Ksenia Krasileva, Professor

Closed (1) Characterising the impact of individual pathogen proteins on duckweed

Closed. This professor is continuing with Spring 2021 apprentices on this project; no new apprentices needed for Fall 2021.

Plants are in a constant battle with pathogens, which greatly outnumber them in the environment. We are interested in how plants are capable of recognising pathogens and in doing so are able to prevent disease. Historically, research has focused on the model plant Arabidopsis thaliana, however the presence of multiple overlapping immune pathways in this species has made it tricky to define the contribution of individual pathways. Our lab previously identified the loss of a major immune pathway in duckweed and plan to utilise this simplified system to further our research on plant immunity. This project will allow a student to investigate duckweeds response to the bacterial plant pathogen Pseudomonas syringae and its virulence molecules called effectors.

The student will need to learn to make sterile media, handling of duckweed, pathogen cultivation, pathogen inoculation and triparental mating to introduce effectors of interest into an effectorless pathogen. The student will be expected to visually identify difference in disease symptoms of duckweed caused by different effectors. The student would also be expected to interpret the virulence consequence of effectors based on visual symptoms and difference in growth rate of innoculated duckweed compared to control plants. The project would require a commitment of 12 hours per week. This project would suit a student interested in plants, molecular biology, immunity and genetics.

Day-to-day supervisor for this project: Erin Baggs , Graduate Student

Qualifications: Basic Laboratory Skills (Bio1A or equivalent)

Weekly Hours: 12 or more hours

Related website: https://krasilevalab.org/

Closed (2) Natural diversity of plant immune receptors

Closed. This professor is continuing with Spring 2021 apprentices on this project; no new apprentices needed for Fall 2021.

Plants have powerful defense mechanisms, which rely on an arsenal of plant immune receptors. A major class of plant immune receptors is Nucleotide Binding Leucine Reach Repeat (NLR) proteins. On the population level, NLRs provide plants with enough diversity to keep up with rapidly evolving pathogens and activate plant immune defenses. How such diversity is generated on the genomic level is not fully understood. The NLR copy number varies in plants from 20-30 in cucumbers to over 2,000 in wheat. This project will use evolutionary and bioinformatics approaches to examine newly sequenced NLR repertoires from 60 wheat species, including wild relatives and domesticated lines. The project will focus on analyzing two types of diversity: 1) structural variation in an NLR clade which evolves rapidly through new gene fusions (that serve as ‘baits’ for the pathogen) and 2) allelic variation in highly variable NLR genes.

Day-to-day supervisor for this project: Pierre Joubert

Qualifications: To do this data analyses, we are looking for student candidates from all backgrounds, that already have experience in Python, bash, or R. The student is expected to work with large datasets using high performance computers. Understanding basic principles of genomics and next generation sequencing is beneficial but not required. This project would suit a student interested in comparative genomics and bioinformatics, computational biology, evolution.

Weekly Hours: 9-11 hrs

Closed (3) Bioinformatics project on the adaptation of fungal plant pathogens to plant defenses

Closed. This professor is continuing with Spring 2021 apprentices on this project; no new apprentices needed for Fall 2021.

Fungal plant pathogens pose a great threat to food security worldwide by causing major yield losses in agriculture. While the development of genetically modified crops that are resistant to these diseases offers an appealing solution, these often only have short term impacts as the pathogens can rapidly adapt to these new defenses. A better understanding of how these pathogens adapt to plant defenses so quickly is vital to implementing disease prevention strategies in the future.

Genomic studies have revealed many interesting characteristics of fungal plant pathogen genomes that could contribute to their adaptability including accessory chromosomes, lineage specific genomic compartments, and the prevalence of transposable elements (TEs). We are interested in gaining a more mechanistic understanding of this adaptability with the hypothesis that TEs actively and passively contribute to genomic plasticity in these fungi.

This project will start with identifying the location and identity of TEs in the genome of Magnaporthe oryzae, the causal agent of the rice blast disease and one of the most important pathogens in agriculture today. We will then answer the following questions:
• How does TE content vary between strains of M. oryzae?
• How do TEs contribute to the evolution of disease-causing genes in M. oryzae?
• How does TE activity change during different stages of infection?

Skills the student will learn through this project include, but are not limited to:
• Using bioinformatics software on the command line
• Writing scripts in bash to automate data processing and visualization
• High performance computing and usage of the UC Berkeley computing cluster
• Understanding of genomics and computational biology

Day-to-day supervisor for this project: China Lunde Shaw, Graduate Student

Qualifications: The student must be a 2nd year or above with a good understanding of genetics and molecular biology. No prior experience required but familiarity with computers and troubleshooting is greatly appreciated as well as any experience with coding. Student should be highly motivated and willing to work independently but not afraid to ask many questions. Student should also be prepared and willing to contribute own ideas and experiments to the project once the project is well under way. The student is expected to dedicate approximately 10 hours a week to the project with flexible hours aside from weekly Zoom meetings with the mentor.

Weekly Hours: 9-11 hrs

Off-Campus Research Site: remote

Closed (4) Characterization of wheat mutants with enhanced resistance to yellow stripe rust

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The Krasileva Lab is looking for an URAP student interested in genetic resistance to pathogens to help characterize a collection of previously identified enhanced disease resistance (EDR) to yellow rust wheat mutants. Stripe rust of wheat (also known as yellow rust) is prevalent throughout the world and causes devastating crop pandemics. The disease is caused by an obligate biotrophic fungus, Puccinia striiformis f. sp. tritici. A combination of economic modeling and field observations estimated that at least $32M USD annual expenditure toward development and deployment of stripe rust-resistant varieties is well-justified to offset yield losses ($979M USD annually). The mutants were created using EMS, and the resulting mutations have been sequenced.

Training will include but not be limited to isolation of nucleic acids, gel electrophoresis, microscopy and plant care. Characterization will include comparing the mutants grown in difference temperatures and their responses to pathogen infection. Early tasks will be routine but with successful completion, initiation of an independent research project is desirable. Summer work would be available to students remaining near Berkeley over the break. Students may also work with bioinformatics methods to do mapping by sequencing and perform downstream data analyses of long-read (Nanopore) sequencing datasets. The project requires a commitment of 9 – 12 hours weekly to be split between lab, greenhouse and home projects including data analysis and image analysis. Successful candidates will show careful attention to detail., Staff Researcher

Qualifications: Careful attention to detail is required. Basic Laboratory Skills (Bio1A or equivalent) desired but not required.

Weekly Hours: 9-11 hrs

Related website: https://krasilevalab.org/
Related website: https://scholar.google.com/citations?hl=en&user=zo9TVCoAAAAJ