Current Experimental and Analytical Methods for Studying Pathogenic Fungi

TOPICAL COLLECTIONS

Guest Editors

Deepika Gunasekaran

University of California, Merced

Dr. Deepika Gunasekaran received her BS and MS in Bioinformatics from Jacobs University and Albert-Ludwigs University in Germany, respectively. During her masters, she worked in the laboratory of Dr. Oliver Schilling, developing methods to quantify high-throughput proteomic data. She received her PhD in Quantitative and Systems Biology from the University of California, Merced in 2023. For her dissertation, she studied mechanisms of evolution and rewiring of transcriptional circuits in pathogenic fungi by integrating multi-omic data. She is currently a postdoctoral scholar in the laboratory of Dr. Clarissa Nobile, where she works on developing computational methods for projects including elucidation of mechanisms of pathogenesis during host-pathogen interactions and studying virulence mechanisms in pathogenic fungal species.

Priyanka Bapat

Revolution Medicines and University of California, Merced

Dr. Priyanka Bapat received her BS in Biotechnology from University of Mumbai, India and moved to University of Missouri- St. Louis, USA to pursue a M.S in Biochemistry and Biotechnology in 2012. There she worked in the laboratory of Dr. James Bashkin to characterize polyamides against Human Papilloma Virus. Dr. Bapat earned her PhD from the Department of Quantitative and Systems Biology, with a track in Molecular and Cell Biology from University of California, Merced in 2021. There she worked in the laboratory of Dr. Clarissa Nobile and described the transcriptional regulation of chlamydospore formation in human fungal pathogen Candida albicans. She also worked to demonstrate that photodynamic therapy is effective against Candida albicans and Candida auris biofilm formation. She is currently pursuing an industrial postdoc at Revolution Medicines, a clinical stage company discovering and delivering targeted medicines for patients living with cancer.

Collection Overview

Fungal infections are increasing globally as new pathogenic fungi emerge, affecting humans and plants. Fungal pathogens have rapidly spread across large geographic ranges, evolved resistance mechanisms to antifungal drugs, developed multiple virulence factors, and can switch between commensal, symbiotic, and pathogenic states. Human fungal infections, such as nosocomial infections, often have high mortality rates, while plant fungal diseases pose a threat to agricultural productivity and food security. Moreover, the lack of approved vaccines to treat fungal infections underscores the need for early detection and identification of viable therapeutic targets.

This Methods Collection focuses on fungal pathogenesis, pathogen detection, mechanisms of fungal virulence, and drug resistance. We aim to compile novel methods for detecting fungal pathogens, identifying new receptors involved in host-pathogen interactions, and developing advanced assays to discover new antifungal treatments.

Examples of methods include:

In vitro and in vivo models of fungal pathogens

Applications of different molecular editing techniques, such as CRISPR-based techniques

High-throughput molecular assays such as CUT&RUN and sequencing methodologies

Computational methods to identify antifungal targets by integrating multi-omics data

Through this curated collection, we aim to provide researchers with a comprehensive resource for advancing research on fungal pathogenesis using systems biology approaches.