iiinova — where your digital self keeps evolving

Leonardo Jo @leonardojo.bsky.social · 04/05/2026

Less than a week left to apply! Come join us at UU Plants!

Leonardo Jo @leonardojo.bsky.social · 16/04/2026

I'm very excited to announce that the Jo Lab is hiring our FIRST EVER PhD candidate! f you're eager to drive discovery in plants, join us at UU Plants! More info: www.uu.nl/en/organisat... Lab website: thejolab.org #Plantbiology #Phd #Job

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Leonardo Jo @leonardojo.bsky.social · 23/03/2026

Cross-section of a large vascular bundle in the maturation zone of a developing rice leaf Author: Sean Robertson(University of Manitoba, Canada) Diagram of Arabidopsis seedlings in control, salt (NaCl) and drought (Sorbitol) conditions Author: Kilian Duijts(Wageningen University, the Netherlands)

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Leonardo Jo @leonardojo.bsky.social · 23/03/2026

It's been a while, but I've finally found the time to included additional maps to ggPlantmap (github.com/leonardojo/ggplantmap), thanks to the contribution of the community.

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Leonardo Jo @leonardojo.bsky.social · 09/03/2026

The Jo Lab website is up! thejolab.org I expect to announce 1 PhD position and 1 Postdoc position in the spring of 2026 (April-May). Stay tuned!

thejolab.org

The Jo Lab - Home

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Leonardo Jo @leonardojo.bsky.social · 09/01/2026

Thanks Li!! I hope we can collaborate in the future!!

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Leonardo Jo @leonardojo.bsky.social · 08/01/2026

Since starting grad school I have dreamed about this moment and I hope to inspire the next generation of plant biologists with the same patience, care and dedication shown to me by the many mentors and colleagues who guided me throughout my journey. Thank you very much for all the help and support!

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Leonardo Jo @leonardojo.bsky.social · 08/01/2026

I'm super excited to join the Plant Stress Resilience group chaired by Rashmi Sasidharan. My research will focus on understanding how the interaction between transcription factors and chromatin states shape plant environmental responses.

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Leonardo Jo @leonardojo.bsky.social · 08/01/2026

I'm very happy to announce that starting February 2026, I'm joining Utrecht University as an Assistant Professor!!!

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Leonardo Jo @leonardojo.bsky.social · 17/09/2024

Today we celebrated the "graduation" of our UU_plants Rclub 2024! We hope to keep empowering young researchers to improve their R skills! Special highlight for the great cake made by PhD candidate Dani (bottom left)! #Rstudio #tidyverse

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Leonardo Jo @leonardojo.bsky.social · 28/08/2024

It took me SEVEN years to figure out that you can save a ggplot as a vectorized .svg file ggsave("file.svg"). The svg file can be opened on pptx/ai/inkspace and it will be completely vectorized, even text are still recognized as text boxes! No more recreating plots on illustrator!!!!

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Leonardo Jo @leonardojo.bsky.social · 05/08/2024

Very happy to share this review with @mnodine1 www.sciencedirect.com/science/arti... Here, we describe what is known (or unknown) about the mechanisms of chromatin reprogramming during the early embryogenesis in plants. A lot of exciting questions that still need to be explored. #plantbiology

sciencedirect.com

“To remember or forget: Insights into the mechanisms of epigenetic reprogramming and priming in early plant embryos”

Chromatin is dynamically modified throughout the plant life cycle to regulate gene expression in response to environmental and developmental cues. Alt…

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Reposted by Leonardo Jo

Kaisa Kajala @kaisakajala.bsky.social · 05/06/2024

Our course Plant Development & Environment 🌱 was the highest rated level 3 in BSc Biology! I love the enthusiastic 🤩 students & the excellent teachers 🙏@daanweits @leonardojo.bsky.social @andruromanowski.bsky.social @dkawa.bsky.social @rsasidharan.bsky.social @viktoriiavoloboeva.bsky.social

Bouquet of flowers and a framed certificate for the best student evaluations

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Leonardo Jo @leonardojo.bsky.social · 16/04/2024

I'm relatively new to building shiny apps, so any comments and suggestions would be greatly appreciated! You can open a ticket on github or send me an email: l.jo@uu.nl Thanks for the help!

