Molecular cloning and characterization of new enzymes employed in biocatalysis ar other commercial applications not assigned GG: industrial companies and partly by FFF
Beginn: 31.12.1994
Ende: 04.11.2025
Small peptides have a variety of uses in industry, for example in medicine, food and cosmetic production as active ingredients, enzymes and flavorings. However, traditional peptide synthesis is harmful to the environment, which is why sustainable alternatives are increasingly being sought, such as biotechnological production. ÖkoPep is dedicated to the goal of studying and improving yeasts as production organisms. The aim is to efficiently produce various relevant peptides with high yield and purity for more sustainable industrial applications.
Beginn: 15.10.2024
Ende: 14.10.2025
Enzymes are the catalysts of Nature. Their mild reactions conditions and high selectivity make them ideal tools for organic synthesis. Many biocatalysts, however, are characterized by limited substrate spectra. This requires methods for the modification of enzymatic mechanisms in order to create new reactivities. The breaking and formation of bonds between carbon atoms is of high interest in view of synthetic applications. However, these reactions are very challenging for biocatalysis. The bacterial enzymes arylmalonate decarboxylase and eudesmol synthase catalyse these reactions with outstanding selectivity. The molecular mechanisms of this selectivity lie in the selective stabilization of reaction intermediates on the one hand, and in targeted quenching of these intermediates on the other hands. On basis of mechanistic studies and computational simulations, we aim to incorporate functional groups at specific positions in order to direct the reactions of both enzymes towards the formation of new products. With the current knowledge, it is extremely difficult to formulate precise predictions on the outcome of any modification of the active site. Therefore, a targeted randomization of sets of amino acids in the active site coupled with a high-throughput screening of selected variants is considered to be the most promising strategy to influence the product formation of both enzymes. For the precise modification of interactions between substrate and protein we plan to incorporate functional groups that are not present in natural enzymes. For this, we will incorporate unnatural amino acids. The approach of Active Site Design is the targeted introduction of novel functional group coupled to a simultaneous variation of the molecular context. The optimal integration of the unnatural amino acids is aimed to achieve novel reactivities. Key for this proceeding is an interdisciplinary collaboration between enzyme engineering, organic synthesis and mechanistic studies.
Beginn: 31.08.2021
Ende: 30.08.2025
A sustainable development of our society is a central and complex multidisciplinary challenge that concerns the future of our planet. For the necessary innovations, the design of new materials plays a pivotal role. In the context of materials suitable for technological innovation, porous materials have the potential to revolutionize several processes:
by controlling their pore size distribution, connectivity, surface functionalization/chemical reactivity, and presence of functional guests, porous materials have demonstrated advantageous functional properties suitable for separation, catalysis, gas storage, pollutant sequestration, drug delivery, and sensing to name a few major applications. In Porous Materials @ Work for Sustainability (PMWS), we contribute to the commitment of TU Graz to sustainable development by creating a consortium of researchers highly interested in porous materials for technological solutions. We decided to capitalize on the know-how developed during our prior Lead Project (Porous Materials @ Work, PMW, phase I) and combine this expertise with the skills and the enthusiasm of new researchers, including early career researchers (ECR).
The project is composed of 20 researchers jointly leading 12 sub-projects focused on catalysis, sensing, and material investigation.
These connected sub-projects will continue a productive initiative fostering cross-fertilization activities between chemists, physicists, materials scientists, engineers, and biotechnologists. Together, we will work on the development and understanding of new porous materials to address specific sustainability challenges, we will reinforce and expand the international collaborations of TU Graz, and we will organize dedicated educational events to inform/stimulate students and the public. By pursuing these goals, this Lead Project, PMWS, will significantly contribute to supporting TU Graz and Austria in progressing towards the commitments of Agenda 2030 the United Nations Sustainable Development Goals (SDGs).
Beginn: 31.08.2022
Ende: 30.08.2025
The aim of this project is to develop a biological (enzyme-assisted) method for splitting carbon / carbon double bonds without the use of the dangerous ‘ozone’. The so-called ozonolysis is a widely used method for the production of so-called "carbonyl compounds". Such carbon / carbon double bond containing compounds can be starting materials to make such as flavor compounds like vanillin or fragrances like Lilial. Ozonolyis is mainly used on a laboratory scale. The reason for this is the toxicity of ozone and the danger of the intermediate products, which are not safe: Some of themhave already caused industrial reactors to explode. We want to find and investigate a safe alternative with enzymes that can split C = C double bonds at room temperature, in water and by means of oxygen. We use a high-throughput detection method that is specifically designed for the detection of aldehydes (carbonyl compounds) in order to examine different protein sequences for their ability to split C = C double bonds. This detection method is highly sensitive, completely independent of structure, easy to use and extremely specific for aldehydes. With this detection method in combination with a special technique, it is possible to examine up to a million protein sequences in a day. It is thus possible to examine known enzymes for their substrate diversity and new enzymes for their activity in a very short time, as quantitatively as possible. After suitable enzymes have been found, we will use them for the production of potential new active pharmaceutical ingredients or flavorings.
Beginn: 31.01.2021
Ende: 30.07.2025
Biocatalysis holds great potential for the utilization of renewable resources, but requires chemical energy from agricultural products. H2value investigates the use of green hydrogen to supply electrons for biocatalytic whole-cell biotransformations. The development of hydrogen-driven biotechnological processes for the synthesis of biobased polymer precursors will allow the coupling of redox biocatalysis to renewable energy and thus make a substantial contribution to a circular economy.
Beginn: 31.12.2023
Ende: 29.06.2025
Lytic polysaccharide monooxygenases (LPMO) and cytochrome P450s (CYPs) are copper- and iron-dependent, respectively, enzymatic systems that perform regio- and stereospecific oxidation of non-activated hydrocarbons in Nature. To control such reactions in modern industry and biotechnology is of utmost importance in creating products of value such as secondgeneration bioethanol and products of value for i.e. the pharmaceutical industry. Due to the major drawbacks of using CYPs, including their partially membrane bound nature and the requirement of a reductase in combination with reducing agents such as NAD(P)H to transfer electrons to the active site for oxygen activation, it is highly desirable to develop new type of catalyst that can perform the same type of reactions. An attractive alternative strategy is to engineer LPMOs to perform CYP catalysis. LPMOs are small, robust, easy to produce in large scale, and rigid water-soluble proteins with a plethora of electron donors. The extended, flat LPMO surface, with huge natural sequence variation and thus, likely, mutability, provides a fantastic scaffold for engineering access to the active site as well as substrate affinity. Thus, we aim in the NewCat project to use LPMOs engineered to accommodate typical CYP substrates and immobilize this on solid supports to provide confinement necessary in bringing the oxygen species together with the C-H bond to be oxidized in a tailored, "closed" environment.
Beginn: 31.05.2022
Ende: 30.05.2025
Nitriles are versatile reactants in organic synthesis. In addition to the presence of the nitrile moiety in drug molecules, agrochemicals and fragrances, they serve as synthons for amines, aldehydes, amides, acids and numerous N-heterocyclic compounds.
This proposal aims to establish a chemoenzymatic cascade reaction as a new cyanide-free route to nitriles from their corresponding carboxylic acids. To cover a diverse range of nitrile products, we need to deepen our understanding about the structure-function relationship of aldoxime dehydratases and use this knowledge to recruit new proteins from this family with particular characteristics.
In our approach, carboxylate reductase enzymes (CARs) in an engineered E. coli strain will be used to reduce carboxylates. The resultant aldehydes are highly reactive and will be trapped immediately as as oximes. A water molecule is then substracted from the oxime by an aldoxime dehydratase (AOxD),
affording the respective nitrile. The best-case scenario of this project is to perform acid to nitrile conversion with a single biocatalyst in one-pot. We will first focus on arylaliphatic substrates to establish the concept and then on aromatic end-products, which are currently not accessible by AOxDs. Hypothetical AOxDs retrieved from databases will be studied by a combination of in silico and in vitro methods in order to assign
functions to sequences and to classify AOxDs into clades.
The reaction concept is new, allows for cyanide free nitrile formation and avoids the isolation and purification of aldehydes that would otherwise be necessary. In depth sequence analysis of AOxDs will lead to more reliable prediction of AOxD function.
Winkler has 16 years of experience in biocatalysis and bioorganic chemistry and Pátek perfectly complements the necessary expertise to carry out the proposed research with his experience in microbiology and enzymology. The team is supported by Rudroff and Gröger, with their expertise in organic
chemistry and application of AOxDs, respectively.
Beginn: 29.02.2020
Ende: 31.07.2024
XRscanning aims to establish novel enzyme engineering techniques for the improvement of carbohydrate-converting enzymes. Aim is increase of the predictive element in enzyme engineering projects and thus the shortening of development-time horizons in the development of biocatalytic processes. The scientific approach combines next-generation sequencing with intracellular selection assays for the identification of improved enzyme variants for a better correlation of sequence modifications with altered function. This so-called fitness landscape provides a systematic data set, whose evaluation is expected to speed up enzyme engineering considerably. The joint development of the expertise in deep mutational scanning is expected to increase the predictive element in enzyme engineering and to allow for a significant improvement of the this methodology. XRscanning focuses on the improvement of enzymes used for the valorization of lignocellulosic biomass.
Beginn: 31.10.2020
Ende: 30.05.2024
The doc.funds CATALOX initiative brings 10 young researchers together to study the mechanisms and applications of so-called oxidoreductases. These biocatalysts are the largest class of enzymes and play an important role in energy metabolism. The associated doctoral program is part of a cooperation between the Graz University of Technology and the University of Graz in the supporting program "NaWI Graz". Within the framework of scientific education, the doctoral students benefit from the international reputation of the working group leaders involved and from the focused research projects. The close cooperation with the Austrian Center for Industrial Biotechnology (ACIB) adds value for the PhD students, especially with regard to the possible applications of the findings. The interdisciplinary approach offers junior researchers the opportunity to prepare for attractive career options in research and development. The unique environment allows for in-depth knowledge in the core areas of biocatalysis and biotechnology - from organic synthesis, mechanistic enzymology, enzyme engineering, structural biology to process engineering.
Beginn: 30.09.2019
Ende: 28.02.2024
FuturoLEAF envisions to exploit know-how in nanocellulose materials and cell biology to revolutionize the field of industrial algal biotechnology by conceptually renewing tailored solid-state cell factories. FuturoLEAF introduces algal-based biocatalysts with functional architecture formulated from nanocellulose building blocks and designed on the principles of plant leaf anatomy and function. Knowledge of bio-based materials science and photosynthesis will be integrated with achievements of synthetic biology and biomolecular engineering to conceive the new technology efficient in capturing CO2 and producing solar-driven biofuels and chemicals. The FuturoLEAF biocatalysts will gain high production efficiency by tailoring nanocellulose matrix performance with utilisation of its highly specific water interactions, resulting in tunable porosity and transport properties. Directed self-assembly as a tool to locate and attach photosynthetic cells in the matrix by their native interaction potential will further improve the performance. The system will maximise light utilization and CO2 capturing by providing controllable influx/efflux of moisture, gases, nutrients, products and substrates, leading to next generation photosynthetic cell factories with high catalytic turn-over time. In addition, the solid-state nature of the system will enable effortless logistical transportation of cell factories without having to move large amounts of water in contrast to current suspension cultures. The FuturoLEAF architecture will be tested under changing environment in a fixedbed high-cell density photobioreactor, which is designed for simulating behaviour of the plant with gas-to-liquid interphase production environment. The proof of the concept will involve evaluation of the approach at TRL3 level in a photobioreactor functioning in continuous mode. FuturoLEAF proposes a significant step away from dependency of fossil sources, towards sustainable energy and chemicals production.
