Master Thesis

The Master’s thesis is the scientific core of your studies: you choose your specialist courses with a view to the topic of your thesis, which you determine before starting your studies. Based on the theoretical foundations of the study programme, you answer a specific question in this research field. You work out solutions that are relevant for research, industry and society, often in co-operation with national and international partners. Depending on your topic, you work in a research group at the Institute of Biotechnology in Wädenswil or externally with an industrial or research partner. Through the thesis you not only demonstrate your knowledge and skills, but also the ability to successfully integrate into a research group and expand your knowledge in your specific field of scientific expertise.

For the Master’s thesis you focus on a particular area of pharmaceutical biotechnology as part of a research group (see next section). You plan and work mainly independently, in consultation with your supervisor and any external research and industry partners. In this way you not only deepen your scientific and technical competence, but also gain useful experience of project management. Pursuing a long-term research project successfully tests and trains your flexibility, for example, when scientific hypotheses need to be reexamined or experimental designs have to be adjusted. A timeframe of eight months is envisaged for the thesis, which you can fit into your studies according to your individual situation.

You select the topic for your Master’s thesis in one of the following research groups:

• Bioprocess development for whole-cell pharmaceutical products (vaccines, recombinant drug delivery platforms)
• Development of novel assays and analysis concepts for at-line and on-line monitoring of virus production processes
• Recombinant targeting entities for prodrug cancer treatment. Bioassay-guided optimization.
• Cell-based, high-throughput diagnostic platforms for parasitic diseases 

Contact: Dr. Lukas Neutsch

• Procaryotic and eucaryotic lipid-binding proteins: Cloning, expression, downstream processing and bioanalytics of lipid-binding proteins for the detection of disease-related lipids.
• Establishment of novel proteins: Cloning, expression and downstream processing of engineered proteins to improve sensitivity of detection systems for human pathogens.
• Establishment of C1q Assay: Cloning, expression and downstream processing of wild type C1q and variants thereof and development of assays to evaluate immune effector functions in 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
• 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.

Contact: Prof. Dr. Sabina Gerber

• Surface functionalization of extracellular vesicles (EVs) for target-specific delivery of therapeutic mRNA molecules to pediatric high grade glioma cells
• Establishing of novel pharmaceutical formulations for bacteriophages / phage proteins
• Characterization of primary fibroblasts from fibrosis patients to identify novel therapeutic targets
• Establishing heterotypic 3D tumor cell culture models to study the efficacy of novel, macrophage-based immunotherapies 
• Developing biofunctionalized nanofiber platforms for localized phage protein therapy and innovative antimicrobial device coatings, collaboration with Markus Huemer, Micreos Pharmaceuticals AG

In collaboration with an industrial partner:

• Automation friendly magnetic bead-based enrichment method                                   a. wet lab, automation, fluid dynamics, robotic programming/scripting, CAD/prototyping, biology & chemistry 
• Automated cell/organoid culturing -> e.g. media exchange, passaging                       a. wet lab, automation, fluid dynamics, robotic programming/scripting, CAD/prototyping, imaging, biology & chemistry
• Automated handling of reactor blocks for small molecule synthesis                            a. robotic programming/scripting, wet lab, automation, CAD/prototyping, chemistry

Contact: Prof. Dr. Steffi Lehmann
 

• Development of plant based biopolymers for the use of pharmaceutical drug delivery systems. 

Contact: Dr. Andrea Baier

• Isolation, characterization, and genome sequence analysis of novel bacteriophages for the specific control of pathogenic bacteria
• Characterization of phagobiomes
• Conservation of bacteriophages by freeze- and spray drying
• Combinatorial effects of bacteriocins and bacteriophages in the control of pathogenic bacteria
• Heterologous cloning, expression, and characterization of phage-encoded endolysins
• Heterologous cloning, expression, and characterization of phage-encoded tail spike proteins
• Construction of recombinant temperate bacteriophages to reprogram the bacterial host
• Phage breeding – expanding phage host ranges by guided evolution
• Optimization of bacteriophage propagation in liquid culture at lab scale 

Contact: Prof. Dr. Lars Fieseler

• Identifizierung neuer Target Sites für kovalente niedermolekulare Antagonisten:Aufreinigung von Proteinen und Charakterisierung von potenziellen Target Sites durch Struktur-Funktions-Studien und Massenspektrometrie.

• Charakterisierung von Protein-Protein-Interaktionen und Proteinstabilität: In vitro-Interaktionsstudien und zelluläre Proteinstabilitätsstudien zur Identifizierung neuer therapeutischer Target Sites in krankheitsrelevanten Proteinen.

