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 Jason Williams, Assistant Director of Inclusion and Research Readiness at the DNA Learning Center at Cold Spring Harbor Laboratory. Jason is also lead for CyVerse Education, Outreach, and Training – the U.S. National Cyberinfrastructure for Life Science. Jason received his B.S. in Biology from SUNY Stonybrook in 2004, then worked as a technician in several labs at Cold Spring Harbor, and then transitioned to multiple roles in the DNA Learning Center In 2009. We discuss an article Jason and colleagues recently published in Science, entitled “Achieving STEM diversity: Fix the classrooms. Outdated teaching methods amount to discrimination”. We also talk about the nuance and complexities around improving diversity, equity and inclusion in STEM education, in planning conferences, and in running scientific societies. Have a listen! Show Notes: Paper: J. Handelsman, S. Elgin, M. Estrada, S. Hays, T. Johnson, S. Miller, V. Mingo, C. Schaffer, and J. Williams. (2022). Science 376:1057-1059. https://pubmed.ncbi.nlm.nih.gov/35653460/ Twitter Handles Liz Haswell Twitter @ehaswell Ivan Baxter Twitter @baxtertwi Jason Williams Twitter @JasonWilliamsNY

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

In this episode, our guest is Olivier Hamant. Olivier is a PI at INRAE in the Plant Reproduction and Development laboratory in Lyon, France. Olivier did his PhD on KNOX homeobox genes in 2003, and then postdocs in Berkeley with Zac Cande and with Jan Traas in Lyon. He took his current position at INRAE in 2012, where he works on the mechanobiology of development. Olivier has received a number of awards in recent years, including Prix Foulon” from the French science academy – 2020. The jumping-off point for our discussion is a commentary that Olivier wrote entitled “Plants Show us the Light”, published in Trends in Plant Science in 2020. There, he argues that evolution favors robustness over efficiency, and cites several recent discoveries in the field of photosynthesis to support his argument. From there, we apply the lens of efficiency versus robustness to a range of applications, including other aspects of biology, lab organization, and even the global economy. We also touch on ways that the COVID pandemic revealed this tension. Show Notes: Olivier Hamant. Plants Show us the Light. Trends Plant Sci. (2020). 26:97-99. https://pubmed.ncbi.nlm.nih.gov/33221171/ Twitter Handles Liz Haswell Twitter @ehaswell Ivan Baxter Twitter @baxtertwi 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

In this episode, our guest is Aman Husbands. Aman is originally from Canada and got his undergraduate degree from the University of Toronto. After completing his PhD at the University of California Riverside, he moved to Cold Spring Harbor Laboratories. In 2018, he moved to The Department of Molecular Genetics at the Ohio State University where he is an Assistant Professor. Aman’s research group focuses on uncovering the properties that allow complex biological processes, like development, to occur reproducibly. Aman shares the story behind a recent publication from his lab entitled “Identifying Cancer-Relevant Mutations in the DLC START Domain Using Evolutionary and Structure-Function Analyses” by Holub et al. 2020 in the International Journal of Molecular Sciences. He describes how his lab was able to identify new funding opportunities outside of plant sciences--and the different cultures of cancer research. We talk about why it is important to tune in to the projects you enjoy doing and discuss the responsibilities PI’s have to their labs and the people that come next. Aman says that it is important to deliberately create an atmosphere within the lab, clearly communicate priorities, and foster collaboration and communication with the group. We also talk about the value of connecting with and getting feedback from those outside your immediate research area. Aman also shares some of the ways he is working to address racism and equality, both on individual and systemic levels. A transcript of this episode was generously provided by Jo Stormer http://bit.ly/S5E5_Taproot Holub AS, Bouley RA, Petreaca RC, Husbands AY. Identifying Cancer-Relevant Mutations in the DLC START Domain Using Evolutionary and Structure-Function Analyses. International Journal of Molecular Sciences. 2020; 21(21):8175. https://doi.org/10.3390/ijms21218175 Community TV show pizza fire GIF http://gph.is/VwCaKS Aman's Email: Husbands.6@osu.edu Twitter Handles @AmanHusbands @ehaswell @baxtertwi @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

In this episode, we talk with Dr. Thelma Madzima, Assistant Professor of Cell and Molecular Biology at the University of Washington, Bothell. A native of Zimbabwe, she received her Ph.D. in Plant Molecular and Cellular Biology from the University of Florida and went on to complete a postdoc with Karen McGinnis in the Department of Biological Science at Florida State University. Her research currently focuses on epigenetic regulation of gene expression in plants using maize (Zea mays) as a model organism. We talk with Thelma about her recent publication in G3 “Epigenetic Regulation of ABA-Induced Transcriptional Responses in Maize”, complete citation. She tells us about characterising a specific epigenetic pathway in maize and how this work identified transposons that induce specific DNA methylations. Perhaps not unexpectedly, she and her authors found that plants that were “pre-stressed” by the loss of epigenetic silencing were also more likely to. Thelma talks about living in the US epicentre of the pandemic and how she is coping with the new “normal” as a Professor at a primarily undergraduate institute. She discusses the setbacks that the pandemic have created for tenure track professors, including those that are specific to PUIs. Additionally, as an immigrant from Zimbabwe, she knows firsthand the hardships an immigrant student faces and what recentchanges have meant to international students. As one of the few Black professors working in academic plant molecular biology in the US, she discusses the changes that need to come about in order to encourage the inclusion of black scientists in the scientific community. A transcript for this episode was generously provided by Jo Stormer http://bit.ly/S5E3_TM Vendramin S, Huang J, Crisp PA, Madzima TF, McGinnis KM (2020) Epigenetic Regulation of ABA-Induced Transcriptional Responses in Maize. G3: Genes|Genomes|Genetics 10: 1727-1743 Twitter Handles @thelma_madzima @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

