Master Thesis

The Master’s thesis is at the heart of your studies. You select modules from Entrepreneurial Skills and Advanced Life Science Skills at an early stage to prepare you for work on your thesis. From the start you are part of a research group at the Institute for Chemistry and Biological Chemistry in Wädenswil or in an external company, organisation or research institute. On the basis of your research you answer specific questions and work out solutions which are relevant for research, business and /or society, often in cooperation with national or international partners. The thesis gives you the opportunity to demonstrate that you can apply the knowledge and competencies you have acquired.

You choose the topic of your Master’s thesis in one of the seven centres shown below. You deepen your experimental abilities in your selected area of research and gain detailed insight into the methodologies needed to carry out demanding research projects.

Contact: Prof. Dr. Rainer Riedl

• Design and synthesis of novel inhibitors for therapeutically relevant drug targets:
  A Structural View on Medicinal Chemistry Strategies against Drug Resistance
  S. Agnello, M. Brand, M. F. Chellat, S. Gazzola, R. Riedl, Angew. Chem. Int. Ed. 2019, 58, 3300.
  Details
  and
  Targeting Antibiotic Resistance
  M. F. Chellat, L. Raguž, R. Riedl, Angew. Chem. Int. Ed. 2016, 55, 6600.
  Details
• Linear and cyclic peptides and peptidomimetics as inhibitors of protein-proteininteractions:
  Drug Design Inspired by Nature: Crystallographic Detection of an Auto- Tailored Protease Inhibitor Template
  F. M. Gall, D. Hohl, D. Frasson, T. Wermelinger, P. R. E. Mittl, M. Sievers, R. Riedl, Angew. Chem. Int. Ed. 2019, 58, 4051.
  Details
• Computer aided and fragment based drug design:
  Merging Allosteric and Active Site Binding Motifs: De novo Generation of Target Selectivity and Potency via Natural-Product-Derived Fragments
  Lanz, J. and Riedl, R. (2015), Merging Allosteric and Active Site Binding Motifs: De novo Generation of Target Selectivity and Potency via Natural-Product-Derived Fragments. ChemMedChem, 10: 451-454. Details

Contact: Dr. Susanne Kern

• Synthesis and characterisation of chiral molecules with infrared spectroscopy
  Mazenauer, Manuel R.; Manov, Stole; Galati, Vanessa M.; Kappeler, Philipp; Stohner, Jürgen, 2017. Synthetic routes for a variety of halogenated (chiral) acetic acids from diethyl malonate. RSC Advances. 7(87), p. 55434-55440.
  Details
• Enantio-separation of small chiral molecules
  Spenger, Benjamin; Stohner, Jürgen, 2016. Verfahren zur gaschromatischen Trennung eines Enantiomerengemisches. Patentnummer EP3069777 A1 (2016-09-21).
  Details
• High-resolution rovibrational spectroscopy of small molecules (relevant in atmospheric and environmental chemistry)
  Hobi, Fabian; Berger, Robert; Stohner, Jürgen, 2013. Investigation of parity violation in nuclear spin-rotation interaction of fluorooxirane. Molecular physics. 111(14-15), p. 2345-2362.
  Details
  (Collaboration with ETH Zurich)
• Determination of the absolute configuration of chiral molecules by new spectroscopic techniques
  Pitzer, Martin; Berger, Robert; Stohner, Jürgen; Dörner, Reinhard; Schöffler, Markus, 2018. Investigating absolute stereochemical configuration with coulomb explosion imaging. Chimia. 72(6), p. 384-388.
  Details
  (Collaboration with University Frankfurt and University Marburg)
• ... mixtures ...
  Böselt, Lennard; Sidler, Dominik; Kittelmann, Tobias; Stohner, Jürgen; Zindel, Daniel; Wagner, Trixie; Riniker, Sereina, 2019. Determination of absolute stereochemistry of flexible molecules using a vibrational circular dichroism spectra alignment algorithm. Journal of chemical information and modeling. 59(5), p. 1826-1838.
  Details
  (Collaboration with Novartis and ETH Zurich)
• Reactor design for a bio-ethanol to acetic acid production via catalytic oxidation in a trickle-bed reactor 
  (Collaboration with Biosimio Chemicals, ETH Zurich Startup)

Contact: Dr Kerstin Gari

• Identification of novel target sites for covalent small-molecule antagonists: Protein purification and characterisation of putative target residues through structure-function studies and mass spectrometry.

• Characterisation of protein-protein interactions and protein stability: In vitro interaction studies and cellular protein stability studies to identify novel therapeutic target sites in disease-relevant proteins.

• Development of small-molecule antagonists for disease-relevant proteins: Screening of libraries, and functional characterisation through biochemical and cellular assays.

• Development of isothermal DNA amplification methods for pathogen detection: This project involves protein purification and assay optimisation.