Beginn: 31.08.2020
Ende: 30.12.2023
A cellular hydrogen sensor for enzyme engineering:
The project H2aseScanning aims to develop a new approach to improve the performance of hydrogenases as they interface between renewable energy and biotechnology. Climate change poses a severe threat to our society and natural resources; carbon dioxide emissions produced as a result of human activity are particularly harmful due to their warming effects. To this end, biotechnological CO2 utilization constitutes an emerging and promising strategy to convert these harmful emissions into valuable chemicals. Nature provides an avenue for CO2 utilization by way of autotrophic microorganisms which have CO2 fixing pathways and a metabolic energy module that provides the chemical energy for its fixation. Unfortunately, it is often difficult to couple these modules to renewable energy sources. In this context, hydrogenases which have the capacity to oxidize of molecular hydrogen to supply reduction equivalents for cellular processes stand out. Hydrogenases can thus provide a unique interface between hydrogen that can be produced from renewable energy and biotechnological processes. They can be applied in cellular processes for the production of valuable chemicals from CO2, in cell-free systems where the hydrogenase supplies electrons for biocatalytic reactions and are elements of biohybrid systems. Unfortunately, the activity and operational stability of hydrogenases leaves much to be desired. Protein engineering is an efficient approach to develop and advance enzymes for industrial applications. H2aseScanning aims to develop a system for the investigation of hydrogenases by deep mutational scanning. The complementation of inactivated genes of subunits of the native hydrogenase with large mutant libraries allows to couple the mutant’s hydrogenase activity to the growth of a hydrogen-utilizing bacterium. This massive high-throughput selection system will then be used to obtain a fitness landscape with comprehensive information of the role of all amino acids on the fitness of the enzyme. The resulting datasets will lay the groundwork for the improvement of hydrogenases by machine-learning methods.
Beginn: 31.12.2021
Ende: 30.12.2023
The insterest within this project lies mainly in the discovery of enzymes, which produce alkyl or alkoxy pryrazines or their precursor, which condense spontaneously to the target pyrazines.
Beginn: 09.02.2020
Ende: 29.09.2023
Posttranslational modifications (PTMs) are key signals modulating the function of eukaryotic proteins, for example by determining their sub-cellular localization. Arginine methylation is an abundant protein modification in eukaryotes, and distorted arginine modification levels are observed in common diseases like cancers and neurodegeneration. The major class of arginine-methylated proteins are RNA-binding proteins (RBPs).
This BioTechMed-Graz Flagship project aims at elucidation of the poorly understood molecular mechanisms by which arginine methylation regulates proteins through determining their sub-cellular localization. We joined our standing research interests and expertises in the fields of PTMs, nuclear import, and phase separation of RBPs, mutually opening up to systems biology, genetics and cell biology, structural biology and synthetic biology approaches. Together, we are studying the impact of arginine methylation on importin-cargo interactions, nuclear import, and formation of membrane-less organelles both in living cells and in vitro on a proteome, biochemical, biophysical and structural level. An improved understanding of PTM dependent signals determining sub-cellular targeting of RBPs will set the basis for pinning causal connections between dysregulated protein modification and disease.
The synergistic nature of this collaborative project is expected to result in a gain of scientific excellence and international recognition of BioTechMed-Graz, providing a fulcrum for the extension of our consortium to a larger Dynamics of subcellular partitioning research focus in Graz.
Beginn: 31.12.2019
Ende: 30.12.2022
PhotoBioCat is a double-degree PhD graduation network. The research deals with the development of light-driven biotechnological processes.
Beginn: 31.12.2017
Ende: 30.12.2022
Establishing a terpenoid screening on modified microorganisms. The screening is supposed to allow medium to high throughput.
Beginn: 31.01.2015
Ende: 30.05.2022
Nature has evolved efficient metabolicsystemsinvolvingmultiple enzymes arranged in pathways or cascadestoprovide robust cellular functions such as growth and reproduction.A key feature of natural pathways isthat they are finely regulated by proteinscalled transcription factors (TFs).TFs bind small molecules from the environment (e.g., nutrients) or sense metabolites inside the cell. Upon binding, TFs can specifically target genomic DNA, which switches on, adapts, and coordinates theproductionof enzymesactive in related metabolic pathwaysto appropriately respond to the stimulus.This project aims at adding this plasticity to artificial pathway designs by implementing customized TFs to regulate the induction and coordinated production of pathway enzymes depending on the presence of cascade-related molecules (e.g., substrates, intermediates, and potential byproducts). Therefore, proof-of-concept cascades consisting ofenzymes from different microorganisms (i.e., different metabolic systems) are introduced, together with pathway-specific TFs,into Escherichia coli, one of the most commonlyused microbialhostsin biotechnology.Customization of TFs follows complementary strategies: (1) screening of known TFs for binding of nonnative but structurally related compounds, (2) expanding binding specificities of known TFs by protein engineering, which is usually applied to engineer enzymes rather than TFs, and (3) identification of novel TFs by screening ofsolute-binding protein (SBP) libraries.Similar to TFs, SBPs bind nutrients and small molecules and transport them inside host cells. The innovation of this research proposal lies in physically linking the binding of pathway-related compounds by SBPs to their localization on microbial genomes. Subsequently, bioinformatic tools are used to analyze the genetic neighborhoods to discover new TFs. This is feasible as SBPs regularly colocalize on microbial chromosomes with their related metabolic pathways and, importantly, the TFs regulating them.Proof-of-concept cascades transform primary alcohol substrates viaaldehyde intermediates into phenylacetylcarbinols, which are precursors for important pharmaceuticals to treat a variety of diseases including hypotension, obesity, or chronic asthma.Implementation of customized TFs enables the timedproductionof all cascade enzymesand dynamic adaption in the amounts needed to efficiently produce the desired phenylacetylcarbinols.This has advantages over current pathway designs that produce enzymes in an all-or-nothingfashion, which burdens host cells and, in turn, can negatively influence synthetic cascade performanceand product yields.Completion ofthis projectrequiresmethodsfrom differentdisciplines includingsynthetic biology, systems biocatalysis, protein engineering, and bioinformatics. Thisinterdisciplinarycharacter is essentialto integrate pathway-specific TFs toauto-regulatethe proof-of-concept cascades. Since this unprecedentedconceptcan be applied toother artificial pathways, this work not only offersecological alternativestotraditional synthetic routes for the production of pharmaceuticals and other chemicalsemployed by the industry, but to auto-regulate and optimize synthetic enzyme cascadessimilar to how nature does it
Beginn: 31.01.2021
Ende: 30.01.2022
The project investigates the effect of synthetically useful reactions on the energy metabolism in cyanobacteria. Focus lies on the understanding, how the cells adapt to stress caused by the reactions. This includes the formation of oxygen radicals by their own photosynthesis. A second risk is the depletion of the energy supply by the biotechnological process as additional consumer. The project studies the genetic adaptation of the cells to the conditions of the catalytic process. Then we will investigate strategies to achieve a balance between photosynthetic energy supply and consumption by catalytic reactions.
Beginn: 30.06.2018
Ende: 30.10.2021
For the selective and effective incorporation of oxygen into biological molecules (oxygenation reaction), several enzyme
types have evolved in nature. They catalyse crucial reactions in various metabolic routes. The chemistry feasible with these
biocatalysts is unrivalled when compared with conventional chemical methods. Therefore, these oxygenating enzymes are
very promising tools in biotechnological approaches. However, when compared with other enzyme classes, such as
hydrolases, oxygenases are still in their infancy considering their biotechnological potential. To fully exploit the catalytic
power of oxygenases, several hurdles have to be taken for which a higher level of knowledge on these enzymes is needed
while also technical aspects have to be solved.
The European Training Network (ETN) OXYTRAIN is a joint academic/non-academic training initiative supporting the
convergence of biochemistry, enzyme engineering and biotechnology. The consortium's mutual goal is developing a new generation of innovative and entrepreneurial early stage researchers (ESRs) to satisfy the need for knowledge and skills to produce and apply oxidative enzymes. This will be achieved by setting up a network and intersectoral programme in which
multiple disciplines will be integrated and exploited. By bringing together 7 academic beneficiaries that are experts in the
field of individual oxygenase groups, the network will provide perfect conditions for cross-fertilization of knowledge, while the
3 industrial beneficiaries and 5 partner organisations will add to the consortium by translating the generated knowledge into
real industrial applications, such as textiles, pharmaceuticals and biorefineries.
Beginn: 31.12.2016
Ende: 30.12.2020
G protein-coupled receptors (GPCRs) are complex proteins located in the plasma membrane that surrounds every cell. The function of a GPCR is to act as an antenna that senses a particular extracellular stimulus and initiates an appropriate intracellular response. Use of a GPCR as a mechanism to detect an extracellular cue developed very early in evolution; hence, GPCRs are found in the plasma membrane of the cells in all eukaryotic organisms - from unicellular microbes, such as yeast, to humans. GPCRs in the human body are responsible for our senses of sight, smell, certain tastes and other perception, especially response to many hormones and other signal molecules. Medically, GPCRs are primary targets of many
clinically used therapeutic agents, both activators (agonists) and inhibitors (antagonists), depending on the condition being treated. However, chronic stimulation of GPCRs can cause inflammatory diseases and certain cancers. Consequently, multiple feedback mechanisms have evolved that act to attenuate GPCRinitiated responses. Recently, it has been shown that special adapter proteins located inside the cell, called alpha-arrestins, can bind to a GPCR and stimulate withdrawal of the GPCR from the plasma membrane,
thereby elegantly terminating the cellular response to an excessive stimulus. Much remains to be learned about how the alpha-arrestins operate and how they, in turn, are controlled. To examine the properties and regulation of alpha-arrestins this study will use yeast cells, which are simple, inexpensive and easy-tohandle, yet exhibit all of the relevant components found in human cells (GPCRs, alpha-arrestins, and regulatory factors). A particular kind of chemical change to an alpha-arrestin, namely attachment of phosphate groups through the action of enzymes known as protein kinases, has been shown to block the ability of an alpha-arrestins to withdraw its cognate GPCR from the plasma membrane. Hence, this project will first investigate how various cellular protein kinases act on alpha-arrestins. To understand the full range of plasma membrane proteins influenced by alpha-arrestins, the second part of this project will apply novel strategies to delineate all the interaction partners of each yeast alpha-arrestin. These studies will be conducted at UC Berkeley. Finally, the knowledge gained will be
applied to human alpha-arrestins and human GPCRs in the lab in Graz. Results of this work could have important impact on the development of next-generation pharmaceuticals because
recent results suggest that modulation of alpha-arrestin function might allow existing drugs to achieve greater potency and suggests routes for the development of new compounds.
Beginn: 31.07.2018
Ende: 30.05.2020
The project aims at the utilization of cyanobacteria as sustainable biocatalysts.
Beginn: 31.10.2017
Ende: 29.04.2020
Enzymatic synthesis of lactones as precursors for polymer production.
Beginn: 31.12.2018
Ende: 30.12.2019
The projects aims at the development and optimization of sustainable enzymatic processes for the utilization of terpenoids waste-streams from the chemical industry. The approach is the development of regio and enantioselective biocatalsts for several bio-based target molecules. The methodological approach uses genome mining and enzyme engineering.
Beginn: 28.02.2018
Ende: 29.06.2019
Oxygen functionalities are key functional groups in many of todays chemicals and materials. The efficient introduction of oxygen-functionalities into raw materials are key chemical transformations in bulk and fine chemicals. Innovative bio-catalytic oxidation routes using molecular oxygen (from air) under benign and mild (pH) conditions such as ambient temperature and pressure can greatly improve the sustainability and economics of processes, but were so far mainly been applied in the pharma segments. In this segment, the enzyme-catalyzed step often represents the highest added value and the high price of the end-product (> 1000/kg) justifies less than optimal enzyme production and limitations in its catalytic efficiency.
Beginn: 31.03.2015
Ende: 30.03.2019
Carboxylic acids are available in abundance from renewable resources and they could serve as economic precursors for bio-based products such as polymers, aldehyde building blocks and alcohols. However, carboxylic acid reduction is a challenge for chemical as well as enzyme catalyzed transformations due to the thermodynamic stability of carboxylates: Whereas chemical reduction methods typically require the use of organic solvents, toxic reagents, undesired reaction conditions, multiple steps or excessive use of reducing equivalents, the enzymatic reduction is poorly understood and only two enzymes are currently available to be used at a preparative scale. A significant number of carboxylate reductase sequences has not yet been elucidated and remains to be explored for biocatalysis. One goal is therefore to identify the primary sequences of enzymes that have already been reported to possess carboxylate reductase activity by a model assisted database mining approach. The putative new carboxylate reductases will then be heterologously expressed in Escherichia coli or Pichia pastoris and their activity will be assessed with a chromatography based in vitro assay. Active carboxylate reductases will be characterized biochemically using a spectrophotometric assay and subjected to crystallization trials in order to solve the first crystal structure of a carboxylate reductase. In addition, molecular model- or x-ray structure-guided site directed mutagenesis will be used to elucidate key residues for substrate binding and catalysis. In summary, we will gain understanding of the fundamentals of enzyme catalyzed reduction of carboxylic acids on the molecular level and provide new enzymes for biocatalysis.
