise the question about the future role of dedicated database biocurators in context of the thousands of crowdsourced, community annotations that are now being stored in wikis.

Making your database available through Wikipedia: the pros and cons

PubMed Central

Finn, Robert D.; Gardner, Paul P.; Bateman, Alex

2012-01-01

Wikipedia, the online encyclopedia, is the most famous wiki in use today. It contains over 3.7 million pages of content; with many pages written on scientific subject matters that include peer-reviewed citations, yet are written in an accessible manner and generally reflect the consensus opinion of the community. In this, the 19th Annual Database Issue of Nucleic Acids Research, there are 11 articles that describe the use of a wiki in relation to a biological database. In this commentary, we discuss how biological databases can be integrated with Wikipedia, thereby utilising the pre-existing infrastructure, tools and above all, large community of authors (or Wikipedians). The limitations to the content that can be included in Wikipedia are highlighted, with examples drawn from articles found in this issue and other wiki-based resources, indicating why other wiki solutions are necessary. We discuss the merits of using open wikis, like Wikipedia, versus other models, with particular reference to potential vandalism. Finally, we raise the question about the future role of dedicated database biocurators in context of the thousands of crowdsourced, community annotations that are now being stored in wikis. PMID:22144683

Stress-Survival Gene Identification From an Acid Mine Drainage Algal Mat Community

NASA Astrophysics Data System (ADS)

Urbina-Navarrete, J.; Fujishima, K.; Paulino-Lima, I. G.; Rothschild-Mancinelli, B.; Rothschild, L. J.

2014-12-01

Microbial communities from acid mine drainage environments are exposed to multiple stressors to include low pH, high dissolved metal loads, seasonal freezing, and desiccation. The microbial and algal communities that inhabit these niche environments have evolved strategies that allow for their ecological success. Metagenomic analyses are useful in identifying species diversity, however they do not elucidate the mechanisms that allow for the resilience of a community under these extreme conditions. Many known or predicted genes encode for protein products that are unknown, or similarly, many proteins cannot be traced to their gene of origin. This investigation seeks to identify genes that are active in an algal consortium during stress from living in an acid mine drainage environment. Our approach involves using the entire community transcriptome for a functional screen in an Escherichia coli host. This approach directly targets the genes involved in survival, without need for characterizing the members of the consortium.The consortium was harvested and stressed with conditions similar to the native environment it was collected from. Exposure to low pH (< 3.2), high metal load, desiccation, and deep freeze resulted in the expression of stress-induced genes that were transcribed into messenger RNA (mRNA). These mRNA transcripts were harvested to build complementary DNA (cDNA) libraries in E. coli. The transformed E. coli were exposed to the same stressors as the original algal consortium to select for surviving cells. Successful cells incorporated the transcripts that encode survival mechanisms, thus allowing for selection and identification of the gene(s) involved. Initial selection screens for freeze and desiccation tolerance have yielded E. coli that are 1 order of magnitude more resistant to freezing (0.01% survival of control with no transcript, 0.2% survival of E. coli with transcript) and 3 orders of magnitude more resistant to desiccation (0.005% survival of

"I Felt Like the Enemy and the Savior All at Once": English Teacher Identity in a Methods Course Wiki

ERIC Educational Resources Information Center

Jewett, Michelle Ann

2012-01-01

This study explores the identity constructions of two cohorts of preservice teachers enrolled in English methods courses during a semester of field experience. This research employs a qualitative methodology and documents the nature of participant's responses posted to online wiki forum. Data sources include archived electronic interactions…

Profiling Hyporheic Microbial Community Nitrogen Cycle and Carbohydrate Active Enzyme Gene Abundances across Seasons

NASA Astrophysics Data System (ADS)

Nelson, W. C.; Graham, E.; Stegen, J.

2016-12-01

The hyporheic zone (HZ) is the permanently inundated sediment layer between a surface channel and adjacent groundwater-saturated sediments. It has been hypothesized to play a major role in macronutrient (C, N, P) cycling in rivers. The correlation between community taxonomic composition dynamics and functional gene representation is poorly understood for hyporheic communities. To explore how microbial communities respond to temporal changes in environmental conditions, metagenomes were derived from communities captured in sterile sandpacks deployed within the HZ of the Columbia River. HMM databases were used to enumerate protein families present. Functional classification of reads allowed a general assessment of community function over time, while targeted assembly of specific genes enabled investigation of the diversity of organisms encoding these functions. Preliminary analysis of nitrogen cycle pathways shows most gene families examined to have quite steady representation across seasons, with most observed changes being less than an order of magnitude. Analysis of ammonia oxidation genes showed bacterial ammonia oxidizers (AOB) to be stably present across the year, while the archaeal amoA gene increased in late summer, peaking sharply in November, mirroring results from 16S rRNA amplicon analysis which showed an increase in Thaumarcheal OTUs during that same period. Most glycosyl hydrolase GH families had low representation. Highly abundant classes of GH included the GH94 (beta-glucosidase), GH95 (1-2-alpha-L-fucosidase) and GH103 (lytic transglycosylase) families, suggesting activity on plant, fungus and insect polysaccharides and peptidoglycans. Further work is investigating the taxonomy of the sequences identified, to determine how changes in the community composition contribute to the stable gene family profiles observed. These results are intended to work towards a greater understanding of the role of species diversity and functional redundancy in the

Zooplankton community analysis in the Changjiang River estuary by single-gene-targeted metagenomics

NASA Astrophysics Data System (ADS)

Cheng, Fangping; Wang, Minxiao; Li, Chaolun; Sun, Song

2014-07-01

DNA barcoding provides accurate identification of zooplankton species through all life stages. Single-gene-targeted metagenomic analysis based on DNA barcode databases can facilitate longterm monitoring of zooplankton communities. With the help of the available zooplankton databases, the zooplankton community of the Changjiang (Yangtze) River estuary was studied using a single-gene-targeted metagenomic method to estimate the species richness of this community. A total of 856 mitochondrial cytochrome oxidase subunit 1 (cox1) gene sequences were determined. The environmental barcodes were clustered into 70 molecular operational taxonomic units (MOTUs). Forty-two MOTUs matched barcoded marine organisms with more than 90% similarity and were assigned to either the species (similarity>96%) or genus level (similarity<96%). Sibling species could also be distinguished. Many species that were overlooked by morphological methods were identified by molecular methods, especially gelatinous zooplankton and merozooplankton that were likely sampled at different life history phases. Zooplankton community structures differed significantly among all of the samples. The MOTU spatial distributions were influenced by the ecological habits of the corresponding species. In conclusion, single-gene-targeted metagenomic analysis is a useful tool for zooplankton studies, with which specimens from all life history stages can be identified quickly and effectively with a comprehensive database.

Using a wiki platform to promote guidelines internationally and maintain their currency: evidence-based guidelines for the nutritional management of adult patients with head and neck cancer.

PubMed

Brown, T; Findlay, M; von Dincklage, J; Davidson, W; Hill, J; Isenring, E; Talwar, B; Bell, K; Kiss, N; Kurmis, R; Loeliger, J; Sandison, A; Taylor, K; Bauer, J

2013-04-01

The present study describes the development of evidence-based practice guidelines for the nutritional management of adult patients with head and neck cancer using a wiki platform to enable wide international stakeholder consultation and maintain currency. A dietitian steering committee and a multidisciplinary steering committee were established for consultation. Traditional methods of evidence-based guideline development were utilised to perform the literature review, assess the evidence and produce a draft document. This was transferred to a wiki platform for stakeholder consultation and international endorsement processes in Australia, New Zealand and the UK. Data were collected on website traffic utilising Google Analytics. In addition to broad stakeholder consultation through the steering committees, an additional twenty comments were received via the wiki by twelve individuals covering six different professions from three different countries, compared to four comments by e-mail. The guidelines were subsequently endorsed by the dietetic associations of Australia, New Zealand and the UK. During a 4-month period monitoring the use of the guidelines, there were 2303 page views to the landing page from 33 countries. The average number of pages accessed per visit was five and the duration of time spent on the website was approximately 6 min. Using a wiki platform for guideline development and dissemination is a successful method for producing high-quality resources that can undergo wide international stakeholder review and include open public consultation. This can replace conventional methods whereby guidelines can quickly become outdated. © 2013 The Authors Journal of Human Nutrition and Dietetics © 2013 The British Dietetic Association Ltd.

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

PubMed Central

Wang, Yu; Zhang, Rui; He, Zhili; Van Nostrand, Joy D.; Zheng, Qiang; Zhou, Jizhong; Jiao, Nianzhi

2017-01-01

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 with

Barriers to prostate cancer prevention and community recommended health education strategies in an urban African American community in Jackson, Mississippi.

PubMed

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.

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

PubMed Central

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

Background 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. Objectives 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. Methods 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. Results 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. Conclusions 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

Development and validation of questionnaires exploring health care professionals' intention to use wiki-based reminders to promote best practices in trauma.

PubMed

Archambault, Patrick Michel; Gagnon, Susie; Gagnon, Marie-Pierre; Turcotte, Stéphane; Lapointe, Jean; Fleet, Richard; Côté, Mario; Beaupré, Pierre; Le Sage, Natalie; Emond, Marcel; Légaré, France

2014-10-03

Little is known about factors influencing professionals' use of wikis. We developed and validated two questionnaires to assess health care professionals' intention to use wiki-based reminders for the management of trauma patients. We developed questionnaires for emergency physicians (EPs) and allied health professions (AHPs) based on the Theory of Planned Behavior and adapted them to the salient beliefs of each, identified in an earlier study. Items measured demographics and direct and indirect theoretical constructs. We piloted the questionnaires with 2 focus groups (5 EPs and 5 AHPs) to identify problems of wording and length. Based on feedback, we adjusted the wording and combined certain items. A new convenience sample of 25 EPs and 26 AHPs then performed a test-retest of the questionnaires at a 2-week interval. We assessed internal consistency using Cronbach alpha coefficients and temporal stability of items with an agreement intraclass correlation coefficient (ICC). Five EPs and 5 AHPs (3 nurses, 1 respiratory therapist, and 1 pharmacist) formed 2 focus groups; 25 EPs and 26 AHPs (12 nurses, 7 respiratory therapists, and 7 pharmacists) completed the test and retest. The EP questionnaire test-retest scores for consistency (Cronbach alpha) and stability (ICC) were intention (test: Cronbach alpha=.94; retest: Cronbach alpha=.98; ICC=.89), attitude (.74, .72, .70), subjective norm (.79, .78, .75), perceived behavioral control (.67, .65, .66), attitudinal beliefs (.94, .86, .60), normative beliefs (.83, .87, .79), and control beliefs barriers (.58, .67, .78) and facilitators (.97, .85, .30). The AHP questionnaire scores for consistency and stability were: intention (test Cronbach alpha=.69, retest Cronbach alpha=.81, ICC=.48), attitude (.85, .87, .83), subjective norm (.47, .82, .62), perceived behavioral control (.55, .62, .60), attitudinal beliefs (.92, .91, .82), normative beliefs (.85, .90, .74), and control beliefs barriers (.58, .55, .66) and facilitators

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

PubMed

Boulos, Maged N Kamel; Maramba, Inocencio; Wheeler, Steve

2006-08-15

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). 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 the context of medical/health education. If

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

PubMed Central

Boulos, Maged N Kamel; Maramba, Inocencio; Wheeler, Steve

2006-01-01

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 the context of medical

Lateral gene transfer in a heavy metal-contaminated-groundwater microbial community

DOE PAGES

Hemme, Christopher L.; Green, Stefan J.; Rishishwar, Lavanya; ...

2016-04-05

Here, unraveling the drivers controlling the response and adaptation of biological communities to environmental change, especially anthropogenic activities, is a central but poorly understood issue in ecology and evolution. Comparative genomics studies suggest that lateral gene transfer (LGT) is a major force driving microbial genome evolution, but its role in the evolution of microbial communities remains elusive.

Functional Gene Differences in Soil Microbial Communities from Conventional, Low-Input, and Organic Farmlands

PubMed Central

Xue, Kai; Wu, Liyou; Deng, Ye; He, Zhili; Van Nostrand, Joy; Robertson, Philip G.; Schmidt, Thomas M.

2013-01-01

Various agriculture management practices may have distinct influences on soil microbial communities and their ecological functions. In this study, we utilized GeoChip, a high-throughput microarray-based technique containing approximately 28,000 probes for genes involved in nitrogen (N)/carbon (C)/sulfur (S)/phosphorus (P) cycles and other processes, to evaluate the potential functions of soil microbial communities under conventional (CT), low-input (LI), and organic (ORG) management systems at an agricultural research site in Michigan. Compared to CT, a high diversity of functional genes was observed in LI. The functional gene diversity in ORG did not differ significantly from that of either CT or LI. Abundances of genes encoding enzymes involved in C/N/P/S cycles were generally lower in CT than in LI or ORG, with the exceptions of genes in pathways for lignin degradation, methane generation/oxidation, and assimilatory N reduction, which all remained unchanged. Canonical correlation analysis showed that selected soil (bulk density, pH, cation exchange capacity, total C, C/N ratio, NO3−, NH4+, available phosphorus content, and available potassium content) and crop (seed and whole biomass) variables could explain 69.5% of the variation of soil microbial community composition. Also, significant correlations were observed between NO3− concentration and denitrification genes, NH4+ concentration and ammonification genes, and N2O flux and denitrification genes, indicating a close linkage between soil N availability or process and associated functional genes. PMID:23241975

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

PubMed

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.

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

NASA Astrophysics Data System (ADS)

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%.

How Does the Scientific Community Contribute to Gene Ontology?

PubMed

Lovering, Ruth C

2017-01-01

Collaborations between the scientific community and members of the Gene Ontology (GO) Consortium have led to an increase in the number and specificity of GO terms, as well as increasing the number of GO annotations. A variety of approaches have been taken to encourage research scientists to contribute to the GO, but the success of these approaches has been variable. This chapter reviews both the successes and failures of engaging the scientific community in GO development and annotation, as well as, providing motivation and advice to encourage individual researchers to contribute to GO.

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

ERIC Educational Resources Information Center

Fong, Shirley S. M.; Chu, Samuel K. W.; Lau, Wilfred W.F.; Doherty, Iain; Hew, K. F.

2017-01-01

Aim/Purpose: To investigate the effectiveness of incorporating wiki technology in an undergraduate 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…

Virtual Communities in the Law Enforcement Environment: Do These Systems Lead to Enhanced Organizational Memory

DTIC Science & Technology

2008-12-01

forwarded to other users. D. DISCUSSION BOARD Discussion boards are commonly referred to as “ forums ” and are used for asynchronous communications.31...This technology allows for open ended communications in written format. A user can start a discussion by adding a posting to a community forum ...and deployed. Some of the built in features include, forums , discussion boards, custom lists, calendar, to-do lists, wiki technology, email

Is Julian Assange an International Version of Daniel Ellsberg and WikiLeaks the Modern Equivalent of the Pentagon Papers?

ERIC Educational Resources Information Center

Freivogel, William H.

