Lightnews — Scholar-powered news

Uriel Urquiza-Garcia

@uurquiza.bsky.social

270 followers 180 following 25 posts

Interested in programming plants with DNA, currently building a Plant Artificial Chromosome and Plant Synthetic Genomics developer|CEPLAS https://www.synthetic-biology.hhu.de/research/urquiza-group

www.synthetic-biology.hhu.de

Posts Media Videos Starter Packs

Pinned

Uriel Urquiza-Garcia @uurquiza.bsky.social · Feb 20

Abundant clock proteins point to missing regulation in the plant circadian clock www.embopress.org/doi/full/10.... first experimental determination of the abundance of transcription factors in Plants and for the circadian clock. It was such a challenge but finally out after peer review !!!

Abundant clock proteins point to missing molecular regulation in the plant circadian clock | Molecular Systems Biology

imageimage~100,000 copies of plant circadian clock proteins per cell were predicted from RNA levels and included in detailed models. Protein levels and DNA-binding were validated, using NanoLUC report...

www.embopress.org

1 8 14

Uriel Urquiza-Garcia @uurquiza.bsky.social · Aug 30

Chemically ?

Reposted by Uriel Urquiza-Garcia

Marcel Dickmanns | 🌿❄️🔬 @madic.bsky.social · Jul 26

Our #cryoET of #plasmodesmata preprint is out! Will write more on it later. 🌿❄️

bioRxivpreprint @biorxivpreprint.bsky.social · Jul 25

In situ architecture of plasmodesmata suggests mechanisms controlling intercellular exchange https://www.biorxiv.org/content/10.1101/2025.07.24.666190v1

1 7 23

Uriel Urquiza-Garcia @uurquiza.bsky.social · Jun 25

Bringing back to life some 10 year old constructs I did during my PhD CCA1pro:NanoLUC-PEST

Reposted by Uriel Urquiza-Garcia

CEPLAS - Cluster of Excellence on Plant Sciences @ceplas.bsky.social · May 22

🎊 We made it!! @dfg.de has just announced that we have been successful with our CEPLAS III proposal in the current funding round of the Excellence Strategy! Many thanks to all our supporters! @hhu.de @unicologne.bsky.social @mpipz.bsky.social @fz-juelich.de @leibnizipk.bsky.social

15 42 110

Uriel Urquiza-Garcia @uurquiza.bsky.social · May 22

@ceplas.bsky.social continues!! Let’s continue delivering excellent plant research now SMARTe plants in dynamic environments!

Reposted by Uriel Urquiza-Garcia

Ralf Reski @reskilab.bsky.social · Mar 28

Moose – Die Gamechanger der Medizin und Forschung!
Mein Interview für #FrischeFische auf YouTube.
#Exzellenzinitiative #Moose #Medizin #Evolution #Forschung #scicomm #wisskomm
@cibss.bsky.social #livMatS @biologyunifreiburg.bsky.social
www.youtube.com/watch?v=JzgL...

🌱 Moose – Die Gamechanger der Medizin und Forschung! 🌱

YouTube video by Gary Silver

www.youtube.com

1 5 7

Reposted by Uriel Urquiza-Garcia

Tonni Andersen @tonnigrubeandersen.bsky.social · Mar 21

Finally!
Im so excited to present to culmination of many years of work from the fantastic Defeng Shen and some great collaborators. For details, I have made a digested thread below, but if you are more interested feel free to reach out (and read the paper of course).
www.science.org/doi/10.1126/...

Apoplastic barriers are essential for nodule formation and nitrogen fixation in Lotus japonicus

Establishment of the apoplastic root barrier known as the Casparian strip occurs early in root development. In legumes, this area overlaps with nitrogen-fixing nodule formation, which raises the possi...

www.science.org

49 110 220

Reposted by Uriel Urquiza-Garcia

Facundo Romani @fromani.bsky.social · Mar 14

After a lot of work, we are finally able to share this project about the cell cycle in Marchantia from the Haseloff lab. If you want to find out how cell division is controlled, you can’t miss out this one… #PlantScience #Synbio #EvoDevo

www.biorxiv.org/content/10.1...

