Dr Ko-Fan Chen

Supervisor Details

Contact Details

Dr Ko-Fan Chen

Department of Genetics and Genome Biology, University of Leicester

Scientific Background

Research Interests

Broadly speaking the Chen lab is interested in two aspects of sleep research:

How environmental factors influence sleep and circadian behaviours?
How sleep-related cellular mechanisms modulate progress of human diseases?

These research questions are addressed using the fruit fly Drosophila melanogaster as an experimental model, allowing the application of diverse methods to identify evolutionary conserved molecular mechanisms.

The group works closely with various research groups across departments in following expertises

Behavioural Neurogenetics
Neurodegeneration
Social Epigenetics
Ophthalmology
Neurophysiology
Cancer

Scientific Inspiration

My attitude towards scientific research was shaped by my former PhD supervisor – Professor Ralf Stanewsky. Under his mentorship, I learnt to be thorough when collecting and describing biological data, and to let the data guide my investigation while keeping an open mind. To see more information about my scientific upbringing and inspiration, please visit https://www.kofanchenlab.net/

Research Groups

Drosophila Sleep Laboratory (Ko-Fan Chen Lab)

Social Epigenetics

Supervision Style

In three words or phrases: Supervisee-oriented, encouraging and inclusive, organised and details-oriented.

Provision of Training

I will provide the student with necessary technical training, either by myself or via arranged collaborations, facilitating their future independence to conduct their own research directions.

Progression Monitoring and Management

Initially we will plan your project goals together and during b-weekly follow-up meetings we will discuss experimental results and general progression. Through these meetings and ad hoc discussions there will also be opportunities for us to troubleshoot and resolve operational issues.

Communication

Apart from in person conversations, we will use emails and video calls to communicate. You should feel free to contact me anytime about matters that require my advice/assistance, but I will respect work-life boundary and to respond to you during the working hours unless it is an emergency.

PhD Students can expect scheduled meetings with me:

In a group meeting

At least once per week

In year 1 of PhD study

At least once per week

In year 2 of PhD study

At least once per week

In year 3 of PhD study

At least once per week

These meetings will be a mixture of face to face and via video chat or telephone, and I am usually contactable for an instant response on every working day.

Working Pattern

Certain tasks in my lab need to occur at set times, and students need to be able to commit to a rota/timetable shared with other members of the team.

Notice Period for Feedback

I need at least 1 week’s notice to provide feedback on written work of up to 5000 words.

MIBTP Project Details

Primary supervisor for:

Identifying the neurogenetic network underlying visually-driven sleep

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).

Identifying the neurogenetic network underlying visually-driven sleep

Secondary Supervisor(s): Professor Ezio Rosato, Dr Roberto Feuda, Dr Nils Reinhart

University of Registration: University of Leicester

BBSRC Research Themes:

Understanding the Rules of Life (Neuroscience and Behaviour)
Integrated Understanding of Health (Ageing)

Project Outline

Sleep is a behavioural quiescence widely observed in the animal kingdom. Evidence indicates that daily light and visual stimuli contribute to sleep pressure; our lab is interested in identifying the elusive molecular and neural basis of such vision-driven sleep. We have identified various genetic components in the light/vision-driven sleep in the fruit fly Drosophila melanogaster. Circuit-based manipulation also indicates parallel neurogenetic pathways linking the visual system and the known sleep homeostatic centre in the fly brain. This PhD project, therefore, aims to combine the latest techniques in connectomics and Drosophila sleep to map out these neural pathways in the fly brain. The student will conduct this exciting project through the following three objectives.

1) Identifying sleep-controlling genetic network: By apply bulk-RNAseq, we will identify common differentially expressed genes (DEGs) in sleep altering visual mutants. In collaboration with Feuda lab, we will then map these DEGs onto scRNA-Seq data (2) to identify the commonly affected neural clusters.

2) Identification of neural connection of vision-sleep pathway: Working with Dr Nils Reinhart, we will use the fly brain connectome (3) to digitally construct neural connection of vision-sleep pathway and examine its overlaps with the DEGs enriched neural clusters. The finding will be confirmed experimentally by confocal brain imaging using customised DEGs-based reporter (2).

3) Verification of the sleep modifying effect of DEGs and associated cell clusters: upon generation of the gene/neural cluster list, automatic high throughput sleep monitor system will be used to test if reduction of these genes modifies the sleep phenotype. The reduction will be implemented in all neurons as well as in the neural clusters identified.

Reference: 1. PMID: 30865587 2. PMID: 37523539 3.PMID: 39638801

Co-supervisor on a project with: Professor Eamonn Mallon