PhD Opportunities

Applications are invited for a research studentship leading to the award of a PhD degree, under the supervision of Dr. Ana Eulalio, to investigate bacterial determinants of the intracellular lifestyle of the bacterial pathogen Staphylococcus aureus, and their impact on pathogenesis and antibiotic treatment.

The post is supported by a bursary and fees (at the UK student rate only) funded by the Department of Life Sciences. The studentship is for 36 months.

Staphylococcus aureus is a leading cause of human infections worldwide, causing a broad range of community- and hospital-acquired infections. Although S. aureus is historically considered an extracellular pathogen, substantial evidence demonstrates that S. aureus can be internalized by various cell types. Recently, our lab characterized the interaction of a large collection of S. aureus clinical isolates collected from patients with bone/joint infections, bacteremia, and infective endocarditis with host cells (epithelial and endothelial cells, osteoblasts and macrophages). This analysis revealed that the vast majority of the isolates are facultative intracellular and identified seven intracellular phenotypes, with various levels of replication, persistence, and host cell death. The presence of S. aureus inside host cells can contribute to its ability to evade antibiotic treatment and immune responses, explaining, at least in part, treatment failure and recurrence of disease.

Despite the relevance of the intracellular lifestyle to S. aureus pathogenicity, a comprehensive identification of host and bacterial factors relevant to this process is yet to be performed. We are addressing this question by applying functional genomics approaches, specifically: i) microscopy-based, high-throughput screenings of S. aureus mutant collections (for bacterial factors) and siRNA/CRISPR libraries (for host factors); ii) transcriptomics and proteomics to identify host and bacterial factors regulated during infection with S. aureus clinical isolates.

The PhD student will pursue a project along the above-described lines of research, particularly focused on characterization of key S. aureus factors controlling the intracellular lifestyle. The PhD student will receive training in microbiology and cell biology approaches, including bacterial and mammalian cell culture, microscopy, transcriptomics, and high-throughput screening.

Supporting publication: Microscopy-based phenotypic profiling of infection by Staphylococcus aureus clinical isolates reveals intracellular lifestyle as a prevalent feature. Rodrigues Lopes I, Alcantara LM, Silva RJ, Josse J, Pedrero Vega E, Cabrerizo AM, Bonhomme M, Lopez D, Laurent F, Vandenesch F, Mano M, Eulalio A (2022) Nature Communications 13(1):7174.

Requirements and eligibility

The studentship provides 3 years of funding (starting date according to availability). Applicants should have a BSc honours degree (at least 2.1 or equivalent) in Biology, Biochemistry, Genetics, or a related discipline. Applicants with a Masters degree (at Merit level or better) in addition to the BSc will be given preference. Intellectual ability, enthusiasm and self-motivation are essential.

Funding provides full support for tuition fees for the three-year duration of the studentship (home fees only), and an annual tax-free stipend of £21,237 per year (rising annually by an amount linked to inflation).

How to apply:

Please direct informal enquiries and requests for further information to Dr. Ana Eulalio (a.eulalio@imperial.ac.uk). Please email a single PDF file including a brief cover letter describing your relevant interests and research experience, your C.V. and names and contact information of three referees. Applications will be considered as they are received, so early applications are encouraged.

In line with our commitment to equality, diversity, and inclusivity, we would be grateful if all applicants who contact supervisors would complete a confidential Equality, Diversity, and Inclusion Questionnaire. This will help us to improve our future policies and processes and provides insight into who is and who isn’t applying. The questionnaire is anonymous and is not seen by potential supervisors. We strongly encourage applications from students from under-represented groups that align with the Department’s equality, diversity and inclusion priorities. These include home (British citizens or residents) students coming from non-Russell group universities and/or are from a minority ethnic group, such as those of Black, Asian or mixed heritage as well as those from white minority ethnic groups (e.g. Gypsy, Roma and Irish Traveller). Candidates must be UK nationals (EU candidates with settled status in the UK may be considered), International students are not eligible.

The Kourelis lab is dedicated to addressing fundamental questions in plant-microbe interactions, particularly focusing on the function and evolution of immune receptors. We are deeply interested in understanding how these receptors work and how they have evolved over time, with the ultimate goal of using this knowledge to bioengineer disease resistance genes that are specifically tailored to meet diverse challenges (see Kourelis et al., 2023 and Marchal et al., 2022). To pursue these objectives, we employ a unique interdisciplinary approach that combines bioinformatics and evolutionary biology with technical expertise in synthetic biology.

