Molecular Cell Biology

Research Output

2018

On display: Autotransporter secretion and application

Van Ulsen, P., Zinner, K. M., Jong, W. S. P. & Luirink, J., 1 Sep 2018, In : FEMS Microbiology Letters. 365, 18, p. 1-10 10 p., fny165.

Research output: Contribution to JournalReview articleAcademicpeer-review

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

Photoswitching the Efficacy of a Small-Molecule Ligand for a Peptidergic GPCR: from Antagonism to Agonism

Gómez-Santacana, X., de Munnik, S. M., Vijayachandran, P., Da Costa Pereira, D., Bebelman, J. P. M., de Esch, I. J. P., Vischer, H. F., Wijtmans, M. & Leurs, R., 3 Sep 2018, In : Angewandte Chemie - International Edition. 57, 36, p. 11608-11612 5 p.

Research output: Contribution to JournalArticleAcademicpeer-review

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

Preliminary studies on ligand-based design and evaluation of new mycobacterial ATP synthase inhibitors

Sellamuthu, S., Asseri, A. H., Goojani, H. G., Nath, G. & Singh, S. K., Jan 2018, In : Current Drug Therapy. 13, 1, p. 56-73 18 p.

Research output: Contribution to JournalArticleAcademicpeer-review

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
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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

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

RD5-mediated lack of PE_PGRS and PPE-MPTR export in BCG vaccine strains results in strong reduction of antigenic repertoire but little impact on protection

Ates, L. S., Sayes, F., Frigui, W., Ummels, R., Damen, M. P. M., Bottai, D., Behr, M. A., van Heijst, J. W. J., Bitter, W., Majlessi, L. & Brosch, R., 18 Jun 2018, In : Plos Pathogens. 14, 6, e1007139.

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

Remote sensing of homochirality: A proxy for the detection of extraterrestrial life

Patty, C. H. L., Ten Kate, I. L., Sparks, W. B. & Snik, F., 2018, Chiral Analysis: Advances in Spectroscopy, Chromatography and Emerging Methods: Second Edition. Polavarapu, P. L. (ed.). 2nd ed. Elsevier Inc., p. 29-69 41 p.

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

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

Simulation of stimulation: Cytokine dosage and cell cycle crosstalk driving timing-dependent T cell differentiation

Barberis, M., Helikar, T. & Verbruggen, P., 2 Aug 2018, In : Frontiers in Physiology. 9, AUGUST, p. 1-17 17 p., 879.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Single-molecule imaging of Escherichia coli transmembrane proteins

Varadajan, A., Oswald, F. & Bollen, Y. J. M., 2018, Methods in Molecular Biology. Peterman, E. (ed.). Humana Press Inc, Vol. 1665. p. 135-144 10 p. (Methods in Molecular Biology; vol. 1665).

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

STRENDA DB: enabling the validation and sharing of enzyme kinetics data

Swainston, N., Baici, A., Bakker, B. M., Cornish-Bowden, A., Fitzpatrick, P. F., Halling, P., Leyh, T. S., O'Donovan, C., Raushel, F. M., Reschel, U., Rohwer, J. M., Schnell, S., Schomburg, D., Tipton, K. F., Tsai, M. D., Westerhoff, H. V., Wittig, U., Wohlgemuth, R. & Kettner, C., 1 Jun 2018, In : FEBS Journal. 285, 12, p. 2193-2204 12 p.

Research output: Contribution to JournalComment / Letter to the editorAcademic

Structural analysis of the interaction between the bacterial cell division proteins FTSQ and FTSB

Kureisaite-Ciziene, D., Varadajan, A., McLaughlin, S. H., Glas, M., Silva, A. M., Luirink, R., Mueller, C., Blaauwen, T. D., Grossmann, T. N., Luirink, J. & Löwe, J., 11 Sep 2018, In : mBio. 9, 5, p. 1-17 17 p., e01346-18.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Open Access
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Subsurface landfill leachate contamination affects microbial metabolic potential and gene expression in the Banisveld aquifer

Taş, N., Brandt, B. W., Braster, M., van Breukelen, B. M. & Röling, W. F. M., 1 Oct 2018, In : FEMS Microbiology Ecology. 94, 10, p. 1-12 12 p., fiy156.

