Student Projects & Teaching

Student projects

We are constantly looking for motivated Bachelors and Masters students from any scientific or engineering background to experience interdisciplinary research with us. Specific currently open projects are listed below, but don’t hesitate to contact us with your interests:

1) Super-resolution live-cell imaging of mitochondrial division

Motivation: Building a biophysical model for mitochondrial division

Background: Mitochondria are respiratory organelles that produce cellular ATP and play important roles in Ca2+ buffering, lipid metabolism and apoptotic cell death. Mitochondria form a highly dynamic network in the cell and constantly undergo fusion and division (fission). Disturbances in mitochondrial dynamics negatively impact cell viability and have been associated with various human diseases, such as neurodegeneration, cancer and cardio-vascular diseases. However, intracellular signals and physiological properties that trigger the division, especially in regard to their distinct function, remain obscure. This lack of understanding is mostly due to the fact that mitochondria are too small to be properly resolved by conventional light microscopy. But developments in super-resolution microscopy now allow to investigate the dynamic behaviour of mitochondria and their interaction partners closer to the molecular scale.

Details: The project will be focused on collecting super-resolution time-lapse movies of living cells using a variety of fluorescent markers and biosensors. The student will be able to acquire expertise in diverse fields, from cell biology to optics and image analysis, while working in a highly interdisciplinary research group.

Skills: Bringing along any or all of the following skills would be a plus:

  • Fluorescence microscopy
  • Cell culture and fluorescent sample preparation
  • Quantitative image analysis (ImageJ)

Figure 1  Structured-illumination microscopy (SIM) of  mitochondria  (magenta) and endoplasmic reticulum (green) in a Cos-7 cell.

Send a mail with your motivation directly to Tatjana Kleele (tatjana.kleele@epfl.ch)

2) Simulating realistic synthetic data sets for developing a self-driving microscope 

Motivation: Many of the breakthroughs made in the fields of computer science and image processing have not yet been applied to the main tools driving biological discovery. The Master project proposed here would contribute to developing a self-driving, or “smart” super-resolution microscope.

Goal: The goal is to build an interactive software (“Flight Simulator”) for generating simulated super-resolution datasets. It should also enable on-the-fly modification of the acquisition parameters in an attempt to mimic, for the first time, what would actually happen on the microscope when an expert does the acquisition. Such an interface is a requirement for the development, validation and comparison of future automated, machine learning driven, routines dedicated to super-resolution microscopy.

Background: Super-resolution microscopy circumvents the diffraction limit of light, allowing nanoscale spatial resolution while retaining the advantages of fluorescence microscopy (e.g. high affinity, multi-color, live cell). As such it offers a unique insight into cells processes and architecture at protein level. Single molecule localization microscopy (SMLM), although providing the biggest gain in spatial resolution, remains paradoxically relatively inaccessible to purely biology laboratories studying complex biological processes. This is due to the high level of expertise required to optimize image acquisition.

Details: The Master project will be shared between two labs (the Laboratory of Experimental Biophysics led by Prof. S. Manley & the Biomedical Imaging Group led by Prof. M. Unser) and under the joint supervision of Dr. Sage and Dr. Griffié, allowing the student to work in a pluri-disciplinary environment.

The focus and scope of this project can be adapted to interests and constraints of the aspirant. Ideal starting time would be spring or summer 2019.

Send a mail with your motivation directly to Juliette Griffié (juliette.griffie@epfl.ch)

3) PAINT the town red. Super-resolution imaging using fluorescently-labeled low-affinity monobodies

The principle of single molecule localization microscopy lies in the separation of individual dye molecules through the induction of photoswitching (blinking). In DNA-PAINT, the transient binding of short dye-labeled oligonucleotides to their complementary target strands creates the necessary ‘blinking’ to enable localization microscopy. We will apply the same principle of transient binding but instead use labelled monobodies that can directly interact with the respective target structure. This new approach has two advantages: (1) monobodies can be selected at different affinities and (2) they directly interact with the protein of interest thereby reducing the size of the label compared to an antibody as in DNA-PAINT.

The project is a collaboration between our group and the labs of Pierre Gönczy and Oliver Hantschel (both SV, EPFL). It is suitable for a MSc thesis and could start in spring or summer 2018. If you’re interested, please apply directly to Christian (christian.sieben@epfl.ch).

4) Biophysics of mitochondrial gene-expression 

Background: Mitochondria are the powerhouse of the cell. Efficient conversion from sugar to ATP – the energy-currency inside all living cells – happens through the Krebs Cycle and Oxidative Phosphorylation (OXPHOS) in the mitochondrial matrix and across the inner mitochondrial membrane. Mitochondria also harbour their own DNA (mtDNA) which encodes for 13 essential protein components of the OXPHOS-machinery and both, tRNAs & rRNAs necessary to translate the mitochondrial transcripts (mtRNA) into the proteins. To orchestrate all of these steps together with nuclear-gene expression and cellular energy demands, mtRNA are heavily processed and regulated. Interestingly, both mtDNA and mtRNA form distinct foci inside mitochondria, together with respective regulatory and processing proteins. These foci are termed nucleoids (mtDNA et al.) and Mitochondrial RNA Granules (MRGs – mtRNA et al.) respectively. Shedding light on their biophysical organisation and interplay are the topic of this project.

Content: This research is placed at the interdisciplinary frontier between fundamental biology, physics and micrsocopy, and biotechnology. A project-student will have the opportunity to learn and develop different superresolved fluorescent microscopy techniques and protocols such as high-throughput Stochastic Optical Reconstruction Microscopy (htSTORM) and instant Structured Illumination Microscopy (iSIM). On top of image acquisition, biological sample preparation as well as quantitative image analysis are key challenges to answer the underlying biological question. Depending on the interest, skills and time-frame of an aspirant, the focus of the project can be set on any or all of these aspects.

Key skills: Bringing along any or all of the following skills would be a plus. But they can just as well constitute the learning outcome.

– Project planning

– Programming (MATLAB, Python, Machine Learning)

– Cell culture and fluorescent sample preparation

– Quantitative image analysis (Fiji, custom scripts)

– Superresolution microscopy

– Biophysical modelling

Duration: The projects are suitable for variable durations, from Semester Project to Master Thesis and can be adapted according to the interests, skills and time-frame of the student. Ideal starting dates are Spring/Summer 2019.

If you’re interested, please apply directly to Timo Rey (timo.rey@epfl.ch).

Courses

Biophysics I

To examine cellular systems through physical models and quantitative approaches to analysis.

MINEUR, 2015, Spring semester, language : en

General Physics I

Students will learn the principles of mechanics to enable a better understanding of physical phenomena, such as the kinematics and dyamics of point masses and solid bodies. Students should acquire the capacity to quantitatively conceptualize and analyze these effects with the appropriate theoretical tools.

ALL SECTIONS, 2014-2016, Fall semester, language : en

Physique générale II: Thermodynamique

Le but du cours de Physique générale est de donner à l’étudiant les notions de base nécessaires à la compréhension des phénomènes physiques. L’objectif est atteint lorsque l’étudiant est capable de prévoir quantitativement les conséquences de ces phénomènes avec des outils théoriques appropriés.

Section de génie mecanique, 2018-, Semestre de printemps, language : fr