Organ on a Chip

Forschungsbereiche und Projekte

ZIEL

ENROL zielt darauf ab, funktionelle Schnittstellen zwischen anorganischen und bio-organischen Systemen zu entwickeln, um sie auf ein neues Niveau des Verständnisses und der technologischen Anwendungen zu bringen. Wir schlagen daher eine kombinierte und synergetische Anstrengung vor, die auf den folgenden drei Forschungsbereichen (RA) basiert:

  • RA1: Theoretische Vorhersage, Modellsysteme und Analyse (Forschungsprojekte 1 bis 7): Die Selbstorganisation von Biomolekülen zu gewünschten Strukturen erfordert ein tieferes Verständnis der Wechselwirkungen zwischen den einzelnen Bestandteilen. Hier sind theoretische Ansätze (Bianchi, Kahl, Hellmich, Grosu) und die Untersuchung von Modellsystemen (Valtiner) unerlässlich, um diese Eigenschaften vorherzusagen. Schließlich erfordern neue Ansätze, wie sie in RA2 entwickelt wurden, auch neue Strategien der Datenanalyse (Heitzinger, Sablatnig).

Partnerorganisationen: (i) CEST, Labdia GmbH, Carl Zeiss Microscopy GmbH (ii) Universität Utrecht, Mines/Universität von Lyon.

  • RA2: Synthese, Strukturierung und Instrumentierung (Forschungsprojekte 8 bis 15): Oberflächen werden durch synthetische Polymerchemie (Baudis, Mihovilovic) oder durch Techniken, die auf der Selbstorganisation von (Bio-)Molekülen und kolloidalen Partikeln basieren (Sevcsik, Bianchi), hergestellt. Die Zwei-Photonen-Polymerisation wird zur Erzeugung dreidimensional strukturierter Materialien eingesetzt (Ovsianikov, Baudis). Neue chemische Verfahren werden den Weg für eine definierte Funktionalisierung eröffnen (Mikula). Neue multimodale Bildgebungsansätze werden für die (automatisierte) Quantifizierung von (multi-)zellulären Reaktionen etabliert (Schütz, Ertl, Lendl, Marchetti-Deschmann, Thurner, Birner-Grünberger).

Partnerorganisationen: (i) Tagworks, SAICO, GenSpeed, TissUse, Carl Zeiss Microscopy GmbH, Optics11, Lithoz (ii) MedUni Wien, Max-Planck-Institut für Biochemie, ETH, BINA, Harvard Medical School, Massachusetts General Hospital

  • RA3: Biologische Anwendungen (Forschungsprojekte 16 bis 24): Synthese und Strukturierung werden sich an spezifischen biologischen Anwendungen orientieren. Sie werden als experimentelle Validierungssysteme verwendet, die es uns ermöglichen, die neuartigen Schnittstellen anhand von funktionellen zellbiologischen Messmodellen zu verfeinern und kontinuierlich zu verbessern, wie z.B. multizelluläre Cluster (Ovsianikov, Guillaume, Andriotis), Immunzellen (Schütz, Sevcsik, Herwig), Pilze (Mach, Aigner-Mach), Neuronen (Wanzenböck) und Kardiomyozyten (Birner-Grünberger).

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


Diese drei Forschungsbereiche sind eng miteinander verknüpft, um einen kontinuierlichen Austausch der neuesten Ergebnisse und einen Know-how-Transfer zwischen den verschiedenen Gruppen zu ermöglichen. Folglich ist jedes PhD-Projekt in ein anregendes Forschungsumfeld eingebettet, das einen kontinuierlichen Prozess der Projektanpassung ermöglicht, um die entwickelten Materialien, die gewählten experimentellen Ansätze und die etablierten theoretischen Vorhersagealgorithmen zu verbessern.

