KLAUS WINZER's Outputs (46)

Gsmodutils: a python based framework for test-driven genome scale metabolic model development (2019)
Journal Article
Gilbert, J., Pearcy, N., Norman, R., Millat, T., Winzer, K., King, J., Hodgman, C., Minton, N., & Twycross, J. (2019). Gsmodutils: a python based framework for test-driven genome scale metabolic model development. Bioinformatics, 35(18), 3397-3403. https://doi.org/10.1093/bioinformatics/btz088

© 2019 The Author(s) 2019. Published by Oxford University Press. Motivation: Genome scale metabolic models (GSMMs) are increasingly important for systems biology and metabolic engineering research as they are capable of simulating complex steady-stat... Read More about Gsmodutils: a python based framework for test-driven genome scale metabolic model development.

Functional genetic elements for controlling gene expression in Cupriavidus necator H16 (2018)
Journal Article
Alagesan, S., Hanko, E. K., Malys, N., Ehsaan, M., Winzer, K., & Minton, N. P. (2018). Functional genetic elements for controlling gene expression in Cupriavidus necator H16. Applied and Environmental Microbiology, https://doi.org/10.1128/AEM.00878-18

A robust and predictable control of gene expression plays an important role in synthetic biology and biotechnology applications. Development and quantitative evaluation of functional genetic elements such as constitutive and inducible promoters, as w... Read More about Functional genetic elements for controlling gene expression in Cupriavidus necator H16.

The butanol producing microbe Clostridium beijerinckii NCIMB 14988 manipulated using forward and reverse genetic tools (2018)
Journal Article
Little, G. T., Willson, B. J., Heap, J. T., Winzer, K., & Minton, N. P. (2018). The butanol producing microbe Clostridium beijerinckii NCIMB 14988 manipulated using forward and reverse genetic tools. Biotechnology Journal, https://doi.org/10.1002/biot.201700711

The solventogenic anaerobe Clostridium beijerinckii has potential for use in the sustainable bioconversion of plant-derived carbohydrates into solvents, such as butanol or acetone. However, relatively few strains have been extensively characterised e... Read More about The butanol producing microbe Clostridium beijerinckii NCIMB 14988 manipulated using forward and reverse genetic tools.

Quantitative isotope-dilution high-resolution-mass-apectrometry analysis of multiple intracellular metabolites in Clostridium autoethanogenum with uniformly 13C-labeled standards derived from Spirulina (2018)
Journal Article
Schatschneider, S., Abdelrazig, S. M., Safo, L., Henstra, A. M., Millat, T., Kim, D.-H., Winzer, K., Minton, N. P., & Barrett, D. A. (2018). Quantitative isotope-dilution high-resolution-mass-apectrometry analysis of multiple intracellular metabolites in Clostridium autoethanogenum with uniformly 13C-labeled standards derived from Spirulina. Analytical Chemistry, 90(7), https://doi.org/10.1021/acs.analchem.7b04758

We have investigated the applicability of commercially available lyophilized spirulina (Arthrospira platensis), a microorganism uniformly labeled with 13C, as a readily accessible source of multiple 13C-labeled metabolites suitable as internal standa... Read More about Quantitative isotope-dilution high-resolution-mass-apectrometry analysis of multiple intracellular metabolites in Clostridium autoethanogenum with uniformly 13C-labeled standards derived from Spirulina.

Polymers for binding of the gram-positive oral pathogen Streptococcus mutans (2017)
Journal Article
Magennis, E. P., Francini, N., Mastrotto, F., Catania, R., Redhead, M., Fernandez-Trillo, F., Bradshaw, D., Churchley, D., Winzer, K., Alexander, C., & Mantovani, G. (2017). Polymers for binding of the gram-positive oral pathogen Streptococcus mutans. PLoS ONE, 12(7), Article e018008. https://doi.org/10.1371/journal.pone.0180087

Streptococcus mutans is the most significant pathogenic bacterium implicated in the formation of dental caries and, both directly and indirectly, has been associated with severe conditions such as multiple sclerosis, cerebrovascular and peripheral ar... Read More about Polymers for binding of the gram-positive oral pathogen Streptococcus mutans.

