Doctoral Student in Environmental Bioengineering 100%

ETH Zurich; Zürich; On-site; CHF 48,000 - 56,000; Full time

Job summary

ETH Zurich in Zürich invites applications for a doctoral student position in the Environmental Microfluidics Group. The project investigates how bacterial chemotaxis accelerates plasmid transfer and the spread of antibiotic resistance, in a collaboration with the University of Warsaw.

This is a primarily experimental PhD at the interface of engineering and microbiology. You will design, build and characterize instrumentation, run conjugation experiments, and analyze imaging data to inform models

Qualifications

• Hands-on engineering mindset with a track record in prototyping and instrument development.
• Experience with control systems, data acquisition and analysis software is preferred.
• Strong written and spoken English; ability to work in an interdisciplinary team.

Responsibilities

• Design, build and characterize instrumentation to couple chemotaxis assays with controlled shear systems.
• Run chemotaxis and conjugation experiments using donor/recipient bacteria and plasmids.
• Image and track bacteria and chemical plumes, and analyze data with pipelines.
• Contribute to mathematical models of plasmid spread in aquatic environments.

Skills

Prototyping & manufacturing

Control systems

Python / MATLAB

Fluency in English

Education

MSc in bioengineering or related

Tools

CAD

3D printing

Machining

Flow cytometry (experience)

Job description

The Environmental Microfluidics Group of Prof. Roman Stocker in the Institute of Environmental Engineering is seeking a dynamic and motivated doctoral student with an engineering background for a project on how bacterial chemotaxis accelerates plasmid transfer, including the spread of antibiotic resistance. The position is funded by a recently awarded SNSF grant, and the project is a joint effort with Prof. Jonasz Slomka at the University of Warsaw. This position will be based in the laboratory of Prof. Roman Stocker.

Project background

Bacterial conjugation, the contact-dependent transfer of plasmids between cells, speeds up bacterial evolution and is a major route for the spread of antibiotic resistance in the environment, which in turn poses a global health threat. Aquatic environments are full of microscale chemical hotspots, such as the nutrient-rich 'phycosphere' around phytoplankton and sinking marine particles, and chemotactic bacteria are known to find and accumulate rapidly at these locations. This project will test the hypothesis that this accumulation enhances plasmid spreading in the environment, contributing to a cutting-edge view of the role of antibiotic resistance in nature.

The project seeks to study when, where and how strongly this enhancement operates across different chemical hotspots, fluid flows and bacterial strains, and what it means for the spread of antibiotic resistance among aquatic bacteria.

Job description

This is a primarily experimental PhD at the interface of engineering and microbiology. The student will:

• Design, build and characterize new instrumentation to couple existing chemotaxis assays to controlled shear systems. This includes mechanical design, 3D printing, control systems and integration with a fluorescence microscope.
• Run chemotaxis and conjugation experiments with bacterial donors and recipients of plasmids and a range of chemoattractants, with the opportunity to learn and use advanced techniques such as flow cytometry and plate-reader-based plasmid transfer quantification.
• Image and track fluorescently labeled bacteria and chemical plumes in shear flow, and analyze the data with quantitative image- and data-analysis pipelines.
• Test clinically relevant bacteria and freshwater (e.g. lake) bacteria, to assess the potential for chemotaxis-driven spread of resistance in the environment.
• Contribute data to mathematical models of plasmid spread.

Profile

We are looking for a hands-on, skilled and curious engineer who loves to build new tools and is interested in using them to answer fundamental scientific questions. Ideal candidates hold an MSc degree in bioengineering, mechanical engineering, mechatronics, electrical engineering, environmental engineering, physics or a related discipline, and have some (not necessarily all) of the following skills:

• Practical experience in prototyping and manufacturing, for example CAD, 3D printing, machining (strongly preferred).
• Experience with control systems and instrumentation, for example motor control, sensors, microcontrollers, and automation or data-acquisition code (Python, MATLAB, LabVIEW or similar) (preferred).
• Openness to gain experience in the microbiology laboratory: bacterial cultures, sterile technique, plate readers and flow cytometry.
• Familiarity with microscopy, image analysis, fluid mechanics or microfluidics (beneficial but not necessary).
• Fluency in English (oral and written), enthusiasm for working in an interdisciplinary and international team, and the drive to pursue scientific excellence (required).

We offer

ETH Zurich is a family-friendly employer with excellent working conditions. You can look forward to an exciting working environment, cultural diversity and attractive offers and benefits.

We value diversity and sustainability

In line with our values, ETH Zurich encourages an inclusive culture. We promote equality of opportunity, value diversity and nurture a working and learning environment in which the rights and dignity of all our staff and students are respected. Visit our Equal Opportunities and Diversity website to find out how we ensure a fair and open environment that allows everyone to grow and flourish. Sustainability is a core value for us - we are consistently working towards a climate-neutral future.

Curious? So are we.