Karen Snover-Clift1, Barb Riker1, Eric Newberry2, Gem Santillana2, Yazmin Rivera2,
and Pat Shiel3
1Cornell University, 2USDA-APHIS-PPQ-S&T, PPCDL, 3USDA-APHIS-PPQ-S&T, DESS
The 2023 workshops marked the 21st anniversary of the collaboration that became the NPDN-PPCDL Advanced Diagnostic Workshops held at the Plant Pathogen Confirmatory Diagnostic Laboratory (PPCDL). The 2023 workshop season used a hybrid approach, offering both virtual and in-person workshops, which resulted in the largest number of workshops offered in a single season. This article provides a review of the 2023 PPCDL workshops that includes the workshop topics presented, the PPCDL scientists that provided instruction, and the NPDN members, partners, and colleagues that received the training.
The statistics are impressive: 11 workshops on 10 different topics, three NEW topics, a return to in-person workshops with 48 spots filled at seven workshops, and 114 spots filled at the four virtual workshops. In total, the workshops covered 25 days over seven weeks for a total of 162 individual trainings.
Three new workshops were offered in 2023.
The Best Laboratory Practices workshop was developed to convey quality management practices, aseptic technique, preventing contamination, and general recommendations for working in a laboratory. Everyone hoping to attend future PPCDL workshops must complete this course before doing so. Offered as a live, 2-hour virtual session in 2023, the planning team members and the instructor, Nicole O’Donahue, are in the process of converting the workshop into an online format to be included in the NPDN’s learning management system (LMS) later this summer. Being available within the LMS will allow for completion at any time.
The Real-Time PCR Basics workshop was presented as a 2.5-hour virtual workshop and included a lecture on the basic principles of TaqMan probe qPCR, instrument features, assay development, method validation, and problem solving.
The Experiential Bioinformatics Module EHTS 102 workshop was an in-person 3-day workshop that was developed for a small group to practice what they learned in the Bioinformatics High Through-Put Sequencing workshop and to do so in the presence of instructors available to assist as questions arose. It covered the latest HTS technologies and analysis tools, allowed participants to generate their own MinION sequence data and analyze it using various sequence analysis software programs.
Other virtual workshops offered using this hybrid format included both bioinformatics modules, Sanger sequencing (module SS) and high through-put sequencing (module HTS). These workshops were chosen for virtual delivery because they are primarily lecture-based with some activities using various types of sequencing software. Having no hands-on laboratory component made them ideal candidates for continuing as virtual workshops.
The 2021 and 2022 workshops could not be delivered following our normal in-person format due to the COVID-19 pandemic. All workshops in those two years required the Herculean task of transforming the workshops to a virtual format. A few of these workshops included hands-on activities in lieu of the in-person laboratory experience, requiring the instructors create, package, and mail individual materials to participants. The return of in-person workshops was a relief to many of us. The instructors and planning team members were holding their collective breath as the workshops’ dates approached. They heard participants express how much they missed the in-person experience. Those of you that have attended in-person workshops understand the benefits to receiving the training with Building 580. When physically present, the participants connect with colleagues and the scientists that developed and/or validated the procedures they are learning, they try out different pieces of equipment and learn what features are needed back at their home lab, they learn while doing and perform the hands-on activities in the presence of experts that can guide them as questions arise and there are no home-base distractions.
The in-person workshops included the Phytophthora 101 workshop, the most requested workshop being offered 16 out of the 21 years. This year required two sessions to accommodate all those wanting to learn how to extract DNA and process samples for Phytophthora ramorum and Phytophthora kernoviae, each using two molecular procedures. The Seed Pathogen Testing workshop was offered in-person for the first time, having been offered in different forms virtually the previous two workshop seasons. This workshop provided an overview of seedborne pathology and the principles of extracting nucleic acids from seed. The Phytoplasmas Molecular Detection workshop covered the taxonomy and disease symptoms produced by phytoplasmas and the laboratory portion allowed participants to prepare samples, extract and purify DNA, perform conventional and qPCR and interpret the results. The Isothermal Amplification workshop covered various technologies, assay design, extraction, LAMP, and RPA using fungal and bacterial targets. The Citrus Canker workshop covered disease characteristics and how samples are processed within the PPCDL. The laboratory portion of the training focused on sample preparation, screening diagnostics, and interpretation of sample results. The Experiential Bioinformatics Module EHTS 102 workshop was described in the section on new workshops.