This week’s Taproot podcast episode is a conversation with Dr. Tanisha Williams A plant researcher, she was inspired this summer by the simultaneous rise of the pandemic and the civil uprising against police brutality to draw Black botanists together for a social media event called #BlackBotanistsWeek. Tanisha is an impressively accomplished early career researcher whose work has ranged from population genomics to the use of herbarium specimens to track climate induced changes in flowering phenology, all with a central thread of preserving plant diversity. She received her PhD from the University of Connecticut Department of Ecology & Evolutionary Biology and now she is the David Burpee Postdoctoral Fellow in the Conservation, Genetics, and Ecology & Evolution of Plant Reproduction Group at Bucknell University. Currently, Tanisha works with Dr. Chris Martine on rare Pennsylvanian plant conservation, Australian Solanum taxonomy, and the way the Martu people of Australia interact with plants. Tanisha takes us on an inspiring journey through her research projects. She has persevered despite numerous setbacks, including those we are all familiar with like the pandemic, and those that are more specific to her experience, such as the dangers of spending time in nature while black and the lack of BIPOC representation in academia. Her social media campaign to provide black plant-lovers with a space to connect and share experiences quickly went viral when it first launched in July and has since expanded into a free virtual lecture series to highlight the work of black botanists. The series is called “Growing Black Roots: The Black Botanical Legacy,” and is hosted virtually by the Holden Arboretum every second Wednesday until September 2021. A transcript for this episode was generously provided by Jo Stormer http://bit.ly/TaprootS5E1_Transcript Tanisha’s website: https://naturesplasticity.weebly.com/research.html @t_marie_wms Tanisha’s Instagram and Twitter Beronda’s website and blog: http://www.berondamontgomery.com/reflect/my-black-botanical-legacy/ @BerondaM Beronda’s Twitter @ehaswell Elizabeth’s Twitter @baxtertwi Ivan’s Twitter @taprootpodcast Taproot Twitter Link to Holden Arboretum Black Botanists Lecture Series https://holdenarb.org/visit/events-lectures/scientist-lecture/ Join the Black Botanist’s Week community: #BlackBotanistsWeek https://blackbotanistsweek.weebly.com/ A story on Dr. Tiffany Knight’s work: https://source.wustl.edu/2013/02/walking-in-the-footsteps-of-19th-and-20thcentury-naturalists-scientists-find-battered-plantpollinator-network/ Burkle, L.A., Marlin, J.C. and T.M. Knight. 2013. Plant-Pollinator Interactions over 120 Years: Loss of Species, Co-Occurrence and Function. Science 339: 1611-1615.

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

In the final episode of Season 4, we talk with Todd Barkman, Professor of Biology at Western Michigan University. Todd earned his PhD in Botany at the University of Texas at Austin with Beryl Simpson, and went on to a postdoc position at Penn State with Claude dePamphilis. He started his lab at Western Michigan in 2000, where his group studies the systematics and evolution of plants, as well as the molecular evolution of biosynthetic pathways. We talk with Todd about his lab’s publication, “Convergent evolution of caffeine in plants by co-option of exapted ancestral enzymes” which was published in PNAS in 2016. Todd tells us the story behind the paper, how flowering plants evolved to make caffeine, and how he became interested in this topic. Todd describes what it is like to work at an “R2, or Research 2” institution such as Western Michigan, where it is important to succeed as both an instructor and as a researcher, and where resources for the latter are modest compared to “R1” institutions. We talk about the pros and cons of this environment, and how to accomplish research goals with limited funds and time. Todd talks about the importance and limitations of collaborations and closes with advice and encouragement for early career scientists considering a career at an R2 or R3 institution. He also advocates for a less deliberate and more open-ended style of experimental planning, and acknowledges the power of serendipity in his work. Huang, R., O’Donnell, A. J., Barboline, J. J., & Barkman, T. J. (2016). Convergent evolution of caffeine in plants by co-option of exapted ancestral enzymes. Proceedings of the National Academy of Sciences, 113(38), 10613-10618. Taproot S4E1: Identifying the Principle Components: Gender Dimorphism in Flowers and Consciously Building a Happy and Rewarding Career in Science http://bit.ly/38QivyY Todd's email: todd.barkman@wmich.edu Twitter Handles @ehaswell @baxtertwi @taprootpodcast

