Proteome maintenance. Many human diseases, such as neurodegenerative diseases are caused by or related to aberrant protein processing. In this project area we have several topics that are focusing on cellular processes involved in proteome maintenance, i.e. protein synthesis, folding, degradation and secretion. The model organism for our studies is yeast Saccharomyces cerevisiae that we use in the study of the unfolded protein response, but also for functional analysis of different human proteins that are involved in regulation of apoptosis. The research involves both experimental work with high-throughput analysis of different mutants and mathematical modelling of cell populations. |
Research directors: |
Jens Nielsen and Dina Petranovic |
| |
|
Nutrient sensing and regulation. Many signal transduction pathways are conserved between yeast and humans. We exploit this evolutionary aspect to studying the regulating of metabolism in yeast and extrapolate the results to humans. The high degree of interconnectivity of carbon, nitrogen and energy metabolism plays a central role in the proper functioning of the cell. As a result, the regulation of these pathways can only be studied using a systems biology approach. Specifically, our focus is on the Snf1 Tor1 and the PKA pathways The research involves a combination of experimental work and integrative analysis of high-throughput data. |
Research directors: |
Jens Nielsen and Goutham Vemuri |
| |
|
Lipid metabolism. Malfunctioning of lipid metabolism is a key factor in the development of many diorders such as diabetes and atherosclerosis Our goal is to understand the regulatory structure of lipid metabolism by quantitative analysis of the flux in lipid biosynthetic pathways and elucidating the role of key transcription factors and protein kinases. Although we use yeast as the model for the fundamental analyses, we also collaborate with other research groups to study lipid metabolism in liver cells. |
Research directors: |
Jens Nielsen and Goutham Vemuri |
| |
|
Metabolic network analysis. We actively construct and curate metabolic network models for different organisms (yeast, filamentous fungi, mouse and human cells) and use them for the analysis of high-througput data and simulation of metabolic functions. Through active collaborations, we also analyze nutrition and obesity-related gene expression data both from mouse studies and different patient cohorts. Through active European collaboration we also study the impact of low or zero gravity on metabolism in yeast (relevant for space flights). |
Research director: |
Jens Nielsen |
| |
|
Comparative and functional genomics of Aspergilli. Our goal is to generate metabolic and regulatory models for industrially relevant Aspergilli such as A. oryzae and A. niger. Based on comparative genomics and transcription analysis, we map the signalling pathways that control energy, carbon and nitrogen metabolism. The work involves both experimental work and detailed data analysis. |
Research director: |
Jens Nielsen |
| |
|
Isoprenoid production by yeast. We are developing a yeast-based platform for the production of isoprenoids, with a special focus on the production of sesquiterpenes that are used as perfumes and fine fragrances. We express plant sesquiterpene synthetases in yeast that has been engineered to have increased flux to the precursor farnesylpyrophosphate. |
Research director: |
Jens Nielsen |
| |
|
Production of commodity chemicals. We address the industry needs to develop sustainable routes for the production of commodity chemicals for use in the chemical and polymer industry by engineering the central carbon metabolism of yeast to design efficient cell factories. We use model-guided approaches to identify targets for rational design of metabolic networks. |
Research director: |
Jens Nielsen |
