Molecular Cell Biology

Research Output

2019

Vaginal microbes in sexual health and disease

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

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

File

Why big-bodied animal species cannot evolve a waste-to-hurry strategy

Augustine, S., Lika, K. & Kooijman, S. A. L. M., Jan 2019, In : Journal of sea research. 143, p. 18-26 9 p.

Research output: Contribution to JournalArticle

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 JournalArticle

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 JournalArticle

Open Access

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 JournalArticle

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 JournalArticle

Open Access

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 Abstract

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 JournalArticle

Open Access

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

Tarazanova, M., Huppertz, T., Kok, J. & Bachmann, H., Jul 2018, In : Microbial Biotechnology. 11, 4, p. 770-780 11 p.

Research output: Contribution to JournalArticle

Open Access

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 JournalArticle

Open Access

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

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 JournalArticle

Open Access

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 article

Open Access

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

Nordholt, N., 2018, 118 p.

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

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

Open Access

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

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 editor

Open Access

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 JournalArticle

Open Access
File

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 JournalArticle

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 JournalArticle

Open Access

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 JournalArticle

Open Access

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 JournalEditorial

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 JournalArticle

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., 13 Aug 2018, In : Plos Pathogens. 14, 8, p. 1-26 26 p., e1007247.

Research output: Contribution to JournalArticle

Open Access

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 JournalArticle

Open Access

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 JournalArticle

Open Access

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 JournalArticle

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 JournalArticle

Open Access

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 JournalArticle

Open Access

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 JournalArticle

Open Access

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 JournalArticle

Open Access

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 JournalArticle

Open Access

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 JournalArticle

Open Access

Integrative Systems Toxicology for Human Health

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

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

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 JournalArticle

File

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 JournalArticle

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 article

Open Access

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 JournalArticle

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 JournalArticle

Open Access

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 JournalArticle

Open Access

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 JournalArticle

Open Access

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 JournalArticle

Open Access

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 JournalArticle

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 survey

Microbial networks for bioremediation of chlorinated ethenes

Vargas Lopez, R., 2018, 214 p.

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

Open Access
File

Modelling, singular perturbation and bifurcation analyses of bitrophic food chains

Kooi, B. W. & Poggiale, J. C., 1 Jul 2018, In : Mathematical Biosciences. 301, p. 93-110 18 p.

Research output: Contribution to JournalArticle

Mutations in ppe38 block PE_PGRS secretion and increase virulence of Mycobacterium tuberculosis

Ates, L. S., Dippenaar, A., Ummels, R., Piersma, S. R., van der Woude, A. D., van der Kuij, K., Le Chevalier, F., Mata-Espinosa, D., Barrios-Payán, J., Marquina-Castillo, B., Guapillo, C., Jiménez, C. R., Pain, A., Houben, E. N. G., Warren, R. M., Brosch, R., Hernández-Pando, R. & Bitter, W., Feb 2018, In : NATURE MICROBIOLOGY. 3, 2, p. 181-188 8 p.

Research output: Contribution to JournalArticle

Mycobacteria employ two different mechanisms to cross the blood-brain barrier

van Leeuwen, L. M., Boot, M., Kuijl, C., Picavet, D. I., van Stempvoort, G., van der Pol, S. M. A., de Vries, H. E., van der Wel, N. N., van der Kuip, M., van Furth, A. M., van der Sar, A. M. & Bitter, W., Sep 2018, In : Cellular Microbiology. 20, 9, p. e12858 e12858.

Research output: Contribution to JournalArticle

Open Access