2011-01-01

History has placed the stamp of approval on the publication of the Pentagon Papers, the top-secret history of the Vietnam War. If WikiLeaks editor-in-chief Julian Assange is another Daniel Ellsberg, then it is possible the website's disclosures will be viewed over time as similarly in the public interest. A classroom discussion on the release of…

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

ERIC Educational Resources Information Center

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…

Development and Validation of Questionnaires Exploring Health Care Professionals' Intention to Use Wiki-Based Reminders to Promote Best Practices in Trauma

PubMed Central

Gagnon, Susie; Gagnon, Marie-Pierre; Turcotte, Stéphane; Lapointe, Jean; Fleet, Richard; Côté, Mario; Beaupré, Pierre; Le Sage, Natalie; Émond, Marcel; Légaré, France

2014-01-01

Background Little is known about factors influencing professionals’ use of wikis. Objective We developed and validated two questionnaires to assess health care professionals’ intention to use wiki-based reminders for the management of trauma patients. Methods We developed questionnaires for emergency physicians (EPs) and allied health professions (AHPs) based on the Theory of Planned Behavior and adapted them to the salient beliefs of each, identified in an earlier study. Items measured demographics and direct and indirect theoretical constructs. We piloted the questionnaires with 2 focus groups (5 EPs and 5 AHPs) to identify problems of wording and length. Based on feedback, we adjusted the wording and combined certain items. A new convenience sample of 25 EPs and 26 AHPs then performed a test-retest of the questionnaires at a 2-week interval. We assessed internal consistency using Cronbach alpha coefficients and temporal stability of items with an agreement intraclass correlation coefficient (ICC). Results Five EPs and 5 AHPs (3 nurses, 1 respiratory therapist, and 1 pharmacist) formed 2 focus groups; 25 EPs and 26 AHPs (12 nurses, 7 respiratory therapists, and 7 pharmacists) completed the test and retest. The EP questionnaire test-retest scores for consistency (Cronbach alpha) and stability (ICC) were intention (test: Cronbach alpha=.94; retest: Cronbach alpha=.98; ICC=.89), attitude (.74, .72, .70), subjective norm (.79, .78, .75), perceived behavioral control (.67, .65, .66), attitudinal beliefs (.94, .86, .60), normative beliefs (.83, .87, .79), and control beliefs barriers (.58, .67, .78) and facilitators (.97, .85, .30). The AHP questionnaire scores for consistency and stability were: intention (test Cronbach alpha=.69, retest Cronbach alpha=.81, ICC=.48), attitude (.85, .87, .83), subjective norm (.47, .82, .62), perceived behavioral control (.55, .62, .60), attitudinal beliefs (.92, .91, .82), normative beliefs (.85, .90, .74), and control beliefs

The Effects of Instruction Enhanced by Video/Photo Blogs and Wikis on Learning the Distinctions of the Spanish Preterite and Imperfect

ERIC Educational Resources Information Center

Castaneda, Daniel A.

2011-01-01

This study investigated the differences in levels of achievement when learning the preterite and imperfect aspects in Spanish, at the recognition and production levels, between students who used instruction with video/photo blogs and wikis, compared to those who used instruction with traditional text-based technologies. Results revealed that there…

Change of microbial community structure and functional gene abundance in nonylphenol-degrading sediment.

PubMed

Wang, Zhao; Yang, Yuyin; He, Tao; Xie, Shuguang

2015-04-01

Biodegradation by autochthonous microbial community is an important way to clean up nonylphenol (NP) from contaminated river sediment. Knowledge of sediment microbial community can aid in our understanding of biological processes related to NP degradation. However, the change in sediment microbial community associated with NP biodegradation remains unclear. The present study investigated the shift in bacterial community structure and NP-degrading gene abundance in response to NP attenuation in river sediment. Sediment microcosms with different levels of 4-NP (0, 100, or 300 μg/g) were constructed. A nearly complete attenuation of NP occurred in the microcosm with 100 μg/g NP after 9 days' incubation, while a residual NP rate of 8.1 % was observed in the microcosm with 300 μg/g NP after 22 days' incubation. Illumina MiSeq sequencing analysis indicated that Gammaproteobacteria, Alphaproteobacteria, and Bacteroidetes predominated in NP-degrading river sediment. Sediment bacterial community structure varied significantly during NP biodegradation and subsequent incubation, which was affected by the level of added NP. The n-alkane biodegradation (alkB) gene abundance showed a significant variation in each NP-amended microcosm (100 or 300 μg/g), while a significant increase in the single component monooxygenase (sMO) gene abundance only occurred in the microcosm spiked with 300 μg/g NP. This study can provide some new insights toward NP-degrading microbial ecology in the environment.

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

PubMed

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.

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

PubMed Central

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

Empirical phylogenies and species abundance distributions are consistent with preequilibrium dynamics of neutral community models with gene flow.

PubMed

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

2017-05-01

Community characteristics reflect past ecological and evolutionary dynamics. Here, we investigate whether it is possible to obtain realistically shaped modeled communities-that is 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 preequilibrium 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 preequilibrium conditions. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

GeoChip-Based Analysis of the Functional Gene Diversity and Metabolic Potential of Microbial Communities in Acid Mine Drainage▿ †

PubMed Central

Xie, Jianping; He, Zhili; Liu, Xinxing; Liu, Xueduan; Van Nostrand, Joy D.; Deng, Ye; Wu, Liyou; Zhou, Jizhong; Qiu, Guanzhou

2011-01-01

Acid mine drainage (AMD) is an extreme environment, usually with low pH and high concentrations of metals. Although the phylogenetic diversity of AMD microbial communities has been examined extensively, little is known about their functional gene diversity and metabolic potential. In this study, a comprehensive functional gene array (GeoChip 2.0) was used to analyze the functional diversity, composition, structure, and metabolic potential of AMD microbial communities from three copper mines in China. GeoChip data indicated that these microbial communities were functionally diverse as measured by the number of genes detected, gene overlapping, unique genes, and various diversity indices. Almost all key functional gene categories targeted by GeoChip 2.0 were detected in the AMD microbial communities, including carbon fixation, carbon degradation, methane generation, nitrogen fixation, nitrification, denitrification, ammonification, nitrogen reduction, sulfur metabolism, metal resistance, and organic contaminant degradation, which suggested that the functional gene diversity was higher than was previously thought. Mantel test results indicated that AMD microbial communities are shaped largely by surrounding environmental factors (e.g., S, Mg, and Cu). Functional genes (e.g., narG and norB) and several key functional processes (e.g., methane generation, ammonification, denitrification, sulfite reduction, and organic contaminant degradation) were significantly (P < 0.10) correlated with environmental variables. This study presents an overview of functional gene diversity and the structure of AMD microbial communities and also provides insights into our understanding of metabolic potential in AMD ecosystems. PMID:21097602

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

ERIC Educational Resources Information Center

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…

The Effects of Faculty Status, Faculty Gender, Field of Study, and Class Size on the Use of Blogs, Wikis, and Discussion Boards

ERIC Educational Resources Information Center

Yang, Dazhi; Spear, Caile E.

2017-01-01

This study examined faculty's use of time intensive Web 2.0 technologies (blogs, discussion forums, and wikis) in teaching during a university's quest for higher research productivity and higher ranking in the Carnegie Classification. Results show there was a difference in using Web 2.0 technologies in teaching between faculty with different…

YTPdb: a wiki database of yeast membrane transporters.

PubMed

Brohée, Sylvain; Barriot, Roland; Moreau, Yves; André, Bruno

2010-10-01

Membrane transporters constitute one of the largest functional categories of proteins in all organisms. In the yeast Saccharomyces cerevisiae, this represents about 300 proteins ( approximately 5% of the proteome). We here present the Yeast Transport Protein database (YTPdb), a user-friendly collaborative resource dedicated to the precise classification and annotation of yeast transporters. YTPdb exploits an evolution of the MediaWiki web engine used for popular collaborative databases like Wikipedia, allowing every registered user to edit the data in a user-friendly manner. Proteins in YTPdb are classified on the basis of functional criteria such as subcellular location or their substrate compounds. These classifications are hierarchical, allowing queries to be performed at various levels, from highly specific (e.g. ammonium as a substrate or the vacuole as a location) to broader (e.g. cation as a substrate or inner membranes as location). Other resources accessible for each transporter via YTPdb include post-translational modifications, K(m) values, a permanently updated bibliography, and a hierarchical classification into families. The YTPdb concept can be extrapolated to other organisms and could even be applied for other functional categories of proteins. YTPdb is accessible at http://homes.esat.kuleuven.be/ytpdb/. Copyright © 2010 Elsevier B.V. All rights reserved.

Detection of Antibiotic Resistance Genes in Source and Drinking Water Samples from a First Nations Community in Canada

PubMed Central

Fernando, Dinesh M.; Tun, Hein Min; Poole, Jenna; Patidar, Rakesh; Li, Ru; Mi, Ruidong; Amarawansha, Geethani E. A.; Fernando, W. G. Dilantha; Khafipour, Ehsan; Farenhorst, Annemieke

2016-01-01

ABSTRACT Access to safe drinking water is now recognized as a human right by the United Nations. In developed countries like Canada, access to clean water is generally not a matter of concern. However, one in every five First Nations reserves is under a drinking water advisory, often due to unacceptable microbiological quality. In this study, we analyzed source and potable water from a First Nations community for the presence of coliform bacteria as well as various antibiotic resistance genes. Samples, including those from drinking water sources, were found to be positive for various antibiotic resistance genes, namely, ampC, tet(A), mecA, β-lactamase genes (SHV-type, TEM-type, CTX-M-type, OXA-1, and CMY-2-type), and carbapenemase genes (KPC, IMP, VIM, NDM, GES, and OXA-48 genes). Not surprisingly, substantial numbers of total coliforms, including Escherichia coli, were recovered from these samples, and this result was also confirmed using Illumina sequencing of the 16S rRNA gene. These findings deserve further attention, as the presence of coliforms and antibiotic resistance genes potentially puts the health of the community members at risk. IMPORTANCE In this study, we highlight the poor microbiological quality of drinking water in a First Nations community in Canada. We examined the coliform load as well as the presence of antibiotic resistance genes in these samples. This study examined the presence of antibiotic-resistant genes in drinking water samples from a First Nations Community in Canada. We believe that our findings are of considerable significance, since the issue of poor water quality in First Nations communities in Canada is often ignored, and our findings will help shed some light on this important issue. PMID:27235436

Detection of Antibiotic Resistance Genes in Source and Drinking Water Samples from a First Nations Community in Canada.

PubMed

Fernando, Dinesh M; Tun, Hein Min; Poole, Jenna; Patidar, Rakesh; Li, Ru; Mi, Ruidong; Amarawansha, Geethani E A; Fernando, W G Dilantha; Khafipour, Ehsan; Farenhorst, Annemieke; Kumar, Ayush

2016-08-01

Access to safe drinking water is now recognized as a human right by the United Nations. In developed countries like Canada, access to clean water is generally not a matter of concern. However, one in every five First Nations reserves is under a drinking water advisory, often due to unacceptable microbiological quality. In this study, we analyzed source and potable water from a First Nations community for the presence of coliform bacteria as well as various antibiotic resistance genes. Samples, including those from drinking water sources, were found to be positive for various antibiotic resistance genes, namely, ampC, tet(A), mecA, β-lactamase genes (SHV-type, TEM-type, CTX-M-type, OXA-1, and CMY-2-type), and carbapenemase genes (KPC, IMP, VIM, NDM, GES, and OXA-48 genes). Not surprisingly, substantial numbers of total coliforms, including Escherichia coli, were recovered from these samples, and this result was also confirmed using Illumina sequencing of the 16S rRNA gene. These findings deserve further attention, as the presence of coliforms and antibiotic resistance genes potentially puts the health of the community members at risk. In this study, we highlight the poor microbiological quality of drinking water in a First Nations community in Canada. We examined the coliform load as well as the presence of antibiotic resistance genes in these samples. This study examined the presence of antibiotic-resistant genes in drinking water samples from a First Nations Community in Canada. We believe that our findings are of considerable significance, since the issue of poor water quality in First Nations communities in Canada is often ignored, and our findings will help shed some light on this important issue. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

AphidBase: A centralized bioinformatic resource for annotation of the pea aphid genome

PubMed Central

Legeai, Fabrice; Shigenobu, Shuji; Gauthier, Jean-Pierre; Colbourne, John; Rispe, Claude; Collin, Olivier; Richards, Stephen; Wilson, Alex C. C.; Tagu, Denis

2015-01-01

AphidBase is a centralized bioinformatic resource that was developed to facilitate community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC). The AphidBase Information System designed to organize and distribute genomic data and annotations for a large international community was constructed using open source software tools from the Generic Model Organism Database (GMOD). The system includes Apollo and GBrowse utilities as well as a wiki, blast search capabilities and a full text search engine. AphidBase strongly supported community cooperation and coordination in the curation of gene models during community annotation of the pea aphid genome. AphidBase can be accessed at http://www.aphidbase.com. PMID:20482635

FoodWiki: Ontology-Driven Mobile Safe Food Consumption System.

PubMed

Çelik, Duygu

2015-01-01

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).

Orthochina.org: case-based orthopaedic Wiki project in China.

PubMed

Ma, Zhen-Sheng; Zhang, Hong-Ju; Yu, Tao; Ren, Gang; Du, Guo-Sheng; Wang, Yong-Hua

2008-10-01

Traditional continuing medical education (CME) depended primarily on periodic courses and conferences. The cost-effectiveness of these courses has not been established, and often the content is not tailored to best meet the needs of the students. Internet training has the potential to accomplish these goals. Over the last 10 years, we have developed a Web site entitled "Orthochina.org," based upon the wiki concept, which uses an interactive, case-based format. We describe the development of online case discussions, and various technical and administrative requirements. As of December 31, 2007, there were 33,984 registered users, 9,759 of which passed the confirmation procedures. In 2007, an average of 211 registrants visited daily. The average number of first page clicks was 4,248 per day, and the average number of posts was 70 per day. All cases submitted for discussion include the patient's complaint, physical examination findings, and relevant images based on specific criteria for case discussion. The case discussions develop well professionally. No spam posting or unauthorized personal advertisement is permitted. In conclusion, online academic discussions proceed well when the orthopaedic surgeons who participate have established their identities.

FoodWiki: Ontology-Driven Mobile Safe Food Consumption System

PubMed Central

Çelik, Duygu

2015-01-01

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). PMID:26221624

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

ERIC Educational Resources Information Center

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…

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

PubMed

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.

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

PubMed Central

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

2011-01-01

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. PMID:20861922

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

PubMed Central

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

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

PubMed Central

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

CYP1A1, GCLC, AGT, AGTR1 gene-gene interactions in community-acquired pneumonia pulmonary complications.

PubMed

Salnikova, Lyubov E; Smelaya, Tamara V; Golubev, Arkadiy M; Rubanovich, Alexander V; Moroz, Viktor V

2013-11-01

This study was conducted to establish the possible contribution of functional gene polymorphisms in detoxification/oxidative stress and vascular remodeling pathways to community-acquired pneumonia (CAP) susceptibility in the case-control study (350 CAP patients, 432 control subjects) and to predisposition to the development of CAP complications in the prospective study. All subjects were genotyped for 16 polymorphic variants in the 14 genes of xenobiotics detoxification CYP1A1, AhR, GSTM1, GSTT1, ABCB1, redox-status SOD2, CAT, GCLC, and vascular homeostasis ACE, AGT, AGTR1, NOS3, MTHFR, VEGFα. Risk of pulmonary complications (PC) in the single locus analysis was associated with CYP1A1, GCLC and AGTR1 genes. Extra PC (toxic shock syndrome and myocarditis) were not associated with these genes. We evaluated gene-gene interactions using multi-factor dimensionality reduction, and cumulative gene risk score approaches. The final model which included >5 risk alleles in the CYP1A1 (rs2606345, rs4646903, rs1048943), GCLC, AGT, and AGTR1 genes was associated with pleuritis, empyema, acute respiratory distress syndrome, all PC and acute respiratory failure (ARF). We considered CYP1A1, GCLC, AGT, AGTR1 gene set using Set Distiller mode implemented in GeneDecks for discovering gene-set relations via the degree of sharing descriptors within a given gene set. N-acetylcysteine and oxygen were defined by Set Distiller as the best descriptors for the gene set associated in the present study with PC and ARF. Results of the study are in line with literature data and suggest that genetically determined oxidative stress exacerbation may contribute to the progression of lung inflammation.

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

NASA Astrophysics Data System (ADS)

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

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

NASA Astrophysics Data System (ADS)

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.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Waldron, P.J.; Wu, L.; Van Nostrand, J.D.

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 butmore » 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.« less

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

PubMed

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.

Developing leadership practices in hospital-based nurse educators in an online learning community.

PubMed

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.

Application of community phylogenetic approaches to understand gene expression: differential exploration of venom gene space in predatory marine gastropods.

PubMed

Chang, Dan; Duda, Thomas F

2014-06-05

Predatory marine gastropods of the genus Conus exhibit substantial variation in venom composition both within and among species. Apart from mechanisms associated with extensive turnover of gene families and rapid evolution of genes that encode venom components ('conotoxins'), the evolution of distinct conotoxin expression patterns is an additional source of variation that may drive interspecific differences in the utilization of species' 'venom gene space'. To determine the evolution of expression patterns of venom genes of Conus species, we evaluated the expression of A-superfamily conotoxin genes of a set of closely related Conus species by comparing recovered transcripts of A-superfamily genes that were previously identified from the genomes of these species. We modified community phylogenetics approaches to incorporate phylogenetic history and disparity of genes and their expression profiles to determine patterns of venom gene space utilization. Less than half of the A-superfamily gene repertoire of these species is expressed, and only a few orthologous genes are coexpressed among species. Species exhibit substantially distinct expression strategies, with some expressing sets of closely related loci ('under-dispersed' expression of available genes) while others express sets of more disparate genes ('over-dispersed' expression). In addition, expressed genes show higher dN/dS values than either unexpressed or ancestral genes; this implies that expression exposes genes to selection and facilitates rapid evolution of these genes. Few recent lineage-specific gene duplicates are expressed simultaneously, suggesting that expression divergence among redundant gene copies may be established shortly after gene duplication. Our study demonstrates that venom gene space is explored differentially by Conus species, a process that effectively permits the independent and rapid evolution of venoms in these species.