Beginn: 28.02.2015
Ende: 27.02.2019
In BIOCASCADES, nine early-stage researchers (ESRs) will investigate the development of sustainable (chemo)enzymatic cascade
reactions under the ‘green chemistry’ philosophy. The proposed BIOCASCADES project combines different techniques such as
compartmentalization, protein engineering and reaction engineering in order to develop commercially viable and environmentally
benign one pot reactions. By avoiding intermediate downstream- and purification-steps, cascade reactions minimize production costs,
energy demand and waste production and are thus expected to make a major contribution for the development of sustainable and
efficient production processes.
Small- and medium sized enterprises (SMEs) are emerging as main drivers of European Research. They are dynamic, explore new
areas and create new ideas, while large companies rely more and more on outsourcing research or involving SMEs by joint ventures.
However, small companies are not strong enough as stand-alone enterprises, which requires them to form networks with other SMEs
and academia. This creates a strong demand for young researchers who can move freely in an international and interdisciplinary
environment. In a tailor-made training program BIOCASCADES aims to provide the nine early stage researchers with specific scientific
and transferable skills for careers in the highly dynamic European biotechnology sector. Training at leading laboratories of biocatalysis
will develop their scientific skills, while secondments to the industry and specific workshops will develop their entrepreneurship. The
graduates of this doctorate program will be highly qualified for collaborative research between European academia and industry.
The consortium is formed by leading academic laboratories from biocatalysis and protein engineering together with a network of four
innovative biotech companies. By combining their versatile expertise, the consortium can achieve a success that would not be possible
in isolated projects.
Beginn: 31.12.2014
Ende: 30.12.2018
Enzyme screening for selective oxyfunctionalization for amino aicids.
Beginn: 14.10.2018
Ende: 14.12.2018
Species of the multicellular fungus Trichoderma are among the most frequent mitosporic fungi (teleomorph Hypocrea, Hypocreales, Ascomycota, Dykaria) commonly detected in cultivation-based surveys. They have been isolated from an innumerable diversity of natural and artificial substrata what demonstrates their high opportunistic potential and adaptability to various ecological conditions. Recent genome sequencing and evolutionary analysis has revealed that the innate nature of Trichoderma is that of a mycotrophic fungus, but that this trait gave rise to development of a broad environmental opportunism from biotrophic interactions with plants and animals to saprotrophic nutrition. Systematic analysis of the genome content of Trichoderma revealed a unique inventory among the Pezizomycotina. The most striking finding is an enrichment of genes coding proteins with ankyrin domains that outnumbers all other fungi, and the combination of these ankyrin domains with HET and NACHT domains. In this project, we are therefore planning a systematic investigation of the ankyrin repertoire of Trichoderma, using a transcriptomic (deep RNA sequencing) and cell biological (gene knock out, gene overexpression) approach to learn the involvement of these proteins in the various life-styles of Trichoderma.
Beginn: 30.06.2013
Ende: 29.06.2018
Background. Functionalized derivatives of heterocyclic five-membered ring structures belong to the most important chiral building blocks for manufacturing of pharmaceuticals, agrochemicals, cosmetics, and natural compounds. The project aims at replacing waste-intensive chemical routes for the synthesis of these important fine chemicals by biohydroxylation, employing substrates and organic solvents from renewable resources. The proposed research is a response to the strong need for novel greener approaches for the selective oxyfunctionalization of biobased and conventional chemical scaffolds and intermediates.
Main objectives. Selective hydroxylations are among the most difficult chemical reactions but enable important direct and indirect functionalization of non-activated C-H bonds to generate key intermediates for chemical synthesis. With this proposal, we specifically address biobased solutions for the direct hydroxylation in the electronically unfavored 3 position of five-membered heterocyclic rings. To our knowledge, there are no currently available economic solutions by metal catalysis to this reaction. The proposed research investigates the biochemical properties and implements the biocatalytic potential of the robust cytochrome P450 family CYP153, aiming at three specific goals:
· access to and development of efficient and selective enzymes for the hydroxylation of simple heterocyclic five-membered ring structures;
· biohydroxylation using substrates and solvents from renewable resources;
· demonstration of the feasibility of biotransformations with commercially useful yields.
By targeting to apply a comparatively unexplored enzyme class to a specifically challenging reaction, the project combines innovative solutions to industrial challenges with scientific progress in a competitive field of biological chemistry.
An international, highly complementary and multidisciplinary team. We will take advantage of the complementary expertise of two participating laboratories, Mattevi’s group in Pavia and the Glieder and Nidetzky groups at the Graz University of Technology, and of the collaboration with Dr. Dr. Z. Li at the National University in Singapore. In a cross-disciplinary approach that combines research in enzymology, organic syntheses, cutting-edge molecular botechnology methods with the joint experience and knowledge in oxygenase-catalyzed biotransformations from previous and ongoing collaborations, we will provide key enabling technologies for bio-based fine chemical industry which has important production sites in northern Italy.
Dissemination and social impact. The project integrates to the bioeconomy chain value by delivering new applications that take advantage of bioderived organic solvents and attractive starting materials for biochemical synthesis and applying nature derived tools for manufacturing. The workplan has a strong emphasis on biobased solutions to support the Italian fine chemical industry with new production technologies and on providing young trained scientists with industrially relevant skills in bioeconomy and technology transfer as well as giving them opportunities to find adequate jobs. Along this line, the proposal has a clear commitment to disseminate and maximize the visibility of the research. The goal is to create a win-win situation by intensifying the already ongoing research collaborations between Universities of Pavia and Graz and their local and international industry networks.
Beginn: 14.06.2016
Ende: 14.06.2018
The DK - Molecular Enzymology is a joint international biomolecular PhD program of 15 research groups from the following two universities: Karl-Franzens-Universität Graz (KFUG), Technische Universität Graz (TUG)
The DK is affiliated with the Faculty of Natural Sciences of the KFUG and the Faculty of Technical Chemistry, Chemical Engineering and Biotechnology of the TU Graz. It is designed to act as an academic complement to existing biomolecular large-scale research networks, such as the SFB Biomembranes, the Kplus Center Applied Biocatalysis and the GENAU-network GOLD: Genomics of Lipid-Associated Disorders.
The aim of the international PhD program in Molecular Enzymology is to provide outstanding scientific training to exceptional young scientists in different areas of the molecular biosciences, including bioorganic chemistry. The interdisciplinarity of the program includes extensive training activities in addition to the project-related PhD research. The laboratory work will be supplemented by seminars, local and international laboratory training courses, and participation in international conferences.
Research Topics:
- the discovery of enzymes
- the molecular structure of enzymes
- the cellular and metabolic function of enzymes
- the biotechnological exploitation of enzymes
PhD Projects:
- Cell biology of neutral lipid formation and mobilization in Saccharomyces cerevisiae
- Lipid assembly in peroxisomal membranes
- Role of yeast TAG lipases in sphingolipid metabolism
- Expression of oxidative enzyme libraries in Schizosaccharomyces pombe
- Alternative oxidases: Elucidation of structural and functional differences between plants and fungi
- Application of lyases to the enantioselective formation of novel C-C bonds
- Molecular identification of lipases in murine bile
- Structure, mechansim and use of bacterial azoreductases
- Structure-Function studies on berberine bridging enzyme (BBE) from the California poppy (Eschscholzia californica)
- The glycogen phosphorylase from Sulfolobus solfataricus
- Aldo-keto reductases from the hyperthermophlic archaeon Sulfolobus solfataricus
- Engineering of enzymes for improved enantioselectivity
Beginn: 31.12.2004
Ende: 30.12.2017
LC-MS/MS data from complex lipid samples carries the potential to elucidate many structural features of lipids. It provides information about the fatty acids and in many cases about their regioisomeric position. However, the MS/MS spectra of lipids can vary tremendously, because the fragmentation process depends on parameters like the used mass spectrometer, fragmentation collision energy, charge state, and adduct ions. Due to this diversity, a generally applicable bioinformatics tool for the automated analysis of lipidomics LC-MS/MS experiments is still missing.
This projects global aim is to develop a versatile and generally applicable method for high throughput determination of lipid structural fatty acid composition from LC-MS/MS data, easily adaptable to different mass spectrometers and experimental setups. The general applicability will be facilitated by a newly developed language for the description of MS/MS fragmentation spectra. Based on this language, a novel algorithm will identify the lipid and its deducible compositional features. The performance of the method will be verified in controlled and biological experiments. Furthermore, we want to supply a graphical user interface for the definition of rules describing the spectra, and supply pre defined rule sets for the most common mass spectrometers.
Beginn: 30.06.2013
Ende: 29.10.2017
CHEM 21 is a project that will develop a broad-based portfolio of sustainable technologies for green chemical intermediate manufacturing in the pharmaceutical industry.
The technology being developed is divided into three work packages based on chemical catalysis and synthetic methods, biocatalysis and synthetic biology. In biocatalysis a range of projects based on the needs identified by the chemical roundtable has been chosen.
Beginn: 30.09.2012
Ende: 29.09.2017
Developement of a production process for recombinant horseradish peroxidases including new enzyme variants.
Beginn: 31.05.2015
Ende: 29.11.2016
Excessive energy intake and diminished energy expenditure are two sides of the same coin leading to overweight and obesity. Both disorders reach pandemic proportions globally with more than 1.5 billion adults overweight (BMI > 25 kg/m2) and at least 500 million of them clinically obese (BMI > 30 kg/m2). As controlling the side of energy intake pharmacologically has failed so far in promoting weight loss, enforcing the side of energy expenditure has recently attracted attention.
Intriguingly, in contrast to early contention, healthy adult individuals possess not only energy-storing white adipocytes but also thermogenic adipocytes which are specialized in combustion of carbohydrates and fats for the purpose of heat production (non-shivering thermogenesis). These thermogenic adipocytes are characterized by multilocular lipid droplets, a high density of mitochondria, and the expression of uncoupling protein 1 (UCP1), a mitochondrial protein that plays the key role in heat production by uncoupling the activity of the respiratory chain from ATP synthesis. Thermogenic adipocytes constitute the brown adipose tissue and - upon cold stimulation - can be found in white adipose tissue, thereby called brite (brown-in-white) / beige adipocytes.
We identified a microRNA that induces UCP1 expression in mature white human adipocytes, thus influencing the white-brite balance. Therefore we propose to characterize the microRNA-induced effects on adipocyte metabolism in vitro and in vivo. In particular, we first aim to generate a human in vitro model system with inducible expression or inhibition of this microRNA. While the inducible microRNA expression will enable us to investigate its thermogenic effects in mature human adipocytes, the inducible microRNA inhibition will provide insight into its regulatory interplay with substances known to influence the white-brite balance. To investigate the role of this microRNA in vivo, we generated a transgenic mouse model that enables an inducible microRNA overexpression exclusively in adipocytes. With these mice, we will investigate the impact of this microRNA on energy homeostasis and thermogenic adipocyte recruitment.
We expect to generate novel insights into the regulation of energy expenditure via non-shivering thermogenesis in adipocytes, which may contribute to novel strategies to combat obesity and associated metabolic disorders.
Beginn: 30.04.2013
Ende: 29.04.2016
During the last two decades cichlid fishes have been established as evolutionary model system.