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

Our guest for this episode is Dr. Holly Bik. Holly obtained her PhD in Molecular Phylogenetics at the University of Southampton, working with John Lambshead at the Natural History Museum of London in conjunction with the UK National Oceanography Center. She completed postdoctoral appointments with Dr. Kelley Thomas at the University of New Hampshire and Dr. Jonathan Eisen at UC Davis before starting her faculty position. In addition to her research, Holly is invested in science communication. She serves as an associate editor for the popular marine blog Deep-Sea News and maintains an active presence on Twitter (@hollybik). Holly has co-authored a number of peer-reviewed articles on the use of social media and online tools in academia, including “An Introduction to Social Media for Scientists” in PLoS Biology and “Ten Simple Rules for Effective Online Outreach” in PLoS Computational Biology. In this episode, we discuss the first paper to come out of Holly’s lab at UC Riverside , entitled “Nematode-associated microbial taxa do not correlate with host phylogeny, geographic region or feeding morphology in marine sediment habitats” (Schuelke et al., 2018). Holly elaborates on the unexpected results from this paper and talks about the many challenges associated with collecting and analyzing marine sediments. In addition to the technical aspects of this paper, we also talk about time management and how Holly set aside time to write a draft in one week. She tells us about her 6-month-long personal work/life balance experiment in time-tracking and shares what she learned from this experience. We discuss the concept of Deep Work and why she continues to fill out weekly review worksheets to help manage stress and productivity. At the time of this recording, Holly was in the process of moving her lab from UC Riverside to The University of Georgia where she is currently an Assistant Professor in the Department of Marine Sciences. We talk about the process of moving and the factors Holly considered when making this important career decision. Holly explains that it's important for early career researchers to understand how long things take, and also be okay with the fact that some things are just going to take way longer than you expect. SHOW NOTES: Paper: Schuelke, T., Pereira, T. J., Hardy, S. M., & Bik, H. M. (2018). Nematode‐associated microbial taxa do not correlate with host phylogeny, geographic region or feeding morphology in marine sediment habitats. Molecular Ecology, 27(8), 1930-1951. A few of Holly’s Twitter threads: Data-driven time management https://twitter.com/hollybik/status/1133750210331496450 Concept of ‘deep work’ https://twitter.com/hollybik/status/1133751166091685888?s=20 Work life balance: https://twitter.com/hollybik/status/1133751739599876106?s=20 The Monday Motivator - weekly emails that provides positive energy, good vibes, and a productivity tip from the National Center of Faculty Development and Diversity Cal Newport (author of Deep Work) https://www.calnewport.com/about/ @hollybik @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 the previous episode, we talked with Dr. Scott Barolo about his research and shared tips for completing written graduate school applications. In this episode, we go to the next step, following up with Scott to discuss what to do once you’ve made it to the interviews. Scott shares tips for how to excel at interviews and offers advice for prospective students to help them make their own evaluations during the process. We talk about how interviews work both ways--you are interviewing the school as much as they are interviewing you--and how to ask the right questions to determine if a particular university, lab or program is the right fit. We leave students with a list of questions to ask that will help them gain a better understanding of lab culture, possibilities, and expectations. Whether you are a prospective student, a faculty member involved in admissions, or just want more insight into a process that can be pretty opaque--this episode is for you! A transcript for this episode generously provided by Joe Stormer can be found here: bit.ly/TRS4E4 SHOW NOTES: 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/ Plantae Mentoring Center https://jobs.plantae.org/ementor/index.cfm @sbarolo @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: bit.ly/TaprootS4E3_Transcript 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. Zen Faulkes about the graduate application process, what program directors are looking for and how hard it is (or indeed impossible) it is to have unbiased selection system. Zen gained a B.A., Psychology at the University of Lethbridge in 1989 and a Ph.D. at the University of Victoria about sand crab digging behaviour in 1996. He was a postdoctoral researcher at McGill University until 1999, and then he was a postdoc at the University of Melbourne until 2001. He is currently a Professor at the University of Texas Rio Grande Valley. Zen writes the “Better Posters” blog, which dispenses advice on how to improve the posters we present at meetings. In this episode, we discuss his publication, “Resolving authorship disputes by mediation and arbitration” in Research Integrity and Peer Review, and also his letter in Science titled “#GRExit's unintended consequences”. As graduate program coordinator, he talks about the pros and cons of GREs. Whilst universities are looking for “successful” people we have a chat about how we could define “success” to begin. Are assessments really consistent and reliable? Hm. We talk through the whole graduate application process step-by-step from both the applicant’s and recruiter’s point of views. We chat about how to structure personal statements and what to expect during interviews but also keeping in mind that everyone is different and perhaps more introverted students might feel at a disadvantage. Zen recommends students to ask program directors what competitive applications look like - they are very likely to give straight answers. While it is good to have a high GPA for a masters program, students really should get to know what the requirements and expectations are for different programs. Zen says, “If you inspire to go to graduate school, you have to be proactive thinking about what your opportunities are.” We leave students with a final piece of advice: every semester get to know one professor slightly better so at least you have a few people who know more about you. Asking for advice from professors and program directors can make graduate school application a whole lot smoother! A transcript for this episode generously provided by Joe Stormer can be found here: bit.ly/TaprootS4E2Transcript SHOW NOTES: Faulkes, Z., 2018. Resolving authorship disputes by mediation and arbitration. Research integrity and peer review, 3(1), p.12. https://researchintegrityjournal.biomedcentral.com/articles/10.1186/s41073-018-0057-z GRE exit - does not predict “success” - Letter in Science https://science.sciencemag.org/content/363/6425/356.2 Better posters site http://betterposters.blogspot.com/ Blog: https://neurodojo.blogspot.com Free pdf: https://faculty.utrgv.edu/zen.faulkes/Presentation_tips.pdf Twitter: @DoctorZen @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: bit.ly/S4E1_TaprootTranscript 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

This season’s theme is “Cultivating a Career”, and we’ll talk about this from both sides--ideas and advice for your own career AND for helping the careers of others.  Be sure to listen to our previous seasons while you wait and stay tuned! Follow us on Twitter: @taprootpodcast @ehaswell @baxtertwi