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

PubMed

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'.

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

PubMed Central

Moody, Paul

2017-01-01

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’. PMID:29278244

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

PubMed

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.

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

PubMed Central

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

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

PubMed

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 < 0.001) increases in the abundance of the GP 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

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

He, Shaomei; Malfatti, Stephanie A.; McFarland, Jack W.

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 greenhousemore » 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

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

DOE PAGES

He, Shaomei; Malfatti, Stephanie A.; McFarland, Jack W.; ...

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 greenhousemore » 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

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

PubMed

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

Abundance of antibiotic resistance genes and bacterial community composition in wild freshwater fish species.

PubMed

Marti, Elisabet; Huerta, Belinda; Rodríguez-Mozaz, Sara; Barceló, Damià; Marcé, Rafael; Balcázar, Jose Luis

2018-04-01

This study was aimed to determine the abundance of four antibiotic resistance genes (bla TEM , ermB, qnrS and sulI), as well as bacterial community composition associated with the intestinal mucus of wild freshwater fish species collected from the Foix and La Llosa del Cavall reservoirs, which represent ecosystems with high and low anthropogenic disturbance, respectively. Water and sediments from these reservoirs were also collected and analyzed to determine the pollution level by antibiotics. The bla TEM gene was only detected in brown trout and Ebro barbel, which were collected from La Llosa del Cavall reservoir. In contrast, the sulI and qnrS genes were only detected in common carp, which were collected from the Foix reservoir. Although the ermB gene was also detected in common carp, the values were below the limit of quantification. Likewise, water and sediment samples from the Foix reservoir had higher concentrations and more classes of antibiotics than those from La Llosa del Cavall. Pyrosequencing analysis of 16S rRNA genes revealed significant differences in bacterial communities associated with the intestinal mucus of fish species. Therefore, these findings suggest that anthropogenic activities are not only increasing the pollution of aquatic environments, but also contributing to the emergence and spread of antibiotic resistance in organisms that inhabit such environments. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

PubMed

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

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

PubMed Central

Edwards, Jennifer L.; Smith, Darren L.; Connolly, John; McDonald, James E.; Cox, Michael J.; Joint, Ian; Edwards, Clive; McCarthy, Alan J.

2010-01-01

Polysaccharides are an important source of organic carbon in the marine environment, degradation of the insoluble, 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, 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, functional genes,, showed that the community was dominated by members of the Gammaproteobacteria, 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, degrade cellulose in the marine environment, to evaluate the glycoside hydrolase (cellulase, chitinase) gene repertoire of that community, in the absence of the biases associated with PCR-based molecular techniques. PMID:24710093

Occurrence and diversity of naphthalene dioxygenase genes in soil microbial communities from the Maritime Antarctic.

PubMed

Flocco, Cecilia G; Gomes, Newton C M; Mac Cormack, Walter; Smalla, Kornelia

2009-03-01

The diversity of naphthalene dioxygenase genes (ndo) in soil environments from the Maritime Antarctic was assessed, dissecting as well the influence of the two vascular plants that grow in the Antarctic: Deschampsia antarctica and Colobanthus quitensis. Total community DNA was extracted from bulk and rhizosphere soil samples from Jubany station and Potter Peninsula, South Shetland Islands. ndo genes were amplified by a nested PCR and analysed by denaturant gradient gel electrophoresis approach (PCR-DGGE) and cloning and sequencing. The ndo-DGGE fingerprints of oil-contaminated soil samples showed even and reproducible patterns, composed of four dominant bands. The presence of vascular plants did not change the relative abundance of ndo genotypes compared with bulk soil. For non-contaminated sites, amplicons were not obtained for all replicates and the variability among the fingerprints was comparatively higher, likely reflecting a lower abundance of ndo genes. The phylogenetic analyses showed that all sequences were affiliated to the nahAc genes closely related to those described for Pseudomonas species and related mobile genetic elements. This study revealed that a microdiversity of nahAc-like genes exists in microbial communities of Antarctic soils and quantitative PCR indicated that their relative abundance was increased in response to anthropogenic sources of pollution.

Beyond Wiki to Judgewiki for Transparent Climate Change Decisions

NASA Astrophysics Data System (ADS)

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.

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

PubMed Central

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

Fungal community and cellulose-degrading genes in the composting process of Chinese medicinal herbal residues.

PubMed

Tian, Xueping; Yang, Tao; He, Jingzhong; Chu, Qian; Jia, Xiaojun; Huang, Jun

2017-10-01

The fungal community and the population of 16S rRNA, 18S rRNA and cellulose-degrading genes during the 30-day composting process of Chinese medicinal herbal residues were investigated using Illumina MiSeq and quantitative real-time PCR. An obvious succession of fungal communities occurred during the composting process. Unidentified fungi predominated in the raw materials. As composting progressed, Ascomycota became the most dominant phylum, with Aspergillus being the most dominant genus, and Aspergillus fumigatus making up 99.65% of that genus. Because of the inoculation of cellulolytic fungi in the mature stage, the cellulose degradation rate in inoculation groups was faster and the relative abundances of Aspergillus and the glycoside hydrolase family 7 genes were significantly higher than those in the control groups. These indicated that the fungal inoculants facilitated the degradation of cellulose, increased cellulolytic fungi and optimized the community structure. Copyright © 2017. Published by Elsevier Ltd.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Ziming; Yang, Sihang; Van Nostrand, Joy D.

Microbial decomposition of soil organic carbon (SOC) in the thawing Arctic permafrost is one of the most important, but poorly understood, processes in determining the greenhouse gases feedback of tundra ecosystems to climate. Here in this paper, we examine changes in microbial community structure during an anoxic incubation at either –2 or 8 °C for up to 122 days using both an organic and a mineral soil collected from the Barrow Environmental Observatory in northern Alaska, USA. Soils were characterized for SOC chemistry, and GeoChips were used to determine microbial community structure and functional genes associated with C degradation andmore » Fe(III) reduction. We observed notable decreases in functional gene diversity (at P < 0.05) in response to warming at 8 °C, particularly in the organic soil. A number of genes associated with SOC degradation, fermentation, methanogenesis, and iron cycling decreased significantly (P < 0.05) after 122 days of incubation, which coincided well with decreasing labile SOC content, soil respiration, methane production, and iron reduction. The soil type (i.e., organic vs. mineral) and the availability of labile SOC were among the most significant environmental factors impacting the functional community structure. In contrast, the functional structure was largely unchanged in the –2 °C incubation due to low microbial activity resulting in less competition or exclusion. These results demonstrate the vulnerability of SOC in Arctic tundra to warming, facilitated by iron reduction and methanogenesis, and the importance of microbial communities in moderating such vulnerability.« less

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

DOE PAGES

Yang, Ziming; Yang, Sihang; Van Nostrand, Joy D.; ...

2017-09-19

Microbial decomposition of soil organic carbon (SOC) in the thawing Arctic permafrost is one of the most important, but poorly understood, processes in determining the greenhouse gases feedback of tundra ecosystems to climate. Here in this paper, we examine changes in microbial community structure during an anoxic incubation at either –2 or 8 °C for up to 122 days using both an organic and a mineral soil collected from the Barrow Environmental Observatory in northern Alaska, USA. Soils were characterized for SOC chemistry, and GeoChips were used to determine microbial community structure and functional genes associated with C degradation andmore » Fe(III) reduction. We observed notable decreases in functional gene diversity (at P < 0.05) in response to warming at 8 °C, particularly in the organic soil. A number of genes associated with SOC degradation, fermentation, methanogenesis, and iron cycling decreased significantly (P < 0.05) after 122 days of incubation, which coincided well with decreasing labile SOC content, soil respiration, methane production, and iron reduction. The soil type (i.e., organic vs. mineral) and the availability of labile SOC were among the most significant environmental factors impacting the functional community structure. In contrast, the functional structure was largely unchanged in the –2 °C incubation due to low microbial activity resulting in less competition or exclusion. These results demonstrate the vulnerability of SOC in Arctic tundra to warming, facilitated by iron reduction and methanogenesis, and the importance of microbial communities in moderating such vulnerability.« less

Bacterial community structure and abundances of antibiotic resistance genes in heavy metals contaminated agricultural soil.

PubMed

Zhang, Fengli; Zhao, Xiaoxue; Li, Qingbo; Liu, Jia; Ding, Jizhe; Wu, Huiying; Zhao, Zongsheng; Ba, Yue; Cheng, Xuemin; Cui, Liuxin; Li, Hongping; Zhu, Jingyuan

2018-04-01

Soil contamination with heavy metals is a worldwide problem especially in China. The interrelation of soil bacterial community structure, antibiotic resistance genes, and heavy metal contamination in soil is still unclear. Here, seven agricultural areas (G1-G7) with heavy metal contamination were sampled with different distances (741 to 2556 m) to the factory. Denaturing gradient gel electrophoresis (DGGE) and Shannon index were used to analyze bacterial community diversity. Real-time fluorescence quantitative PCR was used to detect the relative abundance of ARGs sul1, sul2, tetA, tetM, tetW, one mobile genetic elements (MGE) inti1. Results showed that all samples were polluted by Cadmium (Cd), and some of them were polluted by lead (Pb), mercury (Hg), arsenic (As), copper (Cu), and zinc (Zn). DGGE showed that the most abundant bacterial species were found in G7 with the lightest heavy metal contamination. The results of the principal component analysis and clustering analysis both showed that G7 could not be classified with other samples. The relative abundance of sul1 was correlated with Cu, Zn concentration. Gene sul2 are positively related with total phosphorus, and tetM was associated with organic matter. Total gene abundances and relative abundance of inti1 both correlated with organic matter. Redundancy analysis showed that Zn and sul2 were significantly related with bacterial community structure. Together, our results indicate a complex linkage between soil heavy metal concentration, bacterial community composition, and some global disseminated ARG abundance.

Inquiry Resources Collection as a Boundary Object Supporting Meaningful Collaboration in a Wiki-Based Scientist-Teacher Community

ERIC Educational Resources Information Center

Kim, Hye Jeong; Herbert, Bruce

2012-01-01

Different interpretations of scientific inquiry exist between the two different communities of scientists and science teachers. Thus, in order to achieve a successful partnership between science teachers and scientists in establishing effective communities of practice, the framework for instructional practice in teacher professional development…

Using ZFIN: Data Types, Organization, and Retrieval.

PubMed

Van Slyke, Ceri E; Bradford, Yvonne M; Howe, Douglas G; Fashena, David S; Ramachandran, Sridhar; Ruzicka, Leyla

2018-01-01

The Zebrafish Model Organism Database (ZFIN; zfin.org) was established in 1994 as the primary genetic and genomic resource for the zebrafish research community. Some of the earliest records in ZFIN were for people and laboratories. Since that time, services and data types provided by ZFIN have grown considerably. Today, ZFIN provides the official nomenclature for zebrafish genes, mutants, and transgenics and curates many data types including gene expression, phenotypes, Gene Ontology, models of human disease, orthology, knockdown reagents, transgenic constructs, and antibodies. Ontologies are used throughout ZFIN to structure these expertly curated data. An integrated genome browser provides genomic context for genes, transgenics, mutants, and knockdown reagents. ZFIN also supports a community wiki where the research community can post new antibody records and research protocols. Data in ZFIN are accessible via web pages, download files, and the ZebrafishMine (zebrafishmine.org), an installation of the InterMine data warehousing software. Searching for data at ZFIN utilizes both parameterized search forms and a single box search for searching or browsing data quickly. This chapter aims to describe the primary ZFIN data and services, and provide insight into how to use and interpret ZFIN searches, data, and web pages.

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

PubMed

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.

Linking Microbial Community and Catabolic Gene Structures during the Adaptation of Three Contaminated Soils under Continuous Long-Term Pollutant Stress

PubMed Central

Lima-Morales, Daiana; Jáuregui, Ruy; Camarinha-Silva, Amelia; Geffers, Robert; Vilchez-Vargas, Ramiro

2016-01-01

Three types of contaminated soil from three geographically different areas were subjected to a constant supply of benzene or benzene/toluene/ethylbenzene/xylenes (BTEX) for a period of 3 months. Different from the soil from Brazil (BRA) and Switzerland (SUI), the Czech Republic (CZE) soil which was previously subjected to intensive in situ bioremediation displayed only negligible changes in community structure. BRA and SUI soil samples showed a clear succession of phylotypes. A rapid response to benzene stress was observed, whereas the response to BTEX pollution was significantly slower. After extended incubation, actinobacterial phylotypes increased in relative abundance, indicating their superior fitness to pollution stress. Commonalities but also differences in the phylotypes were observed. Catabolic gene surveys confirmed the enrichment of actinobacteria by identifying the increase of actinobacterial genes involved in the degradation of pollutants. Proteobacterial phylotypes increased in relative abundance in SUI microcosms after short-term stress with benzene, and catabolic gene surveys indicated enriched metabolic routes. Interestingly, CZE soil, despite staying constant in community structure, showed a change in the catabolic gene structure. This indicates that a highly adapted community, which had to adjust its gene pool to meet novel challenges, has been enriched. PMID:26850298

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

PubMed

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.

The BIG Data Center: from deposition to integration to translation

PubMed Central

2017-01-01

Biological data are generated at unprecedentedly exponential rates, posing considerable challenges in big data deposition, integration and translation. The BIG Data Center, established at Beijing Institute of Genomics (BIG), Chinese Academy of Sciences, provides a suite of database resources, including (i) Genome Sequence Archive, a data repository specialized for archiving raw sequence reads, (ii) Gene Expression Nebulas, a data portal of gene expression profiles based entirely on RNA-Seq data, (iii) Genome Variation Map, a comprehensive collection of genome variations for featured species, (iv) Genome Warehouse, a centralized resource housing genome-scale data with particular focus on economically important animals and plants, (v) Methylation Bank, an integrated database of whole-genome single-base resolution methylomes and (vi) Science Wikis, a central access point for biological wikis developed for community annotations. The BIG Data Center is dedicated to constructing and maintaining biological databases through big data integration and value-added curation, conducting basic research to translate big data into big knowledge and providing freely open access to a variety of data resources in support of worldwide research activities in both academia and industry. All of these resources are publicly available and can be found at http://bigd.big.ac.cn. PMID:27899658

The BIG Data Center: from deposition to integration to translation.

PubMed

2017-01-04

Biological data are generated at unprecedentedly exponential rates, posing considerable challenges in big data deposition, integration and translation. The BIG Data Center, established at Beijing Institute of Genomics (BIG), Chinese Academy of Sciences, provides a suite of database resources, including (i) Genome Sequence Archive, a data repository specialized for archiving raw sequence reads, (ii) Gene Expression Nebulas, a data portal of gene expression profiles based entirely on RNA-Seq data, (iii) Genome Variation Map, a comprehensive collection of genome variations for featured species, (iv) Genome Warehouse, a centralized resource housing genome-scale data with particular focus on economically important animals and plants, (v) Methylation Bank, an integrated database of whole-genome single-base resolution methylomes and (vi) Science Wikis, a central access point for biological wikis developed for community annotations. The BIG Data Center is dedicated to constructing and maintaining biological databases through big data integration and value-added curation, conducting basic research to translate big data into big knowledge and providing freely open access to a variety of data resources in support of worldwide research activities in both academia and industry. All of these resources are publicly available and can be found at http://bigd.big.ac.cn. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Monitoring of oil hydrocarbons pollution in the Sea of Japan, based on detection of marker genes in microbial communities

NASA Astrophysics Data System (ADS)

Kim, A. V.; Buzoleva, L. S.; Bogatyrenko, E. A.; Zemskaya, T. I.; Mamaeva, E. V.