Genomic approaches have undergone massive innovation concerning speed and efficiency of
deciphering whole genomes and become increasingly important in evolutionary biology. My research
group has been studying the adaptive radiation of cichlid fishes for more than 15 years, attempting to
understand the pathways of speciation and adaptation to novel ecological niches. The cichlid fishes of
Lake Tanganyika represent the oldest and eco-morphologically most advanced adaptive radiation and
several lineages radiated in parallel. We chose the tribe Tropheini to study adaptive evolution, as they
are much more diverse in terms of ecology, morphology and behavior than any Lake Malawi and
Victoria cichlid, despite being part of a monophyletic and closely related assemblage. To take our
approach further in evo-devo context, we propose to decipher the genomes of two highly divergent
members of the Tropheini, the epilithic algae feeder Tropheus moorii, and the unicellular algae comber
Petrochromis trewavasae. We intend to use 454 sequencing technology in combination with shotgun
approaches to successfully score the two genomes in reasonably complete coverage. The project is
planned as cooperation between three research groups from three Universities, The Karl-Franzens
University of Graz, The Medical University of Graz, and the Graz University of Technology, whereby
each group contributes crucial expertise and resources. The team-members of the Department of
Zoology provide the study system and the research questions and hypotheses, the partners of the
Center of Medical Research of the Medical University of Graz contribute their powerful genome
sequencing unit, the members of the Institute for Genomics and Bioinformatics provide their expertise in
genome assembly and annotation and computing infrastructure, which can cope with the demands of
sequencing large genomes. This project should not be understood as an attempt to undermine ongoing
efforts in cichlid genomics, but as a valuable complement in the common goal to decipher a suite of
wisely chosen cichlid genomes as "natural mutants", to understand the common pattern of cichlid
adaptive evolution and its connection to speciation processes at various stages of adaptive radiation. By
comparing particular structural and regulatory genes in addition to the genome sequencing effort we
hope to find correlates to divergent eco-morphologies, as recently demonstrated e.g. for Lake Malawi
rock cichlids. The advantage and complementary potential of the Lake Tanganyika system would be its
significantly older evolutionary age and the fact of more complete genomic separation, mirrored in the
completed lineage sorting among species in the mtDNA genome.
Beginn: 31.12.2012
Ende: 30.12.2015
The discovery, development and demonstration of biocatalysts for use in the industrial synthesis of chiral chemicals.
Beginn: 30.11.2011
Ende: 29.11.2015
The DIABAT project comprises 19 research partners in 12 european countries and will employ knowledge of the function, dysfunction and physiological regulation of brown adipocytes to develop innovative therapeutic and preventive strategies for type 2 diabetes. Brown adipose tissue (BAT) is currently a worldwide recognized target to combat obesity and diabetes due to last years re-discovery of functional BAT in adult humans by several of the members of the DIABAT network (van Marken LIchtenbelt et al., N. Engl. J. Med. 360, 1500, 2009; Virtanen, Enerbäck & Nuutila, N. Engl. J. Med. 360, 1518, 2009) along with sharp rise in insight in cellular, genetic, and regulatory mechanisms from animal studies. Therefore, the DIABAT project aims at recruiting and re-activating endogenous energydissipating BAT as a preventive and/or remedial measure for weight and blood sugar control in obesity-related type 2 diabetes (diabesity).
Beginn: 30.09.2011
Ende: 29.09.2015
The DIABAT project comprises 19 research partners in 12 european countries and will employ knowledge of the function, dysfunction and physiological regulation of brown adipocytes to develop innovative therapeutic and preventive strategies for type 2 diabetes. Brown adipose tissue (BAT) is currently a worldwide recognized target to combat obesity and diabetes due to last years re-discovery of functional BAT in adult humans by several of the members of the DIABAT network (van Marken LIchtenbelt et al., N. Engl. J. Med. 360, 1500, 2009; Virtanen, Enerbäck & Nuutila, N. Engl. J. Med. 360, 1518, 2009) along with sharp rise in insight in cellular, genetic, and regulatory mechanisms from animal studies. Therefore, the DIABAT project aims at recruiting and re-activating endogenous energydissipating BAT as a preventive and/or remedial measure for weight and blood sugar control in obesity-related type 2 diabetes (diabesity).
Beginn: 30.09.2011
Ende: 29.09.2015
Over 1.6 billion overweight and over 400 million obese people worldwide are causing the biggest epidemic of the 21st century. If the energy intake of modern humans exceeds energy consumption, the natural physiological response is to store energy in white adipose tissue. Brown fat acts diametrically because it burns fat by producing heat (thermogenesis). It was not until 2009 that functional brown adipose tissue was detected in adult humans. This makes a paradigm shift in the treatment of overweight and obesity possible: reduced energy intake is replaced by increased energy consumption. MicroRNAs, a new class of regulators, play a central role in the concert of gene regulation. In order to utilise microRNAs therapeutically, effective microRNA transport - microRNA drug delivery - in fat cells is required. The NANOFAT project aims to develop and validate effective microRNA transport in fat cells.
Beginn: 31.07.2011
Ende: 30.07.2015
The transfer of a methyl group is an essential step in many reactions occurring in every living cell. This transformation is catalyzed by methyltransferases (MTases). All MTases share the need for a cofactor to perform their action. S-adenosyl-L-methionine (SAM, AdoMet) is the most frequently used methyl donor in biological systems. Recent studies showed the ability of DNA-C-MTases as well as small molecule-C-MTases to accept SAM analogues for transfer of extended carbon chains to various substrates. Anyway, the improvement towards a broader range of cofactor analogues is of great interest in terms of both biocatalytic synthesis and DNA diagnostics. This proposal aims to combine directed enzyme evolution with rational protein engineering to obtain C-MTases for improved transfer of extended groups from SAM analogues. In general, it is very difficult to develop selection strategies for MTases. The first part of the proposal describes the directed evolution of the DNA-MTase M.SssI towards cofactor analogues by in vitro selection of positive clones. For this purpose the protection of DNA from fragmentation by cognate restriction endonucleases will be used after in vitro expression of gene variants in water-in-oil emulsion droplets (in vitro compartmentalization). This method links genotype and phenotype and provides an effective selection of evolved variants. The result of M.SssI evolution will afterwards be transferred to rational protein engineering of the small molecule MTase NovO. The fact that both enzymes share high structural similarities of their core fold, which include the cofactor binding site, allows the combination of error-prone mutagenesis for directed evolution of M.SssI and site-directed mutagenesis for rational protein design of NovO. Besides analysis of enzyme activities, also biophysical properties of both enzymes will clarify the mechanism of protein-ligand interaction. Therefore dissociation constants of MTases and cofactors will clarify the importance of individual mutations for cofactor specificity. In sum, the proposed work will give new important insights and stimulate prospective applications of alkyl transfer reactions.
Beginn: 30.09.2014
Ende: 09.07.2015
The rationale of this study is to identify and characterize mRNAs and miRNAs that influence the white to brown conversion of human adipocytes as well as those involved in metabolic activation of brown adipocytes.
Beginn: 31.12.2010
Ende: 30.12.2013
Lactic acid bacteria (LAB) have served humankind all times by preserving food stuff. Examples are the production of yoghurt, sauerkraut or silage. LAB are natural constituents of the healthy intestinal flora, some of which have been proven to have probiotic effects. During the progress of industrialization, production processes using LAB were being more and more specified and demands for these microorganisms increased constantly. Goal of the CD-laboratory for genetically engineered LAB is to understand and learn the basic mechanisms of these microorganisms by using modern methods and new tools of molecular biology and to increase their application potential. Integrating data from qualitative and quantitative genome- transcriptome- and proteome analysis should result in a rational basis for targeted genetic engineering. The CD-laboratory is intended to contribute to science and society by extending the existing knowledge about basic gene structure and regulation and to conduct quantitative analyses about transcription, protein expression and in particular protein secretion. The goal is to exploit the entity of acquired data in an integrative manner in order to construct LAB strains that are feasible for industrial utilization. LAB will be genetically engineered to contain new catabolic and anabolic capacities. Two directions are to be followed, accordingly:
1. Construction of catabolic strains for the over-production of proteins, small peptides and other molecules in industrial fermenters.
2. Construction of anabolic strains, able to degrade macromolecular carbon sources such as cellulose or inulin for more efficient and robust preservation processes.
The main focus of both directions is not only to provide adequate efficiency but also to generate genetically stable and biologically safe, engineered strains. For improved performance of anabolic strains, targeted enzyme engineering is intended to optimize and adapt enzymatic performance. In the long run, the industrial partner will benefit from the hereby created advances in science and technology, and increase its chances within the promising high technology sector of biotechnology.
Beginn: 31.10.2008
Ende: 30.10.2013
In MacroFun, the efforts are focussed on establishing structural and mechanistic know-how to better understand the interface between enzymes and macromolecules, to develop enzymes for the functionalisation of polymer surfaces and the directed and specific assembly, conversion and degradation of biopolymers. Thereby, an improvement of enzymatic processes and novel applications for a selective degradation, activation and functionalisation of natural and synthetic polymers will be developed. New enzyme systems for efficient biotransformation of polymers and the assembly of bioresponsive devices will be established.
Beginn: 30.06.2008
Ende: 29.06.2013
Designer Enzymes - Improved biocatalysts for bioprocesses
Enzymes are increasingly used as efficient biocatalysts to perform a wide range of chemical reactions. Research is needed on how enzymes can be successfully engineered through directed evolution in the laboratory involving rational design over a short timescale. In order to fully harness the power of directed evolution for better catalysts, a sustained effort is needed to develop high-throughput screening methods specifically directed towards enzymes. There is a general need in industrial biotechnology for generic platform technologies and methods for fast and accurate enzyme activity determination and generic methods to improve enzymes are urgently needed.
Beginn: 30.04.2008
Ende: 13.05.2013
Aim 1: Generation and characterization of adipose tissue-specific
APMAP transgenic mice.
In a transcriptomics approach we recently found APMAP to be highly up-regulated during 3T3-L1
differentiation and to play an important role in adipogenesis in vitro [Strauss et al., manuscript in
preparation]. To elucidate the physiological function of this gene we will generate and characterize adipose
tissue-specific transgenic mice will be generated using a plasmid containing the 5.4-kb
mouse aP2 promoter that will be fused to the 1.25 kb APMAP cDNA, linearized, purified, and
microinjected into the fertilized pronuclei of female mice that had been mated before.
Furthermore, the human in vivo function and role of APMAP will be studied by investigation of the
genetic variability within obesity-related phenotypes in human association studies
(C13/Kronenberg).
Aim 2: Functional characterization of genes differentially regulated in fat cell development.
Using microarray analysis described above, a number of genes with yet unknown functions
displaying significant differential regulation during fat cell development was found, such as
APMAP, RIKEN gene 653040D17 (Arxes), 24100004L22, and 4930566A11. First, APMAP will be
studied in more detail in vitro. Hydrolase assays (due to the prediction of sequence analysis by
BINII) will be performed in cooperation with C6/Zechner and C4/Hermetter. Further, the four
predicted Ca-binding sites of APMAP will be mutated to see whether they influence the
differentiation capacity of 3T3-L1 cells. Cloning of YFP and CFP constructs will help to discover the
exact location of APMAP in the cell and whether addition of Ca2+ is translocating APMAP
(microscopy, C10/Kohlwein).
To elucidate the possible function in adipogenesis of the other RIKEN genes listed above, their
expression levels will be studied in various mouse lines under different conditions (C57/Bl6: regular
vs. high fat diet, fasted-fed; OB/OB). In vitro, these genes will be both overexpressed and silenced
in 3T3-L1 cells. We will investigate whether their expression levels have an influence on fat cell
development, TG hydrolysis/accumulation, LD formation, and on the expression levels of
transcription factors known to be important for adipogenesis. In addition, ChIP-qPCR will be
performed to find out whether these genes have binding sites for (and might thus be regulated by)
transcription factors important in fat cell differentiation. In addition, further candidate genes
identified during GOLD III by C2/Trajanoski will be subjected to functional analysis.
