Molecular Cell Biology

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

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

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., 20 Feb 2019, In : Journal of Mathematical Biology. p. 1-22 22 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Canard
Predator-prey Model
Time Scales
Predator
Prey
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

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

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

Senegal
Probiotics
bacterial communities
Fermentation
probiotics

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

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. 010431

Research output: Contribution to JournalArticleAcademicpeer-review

Uganda
Microbiota
Child Development
Mothers
Education

Circular spectropolarimetric sensing of life

Patty, C. H. L., 2019, 174 p.

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

Open Access
File

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

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

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

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

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

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
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

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

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

starter cultures
Uganda
yogurt
probiotics
entrepreneurship

Integrated transcriptomic and proteomic analysis of pathogenic mycobacteria and their esx-1 mutants reveal secretion-dependent regulation of ESX-1 substrates and WhiB6 as a transcriptional regulator

Abdallah, A. M., Weerdenburg, E. M., Guan, Q., Ummels, R., Borggreve, S., Adroub, S. A., Malas, T. B., Naeem, R., Zhang, H., Otto, T. D., Bitter, W. & Pain, A., 2019, In : PLoS ONE. 14, 1, p. e0211003

Research output: Contribution to JournalArticleAcademicpeer-review

Mycobacterium
transcriptomics
Proteomics
proteomics
transcription factors

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

Population Model
RNA
Metabolism
cancer
Cancer

Intrinsic factor recognition promotes T helper 17/T helper 1 autoimmune gastric inflammation in patients with pernicious anemia

Troilo, A., Grassi, A., Petrone, L., Cianchi, F., Benagiano, M., Bella, C. D., Capitani, N., Bitetti, J., D'Elios, S., Tapinassi, S., Azzurri, A., Alnwaisri, H., Romagnoli, J., Bizzaro, N., Bergman, M., Baldari, C. T. & D'Elios, M. M., 23 Apr 2019, In : Oncotarget. 10, 30, p. 2921-2929 9 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Pernicious Anemia
Intrinsic Factor
Stomach
Inflammation
Clone Cells

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

Saccharomycetales
Proteins
Codon
Yeasts
Saccharomyces cerevisiae

Isoniazid bactericidal activity involves electron transport chain perturbation

Zeng, S., Soetaert, K., Ravon, F., Vandeput, M., Bald, D., Kauffmann, J. M., Mathys, V., Wattiez, R. & Fontaine, V., 1 Mar 2019, In : Antimicrobial Agents and Chemotherapy. e01841-18.

Research output: Contribution to JournalArticleAcademicpeer-review

Isoniazid
Electron Transport
Adenosine Triphosphate
Electron Transport Complex IV
NADH Dehydrogenase

Life in the slow lane? A dynamic energy budget model for the western swamp turtle, Pseudemydura umbrina

Arnall, S. G., Mitchell, N. J., Kuchling, G., Durell, B., Kooijman, S. A. L. M. & Kearney, M. R., Jan 2019, In : Journal of sea research. 143, p. 89-99 11 p.

Research output: Contribution to JournalArticleAcademicpeer-review

energy budget
turtle
swamp
energy
estivation

Metabolomics: From Method Development to System Biology

Krumpochova, P., 2019, 215 p.

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

Open Access
File

Mistaken identity: Paracetamol induces amino acid starvation through mimicry of tyrosine and changes ubiquitin homeostasis

Huseinovic, A., 2019, 202 p.

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

Open Access
File

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

Optimization of secretion and surface localization of heterologous OVA protein in mycobacteria by using LipY as a carrier 11 Medical and Health Sciences 1107 Immunology

Burggraaf, M. J., Ates, L. S., Speer, A., Van Der Kuij, K., Kuijl, C. & Bitter, W., 6 Mar 2019, In : Microbial Cell Factories. 18, p. 1-14 14 p., 44.

Research output: Contribution to JournalArticleAcademicpeer-review

Immunology
Ovalbumin
Antigens
Mycobacterium
Allergy and Immunology

Outer membrane vesicles engineered to express membrane-bound antigen program dendritic cells for cross-presentation to CD8 + T cells

Schetters, S. T. T., Jong, W. S. P., Horrevorts, S. K., Kruijssen, L. J. W., Engels, S., Stolk, D., Daleke-Schermerhorn, M. H., Garcia-Vallejo, J., Houben, D., Unger, W. W. J., den Haan, J. M. M., Luirink, J. & van Kooyk, Y., 1 Jun 2019, In : Acta Biomaterialia. 91, p. 248-257 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Cross-Priming
T-cells
Antigens
Dendritic Cells
Membranes

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

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

Aflatoxins
fermented foods
Probiotics
aflatoxins
probiotics

Protease and transmembrane domain of the type VII secretion mycosin protease determine system-specific functioning in mycobacteria

van Winden, V. J. C., Damen, M. P. M., Ummels, R., Bitter, W. & Houben, E. N. G., 28 Jan 2019, In : Journal of Biological Chemistry.

Research output: Contribution to JournalArticleAcademicpeer-review

Mycobacterium
Peptide Hydrolases
Mycobacterium marinum
Membranes
Stabilization

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

Stereoselective Chemoenzymatic Cascade Synthesis of the bis-THF Core of Acetogenins

van Lint, M. J., Hall, M., Faber, K., van Spanning, R. J. M., Ruijter, E. & Orru, R. V. A., 7 Feb 2019, In : European Journal of Organic Chemistry. 2019, 5, p. 1092-1101 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Acetogenins
epoxy compounds
Epoxy Compounds
Biological Products
cascades

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

The number of active metabolic pathways is bounded by the number of cellular constraints at maximal metabolic rates

de Groot, D. H., van Boxtel, C., Planque, R., Bruggeman, F. J. & Teusink, B., 11 Mar 2019, In : PLoS Computational Biology. 15, 3, p. 1-24 24 p., e1006858.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Metabolic Networks and Pathways
biochemical pathways
Pathway
enzyme
Fluxes

The role of low molecular weight thiols in Mycobacterium tuberculosis

Sao Emani, C., Gallant, J. L., Wiid, I. J. & Baker, B., 1 May 2019, In : Tuberculosis. 116, p. 44-55 12 p.

Research output: Contribution to JournalReview articleAcademicpeer-review

Mycobacterium tuberculosis
Sulfhydryl Compounds
Ergothioneine
Molecular Weight
Melanocyte-Stimulating Hormones

Three-dimensional bifurcation analysis of a predator-prey model with uncertain formulation

Aldebert, C., Kooi, B. W., Nerini, D., Gauduchon, M. & Poggiale, J. C., Feb 2019, In : SIAM journal on applied mathematics. 79, 1, p. 377-395 19 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Dimensional Analysis
Predator-prey Model
Bifurcation Analysis
Three-dimensional
Formulation

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

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 JournalArticleAcademicpeer-review

energy budget
energy
assimilation (physiology)
animals
animal
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