The Taproot

In this episode, we speak with Yunde Zhao, a Professor of Cell and Developmental Biology at the University of California San Diego. Yunde earned his Bachelors in Biochemistry from East China University of Science and Technology, received a Ph.D. in Biochemistry from the University of Michigan, and did his postdoctoral training in plant genetics at the Salk Institute, where he was a Howard Hughes Medical Institute Fellow of the Life Sciences Research Foundation. In January 2022, Yunde started his appointment as the Editor-in-Chief of Plant Physiology, one of the oldest plant journals. We discuss a recent paper from Yunde’s lab describing a fast and non-invasive method for monitoring plant transformations, and talk about the transformations that are needed in the publishing world. We also address a recent controversy about diversity among some newly appointed Plant Physiology editors. Show Notes: #DiversifyPlantSci https://rdale1.shinyapps.io/diversifyplantsci/ Plant Physiology Synbio Initiative https://academic.oup.com/plphys/article/190/1/180/6613939 Pandemic-related effects on publishing are gendered: https://www.nature.com/articles/d41586-020-01294-9 https://elifesciences.org/articles/76559 Paper: https://pubmed.ncbi.nlm.nih.gov/33024566/ He, Zhang, Sun, Zhan, and Zhao. A reporter for noninvasively monitoring gene expression and plant transformation. (2020). Horticulture Research 19:152. Twitter Handles: Liz Haswell Twitter @ehaswell Ivan Baxter Twitter @baxtertwi Yunde Zhao Twitter @YundeZhao

In this episode, we speak with Jennifer Robison, an Assistant Professor of Biology at Manchester University in Indiana. Jennifer received her Bachelor’s degree from Dickinson College, her Master’s degree from the University of Delaware and her PhD from Indiana University Purdue University Indianapolis. For her thesis, she studied how thermal stress impact gene expression and physiology in soybean. After getting her PhD, she moved directly to a faculty position, just in time to get her feet wet before the pandemic hit. We discuss Jen’s paper, “Using a Student-Generated Mock Magazine Issue to Improve Students’ Awareness of Diverse Scientists”, which was published in the Journal of Microbiology & Biology Education in 2020. We discuss the importance of approaching our teaching as scientifically and quantitatively as we approach our research. Jen describes the many important (and amusing!) ways she engaged students during pandemic-related remote instruction and the philosophies she’ll be carrying forward as we return to in-person instruction. Show Notes: Paper: Jennifer Robison. J Microbiol Biol Educ. (2020). 21:21/3/75. https://pubmed.ncbi.nlm.nih.gov/33384763/ Blog post: https://jenniferrobison.weebly.com/blog/covid-pivot-turned-me-into-the-cosplay-professor Twitter Handles Liz Haswell Twitter @ehaswell Ivan Baxter Twitter @baxtertwi Jen Robison Twitter @JenRobiSci Taproot Podcast Twitter @taprootpodcast

Taproot S6E1: May I have your attention, please? Searching for causal mutations and for institutional support. In this episode, our guest is Dior Kelley, an assistant professor in the Genetics, Development and Cell Biology department at Iowa State University. Dior received her B.S. in Chemistry from the University of California Santa Cruz in 2000, and her Ph.D. in Plant Biology from the University of California Davis in 2009 before doing an NIH Postdoctoral fellowship with Jeff Long at the Salk Institute and a second postdoc with Mark Estelle. She joined her department as an Adjunct Assistant Professor in 2015 before moving to her current role in 2019. Dior describes “slim shady is a novel allele of PHYTOCHROME B present in the T-DNA line SALK_015201”, which was published in Plant Direct last year. We also discuss the ways in which the already precarious position of the pre-tenure faculty member with kids was exacerbated by the COVID pandemic. We talk about the limitations of giving pre-tenure faculty an extra year to tenure, the challenges of a dual professor couple, and what institutions could be doing–but typically AREN’T–to support young faculty. We hope this conversation helps move us towards solutions both specific to the challenges of the pandemic, but also to more general challenges of young families on the tenure track. Show Notes: Linkan Dash , Robert E McEwan , Christian Montes, Ludvin Mejia, Justin W Walley, Brian P Dilkes, Dior R Kelley. slim shady is a novel allele of PHYTOCHROME B present in the T-DNA line SALK_015201. Plant Direct (2021) 5:e00326. https://pubmed.ncbi.nlm.nih.gov/34136747/ Eminem-The Real Slim Shady https://www.youtube.com/watch?v=eJO5HU_7_1w Ben Barres video about giving tenure at hiring (start around 3:45) https://www.youtube.com/watch?v=Be0KULrnD6E Laura Helen Petersen substack “The Expanding Job”. https://annehelen.substack.com/p/the-expanding-job Twitter Handles: Dior Kelley Twitter @KelleyDior Liz Haswell Twitter @ehaswell Ivan Baxter Twitter @baxtertwi Taproot Podcast Twitter @taprootpodcast

