Job openings in Program 1
Green Cycles of Renewable Materials
PhD student positions
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Project description:
The aim of the project is to identify and verify suitable strategies to strongly bond structural colors formed out of CNCs to the wood substrate and to overcome the disadvantage of the current absence of water resistance. Design principles and approaches found in nature may act as a starting point. As possible approaches we see enzymatic modification of the wood surface to enhance interaction, physical methods to induce energy (heat, rays), green chemical approaches to improve the cohesion of the cellulose assembly or incorporation of fully biobased matrix polymers or waxes.
Background:
Formation of vivid colours is already nicely possible with Cellulose Nanocrystals. For the mechanism of colour adjustment several strategies are established, while the understanding of interaction of wood and its role in colour formation is in the early stage. As main barrier moisture stability is close to zero, as a single drop of water is able to destroy or remove the structure, as the interaction of CNC is based on weak secondary bonds only.
Based on biomimetic approaches, green chemistry or biotechnological methods CNC shall be connected to the wood structure and interconnected with each other.
Research Objectives:
As an outcome an ideally purely lignocellulose based structural colour should be able to coat the lignocellulosic material wood and thus enable realizing a single material concept.
Identifying and analyzing possible modification approaches addressing the interaction within the CNC structure, as well as between wood and the structure
Verify and develop selected strategies
Methods:
Color formation by CNC self-assembly. Biotechnological, chemical or physical methods to be identified depending on approaches selected. Analyses of structural color assemblies by various microscopic techniques on suitable length scales (light microscopy, atomic force microscopy, scanning electron microscopy) including ultramicrotomy as sample preparation. Color determination, surface resistance in dry state and towards water, nanoindentation, …
Main supervisor: Univ.-Prof. Johannes Konnerth
Location: BOKU University (UFT Tulln)
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Description of project
Development of enzymatic cascades in fast growing cyanobacteria based on degradation products of lignin. Predominately ferulic acid and other aromatic phenylpropanoid metabolites should be applied for the production of high value chemicals. The enzyme cascades should contain enzymes from different classes, like phenolic acid decacboxylases, aromatic dioxygenases/isomerases and subsequently either amindehydrogenases or alcohldehydrogenases. The expression of these enzymes will be achieved by the close collaboration with PostDoc#1 from my group who will establish a new expression platform in fast growing cyanobacteria. Additionally it more enzymes for functional group interconversion will be expressed. With the cascade at hand quantitative preparative scale experiments will be performed to prove the feasibility and applicability of the cascade.
Background
The working group has experience in redox biocatalysis and cascade reactions. Additionally the group is well experienced in the genetic modification and cultivation of phototrophic bacteria.
Research Objectives
Efficient utilization of renewable resources and waste streams for the production of fine and bulk chemicals
Identification of bottlenecks in the production of chemicals starting from renewable resources.
Methods
Selection of potential enzyme candidates for suitable cascades.
Cloning of heterologous genes into different fast growing phototrophic bacteria by Gibson cloning.
Testing of single-step and multi-step biocatalysis in different hosts by GC and HPLC analysis
Investigation of different waste and renewable carbon streams on growth and productivity.
Main supervisor: Associate Prof. Florian Rudroff
Co-supervisors : Univ.-Prof Katharina Schröder; Univ.-Prof Oliver Spadiut
International supervisor: Prof. Uwe Bornscheuer
Location: TU Wien (Vienna)
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Are you passionate about pushing the boundaries of sustainable chemistry? Do you dream of working on innovative projects that could shape the future of science? Join our research team as a PhD student and embark on a journey of discovery, growth, and impact!
About the Position
We are seeking a motivated and talented PhD candidate to join our lignin group within our Cluster of Excellence (https://www.circularbioengineering.at), where we tackle some of the most exciting challenges in lignocellulose chemistry focusing on chemical modifications and analytical methods. Our research focuses on ways to deepen the understanding of lignin, including that of technical lignins to provide basic knowledge for future applications and designing novel materials. This is your chance to contribute to work that has real-world applications and scientific significance.What We Offer
Cutting-Edge Research: Work on innovative lignocellulose projects using state-of-the-art techniques and equipment.
Mentorship and Collaboration: Be part of a supportive team led by experienced researchers, with opportunities to collaborate with leading scientists worldwide.
Skill Development: Gain expertise in advanced experimental and analytical methods, as well as transferable skills like scientific writing and project management.
Career Opportunities: Present your work at international conferences, publish in high-impact journals, and build a strong professional network.
Funding and Resources: Competitive funding, access to modern facilities, and a vibrant academic environment.
Salary 2700 € gross (14 times per year) for 3 years
Who We’re Looking For
We are looking for a candidate who is:Curious, creative, and driven to solve complex scientific problems.
Holding a Master’s degree in Chemistry or a related field.
Excited to work in a collaborative and interdisciplinary environment.
