A well-defined double emulsion system for high-throughput biological screening experiments

Water-in-oil-in-water emulsions or double emulsions (DB) could be the next research focus of droplet-based microfluidics. The semi-permeable interface of the DB and the aqueous surrounding environment provide new opportunities for performing high-throughput biological screening experiments. In this project, you will define a DB system and optimize its workflow for the usage in a specific biological task. You will have a lot of fun to play with these lovely DBs. This project is suitable for creative master students.

Contact person

Dr. Yun Ding

High-throughput methods for capturing 3D chromosome conformation

Genome DNA coding is linear. However, the organization of the genome is in a 3D configuration, forming chromosomes. Such 3D configuration of chromosome is complex, dynamic, and crucial for gene regulation. The goal of this project is to develop a high-throughput workflow to perform 3C (chromosome conformation capture) experiments at the single chromosome level. This project is suitable for hardcore master students.

Contact person

Dr. Yun Ding

CRISPR-based electrochemical biosensor for drug-resistance bacteria detection using point-of-care platforms

CRISPR-Cas biosensor has emerged biosensor field in this last few years and empowered analytical performance for point-of-care (POC) diagnostics down to the single nucleotide level. Developing of CRISPR-Cas technology in biosensing are promising for ease-of-use with great sensitivity and selectivity, allowing Cas enzyme manipulation by designing guide-RNA. To develop POC devices, simple, inexpensive, robust, and easy-to-use system is required. Electrochemical detection is one of the most powerful analytical methods, that meets the POC criteria, and thus will be used in this project. To conclude, we aim to develop a novel electroanalytical platform for drug-resistance bacteria (MRSA) detection based on the state-of-the-art electronic nucleic acid knowledge to achieve highly sensitive and promising devices for POC diagnostics.

Contact person

Akkapol Suea-Ngam

Enzymes of Glycobiology on a Chip

Glycobiology is the science of the carbohydrate sugar-coating of Proteins and lipids. Carbohydrate interactions play a role in crucial processes such as immunology, cell-cell interactions, protein quality control and many others. Protein glycosylation starts in the ER and continues in the Golgi apparatus. The enzymes of the glycosylation machinery have recently been studied in the Aebi lab here at ETH.

This project aims to put parts of the glycosylation machinery on a microfluidic platform. The scope of the student’s project can be adjusted according to her or his interests and type of the thesis. Aspects of the project may be:

• expression and purification of enzymes from insect cell cultures

• design, manufacturing, testing and improvement of microfluidic platform

• in vitro and on-chip enzymatic assays

This project is suitable for both part-time and full-time work in bachelor or master studies.

Contact person

Florin Isenrich

Dynamics of Protein and Polymer Self-assembly with Droplet Microfluidics

This project is a collaboration between the groups of Prof. Arosio and Prof. deMello to study protein liquid-liquid phase separation (LLPS) with microfluidic technology.

Protein LLPS is an important biochemical phenomenon. For instance it occurs in cells, when proteins form dynamic membraneless compartments as a response to stress or to control biochemical reactions. In addition to being biologically relevant, LLPS can also be used to create new biomimetic materials for drug delivery and other applications.

Microfluidic technologies represent attractive tools to study thermodynamic and kinetic aspects of LLPS, for features such as low sample consumption, fast heat transfer and excellent spatiotemporal control.

The student will learn the fabrication of the microfluidic device of interest and will perform experiments to study the reversibility and the kinetics of LLPS. Systems of increasing complexity will be studied, from biomimetic polymers to proteins, according to the time availability. The student will analyse the data mainly with Matlab and ImageJ.

Type of work: 70% experimental, 30% data analysis and modelling

Type: master thesis (preferable), bachelor thesis (possible)

Contact person

Alessia Villois

A High-Throughput Optofluidics for Rare Cells Enrichment

Rare cells sorting is important for single cell analysis and disease diagnosis. However, these cells, like circulating tumor cells (CTCs), usually present at very low levels (around 1~10 CTCs per milliliter), which challenges the current benchtop fluorescence-activated cell sorting systems. For this project, a high throughput microfluidic flow cytometer for CTCs enrichment will be developed, the goal of which is to provide a pre-sorting strategy which can enrich the CTCs concentration to a large extent in quite a short time with high accuracy before downstream analysis.

Contact person

Yingchao Meng

Microfluidic System for Extracellular Vesicles Fractionation

Extracellular vesicles (EVs), including apoptotic bodies, microvesicles and exosomes, is a kind of lipid-based vector which contains nucleic acids and proteins for intracellular communication, demonstrating great potential for early disease detection and therapeutic drug delivery systems. Traditional separation methods, e.g. differential centrifugation and ultrafiltration, are time-consuming and labor-intensive, and suffer from low sample purity or low sample yield. Towards this end, a novel and simple microfluidic system for isolation of EVs based on their size will be developed. Downstream analysis, e.g. western blot and sequencing, will be employed, hopefully providing an easy-operating way for early detection of cancer.

Contact person

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Yingchao Meng, Mohammad Asghari

Label-Free Quantitative Detection of Exosomal Protein via a On-chip Integration of Optofluidic Platform for Cancer Diagnosis

Exosomes (EVs) play important roles in cancer development, metastasis, and drug resistance, which makes them promising biomarkers for cancer screening, diagnosis, and monitoring. Exosome isolation followed by bioanalysis would enable a non-invasive and remote biopsy of the tumor mass. The proposed methods include the isolation of exosome by optical force followed by prism-based surface plasmon resonance analysis using an integrated optofluidic chip. Put simply, we aim to develop an on-chip optofluidic platform integrated for non-invasive EVs sorting and characterizing that can be applied to a wide range of biological matrices and addresses the most challenging technological bottleneck in EVs research.

Contact person

Dr. Ying Du