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Saturday, July 27 • 8:00 a.m - 5:00 p.m.
Welcome To the Diagnostic Assay Validation Network (“DAVN”)! Diagnostic Assay Databases, Statistical Tools, User Communities and More on the APS DAVN Network Portal
Diagnostic sciences in Plant Pathology are constantly being strengthened by new tools and discriminatory techniques. Assay developers are acquiring a new array of pathogen detection and diagnostic tools for developing and applying assays specific to their needs, including Next Generation Sequencing, Isothermal Amplification, Point-of-Use, etc. technologies. Confidence requirements are different across a continuum of needs from e.g. regulatory rejection of commodity and ornamental trade to successful surveillance and management of a local or regional outbreak of an emerging pathogen. The ability to ascribe statistically valid confidence to a diagnostic assay is a critical aspect of developing, applying, and reporting a diagnostic protocol. To address these critical issues, a group of APS members conceived and established the Diagnostic Assay Validation Network (DAVN) with USDA funding, and APS has established a robust web portal to host interactive community DAVN resources, including publication databases, statistical tools, and guidance for authors and editors of diagnostics manuscripts. Attendees will participate in breakout exercises to design diagnostic assays across multiple validation Tiers addressing Fitness for Purpose and work hands-on applying the user-friendly online APS-DAVN toolkits for statistical analyses of assay results at multiple levels of assay purpose.
Nanopore Sequencing and Whole Genome Assembly and Annotation with nf-core/pathogensurveillance
Generation and analysis of whole genome sequence data remains challenging. However, new sequencing technologies and automated analysis software are rapidly making whole genome sequencing more accessible. In this workshop, participants will gain hands-on experience with sequencing of a bacterial phytopathogen using Oxford Nanopore long-read sequencing technology. Participants will then use the novel nf-core/pathogensurveillance pipeline developed by the instructors to assemble and annotate the genomes. Throughout the workshop, strategies and tips for sequencing, genome assembly, and data analysis will be discussed. Participants are expected to bring their own laptop, but all computational work will be done in a virtual learning lab at Oregon State University.
Oomycetes Fungicides
Oomycetes include a good number of the most aggressive plant pathogens causing a diverse range of plant diseases including downy mildew, foliar and seedlings blights, damping-off, and root rots. Plant diseases caused by Oomycetes are usually hard to control and one of the key strategies for the management of the diseases is the use of chemical products. In recent years, several Oomycete fungicides have been introduced in the market for the control of downy mildews, Pythium, and Phytophthora diseases. The main objective of the workshop is to learn more about the new technologies being used to determine Oomycetes biodiversity, systematics, and phylogenetics, the evolution of fungicide resistance in new and standards Oomycetes products, to learn more about new Oomycetes products recently introduced in the market, to know more about the risk for resistance development, to discuss past and recent resistance issues, and to discuss the management of Oomycetes diseases with conventional products and the integration of new management strategies such as biocontrol agents.
Saturday, July 27 • 8:00 a.m. - 12:00 p.m.
Advancing Microbiome, Systems Biology Research, and Education Through User-Friendly Online Bioinformatic Platforms
A holistic approach to studying pathosystems is key for establishing sustainable agricultural practices as the demand for food, feed, and fiber increases. Thus, a comprehensive understanding of plants and interactions with their surroundings and associated microbiota is needed to manage emergent and persistent diseases. The increasing availability of techniques and resources are powerful tools for performing such studies. These include multi-omics tools that allow for obtaining large amounts of data that have been critical to elucidate the above mentioned challenges. However, these datasets can be difficult to process and are often analyzed with different pipelines, making it challenging to integrate and reuse the data. This workshop will provide a hands-on learning experience for researchers looking to learn more about microbiome research and plant-microbiome interactions. During this workshop, participants will learn about standardized pipelines to process and analyze multi-omic data by using demonstration datasets provided by the organizers. The workshop will be targeted at teaching two open-source online platforms: NMDC EDGE and KBase. As new technologies and resources arise, it is imperative that researchers can effectively utilize them. Lack of programming knowledge and access to computing resources can be a critical bottleneck for learning bioinformatics, and this workshop aims at reducing these inequalities.
Saturday, July 27 • 1:00 - 5:00 p.m.
Understanding Risk Pathways of Viroid Transmission in Vegetable Seed and Potato Production
Pospiviroids can infect peppers, tomatoes, and potatoes wherever these crops are grown. We still do not completely understand the origin and impact of these Pospiviroid infections. Reports of outbreaks in over the last two decades identified ornamental plants, weeds, and seeds as the origin of infection. Reports of seed as a pathway for the introduction of Pospiviroids as well as levels of seed infection in peppers and tomatoes are contradictory and complicate prevention and management practices. Phytosanitary requirements are now in place to regulate the movement of commercial vegetable seeds around the globe. Are commercial seeds a source of viroid outbreaks in tomato, pepper, and potato production? What have recent disease outbreaks taught us about viroid spread in the field and greenhouse? How can the research community contribute to evidence-based policy decisions related to pathogen testing? Following a guided panel discussion with presenters, the attendees will move into two discussion groups representing potato clean stock or commercial vegetable seed production. Each group will review the risk pathways of viroid introduction and spread, current measures that mitigate spread, and what research is needed to further prevent movement of viroids within the commodity.
Communicating in a Digital World: Introducing New Technologies for Presenting Your Research
The ability to effectively communicate, as an educator or a researcher, is a skill we tend to neglect. It is tough to take what we do and turn it into something that is approachable and memorable. How do you connect with your audience or students? How do you tell a story that will be attention-grabbing and unforgettable? The Office of Public Relations and Outreach proposes an interactive half-day communication workshop. During the first half of the session, participants will hear short presentations from successful communicators on their experience connecting with their audiences using various new digital methods or distance communication options.
Our speakers will showcase their current experience with how new technological opportunities have changed their communications with students and farmers. In the second half, participants will be broken into small work groups to put what they just learned to work, creating their own research pitches, and practicing them with the group.
Network Analysis in Plant Pathology Research: Disentangling Complex Data
Networks play a crucial role in plant pathology and have broad applications in understanding genetics, microbiome science, social systems, and epidemiology. A network comprises nodes and links that represent various relationships. For instance, in a geographic surveillance context, nodes would indicate locations or host populations in the surveillance system, while links would represent the potential pathogen spread between nodes. Analyzing network structures can be useful for understanding pathogen spread patterns in a landscape. Similarly, a network analysis of plant-associated microbiomes enables understanding of potential relationships among observed microbes/pathogens, generating hypotheses about microbial interactions in relation to plant health. This workshop will equip participants with the skills to interpret network analysis and hands-on experience in network analysis. The key learning objectives include a general understanding of fundamental concepts in network science and a practical proficiency in network analysis in R. Participants will engage with examples such as microbiome networks, epidemic networks, and technology spread networks. The workshop will leverage the R programming environment, offering a concise introduction to R.