The minimal cell-cycle control system in Marchantia as a framework for understanding plant cell proliferation

The regulation of cell division is broadly conserved across eukaryotes, governed by cyclins and cyclin-dependent kinases (CDKs) to coordinate progression through the cell cycle. Plants have evolved a ...

www.biorxiv.org

4 33 76

Reposted by Uriel Urquiza-Garcia

Björn Usadel @usadellab.bsky.social · Mar 14

If you are looking for published plant genomes www.plabipd.de/pubplant_mai... might be useful where Rainer is tracking species with genomes for almost 10 years now... time flies. As he has added new useful views, we thought it is time to summarize this. www.biorxiv.org/content/10.1...

1 6 15

Reposted by Uriel Urquiza-Garcia

Ralf Reski @reskilab.bsky.social · Mar 13

Our updated preprint now on bioRxiv:
Production of human papillomavirus type 16 virus-like particles in #Physcomitrella photobioreactors
www.biorxiv.org/content/10.1...

Production of human papillomavirus type 16 virus-like particles in Physcomitrella photobioreactors

Human papillomavirus (HPV) infections are the main causal agent of cervical and other anogenital cancers. Modern HPV vaccines are based on virus-like particles (VLPs), which are self-assembling nanopa...

www.biorxiv.org

5 9

Uriel Urquiza-Garcia @uurquiza.bsky.social · Mar 10

Laura Trimborn, [...] and Ute Hoecker
CRY1 inhibits the activity of COP1 by competitively displacing substrates from COP1
pubmed.ncbi.nlm.nih.gov/40052249/

Cryptochrome 1 promotes photomorphogenesis in Arabidopsis by displacing substrates from the COP1 ubiquitin ligase - PubMed

In blue light, cryptochrome photoreceptors inhibit the key repressor of light signaling, the COP1/SPA ubiquitin ligase, to promote photomorphogenic responses. This inhibition relies on the direct inte...

pubmed.ncbi.nlm.nih.gov

Reposted by Uriel Urquiza-Garcia

James Lloyd 🧬 @jamespblloyd.bsky.social · Mar 9

Our new review in @theplantjournal.bsky.social on synthetic gene circuits is out! I am super proud of this. I hope that it acts as a useful resource for people new to gene circuits.

The switch-liker's guide to plant synthetic gene circuits

onlinelibrary.wiley.com/doi/10.1111/...

The switch‐liker's guide to plant synthetic gene circuits

Synthetic gene circuits have the potential to revolutionise how plants can be engineered by allowing highly customised gene expression patterns to be designed. Gene circuits can sense and integrate m....

onlinelibrary.wiley.com

2 13 37

Reposted by Uriel Urquiza-Garcia

Leo Scheller @leoscheller.bsky.social · Feb 26

I’m happy to share that I will join the LIT in Regensburg (lit.eu) as a Group Leader in Structural Biochemistry in May. We will combine synthetic biology and protein design to develop synthetic receptors and protein therapeutics to improve immunotherapy. Job openings will be available soon!

Leibniz Institute for Immunotherapy

The LIT develops innovative therapies for the treatment of cancer, autoimmunity, and chronic inflammation by reprogramming immune cells.

lit.eu

8 5 26

Uriel Urquiza-Garcia @uurquiza.bsky.social · Mar 2

My first students in Plant Synthetic Genomics put together a nice tool for biodesign automation of random DNA fragments for synthetic genomics applications. "Gearing up Golden Braid assembly for plant synthetic genomics with RepTiles" @hhu.de @ceplas.bsky.social
www.biorxiv.org/content/10.1...