Main supervisor: Univ.-Prof. Antje Potthast
Location: BOKU University (UFT Tulln)
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Background:
Biomass and products from biomass are rich in complex molecules. Often, the unambiguous structural elucidation is necessary to identify unwanted byproducts (e. g. chromophores), to increase the understanding of a process (e. g. degradation products, unintended byproducts), and to describe newly discovered bioactive compounds. The availability of the compounds of interest is often limited either because the effort to isolate sizeable amounts is prohibitive, or because the compounds occur only in minute amounts. Current methodology – the combination of mass spectroscopy after chromatography, nuclear magnetic resonance spectroscopy, infrared spectroscopy – quickly reaches its limit when the available amount of substance is small (microgram). Crystallography allows to determine the structure of organic compounds directly and without ambiguity. The main requirement and obstacle – the availability of single crystals – can be mitigated by two recent developments: crystalline sponges and electron diffraction. These make even volatile and oily substances accessible for structural analysis by crystallography.
Crystalline sponges evade the need to grow single crystals and are compatible with widely available instrumentation for X-ray diffraction. They are porous crystalline metal-organic frameworks (MOFs) that act as a crystalline template for the compounds of interest. The target compounds are dissolved and allowed to diffuse into the MOF that soaks them up like a sponge. In the MOF, the target compounds are adsorbed in an orderly, practically crystalline fashion, which allows a structure elucidation by crystallography.
The field of Crystalline Sponges offers the option to elucidate compounds that so far have evaded a comprehensive analysis or were not available as crystals (examples see “Research objectives”). The combination with chromatographic techniques has been demonstrated and is especially powerful if an adsorption chromatographic method such as supercritical fluid chromatography or normal-phase chromatography is used. Normal-phase thin-layer chromatography with direct bioautographic detection of bioactive molecules that are then embedded in a crystalline sponge for crystallography could become an extremely rapid approach for bioactivity studies.
Research Objectives:
Synthesis of established crystalline sponges (apolar, polar, carbohydrate-based) for first tests with model compounds.
Application of the crystalline sponges to the identification of the target compounds which so far have evaded a comprehensive analysis as they were not available as crystals: a) di- and oligosaccharides of celluloses and hemicelluloses, b) chromophores and byproducts formed during pulp processing, fiber manufacturing and cellulose aging, c) extractives and bioactive compounds form plants (secondary metabolites).
Establishing the combination with preceding chromatographic techniques: supercritical fluid chromatography and high-performance thin-layer chromatography with direct bioautographic detection of bioactive molecules.
Methods:
Synthesis of established crystalline sponges (apolar, polar, carbohydrate based) for first tests with model compounds.
Tests of suitability of different MOFs for different model compounds. Type of MOF and the properties of the solvent for infusion will be screened. Inclusion rate is determined from the supernatant before crystallography. Robustness of the developed methodology is evaluated. If necessary: definition of requirements of MOFs that need to be developed.
Combination of established chromatographic methods – gas chromatography, thin-layer chromatography, liquid chromatography, supercritical fluid chromatography – for selected use cases, e. g. identification of bioactive compounds after bioautography, identification of unknown peaks in gas chromatography
Main supervisor: Univ.-Prof. Thomas Roesenau
Co-supervisors: Univ.-Prof. Antje Potthast, Priv.-Doz. Dr. Stefan Böhmdorfer
Location: BOKU University (UFT Tulln)
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Description of project:
The identification of novel enzymes for industrial applications has been significantly advanced by omics technologies, bioinformatics, and engineering. The identification of new enzyme scaffolds is the first essential step in the development of new biocatalysts. The aim of this project is to identify novel enzymes including oxidoreductases and hydrolases through functional proteomics approaches. To this end, functional proteomic screening of anaerobic fungi and archaea as well as strain collections isolated from selected environments such as wastewater treatment plants, or microbial communities such as rumen or elephant gut microbiome, will be performed in collaboration with Doris Ribitsch to discover new enzyme activities without prior information about their sequence or structure. Three different proteomics approaches will be pursued: Secretomics will reveal proteins expressed and secreted in response to the substrate of interest (e.g. native and artificial polymers, such as lignocellulose). Thermal proteome profiling will reveal proteins binding to native substrates. Activity-based screens using probes for hydrolases and oxidoreductases will allow to identify new enzyme scaffolds. The latter two approaches offer the advantage to screen also otherwise non-culturable microorganisms, in particular new bacterial taxa or unknown bacteria, since it has a high probability of yielding genes encoding novel enzymes. The identified sequences will be produced in expression hosts like E.coli or P.pastoris, purified, validated and characterized in collaboration with Doris Ribitsch.
Background:
The working group has experience in functional proteomics [1-5].