2018-01-01

By means of molecular biology techniques, metabolic potential of microbial communities within the regions of inshore water areas in the Sea of Japan with various anthropogenic load was explored. Presence of functional genes, responsible for oil hydrocarbons destruction, for microbial communities within the regions of inshore water areas in the Sea of Japan was first researched. In total microbial DNA from water mass in the regions with chronic anthropogenic pollution, the genes, responsible for oxidation of broad range of n-alkanes and polycyclic aromatic hydrocarbons, were found. Detection of marker genes in the background water area (in the Vostok Bay) was ever indicating ecological deterioration within this territory. Thereby, it was demonstrated, that molecular genetic methods, aimed at marker gene detection in total bacterial DNA from environment objects, proved themselves to be more effective technique for identification of oil hydrocarbons water pollution, in comparison with trivial culturable methods.

Different impacts of manure and chemical fertilizers on bacterial community structure and antibiotic resistance genes in arable soils.

PubMed

Liu, Peng; Jia, Shuyu; He, Xiwei; Zhang, Xuxiang; Ye, Lin

2017-12-01

Both manure and chemical fertilizers are widely used in modern agriculture. However, the impacts of different fertilizers on bacterial community structure and antibiotic resistance genes (ARGs) in arable soils still remain unclear. In this study, high-throughput sequencing and quantitative PCR were employed to investigate the bacterial community structure, ARGs and mobile genetic elements (MGEs) influenced by the application of different fertilizers, including chemical fertilizers, piggery manure and straw ash. The results showed that the application of fertilizers could significantly change the soil bacterial community and the abundance of Gaiella under phylum Actinobacteria was significantly reduced from 12.9% in unfertilized soil to 4.1%-7.4% in fertilized soil (P < 0.05). It was also found that the application of manure could cause a transient effect on soil resistome composition and the relative abundance of ARGs increased from 7.37 ppm to 32.10 ppm. The abundance of aminoglycoside, sulfonamide and tetracycline resistance genes greatly increased after manure fertilization and then gradually returned to normal levels with the decay of some intestinal bacteria carrying ARGs. In contrast, the application of chemical fertilizers and straw ash significantly changed the bacterial community structure but exerted little effect on soil resistome. Overall, the results of this study illustrated the different effects of different fertilizers on the soil resistome and revealed that the changes of soil resistome induced by manure application mainly resulted from alteration of bacteria community rather than the horizontal gene transfer. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

PubMed

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.

Identification of nitrogen-fixing genes and gene clusters from metagenomic library of acid mine drainage.

PubMed

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.

Identification of Nitrogen-Fixing Genes and Gene Clusters from Metagenomic Library of Acid Mine Drainage

PubMed Central

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

Gene and protein nomenclature in public databases

PubMed Central

Fundel, Katrin; Zimmer, Ralf

2006-01-01

Background Frequently, several alternative names are in use for biological objects such as genes and proteins. Applications like manual literature search, automated text-mining, named entity identification, gene/protein annotation, and linking of knowledge from different information sources require the knowledge of all used names referring to a given gene or protein. Various organism-specific or general public databases aim at organizing knowledge about genes and proteins. These databases can be used for deriving gene and protein name dictionaries. So far, little is known about the differences between databases in terms of size, ambiguities and overlap. Results We compiled five gene and protein name dictionaries for each of the five model organisms (yeast, fly, mouse, rat, and human) from different organism-specific and general public databases. We analyzed the degree of ambiguity of gene and protein names within and between dictionaries, to a lexicon of common English words and domain-related non-gene terms, and we compared different data sources in terms of size of extracted dictionaries and overlap of synonyms between those. The study shows that the number of genes/proteins and synonyms covered in individual databases varies significantly for a given organism, and that the degree of ambiguity of synonyms varies significantly between different organisms. Furthermore, it shows that, despite considerable efforts of co-curation, the overlap of synonyms in different data sources is rather moderate and that the degree of ambiguity of gene names with common English words and domain-related non-gene terms varies depending on the considered organism. Conclusion In conclusion, these results indicate that the combination of data contained in different databases allows the generation of gene and protein name dictionaries that contain significantly more used names than dictionaries obtained from individual data sources. Furthermore, curation of combined dictionaries

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

PubMed

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 < 0.05). In residential buildings, genes of L. pneumomhila, Acanthamoeba and Vermamoeba vermiformis were primarily detected in tanks and taps compared to the mains. Long 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.

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

PubMed

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.

FunGene: the functional gene pipeline and repository.

PubMed

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.

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

PubMed

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.

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

PubMed

Laso Bayas, Juan Carlos; Lesiv, Myroslava; Waldner, François; Schucknecht, Anne; Duerauer, Martina; See, Linda; Fritz, Steffen; Fraisl, Dilek; Moorthy, Inian; McCallum, Ian; Perger, Christoph; Danylo, Olha; Defourny, Pierre; Gallego, Javier; Gilliams, Sven; Akhtar, Ibrar Ul Hassan; Baishya, Swarup Jyoti; Baruah, Mrinal; Bungnamei, Khangsembou; Campos, Alfredo; Changkakati, Trishna; Cipriani, Anna; Das, Krishna; Das, Keemee; Das, Inamani; Davis, Kyle Frankel; Hazarika, Purabi; Johnson, Brian Alan; Malek, Ziga; Molinari, Monia Elisa; Panging, Kripal; Pawe, Chandra Kant; Pérez-Hoyos, Ana; Sahariah, Parag Kumar; Sahariah, Dhrubajyoti; Saikia, Anup; Saikia, Meghna; Schlesinger, Peter; Seidacaru, Elena; Singha, Kuleswar; Wilson, John W

2017-09-26

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 assessment purposes, two additional data sets are provided. The first is a control set of 1,793 sample locations validated by students trained in satellite image interpretation. This data set was used to assess the quality of the crowd as the campaign progressed. The second data set contains 60 expert validations for additional evaluation of the quality of the contributions. All data sets are split into two parts: the first part shows all areas classified as cropland and the second part shows cropland average per location and user. After further processing, the data presented here might be suitable to validate and compare medium and high resolution cropland maps generated using remote sensing. These could also be used to train classification algorithms for developing new maps of land cover and cropland extent.

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

NASA Astrophysics Data System (ADS)

Laso Bayas, Juan Carlos; Lesiv, Myroslava; Waldner, François; Schucknecht, Anne; Duerauer, Martina; See, Linda; Fritz, Steffen; Fraisl, Dilek; Moorthy, Inian; McCallum, Ian; Perger, Christoph; Danylo, Olha; Defourny, Pierre; Gallego, Javier; Gilliams, Sven; Akhtar, Ibrar Ul Hassan; Baishya, Swarup Jyoti; Baruah, Mrinal; Bungnamei, Khangsembou; Campos, Alfredo; Changkakati, Trishna; Cipriani, Anna; Das, Krishna; Das, Keemee; Das, Inamani; Davis, Kyle Frankel; Hazarika, Purabi; Johnson, Brian Alan; Malek, Ziga; Molinari, Monia Elisa; Panging, Kripal; Pawe, Chandra Kant; Pérez-Hoyos, Ana; Sahariah, Parag Kumar; Sahariah, Dhrubajyoti; Saikia, Anup; Saikia, Meghna; Schlesinger, Peter; Seidacaru, Elena; Singha, Kuleswar; Wilson, John W.

2017-09-01

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 assessment purposes, two additional data sets are provided. The first is a control set of 1,793 sample locations validated by students trained in satellite image interpretation. This data set was used to assess the quality of the crowd as the campaign progressed. The second data set contains 60 expert validations for additional evaluation of the quality of the contributions. All data sets are split into two parts: the first part shows all areas classified as cropland and the second part shows cropland average per location and user. After further processing, the data presented here might be suitable to validate and compare medium and high resolution cropland maps generated using remote sensing. These could also be used to train classification algorithms for developing new maps of land cover and cropland extent.

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

PubMed Central

Laso Bayas, Juan Carlos; Lesiv, Myroslava; Waldner, François; Schucknecht, Anne; Duerauer, Martina; See, Linda; Fritz, Steffen; Fraisl, Dilek; Moorthy, Inian; McCallum, Ian; Perger, Christoph; Danylo, Olha; Defourny, Pierre; Gallego, Javier; Gilliams, Sven; Akhtar, Ibrar ul Hassan; Baishya, Swarup Jyoti; Baruah, Mrinal; Bungnamei, Khangsembou; Campos, Alfredo; Changkakati, Trishna; Cipriani, Anna; Das, Krishna; Das, Keemee; Das, Inamani; Davis, Kyle Frankel; Hazarika, Purabi; Johnson, Brian Alan; Malek, Ziga; Molinari, Monia Elisa; Panging, Kripal; Pawe, Chandra Kant; Pérez-Hoyos, Ana; Sahariah, Parag Kumar; Sahariah, Dhrubajyoti; Saikia, Anup; Saikia, Meghna; Schlesinger, Peter; Seidacaru, Elena; Singha, Kuleswar; 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 assessment purposes, two additional data sets are provided. The first is a control set of 1,793 sample locations validated by students trained in satellite image interpretation. This data set was used to assess the quality of the crowd as the campaign progressed. The second data set contains 60 expert validations for additional evaluation of the quality of the contributions. All data sets are split into two parts: the first part shows all areas classified as cropland and the second part shows cropland average per location and user. After further processing, the data presented here might be suitable to validate and compare medium and high resolution cropland maps generated using remote sensing. These could also be used to train classification algorithms for developing new maps of land cover and cropland extent. PMID:28949323

Beyond Social Media: A Cross-Sectional Survey of Other Internet and Mobile Phone Applications in a Community Psychiatry Population.

PubMed

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.

16S rRNA Gene Survey of Microbial Communities in Winogradsky Columns

PubMed Central

Rundell, Ethan A.; Banta, Lois M.; Ward, Doyle V.; Watts, Corey D.; Birren, Bruce; Esteban, David J.

2014-01-01

A Winogradsky column is a clear glass or plastic column filled with enriched sediment. Over time, microbial communities in the sediment grow in a stratified ecosystem with an oxic top layer and anoxic sub-surface layers. Winogradsky columns have been used extensively to demonstrate microbial nutrient cycling and metabolic diversity in undergraduate microbiology labs. In this study, we used high-throughput 16s rRNA gene sequencing to investigate the microbial diversity of Winogradsky columns. Specifically, we tested the impact of sediment source, supplemental cellulose source, and depth within the column, on microbial community structure. We found that the Winogradsky columns were highly diverse communities but are dominated by three phyla: Proteobacteria, Bacteroidetes, and Firmicutes. The community is structured by a founding population dependent on the source of sediment used to prepare the columns and is differentiated by depth within the column. Numerous biomarkers were identified distinguishing sample depth, including Cyanobacteria, Alphaproteobacteria, and Betaproteobacteria as biomarkers of the soil-water interface, and Clostridia as a biomarker of the deepest depth. Supplemental cellulose source impacted community structure but less strongly than depth and sediment source. In columns dominated by Firmicutes, the family Peptococcaceae was the most abundant sulfate reducer, while in columns abundant in Proteobacteria, several Deltaproteobacteria families, including Desulfobacteraceae, were found, showing that different taxonomic groups carry out sulfur cycling in different columns. This study brings this historical method for enrichment culture of chemolithotrophs and other soil bacteria into the modern era of microbiology and demonstrates the potential of the Winogradsky column as a model system for investigating the effect of environmental variables on soil microbial communities. PMID:25101630

Pyrosequence Analysis of the hsp65 Genes of Nontuberculous Mycobacterium Communities in Unchlorinated Drinking Water in the Netherlands

PubMed Central

Heijnen, Leo; van der Kooij, Dick

2013-01-01

Studies have shown that certain opportunistic pathogenic species of nontuberculous mycobacteria (NTM) can be present in distributed drinking water. However, detailed information about NTM population composition in drinking water is lacking. Therefore, NTM communities in unchlorinated drinking water from the distribution system of five treatment plants in the Netherlands were characterized using 454 pyrosequencing of the hsp65 gene. Results showed high diversities in unchlorinated drinking water, with up to 28 different NTM operational taxonomic units (OTUs) in a single sample. Each drinking water sample had a unique NTM community, and most (81.1%) OTUs were observed only once. One OTU was observed in 14 of 16 drinking water samples, indicating that this NTM species is well adapted to unchlorinated drinking water conditions. A clear influence of season, source type (groundwater, surface water), easily assimilable organic carbon (AOC) concentration, biofilm formation rate, and active biomass in treated water on the establishment of an NTM community in drinking water was not observed. Apparently, local conditions are more important for the development of a specific NTM community in the drinking water distribution system. A low (4.2%) number of hsp65 gene sequences showed more than 97% similarity to sequences of the opportunistic pathogens M. avium, M. genavense, and M. gordonae. However, most (95.8%) NTM hsp65 gene sequences were related to not-yet-described NTM species that have not been linked to disease, indicating that most NTM species in unchlorinated drinking water from distribution systems in the Netherlands have a low public health significance. PMID:23913420

Pyrosequence analysis of the hsp65 genes of nontuberculous mycobacterium communities in unchlorinated drinking water in the Netherlands.

PubMed

van der Wielen, Paul W J J; Heijnen, Leo; van der Kooij, Dick

2013-10-01

Studies have shown that certain opportunistic pathogenic species of nontuberculous mycobacteria (NTM) can be present in distributed drinking water. However, detailed information about NTM population composition in drinking water is lacking. Therefore, NTM communities in unchlorinated drinking water from the distribution system of five treatment plants in the Netherlands were characterized using 454 pyrosequencing of the hsp65 gene. Results showed high diversities in unchlorinated drinking water, with up to 28 different NTM operational taxonomic units (OTUs) in a single sample. Each drinking water sample had a unique NTM community, and most (81.1%) OTUs were observed only once. One OTU was observed in 14 of 16 drinking water samples, indicating that this NTM species is well adapted to unchlorinated drinking water conditions. A clear influence of season, source type (groundwater, surface water), easily assimilable organic carbon (AOC) concentration, biofilm formation rate, and active biomass in treated water on the establishment of an NTM community in drinking water was not observed. Apparently, local conditions are more important for the development of a specific NTM community in the drinking water distribution system. A low (4.2%) number of hsp65 gene sequences showed more than 97% similarity to sequences of the opportunistic pathogens M. avium, M. genavense, and M. gordonae. However, most (95.8%) NTM hsp65 gene sequences were related to not-yet-described NTM species that have not been linked to disease, indicating that most NTM species in unchlorinated drinking water from distribution systems in the Netherlands have a low public health significance.

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

PubMed

Currie, Ashleigh R; Tait, Karen; Parry, Helen; de Francisco-Mora, Beatriz; Hicks, Natalie; Osborn, A Mark; Widdicombe, Steve; Stahl, Henrik

2017-01-01

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 CO 2 ) 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 CO 2 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.

Variation of nonylphenol-degrading gene abundance and bacterial community structure in bioaugmented sediment microcosm.

PubMed

Wang, Zhao; Yang, Yuyin; Sun, Weimin; Dai, Yu; Xie, Shuguang

2015-02-01

Nonylphenol (NP) can accumulate in river sediment. Bioaugmentation is an attractive option to dissipate heavy NP pollution in river sediment. In this study, two NP degraders were isolated from crude oil-polluted soil and river sediment. Microcosms were constructed to test their ability to degrade NP in river sediment. The shift in the proportion of NP-degrading genes and bacterial community structure in sediment microcosms were characterized using quantitative PCR assay and terminal restriction fragment length polymorphism analysis, respectively. Phylogenetic analysis indicated that the soil isolate belonged to genus Stenotrophomonas, while the sediment isolate was a Sphingobium species. Both of them could almost completely clean up a high level of NP in river sediment (150 mg/kg NP) in 10 or 14 days after inoculation. An increase in the proportion of alkB and sMO genes was observed in sediment microcosms inoculated with Stenotrophomonas strain Y1 and Sphingobium strain Y2, respectively. Moreover, bioaugmentation using Sphingobium strain Y2 could have a strong impact on sediment bacterial community structure, while inoculation of Stenotrophomonas strain Y1 illustrated a weak impact. This study can provide some new insights towards NP biodegradation and bioremediation.

