Student Projects

Antimicrobial susceptibility testing for aerobic bacteria based on the oxygen consumption measurement

Timeframe
Master Thesis (5-6 months full-time), Internship (2-6 months full-time) or Semester Project (2-4 months part-time)

Contact
Yang LIU (yang.liu@epfl.ch)

Description
For aerobic bacteria, the oxygen consumption is an indicator of their viability. Under the exposure of antimicrobials, bacteria might be killed or inactive and consume no more oxygen.
The oxygen concentration measurement is based on a nanoparticle from a collaborator, for which the fluorescent signal is quenched in the presence of oxygen. Thus, a correlation between the concentration of oxygen and the fluorescent signal is established.
This project consists of
1. To realize of a microfluidic chip to conduct the oxygen concentration measurement by 3D printing or photolithography.
2. To find an appropriate way to sterilize the chip in order to reuse the nanoparticle spot
3. To perform series of experiments with antimicrobials.
4. To construct a data processing program with MATLAB.
Some preliminary experiments to validate of the working principle have been done.

Study of antimicrobial effects on the bacterial motility (E.coli ATCC 25922)

Timeframe
Master Thesis (5-6 months full-time), Internship (2-6 months full-time) or Semester Project (2-4 months part-time)

Contact
Yang LIU (yang.liu@epfl.ch)

Description
Bacterial motility is an important indicator of the bacterial viability. It can be studied with time-lapse imaging.
This project aims to study the antimicrobial effects on bacterial motility. A microfluidic chip with mixing module and observation chamber was designed. Firstly, student will be able to do image acquisition of the swimming bacteria with digital microscopy or optical microscopy (to be discussed). To promote bacterial movement on the surface, surface modification will need to be performed. Then Image processing involves extracting the coordinates of bacteria from the image, bacterial trajectories and extract statistical information such as velocities and bacterial quantity.
Knowledge with MATLAB programming is required; photolithography knowledge and microbiological background will be an advantage.
Main tasks:
• PDMS or UV adhesive chip fabrication and surface modification
• Time lapse imaging with microscopy

Real-time monitoring of dissolved oxygen in a microfluidic chip

Timeframe
Master Thesis (5-6 months full-time), Internship (2-6 months full-time) or Semester Project (2-4 months part-time)

Contact
Roger Krenger (roger.krenger@epfl.ch)

Description
Measurement of the oxygen consumption rate (OCR) of living organisms is a key indicator of metabolic activity. This technology is widely used to characterize mitochondrial respiration in cells and to assess the fitness of top athletes, for example.

The aim of this project is to fabricate a microfluidic device with integrated optical luminescence sensors for the continuous measurement of oxygen content on the chip. These optical sensors are based on the changing intensity of luminescence of a substance which is sensitive to the oxygen concentration in its surroundings. Because PDMS, the most commonly used material for the fabrication of microfluidic chips, is oxygen permeable, it is not suitable for on-chip OCR measurements. In this work, the chips will be made with an alternative fabrication approach.

Upon successful implementation of OCR-sensing on-chip, the device may be applied for experiments on cells or C. elegans.

Microfluidic devices for long-term culture and analysis of C. elegans nematodes

Timeframe
Master Thesis (5-6 months full-time), Internship (2-6 months full-time) or Semester Project (2-4 months part-time)

Contact
Fabien Tâche (fabien.tache@epfl.ch)

Description
The Laboratory of Microsystems (LMIS2) is developing an innovative laboratory device for drug discovery research. The technology employs robotics and computer vision for the automated culture and analysis of micro-organisms within microfluidic chips, as powerful biological models to investigate human diseases and test their potential cures. In this framework, we look for students to contribute to the development of the following microfluidics components:

• Highly-integrated distribution valves with a high number of outputs
• High resolution syringe pumps
• New generation of microfluidic chips, including the optimization of the manufacturing process

The aim of this project is to design one (or several) of the devices listed above, manufacture them, and characterize their performances. If the implementation is successful, the devices will be integrated in the existing robotic platform and used for experiments on C. elegans.

