Leonardo Jo
@leonardojo.bsky.social
Postdoc fellow at Wageningen University
Gene regulatory mechanisms & plant development.
@ucdavis Alumni
First Gen. He/Him.
Gene regulatory mechanisms & plant development.
@ucdavis Alumni
First Gen. He/Him.
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
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
September 17, 2024 at 4:23 PM
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
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
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!!!!
August 28, 2024 at 3:45 PM
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!!!!
[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.
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.
April 16, 2024 at 4:23 PM
[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.
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.
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!
April 11, 2024 at 9:31 PM
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!
The EPS best mentor award goes tooooo.. @kaisakajala.bsky.social !! I'm a bit biased but I believe it was really well deserved!!! 🤣
April 10, 2024 at 6:41 PM
The EPS best mentor award goes tooooo.. @kaisakajala.bsky.social !! I'm a bit biased but I believe it was really well deserved!!! 🤣
March 1, 2024 at 5:45 PM
February 7, 2024 at 11:23 AM
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.
January 28, 2024 at 2:07 PM
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.
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.
January 28, 2024 at 2:06 PM
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.
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.
January 28, 2024 at 2:06 PM
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.
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).
January 28, 2024 at 2:05 PM
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).
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?
January 28, 2024 at 2:05 PM
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?
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.
January 28, 2024 at 2:04 PM
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.
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.
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.
January 17, 2024 at 10:16 PM
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.
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.
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
December 19, 2023 at 3:42 PM
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
You are welcome chatgpt.
December 15, 2023 at 9:08 AM
You are welcome chatgpt.
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
December 6, 2023 at 4:43 PM
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
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
#plantbiology #protoplasts #GFP
November 10, 2023 at 1:18 PM
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
#plantbiology #protoplasts #GFP
October 27, 2023 at 1:10 PM
Just a friendly reminder that I will be giving a brief overview of ggPlantmap this Thursday at 2PM (CEST). I will also discuss ways we can build a supportive community so that everyone can develop skills in R. DM if you would like to receive the link!
October 9, 2023 at 3:04 PM
Just a friendly reminder that I will be giving a brief overview of ggPlantmap this Thursday at 2PM (CEST). I will also discuss ways we can build a supportive community so that everyone can develop skills in R. DM if you would like to receive the link!