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Leonardo Jo @leonardojo.bsky.social · 16/04/2024

It's really raw, but I would like to ask people to try this out on their own ggPlantmaps to see potential errors that can occur. A link for the beta test instructions: github.com/leonardojo/g...

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Leonardo Jo @leonardojo.bsky.social · 16/04/2024

[Beta test] ggPlantmap + shinyapp. Seeking help from the community: I created a function that allows users to create interactive shiny apps to navigate through multiple values (ex: genes) on top of their #ggPlantmap.

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Leonardo Jo @leonardojo.bsky.social · 11/04/2024

OMG! My great mentor John Harada is the recipient of the @aspbofficial.bsky.social Stephen Hales award 2024! This is HUUUGE! He just entered the plant biology hall of fame! Im so happy for him!

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Leonardo Jo @leonardojo.bsky.social · 10/04/2024

The EPS best mentor award goes tooooo.. @kaisakajala.bsky.social !! I'm a bit biased but I believe it was really well deserved!!! 🤣

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Leonardo Jo @leonardojo.bsky.social · 04/03/2024

The final version of the ggPlantmap is out at @JXBot academic.oup.com/jxb/advance-... Come for the information, stay for the beautiful figures! We hope it can encourage people to create their own eFP-viewer!

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Leonardo Jo @leonardojo.bsky.social · 14/02/2024

I'll be happy to try something out if you have already a sample file! Let me know if you have something in mind! All the best!

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Leonardo Jo @leonardojo.bsky.social · 14/02/2024

Hello Javier, It would be super nice to have an automated tool, but finding one-fit-all segmentation tool would be really challenging. What I wanted to try is to check the output file of different automated tracing tools (microscopic, leaf shape,etc) and check how to convert them into a ggplot map.

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Reposted by Leonardo Jo

Hao Yin @haoyin.bsky.social · 13/02/2024

ggPlantmap github.com/leonardojo/g... Convert Icy-traced Plant images into ggPlot Integrable with bulk or sc-RNAseq data Generate .svg for Plant eFP viewer @jxbotany.bsky.social 2024 academic.oup.com/jxb/advance-...

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Leonardo Jo @leonardojo.bsky.social · 07/02/2024

aRt: Building a root barrier. Built using: ggPlantmap and rayshader #plantbio #bioart

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Leonardo Jo @leonardojo.bsky.social · 28/01/2024

This work was co-authored with Julie Pelletier, and concludes the main works I've done during my PhD in John's lab! We hope that this data is useful for people! Let me know if you have comments or suggestions, I'll be happy to address them.

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Leonardo Jo @leonardojo.bsky.social · 28/01/2024

GmWRI1 and GmLEC1 target each other in a positive forward loop to promote FA biosynthesis in seeds. We explored a bit the relationship between these two "master" regulators of seed lipid biosynthesis.

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Leonardo Jo @leonardojo.bsky.social · 28/01/2024

In a transient expression system, we evaluated the function of each motif in GmWRI1 binding sites. To our surprise, mutations in the AW-Box not always resulted in the reduction of enhancer activity, and mutations in the CNC-Box affected the transactivation of CAC2 by GmWRI1.

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Leonardo Jo @leonardojo.bsky.social · 28/01/2024

To further confirm these results, we identified the list of downregulated genes in the Arabidopsis wri1 mutants and upregulated genes by overexpressing GmWRI1 and identified that indeed, both AW-Box and CNC-Box to be enriched in regions downstream the TSS in Arabidopsis as well.

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Leonardo Jo @leonardojo.bsky.social · 28/01/2024

Motif analysis revealed the presence and enrichment of the AW-Box in WRI1 binding sites. It has been shown that this element is bound by WRI1 in vitro. Interestingly we found the presence of another element that we called CNC-Box (CNCCNCC).

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Leonardo Jo @leonardojo.bsky.social · 28/01/2024

When looking at the binding pattern of WRI1, we found that this TF binds preferentially at regions downstream the TSS. This pattern is different from other TFs we studied in the past (LEC1). What could be mechanistic and evolution relevance of this binding pattern?

