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Krasileva Lab

Black lives matter

231 Koshland Hall, Berkeley CA 94720 kseniak [at] berkeley.edu.

Upcoming science presentations at conferences and symposia

Main Presenter - Title - Conference information

Ksenia - "Catching the right mutation: natural and induced diversity in plant immune system" - Oklahoma State University, March 2nd 2022, invited seminar

Pierre Joubert - "The extrachromosomal circular DNAs of the rice blast pathogen Magnaporthe oryzae contain a wide variety of LTR retrotransposons, genes, and effectors" - The 31st Fungal Genetics Conference, March 15-20 2022, selected talk

Fraces (Grace) Stark - "Elucidating Fungal Immune Receptors and Testing the Potential Role of Nucleotide-binding Domain Leucine-rich Repeat-like Proteins (NLR-like) Against Bacterial Antagonists" - The 31st Fungal Genetics Conference, Asilomar March 15-20 2022, selected talk

Ksenia - TBD - Donald Danforth Plant Science Center, March 30th 2022, invited seminar

In 2022, lab members will be attending and presenting at the Fungal Genetics Conference, Maize Genetics conference, The Biology of Genomes, The Molecular Plant Microbe Interaction Congress and more. Watch this space for the announcements.

Past talks (recorded)

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 with a 3 min intro by Ksenia)

Fraces (Grace) Stark - "Fungal Immune Systems with Grace Stark" - Central Texas Mycological Society, Nov 18th 7-9PM CT invited talk. Open to public with livestream on Youtube - link to recording (~1 hr 30 min with discussion)

Ksenia - "Plant immune receptors, pathogen effectors and the evolutionary game of 'Go' that they play", North Carolina State University, Nov 1st 2021. invited seminar - link to recording (director's cut 55 min, with introduction by Prof Peter Balint-Kurti)

Ksenia - Catching the right mutation - enhanced disease resistance mutants in wheat protect against stripe rust and other pathogens, America Phytopathological Society, 2021 - link to recording (12 min)

Ksenia - The highly variable plant immune receptors and how to catch them, iCAR, 2021 - link to recording (9 min)

Pierre Joubert - Investigating the role of extrachromosomal circular DNA in fungal plant pathogen evolution - Computational Biology Departmental Retreat, Spring 2021 - link to recording (9 min)

Who we are and what we do

Krasileva lab an inter-disciplinary group of people who combine new technologies, basic and translational research. Our common goal is to understand innate immunity, a system that maintains plant health. We focus on evolution and function of immune genes, as well as the mechanisms that regulate genetic diversity in plants and fungi.

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, here is how you can approach us:

    • 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.

To read more about specific research projects visit About us and Publications.

My aspiration is to build the lab based on honesty and transparency, to ensure open communication and to maintain the highest quality of research and strongest work ethic without sacrificing our health or wellbeing of our families. Our lab culture is summarized in the Krasileva Lab Charter

If you have any questions about Krasileva Lab, do not hesitate to contact me.

- Ksenia

Lab News

December 2021 - Congratulations Erin on new preprint and completing PhD!

Congratulations to Erin Baggs for completion her outstanding dissertation this month. Dr Baggs is the 1st PhD graduate from the lab! Two of her chapters have been published or pre-printed, and two more will come to the preprint server near you in the next few months.

To read some of Erin's work, see our latest collaborative preprint with the Parker lab, in which we describe evolution and function of plant Toll-Interleukine like (TIR) proteins.

October 2021 - NIH Director's New Innovator Award & new preprint from the lab

Ksenia has been awarded NIH Director's New Innovator Award (read the announcement here) which will provide $1.5 million to the lab to fund high-risk high-reward research program "Cross kingdom health: evolution of immune receptors and their targets" for the next 5 years. Thank you NIH and congratulations to all award recipients.

In our latest preprint, Pierre Joubert describes extra chromosomal circular DNA (eccDNA) from a filamentous fungus, plant pathogen extraordinaire -  Magnaporthe oryzae.
  • Joubert PM and Krasileva KV "The extrachromosomal circular DNAs of the rice blast pathogen Magnaporthe oryzae contain a wide variety of LTR retrotransposons, genes, and effectors"

September 2021 - New grant from USDA-NIFA and welcome Ryan

We are lucky with our funding! Diversity of projects led by lab members is being matched by good funding. This month, we got awarded a 3 year grant by USDA-NIFA (joint initiative with NSF) to study "Genes and pathways that boost wheat resistance to stripe rust" using our wheat mutant lines with enhanced disease resistance. The project is currently led by an experienced geneticist China Lunde. Interested to know more and work with us? Send Ksenia an email at kseniak@berkeley.edu.

