Research Output 1983 2019

2019

Acetogenins: Chemoenzymatic synthesis and molecular probing of respiratory NADH-dehydrogenases

van Lint, M., 12 Sep 2019, 326 p.

Research output: PhD ThesisPhD Thesis - Research VU, graduation VUAcademic

Adaption to glucose limitation is modulated by the pleotropic regulator CcpA, independent of selection pressure strength

Price, C. E., Branco Dos Santos, F., Hesseling, A., Uusitalo, J. J., Bachmann, H., Benavente, V., Goel, A., Berkhout, J., Bruggeman, F. J., Marrink, S. J., Montalban-Lopez, M., De Jong, A., Kok, J., Molenaar, D., Poolman, B., Teusink, B. & Kuipers, O. P., 10 Jan 2019, In : BMC Evolutionary Biology. 19, 1, p. 1-15 15 p., 15.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
strength (mechanics)
glucose
mutation
chemostat
fitness

A genome-scale metabolic network of the aroma bacterium Leuconostoc mesenteroides subsp. cremoris

Özcan, E., Selvi, S. S., Nikerel, E., Teusink, B., Toksoy Öner, E. & Çakır, T., 1 Jan 2019, In : Applied Microbiology and Biotechnology.

Research output: Contribution to JournalArticleAcademicpeer-review

Metabolic Networks and Pathways
Citric Acid
Genome
Bacteria
phosphoketolase

Ampicillin-treated Lactococcus lactis MG1363 populations contain persisters as well as viable but non-culturable cells

van Tatenhove-Pel, R. J., Zwering, E., Solopova, A., Kuipers, O. P. & Bachmann, H., 1 Dec 2019, In : Scientific Reports. 9, 1, 9867.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Lactococcus lactis
ampicillin
antibiotics
viability
cells

A systematic assessment of current genome-scale metabolic reconstruction tools

Mendoza, S. N., Olivier, B. G., Molenaar, D. & Teusink, B., 7 Aug 2019, In : Genome Biology. 20, 1, 158.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Software
genome
Genome
software
Benchmarking

Biodegradation of metformin and its transformation product, guanylurea, by natural and exposed microbial communities

Poursat, B. A. J., van Spanning, R. J. M., Braster, M., Helmus, R., de Voogt, P. & Parsons, J. R., 30 Oct 2019, In : Ecotoxicology and Environmental Safety. 182, p. 1-10 10 p., 109414.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Chemostats
Metformin
Biodegradability
Biodegradation
Sewage

Circular spectropolarimetric sensing of higher plant and algal chloroplast structural variations

Patty, C. H. L., Ariese, F., Buma, W. J., ten Kate, I. L., van Spanning, R. J. M. & Snik, F., May 2019, In : Photosynthesis Research. 140, 2, p. 129-139

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Circular spectropolarimetric sensing of life

Patty, C. H. L., 2019, 174 p.

Research output: PhD ThesisPhD Thesis - Research VU, graduation VUAcademic

Open Access
File

Circular Spectropolarimetric Sensing of Vegetation in the Field: Possibilities for the Remote Detection of Extraterrestrial Life

Patty, C. H. L., Ten Kate, I. L., Buma, W. J., van Spanning, R. J. M., Steinbach, G., Ariese, F. & Snik, F., 30 Jul 2019, In : Astrobiology.

Research output: Contribution to JournalArticleAcademicpeer-review

Exobiology
Forestry
Agriculture
Lighting
Light

Comparative genome analysis of Lactococcus lactis indicates niche adaptation and resolves genotype/phenotype disparity

Wels, M., Siezen, R., Van Hijum, S., Kelly, W. J. & Bachmann, H., 31 Jan 2019, In : Frontiers in Microbiology. 10, January, p. 1-18 18 p., 4.

Research output: Contribution to JournalArticleAcademicpeer-review

Lactococcus lactis
Genotype
Genome
Phenotype
Dairying

Comparative genomics of human Lactobacillus crispatus isolates reveals genes for glycosylation and glycogen degradation: Implications for in vivo dominance of the vaginal microbiota

Van Der Veer, C., Hertzberger, R. Y., Bruisten, S. M., Tytgat, H. L. P., Swanenburg, J., De Kat Angelino-Bart, A., Schuren, F., Molenaar, D., Reid, G., De Vries, H. & Kort, R., 29 Mar 2019, In : Microbiome. 7, 1, p. 1-14 14 p., 49.