Gearing up Golden Braid assembly for plant synthetic genomics with RepTiles

We have developed RepTiles, a system for generating traces of random DNA for synthetic genomics applications. The system uses synthetic random DNA domesticated using the Phytobricks syntax. RepTiles h...

www.biorxiv.org

3 9

Reposted by Uriel Urquiza-Garcia

Sebastian S. Cocioba @atinygreencell.bsky.social · Mar 2

Hey can y'all check to see if the NCBI blastn page is working? Genbank page seems down, too. Same on your end? TYIA

www.ncbi.nlm.nih.gov/genbank/

25 6 30

Uriel Urquiza-Garcia @uurquiza.bsky.social · Mar 2

Is it my imagination or #NCBI is down? cannot access it from Germany

1 2

Uriel Urquiza-Garcia @uurquiza.bsky.social · Feb 22

@andrewmillar.bsky.social provided a very concise thread with broader vision in his thread fediscience.org/@A_J_Millar/... and for others to follow up

Andrew Millar (@[email protected])

1/8 🌱🔬 Exciting developments in biology! Our research investigates the 24-hour, biological clock in plants, now using absolute protein quantification thanks to Uriel Urquiza’s hard work with me, Kare...

fediscience.org

Uriel Urquiza-Garcia @uurquiza.bsky.social · Feb 22

Then joined Andrew and Karen Halliday for dinner down the road at their place as they hosted Mark Stitt and his group form MPI. Though before I discussed just to Andrew that we had done it we got the numbers. The rest well it is history …

Uriel Urquiza-Garcia @uurquiza.bsky.social · Feb 22

I did plate reader measurements for precise quantities and but also decided to fire up the Millar Hamamatsu EMCCD OrcaII cameras cooled down to -70 Celsius to take an image of the plates that showed the circadian pattern synopsis figure show PRR7

Uriel Urquiza-Garcia @uurquiza.bsky.social · Feb 22

Then 2 months before my hard PhD deadline finally after two rounds or circadian sampling 3 days every two hours while purifying MBP-NanoLUC-3Flag-10his standard for the freshest possible enzyme. Adding protease inhibitors and solo working with liquid nitrogen, absolute units protein profiles emerged

1 1

Uriel Urquiza-Garcia @uurquiza.bsky.social · Feb 22

Without any bench fees I could not afford to waste Furomazine for NanoLUC assays until the full circadian tome series so I was in the blind weather the fusions were fully working apart from some preliminary experiments in protoplasts that indicated correct circadian phase in transient transformation

Uriel Urquiza-Garcia @uurquiza.bsky.social · Feb 22

The models informed the selection of lines for creating new reporters using NanoLUC. Went then to rescue mutant lines for CCA1, LHY, PRR7, TOC1 and LUX. Aiming for at least 100 primary T1 events for each line which reduced to around 20 and were then used for a phenotyping FLUC rhythms.

Uriel Urquiza-Garcia @uurquiza.bsky.social · Feb 22

I managed to convince Promega for some free reagents for testing NanoLuc in plants with Andrew’s lab instruments which resulted resulted in expertise to work with it in plants plantmethods.biomedcentral.com/articles/10....

Expanding the bioluminescent reporter toolkit for plant science with NanoLUC - Plant Methods

Background Protein data over circadian time scale is scarce for clock transcription factors. Further work in this direction is required for refining quantitative clock models. However, gathering highl...

plantmethods.biomedcentral.com

Uriel Urquiza-Garcia @uurquiza.bsky.social · Feb 22

The second path heavily experimental was attempt to quantify the amount of protein. Although tagged lines existed the quantifications that could be derived from this lines seemed impossible. Andrew’s expertise pointed to the use of a new reporter luciferase form @promegacorporation.bsky.social

Uriel Urquiza-Garcia @uurquiza.bsky.social · Feb 22

However the question move into how to know if our predictions made any sense. I took a theoretical and experimental path with help from my co supervisor Nacho Molina a path for integrating genome information was set which resulted in matrix based models for binding from extent data for CCA1 and LUX