We hope those that attended these network-wide professional development opportunities in 2023 found them to be beneficial. We love to hear your feedback. You should have received the PPCDL survey forms at the end of your workshop, but if you have additional thoughts, feel free to reach out to anyone of the authors of this article. Thank you to all the PPCDL scientists and leadership for your continued commitment to providing these valuable training opportunities.
2023 PPCDL Workshop Instructors and Participants
February 21 — Best Laboratory Practices Workshop
Instructors: Nicole O’Donahue (USDA-APHIS-PPQ-S&T, PPCDL)
Moderators: Karen Snover-Clift (Cornell University); Matt Stern (Independent Contractor)
Participants: Aimee Thapa (North Dakota State University); Jason Pavel (University of Arkansas); Katherine Bella (USDA-APHIS-PPQ FO – Kansas); Rachel Knier (Pennsylvania Department of Agriculture); Peng Tian (University of Missouri), Jennifer Flynn (University of Minnesota), Pedro Uribe (Texas A&M University); Samantha Knackstadt (Texas A&M University);Rebecca Rodriguez (Texas A&M University); Heather Faubert (University of Rhode Island); Keiddy Urrea-Morawicki (University of Rhode Island); Sandra Jensen (Cornell University); Cora Baggett (Auburn University); Ahmed Hamid (Auburn University); Jennifer Orona (Auburn University);Kellie Bourguignon (Auburn University); Gabby Dunham (Auburn University); Brandice Kopishke (Auburn University); Elliot Cherniak (Auburn University); Kassie Conner (Auburn University); Kyoko Scanlon (Wisconsin Department of Natural Resources); Ethan Wachendorf (Wisconsin Department of Natural Resources); Jen Olson (Oklahoma State University); Sappihitah Dickerson (Washington Department of Agriculture); Sam Brown (Washington Department of Agriculture); Michael Melchert (Washington Department of Agriculture); Telissa Wilson (Washington Department of Agriculture); Nathan Chambers (Washington Department of Agriculture);; John Bonkowski (Purdue University); Sara Bratsch (Minnesota Department of Agriculture); Julie Beale (University of Kentucky); Sara Long (University of Kentucky); Karen Snover-Clift (Cornell University); Sara Wallace (Oklahoma State University); Diane Plewa (University of Illinois); Karen Rane (University of Maryland); Stefanie Rhodes (Michigan Department of Agriculture); Chandler Day (Kansas State University); Adam Schrankler (Minnesota Department of Agriculture); Sunita Young (Minnesota Department of Agriculture); Esneider Mahecha (University of Illinois Champagne-Urbana); Ansuya Jogi (University of Georgia); Alejandra Jimenez Madrid (University of Georgia); Melissa Irizarry (University of Florida); Matt Bertone (North Carolina State University); Swarna Moparthi (North Carolina State University); Giovanna Sassi (University of Vermont); Ann Hazelrigg (University of Vermont); Judy O’Mara University); Jennifer Abshire (Kansas State University); Tashi Gyatso (Virginia Department of Agriculture and Consumer Services); Kyle Broderick (University of Nebraska-Lincoln); James C. Fulton (Florida Department of Agriculture and Consumer Services); Vanessa Gonzalez (University of Florida); Hailey Spier Camposano (USDA-APHIS-PPQ-North Carolina); Jennifer Schoener (Nevada Department Of Agriculture); Jenna Gortari (Nevada Department of Agriculture); Suzette Baldwin (North Dakota State University); Sandesh Dangi (North Dakota State University); Christine Ngoan (North Dakota State University)
