Molecular Cell Physiology

Research Output 1978 2019

2019

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

Bacterial community dynamics in lait caillé, a traditional product of spontaneous fermentation from Senegal

Groenenboom, A. E., Parker, M. E., De Vries, A., De Groot, S., Zobrist, S., Mansen, K., Milani, P., Kort, R., Smid, E. J. & Schoustra, S. E., 10 May 2019, In : PLoS ONE. 14, 5, e0215658.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Senegal
Probiotics
bacterial communities
Fermentation
probiotics

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

Child development, growth and microbiota: follow-up of a randomized education trial in Uganda

Atukunda, P., Muhoozi, G. K. M., van den Broek, T. J., Kort, R., Diep, L. M., Kaaya, A. N., Iversen, P. O. & Westerberg, A. C., Jun 2019, In : Journal of global health. 9, 1, p. 1-11 11 p., 010431.

Research output: Contribution to JournalArticleAcademicpeer-review

Uganda
Microbiota
Child Development
Mothers
Education

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 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

De hygiënehypothese onder de loep

Croon, S., Rijkers, G., Budding, A., de Jong, E., Knol, E., Smits, H., Tool, B. & Kort, R., May 2019, In : Dutch Journal of Allergy, Asthma & Clinical Immunology (NTvAAKI). 19, p. 55-60 6 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Hygiene Hypothesis
Immune System
Hypersensitivity
Eczema
Immune System Diseases

Een praktische gids voor probiotica ter preventie van antibiotica-gerelateerde diarree in Nederland

Agamennone, V., Krul, C., Rijkers, G. & Kort, R., 8 Feb 2019, In : Pharmaceutisch Weekblad. 154, 6, p. 17-24 8 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Probiotics
Netherlands
Diarrhea
Anti-Bacterial Agents
Lactobacillus rhamnosus

Genome annotation and antimicrobial properties of Bacillus toyonensis VU-DES13, isolated from the Folsomia candida gut

Agamennone, V., van Straalen, J., Brouwer, A., de Boer, T. E., Hensbergen, P. J., Zaagman, N., Braster, M., van Straalen, N. M., Roelofs, D. & Janssens, T. K. S., Mar 2019, In : Entomologia experimentalis et applicata. 167, 3, p. 269-285 17 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Folsomia candida
anti-infective properties
antibiotic resistance
genome
digestive system

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

Improving Health and Wealth by Introduction of an Affordable Bacterial Starter Culture for Probiotic Yoghurt Production in Uganda

Westerik, N., Wacoo, A. P., Anyimo, E., Matovu, W., Reid, G., Kort, R. & Sybesma, W., 9 Jan 2019, In : Challenges. 10, 1

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
starter cultures
Uganda
yogurt
probiotics
entrepreneurship

Integration of single-cell RNA-seq data into population models to characterize cancer metabolism

Damiani, C., Maspero, D., Di Filippo, M., Colombo, R., Pescini, D., Graudenzi, A., Westerhoff, H. V., Alberghina, L., Vanoni, M. & Mauri, G., 28 Feb 2019, In : PLoS Computational Biology. 15, 2, p. 1-25 25 p., e1006733.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Population Model
RNA
Metabolism
cancer
Cancer

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

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

Neural plasticity and adult neurogenesis: the deep biology perspective

Colangelo, A., Cirillo, G., Alberghina, L., Papa, M. & Westerhoff, H., 1 Feb 2019, In : Neural Regeneration Research. 14, 2, p. 201-205 5 p.

Research output: Contribution to JournalReview articleAcademicpeer-review

Open Access
Neuronal Plasticity
Neurogenesis
Energy Metabolism
Growth Differentiation Factors
Mitochondrial Dynamics

NEW PROBIOTIC COMPOSITION FOR PREVENTION OF BACTERIAL VAGINOSIS

Kort, R. & van der Veer, C., 17 Jan 2019, 12 Jul 2018, Priority date 12 Jul 2017

Research output: PatentAcademic

File

Phosphofructokinase controls the acetaldehyde-induced phase shift in isolated yeast glycolytic oscillators

Van Niekerk, D. D., Gustavsson, A. K., Mojica-Benavides, M., Adiels, C. B., Goksör, M. & Snoep, J. L., 31 Jan 2019, In : Biochemical Journal. 476, 2, p. 353-363 11 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Phosphofructokinases
Acetaldehyde
Melatonin
Phase shift
Yeast

Potential application of lactic acid starters in the reduction of aflatoxin contamination in fermented sorghum-millet beverages

Byakika, S., Mukisa, I. M., Wacoo, A. P., Kort, R., Byaruhanga, Y. B. & Muyanja, C., 15 Jan 2019, In : International Journal of Food Contamination. 6, 4