Beginn: 31.01.2009
Ende: 29.04.2013
In cells from all organisms studied to date two different types of RNAs are found: messenger RNAs
(mRNAs), which are translated into proteins and so-called non-protein-coding RNAs (ncRNAs), which are
not translated into proteins but function at the level of the RNA itself. Many known ncRNAs, such as
miRNAs, are involved in the regulation of gene expression. Presently, the annotation of ncRNAs in the
genomes of various organisms has been a difficult task for bioinformatics and experimental approaches (e. g.
by the generation of cDNA libraries encoding ncRNAs). Thus, in the human genome the predictions on the
number of ncRNA genes range from about 1.000 up to 400.000 (estimated from tiling-array experiments). In
comparison, about 20.000 human protein-coding genes are being estimated. These findings raise two
important questions to the ncRNA field: 1) how many of these ncRNAs really exist in genomes of model
organisms and 2) what are their functions? Both questions are intimately connected, because it is expected
that novel ncRNAs might fulfill functions that expand the known repertoire of RNA (e.g. induction of
heterochromatin formation). Only if the function of a RNA can be elucidated, this RNA species will be
assigned as a bona fide ncRNA (otherwise, the RNA might represent a spurious transcript or degradation
product without any function). Hence, the proposed application termed: Non-coding RNAs: from
identification to functional characterization deals with these two major questions in genomic research.
By employing sophisticated selection procedures for experimentally identifying novel ncRNAs in various
genomes, we subsequently aim to reveal their cellular role(s). At the same time, we will elucidate the
biological function of some known ncRNAs (specifically miRNAs and riboswitch RNAs) as crucial genetic
switches in the regulation of gene expression. In addition, we will study the roles of selected miRNAs in
neuronal differentiation and in human diseases, such as obesity, atherosclerosis and neuro-degeneration. The
experimental data will be complemented and validated by bioinformatical prediction as well as
classifications of ncRNAs, employing novel computational algorithms. Both, experimental and
computational approaches will enable a better understanding of gene regulation, gene function and
involvement of ncRNAs in human diseases.
Subproject 9: Functional characterization of microRNA-mRNA pairs targeting adipogenesis and obesity
Beginn: 28.02.2009
Ende: 29.04.2012
Objectives:
The aim of our research program is to identify subsets of genes that are particularly relevant to the biology, diagnosis management, treatment, and prevention of lipid-associated disorders and to prioritize the information for further focused studies. We are concentrating our efforts on expression profiling of mouse models using cDNA microarrays and the creation and use of computational tools for combined analyses of genome sequences and gene expression data. Our plan to achieve those goals are outlined in the following specific aims.
Aim 1: To establish a mouse cDNA microarray development and analysis component.
We are installing a core facility to produce >1000 slides per year. The cDNA microarrays will be used to perform transcript profiling in mutant and disease mouse models. We will design and conduct microarray expression assays with the goal of elucidating patterns of gene expression associated with response to environmental stressors in mouse models.
Aim 2: To establish a genomic information management system. We are developing an integrated system for storing and analyzing microarray data. The analytical pipeline includes modules for image processing, cluster analysis, sequence analysis as well as tools for storing and retrieving microarray data (see URL http://genome.tugraz.at).
Aim 3: To establish an education and outreach component. To support this application, we will institute an education and outreach program.
Beginn: 31.10.2002
Ende: 30.01.2012
The flood of data arising from genomic-scale studies performed within the GEN-AU research program poses significant challenges. During the first phase of the GEN-AU program, as part of a strategy to turn these challenges into opportunities and chances, we assembled a consortium of research partners within the Bioinformatics Integration Network (BIN) and established a computational laboratory for the integration of bioinformatics solutions. During this phase we established three thematic nodes with complementary expertise: (i) bioinformatics services and database integration, (ii) sequence annotation and (iii) structural genomics. During the second funding period we expanded and improved the backbone for bioinformatics services and broadened the scope of the thematic nodes by establishing proteomics informatics and evolutionary sequence analysis.
The continuous development and application of novel technologies for generating high-throughput data requires the parallel development of computational methods and tools to manage, store, and analyze the data. The BIN III consortium therefore plans to maintain and enrich the computational laboratory and strengthen interactions with the experimental partners during the third funding period.
The goal of the BIN III project is to provide bioinformatics services and use computational methods to address biological questions arising from the GEN-AU projects. Specifically, our aims are:
- To provide an environment for bioinformatics services and continuously improve bioinformatics resources for the large-scale projects within the Austrian genome research program GEN-AU. The bioinformatics services developed and installed during BIN I and BIN II will be maintained and improved and the available databases, services and systems will be adapted to emerging software technology and new hardware requirements.
- To develop novel computational methods for the analysis of biomolecular data. All individual components will direct major research activities with the aim of developing computational methods for the analysis of biomolecular data and validation of the methods in a biological context. We will focus on two specific areas: gene regulation and the modeling of molecular networks.
- To validate the developed methods and address biological questions posed by the GEN-AU projects. In collaboration with the experimental partners from other GEN-AU projects we will apply the computational methods developed in the preceding aim to address biological questions and/or validate the methods. Experiments will be designed and performed in close collaboration with the computational biologists to generate the necessary data.
- To promote the development of bioinformatics and computational biology in Austria by providing education and training at the undergraduate and graduate levels. We will continue the PhD program with special emphasis on the education of core personnel for bioinformatics. The network will furthermore continue to organize workshops for biologists in the GEN-AU projects, arrange a series of lectures featuring distinguished bioinformatics speakers and offer additional working places for guest scientists at the network nodes.
Beginn: 30.04.2010
Ende: 30.12.2011
The principal goal of our research plan is to link genes to function on a genomic scale in order to facilitate investigations of physiological and pathophysiological mechanisms underlying metabolic diseases. Together, researchers at the Institute of Biomedical Engineering, Graz University of Technology, the company Oridis Biomed, Graz and the company Eccocell, Graz have developed a broad-based response to this challenge in which we will develop a number of reagents, tools, and techniques that will allow us to provide links between physiologically relevant animal models of human disease and the genes that are differentially expressed in those phenotypes. The starting point for our proposed studies are mouse phenotypes that are relevant to liver diseases and obesity, and corresponding human disease tissues. Expression profiling will be performed using murine cDNA microarrays constructed in our laboratory and human disease-specific cDNA microarrays generated by Oridis Biomed as well as genome-sized human microarrays that will be produced. Expression data will be analyzed using: a) large-scale functional prediction on gene sets selected by expression criteria from cDNA microarray data, and b) large-scale comparative analyses of the human and mouse transcripts. Finally, to characterize the biochemical and cellular function of the target proteins, protein expression patterns in normal and diseased tissues will be examined using tissue microarrays.
Beginn: 31.10.2002
Ende: 30.10.2009
Simple and complex carbohydrates have been described as 'the last frontier of molecular and cell biology'. The
carbohydrates, or often 'the sugars', are biomolecules characterised by enormous structural complexity and
functional diversity. To a wider public, they are known mainly because they provide a major caloric portion of the
human diet and sometimes impart a sweet taste to the product. However, physiological roles in which
carbohydrates act as a 'cellular language' have been unveiled and rely on the huge coding potential of the individual
monosaccharides that constitute the functional structure. Among the plethora of carbohydrate-active enzymes, those
which can catalyse the formation of specific linkages between the monosaccharide building blocks to yield
oligosaccharides are especially challenging. This group of enzymes, functionally classified as 'the
glycosyltransferases' (GTs), is large, and its members differ in respect to both amino acid sequence and threedimensional
structure, partly reflecting the complexity of the reaction products of their catalytic action. Obviously,
a very well-defined orchestration of the action of different GTs in a place and time-dependent context is required
to achieve a tight regulation of carbohydrate-mediated cellular responses at all levels of metabolism. In order to
harness fully the newly bequeathed genomic resource in the form of a myriad of open-reading frames whose
translation products that are likely involved in oligosaccharide synthesis, modification and turnover, we need to
understand better how GT sequences relate to enzyme structure, mechanism, and specificity. The project aims at
unraveling some "sweet secrets" of GT structure-function relationships by focusing on a representative enzyme
group within the GT class: the phosphorylases. We will use the genome of the archaeon Sulfolobus solfataricus as
resource of novel and seemingly archetypal variants of glycogen phosphorylase and trehalose phosphorylase, two
important GTs of energy-related carbohydrate metabolism. The archaeal enzymes and selected mutants thereof will
be examined through detailed biochemical and mechanistic characterisation, and their properties compared with
homologues seen in other organisms and cell types. Through this process, means for extrapolation of molecular
information to other sequence-related GTs are provided and strategies for the utilisation of the glycogenomic
resource inspired.
Beginn: 30.09.2005
Ende: 14.01.2009
A recent directive of the European Union proposed that biofuels should represent 2% of the total transportation fuel
consumption by 2005. In order to achieve this ambitious goal, it is clearly necessary to improve the current
biotechnologies for fuel production, particularly if non-conventional feedstocks such as lignocellulose are being
used as raw materials. Lignocellulose is attractive because it is renewable through the process of plant
photosynthesis and available in huge quantities as wastes from forestry, agriculture and the pulp and paper
industries. It is composed of the polysaccharides cellulose and hemicellulose, and lignin. A number of studies have
shown that the economics of a process for lignocellulose conversion require that efficient uses for both cellulose
and hemicellulose be found. Glucose and xylose are the main constituent monosaccharides ('sugars') in cellulose
and hemicellulose, respectively. While glucose can be fermented easily into alcohol, the production of ethanol
from xylose remains a challenge. The classical brewer's or baker's yeasts are unable to utilise xylose unless
engineered with tools of molecular biology to have extra metabolic capabilities. However, the engineered yeast
strains often produce little ethanol, accumulating other by-products. There is a major problem leading to this
shortcoming during xylose fermentation: NAD(P) cofactors are not recycled efficiently between the enzymes
catalyzing the first two steps of xylose assimilation. Therefore, the development of an industrial production
organism requires that the initial steps of xylose utilisation be optimised. Recent studies in the applicant's
laboratory make possible a novel approach to overcome the intrinsic limitations of current recombinant strains
designed to ferment xylose. In this project, enzymes with tailored specificities will be generated by site-directed
mutagenesis, and mutated genes will be introduced into the genome of the yeast Saccharomyces cerevisiae. The
organism expressing the altered genes will now be able to ferment xylose with improved yield and at a reduced
level of by-products. The novel strains produced by metabolic engineering will be tested under fermentation
conditions in bioreactors to provide essential information about physiology and potential industrial application.
Beginn: 30.09.2005
Ende: 14.01.2009
The goal of the project is to maintain, expand, and continuously improve bioinformatics infrastructure, and to create and apply bioinformatics solutions to special requirements emerging from the national genomics and proteomics projects. Efforts are concentrated on the development and use of computational tools for combined analyses of genome sequences, gene expression data, proteomics data, and 3D structural data. The network will focus on the provision of bioinformatics services, development of methods and tools, and training and education. Specifically, the aims of the Bioinformatics Integration Network II (BIN II) are as follows:
To provide bioinformatics services and continuously enrich bioinformatics resources for the projects within GEN-AU. The existing backbone for bioinformatics services will be maintained, improved, and thematically extended. The databases,services, and systems will be adapted to emerging software technologies, frameworks and interfaces. Additionally, the services will be extended to include systems for specific proteomics technologies. The increasing amount and complexity of biological data reaching the limits of the available hardware makes it necessary to migrate to the next generation servers and computing clusters.
To develop novel methods and create databases and software tools for the analysis of biological data generated in GEN-AU projects. The present databases and software tools for microarray data, RNA sequences, protein sequences, and 3D structures will be maintained and improved. The thematic nodes will be complemented by evolutionary sequence and proteomics data analysis.An integrated platform for quantitative proteomics will be developed, including tools for spectrum processing and detection of
posttranslational modifications, storage and validation of results, and data mining tools for high-resolution mass spec data.
To promote the development of bioinformatics and computational biology in Austria by providing education and training at the undergraduate and graduate level.