The PhD project focuses on bioengineering of plant NLR (nucleotide-binding leucine-rich repeat) immune receptors to enhance disease resistance. This research presents an exciting prospect for candidates to expand their skillset within a multidisciplinary research setting, utilizing cutting-edge technologies that integrate protein biochemistry and synthetic biology. The successful candidate will have the opportunity to work with advanced techniques including Gibson Assembly and Golden Gate cloning for receptor engineering, high-throughput functional characterization of bioengineered immune receptors, and CRISPR genome editing. This work will be conducted in a dynamic and supportive research environment, with access to state-of-the-art facilities and a network of international collaborators. The PhD project will offer comprehensive training in these synthetic biology techniques, biochemistry, and plant-pathogen interactions, preparing the candidate not only for the successful completion of their PhD, but also for a competitive edge in their future career in academia or industry.

Requirements and eligibility

We are seeking a final year undergraduate (at least 2.1 or equivalent) or Master's student (at Merit level or better) who is driven by curiosity and fascinated by molecular mechanisms. The ideal candidate will possess basic molecular biology and biochemistry lab skills. However, instead of specific expertise, we are searching for individuals with the right mindset. We value individuals who approach scientific exploration with an open and inquisitive attitude, and who are excited by the prospect of tackling complex biological questions with potential real-world impact.

How to apply:

For more details on the project and the lab, candidates can directly contact me: j.kourelis@imperial.ac.uk

Some technical details about the application process:

• The deadline for application is January 12th. Applicants should send a CV, personal statement, and the contact details of two referees directly to me at: j.kourelis@imperial.ac.uk
• Studentships will be funded for 36 months with an annual tax-free maintenance stipend currently at £21,237 (rising annually by an amount linked to inflation).
• Candidates must be UK nationals (EU candidates with settled status in the UK may be considered). International students are not eligible.
• In line with our commitment to equality, diversity, and inclusivity, we would be grateful if all applicants who contact supervisors would complete a confidential Equality, Diversity, and Inclusion Questionnaire. This will help us to improve our future policies and processes and provides insight into who is and who isn’t applying. The questionnaire is anonymous and is not seen by potential supervisors. We strongly encourage applications from students from under-represented groups that align with the Department’s equality, diversity and inclusion priorities. These include home (British citizens or residents) students coming from non-Russell group universities and/or are from a minority ethnic group, such as those of Black, Asian or mixed heritage as well as those from white minority ethnic groups (e.g. Gypsy, Roma and Irish Traveller). Candidates must be UK nationals (EU candidates with settled status in the UK may be considered), International students are not eligible.

Project Description

Applications are invited for a prestigious EPSRC research studentship leading to the award of a PhD degree, under the supervision of Dr. Alessia David (Dept of Life Science) and Prof Johnson (Dept of Medicine), to develop new bioinformatics approaches for the identification of new genes and genetic variants responsible for human disease. The post is supported by a bursary and fees (at the UK student rate only) are funded by the EPSRC. The studentship is for 36 months from October 2025.

The identification of genes and genetic variation responsible for human disease and the interpretation of their function within a biological network is a crucial step towards personalized medicine and the discovery of novel biomarkers. DNA sequencing projects from individual research groups and the 100K Genomes Project at Genomics England are providing an unprecedented amount of DNA sequencing data that need to be analysed to derive biologically meaningful information. This task cannot be performed manually and requires computational resources.

Recent major development in the field of 3D protein modeling with AlphaFold and the unprecedent wealth of information now available for genome variation in human and model organisms allow to expand the use of multiomics to develop new prediction algorithms to identify genes and genetic variants that can disrupt protein function/structure and biological pathways. In this project you will develop new robust bioinformatics algorithms for predicting the effect of genetic variants and identify new candidate genes for human disease. You will use the wealth of information on gene expression, protein interactions, and three-dimensional protein structure, experimentally determined and modelled by the in house Phyre2 homology modeling software and by the deep learning algorithm AlphaFold. You will apply these new bioinformatics algorithms to genomic and clinical data to interpret their biological relevance. You will have the opportunity to develop effective visualisation web tools to make these new algorithms available to the biomedical community. You will work closely with clinicians to design bespoke approaches that ensure the utilization of these new bioinformatic resources by the biomedical community. Programming experience, preferably in Python, is essential for this position.

The Department of Bioinformatics in the Department of Life Sciences at Imperial College has strong expertise in developing robust bioinformatics resources for the biomedical community, such as the Missense3D prediction algorithm suite for the interpretation of genetic variants (> 8000 users and > 400 citations since its release in 2019) and the Missense3D-DB database, a large catalog of precomputed predictions for 4 million human genetic variant which is included in DECIPHER at the European Bioinformatics Institute. The group of Prof M Johnson, in the Department of Medicine, has extensive expertise in using cell transcriptomics data in particular for the identification of new genetic mechanisms underlying neurological disorders.

