VTechWorks staff will be away for the Thanksgiving holiday beginning at noon on Wednesday, November 27, through Friday, November 29. We will resume normal operations on Monday, December 2. Thank you for your patience.

Browsing by Author "Meyers, Blake C."

Now showing 1 - 2 of 2
  • Thumbnail Image
    Arabidopsis bioinformatics resources: The current state, challenges, and priorities for the future
    Doherty, Colleen; Friesner, Joanna; Gregory, Brian; Loraine, Ann; Megraw, Molly; Meyers, Blake C.; Provart, Nicholas J.; Slotkin, R. Keith; Town, Chris; Assmann, Sarah M.; Axtell, Michael J.; Berardini, Tanya; Chen, Sixue; Gehan, Malia; Huala, Eva; Jaiswal, Pankaj; Larson, Stephen; Li, Song; May, Sean; Michael, Todd; Pires, J. Chris; Topp, Chris; Walley, Justin; Wurtele, Eve (Wiley, 2019-01-01)
    Effective research, education, and outreach efforts by the Arabidopsis thaliana community, as well as other scientific communities that depend on Arabidopsis resources, depend vitally on easily available and publicly-shared resources. These resources include reference genome sequence data and an ever-increasing number of diverse data sets and data types. TAIR (The Arabidopsis Information Resource) and Araport (originally named the Arabidopsis Information Portal) are community informatics resources that provide tools, data, and applications to the more than 30,000 researchers worldwide that use in their work either Arabidopsis as a primary system of study or data derived from Arabidopsis. Four years after Araport's establishment, the IAIC held another workshop to evaluate the current status of Arabidopsis Informatics and chart a course for future research and development. The workshop focused on several challenges, including the need for reliable and current annotation, community-defined common standards for data and metadata, and accessible and user-friendly repositories/tools/methods for data integration and visualization. Solutions envisioned included (a) a centralized annotation authority to coalesce annotation from new groups, establish a consistent naming scheme, distribute this format regularly and frequently, and encourage and enforce its adoption. (b) Standards for data and metadata formats, which are essential, but challenging when comparing across diverse genotypes and in areas with less-established standards (e.g., phenomics, metabolomics). Community-established guidelines need to be developed. (c) A searchable, central repository for analysis and visualization tools. Improved versioning and user access would make tools more accessible. Workshop participants proposed a "one-stop shop" website, an Arabidopsis "Super-Portal" to link tools, data resources, programmatic standards, and best practice descriptions for each data type. This must have community buy-in and participation in its establishment and development to encourage adoption.
  • Thumbnail Image
    CRISPR/Cas9-mediated resistance to cauliflower mosaic virus
    Liu, Haijie; Soyars, Cara L.; Li, Jianhui; Fei, Qili; Peterson, Brenda A.; Meyers, Blake C.; Nimchuk, Zachary L.; Wang, Xiaofeng (Wiley, 2018-02-06)
    Viral diseases are a leading cause of worldwide yield losses in crop production. Breeding of resistance genes (R gene) into elite crop cultivars has been the standard and most cost-effective practice. However, R gene-mediated resistance is limited by the available R genes within genetic resources and in many cases, by strain specificity. Therefore, it is important to generate new and broad-spectrum antiviral strategies. The CRISPR-Cas9 (clustered regularly interspaced palindromic repeat, CRISPR-associated) editing system has been employed to confer resistance to human viruses and several plant single-stranded DNA geminiviruses, pointing out the possible application of the CRISPR-Cas9 system for virus control. Here, we demonstrate that strong viral resistance to cauliflower mosaic virus (CaMV), a pararetrovirus with a double-stranded DNA genome, can be achieved through Cas9-mediated multiplex targeting of the viral coat protein sequence. We further show that small interfering RNAs (siRNA) are produced and mostly map to the 30 end of single-guide RNAs (sgRNA), although very low levels of siRNAs map to the spacer region as well. However, these siRNAs are not responsible for the inhibited CaMV infection because there is no resistance if Cas9 is not present. We have also observed edited viruses in systematically infected leaves in some transgenic plants, with short deletions or insertions consistent with Cas9-induced DNA breaks at the sgRNA target sites in coat protein coding sequence. These edited coat proteins, in most cases, led to earlier translation stop and thus, nonfunctional coat proteins. We also recovered wild-type CP sequence in these infected transgenic plants, suggesting these edited viral genomes were packaged by wild-type coat proteins. Our data demonstrate that the CRISPR-Cas9 system can be used for virus control against plant pararetroviruses with further modifications.