VanDyk, John

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Email Address
jvandyk@iastate.edu
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Title
Manager Business Systems Analysis
Academic or Administrative Unit
Organizational Unit
Entomology

The Department of Entomology seeks to teach the study of insects, their life-cycles, and the practicalities in dealing with them, for use in the fields of business, industry, education, and public health. The study of entomology can be applied towards evolution and ecological sciences, and insects’ relationships with other organisms & humans, or towards an agricultural or horticultural focus, focusing more on pest-control and management.

History
The Department of Entomology was founded in 1975 as a result of the division of the Department of Zoology and Entomology.

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Next-Generation Field Guides

2013-01-01 , Farnsworth, Elizabeth , Chu, Miyoko , Kress, W. John , Neill, Amanda , Courtney, Gregory , Best, Jason , Pickering, John , Stevenson, Robert , 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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Publication

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

2012-01-01 , Doyle, Erin , Booher, Nicholas , Standage, Daniel , Voytas, Daniel , Brendel, Volker , 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;https://boglab.plp.iastate.edu/) 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.