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Sorghum
Aflatoxins
Beverages
millets
aflatoxins

Probiotic Enrichment and Reduction of Aflatoxins in a Traditional African Maize-Based Fermented Food

Wacoo, A. P., Mukisa, I. M., Meeme, R., Byakika, S., Wendiro, D., Sybesma, W. & Kort, R., 25 Jan 2019, In : Nutrients. 11, 2

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Aflatoxins
fermented foods
Probiotics
aflatoxins
probiotics

Ranking network mechanisms by how they fit diverse experiments and deciding on E. coli's ammonium transport and assimilation network

Maeda, K., Westerhoff, H. V., Kurata, H. & Boogerd, F. C., 12 Apr 2019, In : NPJ systems biology and applications. 5, p. 1-11 11 p., 14.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Ammonium
Ammonium Compounds
Escherichia coli
Escherichia Coli
Ranking

Studying Glycolytic Oscillations in Individual Yeast Cells by Combining Fluorescence Microscopy with Microfluidics and Optical Tweezers

Gustavsson, A. K., Banaeiyan, A. A., van Niekerk, D. D., Snoep, J. L., Adiels, C. B. & Goksör, M., Mar 2019, In : Current Protocols in Cell Biology. 82, 1, p. 1-26 26 p., e70.

Research output: Contribution to JournalArticleAcademicpeer-review

Optical Tweezers
Microfluidics
Fluorescence Microscopy
Yeasts
Lab-On-A-Chip Devices

Vaginal microbes in sexual health and disease

van der Veer, C., 11 Jan 2019, 285 p.

Research output: PhD ThesisPhD Thesis - Research external, graduation externalAcademic

File
2018

11-Oxygenated androgen precursors are the preferred substrates for aldo-keto reductase 1C3 (AKR1C3): Implications for castration resistant prostate cancer

Barnard, M., Quanson, J. L., Mostaghel, E., Pretorius, E., Snoep, J. L. & Storbeck, K. H., Oct 2018, In : Journal of Steroid Biochemistry and Molecular Biology. 183, p. 192-201 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Castration
Androgens
Prostatic Neoplasms
Substrates
carbonyl reductase (NADPH)

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

A mechanistic computational model reveals that plasticity of CD4+ T cell differentiation is a function of cytokine composition and dosage

Puniya, B. L., Todd, R. G., Mohammed, A., Brown, D. M., Barberis, M. & Helikar, T., 2 Aug 2018, In : Frontiers in Physiology. 9, AUGUST, p. 1-18 18 p., 878.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Cell Differentiation
Cytokines
T-Lymphocytes
Phenotype
Transcription Factors

A practical guide for probiotics applied to the case of antibiotic-associated diarrhea in The Netherlands

Agamennone, V., Krul, C. A. M., Rijkers, G. & Kort, R., 6 Aug 2018, In : Bmc Gastroenterology. 18, p. 1-12 12 p., 103.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Probiotics
Netherlands
Diarrhea
Anti-Bacterial Agents
Lactobacillus rhamnosus

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

COSMIN guideline for systematic reviews of patient-reported outcome measures

Prinsen, C. A. C., Mokkink, L. B., Bouter, L. M., Alonso, J., Patrick, D. L., de Vet, H. C. W. & Terwee, C. B., 1 May 2018, In : Quality of Life Research. 27, 5, p. 1147-1157 11 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Guidelines
Patient Reported Outcome Measures
Expert Testimony
Routine Diagnostic Tests
Health

Expanding the reach of probiotics through social enterprises

Reid, G., Kort, R., Alvarez, S., Bourdet-Sicard, R., Benoit, V., Cunningham, M., Saulnier, D. M., Van Hylckama Vlieg, J. E. T., Verstraelen, H. & Sybesma, W., 25 May 2018, In : Beneficial Microbes. 9, 5, p. 707-715 9 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Probiotics
Social Media
Economic Models
Prebiotics
Information Dissemination

Feasibility of a novel on-site detection method for aflatoxin in maize flour from markets and selected households in Kampala, Uganda

Wacoo, A. P., Wendiro, D., Nanyonga, S., Hawumba, J. F., Sybesma, W. & Kort, R., Aug 2018, In : Toxins. 10, 8, p. 1-12 12 p., 327.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Aflatoxins
Uganda
Flour
Zea mays
Immunosensors

Formulation and stabilization of an Arthrobacter strain with good storage stability and 4-chlorophenol-degradation activity for bioremediation

Bjerketorp, J., Röling, W. F. M., Feng, X. M., Garcia, A. H., Heipieper, H. J. & Håkansson, S., Feb 2018, In : Applied Microbiology and Biotechnology. 102, 4, p. 2031-2040 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Arthrobacter
Environmental Biodegradation
Soil
Chlorophenols
Controlled Environment

Hydrogen peroxide production by lactobacilli promotes epithelial restitution during colitis

Singh, A. K., Hertzberger, R. Y. & Knaus, U. G., Jun 2018, In : Redox Biology. 16, June, p. 11-20 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Lactobacillus
Colitis
Hydrogen Peroxide
Inflammatory Bowel Diseases
Recovery

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

Integrative Systems Toxicology for Human Health

Sharma, R. P., 2018, 402 p.