Microbial solvent formation revisited by comparative genome analysis (2017)
Journal Article
Poehlein, A., Solano, J. D. M., Flitsch, S. K., Krabben, P., Winzer, K., Reid, S. J., Jones, D. T., Green, E., Minton, N. P., Daniel, R., & Dürre, P. (2017). Microbial solvent formation revisited by comparative genome analysis. Biotechnology for Biofuels, 10, Article 58. https://doi.org/10.1186/s13068-017-0742-z

Background: Microbial formation of acetone, isopropanol, and butanol is largely restricted to bacteria belonging to the genus Clostridium. This ability has been industrially exploited over the last 100 years. The solvents are important feedstocks for... Read More about Microbial solvent formation revisited by comparative genome analysis.

Mathematical modelling of clostridial acetone-butanol-ethanol fermentation (2017)
Journal Article
Millat, T., & Winzer, K. (in press). Mathematical modelling of clostridial acetone-butanol-ethanol fermentation. Applied Microbiology and Biotechnology, 101(6), https://doi.org/10.1007/s00253-017-8137-4

Clostridial acetone-butanol-ethanol (ABE) fermentation features a remarkable shift in the cellular metabolic activity from acid formation, acidogenesis, to the production of industrial-relevant solvents, solventogensis. In recent decades, mathematica... Read More about Mathematical modelling of clostridial acetone-butanol-ethanol fermentation.

Metabolic engineering of Clostridium autoethanogenum for selective alcohol production (2017)
Journal Article
Liew, F., Henstra, A. M., Kӧpke, M., Winzer, K., Simpson, S. D., & Minton, N. P. (2017). Metabolic engineering of Clostridium autoethanogenum for selective alcohol production. Metabolic Engineering, 40, 104-114. https://doi.org/10.1016/j.ymben.2017.01.007

Gas fermentation using acetogenic bacteria such as Clostridium autoethanogenum offers an attractive route for production of fuel ethanol from industrial waste gases. Acetate reduction to acetaldehyde and further to ethanol via an aldehyde: ferredoxin... Read More about Metabolic engineering of Clostridium autoethanogenum for selective alcohol production.

Development and implementation of rapid metabolic engineering tools for chemical and fuel production in Geobacillus thermoglucosidasius NCIMB 11955 (2017)
Journal Article
Sheng, L., Kovács, K., Winzer, K., Zhang, Y., & Minton, N. P. (2017). Development and implementation of rapid metabolic engineering tools for chemical and fuel production in Geobacillus thermoglucosidasius NCIMB 11955. Biotechnology for Biofuels, 10(1), Article 5. https://doi.org/10.1186/s13068-016-0692-x

Background

The thermophile Geobacillus thermoglucosidasius has considerable attraction as a chassis for the production of chemicals and fuels. It utilises a wide range of sugars and oligosaccharides typical of those derived from lignocellulose and... Read More about Development and implementation of rapid metabolic engineering tools for chemical and fuel production in Geobacillus thermoglucosidasius NCIMB 11955.

A genetic assay for gene essentiality in Clostridium (2016)
Journal Article
Walker, D. J., Heap, J. T., Winzer, K., & Minton, N. P. (2016). A genetic assay for gene essentiality in Clostridium. Anaerobe, 42, 40-43. https://doi.org/10.1016/j.anaerobe.2016.07.007

Essential genes of pathogens are potential therapeutic targets, but are difficult to verify. Here, gene essentiality was determined by targeted knockout following engineered gene duplication. Null mutants of candidate essential genes of Clostridium d... Read More about A genetic assay for gene essentiality in Clostridium.

Insights into CO2 fixation pathway of Clostridium autoethanogenumby targeted mutagenesis (2016)
Journal Article
Liew, F., Henstra, A. M., Winzer, K., Kopke, M., Simpson, S. D., & Minton, N. P. (in press). Insights into CO2 fixation pathway of Clostridium autoethanogenumby targeted mutagenesis. mBio, 7(3), Article e00427-16. https://doi.org/10.1128/mBio.00427-16

The future sustainable production of chemicals and fuels from nonpetrochemical resources and reduction of greenhouse gas emissions are two of the greatest societal challenges. Gas fermentation, which utilizes the ability of acetogenic bacteria such a... Read More about Insights into CO2 fixation pathway of Clostridium autoethanogenumby targeted mutagenesis.