The dual oxidase gene BdDuox regulates the intestinal bacterial community homeostasis of Bactrocera dorsalis

PubMed Central

Yao, Zhichao; Wang, Ailin; Li, Yushan; Cai, Zhaohui; Lemaitre, Bruno; Zhang, Hongyu

2016-01-01

The guts of metazoans are in permanent contact with the microbial realm that includes beneficial symbionts, nonsymbionts, food-borne microbes and life-threatening pathogens. However, little is known concerning how host immunity affects gut bacterial community. Here, we analyze the role of a dual oxidase gene (BdDuox) in regulating the intestinal bacterial community homeostasis of the oriental fruit fly Bactrocera dorsalis. The results showed that knockdown of BdDuox led to an increased bacterial load, and to a decrease in the relative abundance of Enterobacteriaceae and Leuconostocaceae bacterial symbionts in the gut. The resulting dysbiosis, in turn, stimulates an immune response by activating BdDuox and promoting reactive oxygen species (ROS) production that regulates the composition and structure of the gut bacterial community to normal status by repressing the overgrowth of minor pathobionts. Our results suggest that BdDuox plays a pivotal role in regulating the homeostasis of the gut bacterial community in B. dorsalis. PMID:26565723

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

PubMed

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.

Gene finding in metatranscriptomic sequences.

PubMed

Ismail, Wazim Mohammed; Ye, Yuzhen; Tang, Haixu

2014-01-01

Metatranscriptomic sequencing is a highly sensitive bioassay of functional activity in a microbial community, providing complementary information to the metagenomic sequencing of the community. The acquisition of the metatranscriptomic sequences will enable us to refine the annotations of the metagenomes, and to study the gene activities and their regulation in complex microbial communities and their dynamics. In this paper, we present TransGeneScan, a software tool for finding genes in assembled transcripts from metatranscriptomic sequences. By incorporating several features of metatranscriptomic sequencing, including strand-specificity, short intergenic regions, and putative antisense transcripts into a Hidden Markov Model, TranGeneScan can predict a sense transcript containing one or multiple genes (in an operon) or an antisense transcript. We tested TransGeneScan on a mock metatranscriptomic data set containing three known bacterial genomes. The results showed that TranGeneScan performs better than metagenomic gene finders (MetaGeneMark and FragGeneScan) on predicting protein coding genes in assembled transcripts, and achieves comparable or even higher accuracy than gene finders for microbial genomes (Glimmer and GeneMark). These results imply, with the assistance of metatranscriptomic sequencing, we can obtain a broad and precise picture about the genes (and their functions) in a microbial community. TransGeneScan is available as open-source software on SourceForge at https://sourceforge.net/projects/transgenescan/.

Vertical Distribution of Bacterial Communities in the Indian Ocean as Revealed by Analyses of 16S rRNA and nasA Genes.

PubMed

Jiang, Xuexia; Jiao, Nianzhi

2016-09-01

Bacteria play an important role in the marine biogeochemical cycles. However, research on the bacterial community structure of the Indian Ocean is scarce, particularly within the vertical dimension. In this study, we investigated the bacterial diversity of the pelagic, mesopelagic and bathypelagic zones of the southwestern Indian Ocean (50.46°E, 37.71°S). The clone libraries constructed by 16S rRNA gene sequence revealed that most phylotypes retrieved from the Indian Ocean were highly divergent from those retrieved from other oceans. Vertical differences were observed based on the analysis of natural bacterial community populations derived from the 16S rRNA gene sequences. Based on the analysis of the nasA gene sequences from GenBank database, a pair of general primers was developed and used to amplify the bacterial nitrate-assimilating populations. Environmental factors play an important role in mediating the bacterial communities in the Indian Ocean revealed by canonical correlation analysis.

Prevalence of Antibiotic Resistance Genes and Bacterial Community Composition in a River Influenced by a Wastewater Treatment Plant

PubMed Central

Marti, Elisabet; Jofre, Juan; Balcazar, Jose Luis

2013-01-01

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. PMID:24205347

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

PubMed

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.

Metatranscriptome sequence analysis reveals diel periodicity of microbial community gene expression in the ocean's interior

NASA Astrophysics Data System (ADS)

Vislova, A.; Aylward, F.; Sosa, O.; DeLong, E.

2016-02-01

Previous work has revealed diel periodicity of gene expression in key metabolic pathways in both autotrophic and heterotrophic microbes in the surface ocean. In this study, we investigated patterns of diel periodicity of gene expression in depth profiles (25, 75, 125 and 250 meters). We postulated that microbial diel transcriptional signals would be increasingly dampened with depth, and that the timing of peak expression of specific transcripts would be shifted in time between depths, in accordance with depth-dependent diel light variability. Bacterioplankton were sampled from four depths every four hours at station ALOHA (22° 45' N 158° W) over 2 days. RNA was extracted from cells preserved on filters, converted to cDNA, and sequenced on the Illumina platform. Surprisingly, harmonic regression analysis revealed an increasing proportion of genes with diel periodic expression patterns with increasing depth between 25- 125 meters. At 250 meters, the proportion of genes exhibiting diel expression patterns decreased an order of magnitude compared to the photic zone. Community composition, functional gene categories, and diel patterns of gene expression were significantly different between the photic zone and 250 meter samples. The signals driving diel periodic gene expression in microbes at 250 meters is under further investigation. These data are now beginning provide a better understanding of the tempo and mode of microbial dynamics among specific taxa, throughout the ocean's interior.

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

PubMed

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

ICT in the ICU: using Web 2.0 to enhance a community of practice for intensive care physicians.

PubMed

Burrell, Anthony R; Elliott, Doug; Hansen, Margaret M

2009-06-01

Contemporary information and communicationstechnology (ICT), particularly applications termed "Web2.0", can facilitate practice development and knowledgemanagement for busy clinicians. Just as importantly, theseapplications might also enhance professional socialinteraction and the development of an interprofessionalcommunity of practice that transcends the boundaries ofthe intensive care unit, health service, jurisdiction andnation.We explore the development of Web 2.0 applications inhealth care, and their application to intensive care practicein Australia and New Zealand. The opportunities for usingpodcasts, blogs, wikis and virtual worlds to support cliniciandevelopment and knowledge exchange are clear in theory.However, strategic leadership from the Colleges is neededto fully exploit these technologies and to enable thedevelopment of a strong and sustainable ICU community ofpractice.

RuBisCO large-subunit gene primers for assessing the CO2-assimilating planktonic community structure in Jiaozhou Bay, China.

PubMed

Chi, Xiang-Qun; Wang, Long; Guo, Ruoyu; Zhao, Dexi; Li, Jia; Zhang, Yongyu; Jiao, Nianzhi

2018-06-19

The protein coding genes (rbcL/cbbL/cbbM) for RuBisCO large subunit, the most abundant protein on earth that drives biological CO2 fixation, were considered as useful marker genes in characterizing CO2-assimilating plankton. However, their community specificity has hindered comprehensive screening of genetic diversity. In this study, six different rbcL/cbbL/cbbM primers were employed to screen clone libraries to identify CO2-assimilating plankton in Jiaozhou Bay. The following community compositions were observed: the community components in Form I A/B rbcL/cbbL clone library mainly comprised Chlorophyta and Proteobacteria, Form ID2 and ID3 libraries consisted of Bacillariophyta, Form II cbbM library consisted of Proteobacteria and Alveolata, and both Form I green and red libraries included Proteobacteria, respectively. At the genus taxonomic level, no overlaps among these clone libraries were observed, except for ID2 and ID3. Overall, the phytoplankton in Jiaozhou Bay mainly consists of Bacillariophyta, Chlorophyta, Cryptophyta, Haptophyceae, and Alveolata. The CO2-assimilating prokaryotes mainly consist of Proteobacteria. Considering the high sequence specificities of these marker genes, we propose that the joint use of multiple primers may be utilized in unveiling the diversity of CO2-assimilating organisms. In addition, designing novel RuBisCO gene primers that generate longer amplicons and have broader phylogenetic coverage may be necessary in the future.

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

PubMed Central

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

2015-01-01

Background 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. Results 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 (P<0.01), but not between nested PCR with 10 cycles in the first round and standard PCR. Operational taxonomic units (OTUs) that had low relative abundance (sum of relative abundance <0.167) accounted for most of the distortion (>27% of total OTUs in stool). Conclusions 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

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

PubMed

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 (P<0.01), but not between nested PCR with 10 cycles in the first round and standard PCR. Operational taxonomic units (OTUs) that had low relative abundance (sum of relative abundance <0.167) accounted for most of the distortion (>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

Identifying Mendelian disease genes with the Variant Effect Scoring Tool

PubMed Central

2013-01-01

Background Whole exome sequencing studies identify hundreds to thousands of rare protein coding variants of ambiguous significance for human health. Computational tools are needed to accelerate the identification of specific variants and genes that contribute to human disease. Results We have developed the Variant Effect Scoring Tool (VEST), a supervised machine learning-based classifier, to prioritize rare missense variants with likely involvement in human disease. The VEST classifier training set comprised ~ 45,000 disease mutations from the latest Human Gene Mutation Database release and another ~45,000 high frequency (allele frequency >1%) putatively neutral missense variants from the Exome Sequencing Project. VEST outperforms some of the most popular methods for prioritizing missense variants in carefully designed holdout benchmarking experiments (VEST ROC AUC = 0.91, PolyPhen2 ROC AUC = 0.86, SIFT4.0 ROC AUC = 0.84). VEST estimates variant score p-values against a null distribution of VEST scores for neutral variants not included in the VEST training set. These p-values can be aggregated at the gene level across multiple disease exomes to rank genes for probable disease involvement. We tested the ability of an aggregate VEST gene score to identify candidate Mendelian disease genes, based on whole-exome sequencing of a small number of disease cases. We used whole-exome data for two Mendelian disorders for which the causal gene is known. Considering only genes that contained variants in all cases, the VEST gene score ranked dihydroorotate dehydrogenase (DHODH) number 2 of 2253 genes in four cases of Miller syndrome, and myosin-3 (MYH3) number 2 of 2313 genes in three cases of Freeman Sheldon syndrome. Conclusions Our results demonstrate the potential power gain of aggregating bioinformatics variant scores into gene-level scores and the general utility of bioinformatics in assisting the search for disease genes in large-scale exome sequencing studies. VEST is

Mechanisms and effects of arsanilic acid on antibiotic resistance genes and microbial communities during pig manure digestion.

PubMed

Sun, Wei; Qian, Xun; Gu, Jie; Wang, Xiao-Juan; Zhang, Li; Guo, Ai-Yun

2017-06-01

High concentrations of residual arsanilic acid occur in pig manure due to its use in feed to promote growth and control diseases. This study compared the effects of arsanilic acid at three concentrations (0, 325, and 650mg/kg dry pig manure) on the abundance of antibiotic resistance genes (ARGs) and the microbial community during anaerobic digestion. Addition of 650mg/kg arsanilic acid enhanced the absolute abundances of tetC, sul2, ermB, and gyrA more than twofold in the digestion product. Redundancy analysis indicated that the change in the microbial community structure was the main driver of variation in the ARGs profile. The As resistance gene arsC co-occurred with four ARGs and intI1, possibly causing the increase in ARGs under pressure by arsanilic acid. High arsanilic acid concentrations can increase the risk of ARGs occurring in anaerobic digestion products. The amount of arsanilic acid used as a feed additive should be controlled. Copyright © 2017. Published by Elsevier Ltd.

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

PubMed

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.

Seasonal and regional diversity of maple sap microbiota revealed using community PCR fingerprinting and 16S rRNA gene clone libraries.

PubMed

Filteau, Marie; Lagacé, Luc; LaPointe, Gisèle; Roy, Denis

2010-04-01

An arbitrary primed community PCR fingerprinting technique based on capillary electrophoresis was developed to study maple sap microbial community characteristics among 19 production sites in Québec over the tapping season. Presumptive fragment identification was made with corresponding fingerprint profiles of bacterial isolate cultures. Maple sap microbial communities were subsequently compared using a representative subset of 13 16S rRNA gene clone libraries followed by gene sequence analysis. Results from both methods indicated that all maple sap production sites and flow periods shared common microbiota members, but distinctive features also existed. Changes over the season in relative abundance of predominant populations showed evidence of a common pattern. Pseudomonas (64%) and Rahnella (8%) were the most abundantly and frequently represented genera of the 2239 sequences analyzed. Janthinobacterium, Leuconostoc, Lactococcus, Weissella, Epilithonimonas and Sphingomonas were revealed as occasional contaminants in maple sap. Maple sap microbiota showed a low level of deep diversity along with a high variation of similar 16S rRNA gene sequences within the Pseudomonas genus. Predominance of Pseudomonas is suggested as a typical feature of maple sap microbiota across geographical regions, production sites, and sap flow periods.

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

PubMed

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.

Signaling network of dendritic cells in response to pathogens: a community-input supported knowledgebase.

PubMed

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

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

PubMed

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.

Primer selection impacts specific population abundances but not community dynamics in a monthly time-series 16S rRNA gene amplicon analysis of coastal marine bacterioplankton.

PubMed

Wear, Emma K; Wilbanks, Elizabeth G; Nelson, Craig E; Carlson, Craig A

2018-03-09

Primers targeting the 16S small subunit ribosomal RNA marker gene, used to characterize bacterial and archaeal communities, have recently been re-evaluated for marine planktonic habitats. To investigate whether primer selection affects the ecological interpretation of bacterioplankton populations and community dynamics, amplicon sequencing with four primer sets targeting several hypervariable regions of the 16S rRNA gene was conducted on both mock communities constructed from cloned 16S rRNA genes and a time-series of DNA samples from the temperate coastal Santa Barbara Channel. Ecological interpretations of community structure (delineation of depth and seasonality, correlations with environmental factors) were similar across primer sets, while population dynamics varied. We observed substantial differences in relative abundances of taxa known to be poorly resolved by some primer sets, such as Thaumarchaeota and SAR11, and unexpected taxa including Roseobacter clades. Though the magnitude of relative abundances of common OTUs differed between primer sets, the relative abundances of the OTUs were nonetheless strongly correlated. We do not endorse one primer set but rather enumerate strengths and weaknesses to facilitate selection appropriate to a system or experimental goal. While 16S rRNA gene primer bias suggests caution in assessing quantitative population dynamics, community dynamics appear robust across studies using different primers. © 2018 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Fungal Community Structure in Disease Suppressive Soils Assessed by 28S LSU Gene Sequencing

PubMed Central

Penton, C. Ryan; Gupta, V. V. S. R.; Tiedje, James M.; Neate, Stephen M.; Ophel-Keller, Kathy; Gillings, Michael; Harvey, Paul; Pham, Amanda; Roget, David K.

2014-01-01

Natural biological suppression of soil-borne diseases is a function of the activity and composition of soil microbial communities. Soil microbe and phytopathogen interactions can occur prior to crop sowing and/or in the rhizosphere, subsequently influencing both plant growth and productivity. Research on suppressive microbial communities has concentrated on bacteria although fungi can also influence soil-borne disease. Fungi were analyzed in co-located soils ‘suppressive’ or ‘non-suppressive’ for disease caused by Rhizoctonia solani AG 8 at two sites in South Australia using 454 pyrosequencing targeting the fungal 28S LSU rRNA gene. DNA was extracted from a minimum of 125 g of soil per replicate to reduce the micro-scale community variability, and from soil samples taken at sowing and from the rhizosphere at 7 weeks to cover the peak Rhizoctonia infection period. A total of ∼994,000 reads were classified into 917 genera covering 54% of the RDP Fungal Classifier database, a high diversity for an alkaline, low organic matter soil. Statistical analyses and community ordinations revealed significant differences in fungal community composition between suppressive and non-suppressive soil and between soil type/location. The majority of differences associated with suppressive soils were attributed to less than 40 genera including a number of endophytic species with plant pathogen suppression potentials and mycoparasites such as Xylaria spp. Non-suppressive soils were dominated by Alternaria, Gibberella and Penicillum. Pyrosequencing generated a detailed description of fungal community structure and identified candidate taxa that may influence pathogen-plant interactions in stable disease suppression. PMID:24699870

Mouse Social Network Dynamics and Community Structure are Associated with Plasticity-Related Brain Gene Expression

PubMed Central

Williamson, Cait M.; Franks, Becca; Curley, James P.