This week’s podcast is a conversation with Dr. Kevin Cox. Kevin earned his PhD at Texas A&M University before returning to his hometown of St Louis, Missouri to do a postdoc with Blake Meyers at The Donald Danforth Plant Science Center. Kevin has won numerous awards and grants and was recently awarded an HHMI Hanna H. Gray fellowship. We talk about Kevin’s work “TAL effector driven induction of a SWEET gene confers susceptibility to bacterial blight of cotton” by Cox et al. 2017 in Nature Communications. He tells us about the molecular mechanisms of bacterial blight on cotton as well as the technologies and collaborations that made this work possible. Kevin shares his path to plant science and how his exposure to new courses and research experiences led him to a career studying plant pathology. We talk about how he now uses multiple online and in-person platforms to share his passion and bridge communication gaps between the science community and the public. We also talk about how the pandemic has affected Kevin’s work as a postdoc and how he was able to balance work responsibilities while supporting his young daughter’s sudden online schooling during the early stages of the pandemic. A transcript for this episode was generously provided by Jo Stormer http://bit.ly/S5E4_KC Cox, K., Meng, F., Wilkins, K. et al. TAL effector driven induction of a SWEET gene confers susceptibility to bacterial blight of cotton. Nat Commun 8, 15588 (2017). https://doi.org/10.1038/ncomms15588 Kevin's YouTube Channel @Bioguy Kevin's Twitch Account @Bioguy Twitter Handles @K_Bioguy_Cox @ehaswell @baxtertwi @taprootpodcast

This week’s podcast is a conversation with Dr. Adán Colón-Carmona, Professor of Biology at the University of Massachusetts Boston. Adán received his PhD from the University of California, Irvine and he did postdoctoral research at the Salk Institute and at the University of California, Davis. His research currently focuses on plant rhizosphere interactions, abiotic stress response, and cell cycle. We talk with Adán about a recent publication in the Journal of Experimental Botany - “Influence of Arabidopsis thaliana accessions on rhizobacterial communities and natural variation in root exudates” (Micallef et al., 2009). He explains that different accessions of Arabidopsis, even when grown in the same starting soil, eventually have unique bacterial communities, and discusses why he thinks their exudates may be the reason. As a Mexican-born immigrant to the USA, Adán describes how the Society for Advancement of Chicanos/Hispanics and Native Americans in Science (SACNAS) has positively impacted his life. Additionally, he points out the value of multiculturalism. He explains how he has relied on his own multiple identities to empathize with, teach, and mentor students whose lives have become increasingly challenging during the COVID lockdowns. A transcript for this episode was generously provided by Jo Stormer http://bit.ly/TaprootS5E2_Transcript Adán's email: adan.colon-carmona@umb.edu @AColonCarmona Adán's Twitter https://www.sacnas.org @ehaswell Elizabeth’s Twitter @baxtertwi Ivan’s Twitter @taprootpodcast Taproot Twitter Micallef SA, Shiaris MP, Colón-Carmona A (2009) Influence of Arabidopsis thaliana accessions on rhizobacterial communities and natural variation in root exudates. Journal of Experimental Botany 60: 1729-1742

