Krasileva Lab
Black lives matter
Full description of lab culture - see Krasileva Lab Charter
231 Koshland Hall, Berkeley CA 94720 kseniak [at] berkeley.edu.
Upcoming presentations
This year, we will be attending: The Plant & Animal Genome Conference, Fungal Genetics, Biology of Genomes, Gordon Research Conference on Cellular and Molecular Fungal Biology, International Plant Protection Congress, iCAR, Plant Pathology 2024
Main Presenter - Title - Conference information
Rakesh Kumar - Durum Wheat, A New Genetic Model For Forward And Reverse Disease Resistance Breeding - Plant & Animal Genome Conference, San Diego, California
Giuseppe Denora - Identification and Characterization of Potential Promoters to Engineer Rust Resistance in Wheat - Plant & Animal Genome Conference, San Diego, California
Ksenia Krasileva - Evolution in overdrive: fungal secreted proteins and innate immune genes - Fungal Genetics, Pacific Grove, California
Frances Grace Stark - Do Fungi have an Immune System? The Neurospora crassa and Pseudomonas syringae pathosystem reveals an initial cellular reaction to bacterial proximity - Fungal Genetics, Pacific Grove, California
Chandler Sutherland - Contributions of mutation and selection to the rapid evolution of plant innate immune receptors - Biology of Genomes, Cold Spring Harbor, NY
Ksenia Krasileva - Fungi as pathogens and hosts: understanding evolution of fungal secreted proteins and innate immune response - Gordon Research Conference on Cellular and Molecular Fungal Biology, Holderness, New Hampshire
Ksenia Krasileva - Evolution in overdrive: NLR diversity generation and maintenance - International Plant Protection Congress, Athens, Greece
Chandler Sutherland - Contributions of mutation and selection to the rapid, intraspecies evolution of Arabidopsis NLRs - iCAR, San Diego, California
Ksenia Krasileva - Evolution in Overdrive: Decoding and Encoding Genomes for Disease Resistance - Plant Pathology 2024, Oxford, UK
Chandler Sutherland - Distinct genomic features are associated with the rapid evolution of NLR receptors in Arabidopsis and Maize - Plant Pathology 2024, Oxford, UK
Past talks (recorded)
Scientific conferences and seminars
Pierre Joubert - "Catching up to Fungal Plant Pathogens" - Pierre Joubert Dissertation Finishing Talk, May 15, 2023 - link to recording (1 hr seminar)
Kyungyong Seong - "Elucidating effector evolution through predicted structures" MPMI Virtual Seminar - Best MPMI Graduate Student Paper Award - link to recording (30 min seminar plus Q&A)
Ksenia - "Comparative structural genomics of pathogen effectors and plant immune receptors: from natural diversity to precise modification" UC Riverside, Sept 30th, invited seminar - link to recording (1 hr seminar)
Pierre Joubert - "Characterizing the extrachromosomal circular DNAs of Magnaporthe oryzae and their potential role in adaptation" - The 31st Fungal Genetics Conference, March 15-20 2022 - link to recording (15 min talk)
Erin Baggs - "Lessons from loss; plant immune signaling pathways and pathogen interactions from land to water" - PhD finishing talk, January 13th - link to recording (46 min seminar with intro by Ksenia)
Outreach
Chandler Sutherland - "How Plants Evolve Their Immune System" The Graduates radio podcast, hosted on on KALX 90.7 link to recording
Chandler Sutherland - "It's Not Easy Staying Green: Understanding Plant Immune Systems" Ask a Science Envoy, hosted by Wonderfest: Bay Area Beacon of Science. " link to recording
Fraces (Grace) Stark - "Fungal Immune Systems with Grace Stark" - Central Texas Mycological Society, Nov 18th 2021 7-9PM CT invited talk. Open to public with livestream on Youtube - link to recording (~1 hr 30 min with discussion)
Who we are and what we do
Krasileva lab an inter-disciplinary group of people. Our common goal is to understand innate immunity; currently we are working with plants and fungi. We focus on evolution and function of immune genes, as well as the mechanisms that regulate genetic diversity. To read more about specific research projects visit About us and Publications.
The lab is located in Koshland Hall, we are part of Department of Plant and Microbial Biology as well as the Innovative Genomics Institute and The Center for Computational Biology at the University of California Berkeley.