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://community.plantae.org/document/5212788406110651806/transcript-taproot-s3e6-yoselin-benitez-alfonso 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 Professor Simon Gilroy to bust the myth that plant scientists are only motivated to feed the world. So, let’s get back to the basics! Simon has been a professor at the University of Wisconsin-Madison since 2007. He completed his Ph.D. at Edinburgh in 1984 in Plant Biochemistry followed by postdoc positions at the University of California, Berkeley and University of Edinburgh. He was an assistant professor at Pennsylvania State University before joining Wisconsin-Madison. He also served on the Steering Committee and the Plant Biology Subcommittee of the 2011 NASA Decadal Survey on Biological and Physical Sciences in Space from the National Academies. We talk about his recent publication with Toyota et al. in the journal Science, "Glutamate triggers long-distance, calcium-based plant defense signaling" and how the videos of calcium spikes in plant leaves after damage caught the public’s imagination and led to his science celebrity status. The research was featured in National Geographic, Science Friday and the New York Times! Arabidopsis plants expressing a GFP-linked calcium sensor revealed rapid, glutamate-mediated long-distance signaling. Plants may have no nerves nor brains (“the big spongy thing on top of our heads”, as Simon would say) but they have a speedy signalling system! Simon shares his curiosity of how the world works, his enthusiasm for fundamental research and asking simple questions. We ask if it is okay to do basic research on taxpayer money and how the accumulation of ‘how this stuff works’ knowledge leads to the next breakthrough in applied science. We discuss how to write broader impact statements for NSF grant proposals for basic research. As we release this episode, Simon is at the Kennedy Space Center on sabbatical, conducting very basic science on Arabidopsis circadian rhythms and oxygen sensing, using space flights as a weird lab environment. According to Simon,, “if astronauts were to develop a taste for Arabidopsis, then all problems with growing food in space would be solved!” We chat about how early career scientists could evaluate if basic or applied science is the next step for them. Simon suggests going for ‘whatever floats your boat’ (e.g. broadly: like cloning genes or going around rainforests in Wellington boots). The basic questions come naturally to him; hence his career path. SHOW NOTES: @ehaswell @baxtertwi @taprootpodcast #TaprootTuesday Facebook page: https://www.facebook.com/gilroylab/ Articles:Toyota, M., Spencer, D., Sawai-Toyota, S., Jiaqi, W., Zhang, T., Koo, A.J., Howe, G.A. and Gilroy, S., 2018. Glutamate triggers long-distance, calcium-based plant defense signaling. Science, 361(6407), pp.1112-1115: http://science.sciencemag.org/content/361/6407/1112 New York Times: Watch Plants Light Up When They Get Attacked https://www.nytimes.com/2018/09/13/science/plant-defenses.html Science Friday: When Plants Sense Danger, They Cry Out With Calcium https://www.sciencefriday.com/segments/when-plants-sense-danger-they-cry-out-with-calcium/ National Geographic: Watch a Mutant Plant Burst Into Action When Attackedhttps://www.nationalgeographic.com/science/2018/09/news-plants-communicate-caterpillar-attack-calcium-video/ Videos: Prof Simon Gilroy checks the reality of the ‘Martian’: https://www.youtube.com/watch?v=b3DFRm0K2R4 Flashes of light show how plants signal distress: https://www.youtube.com/watch?v=txTKICNvpfU Upcoming Plant Cell Meeting: https://www.youtube.com/watch?v=AQZXmFbfNjI Science Videos: https://www.youtube.com/watch?v=LeLSyU_iI9o https://www.youtube.com/watch?v=7-3yFcZSyvo A transcript of this episode, generously provided by Joe Stormer, can be found here: https://community.plantae.org/document/5207577010813011648/transcript-taproot-s3e5-simon-gilroy

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. 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

In this episode, we talk with Dr. Needhi Bhalla to bust the myth that science is set up to be a meritocracy. We discuss one of her recent manuscripts, and how scientists can embrace complexity and diversity as we ask questions and mentor early career researchers. Dr. Needhi Bhalla is currently an Associate Professor in the Molecular, Cell and Developmental Biology department at the University of California, Santa Cruz. She finished her Ph.D. with Dr. Andrew Murray at the University of California, San Francisco and completed a postdoc at the University of California, Berkeley with Dr. Abby Dernberg before becoming an Assistant Professor at Santa Cruz. Needhi is our first guest who is not a plant scientist. Her lab investigates chromosome structure and function in the nematode C. elegans. We talk about one of her recent pre-prints, “PCH-2TRIP13 regulates spindle checkpoint strength” and how her lab learned to tackle paradoxes and think outside of the box to make sense of unintuitive data. In this episode, we also discuss how increasing diversity can provide the perspectives needed to understand scientific complexity. We list ways in which underrepresented groups can find support, and talk about how those in the majority can work to counteract bias and disparity. SHOW NOTES: @NeedhiBhalla @ehaswell @baxtertwi @taprootpodcast Defachelles, L., Russo, A. E., Nelson, C. R., & Bhalla, N. (2018). PCH-2TRIP13 regulates spindle checkpoint strength. bioRxiv, 389080. Lambing, C., Osman, K., Nuntasoontorn, K., West, A., Higgins, J. D., Copenhaver, G. P., … & Franklin, F. C. H. (2015). Arabidopsis PCH2 mediates meiotic chromosome remodeling and maturation of crossovers. PLoS genetics, 11(7), e1005372. Drugmonkey blog @drugmonkeyblog Ginther, D. K., Schaffer, W. T., Schnell, J., Masimore, B., Liu, F., Haak, L. L., & Kington, R. (2011). Race, ethnicity, and NIH research awards. Science, 333(6045), 1015-1019. Montgomery, B. L. (2018). Building and Sustaining Diverse Functioning Networks Using Social Media and Digital Platforms to Improve Diversity and Inclusivity. Frontiers in Digital Humanities, 5, 22. @9replyguys The nine types of reply guys twitter post The Matthew Effect How men can contribute – blog post by Needhi: A Beginner’s Guide for Addressing Sexual Harassment Boynton J.R., Georgiou K., Reid M., Govus A. (2018) Gender Bias in Publishing. The Lancet, 392(10157):1514-1515.

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”. 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

This season we are busting myths, and in this episode, we discuss the myth that mentoring is a one-way street. We talk with our guest Beronda Montgomery, Ph.D., about a cyanobacterium that changes shape in response to stress, and how mentors and trainees also need to change in response to their mutual needs during a research project. Beronda Montgomery is a Michigan State University (MSU) Foundation Professor in the Departments of Biochemistry & Molecular Biology - Microbiology & Molecular Genetics. She is also the Assistant Provost for Faculty Development at  MSU. Beronda completed her Ph.D. at the University of California Davis and was a National Science Foundation-funded postdoctoral fellow at Indiana University. Dr. Montgomery also conducts scholarship and training initiatives on mentoring issues related to diversity, junior scientists, and faculty development. She has received many awards, including recently being elected a fellow of the American Academy of Microbiology. Beronda's laboratory is broadly interested in how photosynthetic organisms, and specifically cyanobacteria, respond to light and nutrient availability. In this episode, we discuss one of her lab's recent publications on the regulation of carboxysome structural proteins and the mentor/mentee dynamics that helped shape the direction of this research. We also talk about Beronda's inspiring mentoring model and the similarities between plants and people (as well as the differences). SHOW NOTES @BerondaM @ehaswell @baxtertwi @taprootpodcast Rohnke, B. A., Singh, S. P., Pattanaik, B., & Montgomery, B. L. (2018). RcaE-Dependent Regulation of Carboxysome Structural Proteins Has a Central Role in Environmental Determination of Carboxysome Morphology and Abundance in Fremyella diplosiphon. mSphere, 3(1), e00617-17. Beronda Montgomery: Growing From Advisor to Mentor Montgomery, B. L. (2017). Mapping a Mentoring Roadmap and Developing a Supportive Network for Strategic Career Advancement. SAGE Open, 7(2), 2158244017710288. IDPS: Vincent BJ et al., (2015). Yearly planning meetings: individualized development plans aren't just more paperwork. https://www.ncbi.nlm.nih.gov/pubmed/26046646 Of possible interest: JAMA article on ‘mentorship malpractice’: https://jamanetwork.com/journals/jama/article-abstract/2512789

