2017 Publications

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Eirik Adim Moreb, Benjamin Hoover, Adam Yaseen, Nisakorn Valyasevi, Zoe Roecker, Romel Menacho-Melgar, and Michael D. Lynch
Managing the SOS Response for Enhanced CRISPR-Cas-Based Recombineering in E. coli through Transient Inhibition of Host RecA Activity
A plasmid-based system was used in which Cas9 and recA mutants are coexpressed, increased efficiency and consistency of CRISPR-Cas9-mediated selection were achieved and recombineered in E. coli, while reducing the induction of the SOS response.
ACS Synth. Biol., 2017, 6 (12), pp 2209–2218, DOI: 10.1021/acssynbio.7b00174
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William C. Morrell, Garrett W. Birkel, Mark Forrer, Teresa Lopez, Tyler W. H. Backman, Michael Dussault, Christopher J. Petzold et al.
The Experiment Data Depot: A Web-Based Software Tool for Biological Experimental Data Storage, Sharing, and Visualization
Experiment Data Depot (EDD), an online repository tool for experimental data and metadata. A variety of data types can be uploaded, visualized, and exported in a standardized fashion for use with predictive algorithms. EDD is utilized for: storage of characterized synthetic biology parts, leveraging proteomics data to improve biofuel yield, and the use of extracellular metabolite concentrations to predict intracellular metabolic fluxes.
American Chemical Society, ACS Synth. Biol. 2017, 6, 2248−2259, DOI: 10.1021/acssynbio.7b00204
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Ertesvåg, H., Sletta, H., Senneset, M., Sun, Y. Q., Klinkenberg, G., Konradsen, T. A., Ellingsen, T. E., and Valla, S.
Identification of genes affecting alginate biosynthesis in Pseudomonas fluorescens by screening a transposon insertion library
When the supplies of fructose 6-phosphate or GTP are diminished, less alginate is produced. This should be taken into account when bacterial strains are designed for industrial polysaccharide production.
BMC genomics vol. 18,1 11. 3 Jan. 2017, doi:10.1186/s12864-016-3467-7
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Virginia Martinez, Ida Lauritsen, Tonja Hobel, Songyuan Li, Alex Toftgaard Nielsen and Morten H. H. Nørholm
CRISPR/Cas9-based genome editing for simultaneous interference with gene expression and protein stability
An efficient genome editing approach that affects specific protein abundances by changing the rates of both RNA synthesis and protein degradation, based on the two cross-kingdom control mechanisms CRISPRi and the N-end rule for protein stability.
Nucleic Acids Research, 45 (20), [gkx797]. DOI: 10.1093/nar/gkx797
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Koepff J., Keller M., Tsolis K.C., Busche T., Rückert C., Hamed M.B., Anné J., Kalinowski J., Wiechert W., Economou A., Oldiges M.
Fast and reliable strain characterization of Streptomyces lividans through micro-scale cultivation
An integrated cultivation workflow for Streptomyces lividans based on a parallelized shaken 48-well microtiter-plate (MTP) cultivation device was developed. Growth performance in 1 mL MTP cultivation against an established 1,000 mL lab-scale cultivation system were validated, and two cultivation regimes were compared with respect to transcriptional and protein secretion activity of Streptomyce.
Biotechnol Bioeng. 2017 Sep; 114(9):2011-2022. doi: 10.1002/bit.26321
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Ladner T., Mühlmann M., Schulte A., Wandrey G. and Büchs J.
Prediction of Escherichia coli expression performance in microtiter plates by analyzing only the temporal development of scattered light during culture
Based on slope at and time of the inflection point, predictions of the standardized expression performance are possible and for a first screen elaborated offline analysis can be avoided; based on 625 E. coli cultures.
Journal of Biological Engineering, 2017, 11:20; DOI: 10.1186/s13036-017-0064-5
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Hosseini R., Kuepper J., Koebbing S., Blank L.M., Wierckx N. and de Winde J.h
Regulation of solvent tolerance in Pseudomonas putidaS12 mediated by mobile elements
The genome of P. putida S12 was sequenced. The mobile genetic elements are described and elaborated on the role of ISS12 in the establishment and maintenance of solvent tolerance in P. putida.
Microbial Biotechnology (2017), doi: 10.1111/1751-7915.12495
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Gupta A., Brockman Reizman I., Reisch C. and Prather K.
Dynamic regulation of metabolic flux in engineered bacteria using a pathway-independent quorum-sensing circuit
The optimal point was identified to redirect glycolytic flux into heterologous engineered pathways in Escherichia coli, resulting in titers of myo-inositol increased 5.5-fold and titers of glucaric acid increased from unmeasurable to >0.8 g/L, compared to the parent strains lacking dynamic flux control.
Nature Biotechnology (2017); doi:10.1038/nbt.3796
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Mühlmann M, Kunze M., Ribeiro J., Geinitz B., Lehmann C., Schwaneberg U., Commandeur U. and Büchs J.
Cellulolytic RoboLector – towards an automated high-throughput screening platform for recombinant cellulase expression
An extended robotic platform is presented to conduct automated high-throughput screenings of clone libraries including preculture synchronization and biomass specific induction. Model organisms: E. coli and K. lactis.
Journal of Biological Engineering (2017), 11:1; doi: 10.1186/s13036-016-0043-2
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Morschett H., Schiprowski D., Rohde J., et al.
Comparative evaluation of phototrophic microtiter plate cultivation against laboratory-scale photobioreactors
Evaluation of the scalability of a microtiter plate-based parallelized micro-photobioreactor against a representative set of established laboratory photobioreactors. Model system: Lipid production by Chlorella vulgaris
Bioprocess Biosyst Eng (2017); doi: 10.1007/s00449-016-1731-5
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Morrell W., Birkel G., Forrer M., Lopez T., Backman T., Dussault M., Petzold C.J., et al.
The Experiment Data Depot: a web-based software tool for biological experimental data storage, sharing, and visualization
The Experiment Data Depot (EDD), an online tool designed as a repository of experimental data and metadata is presented. EDD provides a convenient way to upload a variety of data types, visualize these data, and export them in a standardized fashion for use with predictive algorithms.
CS Synth. Biol., Just Accepted Manuscript, doi: 10.1021/acssynbio.7b00204, Publication Date (Web): August 21, 2017
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Holger Morschett, Stephan Noack, Marco Oldiges
Beschleunigte Bioprozessentwicklung im automatisierten Mikromaßstab
Novel technologies are needed for scalable data acquisition via incorporation of miniaturization, automation and digitalization; and to catalyze their translation from science into industrial application.
Biospektrum (2017) 23: 536; doi: https://doi.org/10.1007/s12268-017-0838-9
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Johannes Hemmerich, Lars Freier, Wolfgang Wiechert, Eric von Lieres, Marco Oldiges
Generic Protocol for Optimization of Heterologous Protein Production Using Automated Microbioreactor Technology
This manuscript describes a generic approach for tailor-made design of microbial cultivation media. This is enabled by an iterative workflow combining Kriging-based experimental design and microbioreactor technology for sufficient cultivation throughput, which is supported by lab robotics to increase reliability and speed in liquid handling media preparation.
Journal of Visualized Experiments ISSUE 130, 12/15/2017; DOI: 10.3791/56234
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