September 2024 – December 2024

Past September, our lab welcomed new postdoc, Dr Danielle Stevens, who brings her expertise in pattern recognition receptors and their bacterial ligands. Danielle will be investigating natural variation in immune responses across plants as well as building ML models for predicting immunogenicity of bacterial ligands and receptor recognition profiles.

Boyan Xu‘s paper on structure-aware annotation of leucine-rich repeat domains and smart use of maths in biology has been published

• Xu B, Cerbu A, Tralie CJ, Lim D, Krasileva K. Structure-aware annotation of leucine-rich repeat domains. PLoS Comput Biol. 2024 Nov 5;20(11):e1012526. doi: 10.1371/journal.pcbi.1012526. PMID: 39499733

Several members of the Krasileva Lab presented their work at local conferences including Inside IGI, Center for Computational Biology (CCB) retreat, and Bay Area Population Genetics Conference and won several awards!

• Wei Wei and Chandler Sutherland were each awarded Best Poster Award at the 2024 CCB retreat.
• Danielle Stevens won Best Poster Award at XXIII Bay Area Pop. Genetics Conference.

Then, several Jedis in our lab joined forces to review the rise of the plant immune resistance at DNA, RNA, and protein levels 💫🚀 check out the preprinted review here: zenodo.org/records/1420.7051

Undergraduate Luyang Zhang received a SPUR Award on understanding the impact of DNA repair pathways on mutation accumulation with her mentor, Chandler Sutherland.

This December, we also welcome our newest grad student cohort in the lab, Nicole Marie Dubbs and Jude Edwards

August 2024

We bid farewell to Rakesh Kumar who has been a postdoc and then staff scientist in the lab for the past two years. Rakesh is moving to USDA, Albany. Rakesh will stay as an affiliate with the lab and continue working on wheat, including some joint projects.

The 9th annual Krasileva Lab retreat, 2024 was at the Russian River. We forward planned our year, discussed strengths, weaknesses, opportunities and threats in the lab, cooked, hiked and enjoyed time together.

New and updated lab publications and pre-prints!

Kyungyong Seong, Wei Wei, Brandon Vega, Amanda Dee, Griselda Ramirez-Bernardino, Rakesh Kumar, Lorena Parra, KseniaKrasileva “Engineering the plant intracellular immune receptor Sr50 to restore recognition of the AvrSr50 escape mutant” bioRxiv 2024.08.07.607039; doi: https://doi.org/10.1101/2024.08.07.607039

Prigozhin DM, Sutherland CA, Rangavajjhala S, Krasileva KV. “Majority of the highly variable NLRs in maize share genomic location and contain additional target-binding domains“. Mol Plant Microbe Interact. 2024 Jul 16. doi: 10.1094/MPMI-05-24-0047-FI. Epub ahead of print. PMID: 39013614

China Lunde, Kyungyong Seong, Rakesh Kumar, Andrew Deatker, Bhavit Chhabra, Meinan Wang, Shivreet Kaur, Sarah Song, Ann Palayur, Cole Davies, William Cumberlich, Upinder Gill, Nidhi Rawat, Xianming Chen, Meriem Aoun, Christopher Mundt, Ksenia V Krasileva “Wheat Enhanced Disease Resistance EMS-Mutants Include Lesion-mimics With Adult Plant Resistance to Stripe Rust“ bioRxiv 2024.05.10.593581; doi: https://doi.org/10.1101/2024.05.10.593581

March and April 2024

New and updated lab publications and pre-prints!

Prigozhin DM, Sutherland CA, Rangavajjhala S, Krasileva KV “Majority of the highly variable NLRs in maize share genomic location and contain additional target-binding domains” bioRxiv 2022.10.05.510735; doi: https://doi.org/10.1101/2022.10.05.510735 Research article v2

• CoLab enabling community to analyse their own receptor and predict ligand binding site using our method: https://colab.research.google.com/github/daniilprigozhin/NLRCladeFinder/blob/main/NLRCladeFinder.ipynb

Sutherland CA, Prigozhin DM, Monroe JG, Krasileva KV. “High allelic diversity in Arabidopsis NLRs is associated with distinct genomic features“. EMBO Rep. 2024 Mar 25. doi: 10.1038/s44319-024-00122-9 Research article

Schuster M, Schweizer G, Reißmann S, Happel P, Aßmann D, Rössel N, Güldener U, Mannhaupt G, Ludwig N, Winterberg S, Pellegrin C, Tanaka S, Vincon V, Presti LL, Wang L, Bender L, Gonzalez C, Vranes M, Kämper J, Seong K, Krasileva K, Kahmann R. Novel Secreted Effectors Conserved Among Smut Fungi Contribute to the Virulence of Ustilago maydis. Mol Plant Microbe Interact. 2024 Mar;37(3):250-263. doi: 10.1094/MPMI-09-23-0139-FI. Epub 2024 Apr 3. PMID: 38416124. Research article

E. Thynne, H. Ali, K. Seong, M. Abukhalaf, M. A. Guerreiro, V. M. Flores-Nunez, R.Hansen, A. Bergues, M. J. Salman, J. J. Rudd, K. Kanyuka, A. Tholey, K. V. Krasileva, G. J.Kettles, E. H. Stukenbrock “An array of Zymoseptoria tritici effectors suppress plant immune responses” bioRxiv 2024.03.12.584321; doi: https://doi.org/10.1101/2024.03.12.584321 Research article

February 2024

Led by China Shaw, the Krasileva Lab hosted students from Latitude High School in Fruitvale. Students toured the lab, saw tomatoes expressing the marker gene RUBY, toured the UC Berkeley Bioimaging Facility and attended a science career panel.

We have also said good bye to visiting student Giuseppe Denora who was mentored by Rakesh Kumar