[Translate to English:] Organ on a Chip

Research Areas and Projects

ENROL aims at engineering functional interfaces between inorganic and bio-organic systems in order to push them towards new levels of understanding and technological applications. We thus propose a combined and synergistic effort based on the following three research areas (RA):

 

  • RA1: Theoretical Prediction, Model Systems, and Analysis (Research Projects 1 to 7): Self-assembly of bio-molecules into desired structures requires a deeper understanding of the interactions of the constituent entities. Here, theoretical approaches (Bianchi, Kahl, Hellmich, Grosu) and the study of model systems (Valtiner) are indispensable to predict these properties. Eventually, new approaches as developed in RA2 demand for new data analysis strategies (Heitzinger, Sablatnig).

Partner organizations: (i) CEST, Labdia GmbH, Carl Zeiss Microscopy GmbH (ii) Utrecht University, Mines/University of Lyon.

  • RA2: Synthesis, Structuring & Instrumentation (Research Projects 8 to 15): Surfaces will be engineered via synthetic polymer chemistry (Baudis, Mihovilovic, Unterlass) or by using techniques based on the self-assembly of (bio‑) molecules and colloidal particles (Sevcsik, Bianchi, Unterlass). Two-photon polymerization will be used to generate 3-dimensionally structured materials (Ovsianikov, Baudis). New chemistry will open the pathway to defined functionalization (Mikula). Novel multimodal imaging approaches will be established for (automated) quantification of (multi-)cellular responses (Schütz, Ertl, Lendl, Marchetti-Deschmann, Thurner, Birner-Grünberger).

Partner organizations: (i) Tagworks, SAICO, GenSpeed, TissUse, Carl Zeiss Microscopy GmbH, Optics11, Lithoz (ii) MedUni Wien, Max Planck Institute of Biochemistry, ETH,   BINA, Harvard Medical School, Massachusetts General Hospital

  • RA3: Biological Applications (Reasearch Projects 15 to 24): Synthesis and structuring will be guided by specific biological applications. They will be used as experimental validation systems, which enable us to refine and continuously improve the novel interfaces based on functional cell biological readout models, such as multicellular clusters (Ovsianikov, Guillaume, Andriotis), immune cells (Schütz, Sevcsik, Herwig), funghi (Mach, Aigner-Mach), neurons (Wanzenböck), and cardiomyocytes (Birner-Grünberger). 

Partner organizations: (i) 3Helix, Optics11, TissUse, Poietis, Novogymes, Clycostem (ii) MedUni Wien, Agroscope.

 

These three research areas are highly interconnected to leverage continuous exchange of the latest results and transfer of know-how between the different groups. In consequence, each PhD project is embedded in a stimulating research environment, which will facilitate a continuous process of project adjustments in order to improve the developed materials, the chosen experimental approaches, and the established theoretical prediction algorithms.

Candidates may also propose their own PhD research project, i.e., different from the ones proposed below. In this case the candidates should first establish contact with the supervisor representing this research field , opens an external URL in a new windowand ask for a letter in support of the project, which they will upload together with a summary of the proposed research project. An Ethics Support Team, opens an external URL in a new window is also in place to assist the candidates during the preparation of their proposed research project should they choose not to apply for one of the proposed ones.

Co-funded by the European Union

[Translate to English:] EU flag

This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 101034277.

Research Project 1

[Translate to English:] Research Project 1

Supervisor

Gerhard Kahl

Self-assembly of biological, bio-related and colloidal macromolecules

The primary aim of this research project is to help guide with computer simulations and artificial intelligence algorithms experimentalists to design and to synthesize biological, bio-related and colloidal macromolecules that self-assemble into desired target structures.

Research Project 2

[Translate to English:] Research Project 2

Supervisor

Christian Hellmich

Atoms-to-beam homogenization of biomacromolecules

The primary aim of this research project is to help to guide with computer simulations and artificial intelligence algorithms experimentalists to design and to synthesize biological, bio-related and colloidal macromolecules that self-assemble into desired target structures.