We are excited to announce that the first episode of Season 3 will be released next Tuesday!  This season, we have some amazing guests joining us and each episode will focus on busting a common science myth. Be sure to listen to Seasons 1 and 2 while you wait and stay tuned! How to listen, download and subscribe to The Taproot podcast Find us on Twitter: @ehaswell @baxtertwi @taprootpodcast

Stayed tuned for Season 3, where our theme will be "myth-busting". While we have some topics, we also want to hear from our audience about their ideas as well. Please take our brief survey: https://goo.gl/forms/a96VBgBG8RwHDieZ2, tell us more about yourself and help us plan for Season 3. Also - if you are attending Plant Biology 2018 in Montreal, stop by the Taproot roundtable discussion in the Plantae Pavilion on Tuesday, July 17 at 12:45-1:30 pm EST to meet Ivan Baxter and Liz Haswell. They'll be answering questions about interviewing scientists, crafting stories, and giving some glimpses into upcoming ideas and episodes. Find us on Twitter: @ehaswell @baxtertwi @taprootpodcast

In the final episode of Season 2, Liz and Ivan talk with Jeff Long, a professor at the University of California, Los Angeles (UCLA). He is the vice chair of the Molecular, Cellular and Developmental Biology department and co-director of the Cell and Developmental Biology graduate program. Jeff has worked on embryogenesis and development in Arabidopsis for most of his career. He earned his Ph.D. at the University of Wisconsin and completed a postdoc at the California Institute of Technology. In 2003, he joined the Salk Institute for Biological studies before moving to UCLA in 2012. Like episode S1.5, which came out between Seasons 1 and 2, in this episode we do not discuss one of our guests’ papers (although we do recommend you look up Jeff’s many impactful publications). Instead, we talk about a recent publication in Nature Biotechnology regarding graduate student mental health. Over 2000 graduate students from many countries and fields beyond plant biology were surveyed, providing astonishing evidence for a mental health crisis in graduate education. The authors report 41% of students scoring high for anxiety issues and 48% scoring high for depression. While these data suffer from responder bias, clearly there is a higher prevalence of mental health issues among graduate students than the general population. Postdocs most likely share this trend. In this study, many students indicate that they feel undervalued and that the Principal Investigators (PIs) in their labs were not providing adequate mentorship, support, or assets to further their career. We explore some of the reasons students might be feeling this way and discuss ways to provide support and mitigate these issues for students. We talk frankly about some of our own experiences and why it is important to think not only about what are we saying, but also how are we being heard. In this season of Taproot, and especially in this episode, we want people who are facing struggles in their careers to know that they aren’t alone and having trouble isn’t unusual. This is the wild type phenotype for scientists, especially while in training! If you are experiencing depression, anxiety, or another mental health issue, please don’t wait for a crisis! Right now, you can reach out to others for help and together we can break down the stigma associated with these struggles. SHOW NOTES Paper: https://www.mcdb.ucla.edu/faculty/jeffalong Evans, T. M., Bira, L., Gastelum, J. B., Weiss, L. T., & Vanderford, N. L. (2018). Evidence for a mental health crisis in graduate education. Nature biotechnology, 36(3), 282. Levecque, K., Anseel, F., De Beuckelaer, A., Van der Heyden, J., & Gisle, L. (2017). Work organization and mental health problems in Ph.D. students. Research Policy, 46(4), 868-879. Ivan Baxter’s tweet regarding this topic; https://twitter.com/BaxterTwi/status/986730085418962944 Find us on Twitter: @ehaswell @baxtertwi @taprootpodcast