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

Open Access
File

Lactobacillus rhamnosus probiotic food as a tool for empowerment across the value chain in Africa

Westerik, N., Kort, R., Sybesma, W. & Reid, G., 10 Jul 2018, In : Frontiers in Microbiology. 9, JULY, p. 1-6 6 p., 1501.

Research output: Contribution to JournalReview articleAcademicpeer-review

Open Access
Lactobacillus rhamnosus
Probiotics
Food
Streptococcus thermophilus
Translational Medical Research

libRCGA: a C library for real-coded genetic algorithms for rapid parameter estimation of kinetic models

Maeda, K., Boogerd, F. C. & Kurata, K., 13 Sep 2018, In : IPSJ Transactions on Bioinformatics. 11, p. 31-40 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Parameter estimation
Genetic algorithms
Kinetics
Constrained optimization
Stars

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

Mens en bacterie

Kort, R., 1 Nov 2018, Ontwikkelingen in de Geneeskunde 2018 . Rotterdam: Erasmus MC, p. 70-76 7 p.

Research output: Chapter in Book / Report / Conference proceedingChapterProfessional

File

Metabolic flexibility of a prospective bioremediator: Desulfitobacterium hafniense Y51 challenged in chemostats

Marozava, S., Vargas-López, R., Tian, Y., Merl-Pham, J., Braster, M., Meckenstock, R. U., Smidt, H., Röling, W. F. M. & Westerhoff, H. V., Jul 2018, In : Environmental Microbiology. 20, 7, p. 2652-2669 18 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Desulfitobacterium hafniense
Desulfitobacterium
Fumarates
chemostat
lactates

Microbial networks for bioremediation of chlorinated ethenes

Vargas Lopez, R., 2018, 214 p.

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

Open Access
File

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

NET works after all? Engineering robustness through diversity

Mondeel, T. D. G. A., Astrologo, S., Zhang, Y. & Westerhoff, H. V., 2018, In : IFAC-PapersOnLine. 51, 19, p. 128-137 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Thermodynamics
Kinetics
Engineers
Planets
Transcription

Oxygen Activation and Energy Conservation by Cytochrome c Oxidase

Wikström, M., Krab, K. & Sharma, V., 14 Mar 2018, In : Chemical Reviews. 118, 5, p. 2469-2490 22 p.

Research output: Contribution to JournalReview articleAcademicpeer-review

Open Access
Electron Transport Complex IV
Protons
Energy conservation
Chemical activation
Oxygen

Predictable irreversible switching between acute and chronic inflammation

Abudukelimu, A., Barberis, M., Redegeld, F. A., Sahin, N. & Westerhoff, H. V., 7 Aug 2018, In : Frontiers in Immunology. 9, AUGUST, p. 1-16 16 p., 1596.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Inflammation
Antigens
Fibroblasts
Phenotype
Antigen-Antibody Complex

Probiotic Fermented Foods: A scalable approach to promote gut health and improve nutrition

Milani, P., Parker, M. E., Kort, R. & Sybesma, W., 13 Aug 2018, In : Sight and Life. 32, 1, p. 53-61 9 p.

Research output: Contribution to JournalArticleProfessional

Open Access
File
Probiotics
Costs and Cost Analysis
Food
Health

Promising prebiotic candidate established by evaluation of lactitol, lactulose, raffinose, and oligofructose for maintenance of a Lactobacillus-dominated vaginal microbiota

Collins, S. L., McMillan, A., Seney, S., van der Veer, C., Kort, R., Sumarah, M. W. & Reid, G., Mar 2018, In : Applied and Environmental Microbiology. 84, 5, p. 1-15 15 p., e02200-17.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
lactitol
Raffinose
Lactulose
lactulose
Prebiotics

Rational cell culture optimization enhances experimental reproducibility in cancer cells

Wright Muelas, M., Ortega, F., Breitling, R., Bendtsen, C. & Westerhoff, H. V., 14 Feb 2018, In : Scientific Reports. 8, 1, p. 1-16 16 p., 3029.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Glutaminase
Cell Culture Techniques
Glutamine
Neoplasms
Metabolomics