You will receive training in the use of genomics, proteomics and 3D protein structures to develop new bioinformatics resources and in their application to analyze patients’ genetic data.

Requirements and eligibility

The studentship provides 3 years of funding starting October 2025.

Applicants should have a BSc honours degree (at least 2.1 or equivalent) in computing, biochemistry, biophysics, computational biology, or bioengineering with additional interest in biology. Applicants with a Master degree (at Merit level or better) in addition to the BSc will be given preference. Interdisciplinarity may be given preference. Candidates should also have demonstrably strong programming skills in a high-level programming language, preferably Python. Enthusiasm and self-motivation are essential. We encourage applications from all backgrounds and communities, and are committed to having a diverse, inclusive team.

Funding provides full support for tuition fees for the three-year duration of the studentship, and an annual tax-free stipend of approx. £21,237 per year.

How to apply:

Please direct informal enquiries and requests for further information to Dr. Alessia David (alessia.david09@imperial.ac.uk). Please email a single PDF file including: a brief cover letter describing your relevant interests, research and coding experience, your C.V. and names and contact information of three referees.

In line with our commitment to equality, diversity, and inclusivity, we would be grateful if all applicants who contact supervisors would complete a confidential Equality, Diversity, and Inclusion Questionnaire. This will help us to improve our future policies and processes and provides insight into who is and who isn’t applying. The questionnaire is anonymous and is not seen by potential supervisors. We strongly encourage applications from students from under-represented groups that align with the Department’s equality, diversity and inclusion priorities. These include home (British citizens or residents) students coming from non-Russell group universities and/or are from a minority ethnic group, such as those of Black, Asian or mixed heritage as well as those from white minority ethnic groups (e.g. Gypsy, Roma and Irish Traveller).

Do you want to design and construct synthetic life-like cells? Is it possible to build synthetic cells that mimic the essential functions of living systems? Could these synthetic cells, equipped with programmable functionalities, perform specialized tasks in biological environments and help uncover the mechanisms underlying cellular processes?

This PhD studentship offers the chance to explore these fundamental questions and contribute to groundbreaking research in bottom-up synthetic biology.

The project focuses on the design and construction of synthetic cells that mimic life-like behaviours. Synthetic cells are minimal systems built from the bottom up using biomolecules and synthetic components and offer unprecedented potential to unravel fundamental biological principles and pave the way for novel biotechnological applications.

The project will explore advanced methodologies to assemble and characterize synthetic cells that mimic features such as motility, fusion, communication, and responsiveness to environmental stimuli. As part of this interdisciplinary research effort, you will gain expertise in advanced techniques such as vesicle fabrication, polymer chemistry, and biophysical characterization, while working in a collaborative and cutting-edge research environment. By leveraging advanced materials science, membrane biophysics, and chemical engineering approaches, the research aims to create synthetic cells with programmable behaviours, thereby advancing our understanding of cellular systems. Moreover, synthetic cells offer the opportunity of producing smart cell-like agents to tackle pressing needs in diagnostics, therapeutics, biosynthesis, and bioremediation.

Funding and Eligibility

A BSc in Biochemistry, Physical Chemistry, Biophysics or related, sciences is required at Upper Second Class level or better and candidates with a master's degree (at Merit level or better), in addition to the BSc, will be given preference. Intellectual ability, enthusiasm and self-motivation are essential.

The studentship will cover UK tuition fees and will provide an annual tax-free maintenance stipend at the standard UKRI level, currently at £21,237 (rising annually by an amount linked to inflation), in 12 monthly instalments. Studentships will be funded for a maximum of 36 months, subject to satisfactory progress. The studentship is expected to start in October 2025.

How to apply

Please direct informal enquiries and requests for further information to Dr. Claudia Contini (c.contini@imperial.ac.uk). Please email a single PDF file including a brief cover letter describing your relevant interests and research experience, your C.V. and names and contact information of three referees. Applications will be considered as they are received, so early applications are encouraged. Deadline for application: 13th February 2025.

In line with our commitment to equality, diversity, and inclusivity, we would be grateful if all applicants who contact supervisors would complete a confidential Equality, Diversity, and Inclusion Questionnaire. This will help us to improve our future policies and processes and provides insight into who is and who isn’t applying. The questionnaire is anonymous and is not seen by potential supervisors. We strongly encourage applications from students from under-represented groups that align with the Department’s equality, diversity and inclusion priorities. These include home (British citizens or residents) students coming from non-Russell group

universities and/or are from a minority ethnic group, such as those of Black, Asian or mixed heritage as well as those from white minority ethnic groups (e.g. Gypsy, Roma and Irish Traveller). Candidates must be UK nationals (EU candidates with settled status in the UK may be considered), International students are not eligible.