VanDyk, John

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Next-Generation Field Guides

2013-01-01 , VanDyk, John , Chu, Miyoko , Kress, W. John , Courtney, Gregory , Best, Jason , Pickering, John , Stevenson, Robert , Courtney, Gregory , VanDyk, John , Ellison, Aaron , Entomology

To conserve species, we must first identify them. Field researchers, land managers, educators, and citizen scientists need up-to-date and accessible tools to identify organisms, organize data, and share observations. Emerging technologies complement traditional, book-form field guides by providing users with a wealth of multimedia data. We review technical innovations of next-generation field guides, including Web-based and stand-alone applications, interactive multiple-access keys, visual-recognition software adapted to identify organisms, species checklists that can be customized to particular sites, online communities in which people share species observations, and the use of crowdsourced data to refine machine-based identification algorithms. Next-generation field guides are user friendly; permit quality control and the revision of data; are scalable to accommodate burgeoning data; protect content and privacy while allowing broad public access; and are adaptable to ever-changing platforms and browsers. These tools have great potential to engage new audiences while fostering rigorous science and an appreciation for nature.

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Use of the internet for information organization, distance learning, and specimen presentation

2003-01-01 , VanDyk, John , VanDyk, John , John Obrycki , Entomology

The advent of the internet has had an effect on the discipline of entomology. The history of the relationship between entomology and the internet is summarized, and several effects are examined in detail. One effect is to create an explosion of available information about insects and pest management, largely available on the world-wide web (WWW). A metadata-based solution to categorizing, searching and filtering this information is presented, along with a case study that used this solution to examine the value added by the use of metadata. In the case study website, one third of the users arrived at web pages containing entomological information by following links that were autogenerated based on metadata. Original software for extracting, assigning and managing metadata across sites is presented. A second effect is the enabling of new teaching methods, including the use of three-dimensional (3D) virtual reality insect models. Photographic 3D models were created using QuickTime VR and compared to standard teaching methodology. The QTVR models were significantly more effective. Lastly, the internet enables distance education. A web-based online introductory distance education course in entomology was constructed and offered for several years. Enrollment increased markedly over the time course was offered. Retention averaged 79% +/- 7.9% in the online section compared to 93% +/- 4.0% in the traditional section. Analysis of log files showed that problems with cheating during online evaluations was rampant, with 15 of 22 students cheating on one or both of the exams analyzed. Potentional solutions to this problem are presented.*;*This dissertation is a compound document (contains both a paper copy and a CD as part of the dissertation).

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TAL Effector-Nucleotide Targeter (TALE-NT) 2.0: tools for TAL effector design and target prediction

2012-01-01 , Booher, Nicholas , Booher, Nicholas , Standage, Daniel , Voytas, Daniel , VanDyk, John , VanDyk, John , Bogdanove, Adam , Plant Pathology and Microbiology , Entomology , Genetics, Development and Cell Biology , Bioinformatics and Computational Biology

Transcription activator-like (TAL) effectors are repeat-containing proteins used by plant pathogenic bacteria to manipulate host gene expression. Repeats are polymorphic and individually specify single nucleotides in the DNA target, with some degeneracy. A TAL effector-nucleotide binding code that links repeat type to specified nucleotide enables prediction of genomic binding sites for TAL effectors and customization of TAL effectors for use in DNA targeting, in particular as custom transcription factors for engineered gene regulation and as site-specific nucleases for genome editing. We have developed a suite of web-based tools called TAL Effector-Nucleotide Targeter 2.0 (TALE-NT 2.0; that enables design of custom TAL effector repeat arrays for desired targets and prediction of TAL effector binding sites, ranked by likelihood, in a genome, promoterome or other sequence of interest. Search parameters can be set by the user to work with any TAL effector or TAL effector nuclease architecture. Applications range from designing highly specific DNA targeting tools and identifying potential off-target sites to predicting effector targets important in plant disease.

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IPM information technology

2009-01-01 , VanDyk, John , VanDyk, John , Entomology

The use of information technology to obtain and manage IPM information will continue to grow. By applying the basic principles of information taxonomies such as tagging information with terms from vocabularies, filtering and aggregation, knowledge workers will have the necessary tools to become increasingly informed about the realm ofiPM.