2016-01-01

Laboratory studies of social behavior have typically focused on dyadic interactions occurring within a limited spatiotemporal context. However, this strategy prevents analyses of the dynamics of group social behavior and constrains identification of the biological pathways mediating individual differences in behavior. In the current study, we aimed to identify the spatiotemporal dynamics and hierarchical organization of a large social network of male mice. We also sought to determine if standard assays of social and exploratory behavior are predictive of social behavior in this social network and whether individual network position was associated with the mRNA expression of two plasticity-related genes, DNA methyltransferase 1 and 3a. Mice were observed to form a hierarchically organized social network and self-organized into two separate social network communities. Members of both communities exhibited distinct patterns of socio-spatial organization within the vivaria that was not limited to only agonistic interactions. We further established that exploratory and social behaviors in standard behavioral assays conducted prior to placing the mice into the large group was predictive of initial network position and behavior but were not associated with final social network position. Finally, we determined that social network position is associated with variation in mRNA levels of two neural plasticity genes, DNMT1 and DNMT3a, in the hippocampus but not the mPOA. This work demonstrates the importance of understanding the role of social context and complex social dynamics in determining the relationship between individual differences in social behavior and brain gene expression. PMID:27540359

Using Contemporary Technology Tools to Improve the Effectiveness of Teacher Educators in Special Education

ERIC Educational Resources Information Center

O'Brien, Chris; Aguinaga, Nancy J.; Hines, Rebecca; Hartshorne, Richard

2011-01-01

Ongoing developments in educational technology, including web-based instruction, streaming video, podcasting, video-conferencing, and the use of wikis and blogs to create learning communities, have substantial impact on distance education and preparation of special educators in rural communities. These developments can be overwhelming, however,…

Pyrosequencing of mcrA and Archaeal 16S rRNA Genes Reveals Diversity and Substrate Preferences of Methanogen Communities in Anaerobic Digesters

PubMed Central

Wilkins, David; Lu, Xiao-Ying; Shen, Zhiyong; Chen, Jiapeng

2014-01-01

Methanogenic archaea play a key role in biogas-producing anaerobic digestion and yet remain poorly taxonomically characterized. This is in part due to the limitations of low-throughput Sanger sequencing of a single (16S rRNA) gene, which in the past may have undersampled methanogen diversity. In this study, archaeal communities from three sludge digesters in Hong Kong and one wastewater digester in China were examined using high-throughput pyrosequencing of the methyl coenzyme M reductase (mcrA) and 16S rRNA genes. Methanobacteriales, Methanomicrobiales, and Methanosarcinales were detected in each digester, indicating that both hydrogenotrophic and acetoclastic methanogenesis was occurring. Two sludge digesters had similar community structures, likely due to their similar design and feedstock. Taxonomic classification of the mcrA genes suggested that these digesters were dominated by acetoclastic methanogens, particularly Methanosarcinales, while the other digesters were dominated by hydrogenotrophic Methanomicrobiales. The proposed euryarchaeotal order Methanomassiliicoccales and the uncultured WSA2 group were detected with the 16S rRNA gene, and potential mcrA genes for these groups were identified. 16S rRNA gene sequencing also recovered several crenarchaeotal groups potentially involved in the initial anaerobic digestion processes. Overall, the two genes produced different taxonomic profiles for the digesters, while greater methanogen richness was detected using the mcrA gene, supporting the use of this functional gene as a complement to the 16S rRNA gene to better assess methanogen diversity. A significant positive correlation was detected between methane production and the abundance of mcrA transcripts in digesters treating sludge and wastewater samples, supporting the mcrA gene as a biomarker for methane yield. PMID:25381241

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

PubMed

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.

Community-managed Data Sharing, Curation, and Publication: SEN on SEAD

NASA Astrophysics Data System (ADS)

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

[Effects of rice straw returning on the community structure and diversity of nitrogen-fixing gene (nifH) in paddy soil].

PubMed

Zhang, Miao-miao; Liu, Yi; Sheng, Rong; Qin, Hong-ling; Wu, Yan-zheng; Wei, Wen-xue

2013-08-01

Taking a long-term fertilization experiment in Taoyuan Agro-ecosystem Research Station under Chinese Academy of Sciences as the platform, and selecting four treatments (no fertilization, CK; rice straw returning, C; nitrogen, phosphorus and potassium fertilization, NPK; and NPK+C) as the objects, soil samples were collected at the tillering, booting and maturing stages of rice, and the abundance, composition and diversity of nifH-containing bacterial community were measured by real-time quantitative PCR and terminal restriction fragment length polymorphism (T-RFLP), aimed to understand the effects of rice straw returning on the nifH-containing bacterial community in paddy soil. Compared with CK, treatments NPK+C and NPK increased the abundance of nifH-containing microorganisms significantly (except at tillering stage), and NPK+C had the highest abundance of nifH-containing microorganisms. Under the effects of long-term fertilization, the composition of nifH gene community in CK differed obviously from that in the other three treatments. The nifH composition had definite difference between C and NPK, but less difference between NPK and NPK+C. Long-term fertilization did not induce significant changes in nifH diversity. Therefore, long-term rice straw returning not only induced the changes of nifH gene community composition, but also resulted in a significant increase in the abundance of nifH-containing community, and hence, the increase of soil nitrogen fixing capacity.

Microbial Communities and Functional Genes Associated with Soil Arsenic Contamination and the Rhizosphere of the Arsenic-Hyperaccumulating Plant Pteris vittata L. ▿ †

PubMed Central

Xiong, Jinbo; Wu, Liyou; Tu, Shuxin; Van Nostrand, Joy D.; He, Zhili; Zhou, Jizhong; Wang, Gejiao

2010-01-01

To understand how microbial communities and functional genes respond to arsenic contamination in the rhizosphere of Pteris vittata, five soil samples with different arsenic contamination levels were collected from the rhizosphere of P. vittata and nonrhizosphere areas and investigated by Biolog, geochemical, and functional gene microarray (GeoChip 3.0) analyses. Biolog analysis revealed that the uncontaminated soil harbored the greatest diversity of sole-carbon utilization abilities and that arsenic contamination decreased the metabolic diversity, while rhizosphere soils had higher metabolic diversities than did the nonrhizosphere soils. GeoChip 3.0 analysis showed low proportions of overlapping genes across the five soil samples (16.52% to 45.75%). The uncontaminated soil had a higher heterogeneity and more unique genes (48.09%) than did the arsenic-contaminated soils. Arsenic resistance, sulfur reduction, phosphorus utilization, and denitrification genes were remarkably distinct between P. vittata rhizosphere and nonrhizosphere soils, which provides evidence for a strong linkage among the level of arsenic contamination, the rhizosphere, and the functional gene distribution. Canonical correspondence analysis (CCA) revealed that arsenic is the main driver in reducing the soil functional gene diversity; however, organic matter and phosphorus also have significant effects on the soil microbial community structure. The results implied that rhizobacteria play an important role during soil arsenic uptake and hyperaccumulation processes of P. vittata. PMID:20833780

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

PubMed

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.

BioGPS and MyGene.info: organizing online, gene-centric information.

PubMed

Wu, Chunlei; Macleod, Ian; Su, Andrew I

2013-01-01

Fast-evolving technologies have enabled researchers to easily generate data at genome scale, and using these technologies to compare biological states typically results in a list of candidate genes. Researchers are then faced with the daunting task of prioritizing these candidate genes for follow-up studies. There are hundreds, possibly even thousands, of web-based gene annotation resources available, but it quickly becomes impractical to manually access and review all of these sites for each gene in a candidate gene list. BioGPS (http://biogps.org) was created as a centralized gene portal for aggregating distributed gene annotation resources, emphasizing community extensibility and user customizability. BioGPS serves as a convenient tool for users to access known gene-centric resources, as well as a mechanism to discover new resources that were previously unknown to the user. This article describes updates to BioGPS made after its initial release in 2008. We summarize recent additions of features and data, as well as the robust user activity that underlies this community intelligence application. Finally, we describe MyGene.info (http://mygene.info) and related web services that provide programmatic access to BioGPS.

Prior knowledge driven Granger causality analysis on gene regulatory network discovery

DOE PAGES

Yao, Shun; Yoo, Shinjae; Yu, Dantong

2015-08-28

Our study focuses on discovering gene regulatory networks from time series gene expression data using the Granger causality (GC) model. However, the number of available time points (T) usually is much smaller than the number of target genes (n) in biological datasets. The widely applied pairwise GC model (PGC) and other regularization strategies can lead to a significant number of false identifications when n>>T. In this study, we proposed a new method, viz., CGC-2SPR (CGC using two-step prior Ridge regularization) to resolve the problem by incorporating prior biological knowledge about a target gene data set. In our simulation experiments, themore » propose new methodology CGC-2SPR showed significant performance improvement in terms of accuracy over other widely used GC modeling (PGC, Ridge and Lasso) and MI-based (MRNET and ARACNE) methods. In addition, we applied CGC-2SPR to a real biological dataset, i.e., the yeast metabolic cycle, and discovered more true positive edges with CGC-2SPR than with the other existing methods. In our research, we noticed a “ 1+1>2” effect when we combined prior knowledge and gene expression data to discover regulatory networks. Based on causality networks, we made a functional prediction that the Abm1 gene (its functions previously were unknown) might be related to the yeast’s responses to different levels of glucose. In conclusion, our research improves causality modeling by combining heterogeneous knowledge, which is well aligned with the future direction in system biology. Furthermore, we proposed a method of Monte Carlo significance estimation (MCSE) to calculate the edge significances which provide statistical meanings to the discovered causality networks. All of our data and source codes will be available under the link https://bitbucket.org/dtyu/granger-causality/wiki/Home.« less

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

PubMed

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.

Exploring the Abundance and Diversity of Bacterial Communities and Quantifying Antibiotic-Related Genes Along an Elevational Gradient in Taibai Mountain, China.

PubMed

Peng, Chu; Wang, He; Jiang, Yingying; Yang, Jinhua; Lai, Hangxian; Wei, Xiaomin

2018-05-10

Thus far, no studies have investigated the soil microbial diversity over an elevational gradient in Taibai Mountain, the central massif of the Qinling Mountain Range. Here, we used Illumina sequencing and quantitative PCR of the 16S rRNA gene to assess the diversity and abundance of bacterial communities along an elevational gradient in representative vegetation soils in Taibai Mountain. We identified the soil, climate, and vegetation factors driving the variations in soil bacterial community structure by Pearson correlation and redundancy analysis. We also evaluated the potential for antibiotic discovery by quantitative PCR of the PKS-I, PKS-II, and NRPS genes from Actinobacteria. The results showed that soil bacterial alpha diversity increased first and then decreased with an elevational rise in both the northern and southern slopes of Taibai Mountain. The bacterial abundance was significantly correlated with soil organic matter and nitrate nitrogen. The average relative abundance of Actinobacteria in Taibai Mountain was markedly higher than those in other mountain forest soils. The absolute abundance of PKS and NPRS gene was significantly higher in the tested soils compared with the gene copy numbers reported in tropical urban soils. Taibai Mountain is rich in actinomycete resources and has great potential for antibiotic excavation.

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

PubMed Central

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

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

PubMed Central

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

2017-01-01

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. PMID:28335539

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.

PubMed

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.

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

PubMed Central

Toth, Courtney R. A.; Gieg, Lisa M.

2018-01-01

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. PMID:29354103

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

PubMed

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.

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.

PubMed

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.

Database Resources of the BIG Data Center in 2018.

PubMed

2018-01-04

The BIG Data Center at Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences provides freely open access to a suite of database resources in support of worldwide research activities in both academia and industry. With the vast amounts of omics data generated at ever-greater scales and rates, the BIG Data Center is continually expanding, updating and enriching its core database resources through big-data integration and value-added curation, including BioCode (a repository archiving bioinformatics tool codes), BioProject (a biological project library), BioSample (a biological sample library), Genome Sequence Archive (GSA, a data repository for archiving raw sequence reads), Genome Warehouse (GWH, a centralized resource housing genome-scale data), Genome Variation Map (GVM, a public repository of genome variations), Gene Expression Nebulas (GEN, a database of gene expression profiles based on RNA-Seq data), Methylation Bank (MethBank, an integrated databank of DNA methylomes), and Science Wikis (a series of biological knowledge wikis for community annotations). In addition, three featured web services are provided, viz., BIG Search (search as a service; a scalable inter-domain text search engine), BIG SSO (single sign-on as a service; a user access control system to gain access to multiple independent systems with a single ID and password) and Gsub (submission as a service; a unified submission service for all relevant resources). All of these resources are publicly accessible through the home page of the BIG Data Center at http://bigd.big.ac.cn. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Database Resources of the BIG Data Center in 2018

PubMed Central

Xu, Xingjian; Hao, Lili; Zhu, Junwei; Tang, Bixia; Zhou, Qing; Song, Fuhai; Chen, Tingting; Zhang, Sisi; Dong, Lili; Lan, Li; Wang, Yanqing; Sang, Jian; Hao, Lili; Liang, Fang; Cao, Jiabao; Liu, Fang; Liu, Lin; Wang, Fan; Ma, Yingke; Xu, Xingjian; Zhang, Lijuan; Chen, Meili; Tian, Dongmei; Li, Cuiping; Dong, Lili; Du, Zhenglin; Yuan, Na; Zeng, Jingyao; Zhang, Zhewen; Wang, Jinyue; Shi, Shuo; Zhang, Yadong; Pan, Mengyu; Tang, Bixia; Zou, Dong; Song, Shuhui; Sang, Jian; Xia, Lin; Wang, Zhennan; Li, Man; Cao, Jiabao; Niu, Guangyi; Zhang, Yang; Sheng, Xin; Lu, Mingming; Wang, Qi; Xiao, Jingfa; Zou, Dong; Wang, Fan; Hao, Lili; Liang, Fang; Li, Mengwei; Sun, Shixiang; Zou, Dong; Li, Rujiao; Yu, Chunlei; Wang, Guangyu; Sang, Jian; Liu, Lin; Li, Mengwei; Li, Man; Niu, Guangyi; Cao, Jiabao; Sun, Shixiang; Xia, Lin; Yin, Hongyan; Zou, Dong; Xu, Xingjian; Ma, Lina; Chen, Huanxin; Sun, Yubin; Yu, Lei; Zhai, Shuang; Sun, Mingyuan; Zhang, Zhang; Zhao, Wenming; Xiao, Jingfa; Bao, Yiming; Song, Shuhui; Hao, Lili; Li, Rujiao; Ma, Lina; Sang, Jian; Wang, Yanqing; Tang, Bixia; Zou, Dong; Wang, Fan

2018-01-01

Abstract The BIG Data Center at Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences provides freely open access to a suite of database resources in support of worldwide research activities in both academia and industry. With the vast amounts of omics data generated at ever-greater scales and rates, the BIG Data Center is continually expanding, updating and enriching its core database resources through big-data integration and value-added curation, including BioCode (a repository archiving bioinformatics tool codes), BioProject (a biological project library), BioSample (a biological sample library), Genome Sequence Archive (GSA, a data repository for archiving raw sequence reads), Genome Warehouse (GWH, a centralized resource housing genome-scale data), Genome Variation Map (GVM, a public repository of genome variations), Gene Expression Nebulas (GEN, a database of gene expression profiles based on RNA-Seq data), Methylation Bank (MethBank, an integrated databank of DNA methylomes), and Science Wikis (a series of biological knowledge wikis for community annotations). In addition, three featured web services are provided, viz., BIG Search (search as a service; a scalable inter-domain text search engine), BIG SSO (single sign-on as a service; a user access control system to gain access to multiple independent systems with a single ID and password) and Gsub (submission as a service; a unified submission service for all relevant resources). All of these resources are publicly accessible through the home page of the BIG Data Center at http://bigd.big.ac.cn. PMID:29036542

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

PubMed

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 < 0.05). Decaying and free-floating 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.

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

PubMed

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

Characterization of Plasmid-Mediated Quinolone Resistance Determinants in High-Level Quinolone-Resistant Enterobacteriaceae Isolates from the Community: First Report of qnrD Gene in Algeria.

PubMed

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.

High-resolution phylogenetic microbial community profiling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Singer, Esther; Bushnell, Brian; Coleman-Derr, Devin

Over the past decade, high-throughput short-read 16S rRNA gene amplicon sequencing has eclipsed clone-dependent long-read Sanger sequencing for microbial community profiling. The transition to new technologies has provided more quantitative information at the expense of taxonomic resolution with implications for inferring metabolic traits in various ecosystems. We applied single-molecule real-time sequencing for microbial community profiling, generating full-length 16S rRNA gene sequences at high throughput, which we propose to name PhyloTags. We benchmarked and validated this approach using a defined microbial community. When further applied to samples from the water column of meromictic Sakinaw Lake, we show that while community structuresmore » at the phylum level are comparable between PhyloTags and Illumina V4 16S rRNA gene sequences (iTags), variance increases with community complexity at greater water depths. PhyloTags moreover allowed less ambiguous classification. Last, a platform-independent comparison of PhyloTags and in silico generated partial 16S rRNA gene sequences demonstrated significant differences in community structure and phylogenetic resolution across multiple taxonomic levels, including a severe underestimation in the abundance of specific microbial genera involved in nitrogen and methane cycling across the Lake's water column. Thus, PhyloTags provide a reliable adjunct or alternative to cost-effective iTags, enabling more accurate phylogenetic resolution of microbial communities and predictions on their metabolic potential.« less

High-resolution phylogenetic microbial community profiling

DOE PAGES

Singer, Esther; Bushnell, Brian; Coleman-Derr, Devin; ...

