EDBB Open positions

This page will be updated more often as we approach the end of 2020, as the EDBB program will be informed of new positions becoming available for the January 20-22, 2021 Hiring Days event at EPFL (or virtual event spread over January-February 2021 depending on the sanitary restrictions). Meanwhile, do not hesitate to contact any EDBB laboratories which interest you to find out whether they have upcoming openings for PhD students.

Laboratory of Molecular Microbiology

We offer the following PhD position on the ecology and evolution of bacterial pathogens. Pathogen frequently emerge due to their adaptation to natural environments or non-human hosts. Within this context, bacteria often engage in interbacterial competition and cooperation. Our laboratory studies these interbacterial interactions at the mechanistic level using microbial cell biology, genetic engineering, and basic biochemistry. Our model organisms are Vibrio cholerae (the causative agent of the ongoing 7th pandemic of cholera) and Acinetobacter baumannii (a common hospital-acquired pathogen that is frequently multi-drug resistant). We are looking for self-motivated enthusiastic PhD candidates with good organizational skills and scientific passion.

CAO Lab

We are seeking highly motivated candidates with interest in nanopore single-molecule sensing to join Dr. Chan Cao’s group at the School of Life Science, EPFL (Switzerland).

This newly established research group is focused on developing novel approaches to address questions in life science and diagnosis at the single-molecule level, especially specialized in nanopore technology. Nanopore measurement is an electrophoretic approach that allows the characterization of molecules of interest in real-time with sub-angstrom resolution and without the need for additional labels/amplification in aqueous solution. It has been successfully applied in sequencing long fragments of DNA and has shown great potential for single-molecule proteomics applications. The main goal of the group is to push the limits of nanopore technology and maximize its potential for as many fields of application as possible. In this position, you will join a dynamic team of computational & structure biologists, biophysicists, biochemists and analytical chemists.

The applicant should have at least one of the following backgrounds: biophysics, biochemistry, analytical chemistry, molecular biology or biomolecule synthesis. Experience in protein production and good programming skills is an advantage. The starting time should be September 2021 at the latest.

The applicant who is interested in this position, please send your resume to Dr. Chan Cao ([email protected])

The position is part of a Swiss National Science Foundation (SNSF) PRIMA project and the student will be co-supervised by Dr. Chan Cao, Prof. Matteo Dal Peraro and/or Prof. Gisou van der Goot. The salary and benefits are very competitive.

https://www.epfl.ch/labs/dangelo-lab/

https://www.epfl.ch/labs/nsbl/

Characterization of spatiotemporal organization of the brain lipidome

Neural cells produce thousands of different lipids, each endowed with peculiar structural features and contributing to specific biological functions. Lipid composition affects neuron firing properties influencing vesicle fusion and fission processes, membrane conductivity, and ion fluxes. Nonetheless, a systematic and fine-grained characterization of lipid composition in the different brain regions is not available.

Lipids also play a fundamental role in brain development. For example, some lipids, such as glycosphingolipids, mediate cell-cell recognition, others like steroid hormones, and phosphoinositides, have a role in stimulating cell growth and signaling.

Furthermore, exposure to teratogenic agents, during development, is associated to cognitive or sensory impairments that might be mediated by interference of these teratogens with lipid biogenesis and metabolism. However, little is known about how the regional specificity of lipids is developmentally established and maintained throughout adulthood.

The doctoral candidate will aim at filling this gap by collecting systematic data necessary to construct a high spatially resolved atlas of the lipidome of the adult and developing mouse brain. We expect this resource to provide numerous cues of the underlying regulation mechanisms; the most interesting observations will be experimentally followed up by the candidate and related to function.

The project offered jointly by the La Manno and D’Angelo labs will allow the candidate to:

– Use super-resolved Imaging Mass Spectrometry (IMS) to reconstruct the spatial lipidome in serial brain sections from adult and developing mice.

– Assess the lipid deregulation resulting from the exposure of different teratogenic conditions.

– Investigate the relation between the lipidome of different stem cell populations and their neural progeny.

– Investigate how perturbation to genes involved in lipid metabolism affects brain development.

– Assess how direct perturbations of lipid composition affect morphogenesis and adult brain structure and composition.

https://deplanckelab.epfl.ch/

Single cell transcriptomics (scRNA-seq) is transforming biomedical research by providing unique insights into a cell’s identity and characteristics. However, several key single cell-related technological limitations remain. As a PhD student focused on technology development, you will be expected to address one key challenge, namely our current inability to link the multi-parametric information of a cell image to a genome-wide, molecular description of that same cell. You will thereby build on technological advances that we made involving microfluids and single cell transcriptomics, as presented in Bues et al. (BioRxiv, 2020), aiming to engineer a platform that couples quantitative, high-resolution microscopy to droplet-based scRNA-seq.