February 27–March 1 — Bioinformatics
Module SS Workshop
Instructors: Eric Newberry; Kurt Zeller; Peter Abrahamian; Schyler Nunziata; Jarred Yasuhara-Bell; Gloria Abad; Adia Damaso Durate (USDA-APHIS-PPQ-S&T, PPCDL)
Moderators: Karen Snover-Clift (Cornell University); Matt Stern (Independent Contractor)
Participants: Todd A. Steinlage (Alaska Department of Natural Resources); Jason Pavel (University of Arkansas); Rebecca Rodriguez (Texas A&M University); Kyoko Scanlon (Wisconsin Department of Natural Resources); Sara Bratsch (Minnesota Department of Agriculture); Michelle Grabowski (Minnesota Department of Agriculture); Esneider Mahecha (University of Illinois Champagne-Urbana); Alejandra Jimenez Madrid (University of Georgia); Melissa Irizarry (University of Florida); Tashi Gyatso (Virginia Department of Agriculture and Consumer Services); Lindsey Theissen (USDA-APHIS-PPQ-Maryland); Geoffrey Dennis (USDA-APHIS-PPQ-North Carolina); Sandesh Dangi (North Dakota State University); Cian Butler (Louisiana State University)
March 6–8 — Phytophthora 101 Workshop
Instructors: John Bienapfl; Kurt Zeller (USDA-APHIS-PPQ-S&T, PPCDL)
Participants: Jillian Smothergill (Pennsylvania Department of Agriculture); Samantha Knackstadt (Texas A&M University); Wei Belisle (California Department of Food and Agriculture); Tashi Gyatso (Virginia Department of Agriculture and Consumer Services); Sienna Turner (Bartlett Tree Experts)
March 9–10 — Seed Pathogen Testing Workshop
Instructors: Bright Agindotan; Dr. Muhammad Ilyas (USDA-APHIS-PPQ-S&T, PPCDL)
Participants: Colette Gabriel (Ohio Department of Agriculture); Bliss Betzen (USDA-APHIS-PPQ FO – Kansas); Samantha Knackstadt (Texas A&M University); Jan Byrne (Michigan State University); Ana Cristina Fulladolsa (Colorado State University); Matias Reynoso Vargas (Colorado State University); Giovanna Sassi (University of Vermont); Patricia Soria (Florida Department of Agriculture and Consumer Services)
March 14–15 — Phytoplasma Molecular
Detection Workshop
Instructor: Stefano Costanzo (USDA-APHIS-PPQ-S&T, PPCDL)
Participants: Jason Pavel (University of Arkansas); Katherine Bella (USDA-APHIS-PPQ FO – Kansas); Bliss Betzen (USDA-APHIS-PPQ FO – Kansas); Lauren Hendricks (Pennsylvania Department of Agriculture); Julie Thommen (Pennsylvania Department of Agriculture); Felicia Millett (University of Connecticut); Romina Gazis-Seregina (University of Florida); Monica Navia-Urrutia (University of Florida); Sara Wallace (Oklahoma State University); Ana Cristina Fulladolsa (Colorado State University); Marcus Vinicius Marin (University of Florida)
March 16–17 — Isothermal Amplification Workshop
Instructors: Gem Santillana; Kurt Zeller; Jarred Yasuhara-Bell (USDA-APHIS-PPQ-S&T, PPCDL)
Participants: Jason Pavel (University of Arkansas); Felicia Millett (University of Connecticut); Pedro Uirbe (Texas A&M University); Romina Gazis-Seregina (University of Florida); Monica Navia-Urrutia (University of Florida); Marcus Vinicius Marin (University of Florida); Kyle Broderick (University of Nebraska-Lincoln); Ruchika Kashyap (University of California, Davis)
March 20–22 — Phytophthora 101 Workshop