2016-02-09

Over the past decade, high-throughput short-read 16S rRNA gene amplicon sequencing has eclipsed clone-dependent long-read Sanger sequencing for microbial community profiling. The transition to new technologies has provided more quantitative information at the expense of taxonomic resolution with implications for inferring metabolic traits in various ecosystems. We applied single-molecule real-time sequencing for microbial community profiling, generating full-length 16S rRNA gene sequences at high throughput, which we propose to name PhyloTags. We benchmarked and validated this approach using a defined microbial community. When further applied to samples from the water column of meromictic Sakinaw Lake, we show that while community structuresmore » at the phylum level are comparable between PhyloTags and Illumina V4 16S rRNA gene sequences (iTags), variance increases with community complexity at greater water depths. PhyloTags moreover allowed less ambiguous classification. Last, a platform-independent comparison of PhyloTags and in silico generated partial 16S rRNA gene sequences demonstrated significant differences in community structure and phylogenetic resolution across multiple taxonomic levels, including a severe underestimation in the abundance of specific microbial genera involved in nitrogen and methane cycling across the Lake's water column. Thus, PhyloTags provide a reliable adjunct or alternative to cost-effective iTags, enabling more accurate phylogenetic resolution of microbial communities and predictions on their metabolic potential.« less

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

PubMed

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.

Community specificity: life and afterlife effects of genes.

PubMed

Whitham, Thomas G; Gehring, Catherine A; Lamit, Louis J; Wojtowicz, Todd; Evans, Luke M; Keith, Arthur R; Smith, David Solance

2012-05-01

Community-level genetic specificity results when individual genotypes or populations of the same species support different communities. Our review of the literature shows that genetic specificity exhibits both life and afterlife effects; it is a widespread phenomenon occurring in diverse taxonomic groups, aquatic to terrestrial ecosystems, and species-poor to species-rich systems. Such specificity affects species interactions, evolution, ecosystem processes and leads to community feedbacks on the performance of the individuals expressing the traits. Thus, genetic specificity by communities appears to be fundamentally important, suggesting that specificity is a major driver of the biodiversity and stability of the world's ecosystems. Copyright © 2012. Published by Elsevier Ltd.

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

PubMed

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/.

Microarray-Based Analysis of Subnanogram Quantities of Microbial Community DNAs by Using Whole-Community Genome Amplification†

PubMed Central

Wu, Liyou; Liu, Xueduan; Schadt, Christopher W.; Zhou, Jizhong

2006-01-01

Microarray technology provides the opportunity to identify thousands of microbial genes or populations simultaneously, but low microbial biomass often prevents application of this technology to many natural microbial communities. We developed a whole-community genome amplification-assisted microarray detection approach based on multiple displacement amplification. The representativeness of amplification was evaluated using several types of microarrays and quantitative indexes. Representative detection of individual genes or genomes was obtained with 1 to 100 ng DNA from individual or mixed genomes, in equal or unequal abundance, and with 1 to 500 ng community DNAs from groundwater. Lower concentrations of DNA (as low as 10 fg) could be detected, but the lower template concentrations affected the representativeness of amplification. Robust quantitative detection was also observed by significant linear relationships between signal intensities and initial DNA concentrations ranging from (i) 0.04 to 125 ng (r2 = 0.65 to 0.99) for DNA from pure cultures as detected by whole-genome open reading frame arrays, (ii) 0.1 to 1,000 ng (r2 = 0.91) for genomic DNA using community genome arrays, and (iii) 0.01 to 250 ng (r2 = 0.96 to 0.98) for community DNAs from ethanol-amended groundwater using 50-mer functional gene arrays. This method allowed us to investigate the oligotrophic microbial communities in groundwater contaminated with uranium and other metals. The results indicated that microorganisms containing genes involved in contaminant degradation and immobilization are present in these communities, that their spatial distribution is heterogeneous, and that microbial diversity is greatly reduced in the highly contaminated environment. PMID:16820490

High-resolution phylogenetic microbial community profiling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Singer, Esther; Coleman-Derr, Devin; Bowman, Brett

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 ourmore » 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.« less

ESIP Federation: A Case Study on Enabling Collaboration Infrastructure to Support Earth Science Informatics Communities

NASA Astrophysics Data System (ADS)

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

Molecular analysis of fungal communities and laccase genes in decomposing litter reveals differences among forest types but no impact of nitrogen deposition

USGS Publications Warehouse

Blackwood, C.B.; Waldrop, M.P.; Zak, D.R.; Sinsabaugh, R. L.

2007-01-01

The fungal community of the forest floor was examined as the cause of previously reported increases in soil organic matter due to experimental N deposition in ecosystems producing predominantly high-lignin litter, and the opposite response in ecosystems producing low-lignin litter. The mechanism proposed to explain this phenomenon was that white-rot basidiomycetes are more important in the degradation of high-lignin litter than of low-lignin litter, and that their activity is suppressed by N deposition. We found that forest floor mass in the low-lignin sugar-maple dominated system decreased in October due to experimental N deposition, whereas forest floor mass of high-lignin oak-dominated ecosystems was unaffected by N deposition. Increased relative abundance of basidiomycetes in high-lignin forest floor was confirmed by denaturing gradient gel electrophoresis (DGGE) and sequencing. Abundance of basidiomycete laccase genes, encoding an enzyme used by white-rot basidiomycetes in the degradation of lignin, was 5-10 times greater in high-lignin forest floor than in low-lignin forest floor. While the differences between the fungal communities in different ecosystems were consistent with the proposed mechanism, no significant effects of N deposition were detected on DGGE profiles, laccase gene abundance, laccase length heterogeneity profiles, or phenol oxidase activity. Our observations indicate that the previously detected accumulation of soil organic matter in the high-lignin system may be driven by effects of N deposition on organisms in the mineral soil, rather than on organisms residing in the forest floor. However, studies of in situ gene expression and temporal and spatial variability within forest floor communities will be necessary to further relate the ecosystem dynamics of organic carbon to microbial communities and atmospheric N deposition. ?? 2007 The Authors; Journal compilation ?? 2007 Society for Applied Microbiology and Blackwell Publishing Ltd.

The Potential Transformative Impact of Web 2.0 Technology on the Intelligence Community

DTIC Science & Technology

2008-12-01

wikis, mashups and folksonomies .24 As the web is considered a platform, web 2.0 lacks concrete boundaries; instead, it possesses a gravitational...engagement and marketing Folksonomy The practice and method of collaboratively creating and managing tags147 to annotate and categorize content

Gene Ontology Consortium: going forward

PubMed Central

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. PMID:25428369

Metabolonote: A Wiki-Based Database for Managing Hierarchical Metadata of Metabolome Analyses

PubMed Central

Ara, Takeshi; Enomoto, Mitsuo; Arita, Masanori; Ikeda, Chiaki; Kera, Kota; Yamada, Manabu; Nishioka, Takaaki; Ikeda, Tasuku; Nihei, Yoshito; Shibata, Daisuke; Kanaya, Shigehiko; Sakurai, Nozomu

2015-01-01

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 “Togo Metabolome Data” (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 facilitate 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: a wiki-based database for managing hierarchical metadata of metabolome analyses.

PubMed

Ara, Takeshi; Enomoto, Mitsuo; Arita, Masanori; Ikeda, Chiaki; Kera, Kota; Yamada, Manabu; Nishioka, Takaaki; Ikeda, Tasuku; Nihei, Yoshito; Shibata, Daisuke; Kanaya, Shigehiko; Sakurai, Nozomu

2015-01-01

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 "Togo Metabolome Data" (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 facilitate 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/.

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

PubMed

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.

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

PubMed

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.

Influence of zeolite and superphosphate as additives on antibiotic resistance genes and bacterial communities during factory-scale chicken manure composting.

PubMed

Peng, Shuang; Li, Huijie; Song, Dan; Lin, Xiangui; Wang, Yiming

2018-04-30

Factory-scale chicken manure composting added with zeolite (F), superphosphate (G), or zeolite and ferrous sulfate (FL) simultaneously, were evaluate for their effects on the behaviors of antibiotic resistance genes (ARGs) and bacterial communities. After composting, ARGs in manure decreased by 67.3% in the control, whereas the reductions were 86.5%, 68.6% and 72.2% in F, G and FL, respectively. ARGs encoding ribosomal protection proteins (tetO, tetB(P), and tetM) were reduced to a greater extent than tetG, tetL, sul1 and sul2. Bacteria pathogens were also effectively removed by composting. Network analysis showed that Firmicutes were the important potential host bacteria for ARGs. The bacterial communities and environmental factors, as well as the intI gene, contributed significantly to the variation of ARGs. The ARGs and integrons were reduced more when zeolite was added than when superphosphate was added; thus, it may be useful for reducing the risks of ARGs in chicken manure. Copyright © 2018 Elsevier Ltd. All rights reserved.

Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities

PubMed Central

Dupont, Chris L; McCrow, John P; Valas, Ruben; Moustafa, Ahmed; Walworth, Nathan; Goodenough, Ursula; Roth, Robyn; Hogle, Shane L; Bai, Jing; Johnson, Zackary I; Mann, Elizabeth; Palenik, Brian; Barbeau, Katherine A; Craig Venter, J; Allen, Andrew E

2015-01-01

Transitions in community genomic features and biogeochemical processes were examined in surface and subsurface chlorophyll maximum (SCM) microbial communities across a trophic gradient from mesotrophic waters near San Diego, California to the oligotrophic Pacific. Transect end points contrasted in thermocline depth, rates of nitrogen and CO2 uptake, new production and SCM light intensity. Relative to surface waters, bacterial SCM communities displayed greater genetic diversity and enrichment in putative sulfur oxidizers, multiple actinomycetes, low-light-adapted Prochlorococcus and cell-associated viruses. Metagenomic coverage was not correlated with transcriptional activity for several key taxa within Bacteria. Low-light-adapted Prochlorococcus, Synechococcus, and low abundance gamma-proteobacteria enriched in the>3.0-μm size fraction contributed disproportionally to global transcription. The abundance of these groups also correlated with community functions, such as primary production or nitrate uptake. In contrast, many of the most abundant bacterioplankton, including SAR11, SAR86, SAR112 and high-light-adapted Prochlorococcus, exhibited low levels of transcriptional activity and were uncorrelated with rate processes. Eukaryotes such as Haptophytes and non-photosynthetic Aveolates were prevalent in surface samples while Mamielles and Pelagophytes dominated the SCM. Metatranscriptomes generated with ribosomal RNA-depleted mRNA (total mRNA) coupled to in vitro polyadenylation compared with polyA-enriched mRNA revealed a trade-off in detection eukaryotic organelle and eukaryotic nuclear origin transcripts, respectively. Gene expression profiles of SCM eukaryote populations, highly similar in sequence identity to the model pelagophyte Pelagomonas sp. CCMP1756, suggest that pelagophytes are responsible for a majority of nitrate assimilation within the SCM. PMID:25333462

Occurrence and expression of gene transfer agent genes in marine bacterioplankton.

PubMed

Biers, Erin J; Wang, Kui; Pennington, Catherine; Belas, Robert; Chen, Feng; Moran, Mary Ann

2008-05-01

Genes with homology to the transduction-like gene transfer agent (GTA) were observed in genome sequences of three cultured members of the marine Roseobacter clade. A broader search for homologs for this host-controlled virus-like gene transfer system identified likely GTA systems in cultured Alphaproteobacteria, and particularly in marine bacterioplankton representatives. Expression of GTA genes and extracellular release of GTA particles ( approximately 50 to 70 nm) was demonstrated experimentally for the Roseobacter clade member Silicibacter pomeroyi DSS-3, and intraspecific gene transfer was documented. GTA homologs are surprisingly infrequent in marine metagenomic sequence data, however, and the role of this lateral gene transfer mechanism in ocean bacterioplankton communities remains unclear.

GeneLab

NASA Technical Reports Server (NTRS)

Berrios, Daniel C.; Thompson, Terri G.

2015-01-01

NASA GeneLab is expected to capture and distribute omics data and experimental and process conditions most relevant to research community in their statistical and theoretical analysis of NASAs omics data.

Gene Ontology Consortium: going forward.

PubMed

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.

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

NASA Astrophysics Data System (ADS)

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

Presence or Absence of mlr Genes and Nutrient Concentrations Co-Determine the Microcystin Biodegradation Efficiency of a Natural Bacterial Community

PubMed Central

Lezcano, María Ángeles; Morón-López, Jesús; Agha, Ramsy; López-Heras, Isabel; Nozal, Leonor; Quesada, Antonio; El-Shehawy, Rehab

2016-01-01

The microcystin biodegradation potential of a natural bacterial community coexisting with a toxic cyanobacterial bloom was investigated in a water reservoir from central Spain. The biodegradation capacity was confirmed in all samples during the bloom and an increase of mlrA gene copies was found with increasing microcystin concentrations. Among the 24 microcystin degrading strains isolated from the bacterial community, only 28% showed presence of mlrA gene, strongly supporting the existence and abundance of alternative microcystin degradation pathways in nature. In vitro degradation assays with both mlr+ and mlr− bacterial genotypes (with presence and absence of the complete mlr gene cluster, respectively) were performed with four isolated strains (Sphingopyxis sp. IM-1, IM-2 and IM-3; Paucibacter toxinivorans IM-4) and two bacterial degraders from the culture collection (Sphingosinicella microcystinivorans Y2; Paucibacter toxinivorans 2C20). Differences in microcystin degradation efficiencies between genotypes were found under different total organic carbon and total nitrogen concentrations. While mlr+ strains significantly improved microcystin degradation rates when exposed to other carbon and nitrogen sources, mlr− strains showed lower degradation efficiencies. This suggests that the presence of alternative carbon and nitrogen sources possibly competes with microcystins and impairs putative non-mlr microcystin degradation pathways. Considering the abundance of the mlr− bacterial population and the increasing frequency of eutrophic conditions in aquatic systems, further research on the diversity of this population and the characterization and conditions affecting non-mlr degradation pathways deserves special attention. PMID:27827872

Presence or Absence of mlr Genes and Nutrient Concentrations Co-Determine the Microcystin Biodegradation Efficiency of a Natural Bacterial Community.

PubMed

Lezcano, María Ángeles; Morón-López, Jesús; Agha, Ramsy; López-Heras, Isabel; Nozal, Leonor; Quesada, Antonio; El-Shehawy, Rehab

2016-11-03

The microcystin biodegradation potential of a natural bacterial community coexisting with a toxic cyanobacterial bloom was investigated in a water reservoir from central Spain. The biodegradation capacity was confirmed in all samples during the bloom and an increase of mlr A gene copies was found with increasing microcystin concentrations. Among the 24 microcystin degrading strains isolated from the bacterial community, only 28% showed presence of mlr A gene, strongly supporting the existence and abundance of alternative microcystin degradation pathways in nature. In vitro degradation assays with both mlr ⁺ and mlr - bacterial genotypes (with presence and absence of the complete mlr gene cluster, respectively) were performed with four isolated strains ( Sphingopyxis sp. IM-1, IM-2 and IM-3; Paucibacter toxinivorans IM-4) and two bacterial degraders from the culture collection ( Sphingosinicella microcystinivorans Y2; Paucibacter toxinivorans 2C20). Differences in microcystin degradation efficiencies between genotypes were found under different total organic carbon and total nitrogen concentrations. While mlr ⁺ strains significantly improved microcystin degradation rates when exposed to other carbon and nitrogen sources, mlr - strains showed lower degradation efficiencies. This suggests that the presence of alternative carbon and nitrogen sources possibly competes with microcystins and impairs putative non- mlr microcystin degradation pathways. Considering the abundance of the mlr - bacterial population and the increasing frequency of eutrophic conditions in aquatic systems, further research on the diversity of this population and the characterization and conditions affecting non- mlr degradation pathways deserves special attention.