WICHTIGE INFORMATION

Die Kandidaten können auch ein eigenes PhD-Forschungsprojekt vorschlagen, das sich von den unten vorgeschlagenen Projekten unterscheidet. In diesem Fall sollten die Kandidaten zunächst Kontakt mit dem Betreuer aufnehmen, der diesen Forschungsbereich vertritt, und um ein Unterstützungsschreiben für das Projekt bitten, das sie zusammen mit einer Zusammenfassung des vorgeschlagenen Forschungsprojekts hochladen werden. Ein Ethik-Support-Team steht den Bewerbern bei der Vorbereitung ihres vorgeschlagenen Forschungsprojekts zur Seite, falls sie sich nicht für eines der vorgeschlagenen Projekte bewerben möchten.

 

Acknowledgement

Engineering for Life Sciences - Doctoral Programme

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Research Project 1: ALREADY ASSIGNED

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. Click here, öffnet eine Datei in einem neuen Fenster for more information.

Research Project 2: CLOSED

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. Click here, öffnet eine Datei in einem neuen Fenster for more information.

Research Project 3: CLOSED

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. Click here, öffnet eine Datei in einem neuen Fenster for more information.

Research Project 4: ALREADY ASSIGNED

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. Click here, öffnet eine Datei in einem neuen Fenster for more information.

Research Project 5: ALREADY ASSIGNED

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. Click here, öffnet eine Datei in einem neuen Fenster for more information.

Research Project 9: CLOSED

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. Click here, öffnet eine Datei in einem neuen Fenster for more information.

Research Project 10: ALREADY ASSIGNED

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. Click here, öffnet eine Datei in einem neuen Fenster for more information.

Research Project 11: ALREADY ASSIGNED

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. Click here, öffnet eine Datei in einem neuen Fenster for more information.

Research Project 12: ALREADY ASSIGNED

Research Project 12

Supervisor

Philipp Thurner

Development of a constitutive model of individual collagen fibrils informed by experiments

The goals of this research project is the characterization of the nanomechanical properties of the collagen fibrils, the development of a corresponding constitutive model for collagen fibrils as well as the parameter determination and validation.

Research Project 13: ALREADY ASSIGNED

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. Click here, öffnet eine Datei in einem neuen Fenster for more information.

Research Project 14:CLOSED

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.). Click here, öffnet eine Datei in einem neuen Fenster for more information.

 

Research Project 15: ALREADY ASSIGNED

Research Project 15

Supervisor

Peter Ertl

CellChemChip – Multi-dimensional Tracing of Cells & Molecules

This study aims to combine the key strengths of 3D cell biology, lab-on-a-chip systems, bioorthogonal chemistry, and molecular imaging to enable new approaches to study crucial processes with molecular precision; literally at the interface of chemistry (molecules) and biology (cells).

Research Project 17: ALREADY ASSIGNED

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. Click here, öffnet eine Datei in einem neuen Fenster for more information.

Research Project 19: ALREADY ASSIGNED

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. Click here, öffnet eine Datei in einem neuen Fenster for more information.

Research Project 20: ALREADY ASSIGNED

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. Click here, öffnet eine Datei in einem neuen Fenster for more information.

Research Project 21: ALREADY ASSIGNED

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. Click here, öffnet eine Datei in einem neuen Fenster for more information.

Research Project 22: ALREADY ASSIGNED

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. Click here, öffnet eine Datei in einem neuen Fenster for more information.

Research Project 23: ALREADY ASSIGNED

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). Click here, öffnet eine Datei in einem neuen Fenster for more information.

Research Project 25: ALREADY ASSIGNED

Research Project 25

Supervisor

Christian Dank

Synthesis of Novel Compounds with Potential Therapeutic Activity for the Treatment of Respiratory Diseases

The target is to contribute to the fight against respiratory diseases by providing molecules that mitigate symptoms, reduce inflammation, or improve lung function. Respiratory disorders such as asthma, chronic obstructive pulmonary disease (COPD), cystic fibrosis, pulmonary hypertension, etc. are possible targets.