Research output: Contribution to JournalArticleAcademicpeer-review

File
Microbiota
Genomics
Glycogen
Glycosylation
Lactobacillus

Dynamic Metabolic Rewiring Enables Efficient Acetyl Coenzyme A Assimilation in Paracoccus denitrificans

Kremer, K., van Teeseling, M. C. F., Schada von Borzyskowski, L., Bernhardsgrütter, I., van Spanning, R. J. M., Gates, A. J., Remus-Emsermann, M. N. P., Thanbichler, M. & Erb, T. J., 9 Jul 2019, In : mBio. 10, 4, p. 1-15 15 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Paracoccus denitrificans
Acetyl Coenzyme A
Carbon
Growth
Biomass

Finding functional differences between species in a microbial community: Case studies in wine fermentation and Kefir culture

Melkonian, C., Gottstein, W., Blasche, S., Kim, Y., Abel-Kistrup, M., Swiegers, H., Saerens, S., Edwards, N., Patil, K. R., Teusink, B. & Molenaar, D., 25 Jun 2019, In : Frontiers in Microbiology. 10, JUNE, p. 1-14 14 p., 01347.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Wine
Fermentation
Metagenomics
Gluconobacter
Pantoea

From functional potential of soil bacterial communities towards petroleum hydrocarbons bioremediation

Iturbe Espinoza, P. A., Bonte, M., Brown, D. M. & van Spanning, R., 2019, In : Journal of Biology, Agriculture and Healthcare. 9, 10, 24 p.

Research output: Contribution to JournalReview articleAcademicpeer-review

petroleum hydrocarbon
bioremediation
hydrocarbon
microbial community
gene

Harmonizing semantic annotations for computational models in biology

Neal, M. L., König, M., Nickerson, D., Misirli, G., Kalbasi, R., Dräger, A., Atalag, K., Chelliah, V., Cooling, M. T., Cook, D. L., Crook, S., De Alba, M., Friedman, S. H., Garny, A., Gennari, J. H., Gleeson, P., Golebiewski, M., Hucka, M., Juty, N., Myers, C. & 8 othersOlivier, B. G., Sauro, H. M., Scharm, M., Snoep, J. L., Touré, V., Wipat, A., Wolkenhauer, O. & Waltemath, D., 22 Mar 2019, In : Briefings in bioinformatics. 20, 2, p. 540-550 11 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Semantics
Research Personnel
Biota
Biological Science Disciplines
Theoretical Models

Implications of microbial adaptation for the assessment of environmental persistence of chemicals

Poursat, B. A. J., van Spanning, R. J. M., de Voogt, P. & Parsons, J. R., 1 Jan 2019, In : Critical Reviews in Environmental Science and Technology.

Research output: Contribution to JournalReview articleAcademicpeer-review

Open Access
Biodegradability
persistence
Biodegradation
Organic chemicals
biodegradation

In vivo characterisation of fluorescent proteins in budding yeast

Botman, D., de Groot, D. H., Schmidt, P., Goedhart, J. & Teusink, B., 19 Feb 2019, In : Scientific Reports. 9, p. 1-14 14 p., 2234.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Saccharomycetales
Proteins
Codon
Yeasts
Saccharomyces cerevisiae

Metabolomics: From Method Development to System Biology

Krumpochova, P., 2019, 215 p.

Research output: PhD ThesisPhD Thesis - Research VU, graduation VUAcademic

Open Access
File

Microbial Communities in Sediments From Four Mildly Acidic Ephemeral Salt Lakes in the Yilgarn Craton (Australia) - Terrestrial Analogs to Ancient Mars

Aerts, J. W., van Spanning, R. J. M., Flahaut, J., Molenaar, D., Bland, P. A., Genge, M. J., Ehrenfreund, P. & Martins, Z., 6 May 2019, In : Frontiers in Microbiology. 10

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Physical biology of GPCR signalling dynamics inferred from fluorescence spectroscopy and imaging

Chavez-Abiega, S., Goedhart, J. & Bruggeman, F. J., 1 Apr 2019, In : Current Opinion in Structural Biology. 55, p. 204-211 8 p.