Ryan Kenneally joins the lab for his first PhD rotation to work on #project-wheat. Welcome Ryan!

July 2021 - Chandler is awarded Grace Kase-Tsujimoto Graduate Fellowship

Congratulations to Chandler Sutherland for being awarded the 2021-22 Grace Kase-Tsujimoto Graduate Fellowship for her exceptional academic and rotation performance during first year as a graduate student. Chandler joined our lab to study evolution and diversity generation mechanisms in plant immune receptors.

The Grace Kase-Tsujimoto Fellowship celebrates Mr. Harry Tsujimoto's (Grace Kase's husband) long and productive affiliation with and career at UC Berkeley. After graduating from Cornell, Mr. Tsujimoto received a Master of Science degree with the late Professor Daniel Arnon and continued working closely with him in the then Cell Physiology department for over 30 years. After his retirement, Mr. Tsujimoto and his wife, Grace Kase, established the K/T Foundation that set up an endowment in our department to provide ongoing support for the Grace Kase fellowship and the annual Tsujimoto and Buchanan Lectures.

July 2021 - Wow Grace!

Congratulations to Frances (Grace) Stark for winning a highly prestigious Graduate Level Scholarship at the Sonoma County Mycological Association. Grace, a molecular mycologist and PhD candidate in our lab, will give an invited lecture in January at the SOMA camp alongside biggest mycology experts (check here for updates).

Grace defended her QE on fungal-bacterial interactions in April*, a project she brought to Krasileva laboratory and is developing very rapidly into a fantastic study. She is open, collaborative, and you can find her project description (Do fungi also have innate immune responses?) here

You can also follow Grace into the world of all things fungi and more on Instagram @the_molecular_mycologist

*we gathered to celebrate Grace's quals in April at the UC Berkeley Botanical Gardens - the first time we saw each other in person since the lockdown

June 2021 - Congrats to Boyan Xu for passing his QE

Boyan Xu successfully defended Qualification Exams in the areas of Biological Sequence Analysis, Machine Learning and Topology. Congrats to our newest PhD candidate!

May 2021 - Welcome to two new graduate students and a farewell to Mark

We welcome two graduate students who joined the lab this May after completing their rotation year. Kyungyong Seong joins us as a Microbiology student with Designated Emphasis in Genomics and Computational biology. Chandler Sutherland joins us as a Plant Biology student, also with a deep interest in genomics and genome evolution.

We are also saying farewell to Mark Tiersma, who is graduating with BA degree in Molecular and Cell Biology with an emphasis in genetics. After spending two year doing research with us, Mark will be now joining  Prof Maya Kasowski lab at Stanford as a predoctoral laboratory technician working on single cell genomics.

January 2021 - starting the year strong with preprints and publications

It is exciting to start the new year with several publications.

We are opening the year with new age of computational structural genomics, led by Kyungyong Seong and accomplished during his rotation. In his preprint, Kyungyong shows the power of latest machine learning algorithms and high throughput structure predictions to cluster virulence factors that are highly divergent in their sequences and to uncover new patterns of their evolution.

A paper started last year on phylogenomics and using information theory plus structural analyses to identify highly variable NLRs and predict their rapidly evolving ligand binding sites, is now published (and includes 2.5 new figures that were not in the original preprint):

Erin Baggs' analyses of immune receptors in maize are included in this latest preprint:

  • Hufford MB, Seetharam A, Woodhouse M, Chougule K, Ou S, Liu J, Ricci WA, Guo T, Olson A, Qiu Y, Coletta RD, Tittes S, Hudson AI, Marand A, Wei S, Lu Z, Wang B, Wang N, Kim D, Zeng Y, Piri R, O’Connor C, Li X, Gilbert A, Baggs E, Krasileva KV, Portwood J, Cannon E, Andorf C, Manchanda N, Snodgrass S, Hufnagel D, Jiang Q, Pedersen S, Syring M, Kudrna DA,  McGaugh S, Schmitz RJ, Llaca V, Fengler K, Ross-Ibarra J, Yu J, Gent JI, Hirsch CN, Ware D, Dawe RK "De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes" bioRxiv Jan 2021 https://doi.org/10.1101/2021.01.14.426684 Research article

December 2020 - The plant that lost its NLRs

Congratulations to Erin Baggs on collaborative work on a duckweed Wolffia! Wolffia is one of the plant species that has fewest NLRs (only 1 left), yet it is resistant to pathogens.