Beginn: 31.12.2005
Ende: 30.12.2008
Comparative transcriptomics of models of lipid-associated disorders Disease phenotypes arise from complex interactions of organisms with their environments. While we have along history of associating genes and gene defects with a large array of diseases, a growing body of datasuggests that many disease phenotypes arise from the interactions of genes with their environments -including the genetic background in which those genes are expressed. The goal in this project is to explore these interactions using cDNA microarray technology, in conjunction with the characterization of mousephenotypes relevant to lipid-associated disorders, and to identify genes, pathways, and environmental factors that contribute to the development of the disease state.The overall goal of this component is to identify subsets of genes that are particularly relevant to the biology of lipid-associated disorders and to prioritize the information for further focused studies. We are concentrating our efforts on expression profiling using mouse models of lipid-associated disorders, comparative analyses of the generated profiles, and ChIP on chip assays. Specifically, we aim to: Develop a molecular atlas of wild-type and mutant mouse adipocytes. We have developed a mouse microarray and aim to enrich this array with an additional library and to conduct expression assays to establish a wild-type and mutant gene expression atlas of mouse adipocytes. Identify regulators involved in fat cell differentiation.We have established an in vitro adipocyte differentiation assay using calvariae calvariae cells of newborn mice (mesenchymal precursor cells) to identify genes important for adipocyte differentiation. We will compare transcriptional profiles of differentiating wild-type cells with differentiating cells from transgenic mice. Develop ChIP on chip (Chromatin immunoprecipitation on microarray). We aim to develop a mouse promoter microarray to identify target genes of key transcription factors selectedin the previous aims and in other subprojects.
Beginn: 30.11.2005
Ende: 29.11.2008
Previous data suggest that JunB is important for the control of adipocyte differentiation and lipid metabolism. Therefore we want to define the physiological pathways that depend on JunB to decipher the key signaling molecules which are transcriptionally regulated by JunB. The long term goal of this project is to explore the role of the AP-1 transcription factor family in energy and fat metabolism. To investigate the function of JunB in adipose tissue development. JunB delta/delta and UbiJunB mice will be used for phenotypical characterization focusing on adipogenesis and lipid metabolism. RNA samples of several tissues will be subjected to microarray analysis to identify genes involved in adipogenesis and lipid metabolism that are regulated by JunB. ChIP on chip assays will be used to identify target genes of the AP-1 transcription factor family. To generate and characterize adipose tissue specific AP-1 knock out mice and to identify differentially expressed genes. Adipose tissue specific ko mice will be compared to the conventional ko-mice analyzed in Aim 1. Genes newly identified by microarray analysis will be tested for their functional relevance in vitro.
Beginn: 30.11.2005
Ende: 29.11.2008
The dramatic increase of overweight and obesity has reached globally the status of the epidemic of the 21st century. Globally, more than 1 billion adults are overweight (BMI > 25) - at least 300 million of them clinically obese (BMI > 30) - and the increasing incidence of obesity in developing countries as well as of child obesity is alarming causing tremendous costs for our health care systems. Obesity is characterized on the cellular level by excess adipose (fat) tissue. The identification of protein-coding genes that are involved in the regulation of fat cell (adipocyte) development has greatly increased our knowledge of the mechanisms that underlie this condition. But still, we are far from a complete picture of molecular events in adipocyte differentiation. Especially, the early stage of adipocyte differentiation is not well understood also due to a lack of appropriate in vitro cell models. Recently, a novel class of tiny regulators - called microRNAs - has been identified to be involved in cellular differentiation which are recruited from the 97% of the human genome that does not encode proteins. To date, more than 350 mouse and 450 human candidates of this novel class of regulators have been identified predicted to regulate 30% of all genes. A small number of microRNAs has been associated with diseases, with the potential for many more. This proposed project addresses the identification of microRNAs regulated across species in the early stage of adipocyte differentiation (adipogenesis) in mammals with relevance in vivo.
Therefore, the specific aims of this project are to profile mouse microRNA and mRNA expression during adipogenesis in vitro, to profile mouse microRNA and mRNA expression during adipogenesis in vivo, to identify cross-species regulated microRNAs between human (previous work) and mouse in vitro and in vivo, and to validate adipo-specific miRNAs by inversely regulated target genes.
The results obtained will make an important contribution to the understanding molecular mechanisms of fat cell development and the pathogenesis of obesity as one of the most daunting health challenges facing medicine today, thereby also laying the foundations for possible commercial applications.
Beginn: 30.09.2007
Ende: 29.09.2008
Natural biodiversity represents a nearly unlimited pool of biostructures and therefore it is the major source for
obtaining enzymes and metabolites to be used in various industrial, medical, agricultural and environmental
applications. Especially the microbial world reflects a huge genetic and metabolic biodiversity, which is to a great
extent not yet explored, but offers a very high application potential. However, only a very small percentage of
microbial species can be cultivated but in the last years methods to explore the uncultivable microbial world have
been developed. One major fact determining the available pool of biostructures is the specific habitat of a microbial
community which determines the composition of the available enzymatic and metabolic activities. One such
interesting habitat are endophytic microbial populations of plants. This habitat reflects intense interactions between
the microbial and the plant biological activities. Therefore it can be expected that it contains very specific
biostructures, both at the enzymatic and the metabolic level.
This project intends to explore plant endophytic habitats with a focus on obtaining a new diversity of biostructures,
having a high potency for biocatalytic and agricultural applications. Metagenomic libraries of the microbial
community present in such specific habitats will be set up to create a novel bioresource at the metagenome level.
Though this project focusses on recruiting interesting new enzymes, the basic setup of metagenomic libraries will
address both, creating a new resource for enzymes as well as for metabolites. Expression libraries of small
fragments will be generated on the one hand to serve as a source for novel enzymes. On the other hand the creation
of libraries which contain large genomic fragments will allow also to explore the metabolic diversity. Libraries will
be established from two interesting habitats, one being a wild plant known to be able to efficiently grow at low
temperatures (Crocus albiflorus) and the other being a plant of high agricultural interest (potato).
One problem in exploring metagenomic populations for novel enzymes is functional expression in heterologous
hosts. Therefore suitable host-vector systems which in addition to E.coli should serve as potent expression systems
will be established, focussing on a Gram-positive Bacillus system and on a Streptomyces system.
Established libraries will be screened by high-throughput techniques for novel enzymes with a focus on hydrolytic
enzymes. Identified hits will be further explored for biocatalytic features and a comparison characterized at the
molecular level. In addition, libraries are screened for ACC terminases serving as a basis for agricultural and
environmental applications
The combination of the specific expertises at the ARC Seibersdorf in exploring endophytes and of the Institute of
Molecular Biotechnology of the TU Graz in molecular enzymology and screening will provide the basis to reach
the major outcome of this project which will be:
- the availability of metagenomic libraries from specific microbial communities
- established tools for screening expression libraries using different hosts
- sets of new enzymes being of high potential for biocatalytic and agricultural or environmental applications
- extended scientific knowledge on the diversity of the endophytic communities of plants, including uncultivable
species
Beginn: 31.01.2005
Ende: 29.04.2008
The dramatic increase of overweight and obesity has reached globally the status of the epidemic of the 21st century. Over the last decade, the prevalence of obesity in Western and Westernizing countries has more than doubled, and the increasing incidence of obesity in developing countries as well as of child obesity is alarming. Globally, more than 1 billion adults overweight (BMI > 25) - at least 300 million of them clinically obese (BMI > 30) - cause tremendous costs for our health care systems. The development of obesity is influenced by a combination of environmental factors and inherited genetic predispositions. On the cellular level, obesity is characterized by the excess of adipose tissue. Adipocytes, the principal component of fat tissue, derive from adult mesenchymal stem cells and undergo a multi-stage differentiation called adiopogenesis in order to become mature adipocytes. The identification of protein-coding genes that are involved in the regulation of fat cell (adipocyte) development has greatly increased our knowledge of the mechanisms that underlie this condition. But still, we are far from a complete picture of molecular events in adipocyte differentiation. Especially, the early stage of adipocyte differentiation is not well understood also due to a lack of appropriate cell models. Recently, a novel class of tiny regulators - called microRNAs - has been identified to be involved in cellular differentiation which are recruited from the 97% of the human genome that does not encode proteins, but can downregulate the activity of thousands of genes. More than 300 candidates of this novel class of regulators have been identified predicted to regulate more than 10% of all genes. A small number of microRNAs has been associated with diseases, with the potential for many more. This proposed project addresses the identification of microRNA candidates in the early stage of human adipocyte differentiation (adipogenesis).
Therefore, the project goals are to develop a method for the highly-parallel identification of expressed candidates of this novel class of regulators based on microarray technology, to elucidate microRNA expression profiles during early human adipogenesis, and to identify dynamically expressed microRNAs during early human adipogenesis and their corresponding target genes identified by microRNA binding motifs within the target transcripts and validated by their reciprocal expression profile.
The results obtained will make an important contribution to understanding cellular differentiation mechanisms and the pathogenesis of extremely frequent diseases of civilization, thereby also laying the foundations for possible commercial applications.
Beginn: 28.02.2006
Ende: 27.02.2007
Die in den letzten Jahren entstandenen Methoden zur Genespressionsermittlung haben besonders durch die Microarray- Technologie zu äußerst umfangreichen Datenmengen geführt denen aber Defizite im Bereich der Auswertung und Interpretation dieser Datenfülle gegenüberstehen. Diese Defizite haben ihre Ursache in eben jenem Umfang an Datenmaterial und den damit verbundenen Problemen der Strukturierung und Interpretation.
Auf einen einfachen Nenner gebracht, kann gesagt werden, ein zentrales Problem im Bereich der Genominterpretation liegt darin, dass der qualitative Sprung von Datengenerierung zu erkenntniskräftiger Information immer schwieriger zu bewältigen ist. Besonders Augenfällig wird diese zentrale Schwierigkeit in den bereichen Diagnostik und diagnostischer Forschung. Die in diesem Feld notwendige interpretatorische Gegenüberstellung von Genexpressionsdaten mit anderen klinischen Daten wird aktuell durch ein nur mangelhaftes Instrumentarium unterstützt.
Das Projekt Con_Benetic soll helfen diese Defizite zu mindern, indem es, aufbauendauf existierende Standards der Genexpressionsanalyse- und - visualisierung, folgende Beiträge leistet:
1. Kontextualisierung von Genomdaten und klinischen Daten aus verschiedenen Analysesverfahren.
2. Einsatz von Methoden der Visualisierung und Interaktion um komplexe bioinformatische Daten für Forschung und Diagnostik überschaubar, erfassbar und effizienter nutzbar zu machen.
Beginn: 28.02.2005
Ende: 27.02.2007
Beginn: 31.05.2000
Ende: 30.12.2006
Beginn: 30.11.2003
Ende: 30.12.2006
Lipidomics -genomics of lipid metabolism- is the common denominator of the concerted research effort of SFB (Spezialforschungsbereich) Biomembranes. The goal is to make a major contribution to the understanding of the biosynthesis, function and dysfunction of lipids and biological membranes. Biological membranes are central elements in all living systems that recognize and separate inside from outside. They provide an interface with the environment, harbor metabolic enzymes, control electrochemical gradients, and divide interior of the cell into intracellular compartments. Membrane alterations are involved in the pathogenesis of prevalent diseases such as atherosclerosis and obesity. Understanding the mechanisms of membrane assembly, membrane function, and their interaction with other cellular components is thus not only a significant and fascinating experimental challenge, but also of great medical relevance.
The SFB Biomembranes will offer interdisciplinary doctoral training in bioinformatics, genetics, biochemistry, molecular biology, and biophysics through the use of state-of-the-art molecular biology and genomic techniques. The trainees will participate in current experiments to address the questions related to lipid metabolism and membrane biology from diverse angles and will benefit of the scientific background of this internationally recognised group.
Beginn: 30.06.2002
Ende: 30.07.2006
siehe www.cis.tugraz.at/biote/
Beginn: 28.02.2002
Ende: 27.02.2006
The long-term goal of this proposal is to establish bioinformatics infrastructure and support genomic initiatives at the academic institutions in Austria. We are concentrating our efforts on the creation and use of computational tools for combined analyses of genome sequences, gene expression data and 3D structural data. The network will focus on the development of computational environments, software support systems and the accumulation of specific know-how.
The overall specific aims of the Austrian bioinformatics integration network (BIN) are as follows:
1) Provide an environment for building bioinformatics capabilities in Austria, through establishing bioinformatics services, research, networking, training for both researchers and industry, and support for commercialization.
2) Create an integrative research program, using an Open Source platform of freely available source code, by establishing connections across multiple information resources-such as data on genomics, proteins, and clinical medicine -as well as across multiple disciplines, including mathematics, statistics, physics, computer science and life sciences.