Contact: PD Dr. Mathias Schmelcher

• Recombinant production and characterization of antibacterial proteins, such as cell wall-degrading enzymes from bacteriophages
• Generation of antimicrobial agents with novel properties through protein engineering
• Development of new delivery strategies for antimicrobial agents

Contact: Prof. Dr. Sabina Gerber

• Monoclonal therapeutic antibodies: Recombinant expression and downstream processing of monoclonal antibodies, fragments thereof and new generation antibody formats. Analysis of physicochemical properties and quantification of binding interactions with antigens and Fc receptors.
• Fc receptors for analytics of monoclonal therapeutic antibodies: Recombinant expression, downstream processing and bioanalytics of human receptors and quantification of binding interactions with monoclonal therapeutic IgG antibodies.
• Post-translational modification of therapeutically relevant antigens: Role of N-glycosylation in antigens for binding interaction with monoclonal therapeutic antibodies.
• Structure-activity relationship and reaction mechanism of bacteriophage tailspike proteins: Cloning, recombinant expression, downstream processing, bioanalytics of tailspike proteins and assay development for the characterization of catalysis and specificity for lipopolysaccharide substrates.

Contact: Dr. Margit Winkler

• Hydrogen driven enzymatic reactions: Molecular hydrogen is the most atom efficient reducing agent. Some enzymes and microbes are able to transfer electrons from hydrogen gas to small molecules. In this project, we are exploring enzyme catalysed reduction reactions in a customized hydrogen reactor that allows investigation of multiple reactions at the same time. The workflow includes biocatalyst preparation (cultivation, protein enrichment or purification), reaction engineering (variation of reaction parameters in H2-reactor) and analyses (SDS-Page, gas chromatography and/or high performance liquid chromatography). This research is in collaboration with the Austrian Center of Industrial Biotechnology and other academic and industrial partners.
• Novel enzymes for fragrance synthesis: Many aldehydes come with very characteristic smell – think of cinnamaldehyde and vanillin. Their chemical synthesis is challenging, but a number of enzymes are able to convert more stable and less volatile precursor molecules to valuable aldehydes. In this project, we aim for enzyme discovery by database mining, expression of novel target sequences in E. coli or K. phaffii, experimental proof of enzymatic activity and enzyme characterization. The workflow includes catalyst design (database mining, generation of expression vectors), enzyme production (cultivation, enzyme purification), analyses (Gel-electrophoresis, SDS-Page, gas chromatography and/or high performance liquid chromatography) and enzyme characterisation (substrate scope, ph/T-optima, binding affinities, kinetic parameters). This research is in collaboration with TUWien and the University Zagreb.
• Bringing enzymes that catalyze rare transformations closer to applications: Biosynthetic gene-clusters are composed of multiple components which work together like molecular assembling machines. Some of these clusters are very unique and possess modules which catalyze rare but synthetically valuable reactions. The workflow in the lab may include enzyme production design (generation of expression vectors, evaluation of expression strategies, cultivation, enzyme purification), analyses (Gel-electrophoresis, SDS-Page, GC and/or HPLC), optimization of reaction conditions (substrate concentration, ph, temperature, co-solvents) and enzyme improvement (rational design or directed evolution). One example is a ring-hydroxylase with a rare activity that is investigated in collaboration with the Rheinland-Pfälzischen Technischen Universität.

Contact: Dr. Thomas Schwander

• Biotechnological production of enzymes in fermentation scale and optimization of fermentation conditions with regard to enzyme activity and product formation.
• Combination of enzymes from different microorganisms to integrate novel metabolic pathways into E. coli or yeast.
• Establishment of new enzyme cascades for the production of fine chemicals.

Contact: PD Dr. Christian Frech

• The development of cross-coupling catalysts, which once will find their application in organic laboratories and/or industrial processes is of great importance. We are working in that field and aim the development of such catalyst systems for C-C cross-coupling reactions.
• We are working on the development of patent non-infringing, scalable synthetic routes of pharmaceutically active ingredients.

Contact: Dr. Peter Riedlberger

• Opportunities of micro reaction systems for controllable preparation of particle
• Impact of complex fluids in microchannel flows. Details
• Continuous synthesis of heterogeneous catalysts. Details
• Continuous production of high value products in a microreactor
• Sustainable Engineering – from concept to real plant

Contact: Prof. Dr. Michael Raghunath

• Stem cell applications: Nutraceutical platform based on human progenitor cells (brown and white adipose tissue); Induced pluripotent stem cells, exosome typing, Reporter assays
• Biofabrication: development of enzymatic bio-ink, bioprinted skeletal muscle, voxelated tissue assembly (cancer models, pancreas, fat)
• Immuno-bioengineering: Immunogenic expression of cell membrane structures; 3D bone marrow models
• 3D epithelial constructs: Skin Photobiology; immuncompetent skin models; renal tubules

• Biocatalysis: Production and application of biocatalysts (enzymes and whole cells).
• Process Analytical Technologies (PAT): Fluorescent reporter molecules for bioprocess monitoring and control In-situ process spectroscopy and real-time chemometric evaluation.