Research output: Contribution to JournalArticleAcademicpeer-review

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

The AmP project: Comparing species on the basis of dynamic energy budget parameters

Marques, G. M., Augustine, S., Lika, K., Pecquerie, L., Domingos, T. & Kooijman, S. A. L. M., 9 May 2018, In : PLoS Computational Biology. 14, 5, e1006100.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

The anti-mycobacterial activity of the cytochrome bcc inhibitor Q203 can be enhanced by small-molecule inhibition of cytochrome bd.

Lu, P., Asseri, A. H. O., Kremer, M., Maaskant, J., Ummels, R., Lill, H. & Bald, D., 8 Feb 2018, In : Scientific Reports. 8, 1, 2625.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File

The Arabidopsis GORK K+-channel is phosphorylated by calcium-dependent protein kinase 21 (CPK21), which in turn is activated by 14-3-3 proteins

van Kleeff, P. J. M., Gao, J., Mol, S., Zwart, N., Zhang, H., Li, K. W. & de Boer, A. H., Apr 2018, In : Plant Physiology and Biochemistry. 125, p. 219-231 13 p.

Research output: Contribution to JournalArticleAcademicpeer-review

The novel antibiotic rhodomyrtone traps membrane proteins in vesicles with increased fluidity

Saeloh, D., Tipmanee, V., Jim, K. K., Dekker, M. P., Bitter, W., Voravuthikunchai, S. P., Wenzel, M. & Hamoen, L. W., 16 Feb 2018, In : Plos Pathogens. 14, 2, e1006876.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

The probiotic Lactobacillus rhamnosus for alleviation of helicobacter pylori-associated gastric pathology in East Africa

Westerik, N., Reid, G., Sybesma, W. & Kort, R., 14 Aug 2018, In : Frontiers in Microbiology. 9, AUGUST, p. 1-13 13 p., 1873.

Research output: Contribution to JournalReview articleAcademicpeer-review

Open Access

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

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

Tuberculous meningitis at the host-pathogen interface

van Leeuwen, L. M., 2018, 330 p.

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

Open Access
File

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

Utilization of Solid Waste as a Substrate for Production of Oil from Oleaginous Microorganisms

Laker, F., Agaba, A., Akatukunda, A., Gazet, R., Barasa, J., Nanyonga, S., Wendiro, D. & Wacoo, A. P., 16 May 2018, In : JOURNAL OF LIPIDS. 2018, p. 1 - 6 6 p., 1578720.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
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

A fluorescence-based reporter for monitoring expression of mycobacterial cytochrome bd in response to antibacterials and during infection.

Boot, M., JIm, K. K., Liu, T., Commandeur, S., Lu, P., Verboom, T., Lill, H., Bitter, W. & Bald, D., 2017, In : Scientific Reports. 7, 1, 10665.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

A metabolic core model elucidates how enhanced utilization of glucose and glutamine, with enhanced glutamine-dependent lactate production, promotes cancer cell growth: The WarburQ effect

Damiani, C., Colombo, R., Gaglio, D., Mastroianni, F., Pescini, D., Westerhoff, H. V., Mauri, G., Vanoni, M. & Alberghina, L., 1 Sep 2017, In : PLoS Computational Biology. 13, 9, e1005758.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

An ecoepidemic model with prey herd behavior and predator feeding saturation response on both healthy and diseased prey

Banerjee, M., Kooi, B. W. & Venturino, E., 21 Apr 2017, In : Mathematical Modelling of Natural Phenomena. 12, 2, p. 133-161 29 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Application of an E. coli signal sequence as a versatile inclusion body tag

Jong, W. S. P., Vikström, D., Houben, D., Berg van Saparoea, H. B., de Gier, J. W. & Luirink, J., 21 Mar 2017, In : Microbial Cell Factories. 16, 1, 50.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

A systematic review on the role of imiquimod in lentigo maligna and lentigo maligna melanoma: need for standardization of treatment schedule and outcome measures

Tio, D., van der Woude, J., Prinsen, C. A. C., Jansma, E. P., Hoekzema, R. & van Montfrans, C., 1 Apr 2017, In : Journal of the European Academy of Dermatology and Venereology. 31, 4, p. 616-624 9 p.