Production of a functional cell wall-anchored minicellulosome by recombinant Clostridium acetobutylicum ATCC 824 (2016)
Journal Article
Willson, B. J., Kovács, K., Wilding-Steele, T., Markus, R., Winzer, K., & Minton, N. P. (2016). Production of a functional cell wall-anchored minicellulosome by recombinant Clostridium acetobutylicum ATCC 824. Biotechnology for Biofuels, 9(1), Article 109. https://doi.org/10.1186/s13068-016-0526-x

Background: The use of fossil fuels is no longer tenable. Not only are they a finite resource, their use is damaging the environment through pollution and global warming. Alternative, environmentally friendly, renewable sources of chemicals and fuels... Read More about Production of a functional cell wall-anchored minicellulosome by recombinant Clostridium acetobutylicum ATCC 824.

Dendrimer mediated clustering of bacteria: improved aggregation and evaluation of bacterial response and viability (2016)
Journal Article
Leire, E., Amaral, S. P., Louzao, I., Winzer, K., Alexander, C., Fernandez-Megia, E., & Fernandez-Trillo, F. (2016). Dendrimer mediated clustering of bacteria: improved aggregation and evaluation of bacterial response and viability. Biomaterials Science, 4(6), https://doi.org/10.1039/C6BM00079G

Here, we evaluate how cationic gallic acid-triethylene glycol (GATG) dendrimers interact with bacteria and their potential to develop new antimicrobials. We demonstrate that GATG dendrimers functionalised with primary amines in their periphery can in... Read More about Dendrimer mediated clustering of bacteria: improved aggregation and evaluation of bacterial response and viability.

Mutant generation by allelic exchange and genome resequencing of the biobutanol organism Clostridium acetobutylicum ATCC 824 (2016)
Journal Article
Ehsaan, M., Kuit, W., Zhang, Y., Cartman, S. T., Heap, J. T., Winzer, K., & Minton, N. P. (2016). Mutant generation by allelic exchange and genome resequencing of the biobutanol organism Clostridium acetobutylicum ATCC 824. Biotechnology for Biofuels, 9(1), Article 4. https://doi.org/10.1186/s13068-015-0410-0

Background

Clostridium acetobutylicum represents a paradigm chassis for the industrial production of the biofuel biobutanol and a focus for metabolic engineering. We have previously developed procedures for the creation of in-frame, marker-less de... Read More about Mutant generation by allelic exchange and genome resequencing of the biobutanol organism Clostridium acetobutylicum ATCC 824.

Whole genome sequence and manual annotation of Clostridium autoethanogenum, an industrially relevant bacterium (2015)
Journal Article
Humphreys, C. M., McLean, S., Schatschneider, S., Millat, T., Henstra, A. M., Annan, F. J., Breitkopf, R., Pander, B., Piatek, P., Rowe, P., Wichlacz, A. T., Woods, C., Norman, R., Blom, J., Goesman, A., Hodgman, C., Barrett, D., Thomas, N. R., Winzer, K., & Minton, N. P. (2015). Whole genome sequence and manual annotation of Clostridium autoethanogenum, an industrially relevant bacterium. BMC Genomics, 16(1), Article 1085. https://doi.org/10.1186/s12864-015-2287-5

© 2015 Humphreys et al. Background: Clostridium autoethanogenum is an acetogenic bacterium capable of producing high value commodity chemicals and biofuels from the C1 gases present in synthesis gas. This common industrial waste gas can act as the so... Read More about Whole genome sequence and manual annotation of Clostridium autoethanogenum, an industrially relevant bacterium.