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Leonardo Jo @leonardojo.bsky.social · 28/01/2024

After many failed attempts, we finally obtained a good GmWRI1 antibody that allowed us to perform a ChIP-Seq that passed ENCODE QC. With this dataset identified the list of potential target genes of GmWRI1 As expected, these genes encoded for many lipid related genes in seeds.

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Leonardo Jo @leonardojo.bsky.social · 28/01/2024

It is a pretty descriptive work, but we hope to provide resources and insights that can help people who are studying ways to improve oil content in seeds. We will make all the datasets (ChIP-seq, RNA-seq) available upon final publication.

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Leonardo Jo @leonardojo.bsky.social · 28/01/2024

I’m happy to finally submit the final chapter of my PhD dissertation. Here we studied a very known TF in the field of seed lipid content - WRINKLED1. To our surprise, this was the first comprehensive study of genome-wide binding pattern of WRI1. #plantbio #seeds #lipids

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Leonardo Jo @leonardojo.bsky.social · 17/01/2024

I would love to see ggPlantmaps created by the community being uploaded into biocons (bioicons.com) or plant illustrations (figshare.com/authors/Plan...) Can't wait to see! #ggPlantmap #bioicons #dataviz

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Leonardo Jo @leonardojo.bsky.social · 17/01/2024

Note: ggPlantmap small update (v1.1). ggPlantmap.to.SVG() converts your ggPlantmap into a SVG file that is compatible with an ePlant EFP pipeline or any graphic software (like powerpoint). The polygons will be grouped based on an assigned column.

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Reposted by Leonardo Jo

Ronald Pierik @ronaldpierik.bsky.social · 23/12/2023

Our latest preprint: postdoc Pierre Gautrat devoted his EMBO fellowship to resolving how nutrient and light cues interact to control shade avoidance. With @andruromanowski.bsky.social. The answer is PIF-dependent regulation of cytokinin response regulators. Read all about it in this preprint.

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Leonardo Jo @leonardojo.bsky.social · 19/12/2023

If you use the background_image() function from ggpubr (rpkgs.datanovia.com/ggpubr/refer...), you can display your ggPlantmap on top of a image. There is a small y-axis offset, but it can do the trick. I will work on implementing this function whenever I have some free time. #ggPlantmap

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Leonardo Jo @leonardojo.bsky.social · 15/12/2023

As long as the candidate doesnt fail miserably during the demonstration (really rare cases), being an average or inexperienced teacher is easily acceptable. This standard is never true when discussing research.

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Leonardo Jo @leonardojo.bsky.social · 15/12/2023

Based on a few experiences I had: Requiring teaching statements/talks doesn't necessarily mean teaching is taken seriously for the hiring committee. More often research is the focus. Teaching often comes as an accessory that can be ignored if the candidate has an excellent research track.

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Leonardo Jo @leonardojo.bsky.social · 15/12/2023

This is just sad, but not at all surprising. R1 hiring is all about grants and research, and let's hope the top candidate actually care about teaching. Oh, look, in their teaching statement they mentioned active learning and critical thinking. Thats good enough right?

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Leonardo Jo @leonardojo.bsky.social · 06/12/2023

Contrary to my previous belief, root size doesn't seem to determine the number of xylem poles. Legume roots of different "thickness" can display 3 or 4 xylem poles. What could be the genetic basis (evo-devo) of different xylem pole numbers? #rootbiology #plantbiology

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Leonardo Jo @leonardojo.bsky.social · 04/12/2023

Our ggPlantmap manuscript is out at biorxiv. A bit awkward writing it honestly, but we made it! At the same time, I've seen some people using it and creating nice maps! I hope it empowers people to find new ways to explore their data!

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Leonardo Jo @leonardojo.bsky.social · 10/11/2023

Great work by bachelor student Martijn Posthumus during his 10-week internship. He built tagged versions of GFP that are transported to different cellular compartments. We will use it to study protein sub-cellular localization in plants. #plantbiology #protoplasts #GFP

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