Research output: Contribution to JournalReview articleAcademicpeer-review

A Tonoplast P3B-ATPase Mediates Fusion of Two Types of Vacuoles in Petal Cells

Faraco, M., Li, Y., Li, S., Spelt, C., Di Sansebastiano, G. P., Reale, L., Ferranti, F., Verweij, W., Koes, R. & Quattrocchio, F. M., 20 Jun 2017, In : Cell Reports. 19, 12, p. 2413-2422 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Benzene degradation in a denitrifying biofilm reactor: activity and microbial community composition

van der Waals, M. J., Atashgahi, S., da Rocha, U. N., van der Zaan, B. M., Smidt, H. & Gerritse, J., 1 Jun 2017, In : Applied Microbiology and Biotechnology. 101, 12, p. 5175-5188 14 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Cell envelope stress in mycobacteria is regulated by the novel signal transduction ATPase IniR in response to trehalose

Boot, M., van Winden, V. J. C., Sparrius, M., van de Weerd, R., Speer, A., Ummels, R., Rustad, T., Sherman, D. R. & Bitter, W., Dec 2017, In : PLoS Genetics. 13, 12, p. e1007131 e1007131.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

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, 1691.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Circular spectropolarimetric sensing of chiral photosystems in decaying leaves

Patty, C. H. L., Visser, L. J. J., Ariese, F., Buma, W. J., Sparks, W. B., van Spanning, R. J. M., Röling, W. F. M. & Snik, F., 1 Mar 2017, In : Journal of Quantitative Spectroscopy and Radiative Transfer. 189, p. 303-311 9 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Combining bifurcation and sensitivity analysis for ecological models: Model analysis, and the allegory of the cave

van Voorn, GAK. & Kooi, B. W., 2017, In : European Physical Journal. Special Topics. 226, 9, p. 2101-2118 18 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File

Comment on the ecophysiology of the Greenland shark, Somniosus microcephalus

Kooijman, S. A. L. M., 2017, In : Polar Biology. 40, 12, p. 2429-2533 5 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File

Comparison of landfarming amendments to improve bioremediation of petroleum hydrocarbons in Niger Delta soils

Brown, D. M., Okoro, S., van Gils, J., van Spanning, R., Bonte, M., Hutchings, T., Linden, O., Egbuche, U., Bruun, K. B. & Smith, J. W. N., 15 Oct 2017, In : Science of the Total Environment. 596-597, p. 284-292 9 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Compositional Stability of the Bacterial Community in a Climate-Sensitive Sub-Arctic Peatland

Weedon, J. T., Kowalchuck, G. A., Aerts, M. A. P. A., Freriks, S., Roling, W. F. M. & van Bodegom, P. M., 2017, In : Frontiers in Microbiology. 8, MAR, 317.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

COSMIN Risk of Bias checklist for systematic reviews of Patient-Reported Outcome Measures

Mokkink, L. B., de Vet, H. C. W., Prinsen, C. A. C., Patrick, D. L., Alonso, J., Bouter, L. M. & Terwee, C. B., 19 Dec 2017, (Accepted/In press) In : Quality of Life Research. 27, 5, p. 1-9 9 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File

De microbemens: Het belang van het onzichtbare leven

Translated title of the contribution: Microbe man: The importance of invisible life Kort, R., 26 Sep 2017, Amsterdam: Athenaeum, Polak & Van Gennep. 240 p.

Research output: Book / ReportBook

Draft genome Sequences of 11 Lactococcus lactis subsp. cremoris strains

Wels, M., Backus, L., Boekhorst, J., Dijkstra, A., Beerthuyzen, M., Siezen, R. J., Bachmann, H. & van Hijum, S. A. F. T., 2017, In : Genome Announcements. 5, 11, p. e01739-16 e01739-16.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Draft genome sequences of 24 Lactococcus lactis strains

Backus, L., Wels, M., Boekhorst, J., Dijkstra, A. R., Beerthuyzen, M., Kelly, W. J., Siezen, R. J., van Hijum, S. A. F. T. & Bachmann, H., 2017, In : Genome Announcements. 5, 13, p. e01737-16 e01737-16.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Open Access
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