Molecular Cell Biology

Research Output 1978 2020

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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 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

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

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
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

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 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

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

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 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

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

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

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

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

Genome-Scale Metabolic Reconstruction of Acetobacter pasteurianus 386B, a Candidate Functional Starter Culture for Cocoa Bean Fermentation

Pelicaen, R., Gonze, D., Teusink, B., De Vuyst, L. & Weckx, S., 5 Dec 2019, In : Frontiers in Microbiology. 10, 2801.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Acetobacter
Fermentation
Genome
Growth
Genomics

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

Open Access
Semantics
Research Personnel
Biota
Biological Science Disciplines
Theoretical Models

Identifying indigenous practices for cultivation of wild saprophytic mushrooms: responding to the need for sustainable utilization of natural resources

Wendiro, D., Wacoo, A. P. & Wise, G., 12 Dec 2019, In : Journal of Ethnobiology and Ethnomedicine. 15, 1, 1 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Agaricales
mushrooms
natural resources
utilization
Musa

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

Open Access
starter cultures
Uganda
yogurt
probiotics
entrepreneurship

Inhibition of autotransporter biogenesis by small molecules

Steenhuis, M., Abdallah, A. M., de Munnik, S. M., Kuhne, S., Sterk, G. J., van den Berg van Saparoea, B., Westerhausen, S., Wagner, S., van der Wel, N. N., Wijtmans, M., van Ulsen, P., Jong, W. S. P. & Luirink, J., Jul 2019, In : Molecular Microbiology. 112, 1, p. 81-98 18 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Membrane Proteins
Virulence Factors
Libraries
Hemoglobins
Peptide Hydrolases

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

Open Access
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

Open Access
Population Model
RNA
Metabolism
cancer
Cancer

Interrogating the essential bacterial cell division protein FtsQ with fragments using target immobilized NMR screening (TINS)

Glas, M., Eiso, A. B., Hollander, J., Siegal, G., Luirink, J. & de Esch, I., 1 Aug 2019, In : International Journal of Molecular Sciences. 20, 15, 3684.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
cell division
Cell Division
affinity
Screening
screening

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

Open Access
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

Open Access
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

Microbial Communities in Sediments From Four Mildly Acidic Ephemeral Salt Lakes in the Yilgarn Craton (Australia) - Terrestrial Analogs to Ancient Mars

Aerts, J. W., van Spanning, R. J. M., Flahaut, J., Molenaar, D., Bland, P. A., Genge, M. J., Ehrenfreund, P. & Martins, Z., 6 May 2019, In : Frontiers in Microbiology. 10

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

Modelling the variable incorporation of aromatic amino acids in the tyrocidines and analogous cyclodecapeptides

Vosloo, J. A., Snoep, J. L. & Rautenbach, M., 1 Dec 2019, In : Journal of Applied Microbiology. 127, 6, p. 1665-1676 12 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Tyrocidine
Aromatic Amino Acids
Peptides
Competitive Binding
Brevibacillus

Natural Microbial Communities Can Be Manipulated by Artificially Constructed Biofilms

Rijavec, T., Zrimec, J., van Spanning, R. & Lapanje, A., 1 Jan 2019, In : Advanced Science. 1901408.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
biofilms
Biofilms
Corrosion
Biofouling
corrosion

New Insights Into Cinnamoyl Esterase Activity of Oenococcus oeni

Collombel, I., Melkonian, C., Molenaar, D., Campos, F. M. & Hogg, T., 8 Nov 2019, In : Frontiers in Microbiology. 10, p. 1-14 14 p., 2597.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Oenococcus
Esterases
Wine
Cell Extracts
Esters

On the role of vector modeling in a minimalistic epidemic model

Rashkov, P., Venturino, E., Aguiar, M., Stollenwerk, N. & Kooi, B. W., 1 Jan 2019, In : Mathematical Biosciences and Engineering. 16, 5, p. 4314-4338 25 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Epidemic Model
Virus Diseases
Infection
Ecology
Modeling