Microbial community structure with trends in methylation gene diversity and abundance in mercury-contaminated rice paddy soils in Guizhou, China

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vishnivetskaya, Tatiana A.; Hu, Haiyan; Van Nostrand, Joy D.

In this paper, paddy soils from mercury (Hg)-contaminated rice fields in Guizhou, China were studied with respect to total mercury (THg) and methylmercury (MeHg) concentrations as well as Bacterial and Archaeal community composition. Total Hg (0.25–990 μg g –1) and MeHg (1.3–30.5 ng g –1) varied between samples. Pyrosequencing (454 FLX) of the hypervariable v1–v3 regions of the 16S rRNA genes showed that Proteobacteria, Actinobacteria, Chloroflexi, Acidobacteria, Euryarchaeota, and Crenarchaeota were dominant in all samples. The Bacterial α-diversity was higher in samples with relatively Low THg and MeHg and decreased with increasing THg and MeHg concentrations. In contrast, Archaeal α-diversitymore » increased with increasing of MeHg concentrations but did not correlate with changes in THg concentrations. Overall, the methylation gene hgcAB copy number increased with both increasing THg and MeHg concentrations. The microbial communities at High THg and High MeHg appear to be adapted by species that are both Hg resistant and carry hgcAB genes for MeHg production. The relatively high abundance of both sulfate-reducing δ- Proteobacteria and methanogenic Archaea, as well as their positive correlations with increasing THg and MeHg concentrations, suggests that these microorganisms are the primary Hg-methylators in the rice paddy soils in Guizhou, China.« less

Microbial community structure with trends in methylation gene diversity and abundance in mercury-contaminated rice paddy soils in Guizhou, China

DOE PAGES

Vishnivetskaya, Tatiana A.; Hu, Haiyan; Van Nostrand, Joy D.; ...

2018-03-05

In this paper, paddy soils from mercury (Hg)-contaminated rice fields in Guizhou, China were studied with respect to total mercury (THg) and methylmercury (MeHg) concentrations as well as Bacterial and Archaeal community composition. Total Hg (0.25–990 μg g –1) and MeHg (1.3–30.5 ng g –1) varied between samples. Pyrosequencing (454 FLX) of the hypervariable v1–v3 regions of the 16S rRNA genes showed that Proteobacteria, Actinobacteria, Chloroflexi, Acidobacteria, Euryarchaeota, and Crenarchaeota were dominant in all samples. The Bacterial α-diversity was higher in samples with relatively Low THg and MeHg and decreased with increasing THg and MeHg concentrations. In contrast, Archaeal α-diversitymore » increased with increasing of MeHg concentrations but did not correlate with changes in THg concentrations. Overall, the methylation gene hgcAB copy number increased with both increasing THg and MeHg concentrations. The microbial communities at High THg and High MeHg appear to be adapted by species that are both Hg resistant and carry hgcAB genes for MeHg production. The relatively high abundance of both sulfate-reducing δ- Proteobacteria and methanogenic Archaea, as well as their positive correlations with increasing THg and MeHg concentrations, suggests that these microorganisms are the primary Hg-methylators in the rice paddy soils in Guizhou, China.« less

Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities

DOE PAGES

Dupont, Chris L.; McCrow, John P.; Valas, Ruben; ...

2014-10-21

Here, transitions in community genomic features and biogeochemical processes were examined in surface and subsurface chlorophyll maximum (SCM) microbial communities across a trophic gradient from mesotrophic waters near San Diego, California to the oligotrophic Pacific. Transect end points contrasted in thermocline depth, rates of nitrogen and CO 2 uptake, new production and SCM light intensity. Relative to surface waters, bacterial SCM communities displayed greater genetic diversity and enrichment in putative sulfur oxidizers, multiple actinomycetes, low-light-adapted Prochlorococcus and cell-associated viruses. Metagenomic coverage was not correlated with transcriptional activity for several key taxa within Bacteria. Low-light-adapted Prochlorococcus, Synechococcus, and low abundance gamma-proteobacteriamore » enriched in the>3.0-μm size fraction contributed disproportionally to global transcription. The abundance of these groups also correlated with community functions, such as primary production or nitrate uptake. In contrast, many of the most abundant bacterioplankton, including SAR11, SAR86, SAR112 and high-light-adapted Prochlorococcus, exhibited low levels of transcriptional activity and were uncorrelated with rate processes. Eukaryotes such as Haptophytes and non-photosynthetic Aveolates were prevalent in surface samples while Mamielles and Pelagophytes dominated the SCM. Metatranscriptomes generated with ribosomal RNA-depleted mRNA (total mRNA) coupled to in vitro polyadenylation compared with polyA-enriched mRNA revealed a trade-off in detection eukaryotic organelle and eukaryotic nuclear origin transcripts, respectively. Gene expression profiles of SCM eukaryote populations, highly similar in sequence identity to the model pelagophyte Pelagomonas sp. CCMP1756, suggest that pelagophytes are responsible for a majority of nitrate assimilation within the SCM.« less

Denitrification gene expression in clay-soil bacterial community

NASA Astrophysics Data System (ADS)

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.

Diversity and Gene Expression of Phosphatase Genes Provide Insight into Soil Phosphorus Dynamics in a New Zealand Managed Grassland

NASA Astrophysics Data System (ADS)

Dunfield, K. E.; Gaiero, J. R.; Condron, L.

2017-12-01

Healthy and diverse communities of soil organisms influence key soil ecosystem services such as carbon sequestration, water quality protection, climate regulation and nutrient cycling. Microbially driven mineralization of organic phosphorus is an important contributor to plant available inorganic orthophosphates. In acidic soils, microbes produce non-specific acid phosphatases (NSAPs) which act on common forms of organic phosphorus (P). Our current understanding of P turnover in soils has been limited by lack of research tools capable of targeting these genes. Thus, we developed a set of oligonucleotide PCR primers that targeted bacteria with the genetic potential for acid phosphatase production. A long term randomized-block pasture trial was sampled following 22 years of continued aerial biomass removal and retention. Primers were used to target genes encoding alkaline phosphatase (phoD) and the three classes (CAAP, CBAP, CCAP) of non-specific acid phosphatases. PCR amplicons targeting total genes and gene transcripts were sequenced using Illumina MiSeq to understand the diversity of the bacterial phosphatase producing communities. In general, the majority of operational taxonomic units (OTUs) were shared across both treatments and across metagenomes and transcriptomes. However, analysis of DNA OTUs revealed significantly different communities driven by treatment differences (P < 0.05). Transcript expression was highest in the removed biomass treatment which corresponded the reduced Olsen P levels (15 vs. 36 mg kg-1 in retained treatment). Acid phosphatase activity was measured in all samples, and found to be highest in the biomass retained treatment (16.8 vs. 11.4 µmol g-1 dry soil h-1), likely elevated due to plant-derived enzymes; however, was still correlated to bacterial gene abundances. Overall, the phosphatase producing microbial communities responded to the effect of consistent P limitation as expected, through alteration in the composition of the

Occurrence and Expression of Gene Transfer Agent Genes in Marine Bacterioplankton▿

PubMed Central

Biers, Erin J.; Wang, Kui; Pennington, Catherine; Belas, Robert; Chen, Feng; Moran, Mary Ann

2008-01-01

Genes with homology to the transduction-like gene transfer agent (GTA) were observed in genome sequences of three cultured members of the marine Roseobacter clade. A broader search for homologs for this host-controlled virus-like gene transfer system identified likely GTA systems in cultured Alphaproteobacteria, and particularly in marine bacterioplankton representatives. Expression of GTA genes and extracellular release of GTA particles (∼50 to 70 nm) was demonstrated experimentally for the Roseobacter clade member Silicibacter pomeroyi DSS-3, and intraspecific gene transfer was documented. GTA homologs are surprisingly infrequent in marine metagenomic sequence data, however, and the role of this lateral gene transfer mechanism in ocean bacterioplankton communities remains unclear. PMID:18359833

Hypervisors as a Foothold for Personal Computer Security: An Agenda for the Research Community

DTIC Science & Technology

2012-01-13

unintrusive solutions that boost security. For example, gamers are even buying hardware tokens to protect their World of Warcraft accounts [5]. Build...security technology. http://www. vmware.com/technology/security/vmsafe.html. [4] VNC. http://en.wikipedia.org/wiki/VNC. [5] World of warcraft to sell

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms

PubMed Central

Joyce, Blake L.; Haug-Baltzell, Asher K.; Hulvey, Jonathan P.; McCarthy, Fiona; Devisetty, Upendra Kumar; Lyons, Eric

2017-01-01

This workflow allows novice researchers to leverage advanced computational resources such as cloud computing to carry out pairwise comparative transcriptomics. It also serves as a primer for biologists to develop data scientist computational skills, e.g. executing bash commands, visualization and management of large data sets. All command line code and further explanations of each command or step can be found on the wiki (https://wiki.cyverse.org/wiki/x/dgGtAQ). The Discovery Environment and Atmosphere platforms are connected together through the CyVerse Data Store. As such, once the initial raw sequencing data has been uploaded there is no more need to transfer large data files over an Internet connection, minimizing the amount of time needed to conduct analyses. This protocol is designed to analyze only two experimental treatments or conditions. Differential gene expression analysis is conducted through pairwise comparisons, and will not be suitable to test multiple factors. This workflow is also designed to be manual rather than automated. Each step must be executed and investigated by the user, yielding a better understanding of data and analytical outputs, and therefore better results for the user. Once complete, this protocol will yield de novo assembled transcriptome(s) for underserved (non-model) organisms without the need to map to previously assembled reference genomes (which are usually not available in underserved organism). These de novo transcriptomes are further used in pairwise differential gene expression analysis to investigate genes differing between two experimental conditions. Differentially expressed genes are then functionally annotated to understand the genetic response organisms have to experimental conditions. In total, the data derived from this protocol is used to test hypotheses about biological responses of underserved organisms. PMID:28518075

Mechanisms of pollution induced community tolerance in a soil microbial community exposed to Cu.

PubMed

Wakelin, Steven; Gerard, Emily; Black, Amanda; Hamonts, Kelly; Condron, Leo; Yuan, Tong; van Nostrand, Joy; Zhou, Jizhong; O'Callaghan, Maureen

2014-07-01

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. EC50 values were determined using substrate induced respiration and correlations made against soil physicochemical properties, microbial community structure, physiological status (qCO2; metabolic quotient), and abundances of genes associated with metal and antibiotic resistance. Previous level of exposure to copper was directly (P < 0.05) associated with tolerance to addition of new Cu(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 < 0.05) with increased metabolic quotient, potentially indicating that the community directed more energy towards cellular maintenance rather than biomass production. Neither bacterial or fungal community composition nor changes in the abundance of genes involved with metal resistance were related to PICT or co-tolerance mechanisms. Copyright © 2014 Elsevier Ltd. All rights reserved.

The promise and peril of chemical probes

PubMed Central

Arrowsmith, Cheryl H; Audia, James E; Austin, Christopher; Baell, Jonathan; Bennett, Jonathan; Blagg, Julian; Bountra, Chas; Brennan, Paul E; Brown, Peter J; Bunnage, Mark E; Buser-Doepner, Carolyn; Campbell, Robert M; Carter, Adrian J; Cohen, Philip; Copeland, Robert A; Cravatt, Ben; Dahlin, Jayme L; Dhanak, Dashyant; Frederiksen, Mathias; Frye, Stephen V; Gray, Nathanael; Grimshaw, Charles E; Hepworth, David; Howe, Trevor; Huber, Kilian V M; Jin, Jian; Knapp, Stefan; Kotz, Joanne D; Kruger, Ryan G; Lowe, Derek; Mader, Mary M; Marsden, Brian; Mueller-Fahrnow, Anke; Müller, Susanne; O'Hagan, Ronan C; Overington, John P; Owen, Dafydd R; Rosenberg, Saul H; Ross, Ruth; Roth, Bryan; Schapira, Matthieu; Schreiber, Stuart L; Shoichet, Brian; Sundström, Michael; Superti-Furga, Giulio; Taunton, Jack; Toledo-Sherman, Leticia; Walpole, Chris; Walters, Michael A; Willson, Timothy M; Workman, Paul; Young, Robert N; Zuercher, William J

2016-01-01

Chemical probes are powerful reagents with increasing impacts on biomedical research. However, probes of poor quality or that are used incorrectly generate misleading results. To help address these shortcomings, we will create a community-driven wiki resource to improve quality and convey current best practice. PMID:26196764

GeneSigDB—a curated database of gene expression signatures

PubMed Central

Culhane, Aedín C.; Schwarzl, Thomas; Sultana, Razvan; Picard, Kermshlise C.; Picard, Shaita C.; Lu, Tim H.; Franklin, Katherine R.; French, Simon J.; Papenhausen, Gerald; Correll, Mick; Quackenbush, John

2010-01-01

The primary objective of most gene expression studies is the identification of one or more gene signatures; lists of genes whose transcriptional levels are uniquely associated with a specific biological phenotype. Whilst thousands of experimentally derived gene signatures are published, their potential value to the community is limited by their computational inaccessibility. Gene signatures are embedded in published article figures, tables or in supplementary materials, and are frequently presented using non-standard gene or probeset nomenclature. We present GeneSigDB (http://compbio.dfci.harvard.edu/genesigdb) a manually curated database of gene expression signatures. GeneSigDB release 1.0 focuses on cancer and stem cells gene signatures and was constructed from more than 850 publications from which we manually transcribed 575 gene signatures. Most gene signatures (n = 560) were successfully mapped to the genome to extract standardized lists of EnsEMBL gene identifiers. GeneSigDB provides the original gene signature, the standardized gene list and a fully traceable gene mapping history for each gene from the original transcribed data table through to the standardized list of genes. The GeneSigDB web portal is easy to search, allows users to compare their own gene list to those in the database, and download gene signatures in most common gene identifier formats. PMID:19934259

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

PubMed

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.

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).

PubMed

Bhatta, Dharm R; Cavaco, Lina M; Nath, Gopal; Kumar, Kush; Gaur, Abhishek; Gokhale, Shishir; Bhatta, Dwij R

2016-05-15

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 and negative MRSA isolates. Out of 139 MRSA isolates, 79 (56.8 %) were PVL positive. The majority of the community acquired MRSA (90.4 %) were PVL positive (Positive predictive value: 94.9 % and negative predictive value: 86.6 %), while PVL was detected only in 4 (7.1 %) hospital associated MRSA strains. None of the MRSA isolates from hospital environment was found positive for the PVL genes. The majority of the PVL positive strains (75.5 %) were isolated from pus samples. Antibiotic resistance among PVL negative MRSA isolates was found higher as compared to PVL positive MRSA. Our study showed high prevalence of PVL among community acquired MRSA isolates. Absence of PVL among MRSA isolates from hospital environment indicates its poor association with hospital acquired MRSA and therefore, PVL may be used a marker for community acquired MRSA. This is first study from Nepal, to test PVL among MRSA isolates from hospital environment.

Wikipedia: a key tool for global public health promotion.

PubMed

Heilman, James M; Kemmann, Eckhard; Bonert, Michael; Chatterjee, Anwesh; Ragar, Brent; Beards, Graham M; Iberri, David J; Harvey, Matthew; Thomas, Brendan; Stomp, Wouter; Martone, Michael F; Lodge, Daniel J; Vondracek, Andrea; de Wolff, Jacob F; Liber, Casimir; Grover, Samir C; Vickers, Tim J; Meskó, Bertalan; Laurent, Michaël R

2011-01-31

The Internet has become an important health information resource for patients and the general public. Wikipedia, a collaboratively written Web-based encyclopedia, has become the dominant online reference work. It is usually among the top results of search engine queries, including when medical information is sought. Since April 2004, editors have formed a group called WikiProject Medicine to coordinate and discuss the English-language Wikipedia's medical content. This paper, written by members of the WikiProject Medicine, discusses the intricacies, strengths, and weaknesses of Wikipedia as a source of health information and compares it with other medical wikis. Medical professionals, their societies, patient groups, and institutions can help improve Wikipedia's health-related entries. Several examples of partnerships already show that there is enthusiasm to strengthen Wikipedia's biomedical content. Given its unique global reach, we believe its possibilities for use as a tool for worldwide health promotion are underestimated. We invite the medical community to join in editing Wikipedia, with the goal of providing people with free access to reliable, understandable, and up-to-date health information.