Research output: Contribution to JournalReview articleAcademicpeer-review

Optical Imaging
Fluorescence Spectrometry
G-Protein-Coupled Receptors
GTP-Binding Proteins
Carrier Proteins

Stereoselective Chemoenzymatic Cascade Synthesis of the bis-THF Core of Acetogenins

van Lint, M. J., Hall, M., Faber, K., van Spanning, R. J. M., Ruijter, E. & Orru, R. V. A., 7 Feb 2019, In : European Journal of Organic Chemistry. 2019, 5, p. 1092-1101 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Acetogenins
epoxy compounds
Epoxy Compounds
Biological Products
cascades

Taxonomic and functional characterization of the microbial community during spontaneous in vitro fermentation of riesling must

Sirén, K., Mak, S. S. T., Melkonian, C., Carøe, C., Swiegers, J. H., Molenaar, D., Fischer, U. & Thomas P Gilbert, M., 1 Jan 2019, In : Frontiers in Microbiology. 10, APR, 697.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Fermentation
Metagenomics
Saccharomyces
Metschnikowia
Biodiversity

The number of active metabolic pathways is bounded by the number of cellular constraints at maximal metabolic rates

de Groot, D. H., van Boxtel, C., Planque, R., Bruggeman, F. J. & Teusink, B., 11 Mar 2019, In : PLoS Computational Biology. 15, 3, p. 1-24 24 p., e1006858.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Metabolic Networks and Pathways
biochemical pathways
Pathway
enzyme
Fluxes
2018

A benzene-degrading nitrate-reducing microbial consortium displays aerobic and anaerobic benzene degradation pathways

Atashgahi, S., Hornung, B., Van Der Waals, M. J., Da Rocha, U. N., Hugenholtz, F., Nijsse, B., Molenaar, D., Van Spanning, R., Stams, A. J. M., Gerritse, J. & Smidt, H., 14 Mar 2018, In : Scientific Reports. 8, 1, p. 1-12 12 p., 4490.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Microbial Consortia
Benzene
Nitrates
Oxygen
Genes

Adaptation of microbial communities to emerging pollutants in chemostat systems

Poursat, B., Braster, M., Helmus, R., van Spanning, R., de Voogt, P. & Parsons, J., 18 Mar 2018, In : Abstracts of Papers - American Chemical Society. 255

Research output: Contribution to JournalMeeting AbstractAcademic

Alignment of microbial fitness with engineered product formation: Obligatory coupling between acetate production and photoautotrophic growth

Du, W., Jongbloets, J. A., van Boxtel, C., Hernández, H. P., Lips, D., Olivier, B. G., Hellingwerf, K. J. & dos Santos, F. B., 13 Feb 2018, In : Biotechnology for Biofuels. 11, 38, p. 1-13 13 p., 38.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
acetate
Acetates
fitness
Cyanobacteria
production system

Altering textural properties of fermented milk by using surface-engineered Lactococcus lactis

Tarazanova, M., Huppertz, T., Kok, J. & Bachmann, H., 9 May 2018, In : Microbial Biotechnology.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Fermented milk
Lactococcus lactis
Milk
Dairy products
Hydrophobicity

An integrated model quantitatively describing metabolism, growth and cell cycle in budding yeast

Palumbo, P., Vanoni, M., Papa, F., Busti, S., Wortel, M., Teusink, B. & Alberghina, L., 2018, Artificial Life and Evolutionary Computation - 12th Italian Workshop, WIVACE 2017, Revised Selected Papers. Springer/Verlag, p. 165-180 16 p. (Communications in Computer and Information Science; vol. 830).

Research output: Chapter in Book / Report / Conference proceedingConference contributionAcademicpeer-review

Integrated Model
Cell Cycle
Metabolism
Yeast
Cells

Balance on many scales: growth and gene expression in Bacillus subtilis

Nordholt, N., 2018, 118 p.

Research output: PhD ThesisPhD Thesis - Research VU, graduation VUAcademic

Open Access
File

Constraint-based models of microbial physiology: Surprisingly versatile

Teusink, B., Planqué, B., Molenaar, D. & Bruggeman, F., 1 Jan 2018, 10th International Conference on Simulation and Modelling in the Food and Bio-Industry 2018, FOODSIM 2018. Eurosis, p. 5-10 6 p.

