Dr Hung-Ji Tsai

Supervisor Details

Contact Details

School of Biosciences, University of Birmingham

Scientific Background

Research Interests

Dr Hung-Ji Tsai is interested in how aneuploidy, an unbalanced genomic state with gain or loss of chromosomes, enables rapid adaptation to diverse environment. His research focus is to understand the distinct cellular processes driven by aneuploidy (and other large-scale genome instability) during the acquisition of antifungal drug resistance.

Our research group is broadly interested in how cells survive stress conditions. A major focus is to investigate the molecular mechanisms in response to stress in cells with ongoing large-scale genome instability, mainly in aneuploid cells. While aneuploidy is frequently observed in eukaryotic genome and generates genetic diversity, the physiological impact of aneuploidy contributing to cellular adaptation under stress remains poorly known. We aim to study:

How do aneuploid cells respond to stress?
How do aneuploid fungi interact with the host during the evolution of drugs?

Our group employs molecular tools, experimental evolution, genomics and cell biological techniques to address fundamental questions in fungal species, including Saccharomyces cerevisiae and Candida albicans.

Supervision Style

In three words or phrases: supportive, goal-driven, collaborative.

Provision of Training

At the beginning of your training, I will work alongside the student to support the development of experimental skills and to help the student establish a solid foundation of scientific methods and experimental discipline. By the end of the PhD, I expect the student could have the ability to initiate new ideas/projects with rational, feasible experimental plans and meanwhile possess the ability to write research manuscripts and proposals, as an independent scientist.

Progression Monitoring and Management

I expect the student to take full ownership of the project progression, but I will be available for troubleshooting to facilitate the student’s project. A weekly personal meeting will also be set up to discuss plans of action and related lab matters.

Communication

I reply emails from my team at all hours (not expect the student to do the same), in response to any timely needs in the lab or data analyses, and a lab SLACK group is set up for the lab members to facilitate the communication. I am also happy to discuss any issues regarding career development in personal meetings and will proactively initiate the conversations at every milestone during the training.

PhD Students can expect scheduled meetings with me:

In a group meeting

At least once per fortnight

In year 1 of PhD study

At least once per week

In year 2 of PhD study

At least once per fortnight

In year 3 of PhD study

At least once per fortnight

These meetings will mainly be face to face, and I am usually contactable for an instant response on every working day.

Working Pattern

The timing of work in my lab is completely flexible, and (other than attending pre-arranged meetings), I expect students to manage their own time.

Notice Period for Feedback

I need at least 2 weeks' notice to provide feedback on written work of up to 5000 words.

MIBTP Project Details

Current Projects (2025-26)

Primary supervisor for:

Explore the mutational trajectories shaping fungal adaptation

See the PhD Opportunities section to see if this project is currently open for applications via MIBTP.

Please Note: The main page lists projects via BBSRC Research Theme(s) quoted and then relevant Topic(s).

Explore the mutational trajectories shaping fungal adaptation

Secondary Supervisor(s): Dr Megan McDonald

University of Registration: University of Birmingham

BBSRC Research Themes: Understanding the Rules of Life (Microbiology, Systems Biology)

Project Outline

The rapid emergence of fungal diseases is a global threat to animal, plant and our ecosystem, while fungal infections affect billions of people, including >1.5 million global deaths each year. Within a fifteen-year period (1995-2010), fungi have caused species extinction of 39 animal and four plant species [1], and there are only three classes of antifungal drugs available in the clinic in the past four decades. Inevitably, multidrug resistance has become an urgent problem for the agricultural industries and human medicine. Additionally, with climate change, extreme weathers also facilitate the interactions between fungal pathogens and their host (and/or environment), and many environmental fungi now can overcome growth temperature barriers (12–30°C) to affect human [2]. The development of stress (thermo-) tolerance phenotypes likely results from the high genome plasticity in fungal genome, while aneuploidy, an unbalanced genomic state with gain or loss of chromosomes, is prevalent in wild and clinical fungal isolates. Whether and how aneuploidy contributes to the selection processes to adaptive traits in fungi remains elusive.

This project aims to investigate the mutational trajectories across the adaptation history in the context of aneuploidy and to identify the key genetic and non-genetic determinants enabling antifungal resistance.

Objective and Methods:

We will use both the model organism Saccharomyces cerevisiae and multiple fungal pathogens (mainly Candida species), together with animal, cell line infection models to investigate the mutational cues for adaptive phenotypes.

Objective 1: Investigate the fungal genomic plasticity at the host-fungal interface.

As fungi possess a high level of genome plasticity, we will identify the types of genomic alterations (mutations/CNV/ploidy variations) when fungal pathogens encounter the host and environmental stress in a temporal manner. Importantly, the mutual relationship between each type of genomic abnormalities will be investigated. For example, whether ploidy variations “buffer” or promote DNA damage responses? Both genomics and cell biological methods will be used to reveal the mutational evolution in the adaptive process.

Objective 2: Explore the mutational cues in response to genetic variation in fungi.

While genome-phenome gap is the main obstacle allowing us to combat antifungal drug resistance, we will use experimental evolution approaches to monitor the relationship between mutational complexity and phenotypic outcomes (e.g., tolerance and fitness) based on our recent observations of “genome instability burst”.

Together, this project will leverage both genomics, proteomics, biochemistry and cell biological approaches to understand the molecular evolution of fungal diseases from the interactions of hosts, fungal pathogens and their microenvironment.

References

1. Fisher, M., Henk, D., Briggs, C. et al. Emerging fungal threats to animal, plant and ecosystem health. Nature 484, 186–194 (2012). https://doi.org/10.1038/nature10947.

2. Case NT, Berman J. et al. The future of fungi: threats and opportunities. G3 (Bethesda). 2022 Nov 4;12(11) https://doi.org/10.1093/g3journal/jkac224.

Previous Projects (2024-25)

Primary supervisor for:

Investigating the effects of microenvironment cues on fungal adaptation

Co-supervisor on a project with Dr Megan McDonald.

Previous Projects (2023-24)

Primary supervisor for:

Investigating how the host immunity shapes the evolution of antifungal resistance