3) Through a national virtual laboratory, accelerate the pace of life sciences knowledge discovery by providing new ways of viewing and analyzing biological data, facilitating research and understanding of databases from both technical and biological perspectives. not assigned KP: Bioinformatik, Institut für Molekulare Pathologie
Beginn: 31.12.2002
Ende: 30.12.2005
This programme will demonstrate that the transfer of specific genes from an Aspergillums Niger strain, which produces citric acid with close to theoretical efficiency, into other commercial micro-organisms will enhance the pool of precursors in those organisms and lead to increased yield and production rates for their end products. The two key enzymes, pike and axle, lead to increased glycol tic flux and the uncoupling of respiration from ATP production respectively, which, together with high glucose levels, will lead to increased metabolic fluxes and steady state levels of intermediates. Such a demonstration of high yield and productivity will then be transferred directly to the production strains of European manufacturers.
Beginn: 31.01.2003
Ende: 30.10.2005
Increasing our understanding of the assembly, function and pathophysiology of biomembranes, and their interaction with lipoproteins is the principal objective of this SFB. Disturbances of lipid and membrane function, initiated by exogenous or endogenous determinants, play an important role in the pathogenesis and progression of diseases such as atherosclerosis and obesity. The cellular and molecular mechanisms causing these distortions are still not well understood. It is, therefore, a key issue of our concerted efforts to elucidate the underlying events in healthy and diseased states at the cellular and molecular levels.
Nine research projects, and one administration project, provide the scientific and administrative infrastructure for this research program. The close interaction between this number of research groups from the Graz University of Technology and from both the medical and natural sciences faculties of the University of Graz provides the critical mass and competitive environment for both rapid advances in research and a challenging program of graduate student education in biochemical, molecular and medical research.
not assigned KP: Institute der Karl-Franzens-Universität Graz not assigned KP: SFB Biomembranen F700
Beginn: 30.09.1995
Ende: 29.09.2005
In 1993 the Special Research Area (SFB) Biocatalysis was established at Graz University of Technology as the first SFB ("Spezialforschungsbereich") in Austria.
This meant a concentration of Austrian biocatalytic research in Graz.
What is Biocatalysis? It is the technique which makes use of the special properties of nature's catalysts, enzymes. They are characterized by high selectivities, mild reaction conditions and minimum waste which makes them ideal for solving today's trenchant problems in chemistry, technology and ecology.
Major aims of the research:
1. to investigate mechanisms of enzymatic catalysis,
2. to explore possibilities of optimizing catalytic performance
3. to develop systems suitable for practical application.
The methods employed are based on classical procedures of chemistry, enzymology, protein chemistry, microbiology, and chemical engineering. In addition, advanced techniques are used to determine the structure of proteins, and to modify their structures either by chemical derivatization or by site-directed mutagenesis. not assigned KP: Institute der Karl-Franzens-Universität Graz not assigned KP: SFB not assigned KP: SFB Biokatalyse
Beginn: 31.03.1993
Ende: 30.01.2003
Beginn: 31.12.2000
Ende: 30.01.2003
To identify mechanism(s) by which Troglitazone improves insulin resistance we will study the effects of Troglitazone on lipid metabolism in obese Zucker rats. Our specific goals are: 1) is to assess lipolysis during euglycemic conditions in lean and obese Zucker rats and obese Zucker rats treated with Troglitazone; and 2) to estimate glucose turnover rates in obese Zucker rats treated with Troglitazone during euglycemic conditions and elevated FFA levels.
Beginn: 28.02.1999
Ende: 30.12.2002
not assigned KP: Forum Qualitätssicherung in der Diabetologie (Deutschland und Österreich) not assigned KP: Qualitätssicherungsbeirat der KAGES not assigned KP: Steirische Diabetologenrunde
Beginn: 31.12.1996
Ende: 30.12.2002
The START Y144-N04 program is about the noninvasive imaging of cardiac electrical function in the human heart for purpose of diagnosis of complex arrhythmias.
The electrical function within the cardiac muscle is reconstructed by coupling anatomical and electrical information. Great expectations persist on the part of the developer and potential users of this novel method, in particular in view of a better localization of the onset cardiac arrhythmias.
Due to novel and improved measurement techniques and the availability of enormous computer capacity, coupled with physical and physiological knowledge about the target organ, medical imaging is becoming of particular importance in diagnosis. Beside pure anatomical imaging, during the last years major efforts have been undertaken, in devel-oping high-dimensional functional imaging.
The most important target organs are the human brain and heart. With respect to the human heart, novel methods are under development for the imaging of movement, contraction, perfusion, metabolism and electrical function.
This six-year research program started in September 2000 and its goal is to extend the imaging modalities like magnetic resonance imaging (MR), computed tomography (CT), ultrasound (US), and biplane-fluoroscopy (BF) by the imaging of electrical function.
The project is continued at the
University of Health Sciences in Insbruck.
Beginn: 31.08.2000
Ende: 30.12.2002
BACKGROUND: High throughput techniques are becoming more and more important in many areas of basic and applied biomedical research. Microarray techniques using cDNAs or oligonucleotides are such high throughput approaches for large-scale gene expression analysis and enable the investigation of mechanisms of fundamental processes and the molecular basis of diseases on a genomic scale. Microarray experiments have been used to identify differentially expressed genes in a highly parallel manner. Beyond simple discrimination of differentially expressed genes, functional annotation of coexpressed genes (guilt-by-association), diagnostic classification, and investigation of regulatory mechanisms (coregulation from coexpression) require clustering of genes into sets with similar expression patterns. In collaboration with The Institute for Genomic Research (TIGR), Rockville, MD/USA, we have recently developed a versatile, comprehensive, portable and easy to use JAVA tool (Quackenbush J. Computational Analysis of Microarray Data. Nat. Genet. Rev., 2:418-427, 2001) for large-scale gene expression studies. The implemented clustering and classification procedures in combination with the appropriate filtering, normalization, and similarity distance measurement, enable researchers to analyse the data in a systematic and reproducible way for a given set of experiments. However, presently the software has to be installed on a high-end NT/UNIX platforms...(this text has been cut automatically)
Beginn: 14.12.2001
Ende: 30.12.2002
The broad, long-term objective of this proposal is the application of minimally invasive and noninvasive state-of-the-art techniques for assessment of whole-body and regional metabolism to investigate the physiological and pathophysiological mechanisms that regulate hypoglycemic counterregulation. It is our aim to apply stable isotope dilution techniques (to assess systemic and local lipolysis) with the unique combination of open-flow microperfusion (to characterize the microenvironment in adipose and muscle interstitial fluid), indirect calorimetry (for the measurement of fuel oxidation), and 1H-NMR spectroscopy (to measure intramuscular lipid content) to examine lipolysis during prolonged moderate hypoglycemia in well-controlled patients with type 1 diabetes mellitus and nondiabetic subjects.
Beginn: 31.07.2000
Ende: 30.07.2002
Obesity is an increasing health problem reaching epidemic proportions in most western societies. It is the main precursor state of diabetes and other diseases such as hypertension, dyslipidaemia, and cardiovascular disease are also attributable to obesity. The development of obesity requires the continuous differentiation of new adipocytes throughout life, which is regulated by a complex transcriptional cascade. Recently, a protein member of the nuclear hormone receptor superfamily designated PPARg (peroxisome proliferator-activated receptor gamma) was discovered and its central role in adipose differentiation was identified. Despite intensive research efforts, due to the extraordinarily diverse spectrum of responses in different biological settings, the actual identities of many PPARg-regulated gene products have remained elusive. The broad, long-term objective of the studies in this project is to delineate transcriptional regulatory networks of adipocyte differentiation using combined analysis of genome sequence and gene expression data. The specific aim is to identify additional downstream PPAR? target genes. For this purpose advantage will be taken of the availability of cellular model systems, the specificity provided by synthetic PPARg ligands, and the cDNA microarray technology. Hypotheses were first generated by performing database searches and using computational techniques for modeling transcription factor binding sites. Base...(this text has been cut automatically)
Beginn: 31.12.2000
Ende: 30.01.2002
Beginn: 31.12.1994
Ende: 30.01.2002
Beginn: 31.12.1997
Ende: 30.12.2001
Beginn: 31.12.1997
Ende: 30.12.2001
The focus of this project is to assess local thermogenesis in skeletal muscle and to characterize muscle thermogenic regulation by employing state-of-the-art techniques as this particular tissue bed plays a critical role in whole body fuel metabolism and is thought to play a key role in the pathophysiology of obesity and insulin resistance. It is our aim to apply the unique combination of on-line measurement of pO2, pCO2, pH and temperature in muscle ICF and techniques for assessment of lipolysis, muscle sympathetic nervous activity, and oxidative fuel metabolism to investigate thermogenesis in skeletal muscle.
Beginn: 31.12.1998
Ende: 30.07.2001
Beginn: 29.02.2000
Ende: 19.04.2001
Noninvasive imaging of cardiac electrical function from body surface potential or magnetic field data has attained increasing interest. In combination with imaging modalities like magnetic resonance imaging it has become possible to reconstruct the primary sources in the human heart fully noninvasively with temporal resolution in the order of milliseconds and spatial resolution of millimeters. Till now, no other modality for functional imaging allowed resolution of electrical function of comparable order. In near future this modality will assist cardiologists performing functional electrical diagnostics. The objective of this project was to compare reconstruction from BSP and MCG data. An inverse method for the estimation of the activation time map on the epi-and endocardium was applied.
In a first step a three-dimensional cellular automaton model of the human left and right ventricle was adapted to simulate the AT pattern and the BSP and MCG in the forward problem for normal ventricular depolarization. Afterwards in the inverse problem the AT pattern was estimated from these simulated synthetic BSP and MCG data. In a second step the same inverse approach was applied to measured BSP and MCG data from a healthy volunteer.
Beginn: 31.12.1996
Ende: 30.12.2000
Noninvasive electrophysiology has attained more interest during the last years because of the availability of multichannel cardiomagnetometer and body surface potential mapping systems. The main focus is the determination of the impressed electrical sources in the human heart from body surface potential (BSP) and magnetocardiogram (MCG) mapping data. The noninvasive procedure should help to shorten invasive surgery time e.g. in the case of catheter ablation and help to decide whether an invasive procedure is necessary or not.
The objective of this project is the development of inverse algorithms for the estimation of the activation time (AT) map including temporal and spatial regularization considering an inhomogeneous boundary element (BE) torso model. Electrical anisotropy is neglected in the BE approach. The estimation of the AT map (phase 0) enables the imaging of the propagation pattern on the endocardium and epicardium. The applied analytical description of the surface transmembrane potential for phase 0 is based on an analytical function and includes the following parameters: activation time, rise time, action potential amplitude and resting membrane potential. Each of these parameters, except the activation time are assumed to be constant at the BE nodes of the surface of the heart. The AT map is estimated applying the critical point theorem and a subsequent nonlinear optimization approach.
Beginn: 31.12.1997
Ende: 30.12.2000
Hyperglycemia per se can enhance glucose uptake (GU) and inhibit endogenous glucose production (EGP) in man. The aim of the current study was to assess the relative contributions of hyperglycemia's actions on GU and EGP in insulin-dependent diabetic subjects. Therfore, six diabetic subjects who had no residual insulin secretion underwent a labeled intravenous glucose tolerance test (LIVGTT) under conditions of basal insulin levels. The time course of the endogenous glucose concentration was calculated from the measured total glucose and tracer enrichment in the plasma samples. Endogenous glucose concentrations remained at basal levels during the LIVGTTs (P>0.12). Thus, in the presence of basal insulin levels, hyperglycemia per se did not significantly alter basal EGP. Therefore, in diabetic subjects, glucose decline during the LIVGTT is dominated by the effect of hyperglycemia per se to enhance GU.
