Current Projects

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CompuGene

CompuGene is an interdisciplinary consortium of natural science and engineering with the aim to develop computer-aided designs of complex, synthetic genetic circuits. In this framework it is the task of the kabisch-lab to develop methods for the rapid prototyping of these circuits. For this we examined a variety of DNA assembly methods in respect to their automation potential. After identifying the ligase cycling reaction (LCR) as most suited we have begun to evaluate the limits of the method, started building models, as well as creating computer-aided design tools enabling us model optimal assembly designs. Furthermore we down-scaled the DNA assembly reactions to 1 µl using a nanoliter dispenser.

Drop-In Biofuels

We research and optimize oleaginous microorganisms such as the yeast Yarrowia lipolytica in respect to their oil body formation capabilities and methods to transform these into a renewable gasoline replacements. Our second host, the Gram-positive bacterium Bacillus subtilis, is being optimized with the goal to produce hydrocarbons of varying length.

Eternal Cell

Deciphering the physiological function of fundamental cellular processes has until recently been hindered by the lack of molecular tools to manipulate essential genes in vivo. Recent breakthroughs in the technology for genome engineering, such as CRISPR-Cas9, have allowed the characterization of these under-studied processes. In the frame of this project we propose to use these new tools for the creation of a cell that will lose central mechanisms of the bacterial life cycle.

CASCADE-KIT

Will not be disclosed.

Publications

2018

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Bruder, S., Moldenhauer, E.J., Ledesma-Amaro, R., Kabisch, J., Drop-In Biofuel production by using fatty acid photodecarboxylase from Chlorella variabilis in the oleaginous yeast Yarrowia lipolytica. bioRxiv 468876 (2018).
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Nadler, F.,Bracharz, F.,, Kabisch, J., CopySwitch - in vivo optimization of gene copy numbers for heterologous gene expression in Bacillus subtilis. bioRxiv 446393 (2018).
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Bruder, S., Hackenschmidt, S., Moldenhauer, E.J., Kabisch, J., Chapter 12 - Conventional and Oleaginous Yeasts as Platforms for Lipid Modification and Production. in Book: Lipid Modification by Enzymes and Engineered Microbes. AOCS Press, pp. 257-292. (2018).
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Kohl, A., Srinivasamurthy, V., Boettcher, D., Kabisch, J., Bornscheuer, U.T., Co-expression of an alcohol dehydrogenase and a cyclohexanone monooxygenase for cascade reactions facilitates the regeneration of the NADPH cofactor. Enzyme and Microbial Technology 108, 53-58 (2018).

2017

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Hehemann, J.-H. et al. Aquatic adaptation of a laterally acquired pectin degradation pathway in marine gammaproteobacteria. Environ Microbiol 19, 2320-2333 (2017).
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Junne, S. & Kabisch, J. Fueling the future with biomass: Processes and pathways for a sustainable supply of hydrocarbon fuels and biogas. Eng. Life Sci. 17, 14-26 (2017).

2016

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Mikolasch, A. et al. From oil spills to barley growth - oil-degrading soil bacteria and their promoting effects. J. Basic Microbiol. 56, 1252-1273 (2016).
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Hofmeyer, T. et al. Draft Genome Sequence of Cutaneotrichosporon curvatus DSM 101032 (Formerly Cryptococcus curvatus), an Oleaginous Yeast Producing Polyunsaturated Fatty Acids. Genome Announc. 4, e00362-16 (2016).
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Hoehne, M. & Kabisch, J. Schmerzmittel brauen: Eine Hefe-Zellfabrik produziert Opiate aus Zucker. Angew. Chem. 12, 1266-1268 (2016).
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Hoehne, M. & Kabisch, J. Brewing Painkillers: A Yeast Cell Factory for the Production of Opioids from Sugar. Angew. Chem. Int. Ed. 55, 1248-1250 (2016).

Before...

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Kumpfmueller, J., Kabisch, J. & Schweder, T. An optimized technique for rapid genome modifications of Bacillus subtilis. Journal of Microbiological Methods 95, 350-352 (2013).
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Kabisch, J. et al. Metabolic engineering of Bacillus subtilis for growth on overflow metabolites. Microbial Cell Factories 12, 72 (2013).
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Kabisch, J. et al. Characterization and optimization of Bacillus subtilis ATCC 6051 as an expression host. Journal of Biotechnology 163, 97-104 (2013).
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Gardebrecht, A. et al. Physiological homogeneity among the endosymbionts of Riftia pachyptila and Tevnia jerichonana revealed by proteogenomics. ISME J 6, 766-776 (2012).
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Uhlig, C. et al. Heterologous expression, refolding and functional characterization of two antifreeze proteins from Fragilariopsis cylindrus (Bacillariophyceae). Cryobiology 63, 220-228 (2011).
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Junne, S., Klingner, A., Kabisch, J., Schweder, T. & Neubauer, P. A two-compartment bioreactor system made of commercial parts for bioprocess scale-down studies: Impact of oscillations on Bacillus subtilis fed-batch cultivations. Biotechnology Journal 6, 1009-1017 (2011).