Molecular Cell Biology

Research Output 1978 2020

2020

Analysis of a predator–prey model with specific time scales:a geometrical approach proving the occurrence of canard solutions

Poggiale, J. C., Aldebert, C., Girardot, B. & Kooi, B. W., 2020, In : Journal of Mathematical Biology. p. 39-60 21 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Canard
Predator-prey Model
Time Scales
Predator
Prey

A new target for an old enemy: The Cytochrome P450 system from Mycobacterium tuberculosis

Ortega Ugalde, S., 2020, 204 p.

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

Open Access
File

A safe harbor can protect an endangered species from its predators

Banerjee, M., Kooi, B. & Venturino, E., 2020, (Accepted/In press) In : Ricerche di Matematica.

Research output: Contribution to JournalArticleAcademicpeer-review

endangered species
harbor
predator
bifurcation
Allee effect

Current Trends in Dynamical Systems in Biology and Natural Sciences

Aguiar, M. (ed.), Braumann, C. (ed.), Kooi, B., Pugliese, A. (ed.) & Stollenwerk, N., 21 Jun 2020, (Accepted/In press) Springer. (SEMA SIMAI Springer Series; vol. 21)

Research output: Book / ReportBook editingAcademic

Epidemiology
Ecology
Biology
Dynamical system
Recycling

Elementary Growth Modes provide a molecular description of cellular self-fabrication

de Groot, D. H., Hulshof, J., Teusink, B., Bruggeman, F. J. & Planqué, R., 1 Jan 2020, In : PLoS Computational Biology. 16, 1, e1007559.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Fabrication
phenotype
Growth
Phenotype
enzyme kinetics

Fermented foods in a global age: East meets West

Tamang, J. P., Cotter, P. D., Endo, A., Han, N. S., Kort, R., Liu, S. Q., Mayo, B., Westerik, N. & Hutkins, R., 3 Jan 2020, In : Comprehensive Reviews in Food Science and Food Safety. 19, 1, p. 184-217 34 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
fermented foods
Food
Food and Beverages
starter cultures
microorganisms

Long-term exposure of activated sludge in chemostats leads to changes in microbial communities composition and enhanced biodegradation of 4-chloroaniline and N-methylpiperazine

Poursat, B. A. J., van Spanning, R. J. M., Braster, M., Helmus, R., de Voogt, P. & Parsons, J. R., 1 Mar 2020, In : Chemosphere. 242, 125102.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Chemostats
chemostat
Sewage
Biodegradation
community composition

Microdroplet screening and selection for improved microbial production of extracellular compounds

van Tatenhove-Pel, R. J., Hernandez-Valdes, J. A., Teusink, B., Kuipers, O. P., Fischlechner, M. & Bachmann, H., Feb 2020, In : Current Opinion in Biotechnology. 61, p. 72-81 10 p.

Research output: Contribution to JournalReview articleAcademicpeer-review

Open Access
Fermentation
Screening
Emulsions
Throughput
Industry

Mutagenesis-Based Characterization and Improvement of a Novel Inclusion Body Tag

Jong, W. S. P., ten Hagen-Jongman, C. M., Vikström, D., Dontje, W., Abdallah, A. M., de Gier, J. W., Bitter, W. & Luirink, J., 10 Jan 2020, In : Frontiers in Bioengineering and Biotechnology. 7, 442.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Mutagenesis
Inclusion Bodies
Protein Sorting Signals
Agglomeration
Proteins

Sensing Extracellular Calcium – An Insight into the Structure and Function of the Calcium-Sensing Receptor (CaSR)

Chavez-Abiega, S., Mos, I., Centeno, P. P., Elajnaf, T., Schlattl, W., Ward, D. T., Goedhart, J. & Kallay, E., 2020, Calcium Signaling. Islam, S. (ed.). 2nd ed. Cham: Springer Nature Switzerland AG, p. 1031-1063 33 p. (Advances in Experimental Medicine and Biology; vol. 1131).

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

Calcium-Sensing Receptors
Calcium
Tissue
Secondary Hyperparathyroidism
Parathyroid Glands
Open Access
Growth
Metabolic Networks and Pathways
Saccharomyces cerevisiae
Theoretical Models
Adenosine Triphosphate

Trumping the Trumps: Addressing complexities through BioLogical rationality

Westerhoff, H. V., 17 Jan 2020, Amsterdam: Vrije Universiteit Amsterdam. 37 p.

Research output: Book / ReportValedictory speechProfessional

Open Access
File
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

Ample arsenite bio-oxidation activity in Bangladesh drinking water wells: A bonanza for bioremediation?

Hassan, Z., Sultana, M., Khan, S. I., Braster, M., Röling, W. F. M. & Westerhoff, H. V., Aug 2019, In : Microorganisms. 7, 8, p. 1-22 22 p., 246.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Water Wells
Environmental Biodegradation
Bangladesh
Drinking Water
Comamonas

Analysis of Arabidopsis thaliana HKT1 and Eutrema salsugineum/botschantzevii HKT1;2 Promoters in Response to Salt Stress in Athkt1:1 Mutant

Nawaz, I., Iqbal, M., Hakvoort, H. W. J., de Boer, A. H. & Schat, H., 1 Jun 2019, In : Molecular Biotechnology. 61, 6, p. 442-450 9 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Arabidopsis
Salts
Agricultural Crops
Cathode ray tubes
Level control

A new phase in DEB research

Augustine, S. & Kooijman, S. A. L. M., Jan 2019, In : Journal of sea research. 143, p. 1-7 7 p.