• Entwicklung von niedermolekularen Antagonisten für krankheitsrelevante Proteine: Screening von Bibliotheken und funktionale Charakterisierung durch biochemische und zelluläre Assays.

• Entwicklung von isothermalen DNA-Amplifikationsmethoden zum Nachweis von Pathogenen: Dieses Projekt beinhaltet Proteinaufreinigung und Assay-Optimierung.

Contact: Dr. Kerstin Gari

• 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 administration strategies for antimicrobial agents

Contact: PD Dr. Mathias Schmelcher

• Development of bacterial reporter strains to monitor the efficacy of novel antimicrobial agents in vitro and in vivo
• Development of assays to evaluate the antimicrobial efficacy of novel compounds

Contact: Dr. Gottfried Dasen

• Topic 1: Comparative genomics to determine the phytopathological potential of Erwinia oleae DAPP PG-531
  Erwinia oleae DAPP PG-531 (LMG 25322^T) was isolated as olive knot endophyte but can in collaboration with Pseudomonas savastanoi pv. savastanoi cause disease of olive trees, called olive knot disease. The genome of this strain has been sequenced, autoassembled and published as a draft genome. An improvement of the genome assembly still is required to work well with it for comparative genomics and to draw some important conclusions. For this, the genome will have to be sequenced using a long-read technology. Additional, using comparative genomics with genomes from other Erwinia spp., the potential to be a pathogen will be examined in detail.
• Topic 2: Comparative genomics of Phytobacter spp. and related species
  Novel clinical isolates are appointed as members of the Enterobacteriaceae, all belonging to the genus Phytobacter. Some of the current isolates are highly resistant to different antibiotics. Different genomes of Phytobacter spp. were determined in the last years. Some of these still require a more detailed assembly, while others are fine for comparison. Comparative genomics of the different members of this genus will be done to determine differences between the different species within this interesting genus.
• Topic 3: Assembly and analysis of the genomes of two clinical Pantoea agglomerans isolates.
  We recently obtained and sequenced two Pantoea agglomerans strains that were isolated from a thorn wound. To be able to compare and visualize differences to the already available collection of P. agglomerans strains, the genomes will have to be assembled and annotated. Based on comparative genomics, we will draw first conclusions on the potential of the two strains in the field of pathogenicity, antibiotic resistances, biocontrol, or metabolism.
• Topic 4: Degradation of 17b-estradiol-3-sulfate (E2-3S) by Pseudomonas spp.: a genomics approach
  In a recent master work, we isolated many different bacterial species able to degrade E2-3S, a potential endocrine disruptor that appears to be present in the environment. Some of the isolates were members of the Pseudomonas putida group, closely related to Pseudomonas japonica based on 16S rRNA gene sequencing. In this study, we will do complete genome sequencing of one of these isolates and characterization of the biodegradation potential, both in silico and in vitro. Additionally, we will perform comparative genomics with other members of this group and determine whether Pseudomonas wadenswilerensis and further members are able to grow with E2-3S, also both in silico and in vitro.

Contact: Prof. Dr. Theo H.M. Smits

• Process developments for the production of plant cell culture-based foods (e.g. cocoa, guacamole, together with ILGI)
• Stem cell cultivations for food applications
• Intensified and continuous upstream processing in animal cell-based productions of biotherapeutics (e.g. monoclonal antibodies)
• Development of production processes for cell therapeutics (human mesenchymal stem cells, human induced pluripotent stem cells)
• Novel single-use technologies (together with industrial partners) 

Contact: Prof. Dr. Regine Eibl

• Scale-Down and Scale-Up of Biopharmaceutical Production Processes Based on Microorganisms and Fungal Cultures (The Topic May Include Medium Development)
• Bioreactor Characterization, Design, and Tests for Biopharmaceutical Applications (Usage of Classical Bioengineering Tools and Modern Methods Such as Computational Fluid Dynamics, etc.)
• Novel Cellular Agricultural Approaches for Microorganism-Based Products Suitable for Human Nutrition (e.g., Single Cell Protein, Mushrooms)
• Integration of Digital Twins and AI-Driven Models in Bioreactor Characterization and Optimization for Biopharmaceutical and Food Applications: Development of Automated Concepts and Prototypes
• Contact: Dr.-Ing. Cedric Schirmer

• 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: Dr. Thomas Schwander

• Lignocellulose pretreatment for enhanced bioconversion in a biorefinery
  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 will be treated in a special steam process and its effect on bioconversion investigated. The corresponding studies include enzymatic cellulose conversion (cellulases), enzyme deactivation and fermentation.
• Bioprocess development for sustainable hyaluronic acid production
  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 addition, the use of more sustainable feedstocks (sugars obtained from lignocellulose) will be investigated. The hyaluronic acid produced in the process will be analysed and tested for cosmetic applications with the help of an industrial partner. 