Instructors: John Bienapfl; Kurt Zeller (USDA-APHIS-PPQ-S&T, PPCDL)
Participants: Jason Pavel (University of Arkansas); Yonghao Li (Connecticut Agricultural Experiment Station); Ruchika Kashyap (University of California, Davis); Christian J. Cumagun (University of Idaho); Jennifer McCallister (USDA-APHIS-PPQ FO – Maryland); Madeleine Hassett (University of New Hampshire)
March 27–28 — Citrus Canker Workshop
Instructors: Gem Santillana; Jarred Yasuhara-Bell (USDA-APHIS-PPQ-S&T, PPCDL)
Participants: Michael Melzer (University of Hawaii); Alejandra Jimenez Madrid (University of Georgia); Jennifer McCallister (USDA-APHIS-PPQ FO – Maryland); Jennifer Schoener (Nevada Department of Agriculture); Jenna Gortari (Nevada Department of Agriculture)
March 27–29 — Bioinformatics Module HTS Workshop
Instructors: Schyler Nunziata; Gloria Abad; Peter Abrahamian; Eric Newberry; Yazmin Rivera (USDA-APHIS-PPQ-S&T, PPCDL)
Moderators: Karen Snover-Clift (Cornell University); Matt Stern (Independent Contractor)
Participants: Kassandra Breckenridge (Corteva Agrisciences); Katherine Bella (USDA-APHIS-PPQ FO – Kansas); Bliss Betzen (USDA-APHIS-PPQ FO – Kansas); Rebecca Rodriguez (Texas A&M University); Marcus Vinicius Marin (University of Florida); Sara Bratsch (Minnesota Department of Agriculture); Sandesh Dangi (North Dakota State University); Michelle Grabowski (Minnesota Department of Agriculture); Melissa Irizarry (University of Florida); Brianna Benitez (University of Florida); Patricia Soria (Florida Department of Agriculture and Consumer Services); Hailey Spier Camposano (USDA-APHIS-PPQ – North Carolina); Chandler Day (Kansas State University); Sienna Turner (Bartlett Tree Experts); Lindsey Thiessen (USDA-APHIS-PPQ – Maryland); Krishna Puri (Missouri Department of Agriculture)
March 30 — Real-Time PCR Basics Workshop
Instructor: Zonghe Yan (USDA-APHIS-PPQ-S&T, PPCDL)
Moderators: Karen Snover-Clift (Cornell University); Matt Stern (Independent Contractor)
Participants: Jason Pavel (University of Arkansas); Peng Tian (University of Missouri); Aimee Thapa (North Dakota State University); Ruchika Kashyap (University of California, Davis); Samantha Knackstadt (Texas A&M University); Rebecca Rodriguez (Texas A&M University); Phillip Lujan (New Mexico State University); Cora Baggett (Auburn University); Kassie Conner (Auburn University); Krishna Puri (Missouri Department of Agriculture); Jen Olson (Oklahoma State University); Sam Brown (Washington Department of Agriculture); Sapphitah Dickerson (Washington Department of Agriculture); Stefanie Rhodes (Michigan Department of Agriculture) Sara Bratsch (Minnesota Department of Agriculture); Julie Beale (University of Kentucky); Karen Rane (University of Maryland); Chandler Day (Kansas State University); Ansuya Jogi (University of Georgia); Kyoko Scanlon (Wisconsin Department of Natural Resources)
April 25–27 — Experiential Bioinformatics
HTS-102 Workshop
Instructors: Schyler Nunziata; Eric Newberry; Chellappan Padmanabhan; Phillip Lake; Yazmin Rivera (USDA-APHIS-PPQ-S&T, PPCDL)
Participants: Sebastian Albu (California Department of Food and Agriculture); Sandesh Dangi (North Dakota State University); Katie Posis (California Department of Food and Agriculture); Ying Yi Guo (California Department of Food and Agriculture); Sienna Turner (Bartlett Tree Experts)