In this episode, Ivan and Liz talk with Gina Baucom, Assistant Professor in Department of Ecology and Evolutionary Biology at the University of Michigan. Gina earned her PhD and completed a postdoc at the University of Georgia. She joined the faculty at University of Cincinnati in 2010 before moving to the University of Michigan in 2013. Gina’s lab integrates ecology, evolution, and genetics in order to understand the persistence of noxious agricultural weeds as well as the evolution of important plant functional traits. In this episode we discuss a recent paper from the Baucom lab: “Shifts in outcrossing rates and changes to floral traits are associated with the evolution of herbicide resistance in the common morning glory” Kuester et al., Ecology letters 20(1), 41-49, 2017). Gina describes how she became interested in morning glories and how their recent work illustrates ways in which herbicide resistance can influence mating and thereby evolution of non-agricultural systems. We also talk about how Gina unintentionally “broke Twitter” with a tweet about sexism in academia. We go over some of the data that demonstrate an unfair disadvantage for women and minorities pursuing careers in science. Gina outlines four major areas surrounding this issue and discusses a number of concrete actions men and women in positions of power can take to invite women scientists into the room AND give them a seat at the table. SHOW NOTES Paper: Kuester, A., Fall, E., Chang, S. M., & Baucom, R. S. (2017). Shifts in outcrossing rates and changes to floral traits are associated with the evolution of herbicide resistance in the common morning glory. Ecology letters, 20(1), 41-49. Baucom Lab Website: https://baucomlab.wordpress.com/ Diversify EB: https://diversifyeeb.wordpress.com Dynamic Ecology Blogpost: The Day @gbaucom Broke Twitter Possible Responses to Gender Discrimination: https://dynamicecology.wordpress.com/2017/07/10/guest-post-the-day-i-broke-some-twitter-feeds-insights-into-sexism-in-academia-part-2/ @NeedhiBhalla “What can I Do? Twitter thread: https://twitter.com/NeedhiBhalla/status/924383367704993793 Adrienne LaFrance article about gender differences in sources for her reporting: https://www.theatlantic.com/technology/archive/2016/02/gender-diversity-journalism/463023/ Ed Yong did a similar analysis: https://www.theatlantic.com/science/archive/2018/02/i-spent-two-years-trying-to-fix-the-gender-imbalance-in-my-stories/552404/ Gender Bias in Science--a Short Bibliography Clancy, K. B., Nelson, R. G., Rutherford, J. N., & Hinde, K. (2014). Survey of academic field experiences (SAFE): Trainees report harassment and assault. PLoS One, 9(7), e102172: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0102172 Zeng, X. H. T., Duch, J., Sales-Pardo, M., Moreira, J. A., Radicchi, F., Ribeiro, H. V., ... & Amaral, L. A. N. (2016). Differences in collaboration patterns across discipline, career stage, and gender. PLoS biology, 14(11), e1002573: http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1002573 Sex assaults, harassment reported in science fieldwork by Hoai-Tran Bui: https://www.usatoday.com/story/news/nation/2014/07/16/sexual-assault-harassment-science-fieldwork-studies-research-study/12735343/ Google Doc Sexual Harassment In the Academy: A Crowdsource Survey. By Dr. Karen Kelsky: https://docs.google.com/spreadsheets/u/1/d/1S9KShDLvU7C-KkgEevYTHXr3F6InTenrBsS9yk-8C5M/htmlview#gid=1530077352 Find us on Twitter: @gbaucom @DiversifyEEB @ehaswell @baxtertwi @taprootpodcast

In this episode, Ivan and Liz talk with Rosangela (Ross) Sozzani about her research and career path. Ross received her Ph.D. at the University of Pavia. After her post-doctoral studies at Duke University, Ross received the Armenise-Harvard Career Development Award for outstanding early-career scientists and moved back to Italy as an assistant professor, also at the University of Pavia. In 2013, Ross joined North Carolina State University’s Department of Plant and Microbial Biology, where she currently resides. Her research incorporates gene expression, genetics, mathematics, and computational biology to understand the function of biological circuits involving Arabidopsis root stem cells. We discuss a recent paper from Sozzani’s lab, “Predicting gene regulatory networks by combining spatial and temporal gene expression data in Arabidopsis root stem cells” (Balaguer et al., PNAS, 2017). We talk about how perspectives from outside plant sciences enabled this work (interestingly, the first author on this paper is an electrical engineer!) as well the limitations of technology and the importance of understanding what you can and cannot measure with tools available. In this episode, we also discuss some of the many struggles associated with being an early career scientist, such as choosing where to work, starting a lab, and figuring out when to try to fix a problem, when to accept it, and when to go a different direction. We talk about Ross’ experiences setting up her first lab at the University of Pavia and the factors she had to consider before she ultimately chose to “break the circuit” and start again elsewhere. SHOW NOTES Paper: de Luis Balaguer, M. A., Fisher, A. P., Clark, N. M., Fernandez-Espinosa, M. G., Möller, B. K., Weijers, D., ... & Sozzani, R. (2017). Predicting gene regulatory networks by combining spatial and temporal gene expression data in Arabidopsis root stem cells. Proceedings of the National Academy of Sciences, 114(36), E7632-E7640. http://www.pnas.org/content/114/36/E7632 Ross’ Websites: https://pmb.cals.ncsu.edu/people/people-table/dr-rosangela-ross-sozzani/ https://pmb.cals.ncsu.edu/sozzani-lab/ Find us on Twitter: @RossSozzani @ehaswell @baxtertwi @taprootpodcast

Message from Ivan and Liz: We want to bring listeners attention to this blogpost on Biofortified. https://biofortified.org/2018/08/kevin-folta-coi/ We believe that evidence presented here contradicts several of Kevins assertions in the episode about ‘radical transparency’ and urge listeners to consider them while processing our conversation. ########## In this episode, Ivan and Liz talk to Kevin Folta, Professor and Chairman of the Horticultural Sciences Department at the University of Florida. Kevin’s research focuses on the functional genomics of small fruit crops, photomorphogenesis, and plant transformation. In addition to his many impressive publications, Kevin has been deeply involved in student education and communication of science to the public for many years. Unfortunately, his success in scientific communication has also made him a target. In 2015, a Freedom of Information Act (FOIA) request was filed to the University of Florida by US Right to Know as part of a campaign targeting the emails of public scientists who have spoken out in favor of biotechnology. In this emotional episode, Kevin describes the whirlwind of fake news and misinformation that ensued after the FOIA request. We talk about the spiral of silence these efforts intend to create and why it is absolutely vital to keep speaking up for science and for the scientists under attack. SHOW NOTES Paper: Bao, Z., Clancy, M. A., Carvalho, R. F., Elliott, K., & Folta, K. M. (2017). Identification of novel growth regulators in plant populations expressing random peptides. Plant Physiology, pp-00577. http://www.plantphysiol.org/content/early/2017/08/14/pp.17.00577 Kevin’s Websites http://www.talkingbiotechpodcast.com/ http://kfolta.blogspot.com/ http://arabidopsisthaliana.com/ Links to Real News https://www.forbes.com/sites/davidkroll/2015/09/10/what-the-new-york-times-missed-on-kevin-folta-and-monsantos-cultivation-of-academic-scientists/#f3e425b619ad https://www.chronicle.com/blogs/ticker/jp/criticized-by-activists-professor-gives-grant-from-monsanto-to-food-pantry https://www.chronicle.com/blogs/ticker/academic-scientists-are-foot-soldiers-in-lobbying-battle-over-bioengineered-foods/104167 https://theness.com/neurologicablog/index.php/how-to-attack-a-public-scientist/ http://scibabe.com/folta/ https://respectfulinsolence.com/2015/11/05/a-sad-day-for-public-science-advocacy/ http://croplife.ca/theres-a-new-void-to-fill-in-science-communication/ Find us on Twitter: @kevinfolta @talkingbiotech @ehaswell @baxtertwi @taprootpodcast taproot@plantae.org