Contact: Dr. Thomas Pielhop

• Development of sensors for critical process parameters in (bio)process control (pH, pO2, biomass concentration, ion concentration, substrates and metabolites) based on electrochemical and optical methods and dielectric spectroscopy
• Application of sensors in on-line bioprocess monitoring and control, with a special focus on single-use systems
• Development of methods for near-line and off-line process analysis of metabolites and substrates in biotechnological cultivations (HPLC, spectroscopy, LC/MS)

Contact: Prof. Dr. Caspar Demuth

• From Medicinal Plant to Product: Quality assurance along the value chain of herbal medicines and other plant based health products in collaboration with our industry partners in Pharma, Food and Cosmetics
• Standardized extracts of the European Pharmacopoeia: Research contributing to rational and evidence-based phytotherapy
• Phytochemical Analysis: Analytical studies involving UHPLC-DAD-FLR-ELSD-RI-MS, GC-FID, HPTLC
• Bioautography: Bioassay-linked chromatography for pharmacological and toxicological screening of natural products
• Fractionation and isolation of plant-based natural products
• Galenic formulation: Forms of application including cremes, tablets, pastilles and liquid formulations for herbal drugs
• Ethnopharmacology: Research of traditionally used medicinal plants

Contact: Dr. Andreas Lardos

• Microbiology and metabolism of anaerobic fungi: Laboratory work, microbiological & bioprocess oriented.
• Cultivation and kinetics of methanogenic archaea: Laboratory work, microbiological & bioprocess engineering oriented
• Detection and reduction of microplastics in soils: Laboratory & field work, analytically oriented
• Power-2-Gas: Bioprocess engineering of microbiological methanation of hydrogen to methane. laboratory work, bioprocess oriented
• P-recovery from sewage sludge by means of hydrothermal carbonization: Laboratory & pilot work, process engineering and analytically oriented. 

Contact: Dr. Hajo Nägele

The Cell Physiology and Cell Engineering group focuses on the development of advanced human cell-based model systems for translational biotechnology. Our research combines stem cell technologies, genetic engineering, immuno-oncology, and physiologically relevant 3D tissue models to investigate complex cellular functions and disease-related mechanisms in vitro.

Current Master’s thesis projects

• Human iPSC-derived blood–brain barrier models
  Generation of brain microvascular endothelial cells (BMECs) from human induced pluripotent stem cells (iPSCs) and establishment of functional in vitro blood–brain barrier models for permeability and transport studies.
• Genetically engineered 3D human skin models
  Development of full-thickness 3D skin equivalents incorporating stable reporter systems to quantitatively assess oxidative, mitochondrial, endoplasmic reticulum, and hypoxic stress responses.
• Immuno-oncology assays with CAR-engineered NK cells
  Design and expression of novel chimeric antigen receptor (CAR) constructs in natural killer (NK) cells, followed by in vitro evaluation of cancer cell targeting, cytotoxicity, and functional activation.
• Antibody development against complex membrane proteins
  Generation of high-affinity antibodies using full-length human membrane proteins in their native conformation, enabling targeting of clinically relevant receptors and ion channels.

Key methodologies

• Human iPSC culture and directed differentiation
• Genetic engineering using CRISPR/Cas and viral systems
• 3D cell and tissue culture technologies
• Cell-based functional assays, flow cytometry, and confocal laser scanning microscopy

Contact: Prof. Dr. Jack Rohrer

• Engineering of CH-activating enzymes for pharmaceutical applications
• Bioinformatic analysis of PETase variants (plastic degrading enzymes)
• Optimization of enzyme engineering techniques
• Screening Nature’s genetic diversity for novel biocatalysts 

Contact: Prof. Dr. Rebecca Buller

• Development and Optimization of a novel Cell-free Expression System for the High-throughput Screening of Diagnostic Antigens
• Recombinant Production and Screening of Novel Antigens for the Diagnosis of Neglected Parasitic Infections
• Evaluation of the Diagnostic Capacity of Parasite Extracellular Vesicles

Contact: Dr. Ramon Eichenberger