It has been quite a few months since our last episode! We intended to have a new season out by now, but as you might imagine, a few things got in the way. We are, however, back to working on topics and guests for Season 5 so stay tuned for new episodes this Fall! In the meantime, we want to hear from you! Tell us how you're navigating these chaotic and unusual times. Or... if what you're doing can't really be characterized as navigating, tell us about that instead! Let us know how you're trying to work right now, how you're navigating the next step in your career, or how the renewed attention on systemic racism in science and the world around us has affected you. We're planning on playing a few of these in every episode. So tell us a little bit about yourself by recording a short voicemail on your phone and email it to us at Tapoot@Plantae.org. We look forward to hearing from you! Be sure to listen to our previous seasons while you wait and stay tuned How to listen, download and subscribe to The Taproot podcast. Questions, feedback, suggestions? Contact us at taproot@plantae.org. Follow us on Twitter @TaprootPodcast @ehaswell @baxtertwi

This episode, we continue our discussions about cultivating a career with guest Kelly Gillespie, Nursery Solutions Lead at Bayer Crop Science. Kelly got her bachelor's degree at Knox College, a small liberal arts college in Illinois. She then moved on to do a PhD with Lisa Ainsworth at the University of Illinois. She did a short postdoc with Dick Sayre at the Danforth Center before moving to Monsanto, where she has worked for 9 years, staying with the company through the merger with Bayer. We talk with Kelly about her publication, “Greater antioxidant and respiratory metabolism in field‐grown soybean exposed to elevated ozone under both ambient and elevated CO2”, which was published in 2011 in Plant Cell & Environment. She talks about what it was like to work at the USDA Free Air Concentration Enrichment (FACE) site, the teamwork that was needed to collect her data, and how this experience taught her to work in highly collaborative environments. Kelly also shares her career journey and the factors she considered when choosing to make the transition from academia to industry. Kelly emphasizes a “milestone-based” approach, where each decision is broken into small steps and evaluated at checkpoints along the way. She talks about what it takes to succeed in a science career in industry, what might be familiar and what might be surprising to someone with an academic background, and emphasizes the value of making connections with other professionals. SHOW NOTES: Gillespie, K. M., Xu, F., Richter, K. T., Mcgrath, J. M., Markelz, R. C., Ort, D. R., ... & Ainsworth, E. A. (2012). Greater antioxidant and respiratory metabolism in field‐grown soybean exposed to elevated O3 under both ambient and elevated CO2. Plant, Cell & Environment, 35(1), 169-184. Join ASPB http://bit.ly/PCASPBMembership Plantae Webinar: Ask Me Anything: Plant Science Careers in Industry http://bit.ly/IndustryCareer_Seminar The Awesomest Seven Year Postdoc http://bit.ly/2Os6mbp Plantae Webinar: Prioritization and Work / Life Balance: Do Less, Work Better http://bit.ly/2vMYrit Plantae Mentoring Center - Sign up to be a mentor or mentee http://bit.ly/395XWOT Kelly’s LinkedIn Profile http://bit.ly/3b8bVWh Twitter Handles @kmgillespie @ehaswell @baxtertwi @taprootpodcast

In this episode, we talk with Laura Klasek who is a Plant Biology Ph.D. Candidate at the University of California, Davis about her research and experiences as a graduate student. Laura received her undergraduate degree from Hendrix College, where she double-majored in Biology and English with a creative writing focus. She was a 2018-2019 ASPB Conviron Scholar, is currently serving as a Plantae Community Network Leader for the Student Space Network, and is an Early Career Representative for the ASPB Plant Biology Program committee. For her dissertation, Laura is examining how the photosynthetic apparatus of the chloroplast develops. She is specifically interested in how proteins are targeted and folded within the chloroplast to facilitate improvements in how efficiently plants use light, water, and nutrients. Laura began her graduate studies in 2014 with Dr. Kentaro Inoue. In August 2016 - two weeks before Laura’s qualifying exams - Dr. Inoue tragically died in a traffic accident. The sudden loss of her advisor at a time when many graduate students already question whether to continue forced Laura to actively make difficult decisions about her career in a stressful and unexpected environment. In this episode, Laura shares how she navigated her situation with honesty. We discuss graduate student agency and how options are not unlimited. We talk about how it is important to work through the panic when our experiments and careers do not go as planned and how to decide if something is salvageable or if it is time to walk away. Finally, Laura suggests ways in which graduate programs and universities might help students by having systems already in place that provide support when faculty are sick, moving, or otherwise suddenly unavailable to mentor and to provide financial stability. SHOW NOTES: View From the Trenches - Advice if your PhD Advisor Unexpectedly Dies by Laura Klasek Hope is not a Strategy - Designing an IDP for a graduate program by Laura Klasek Plantae Webinar with Katie Murphy and Laura Klasek All aboard the mentor-ship: making and using an Individual Development Plan Follow on Twitter @EBibliophile @ehaswell @baxtertwi @taprootpodcast

