The Taproot

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 [email protected].

A transcript of this episode, generously provided by Joe Stormer, can be found here: https://bit.ly/3bq6z9K

SHOW NOTES:

Paper: Gaudioso-Pedraza et al., Callose-Regulated Symplastic Communication Coordinates Symbiotic Root Nodule Development. Current Biology 2018

https://www.cell.com/current-biology/fulltext/S0960-9822(18)31226-0

Benitez-Alfonso lab website: https://benitezalfonso.wordpress.com/the-lab/

@benitez_lab

@ehaswell

@baxtertwi

@taprootpodcast

#TaprootTuesday

In this episode, Liz and Ivan talk with 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.

A transcript for this episode was generously provided by Joe Stormer https://bit.ly/3dsbKZB

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.

A transcript of this episode was generously provided by Joe Stormer https://bit.ly/3dxNwNt

SHOW NOTES: 

@RishiMasalia

@ehaswell

@baxtertwi

@taprootpodcast

#aspbforward

#TaprootTuesday

Rishi’s website: https://rishimasalia.com/

LeafWorks https://www.leafworks.com/

Athens Science Cafe https://athenssciencecafe.wordpress.com/

Athens Science Observer

https://athensscienceobserver.com/

UGA Science, Policy, Education, Advocacy and Research (SPEAR) organization: https://ugaspear.wordpress.com/

Article: Masalia, R.R., A.A. Temme, N. de leon Torralba, J.M. Burke. 2018. Multiple genomic regions influence root morphology and seedling growth in cultivated sunflower (Helianthus annuus L.) under well-watered and water-limited conditions. Plos One, 13(9): e0204279.

Early Career Professionals to ASPB Committees: https://blog.aspb.org/early-career-professionals-to-aspb-committees/

Resources for Early Career Scientists by the Union of Concerned Scientists: https://www.ucsusa.org/action/science_network/career-resources-early-career-scientists

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”.

A transcript of this episode, generously provided by Joe Stormer can be found here https://bit.ly/3bjjavz

SHOW NOTES: 

@SpicyBotrytis ‏

@ehaswell

@baxtertwi

@taprootpodcast

Corwin, J. A., Copeland, D., Feusier, J., Subedy, A., Eshbaugh, R., Palmer, C., ... & Kliebenstein, D. J. (2016). The quantitative basis of the Arabidopsis innate immune system to endemic pathogens depends on pathogen genetics. PLoS genetics, 12(2), e1005789.

Brady, S. M., Burow, M., Busch, W., Carlborg, Ö., Denby, K. J., Glazebrook, J., ... & Springer, N. M. (2015). Reassess the t test: interact with all your data via ANOVA. The Plant Cell, tpc-15.

Additional Papers Mentioned:

Stoeger, T., Gerlach, M., Morimoto, R. I., & Amaral, L. A. N. (2018). Large-scale investigation of the reasons why potentially important genes are ignored. PLoS biology, 16(9), e2006643.

Su, A. I., & Hogenesch, J. B. (2007). Power-law-like distributions in biomedical publications and research funding. Genome biology, 8(4), 404.

Edwards, A. M., Isserlin, R., Bader, G. D., Frye, S. V., Willson, T. M., & Frank, H. Y. (2011). Too many roads not taken. Nature, 470(7333), 163.

Monroe, J. G., Powell, T., Price, N., Mullen, J., Howard, A., Evans, K., ... & McKay, J. (2018). Drought adaptation in nature by extensive genetic loss-of-function. bioRxiv, 372854.

Terminology:

GWAS - Genome Wide Association Mapping; a method of looking at the association between genetic markers which we will call SNPs (Single Nucleotide Polymorphisms) in this discussion

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