UPGON

Mechanisms directing centriole fate during muscle development in zebrafish and human iPS cells. The project aims at monitoring centriole and centrosome dynamics during muscle formation and regeneration in zebrafish embryos using light sheet microscopy, in collaboration with the Oates laboratory. The work will be complemented by inducing muscle formation from human iPS cells, with the goal of discovering the fate and the importance of centrioles during this differentiation program.

LBNC

We expect to hire 1-2 PhD students in 2020 in the area of cell-free synthetic biology / synthetic cell engineering.

https://www.p-lab.science/

PhD position in microscopy and biophysics

The lab is looking for a student interested in implementing interferrometric scattering microscopy for the visualization of bacterial extracellular filaments like flagella and pili (see Tala et al., Nature Microbiology 2019). The ideal candidate is a student interested in bioengineering or biophysical problems eager to implement new microscopy methodologies, or a microscopist interested exploring new frontiers of biophysics, all with applications to infectious diseases. 

More generally, our lab investigates mechanical regulation of bacterial physiology and infection, in particular via mechanosensing. Our team is highly multidisciplinary, combining techniques from physics, engineering and biology.

LBI

Project title: Engineering immunity-disease interactions for enhanced cancer immunotherapy

 

Tang lab’s research aims at developing novel strategies to engineer immunity-disease interactions, an emerging field called ‘immunoengineering’, through chemical, metabolic, and mechanical means in order to treat cancer safely and effectively with immunotherapies. We are actively looking to recruit a PhD student who is interested in this new field and would like to work in a highly interdisciplinary environment. For more information, please see our publications below and reach out to [email protected].

 

Highly motivated and talented students (bachelor or master) with excellent academic achievements in a major field of Immunology, Cancer Biology, Bioengineering, or a closely related discipline, are encouraged to apply for the EPFL doctoral programs.

 

-Metabolic immunoengineering:

Guo, Y.#; Xie, Y.-Q.#; Gao, M.; Zhao, Y.; Franco, F.; Wenes, M.; Siddiqui, I.; Bevilacqua, A.; Wang, H.; Yang, H.; Feng, B.; Xie, X.; Sabatel, C.M.; Tschumi, B.; Chaiboonchoe, A.; Wang, Y.; Li, W.; Xiao, W.; Held, W.; Romero, P.; Ho, P.-C.*; Tang, L.* “Metabolic Reprogramming of Terminally Exhausted CD8+ T-cells by IL-10/Fc Enhances Anti-Tumor Immunity”, Nat. Immunol. 2021, in press.

 

-Mechanical immunoengineering:

  1. Lei, K.; Tang, L.* “T Cell Force-Responsive Delivery of Anticancer Drugs Using Mesoporous Silica Microparticles”, Hori. 2020, 7, 3196-3200. Cover story of Materials Horizons Issue 12, December. Highlighted: EPFL News; Materials Horizons Emerging Investigator Series.
  2. Lei, K.; Kurum, A.; Tang, L.* “Mechanical Immunoengineering of T-cells for Therapeutic Applications”, Chem. Res. 2020, 53, 2777–2790.

 

-Chemical immunoengineering:

  1. Wei, L.; Zhao, Y.; Hu, X.; Tang, L.* “Redox-Responsive Polycondensate Neoepitope for Enhanced Personalized Cancer Vaccine”, ACS Cent. Sci. 2020, 6, 404-412.
  2. Guo, Y.; Lei, K.; Tang, L.* “Neoantigen Vaccine Delivery for Personalized Anticancer Immunotherapy”, Immunol. 2018, 9, 1499. 23,553 views, 5,445 downloads, >99% all Frontiers articles.
  3. Tang, L.*; Zheng, Y.; Melo, M.B.; Mabardi, L.; Castaño, A.P.; Xie, Y.-Q.; Li, N.; Kudchodkar, S.B.; Wong, H.C.; Jeng, E.K.; Maus, M.V. and Irvine, D.J.* “Enhancing T-cell Therapy Through TCR Signaling-Responsive Nanoparticle Drug Delivery”, Biotech. 2018, 36, 707-716. Cover story of Nature Biotechnology, Volume 36 Issue 8, August 2018.

For more details, see web pages of the EDBB program’s potential thesis directors.