In this episode, we talk with Dr. Scott Barolo about how he made a popular board game into a teaching tool, and we start a two-part discussion about the grad school application process. Scott gained his BSc at Penn State University and his Ph.D. in biology at the University of California, San Diego. He was then a postdoctoral fellow at the same university and started his lab in 2003 at the University of Michigan Medical School. Scott’s lab studies transcriptional pathways, repressors, and enhancers in Drosophila melanogaster. He has been the director of the graduate training Program in Biological Sciences (PIBS) since 2012. He is also a co-founder of the “9 Reply Guys” - inspired by #MeTooSTEM - where he humorously categorizes unconstructive Twitter behavior of men/women into 9 types. In this episode, we discuss a publication with Amy Strom, who was then an undergraduate student, titled “Using the Game of Mastermind to Teach, Practice, and Discuss Scientific Reasoning Skills”, published in PLOS One in 2011. We discuss how he “forced” his students to play this codebreaker game and how it helped them think about good experimental design, hypothesis testing, and biases. This paper helped provide some insight into aspects of scientific design that are often not explicitly explained to trainees. In the same vein, we ask Scott to describe the process of applying to graduate school. We talk about the advantages of taking off a couple of years first and getting lab experience to see if graduate school is a good fit. We get into a time machine and recall our own applications and how not to randomly apply to universities and programs. Scott says when he evaluates large stacks of applications, being an overachiever is great but the applications he remembers are from people who are different in some way. He recommends students to ‘show a bit of themselves’ in personal statements. They should not be afraid to share some of their out-of-academia interests either! The conversation was so great we decided to split the episode into two sections so look out for the continuation in our next episode where Scott demystifies the interview process! A transcript for this episode generously provided by Joe Stormer can be found here: https://bit.ly/3do5FNM SHOW NOTES: Strom, A.R. and Barolo, S., 2011. Using the game of mastermind to teach, practice, and discuss scientific reasoning skills. PLoS biology, 9(1), p.e1000578. https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1000578 Barolo Lab website: https://www.barololab.net/ Should you go to grad school? (Via Plantae) https://plantae.org/blog/should-you-go-to-grad-school-from-science-careers/ Twitter link to 9 reply guys introduction: https://twitter.com/sbarolo/status/1036685010869407744 Twitter: @9replyguys @sbarolo @ehaswell @baxtertwi @taprootpodcast #TaprootTuesday

In this episode, we talk with Dr. Ambika Kamath, a behavioral ecologist and a postdoctoral fellow at UC Berkeley, about her undergraduate research and how to make value-based career decisions. Ambika is originally from India and gained her B.A. in Biology at Amherst College in 2011. She received the Schupf Scholarship at Amherst which provided unlimited funding for her independent research on the evolution of flower morphology. She completed her Ph.D. at Harvard University studying the behavioral ecology of lizards. As a postdoctoral researcher at UC Berkeley, she received a Miller Institute for Basic Research in Science Postdoctoral Fellowship. Earlier this year she was awarded the 2019 American Society of Naturalists’ Young Investigator Award. In this episode, we discuss her publication, “Floral size and shape evolution following the transition to gender dimorphism” which was the outcome of her undergraduate research. She shares how her interest in mathematics led her to ecology, how much she enjoyed the fieldwork, and statistics behind the paper. Picking her graduate school was not a ‘no brainer decision’ so she talked to her supervisors, and made a list of things that she wanted before even having opportunities. This proactive decision system - instead of a reactive one - helped her choosing her graduate school and deciding to continue in academia as a postdoc. Ambika also talks about how helpful therapy was in her last year of graduate school and she shares some of the values she used when deciding to pursue a postdoc. We discuss how ‘sitting with your feelings’ is probably the best advice to everyone deciding on their career choices - it is hard to formulate general advice for everyone but list making is a great first step! Finally, Ambika shares some advice for established researchers who want to encourage trainees to stay in science. We leave you with the best advice she has ever received: "You are really good at being you, and you've gotten to where you are by being you. Just keep being you, there's no reason to stop now." A transcript of this episode generously provided by Joe Stormer can be found here: https://bit.ly/3scjp2q SHOW NOTES: Paper: Kamath, A., Levin, R.A. and Miller, J.S., 2017. Floral size and shape evolution following the transition to gender dimorphism. American Journal of Botany, 104(3), pp.451-460. https://bsapubs.onlinelibrary.wiley.com/doi/10.3732/ajb.1600442 Ambika’s blog: https://ambikamath.wordpress.com/blog/ @ambikamath @ehaswell @baxtertwi @taprootpodcast #TaprootTuesday