Research Project 3

[Translate to English:] Research Project 3

Supervisor

Emanuela Bianchi

Design of anisotropic DNA origami nanoparticles for programmed self-assembly

The primary aim of this research project to precisely tackle the design principles that govern the self-assembly of functionalized DNA-origami as building blocks of tailored materials.

Research Project 4

[Translate to English:] Research Project 4

Supervisor

Markus Valtiner

Soft matter in confinement and under potential control

The primary aim of this research project is to measure and simulate consequences of confinement and approach of two cell membranes, while varying their surface potential. Structures and forces will be evaluated, mediated by the assembly of polymeric model compounds that resemble typical plasma membrane structures.

Research Project 5

[Translate to English:] Research Project 5

Supervisor

Radu Grosu

Reinforcement and Supervised Learning with Neural Circuit Policies

The purpose of this research project is to develop supervised and reinforcement learning techniques for NCPs, and apply them in the control of the autonomous microscopy system for adaptive experimentation in cell biology, available in the lab of our project partner Gerhard Schütz.

Research Project 6

[Translate to English:] esearch Project 6

Supervisor

Clemens Heitzinger

Advanced Probabilistic Clustering Algorithms for Super-Resolution Microscopy

This PhD project focuses on the development of advanced probabilistic clustering algorithms to advance super-resolution microscopy.

Research Project 7

[Translate to English:] Research Project 7

Supervisor:

Robert Sablatnig

Immunophenotyping for Diagnosis in Childhood Leukemia

The primary aim of this research project is to improve the treatment of children with acute leukemia using machine learning technology.

Research Project 8

[Translate to English:] Research Project 8

Supervisor

Stefan Baudis

A Material Platform for 4D Tissue Models

The primary aim of this research project is the design, synthesis and application of a material platform based on photocurable hydrogels.

Research Project 9

[Translate to English:] Research Project 9

Supervisor

Marko Mihovilovic

A Generic Approach for Target Identification of Natural Products Employing a Tandem Photoaffinity-Clicking Strategy

The primary aim of this research project involves the synthetic implementation of the multi-functional platform exemplified on currently worked on natural compound targets in the area of lignans with anti-inflammatory activity. In addition, stereoselective synthetic access to natural product molecules of interest shall be established and optimized in order to also enable structure-activity profiling and scaffold development.

Research Project 10

[Translate to English:] Research Project 10

Supervisor

Hannes Mikula

Bioorthogonal Turn-off and Dual-release

This PhD project focuses on the development of bioorthogonal bond-cleavage reactions with unmatched chemical performance and unique capabilities. The candidate will design, prepare and investigate next-generation chemical tools that achieve exceptional reaction kinetics, high stability, selectivity and biocompatibility.

Research Project 11

[Translate to English:] Research Project 11

Supervisor

Martina Marchetti-Deschmann

Multimodal imaging – a picture says more than a thousand datapoints

The primary aim of this PhD thesis is to determine UV effects on epidermal keratinocytes and the extracellular matrix (mainly collagen) by using different analytical imaging modalities in order to achieve holistic information on UV damage in the tissue context upon correlation of generated data.

Research Project 12

[Translate to English:] Research Project 12

Supervisor

Philipp Thurner

Correlative multimodal imaging of human meniscal tissue

The primary aim and goal of this research project is to develop a protocol to enable cross-comparison of chemical µMRI images with spatially resolved mechanical data from AFM/NI and MALDI-TOF imaging.

Research Project 13

[Translate to English:] Research Project 13

Supervisor

Gerhard Schütz

Development of an Autonomous Microscopy Platform for Adaptive Experimentation in Cell Biology

The aim of this research project is to develop an autonomous microscopy system, which enables the automated interpretation of cell biological images, and – based on a set of user-defined rules – a corresponding response exerted on the cell by the microscopy system. The autonomous system will be based on a combined super-resolution – atomic force microscopy setup, which shall be used for studying early T cell activation.

Research Project 14

[Translate to English:] Research Project 14

Supervisor

Bernhard Lendl

Next Generation Super-resolution Chemical Imaging

The aim of this research project is the design and construction of a novel, mid-IR laser based set-up for photothermal spectroscopy and imaging below the diffraction limit as well as the application of the developed set-ups to a variety of different samples available within ENROL ranging from aqueous solutions, cells to biological materials (bones, joints etc.).

