Doctoral Scholarship Opportunity in Single Cell Biology

Project: A cell atlas of trained immunity in BCG vaccinated African infants

Project Summary
The main goal of our project is to build a high-resolution single-cell paediatric atlas of healthy peripheral blood myeloid and lymphoid cell development, following BCG vaccination in the first year of life. This atlas will be built as part of the Human cell atlas (HCA) consortia and aims to increase representation of African people in the existing body of HCA atlases and will be used as a healthy pediatric reference atlas for myeloid and lymphoid developmental cell lineages.

Our secondary aim is determining whether BCG induces trained immunity or ‘memory’ in myeloid cells through measurable histone modifications detected in open regions of chromatin and whether these modifications are long lasting.

Our project will collect samples from Malawian newborns, across sex and at 5 timepoints up to one year of age for scRNAseq and scATACseq. We will include proteomic analysis to complement the cell atlas data and immunological assays for trained immunity.

Single cell sequencing and proteomics will be done at our collaborator labs in the Netherlands, whilst data hosting and analysis will be done in Malawi. Our strategies include recruitment across socioeconomic, ethnic, and marginalised community lines, to increase representation of understudied populations within Malawi. We will implement a strong community engagement plan with a dedicated Malawian CE officer, to sensitise communities, health facilities, local chiefs, and stakeholders through the duration of the project. We will establish long-lasting
international partnerships, engage with the existing HCA community and with Malawian community members within healthcare centres, stakeholders, district health offices, national policymakers, and local researchers at MLW.

Our group commits to hiring racially diverse, gender balanced, Malawian staff and to implement equity in salary, caregiving support and create opportunities and access to advanced RNAseq training, particularly, to women to build capacity within Malawi.

The PhD Candidate
Applications are invited from suitably qualified Malawian candidates to pursue a fully funded PhD in Immunology and Bioinformatics using single cell techniques. Applicants must hold a master’s degree in bioinformatics, Computer Science or its equivalent with strong bias in programming and computation and have wet lab experience in immunological techniques.

The successful candidate will be hands on in the lab conducting immunological experiments with samples and address research questions using single cell data to understand the effect of cell development within the first of life following BCG vaccination. The candidate will be supervised by Dr Louise Afran from Malawi Liverpool Wellcome Trust, Dr Benjamin Kumwenda, KUHeS Bioinformatics and Dr Anmol Kiran, MLW.

Requirements for the Doctoral Scholarship:

  1. Master’s degree in bioinformatics, Computer Science or any equivalent qualification with strong bias in computer programming.
  2. Experience in immunological techniques, molecular biology or cell biology.
  3. Knowledge and experience in single cell sequencing data, transcriptomics and/ or human genomics will be an added advantage;
  4. The scholar must successfully apply and be accepted to the KUHeS Postgraduate Office to enroll in 2022.

Application Details:
Once selected by the project, the candidate will submit an application for admission to KUHeS Institute of Postgraduate Studies and Research. Application forms can be obtained online at the Postgraduate Institute Office or on KUHeS website. The candidate will have to present their concept and general preparedness to pursue doctoral studies.

KUHeS Ph.D application requirements:
1. Transcripts
2. Personal statement
3. Resume or CV
4. One Page Research Concept and a power point presentation to be made to a panel
5. Proof of finances or financial support

Due Date
Applications are due on May 26th 2022 at 11:59pm CAT. Late applications will not be accepted.

Post expires at 11:59pm on Thursday May 26th, 2022