In this episode, we talk with Dr. Yoselin Benitez-Alfonso who is a faculty member at the University of Leeds in the United Kingdom to bust the myth competition is a part of science that cannot be avoided. Dr. Yoselin Benitez-Alfonso is originally from Cuba, and completed her graduate studies at the Universidad de Córdoba in Spain. After graduating with her Ph.D., she did two postdocs, one at Cold Spring Harbor Laboratories and another at the John Innes Center. She started her independent faculty position at University of Leeds in 2013 where she currently studies plasmodesmata, a kind of communication channel between plant cells. In this episode, we discuss one of her recent publications, “Callose-Regulated Symplastic Communication Coordinates Symbiotic Root Nodule Development” which was made possible by collaborating with Carvalho-Niebel’s lab in France. Using this project as an example, Yoselin explains how “with a bit of trust your alleged competition can become a friend and an amazing collaborator.” We also discuss the pros and cons of competition, why you should not be afraid or avoid it, and how to determine when collaboration will help you cover more ground and help further scientific advancement. But wait, there’s more! We’re planning an upcoming show – “Interrogate the Taproot”, in which we answer your questions. Please submit any questions for Liz and Ivan (about science, science careers or scientific culture) to @taprootpodcast or email us at taproot@plantae.org. A transcript of this episode, generously provided by Joe Stormer, can be found here: https://bit.ly/3bq6z9K SHOW NOTES: Paper: Gaudioso-Pedraza et al., Callose-Regulated Symplastic Communication Coordinates Symbiotic Root Nodule Development. Current Biology 2018 https://www.cell.com/current-biology/fulltext/S0960-9822(18)31226-0 Benitez-Alfonso lab website: https://benitezalfonso.wordpress.com/the-lab/ @benitez_lab @ehaswell @baxtertwi @taprootpodcast #TaprootTuesday

In this episode, Liz and Ivan talk with Dr. Rishi R. Masalia to bust the myth that early to late-career scientists should not speak up and make a difference to training programs and local communities. But how can we know when to or when not to STFU? (Listen to the episode to find out what that stands for.)Rishi is currently the Director of Bioinformatics at LeafWorks, a herbal genetics company. Rishi received his B.S. degree from the University of Arizona with a double major in Biology and Molecular and Cellular Biology. He finished his PhD in Plant Evolutionary Genetics in 2018 with a focus on cultivated sunflower genomics at the University of Georgia. During his graduate training, he co-founded Athens Cafe Observer, Athens Science Cafe, and the SPEAR science communication organization at Georgia. He started out as an ASPB Graduate Student Ambassador in 2015 and he is currently a member of the ASPB Membership Committee and the Plantae Steering Committee. We talk about his recent publication "Multiple genomic regions influence root morphology and seedling growth in cultivated sunflower under well-watered and water-limited conditions" and his transition to industry after his PhD. While his PhD project technically prepared him for a career in industry, he noticed many gaps in his graduate education. We chat about the #ASPBforward movement as we ask questions about graduate training and underrepresentation of early career scientists. Rishi also shares the story of the Town Hall Meeting at the ASPB Plant Biology conference in Montreal, where he stood up and told the board: “rather than talking about us [early career scientists], talk directly to us!”.While Rishi’s experience illustrates the power of “speaking your truth”, we also discuss how speaking up also depends on the individual’s situation and comfort zone. We make recommendations on how to voice your opinion in a respectful manner and suggest finding your people who share your opinions, especially within societies such as ASPB. A transcript of this episode was generously provided by Joe Stormer https://bit.ly/3dxNwNt SHOW NOTES: @RishiMasalia @ehaswell @baxtertwi @taprootpodcast #aspbforward #TaprootTuesday Rishi’s website: https://rishimasalia.com/ LeafWorks https://www.leafworks.com/ Athens Science Cafe https://athenssciencecafe.wordpress.com/ Athens Science Observer https://athensscienceobserver.com/ UGA Science, Policy, Education, Advocacy and Research (SPEAR) organization: https://ugaspear.wordpress.com/ Article: Masalia, R.R., A.A. Temme, N. de leon Torralba, J.M. Burke. 2018. Multiple genomic regions influence root morphology and seedling growth in cultivated sunflower (Helianthus annuus L.) under well-watered and water-limited conditions. Plos One, 13(9): e0204279. Early Career Professionals to ASPB Committees: https://blog.aspb.org/early-career-professionals-to-aspb-committees/ Resources for Early Career Scientists by the Union of Concerned Scientists: https://www.ucsusa.org/action/science_network/career-resources-early-career-scientists

