Join our lab
Master and PhD projects
Contact (Head of Lab): srsousa@i3s.up.pt
PhD student opportunity
We are recruiting motivated individuals to join our research team as PhD candidates! At the group of Cell Biology of Bacterial Infections (https://www.i3s.up.pt/research-group.php?groupid=137) in Instituto de Investigação e Inovação em Saúde (i3S), we are dedicated to explore the mechanisms of plasma membrane repair responding to infectious damage. As a PhD candidate, you will have the opportunity to engage in cutting-edge research, collaborate with field experts, and develop skills that will shape your future career.
What We Offer:
- Mentorship: We provide you with personalized support throughout your PhD journey.
- Research Opportunities: Dive into exciting research projects that tackle real-world problems and contribute to advancing knowledge in an area that interests you.
- Professional Development: Enhance your skills through workshops, seminars, and conferences. Gain valuable experience in presenting and publishing your research findings.
- Collaborative Environment: Join a community of researchers who are leaders in their fields. Build collaborative networks with researchers from diverse backgrounds.
- Funding: The candidate must be willing to apply to the national call for PhD fellowships (FCT), open until 18th April 2024. We support you in all steps of the application.
Who We are Looking For:
- Highly motivated individuals with strong academic background and passionate for research.
- Individuals able to work independently and collaborate in a multidisciplinary environment.
To apply, please submit the following documents until 6 April 2024:
- Curriculum vitae (CV)
- Motivation letter outlining your research interests, career goals, and why you are interested in pursuing a PhD with us.
For informal inquiries and to submit your application, please contact: srsousa@i3s.up.pt. We are committed to diversity, equity, and inclusion.
We welcome applications from individuals of all backgrounds and identities.
PhD level
RepairBleb
Exploring the ultrastructure of plasma membrane damage sites inflicted by toxins, bacteria and viruses
Project Summary
CONTEXT: The airway epithelium is exposed to infectious agents that compromise the integrity of its plasma membrane (PM), such as influenza virus and pneumococci, two major causes of global mortality.
Altogether viruses, bacteria or their secreted toxins cause the disruption of epithelial and endothelial barriers, and trigger inflammatory responses that exacerbate lung damage. To survive, injured cells activate PM repair mechanisms, namely: wound blockade, reshaping of PM lipid composition, vesicular shedding and PM blebbing. Coordinated PM blebbing requires reorganization of cortical actomyosin cytoskeleton and its crosstalk with the endoplasmic reticulum. If this crosstalk is impaired, cells undergo uncontrolled blebbing, repair fails, and host susceptibility to infection increases.
AIM: The aim of this project is to establish if PM blebs supports damage confinement and serves to expel viral or bacterial toxins from the plasma membrane, thus allowing survival of the affected cell.
PUBLIC HEALTH IMPACT: Data generated should impact public health, as understanding in detail PM repair should help to define strategies to modulate PM repair pathways and ultimately control lung infections. Given the urgent need for better therapeutic interventions to overcome the widespread antiviral and antibiotic resistance, this work is timely and critical.
Work to be developed by the student
This project will include the following tasks and methodologies:
- Intoxicate (pneumolysin) or infect (pneumococcus, influenza A virus) lung epithelial cells and 3D lung models (by cell culture, infection at BSL2 level)
- Track the dynamics of plasma membrane upon intoxication or infection (by live cell imaging, super resolution microscopy)
- Characterize the ultrastructure of the damaged sites (by Correlative Light and Electron Microscopy, electron tomography or immunogold labeling).
This combined approach is expected to resolve bleb 3D architecture and allow the detection of pneumolysin in blebs, so as to support the role of blebs in damage confinement, toxin expulsion and infection control.
References
- Mesquita FS, Brito C, Mazon Moya MJ, Pinheiro JC, Mostowy S, Cabanes D, Sousa S. "Endoplasmic reticulum chaperone Gp96 controls actomyosin dynamics and protects against pore-forming toxins." EMBO Rep. (2017) 18:303-318. DOI: 10.15252/embr.201642833.