Contact: PD Dr. Dominik Brühwiler

• Nanoporous materials with multimodal pore systems and core-shell structures
  M. J. Reber, D. Brühwiler, Dalton Trans. 44 (2015) 17960.
  Details
• Selective functionalization of silica surfaces
  N. Zucchetto, D. Brühwiler, Chem. Mater. 30 (2018) 7280.
  Details
• Novel pigments based on host-guest materials
  P. Woodtli, S. Giger, P. Müller, L. Sägesser, N. Zucchetto, M. J. Reber, A. Ecker, D. Brühwiler, Dyes and Pigments 149 (2018) 456.
  Details
• Mesoporous silica particles for climate research
  R. O. David, C. Marcolli, J. Fahrni, Y. Qiu, Y. A. Perez Sirkin, V. Molinero, F. Mahrt, D. Brühwiler, U. Lohmann, Z. A. Kanji, Proc. Natl. Acad. Sci. 116 (2019) 8184.
  Details

Contact: Dr. Thomas Pielhop

• Pretreatment of lignocellulosic biomass for renewable chemicals production
  Non-edible biomass such as wood or straw (lignocellulose) is a sustainable alternative to fossil raw materials. However, this biomass must first be pretreated, to enable the enzymatic saccharification of the cellulose and thus the fermentative production of various chemicals. In this project, the biomass is treated in a special steam process involving the addition of chemicals (carbocation scavengers), and their effect on cellulose bioconversion and lignin quality will be investigated. The corresponding studies include pretreatment, enzymatic cellulose conversion (cellulases) and lignin analysis (e.g. GPC, NMR).
• Use of lignin in renewable polymers
  Lignin is the second most abundant natural polymer and the main component of non-edible biomass such as straw or wood. It is a promising alternative to reduce or even replace the use of fossil resources in synthetic polymers, without competing with food production. In this project, lignin will be isolated from lignocellulose in a mild process, in order to obtain a lignin of high quality. The process includes biomass pretreatment with carbocation scavengers and lignin isolation by cellulose hydrolysis or by extraction with organic solvents. The quality of the obtained lignin will be analysed using various methods (e.g. GPC, NMR, FTIR). The lignin will then be chemically functionalised, in order to tailor it for its final application, such as plasticiser in concrete or battery applications.
• Sustainable hyaluronic acid production from lignocellulose
  Hyaluronic acid is a polymer that occurs in almost all mammalian tissues and is also used as an active ingredient in cosmetic or medical applications. In this project, the fermentation with a recombinant E.Coli strain will be optimised for hyaluronic acid production. In particular, the use of more sustainable feedstocks (sugars obtained from lignocellulose, molasses) will be investigated. The hyaluronic acid produced in the process will be analysed (e.g. GPC, NMR) and tested for its suitability in cosmetic applications with the help of an industrial partner (Givaudan SA).

Contact: Prof. Dr. Bastian Brand

• Automated synthesis of ion chromatography columns
  Polymer substrate particles are packed into a column and subsequently functionalised layer by layer using flow chemistry. Theses are available in a number of fields with focus on synthesis, automation or analytics.
• Sugar-based surface functionalisation
  Using glycosylation reactions, a sugar-based surface functionalisation is introduced onto hydroxyl-bearing surfaces using grafting-from techniques. The reagent for glycosylation is produced in our group. The proof of concept for this synthesis pathway has been recently accomplished, opening the field for more detailed investigations into the structure of the graft layer and its effects on the material properties.
• Ceramics based stationary phases
  Polymeric and silica-based stationary phases are common in all fields of liquid chromatography. Materials based on ceramics, such as Zirconia, are less abundant due to their difficult functionalisation process. In collaboration with ceramics experts from the School of Engineering we 3D print chromatography columns and functionalise them.
• Monodisperse polymer particle synthesis using Pickering emulsion
  Dispersion polymerisation is commonly used to prepare highly monodisperse polymer particles in a diameter range of 2-10 um. Smaller or larger particles are possible, but usually at the expense of higher polydispersity.
  Recently a method using nanoparticles as stabilisers in the dispersion process has been published (https://doi.org/10.1016/j.colsurfa.2017.11.069) that allows for highly monodisperse dispersion particles smaller than 1 um.
  In this project we would like to synthesise sub-micron particles using this Pickering emulsion technique and apply them in the synthesis of porous polymer particles for chromatography.
• Brown sauce synthesis
  The flexitarian food trend asks for a lot of innovation from flavour manufacturers. Typically meat-based flavours, like brown sauce concentrate, are highly demanded as plant-based alternatives. These sauces obtain their flavour from proteins undergoing Maillard reactions. Plant-based proteins, however, deliver sensorically worse results than those based on meat. Food scientists attribute this to the higher fat content in meat than in plant-based alternatives. In this project we are going to investigate the effects of the presence of emulsified oils in the reaction.