Molecular Cell Biology

Research Output 1978 2019

2019

Neural plasticity and adult neurogenesis: the deep biology perspective

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

Research output: Contribution to JournalReview articleAcademicpeer-review

Open Access
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

Accelerating early antituberculosis drug discovery by creating mycobacterial indicator strains that predict mode of action

Boot, M., Commandeur, S., Subudhi, A. K., Bahira, M., Smith, T. C., Abdallah, A. M., van Gemert, M., Lelièvre, J., Ballell, L., Aldridge, B. B., Pain, A., Speer, A. & Bitter, W., Jul 2018, In : Antimicrobial Agents and Chemotherapy. 62, 7, e00083-18

Research output: Contribution to JournalArticleAcademicpeer-review

Drug Discovery
Anti-Bacterial Agents
Mycobacterium marinum
Dermatoglyphics
Tuberculosis

Acetaminophen reduces the protein levels of high affinity amino acid permeases and causes tryptophan depletion

Huseinovic, A., Dekker, S. J., Boogaard, B., Vermeulen, N. P. E., Kooter, J. M. & Vos, J. C., Oct 2018, In : Amino Acids. 50, 10, p. 1377-1390 14 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Amino Acid Transport Systems
Acetaminophen
Tryptophan
Proteins
Yeast

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

Altricial-precocial spectra in animal kingdom

Augustine, S., Lika, K. & Kooijman, S. A. L. M., 21 Apr 2018, In : Journal of sea research. p. 1-8 8 p.

Research output: Contribution to JournalArticleAcademicpeer-review

puberty
mammal
animal
mammals
bird

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

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

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

Bacterial secretion chaperones: The mycobacterial type VII case

Phan, T. H. & Houben, E. N. G., 1 Sep 2018, In : FEMS Microbiology Letters. 365, 18, p. 1-8 8 p., fny197

Research output: Contribution to JournalReview articleAcademicpeer-review

Open Access
Secretory Pathway
Protein Folding
Protein Transport
Mycobacterium
Cytosol

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

Biomass conversion at population level

Kooijman, S. A. L. M., 2018, Individual-Based Models and Approaches in Ecology: Populations, Communities and Ecosystems. CRC Press, p. 338-358 21 p.

Research output: Chapter in Book / Report / Conference proceedingChapterAcademicpeer-review

Biomass
Predator
Prey
Harvesting
Energy

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., 23 Aug 2018, In : Photosynthesis Research.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Photosynthesis
Chloroplasts
Algae
algae
chloroplasts

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., Tytgat, H., Swanenburg, J., de Kat Angelino-Bart, A., Schuren, F., Molenaar, D., Reid, G., de Vries, H. & Kort, R., 13 Oct 2018, In : bioRxiv. p. 1-30 30 p.

Research output: Contribution to JournalArticleAcademic

File
Microbiota
Genomics
Glycogen
Glycosylation
Lactobacillus

Comparing autotransporter β-domain configurations for their capacity to secrete heterologous proteins to the cell surface

Jong, W. S. P., Schillemans, M., ten Hagen-Jongman, C. M., Luirink, J. & van Ulsen, P., 7 Feb 2018, In : PLoS ONE. 13, 2, e0191622

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
IgA-specific serine endopeptidase
recombinant proteins
Membrane Proteins
Recombinant Proteins
Membranes

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 others Bonnet, 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

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

Display of recombinant proteins on bacterial outer membrane vesicles by using protein ligation

van den Berg van Saparoea, H. B., Houben, D., de Jonge, M. I., Jong, W. S. P. & Luirink, J., Apr 2018, In : Applied and Environmental Microbiology. 84, 8, p. 1-17 17 p., e02567-17

Research output: Contribution to JournalArticleAcademicpeer-review

hemoglobin
vesicle
Recombinant Proteins
recombinant proteins
Ligation

Drug toxicity profiling of a Saccharomyces cerevisiae deubiquitinase deletion panel shows that acetaminophen mimics tyrosine

Huseinovic, A., van Dijk, M., Vermeulen, N. P. E., van Leeuwen, F., Kooter, J. M. & Vos, J. C., Mar 2018, In : Toxicology in Vitro. 47, p. 259-268 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Acetaminophen
Drug-Related Side Effects and Adverse Reactions
Yeast
Toxicity
Saccharomyces cerevisiae