Cationic polymer mediated bacterial clustering: cell-adhesive properties of homo- and copolymers (2015)
Journal Article
Louzao, I., Sui, C., Winzer, K., Fernandez-Trillo, F., & Alexander, C. (2015). Cationic polymer mediated bacterial clustering: cell-adhesive properties of homo- and copolymers. European Journal of Pharmaceutics and Biopharmaceutics, 95, 47-62. https://doi.org/10.1016/j.ejpb.2015.05.026

New anti-infective materials are needed urgently as alternatives to conventional biocides. It has recently been established that polymer materials designed to bind to the surface of bacteria can induce the formation of cell clusters which enhance the... Read More about Cationic polymer mediated bacterial clustering: cell-adhesive properties of homo- and copolymers.

Coenzyme A-transferase-independent butyrate re-assimilation in Clostridium acetobutylicum - evidence from a mathematical model (2014)
Journal Article
Millat, T., Voigt, C., Janssen, H., Cooksley, C. M., Winzer, K., Minton, N. P., Bahl, H., Fischer, R.-J., & Wolkenhauer, O. (2014). Coenzyme A-transferase-independent butyrate re-assimilation in Clostridium acetobutylicum - evidence from a mathematical model. Applied Microbiology and Biotechnology, 98(21), https://doi.org/10.1007/s00253-014-5987-x

The hetero-dimeric CoA-transferase CtfA/B is believed to be crucial for the metabolic transition from acidogenesis to solventogenesis in Clostridium acetobutylicum as part of the industrial-relevant acetone-butanol-ethanol (ABE) fermentation. Here, t... Read More about Coenzyme A-transferase-independent butyrate re-assimilation in Clostridium acetobutylicum - evidence from a mathematical model.

Bacteria-instructed synthesis of polymers for self-selective microbial binding and labelling (2014)
Journal Article
Magennis, E. P., Fernandez-Trillo, F., Sui, C., Spain, S. G., Bradshaw, D., Churchley, D., Mantovani, G., Winzer, K., & Alexander, C. (2014). Bacteria-instructed synthesis of polymers for self-selective microbial binding and labelling. Nature Materials, 13(7), 748-755. https://doi.org/10.1038/nmat3949

The detection and inactivation of pathogenic strains of bacteria continues to be an important therapeutic goal. Hence, there is a need for materials that can bind selectively to specific microorganisms for diagnostic or anti-infective applications, b... Read More about Bacteria-instructed synthesis of polymers for self-selective microbial binding and labelling.

Bacteria clustering by polymers induces the expression of quorum sense controlled phenotypes (2013)
Journal Article
Lui, L. T., Xue, X., Sui, C., Brown, A., Pritchard, D. I., Halliday, N., Winzer, K., Howdle, S. M., Fernandez-Trillo, F., Krasnogor, N., & Alexander, C. (2013). Bacteria clustering by polymers induces the expression of quorum sense controlled phenotypes. Nature Chemistry, 5(12), https://doi.org/10.1038/nchem.1793

Bacteria deploy a range of chemistries to regulate their behaviour and respond to their environment. Quorum sensing is one mean by which bacteria use chemical reactions to modulate pre-infection behaviour such as surface attachment. Polymers that can... Read More about Bacteria clustering by polymers induces the expression of quorum sense controlled phenotypes.

Secretion and assembly of functional mini-cellulosomes from synthetic chromosomal operons in Clostridium acetobutylicum ATCC 824 (2013)
Journal Article
Kovacs, K., Willson, B. J., Schwarz, K., Heap, J. T., Jackson, A., Bolam, D. N., Winzer, K., & Minton, N. P. (2013). Secretion and assembly of functional mini-cellulosomes from synthetic chromosomal operons in Clostridium acetobutylicum ATCC 824. Biotechnology for Biofuels, 6(117), https://doi.org/10.1186/1754-6834-6-117

BACKGROUND:

Consolidated bioprocessing (CBP) is reliant on the simultaneous enzyme production, saccharification of biomass, and fermentation of released sugars into valuable products such as butanol. Clostridial species that produce butanol are, h... Read More about Secretion and assembly of functional mini-cellulosomes from synthetic chromosomal operons in Clostridium acetobutylicum ATCC 824.