Research output: Chapter in Book / Report / Conference proceedingConference contributionAcademicpeer-review

microbial physiology
Physiology
Fluxes
Microbiological Phenomena
Growth

Correction to: Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)

Waltemath, D., Bergmann, F. T., Chaouiya, C., Czauderna, T., Gleeson, P., Goble, C., Golebiewski, M., Hucka, M., Juty, N., Krebs, O., Le Novère, N., Mi, H., Moraru, I. I., Myers, C. J., Nickerson, D., Olivier, B. G., Rodriguez, N., Schreiber, F., Smith, L., Zhang, F. & 1 othersBonnet, E., 9 Aug 2018, In : Standards in Genomic Sciences. 13, 1, p. 1-1 1 p., 17.

Research output: Contribution to JournalComment / Letter to the editorAcademic

Open Access
Publications
Education
Research

Dynamic elementary mode modelling of non-steady state flux data

Folch-Fortuny, A., Teusink, B., Hoefsloot, H. C. J., Smilde, A. K. & Ferrer, A., 18 Jun 2018, In : BMC Systems Biology. 12, p. 1-15 15 p., 71.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Metabolic Flux Analysis
Fluxes
Discriminant Analysis
Metabolic Networks and Pathways
Modeling

Editorial overview: Special Section: Single cell systems biology

Bruggeman, F. J. & Swain, P., Apr 2018, In : Current Opinion in Systems Biology. 8, p. vi-vi 1 p.

Research output: Contribution to JournalEditorialAcademicpeer-review

Further elucidation of galactose utilization in Lactococcus lactis MG1363

Solopova, A., Bachmann, H., Teusink, B., Kok, J. & Kuipers, O. P., 3 Aug 2018, In : Frontiers in Microbiology. 9, AUGUST, p. 1-9 9 p., 1803.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Lactococcus lactis
Galactose
Lactose
Lactococcus
Membrane Transport Proteins

Imaging linear and circular polarization features in leaves with complete Mueller matrix polarimetry

Patty, C. H. L., Luo, D. A., Snik, F., Ariese, F., Buma, W. J., ten Kate, I. L., van Spanning, R. J. M., Sparks, W. B., Germer, T. A., Garab, G. & Kudenov, M. W., Jun 2018, In : Biochimica et Biophysica Acta - General Subjects. 1862, 6, p. 1350-1363 14 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Circular polarization
Polarimeters
Veins
Acer
Imaging techniques

Influence of lactococcal surface properties on cell retention and distribution in cheese curd

Tarazanova, M., Huppertz, T., Kok, J. & Bachmann, H., Oct 2018, In : International Dairy Journal. 85, p. 73-78 6 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Surface Properties
milk curds
Cheese
cheeses
cells

Low affinity uniporter carrier proteins can increase net substrate uptake rate by reducing efflux

Bosdriesz, E., Wortel, M. T., Haanstra, J. R., Wagner, M. J., De La Torre Cortés, P. & Teusink, B., 3 Apr 2018, In : Scientific Reports. 8, 1, p. 1-9 9 p., 5576.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Facilitated Diffusion
Facilitative Glucose Transport Proteins
Glycolysis
Saccharomyces cerevisiae
Carrier Proteins

Maintaining maximal metabolic flux by gene expression control

Planqué, R., Hulshof, J., Teusink, B., Hendriks, J. C. & Bruggeman, F. J., 20 Sep 2018, In : PLoS Computational Biology. 14, 9, p. 1-20 20 p., e1006412.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Metabolites
Metabolic Networks and Pathways
Gene expression
Gene Expression
gene expression

Metabolic enzyme cost explains variable trade-offs between microbial growth rate and yield

Wortel, M. T., Noor, E., Ferris, M., Bruggeman, F. J. & Liebermeister, W., 16 Feb 2018, In : PLoS Computational Biology. 14, 2, e1006010.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
variable costs
microbial growth
Enzymes
Trade-offs
enzyme

Metabolite Depletion Affects Flux Profiling of Cell Lines

Nilsson, A., Haanstra, J. R., Teusink, B. & Nielsen, J., Jun 2018, In : Trends in Biochemical Sciences. 43, 6, p. 395-397 3 p.