If you are interested in joining the lab:
Undergraduate research: reach out to us directly before the semester begins or look for projects at URAP and SPUR.
Graduate students: we are part of graduate programs in Microbiology and Plant Biology as well as Center for Computational Biology. To discuss a rotation, please reach out a few weeks in advance.
Postdocs: please send Ksenia your CV and a list of postdoc fellowships you would like to apply for.
Staff: occassionally, positions become available. Please, watch this space or send us a note.
Our lab culture, summarized in the Krasileva Lab Charter, is built on honesty and transparency and open communication. We aim to maintain the highest quality of research and strongest work ethic without sacrificing our health or wellbeing of our families. If you have any questions about Krasileva Lab, do not hesitate to reach out to any lab members.
Lab News
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
September 2023 - New lab members and outreach
What a summer! We traveled to several conferences, submitted one tenure package and a few grants led both by different lab members.
We had fun at our 8th Annual Forward Planning Symposium (aka Lab retreat).
We bid farewell to Anne Nakamoto, who started PhD in Genomics and Computational Biology at UC Santa Cruz.
This fall we also welcome new lab members (https://krasilevalab.org/people/):
- Giuseppe Denora is a visiting graduate student researcher from IDEAS Innovation Development in AgriFood Systems, University of Bari Aldo, Italy. He will be working on #projectwheat transforming wheat in both literal and symbolic sense for better plant health.
- Yuting Lin, Luyang Zhang and Doogie Kim are our newest undergraduate research student apprentices trained through the URAP program at Berkeley.
In outreach news:
- Chandler Sutherland did a podcast on "How Plants Evolve Their Immune System" with The Graduates radio, KALX 90.7 link to recording
- Grace Stark is continuing to lead UC Berkeley Mycology Club. Here is the Cal Mycology Discord. You can also follow Grace's observations on iNaturalist: https://www.inaturalist.org/people/grace_stark
May 2023 - Happy graduation!
Congratulations Dr Pierre Joubert! Pierre received PhD in Microbiology with DE in Genomics and Computational Biology this spring.
You can watch his finishing talk here - link
March 2023 - Hello Spring!
Happy St Patrick's day, Spring break and other holidays!
This month, we welcome new undergraduate, Ann Palayur, who will be working with China and Rakesh on understanding and improving plant immunity in #project-wheat.
Congrats Pierre, and Kyungyong on recent preprint and publications!
It's online! Altering specificity and auto-activity of plant immune receptors Sr33 and Sr50 via a rational engineering approach doi.org/10.1094/MPMI-0 by @JaninaTamborski @KyungyongS together with @FurongLiu @bstask you all saw it first @biorxivpreprint
We have new preprint! Pathogens evolve as fast as their hosts. We looked into which genomic features are associated with rapid gene presence absence variation. Read new study by @pmjoubert to find out more:
January 2023 - Happy New Year - recent news from the lab
Happy New Year, Lunar New Year and Chinese Spring Festival to everyone.
Thumbs up to Grace for outstanding re-launch of UC Berkeley Mycology Club!
Congrats Chandler, Anne, Pierre, and Kyungyong on recent preprint and publications!
Sutherland CA, Prigozhin DM, Monroe JG, Krasileva KV “High intraspecies allelic diversity in Arabidopsis NLR immune receptors is associated with higher transcription, gene body hypomethylation, and proximity to transposable elements" bioRxiv 2023.01.12.523861; doi: https://doi.org/10.1101/2023.01.12.523861 Research article
Seong K, Krasileva KV. "Prediction of effector protein structures from fungal phytopathogens enables evolutionary analyses". Nat Microbiol.2023 Jan;8(1):174-187. doi: https://doi.org/10.1038/s41564-022-01287-6. Research article
Baggs EL, Stark FG, Tiersma MB, Krasileva KV "Pseudomonas isolates from ponds populated with duckweed prevent disease caused by pathogenic Pseudomonas species” bioRxiv 2022.12.09.519836; doi: https://doi.org/10.1101/2022.12.09.519836 Research article
Krasileva Lab News recaps
2022 lab news recap - link
2021 lab news recap - link
2020 lab news recap - link
2019 lab news recap - link