STUDYING FUNGAL GENOMES

Dr. Shira Milo Cochavi, Va’adia BARD postdoc fellow at University of Massachusetts’ department of biochemistry and molecular biology is studying genomic aspects of DNA damage and repair in fungi

What is the main focus of your postdoc work?

The aim of my postdoctoral work is to better understand genomic aspects of DNA damage and repair in the fungal pathogen Fusarium oxysporum. I am currently leading three primary projects involving both molecular biology and computational approaches. The first project studies a unique expansion of the poly(ADP) ribose polymerase (PARP) protein family in F. oxysporum. PARPs are important cellular coordinators involved in DNA repair, chromatin remodeling, transcription regulation, apoptosis and more. We’ve developed several hypotheses and are using a comparative system of different F. oxysporum strains to answer our questions. The second project studies the emergence of different races of the tomato pathogen F. oxysporum f. sp. lycopersici from an evolutionary standpoint. This project is expected to shed light on the evolutionary mechanisms that allowed this pathogen to continuously overcome host resistance and rapidly adapt to new environments. The third project focuses on the development of an efficient and reliable CRISPR/Cas9 genome editing method in F. oxysporum that can be used both for gene knockout and complementation. Joining the lab of Prof. Li-Jun Ma in U Mass Amherst has given me a wonderful opportunity to study the scientific questions that I’m interested in and at the same time learn new methods and techniques while given an endless support and encouragement.   

What got you interested in fungal genomic research?

Fungi are unique organisms in so many levels. They are extremely diverse and can be found in a wide range of environments and ecological niches. The genomes of fungal pathogens often show high plasticity and a remarkable ability to undergo genomic changes in a relatively short period of time allowing them to quickly adapt to new environments and overcome commonly used fungicides. Given their “genomic background”, pathogenic fungi can serve as a wonderful and interesting system to study evolutionary trajectories as well as the molecular mechanisms that contribute to the emergence of successful pathogens.

How did the Covid-19 pandemic impact your work?

We moved to the U.S in the middle of the pandemic and had to rebuild our life under several constraints and plenty of uncertainties. As always in life, difficulties may also open a window to new opportunities, and I must admit that I like certain work and academic customizations that had been made to eliminate the spread, such as the ability to (virtually) attend international seminars and conferences no matter where you reside. I think that it enriches the scientific community and contributes to collaborations and data sharing which are the most important things when doing science.

What are your plans once you complete your postdoctoral work?

I’m planning to join any organization (either academic or industrial) to which I will be able to contribute my skills and knowledge, but at the same time will allow me to grow both as a scientist and a human being.

What tip would you give someone just beginning a career in agricultural research?

The best tip would be to develop a unique set of skills that can be used in a multi-approach research. The ability to both predict and analyze big data and then enter the lab and test your predictions and hypotheses is very much needed and highly demanded.