November, 2020 - Welcome Lorena, Kyungyang, Boyan and Dean

Lorena Parra joined us this month as a postdoc on a grant funded by Foundation for Food and Agriculture Research, 2Blades Foundation and Innovative Genome Institute to improve disease resistance in wheat. Dr Parra obtained her PhD in University of California, Davis, working with Prof Richard Michelmore. In her project with us, she will establish high throughput assays for engineering new NLR binding specificities.

We are hosting graduate students for rotations this year despite all obstacles. Kyungyong Seong, Boyan Xu and Dean Pettinga join for the second rotation. They come from different programs: Microbiology, Plant Biology and Math, respectively, yet all are computational biologists - this is the power of cross cutting research. Welcome to the virtual reality of our lab today, and we hope for safe interactions in person in 2021!

October, 2020 - Ksenia joins UC Berkeley Center for Computational Biology

UC Berkeley Center for Computational Biology (https://ccb.berkeley.edu) is a unique interdisciplinary hub of faculty and students from over 12 departments that are united by common research interest and hold events, seminar and retreats together. The center offers a Computational Biology PhD program (link) as well as an opportunity for graduate students from any UC Berkeley department to join the Center through the Designated Emphasis in Computational Biology (DE link). Pierre Joubert in our lab is part of the DE program. It's exiting to join this rich community!

September, 2020 - Welcome Anne Nakamoto and Yiling Fang (and welcome back Mark and Daniel)

As the pandemic affects all aspects of our lives, we strive to provide the training to undergraduates that we can. Anne Nakamoto, an undergraduate student in MCB with minor in Computer Science and a URAP student joins Pierre Joubert on a computational project. Anne will be working on genomics of a devastating (and fascinating) fungal pathogen of wheat, Magnaporthe oryzae. Mark Tiersma and DanielChoAhn come back also as URAP students to work with Erin Baggs on duckweed.

Yiling Fang, 1st year graduate student in Plant Biology, joins the lab for a 10 week rotation to work on NLR designs with Janina Tamborski.

July, 2020 - Collaborative preprint on NLR phylogenomics and binding sites prediction

A new preprint from the lab (link). We applied phylogeny-based clustering and information theory to examine the evolution of plant NLR immune receptors. The question we sought to answer was: how can plants with only innate immune receptors develop new recognition specificities? We found that a subset of plant NLRs are highly variable and this variation mostly clusters on the surfaces of their C-terminal LRR and post-LRR domains. We also made a key observation that recognition of plant's own molecules adapted for indirect recognition of pathogen activity on the cell evolved as a functional byproduct of direct recognition of any molecules (mostly used to catch pathogen-derived proteins). This unifies a previously proposed 'Birth and Death' theory of plant immunity evolution (Michelmore and Meyers, 1998) with current understanding of how these receptors function inside the cell.

This study is a product of long-term discussions with Daniil Prigozhin who has been trained in mathematics, molecular and cellular biology and structural biology and is currently a project scientist at LBNL (and for full COI disclosure, Ksenia's husband).

June, 2020 - Lab statement against racism

In Krasileva Lab, we condemn any racist actions, opinions and behavior. We aim to be proactively anti-racist and help to introduce structural and societal change.

Please, take a minute to read a powerful message written by Marco Lindsey, Associate Director of Diversity, Equity and Inclusion at the Haas School of Business "Thoughts from your Black colleague"

If you do not have time, this is the essence: "If you read no further, understand this: Black Lives Matter = if anyone kills a Black person, their punishment should be the same as if they killed someone from any other race."

June, 2020 - A new paper led by Erin comes out in The Plant Cell

We have a new publication from the lab (link). Conceptualized and led by a graduate student Erin L Baggs, our new study provides a comparative analysis of plant immune receptors and signaling pathways across plants. Erin discovered that at least five plant species that belong to different lineages, including duckweed and asparagus, convergently lost most of NLR immune receptors as well as a key EDS1/PAD4 signaling pathway. Erin took this analysis further to look for other genes convergently lost in these species and predicted other possible components of plant immunity. She also uncovered an intriguing link between immunity and drought response that connects these genes on a transcriptional level.