In this episode, Ivan and Liz talk with Elizabeth ‘Toby’ Kellogg about her research interests and career path. Toby received her PhD at Harvard University, then completed a postdoc with R.A. Howard, also at Harvard University. She worked at the Harvard Herbarium before being becoming an Associate Professor of Biology at Harvard University. From there she became E. Desmond Lee and Family Professor of Botanical Studies at the University of Missouri-St. Louis. In 2014, she joined the Donald Danforth Plant Science Center where she currently resides as a Robert E. King Distinguished Investigator. Read more about this episode: https://plantae.org/taproot-s2e2-minding-the-gap-with-elizabeth-toby-kellogg/ SHOW NOTES Intraspecific and interspecific variation in 5S RNA genes are decoupled in diploid wheat relatives (Kellogg et al., 1995) http://www.genetics.org/content/140/1/325.short http://kellogglab.weebly.com/ Research Fellowships for STEM professionals returning to their careers after a break: http://www.daphnejackson.org/fellowships Find us on Twitter: @TheKelloggLab @ehaswell @baxtertwi @taprootpodcast

To kick off Season 2, Ivan and Liz talk with Guillaume Lobet, Assistant Professor at the Forschungszentrum Jülich and the Université Catholique de Louvain. He was also a graduate student at UCL and took three postdoctoral positions in Germany and Belgium before returning and starting his faculty position in 2016. His work focuses on development of image analysis and phenotyping tools to help researchers improve their scientific workflow. He won the Plant Cell Teaching Tools in Plant Biology competition in 2015 and is an Academic Editor at Plant Direct. ----- Read more about this episode: https://plantae.org/taproot-s2e1-phenotyping-roots-without-pulling-up-your-own-with-guillaume-lobet/ ----- ----- SHOW NOTES ----- Root system markup language: toward a unified root architecture description language, Lobet et al. 2015 http://www.plantphysiol.org/content/167/3/617 https://figshare.com/ Guillaume’s personal webpage http://www.guillaumelobet.be// Recent eLIFE community essay about “mandatory” research training abroad https://elifesciences.org/articles/30183 Find us on Twitter @guillaumelobet @ehaswell @baxtertwi @taprootpodcast

In Season 1 of The Taproot, co-hosts Liz Haswell and Ivan Baxter dug beneath the surface of a manuscript to understand how scientific publications in plant biology are made. This season we will be talking to five guests who have succeeded despite facing huge challenges--challenges like resisting the pressure to relocate, taking time off to raise a family, facing gender discrimination, recovering from big mistakes, and being targeted by anti-science activists. SHOW NOTES: Taproot in the News http://news.stlpublicradio.org/post/2-st-louis-plant-scientists-use-podcast-dig-deep-struggles-research#stream/0 https://www.gdcb.iastate.edu/lawrence-dill-discusses-grad-school-paper-taproot-plantae-podcast https://artsci.wustl.edu/ampersand/bar-talk-haswell-hosts-new-science-podcast https://source.wustl.edu/2017/08/listening-in/ https://aspb.org/newsletter/archive/2017/NovDec17.pdf @taprootpodcast @ehaswell @baxtertwi taproot@plantae.org

In this episode, we take a different approach than usual- we bring a conversation we were having offline with our friend Brian Dilkes about a paper that tries to define the key variables that predict a ‘successful’ faculty member. We talk about some really important flaws of the paper, how to define “success”, and what impact really means and how one could/should/would measure it. Read more about this episode at https://plantae.org/taproot-podcast-s1-5esessile-measuring-mentoring-and-other-bleeps-with-brian-dilkes/ Show Notes: Planet Dilkes websites: https://ag.purdue.edu/cpb/ https://ag.purdue.edu/biochem/Pages/Profile.aspx?strAlias=bdilkes https://www.purdue.edu/gradschool/pulse/groups/profiles/faculty/dilkes.html https://twitter.com/BrianDilkes https://openwetware.org/wiki/Dilkes The paper we are discussing: https://peerj.com/articles/1262/ Paper that defines success as whether your faculty advisor thought you were successful: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3923635/ Letter Liz and colleagues wrote in response: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4072567/ For those who wish to make the metric the target (DON’T DO IT!!!!): Liz Google Scholar Page: https://scholar.google.com/citations?user=L7pWt14AAAAJ&hl=en Ivan Google Scholar Page: https://scholar.google.com/citations?hl=en&user=M68cB1AAAAAJ&view_op=list_works&gmla=AJsN-F6Vs2Z0EJFPnUog3VS8ExzbJsd9xu6_RRBmJm-SoiXtlVV3GXBGmTzqXHLc-enjsrR6JWux3L1oXYkH5tqiBI7FIDdSUFnW-KI320MNnLDDgpCVQRA Brian Google Scholar Page: https://scholar.google.com/citations?user=Rkx4gSoAAAAJ https://profiles.impactstory.org/u/0000-0003-2799-954X http://www.researcherid.com/rid/C-9293-2012 Twitter handles: @ BrianDilkes @ehaswell @baxterTWI