Research output: Contribution to JournalEditorialAcademicpeer-review

energy budget
energy
state of the art

A Photoswitchable Agonist for the Histamine H 3 Receptor, a Prototypic Family A G-Protein-Coupled Receptor

Hauwert, N. J., Mocking, T. A. M., Da Costa Pereira, D., Lion, K., Huppelschoten, Y., Vischer, H. F., De Esch, I. J. P., Wijtmans, M. & Leurs, R., 26 Mar 2019, In : Angewandte Chemie - International Edition. 58, 14, p. 4531-4535 5 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Histamine Agonists
G-Protein-Coupled Receptors
Histamine
Proteins
Chemical activation

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

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

Bacterial inclusion bodies function as vehicles for dendritic cell-mediated T cell responses.

Schetters, S. T. T., Jong, W., Kruijssen, L. J. W., van den Berg van Saparoea, B., Engels, S., Unger, W. W. J., Houben, D., den Haan, J. M. M., Luirink, J. & van Kooyk, Y., 8 Oct 2019, In : cellular & molecular immunology.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

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

Body size as emergent property of metabolism

Lika, K., Augustine, S. & Kooijman, S. A. L. M., Jan 2019, In : Journal of sea research. 143, p. 8-17 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

body size
metabolism
assimilation (physiology)
body mass
breathing

Chaperones and substrate specificity, type VII secretion systems reconnected

Phan, T. H., 2019, 194 p.

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

Open Access
File

Checks and balances in bacterial cell division

Den Blaauwen, T. & Luirink, J., 1 Jan 2019, In : mBio. 10, 1, e00149-19.

Research output: Contribution to JournalComment / Letter to the editorAcademic

Open Access
Peptidoglycan
Cell Division
Gram-Positive Bacteria
Proteins
Anti-Bacterial Agents

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., 3 Oct 2019, In : Astrobiology. 19, 10, p. 1221-1229 9 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Exobiology
extraterrestrial life
circular polarization
vegetation
polarization

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

Open Access
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

Comparative physiological energetics of Mediterranean and North Atlantic loggerhead turtles

Marn, N., Jusup, M., Catteau, S., Kooijman, S. A. L. M. & Klanjšček, T., Jan 2019, In : Journal of sea research. 143, p. 100-118 19 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Caretta caretta
energy budget
turtle
energetics
sexual maturity

Comprehensive characterization of the attenuated double auxotroph mycobacterium tuberculosisΔleudΔpanCD as an alternative to h37Rv

Mouton, J. M., Heunis, T., Dippenaar, A., Gallant, J. L., Kleynhans, L. & Sampson, S. L., 1 Jan 2019, In : Frontiers in Microbiology. 10, AUG, 1922.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Mycobacterium
Mycobacterium tuberculosis
Tuberculosis
Mycobacterium smegmatis
Latent Tuberculosis
Open Access
Cytochromes
Electron Transport
Mycobacterium tuberculosis
Proteins
Infection

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

Development and evaluation of a harmonized whole body physiologically based pharmacokinetic (PBPK) model for flutamide in rats and its extrapolation to humans

Sharma, R. P., Kumar, V., Schuhmacher, M., Kolodkin, A. & Westerhoff, H. V., 26 Nov 2019, In : Environmental Research. 182, p. 1-14 14 p., 108948.

Research output: Contribution to JournalArticleAcademicpeer-review

Flutamide
Pharmacokinetics
Extrapolation
Rats
drug

Differential Salt Sensitivity in Potato Cultivars: The Role of Na+ Tissue Distribution and Vacuolar Na+ Sequestration

Jaarsma, R., 2019, 113 p.

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

Open Access
File

Distinct requirements for tail-anchored membrane protein biogenesis in escherichia coli

Peschke, M., Le Goff, M., Koningstein, G. M., Vischer, N. O., Abdel-Rehim, A., High, S., Van Ulsen, P. & Luirink, J., 1 Jan 2019, In : mBio. 10, 5, e01580-19.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Membrane Proteins
Escherichia coli
Hydrophobic and Hydrophilic Interactions
Signal Recognition Particle
Membranes

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

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

Effects of antimony on enzymatic and non-enzymatic antioxidants in a metallicolous and a non-metallicolous population of Salvia spinosa L

Rajabpoor, S., Ghaderian, S. M. & Schat, H., 1 Nov 2019, In : Plant Physiology and Biochemistry. 144, p. 386-394 9 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Salvia
antimony
Antimony
Antioxidants
Ascorbate Peroxidases

Eighth annual conference of in VIVO planetary health: From challenges to opportunities

VIVO Planetary Health of the Worldwide Universities Network (WUN), 5 Nov 2019, In : International Journal of Environmental Research and Public Health. 16, 21, p. 1-62 62 p., 4302.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Health
Urban Renewal
Planets
Urbanization
Creativity

Erratum for den Blaauwen and Luirink, "Checks and Balances in Bacterial Cell Division"

den Blaauwen, T. & Luirink, J., 16 Apr 2019, In : mBio. 10, 2

Research output: Contribution to JournalComment / Letter to the editorAcademic

Open Access

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

Fitting multiple models to multiple data sets

Marques, G. M., Lika, K., Augustine, S., Pecquerie, L. & Kooijman, S. A. L. M., Jan 2019, In : Journal of sea research. 143, p. 48-56 9 p.

Research output: Contribution to JournalArticleAcademicpeer-review

energy budget
energy
prediction
methodology
parameter

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

Function, essentiality, and expression of cytochrome P450 enzymes and their cognate redox partners in Mycobacterium tuberculosis: are they drug targets?

Ortega Ugalde, S., Boot, M., Commandeur, J. N. M., Jennings, P., Bitter, W. & Vos, J. C., 2 May 2019, In : Applied Microbiology and Biotechnology. 103, 9, p. 3597-3614 18 p.

Research output: Contribution to JournalArticleAcademicpeer-review

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

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