Baggs et al Plant Cell "Convergent Loss of an EDS1/PAD4 Signaling Pathway in Several Plant Lineages Reveals Co-evolved Components of Plant Immunity and Drought Response" The Plant Cell 2020 (link)

Recognizing Plant Cell authors: Erin Baggs (link)

Plantae IN BRIEF: ASTREL Projection: Comparative Phylogenomics Uncovers Novel Genes Co-eliminated with the EDS1 Immune Pathway (link)

May, 2020 - New PhD student joins the lab

A very warm welcome to Frances (Grace) Stark who joins the lab this year. Grace got her BSc in University of Texas at Austin. She is "a mycologist fascinated by plant/fungal symbioses and the molecular mechanisms driving their relationships!" Whoo hoo!

April, 2020 - A collaborative pre-print: Wolffia genome has only 1 NLR left

Todd P. Michael, Evan Ernst, Nolan Hartwick, Philomena Chu, Douglas Bryant, Sarah Gilbert, Stefan Ortleb, Erin L. BaggsK. Sowjanya Sree, Klaus J. Appenroth, Joerg Fuchs, Florian Jupe, Justin P. Sandoval, Ksenia V. Krasileva, Ljudmylla Borisjuk, Todd C. Mockler, Joseph R. Ecker, Robert A. Martienssen, Eric Lam "Genome and time-of-day transcriptome of Wolffia australiana link morphological extreme minimization with un-gated plant growth" bioRxiv April 2020 (link)

Our analyses of the genome of a duckweed Wolffia reveals a single canonical NLR (plus 2 non-canonical) in its reductionist immune system. NLR work by Erin L. Baggs.

March, 2020 - Collaborative paper describes NLR in wheat

Burkhard Steuernagel, Kamil Witek, Simon G. Krattinger, Ricardo H. Ramirez-Gonzalez, Henk-jan Schoonbeek, Guotai Yu, Erin Baggs, Agnieszka Witek, Inderjit Yadav, Ksenia V Krasileva, Jonathan D Jones, Cristobal Uauy, Beat Keller, Christopher James Ridout, Brande B Wulff "The NLR-Annotator tool enables annotation of the intracellular immune receptor repertoire" Plant Physiology March 2020 (link)

This paper describes a new tool, NLR-Annotator developed by Dr Burkhard Steuernagel that can mine for NLR motifs in unannotated genomes. We have used NLR-Annotator on a number of genomes in our studies, and find it very useful and complementary to other approaches, such as domain-based searches implemented in plant_rgenes. We now routinely use NLR-Annotator as a quality check of NLR annotations in proteomes.

Secondly, this paper carefully catalogs NLRs in hexaploid wheat and provides an annotated phylogeny which is openly available in interactive mode (link).

February, 2020 - New review article from our lab

Janina Tamborski and Ksenia Krasileva "Evolution of Plant NLRs: From Natural History to Precise Modifications" Annual Review of Plant Biology v71, 2020 (link)

January, 2020 - Welcome China Lunde Shaw, our new lab manager!

Joseph Brodsky once said "A school is a factory is a poem is a prison is academia is boredom, with flashes of panic" (J. Brodsky, Less than One, 1976). We are excited for China to join our lab, she will keep down our flashes of panic when it comes to lab organization, ordering and running the lab while enjoying the bits of poetry that is research.

The Gordon and Betty Moore Innovator 2019 Fellowship

We are thrilled to have our first grant at UC Berkeley. Ksenia and our lab were selected as one of only 5 recipients of the grant this year. The grant is focused on sustainable agriculture and boosting plant health through new protein engineering approaches (akin to antibody therapy for us humans) that will be able to recognize invading pathogens. This project stems directly from our discovery of plant immune receptors naturally prone to new protein fusions that can function as 'baits' for the pathogen.

Read The Gordon and Betty Moore Foundation announcement.

Pierre awarded Grace Kase Fellowship

Congratulations Pierre on receiving Grace Kase Graduate Fellowship Award 2019-2020 to investigate evolution of 'Genomes under stress'.

New preprint: What genomics can tell us about aquatic vs terrestrial plant lifestyle

Erin Baggs has her new paper out on bioarxiv preprint: "Convergent gene loss in aquatic plants predicts new components of plant immunity and drought response"

Welcome our first rotation students at Berkeley!

Two new students, Pierre Joubert (microbiology) and Lorenzo Washington (plant) start their 3rd rotation with us today. Welcome to the Lab.

Other News