The overall project holds great potential to represent a breakthrough in biomedical research and, as such, resides at the core of a startup project (Nagi Bioscience).

Biological assays on C. elegans nematodes using new generation microfluidic platform

Timeframe
Master Thesis (5-6 months full-time), Internship (2-6 months full-time) or Semester Project (2-4 months part-time)

Contact
Fabien Tâche (fabien.tache@epfl.ch)

Description
The Laboratory of Microsystems (LMIS2) is developing an innovative laboratory device for drug discovery research. The technology employs robotics and computer vision for the automated culture and analysis of micro-organisms within microfluidic chips, as powerful biological models to investigate human diseases and test their potential cures. In this framework, we look for students to contribute to the development of experimental protocols and run biological assays. This includes the following tasks:

• Definition of experimental protocols
• Implementation and optimization of protocols (manipulation of C. elegans using microfluidics, feeding of worms, control of worm chamber temperature, …)
• Perform biological assays to validate the technology and protocols

This project is highly multidisciplinary, because it is at the interface of technology, life sciences and entrepreneurship.

The overall project holds great potential to represent a breakthrough in biomedical research and, as such, resides at the core of a startup project (Nagi Bioscience).

Tracking and analysis of C. elegans nematodes at single-organism resolution

Timeframe
Master Thesis (5-6 months full-time), Internship (2-6 months full-time) or Semester Project (2-4 months part-time)

Contact
Fabien Tâche (fabien.tache@epfl.ch)

Description
The Laboratory of Microsystems (LMIS2) is developing an innovative laboratory device for drug discovery research. The technology employs robotics and computer vision for the automated culture and analysis of micro-organisms within microfluidic chips, as powerful biological models to investigate human diseases and test their potential cures. In this framework, we look for students to contribute to the development of a tracking and analysis software. This project includes the following tasks:

• Implementation of worm tracking algorithms
• Implementation of a worm phenotype analysis software
• Characterization, optimization and validation of algorithms
• Implementation of a graphical user interface (GUI) displaying the results of automated analysis

This project requires good software development and image processing skills. Machine learning knowledge is a plus.

The overall project holds great potential to represent a breakthrough in biomedical research and, as such, resides at the core of a startup project (Nagi Bioscience).

A microfluidic single worm dispenser

Timeframe
Master Thesis (5-6 months full-time), Internship (2-6 months full-time) or Semester Project (2-4 months part-time)

Contact
H. Baris Atakan (baris.atakan@epfl.ch)

Description
The nematode C. elegans is of great interest in biomedical research, as it is a useful model organism to study drug screening, aging and longevity due to its short life span, hermaphrodite behavior and genetic similarity with humans. As C. elegans are normally cultured in colonies, it is quite challenging to isolate a single nematode from the rest. Traditional approaches to handle C. elegans at single worm resolution are extremely tedious and time consuming.

The aim of this project is to improve our previously fabricated single C. elegans dispenser and enable off-chip culturing studies.

For this project, the student will be working mostly in our laboratory and, if required, in the cleanroom. A basic knowledge of SU8 photolithography and PDMS casting can be advantageous.

Permeabilizing C. elegans embryos

Timeframe
Master Thesis (5-6 months full-time), Internship (2-6 months full-time) or Semester Project (2-4 months part-time)

Contact
H. Baris Atakan (baris.atakan@epfl.ch)

Description
Embryos of the nematode C. elegans are trending in the research, as it can be a proper model organism with a shorter development duration compared to its larvae. Permeabilization of embryo shell is of utmost importance as this development may enable possibility of various drug screening studies in a short time span.

The aim of this project is to build a microfluidic platform to permeabilize C. elegans embryo shell with bleach solution. A controlled study of bleach solution intake is required to create permeabilized embryo shells.

For this project, the student will be working part-time in the cleanroom and part-time in our laboratory. A basic knowledge of SU8 photolithography, Bosch process and PDMS casting will be advantageous.