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 Outdated teaching methods amount to discrimination”.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: [email protected]

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: [email protected]

@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.