In this episode, we discuss a relatively recent paper from Jeff’s lab that illustrates the pros and cons of planning authorship lists in advance. We have an honest discussion about publishing in “high impact” journals (please note the ironic air quotes) as a pre-tenure professor and how his lab members made deliberate trade-offs in work-life balance to get experiments done quickly. Today’s paper is Hufford et al. “Comparative population genomics of maize domestication and improvement”, published in Nature Genetics in 2012. Read more about this episode on Plantae at: https://plantae.org/blog/taproot-podcast-s1e6-population-genetics-authorship-lists-worklife-balance-and-raining-cockroaches-with-jeffrey-ross-ibarra/ Show Notes: Hufford et al. https://www.ncbi.nlm.nih.gov/pubmed/22660546 Github site with successful faculty and grant applications-- https://github.com/RILAB/statements The Maize Diversity Project https://www.panzea.org Twitter handles @jrossibarra (it’s the cool cow with sunglasses) @ehaswell @baxterTWI

In this episode, Ivan and Liz talk with José Dinneny, a staff member at the Carnegie Institute for Sciences in Palo Alto, CA. We discuss a recent paper that describes a novel system for imaging root growth that balances the need for visualization with the need for more physiological growth conditions. The paper is Rellan-Alvarez et al., “GLO-roots: an imaging platform enabling multidimensional characterization of soil-grown root systems”, published in 2015. Read more about this episode at Plantae: https://plantae.org/blog/taproot-podcast-s1e5-finding-glory-the-power-of-new-technology-to-spur-innovation-with-jose-dinneny/ Show Notes: Rellan-Alvarez et al., 2015 https://elifesciences.org/articles/07597 Twitter handles @JoseDinneny @ehaswell @baxterTWI

In this episode Ivan and Liz talk with Siobhan Braybrook, Career Development Fellow at The Sainsbury Laboratory, University of Cambridge and soon-to-be Assistant Professor of Molecular, Cell and Developmental Biology at UCLA. We discuss two of her papers and discuss how to handle the grey areas of science and of scientific careers. And, maybe, we talk a bit about scientific impact). The papers are Peaucelle et al., 2011 and Braybrook & Peaucelle, 2013. Learn more about this episode on Plantae: https://plantae.org/blog/taproot-podcast-s1e4-embracing-uncertainty-in-science-and-science-careers-with-siobhan-braybrook/ Show Notes Peaucelle et al., 2011: http://www.sciencedirect.com/science/article/pii/S0960982211009638 Braybrook & Peaucelle, 2013: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0057813 Siobhan’s Kanban board: https://twitter.com/BraybrookSA/status/847098317758705664 Siobhan’s website: www.plantmechanome.org Twitter handles @BraybrookSA @ehaswell @baxterTWI

In this episode, Ivan and Liz talk with Luca Comai, a Professor of Plant Biology at the Genome Center at University of California, Davis. We discuss a paper he published as part of his transition from industry to academia that he feels illustrates a mistake he made in choosing a research direction. We have a fascinating conversation about the power and the peril of striking out in new research directions and Luca gives his advice on grant-writing. The paper is “Developmental expression of tomato heat shock cognate protein 80"  by Koenig & Comai, Plant Phys 1992. Learn more about this episode on Plantae: https://plantae.org/blog/s1e3-academic-industry-and-pivoting-on-projects-with-luca-comai/ SHOW NOTES: Paper: https://www.ncbi.nlm.nih.gov/pubmed/16653061 Lords of the Harvest: https://www.amazon.com/Lords-Of-The-Harvest-Biotech/dp/073820773X/gristmagazine Luca’s Teaching website http://flipping101genetics.blogspot.com

In this episode, Ivan and Liz talk with Carolyn Lawrence-Dill, an Associate Professor of Genetics, Development and Cell Biology as well as Agronomy at Iowa State University. We discuss a paper from her grad school days that has a great back story about how to bring a large number of people together to agree on a common system of nomenclature. It turns out that it’s both important and challenging to do and we had a great conversation touching on egos, politics and grad student projects. Read more about this episode: https://plantae.org/blog/taproot-podcast-s1e2-normalizing-nomenclature-and-the-idealism-of-youth-with-carolyn-lawrence-dill/ SHOW NOTES: Lawrence et al., 2004 http://jcb.rupress.org/content/167/1/19.long Maize GDB https://www.maizegdb.org Carolyn’s website https://dill-picl.org Ron Vale shows animation of kinesin walking (start at 25:00) https://www.youtube.com/watch?v=9RUHJhskW00 @IAcornflake @ehaswell @BaxterTWI taproot@plantae.org

In this episode, the hosts and Sophien discuss a recent collaborative paper (Islam et al., 2016, BMC Biology) that really embodies the concepts of open science. It addresses the source and characterization of a newly discovered wheat blast in Bangladesh. Wheat blast is a fungal disease that affects grasses that are a huge threat to food security. The authors report the geographical distribution of this new disease, characterize the disease symptoms of affected plants, and isolate and validate the causal fungus. Most strikingly, they performed RNA sequencing on symptomatic and asymptomatic leaves and show that RNA from these infected leaves aligns to the genome of a Brazilian wheat blast strain. They conclude that the Bangladesh isolate of wheat blast is phylogenetically related to the Brazilian wheat blast, rather than an unknown or new lineage. _____ Islam et al. 2016 https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-016-0309-7 Kamoun, 2012 http://kamounlab.dreamhosters.com/pdfs/MicrobiologyToday_2012.pdf Open Wheatblast http://s620715531.websitehome.co.uk/owb/ ASAPBio http://asapbio.org BioRxiv http://www.biorxiv.org @KamounLabTwitter Kamoun Lab webpage http://kamounlab.tumblr.com @baxterTWI @ehaswell Contact: taproot@plantae.org _____ Read more about this episode: https://plantae.org/blog/taproot-episode-1-season-1-extreme-open-science-and-the-meaning-of-scientific-impact-with-sophien-kamoun/

The Taproot is the podcast that digs beneath the surface to understand how scientific publications are created. In each episode, we take a paper from the plant biology literature and talk about the story behind the science with one of the authors.