 

Research Project 15

[Translate to English:] Research Project 15

Supervisor

Peter Ertl

μMechanoLymph

This study will address the following research questions: 1) Can a chip-based blood-lymph interstitial interface model reproduce physiologic interstitial flow conditions to study molecule movement from the bloodstream into the interstitial space to subsequent uptake into the lymphatic system and 2) to what extent do lymphatic endothelial cells actively transport molecules across the lymphatic endothelium via receptor-mediated transport (LYVE-1, hyaluronan) and vesicular (clathrin, albumin) transport.

Research Project 16

[Translate to English:] Research Project 16

Supervisor

Aleksandr Ovsianikov

Controlled Vascularization for Organ-on-Chips

The primary aim of this PhD thesis is to develop a versatile toolset to create controlled microvascular networks in different tissues. The outcomes of this work have the potential to revolutionize the Organ-on-Chip field.

Research Project 17

[Translate to English:] Research Project 17

Supervisor

Orestis Andriotis

Micromechanical assessment of cell clusters

The primary aim of this research project is to develop, build, validate and use an instrument for micro- and nanoscale mechanical characterization of cell clusters. The development and realization of the instrument will in a large part be based on a recently developed prototype for nanotensile testing.

Research Project 18

[Translate to English:] Research Project 18

Supervisor

Olivier Guillaume

Bioprinting of 3D Immunogenic Skin Model

The primary aim of this research project is to develop in vitro a skin equivalent tissue, integrating not only skin cells, but also a viable immune compartment.

Research Project 19

[Translate to English:] Research Project 19

Supervisor

Robert Mach

An albino Aureobasidium pullulans for biotechnological application (ALABAMA)

The primary aim of this research project is to understand which regulatory pathways and mechanisms (cAMP signaling, MAP kinase pathway, epigenetic mechanisms, yet unknowns, etc.) are responsible for the production of pullulan and melanin in A. pullulans. Ultimately, this knowledge shall contribute to the design of strain that produce melanin-free pullulan.

Research Project 20

[Translate to English:] Research Project 20

Supervisor

Astrid Mach-Aigner

Secretory stress management in Trichoderma reesei

This research project focuses on studying the expression of cellulases by the industrially employed fungus Trichoderma reesei. The major aim is to learn whether the unwanted reduction of transcript levels of genes coding for these cellulases happens in T. reesei only at a transcriptional level, possibly by a mechanism called RESS (repression under secretion stress), or also on a post-transcriptional level.

Research Project 21

[Translate to English:] Research Project 21

Supervisor

Eva Sevcsik

Stimuli-responsive nanostructured biointerfaces for T-cell activation

The aim of this research project is to probe the molecular mechanisms of early T-cell signaling. Generating 3D DNA origami structures will allow to manipulate the axial position of ligands; heterobifunctional DNA origami structures will be employed to decipher the effect of co-receptors and antagonists.

Research Project 22

[Translate to English:] Research Project 22

Supervisor

Ruth Birner-Gruenberger

Functional Proteomics of GliFlozin Drug (Off) Targets

The primary aim of this research project is to elucidate the cellular effects and molecular mechanism of gliflozins on cardiomyocytes. To this end, the ESR will use cardiomyocyte cell models and perform functional phenotyping

Research Project 23

[Translate to English:] Research Project 23

Supervisor

Heinz Wanzenboeck

Electrophysiology on a Microchip

This research project focuses on the development of a beating human mini-heart on a microelectronic chipby using the unique capabilities of microfabrication  to (i) replicate the in-vivo environment of the human organism on a microchip and (ii) utilize electrical recordings with the microelectrodes on the chip to monitor the beating activity of a human “miniature heart” (aka cardioid).

Research Project 24

[Translate to English:] Research Project 24

Supervisor

Christoph Herwig

Digital twin-based bioprocess development for cell and gene therapy

The primary aim of this research project is to develop and deploy digital twins to technologize and enable robust ATMP processes, using NK cells as a model system.