This season of the Taproot is all about busting myths. In this episode, we talk with Dan Kliebenstein and bust the myth that if p < 0.5 your conclusion is correct. Dan Kliebenstein is a full professor at the University of California Davis, as well as a visiting professor at the University of Copenhagen. Before moving to California, Dan completed his Ph.D. at Cornell University under the advisement of Rob Last and then did a postdoc at the Max Planck Institute with Dr. Thomas Mitchell-Olds and Jonathan Gershenzon. Dan is currently an editor at four journals including the Plant Cell and eLife. Dan has many publications to choose from, but in this episode, we talk with him about a recent paper from his lab, "The quantitative basis of the Arabidopsis innate immune system to endemic pathogens depends on pathogen genetics." This work looks into how many genes actually control a host-pathogen interaction and what their identities might be. We talk about judgment calls his lab had to make when looking at their data, ambiguity, and how they dealt with it. We also discuss what led Dan to lead a Plant Cell perspective article on reassessing the t-test and explore how the scientific community can avoid incorrect conclusions, and putting undue emphasis on “mechanism” and “novelty”. A transcript of this episode, generously provided by Joe Stormer can be found here https://bit.ly/3bjjavz SHOW NOTES: @SpicyBotrytis ‏ @ehaswell @baxtertwi @taprootpodcast Corwin, J. A., Copeland, D., Feusier, J., Subedy, A., Eshbaugh, R., Palmer, C., ... & Kliebenstein, D. J. (2016). The quantitative basis of the Arabidopsis innate immune system to endemic pathogens depends on pathogen genetics. PLoS genetics, 12(2), e1005789. Brady, S. M., Burow, M., Busch, W., Carlborg, Ö., Denby, K. J., Glazebrook, J., ... & Springer, N. M. (2015). Reassess the t test: interact with all your data via ANOVA. The Plant Cell, tpc-15. Additional Papers Mentioned: Stoeger, T., Gerlach, M., Morimoto, R. I., & Amaral, L. A. N. (2018). Large-scale investigation of the reasons why potentially important genes are ignored. PLoS biology, 16(9), e2006643. Su, A. I., & Hogenesch, J. B. (2007). Power-law-like distributions in biomedical publications and research funding. Genome biology, 8(4), 404. Edwards, A. M., Isserlin, R., Bader, G. D., Frye, S. V., Willson, T. M., & Frank, H. Y. (2011). Too many roads not taken. Nature, 470(7333), 163. Monroe, J. G., Powell, T., Price, N., Mullen, J., Howard, A., Evans, K., ... & McKay, J. (2018). Drought adaptation in nature by extensive genetic loss-of-function. bioRxiv, 372854. Terminology: GWAS - Genome Wide Association Mapping; a method of looking at the association between genetic markers which we will call SNPs (Single Nucleotide Polymorphisms) in this discussion