The Taproot

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.

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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

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.

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Read more about this episode:

https://plantae.org/taproot-s2e1-phenotyping-roots-without-pulling-up-your-own-with-guillaume-lobet/

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SHOW NOTES

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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

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