Research output: Contribution to JournalShort surveyAcademicpeer-review

Metabolites
Cells
Fluxes
Cell Line
Growth

Naturally fermented milk from northern Senegal: Bacterial community composition and probiotic enrichment with Lactobacillus rhamnosus

Parker, M., Zobrist, S., Donahue, C., Edick, C., Mansen, K., Nadjari, M. H. Z., Heerikhuisen, M., Sybesma, W., Molenaar, D., Diallo, A. M., Milani, P. & Kort, R., 21 Sep 2018, In : Frontiers in Microbiology. 9, September, p. 1-12 12 p., 2218.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Regulatory and metabolic networks

Sauer, U. & Teusink, B., Apr 2018, In : Current Opinion in Systems Biology. 8, p. iv-v 2 p.

Research output: Contribution to JournalEditorialAcademicpeer-review

SBML Level 3 Package: Flux Balance Constraints version 2

Olivier, B. G. & Bergmann, F. T., 9 Mar 2018, In : Journal of Integrative Bioinformatics. 15, 1, p. 1-39 39 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Social Planning
Genome
Proteins

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3)

Bergmann, F. T., Cooper, J., König, M., Moraru, I., Nickerson, D., Le Novère, N., Olivier, B. G., Sahle, S., Smith, L. & Waltemath, D., 19 Mar 2018, In : Journal of Integrative Bioinformatics. 15, 1, p. 1-98 98 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Language
Reproduction
Software
Research

Sulfur cave (Romania), an extreme environment with microbial mats in a Co2-H2S/O2 gas chemocline dominated by mycobacteria

Sarbu, S. M., Aerts, J. W., Flot, J. F., van Spanning, R. J. M., Baciu, C., Ionescu, A., Kis, B. M., Incze, R., Siko-Barabasi, S., Para, Z., Hegyeli, B., Atudorei, N. V., Barr, C., Nealson, K. H., Forray, F. L., Lascu, C., Fleming, E. J., Bitter, W. & Popa, R., 1 Jan 2018, In : International Journal of Speleology. 47, 2, p. 173-187 15 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
microbial mat
cave
sulfur
gas
biofilm

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core

Hucka, M., Bergmann, F. T., Dräger, A., Hoops, S., Keating, S. M., Le Novère, N., Myers, C. J., Olivier, B. G., Sahle, S., Schaff, J. C., Smith, L. P., Waltemath, D. & Wilkinson, D. J., 9 Mar 2018, In : Journal of Integrative Bioinformatics. 15, 1, p. 1-182 182 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Systems Biology
Language
Software
Biological Phenomena
Metabolic Networks and Pathways

Training for translation between disciplines: A philosophy for life and data sciences curricula

Anton Feenstra, K., Abeln, S., Westerhuis, J. A., Brancos Dos Santos, F., Molenaar, D., Teusink, B., Hoefsloot, H. C. J. & Heringa, J., 1 Jul 2018, In : Bioinformatics. 34, 13, p. i4-i12 9 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Understanding start-up problems in yeast glycolysis

Overal, G. B., Teusink, B., Bruggeman, F. J., Hulshof, J. & Planqué, R., May 2018, In : Mathematical Biosciences. 299, May, p. 117-126 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Glycolysis
Start-up
glycolysis
Yeast
Yeasts
2017

Aerobic and anaerobic bacteria – Respiration without oxygen

van Spanning, R., van der Oost, J. & Richardson, D., 2017, Mighty Microbes: The amazing world of microorganisms. van Doorn, J., Luirink, J., van der Oost, J., Oudega, B., Robertson, L., Smit, H. & Willemsen, P. (eds.). Microcanon Foundation / Stichting Microcanon, p. 56-58

Research output: Chapter in Book / Report / Conference proceedingChapterPopular

Aerobic Bacteria
Anaerobic Bacteria
cell respiration
Bacteria
Respiration

Cell surface properties of Lactococcus lactis reveal milk protein binding specifically evolved in dairy isolates

Tarazanova, M., Huppertz, T., Beerthuyzen, M., van Schalkwijk, S., Janssen, P. W. M., Wels, M., Kok, J. & Bachmann, H., 7 Sep 2017, In : Frontiers in Microbiology. 8, SEP

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Lactococcus lactis
Surface Properties
Milk Proteins
Protein Binding
Hydrophobic and Hydrophilic Interactions