Beginn: 31.12.1996
Ende: 30.12.2000
Beginn: 31.12.1997
Ende: 29.09.2000
Diabetes is also characterized by derangement of lipid metabolism. However, sampling of adipose tissue interstitial fluid substances with high molecular weight (e.g., free fatty acid) was not possible so far. The aim of this study was to evaluate the microperfusion method for sampling interstitial fluid substances of high molecular weight. The double lumen catheter of the system was inserted in the adipose tissue and was perfused through the inner lumen with ion-free solution. Due to the perforations of the catheter, the interstitial fluid equilibrated partially with the perfusion fluid. In this way, interstitial fluid samples were obtained from healthy volunteers during fasting and from patients with IDDM during a hypoglycaemic hyperinsulinemic clamp experiment. It could be shown that sampling of substances even with a high molecular weight like free fatty acid and albumin is possible under these experimental conditions. not assigned GG: Max Kade Inc.
Beginn: 31.01.1997
Ende: 30.01.2000
In many medical check-ups Magnetic Resonance Imaging (MRI) is involved. This project deals with calculations of induced current densities and energy deposition in the simulated human body during MRI and enables thus an estimation of a possible hazard. The geometric and electrical properties of the human torso, as well as the operational conditions of coils generating switched gradients of the low-frequency magnetic fields and radio-frequency magnetic fields of 1.5 T MRI machines for medical diagnosis have been simulated. The human torso has been modeled from MR scans of a volunteer by Finite Element Method. The FE software has been developed at Institute for Fundamentals and Theory in Electrical Engineering. The FE formulation has been A,V/Phi. The model consists of 20 layers, spaced 3 cm apart.
This gives altogether 2596 elements, 636 of which are needed for fulfilling the boundary condition (F should be zero at the farthest boundaries). In this model thirteen different kinds of tissues have been modelled: bone, cartilage, fat, lungs, intestines, skin, muscle, blood, liver, heart muscle, kidney, nerves and spleen, with the following organs being distinguished: kidneys, heart muscle, lungs, spinal cord, liver and spleen. The simulated frequency has been 64 MHz, corresponding to 1.5 MRI machine. Simulated exposure system has been the so-called bird-cage coil with 12 rods with capacitors in the ring.
Beginn: 31.12.1994
Ende: 30.12.1999
The reconstruction of cardiac electrical sources from body surface potential maps and from maps of the cardiac magnetic field has been of scientific interest during the last years. Several efforts were made to develop powerful recording techniques and mathematical approaches for a proper estimation of the primary sources. Besides measurement techniques, powerful modeling approaches have to be applied in order to estimate the primary source structure. For volume conductor modeling, the finite element method and the boundary element method are the state-of-the-art techniques. Regarding the modeling approaches, linear and nonlinear methods for the determination of the transmembrane potential pattern on the surface of the heart were developed.
The objective of the project is the development of an inverse approach including temporal and spatial regularization for the estimation of the activation time (i.e. of the onset of the transmembrane potential) map during ventricular depolarization. The activation times on the endo- and epicardium are reconstructed by a quasi-Newton method (BFGS, Broyden-Fletcher-Goldfarb-Shanno method). The starting column matrix for the activation times is estimated applying the critical point theorem.
Beginn: 31.12.1996
Ende: 30.12.1999
The reconstruction of cardiac electrical sources from body surface potential maps (BSPM) and from maps of the cardiac magnetic field MCG is of increasing scientific interest. The goal is the development of a noninvasive functional cardiac source imaging modality for clinical purposes. In a first step the epi- and endocardial activation time map during ventricular polarization is estimated from BSP and ECG data applying the critical point theorem. This result is then used as a starting vector for a successive optimization procedure. Several optimization strategies (e.g. BFGS) are investigated in order to increase the spatial and temporal resolution obtained. The ventricular AT pattern was estimated with a relative error of 0.1 from simulated ECG data after adding Gausian noise with a singal to noise ratio of 35dB.
Beginn: 31.12.1996
Ende: 30.12.1999
The objective of this project is the development of a 63 channel body surface potential (BSP) mapping system for solving the electrocardiographic inverse problem for noninvasive functional cardiac electrical diagnosis. The measurement of the electric potential on the outer thorax surface using multichannel mapping systems allows, in addition to conventional signal processing in time and frequency domains, the noninvasive estimation of cardiac electrical sources (transmembrane potentials or activation time maps on the endo- and epicardium) when morphological information about the volume conductor is included. This is obtained in most cases by using magnetic resonance imaging in order to build up a boundary element thorax model for a mathematical formulation of the forward and inverse problem.
The signal conditioning unit consits of the instrumentation amplifier, an isolation and output amplifier and a filtering circuit. The data acquisition unit of a Pentium 133 MHz personal computer with 16 MByte RAM and a 1GByte SCSI hard disc. A/D converting is performed by an AT-MIO-64E-3 card (National Instruments, Austin, TX, USA) with a 64 single ended or 32 differential channel configuration. The software package LabVIEW (National Instruments, Austin, TX) allows graphical programming and is used for the development of routines for data sampling and processing and for data display.
Beginn: 31.12.1995
Ende: 30.12.1999
For many routine or research investigations in medicine repeated blood samples of ambulatory subjects or animals are necessary for obtaining hormonal or metabolic profiles. However, the necessity of the presence of skilled medical staff for drawing the blood samples can be limiting factors in these studies. The aim of this project was to develop a portable device for continuous fractionated blood sampling and continuous ex vivo monitoring using flow chamber with biosensors in the sampling line. The fabricated sampling device is based on a double lumen catheter for extracorporeal blood heparisation and an automatic fluid sampler. The double lumen catheter is placed in a peripheral vein and the inner lumen is then connected to a 10 ml syringe containing heparin solution. The outer lumen is linked to a roller pump with programmable speed. A needle which can be moved in two directions supplies 56 vacuum tubes with the collected blood.
Beginn: 31.01.1996
Ende: 30.12.1999
Monitoring of adipose tissue lactate concentration during exercise was not possible so far. The aim of this study was to evaluate the measurement of subcutaneous lactate concentration during exercise by combining open flow microperfusion, lactate and conductivity sensoring. The lactate sensor was based on the measurement of H2O2 which is produced by the membrane-enclosed enzyme lactate oxidase. The conductivity sensor was used to calculate the recovery of the sampled interstitial fluid. In 5 healthy subjects, the microperfusion catheter was inserted into the adipose tissue and the electronic unit was fixed at the hips. The subjects started with a 6 min warm up at 50 watts. The exercise was then increased by 50 watts every 3 min until exhaustion. The results show that during exercise the lactate concentration in the interstitial fluid can be measured on line and continuously by this method.
Beginn: 31.12.1995
Ende: 30.12.1999
In diabetic subjects who have no residual insulin secretion, the restoration of normoglycemia after oral or intravenous glucose administration occurs only via glucose-mediated stimulation of glucose disappearance. The aim of this study was to assess the ability of several mathematical models to account for glucose-mediated glucose disappearance (GMGD). Therfore, six C-peptide negative diabetic subjects underwent an intravenous glucose tolerance test (IVGTT) under conditions of basal insulin levels. The considered mathematical models were identified from the data obtained during the IVGTTs. We found that the widely used minimal model of glucose kinetics failed to describe the observed GMGD. In contrast, a proposed two-compartment model was able to account for the measured glucose dynamics throughout the IVGTT.
Beginn: 31.12.1995
Ende: 30.12.1999
A three dimensional cellular automaton model is used for modeling the spread of activation and repolarization in the entire human heart. Spatial distribution of refractory periods and conduction velocities in different cardiac tissues, the anisotropy of conduction in the ventricle as well as the dependence of the effective refractory period on the diastolic interval is taken into account. The algorithm calculating the activation process is based on a modified version of Huygen's principle. Similar to programmed stimulation in patients with heart disease, the computer model can be used as a noninvasive tool to assess the inducibility of ventricular tachycardia and fibrillation. Recently the inducibility of bundle branch reentrant tachycardia was tested for different ventricular stimulus sites.
Beginn: 31.12.1994
Ende: 30.12.1998
During the last years a method for continuous on-line ex vivo monitoring of the subcutaneous tissue glucose was developed at the Department of Biophysics. This method combines open-flow microperfusion of subcutaneous adipose tissue with extracorporeal sensing of perfusate glucose and perfusate conductivity, thus allowing the estimation of interstitial glucose concentration without any in vivo calibration. The aim of the current study was to assess the accuracy of this monitoring technique under various experimental conditions in humans. Therefore, healthy volunteers as well as patients with type I diabetes participate in hyper- hypo- and euglycaemic clamp studies where the plasma glucose levels are clamped to different targets. The results show that under those experimental conditions the continuous monitoring of subcutaneous adipose tissue glucose concentration was possible with good accuracy.
Beginn: 31.12.1995
Ende: 30.12.1998
For computation of forward and inverse solutions in bioelectromagnetism, digitized models of the associated volume conductor (human torso, human head) are required. Often a piecewise homogeneous model considering internal inhomogeneities (e.g. the lungs and the cavities of the heart; the skull and the cortex) is build up from MRI scans. In order to provide an explicit and compact representation of anatomical surfaces a semiautomatic meshing procedure has been developed. In a first step point clouds of the surfaces which have to be modeled are extracted manually from the MRI-scans. Then those surfaces are approximated by a double Fourier series or Legendre polynomials in a second step and the Boundary Element mesh is generated automatically.
Beginn: 31.12.1995
Ende: 30.12.1997
The relationship between the primary electrical sources within a human heart model and the simulated magnetocardiogram (MCG) including an boundary-element (BE) thorax model for the inverse problem is investigated.
A cellular automaton model of the entire human heart considering 15 different tissue types and the dependence of the refractory period and conduction velocity on the cycle length is adopted. Anisotropy of the conduction velocities and optionally of the electrical conductivities in the ventricles is assumed. The Huygen´s propagation principle is applied for calculating the isochrones. The primary current dipoles are computed by the bidomain theory. The heart model is positioned inside the BE thorax model. The MCG is calculated closely above the thorax surface at 74 observation points.
In case of the UDL theory (the PCDs are perpendicular to the wavefront) no MCG can be detected outside the thorax as long as the excitation wave does not reach the heart´s surfaces (epi- or endocardium). In case of the ODL theory (the PCDs are directed oblique to the wavefront), an additional contribution to the MCG is generated. In case of electrical isotropy the real signal generators are located on the heart´s surfaces only (i.e. the transmembrane potential distribution). Reconstructing sources from the MCG one can consequentely try to estimate the transmembrane potential distribution or the activation time map on the endo- and epicardium.
Beginn: 31.12.1994
Ende: 30.12.1997
The overall objective of NEMY is to improve the diagnostic information content of electro- and magnetocardiographic data by developing standardized systems for noninvasive exa-mination of the heart. The individual objectives are to harmonize methods for BSP and MCG mapping, to harmonize methods for modelling, to create an environment for the exchange of measurement and modelling data, create a library of anatomical models and electromagnetic data for both normal and pathological cardiac conditions, derive the specifications and assess the feasibility of a standardized methodology for accurate indirect sensing of myocardial condition and to improve the reliability, accuracy and sensitivity of noninvasive methods of diagnosis, monitoring and treatment of cardiac patients.
Our group is involved as an associated partner in the field of cardiac forward and inverse modelling. The forward and inverse methods developed should be harmonized with those of the other modelling groups involved in NEMY I.
The standardization of modelling the volume conductor and of the inverse method is of specific interest when noninvasive functional imaging is evaluated. Such a standardization allows the evaluation of the different methods as well as the evaluation of different data sets. Software tools were developed by our group which enables a transformation of different boundary element data formats into each other.
Beginn: 31.12.1994
Ende: 30.12.1997
The framework of the project included: 1) development of devices for continuous ex vivo glucose monitoring; 2) modelling and simulation studies, and 3) experimental studies on glucose metabolism. Two portable devices were developed and evaluated during standardized conditions: a continuous ambulatory blood sampler with a miniaturized thin-film glucose sensor in the sampling line and a subcutaneous tissue glucose monitoring device using open flow microperfusion and measurement of glucose and conductivity for the calculation of absolute subcutaneous glucose concentration. The latter device was designed for hypoglycemia detection and in combination with an insulin pump for closed-loop control of glucose using the subcutaneous route. Experimental studies were used to evaluate the devices whereas the numerical studies were performed to investigate various control approaches.
Beginn: 31.12.1990
Ende: 30.12.1993