- Pereira JM, Xu S, Leong JM, and Sousa, S. "The Yin and Yang of Pneumolysin during Pneumococcal Infection". Frontiers Immunol. (2022)13: 878244. DOI: 10.3389/fimmu.2022.878244
Master level
Copines
Novel players in the repair of plasma membrane damage triggered by pneumococcal toxins
Project Summary
CONTEXT: Plasma membrane (PM) is a selectively permeable structure that separates inside and outside cellular environments. PM disruption causes cell death and tissue inflammation. Several human pathogens produce pore-forming toxins (PFTs) that form PM pores, disrupting cell homeostasis and promoting bacterial dissemination. Streptococcus pneumoniae is the most common cause of deadly pneumonia. Its major virulence factor, the PFT pneumolysin (PLY), triggers overwhelming immune response and extensive tissue damage. At low PLY concentrations, cells recover from PLY-induced PM damage through understudied repair mechanisms.
AIM: We recently proposed that Copines are required for the repair of PLY pores. This project aims to identify Copine partners and validate their function in PM repair during PLY intoxication or pneumococcus infection.
PUBLIC HEALTH IMPACT: Data generated should improve our understanding of host survival responses to PTFs and provide clues for the development of therapeutic approaches aiming to modulate PM repair. Given the urgent need for better therapeutic interventions to overcome the widespread antibiotic resistance, this work is critical for public health.
Work to be developed by the student
This project will include the following tasks and methodologies:
- Establish molecular biology tools for the identification of Copines partners in PM repair (BioID-Copines construct, lung cell line that stably expresses the construct)
- Intoxicate (PLY) or infect (pneumococcus) lung epithelial cells expressing BioID-Copines (cell culture, infection at BSL2 level)
- Identify Copine partners (by complementary label-free quantitative mass spectrometry (MS)-based proteomics: IP-MS and BioID).
- Validate best hits for their role in PM repair in lung cell monolayers and 3D lung models of PLY intoxication or pneumococcal infection (immunoprecipitation, flow cytometry, microscopy).
This approach is expected to reveal new players involved in PM repair, acting in concert with Copines.
References
- Alves S, Pereira JM, Mayer RL, Goncalves ADA, Impens F, Cabanes D, Sousa S: Cells Responding to Closely Related Cholesterol-Dependent Cytolysins Release Extracellular Vesicles with a Common Proteomic Content Including Membrane Repair Proteins. Toxins 2022, 15(1):1-22.
- Pereira JM, Xu S, Leong JM, and Sousa, S. "The Yin and Yang of Pneumolysin during Pneumococcal Infection". Frontiers Immunol. (2022)13: 878244. DOI: 10.3389/fimmu.2022.878244
Master level
ToxicMuscle
An unusual
model to approach repair in muscle disorders
Project Summary
CONTEXT: Damage to the plasma membrane (PM) occurs in healthy muscle cells due to mechanical tearing, as well as in dystrophic muscles due to aberrant expression or absence of PM repair proteins. We have uncovered a key player, the endoplasmic reticulum chaperone Gp96, that is involved in repairing PM damage induced by pore-forming toxins secreted by highly pathogenic bacteria. These toxins are simple to manipulate and cause reproducible and easily controlled damage in any cell type, intrinsic properties that make them valuable tools in fields of research other than infectiology. We propose that studies on PM damage induced by these toxins are of great value to identify new players and signalling pathways that can be modulated to promote PM repair in the muscle.
AIM: The goal here is to demonstrate that Gp96 and other proteins promoting PM repair upon toxin-induced damage are also involved in muscle repair upon mechanical damage.
PUBLIC HEALTH IMPACT: The intimate link between PM injury and muscular disease needs urgent addressing, and the principles of PM repair need to be detailed as they can potentially be translated into tailored therapies.
Work to be developed by the student
This project will include the following tasks and methodologies:
- Deplete Gp96 (and related proteins involved in PM repair) in human muscle cells, or possibly establish muscle cell lines stably depleted of those proteins (by siRNA or CRISPR/Cas9 technology, lentiviral transduction)
- Evaluate muscle cell resistance to PM damage induced by microinjuries in those cells expressing or not Gp96 (by immunofluorescence, light and electron microscopy).
This approach should provide proof-of-concept that PFT-induced damage is a relevant model to identify the machinery and pathways involved in muscle repair. Eventually, the impact of Gp96 and related proteins in PM repair can be validated in well-established and relevant muscular dystrophy animal models (like zebrafish).
References
- Mesquita FS, Brito C, Mazon Moya MJ, Pinheiro JC, Mostowy S, Cabanes D, Sousa S. "Endoplasmic reticulum chaperone Gp96 controls actomyosin dynamics and protects against pore-forming toxins." EMBO Rep. (2017) 18:303-318. DOI: 10.15252/embr.201642833.
Master level