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

Environmental Mycobacterium avium subsp. hominissuis have a higher probability to act as a recipient in conjugation than clinical strains

Shoulah, S. A., Oschmann, A. M., Selim, A., Semmler, T., Schwarz, C., Kamal, E., Hamouda, F., Galila, E., Bitter, W. & Lewin, A., Jan 2018, In : Plasmid. 95, p. 28-35 8 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Mycobacterium avium
Plasmids
DNA Restriction-Modification Enzymes
Genes
Genomic Islands

EspH is a hypervirulence factor for Mycobacterium marinum and essential for the secretion of the ESX-1 substrates EspE and EspF

Phan, T. H., van Leeuwen, L. M., Kuijl, C., Ummels, R., van Stempvoort, G., Rubio-Canalejas, A., Piersma, S. R., Jiménez, C. R., van der Sar, A. M., Houben, E. N. G. & Bitter, W., 1 Aug 2018, In : Plos Pathogens. 14, 8, e1007247

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Mycobacterium marinum
Virulence
Zebrafish
Phagocytes
Infection

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

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

Fluorescent Benzothiazinone Analogues Efficiently and Selectively Label Dpre1 in Mycobacteria and Actinobacteria

Sommer, R., Neres, J., Piton, J., Dhar, N., van der Sar, A., Mukherjee, R., Laroche, T., Dyson, P. J., McKinney, J. D., Bitter, W., Makarov, V. & Cole, S. T., 16 Nov 2018, In : Acs chemical biology. 13, 11, p. 3184-3192 9 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Smegma
Corynebacterium glutamicum
Lead compounds
Nocardia
Fluorophores

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
Controlled Environment
Poisons

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

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

Immunization with Skp delivered on outer membrane vesicles protects mice against enterotoxigenic Escherichia coli CHALLENGE

Hays, M. P., Houben, D., Yang, Y., Luirink, J. & Hardwidge, P. R., 1 May 2018, In : Frontiers in Cellular and Infection Microbiology. 8, MAY, 132

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Enterotoxigenic Escherichia coli
Immunization
Glutathione Transferase
Membranes
Antigens

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

Tarazanova, M., Huppertz, T., Kok, J. & Bachmann, H., 1 Oct 2018, In : International Dairy Journal. 85, p. 73-78 6 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Surface Properties
milk curds
Cheese
cheeses
cells

Integrative Systems Toxicology for Human Health

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

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

Open Access
File

Ionophoric effects of the antitubercular drug bedaquiline

Hards, K., McMillan, D. G. G., Schurig-Briccio, L. A., Gennis, R. B., Lill, H., Bald, D. & Cook, G. M., 10 Jul 2018, In : Proceedings of the National Academy of Sciences of the United States of America. 115, 28, p. 7326-7331 6 p.

Research output: Contribution to JournalArticleAcademicpeer-review

File
bedaquiline
Antitubercular Agents
Adenosine Triphosphate
Escherichia coli
Proton-Motive Force

Is structural sensitivity a problem of oversimplified biological models? Insights from nested Dynamic Energy Budget models

Aldebert, C., Kooi, B. W., Nerini, D. & Poggiale, J-C., 7 Jul 2018, In : Journal of Theoretical Biology. 448, p. 1-8 8 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Biological Models
Budgets
Theoretical Models
Prediction Model
Sensitivity Analysis

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., 2018, In : IPSJ Transactions on Bioinformatics. 11, p. 31-40 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Linking cytochrome P450 enzymes from Mycobacterium tuberculosis to their cognate ferredoxin partners

Ortega Ugalde, S., de Koning, C. P., Wallraven, K., Bruyneel, B., Vermeulen, N. P. E., Grossmann, T. N., Bitter, W., Commandeur, J. N. M. & Vos, J. C., Nov 2018, In : Applied Microbiology and Biotechnology. 102, 21, p. 9231-9242 12 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Ferredoxins
Mycobacterium tuberculosis
Cytochrome P-450 Enzyme System
Oxidation-Reduction
Genome

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

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 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

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

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

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

Modelling, singular perturbation and bifurcation analyses of bitrophic food chains

Kooi, B. W. & Poggiale, J. C., 22 Apr 2018, In : Mathematical Biosciences. 301, p. 93-110 18 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Food Chain
Explosions
Singular Perturbation
food chain
Bifurcation