Research Objective:
Identification of new biocatalysts for decomposition of natural and synthetic polymers
Decomposition of natural and synthetic polymer substrates into defined, low-molecular-weight products that will be used to develop novel and sustainable materials
Methods:
Establishment of functional proteomics screening assays with target substrates (secretomics, thermal proteome profiling)
Establishment of activity-based proteomics of hydrolases and oxidoreductases
Establishment of habitat specific metaproteomics workflows
Screening of strains (anaerobe, aerobe) and microbial communities from underexplored sources for new enzyme activities
Recombinant production of enzymes and validation of enzymatic activities
Krammer L, Darnhofer B, Kljajic M, Liesinger L, Schittmayer M, Neshchadin D, Gescheidt G, Kollau A, Mayer B, Fischer RC, Wallner S, Macheroux P, Birner-Gruenberger R*, Breinbauer R. (2025) A general approach for activity-based protein profiling of oxidoreductases with redox-differentiated diarylhalonium warheads. Chem Sci; doi: 10.1039/d4sc08454c. Epub ahead of print. PMID: 40103729; PMCID: PMC11912224. (#co-first author, *co-corresponding author)
Honeder SE, Tomin T, Schinagl M, Pfleger R, Hoehlschen J, Darnhofer B, Schittmayer M, Birner-Gruenberger R. (2023) Research advances through activity-based lipid hydrolase profiling. Israel Journal of Chemistry; doi: 10.1002/ijch.202200078
Schittmayer, M., Vujic, N., Darnhofer, B., Korbelius, M., Honeder, S., Kratky, D., Birner-Gruenberger, R. (2020) Spatially Resolved Activity-based Proteomic Profiles of the Murine Small Intestinal Lipases. Molecular & Cellular Proteomics, 19:2104-2115. DOI:10.1074/mcp.RA120.002171
Wallace, P. W., Haernvall, K., Ribitsch, D., Zitzenbacher, S., Schittmayer, M., Steinkellner, G., Gruber, K., Guebitz, G. M., Birner-Gruenberger, R. (2017) PpEst is a novel PBAT degrading polyesterase identified by proteomic screening of Pseudomonas pseudoalcaligenes. Applied Microbiology and Biotechnology, 101:2291–2303. DOI:10.1007/s00253-016-7992-8
Sturmberger, L., Wallace, P. W., Glieder, A., Birner-Gruenberger, R. (2016) Synergism of proteomics and mRNA sequencing for enzyme discovery. Journal of Biotechnology, 235:132-138. DOI:10.1016/j.jbiotec.2015.12.015
Main supervisor: Univ.-Prof. Ruth Birner-Gruenberger
Co-supervisors: Priv.-Doz. Dr. Doris Ribitsch
Duration: 4 years (30 h/week)
Location: TU Wien, Research Group Bioanalytics: https://www.tuwien.at/en/tch/bioanalytics
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Description of the project:
Protein engineering is a powerful tool to change the activity of enzymes. This project investigates how carbohydrate binding modules (CBMs) can alter the binding and activity of an enzyme towards cell wall polymers like cellulose and hemicelluloses. The enzyme lytic polysaccharide monooxygenase (LPMO) will be engineered to produce variants and fusion enzymes with an altered substrate interaction to study the influence of CBMs on substrate targeting and activity. This project is correlated with Program 3 of Circular Bioengineering, but financed by BIOTOPIA, the biomolecular technology of protein interactions PhD program (https://biotop.boku.ac.at). The selection process will give you the opportunity to enroll in this PhD program without further selection process.
Background:
Many enzymes feature substrate binding domains that are not part of their active site and located in a different domain. Cellulosic and hemicellulosic enzymes often feature carbohydrate binding modules (CBMs). CBMs bind the enzyme to their substrate and establish an equilibrium of bound and soluble enzymes. Only substrate-bound enzymes are catalytically active and their activity is influenced by the binding strength of the CBM. Soluble enzymes can target newly created positions in the cell wall’s polymer network. The affinity of a CBM therefore not only regulates the catalytic activity, but also influences the efficiency of other enzymes by targeting mutually beneficial positions for subsequent catalytic action.
Aims:
After the selection and engineering of CBMs to achieve varying affinities towards cellulose, they will be fused to LPMO. The hypothesis is that a weak binding increases the soluble fraction of LPMO and therefore supports the targeting of new plant cell wall areas for its catalytic action, whereas a CBM with a high affinity restricts the mobility of an enzyme, but increases its activity locally. Th project aims to modulate the affinity of the LPMO-CBM fusion enzyme to optimize binding and mobility for maximum enzymatic activity on cellulose and other carbohydrate polymers.
Methods:
Bioinformatic (sequence and structure based) selection of CBMs and LPMOs.
Structure-based protein engineering
Enzyme production and purification in a yeast expression system
Biochemical characterization (protein analysis and kinetic measurements)
Fluorescence microscopy and electrochemical detection methods
Small-scale application studies in COE Program 1.
Main supervisor: Associate Prof. Roland Ludwig
Co-supervisors: Univ.-Prof. Chris Oostenbrink
Location: BOKU University (Muthgasse)