List of works - Douwe Molenaar

A heat shock following electroporation induces highly efficient transformation of Corynebacterium glutamicum with xenogeneic plasmid DNA.

scientific article published in October 1999

A high-throughput cheese manufacturing model for effective cheese starter culture screening

scientific article published on 01 December 2009

Amino acid analysis using chromatography-mass spectrometry: An inter platform comparison study

scientific article

AmtB-mediated NH3 transport in prokaryotes must be active and as a consequence regulation of transport by GlnK is mandatory to limit futile cycling of NH4(+)/NH3.

scientific article

An additional PII in Escherichia coli: a new regulatory protein in the glutamine synthetase cascade

scientific article published in October 1995

An agr-like two-component regulatory system in Lactobacillus plantarum is involved in production of a novel cyclic peptide and regulation of adherence

scientific article published on August 2005

An alternative PII protein in the regulation of glutamine synthetase in Escherichia coli

scientific article published in July 1996

Analysis of growth of Lactobacillus plantarum WCFS1 on a complex medium using a genome-scale metabolic model

scientific article published on 24 October 2006

Availability of public goods shapes the evolution of competing metabolic strategies

scientific article published on 12 August 2013

Binding proteins enhance specific uptake rate by increasing the substrate-transporter encounter rate

scientific article published on 24 April 2015

Biochemical and genetic characterization of the membrane‐associated malate dehydrogenase (acceptor) from Corynebacterium glutamicum ⬇️

scientific article published on June 1, 1998

Biodiversity-based identification and functional characterization of the mannose-specific adhesin of Lactobacillus plantarum.

scientific article

Bioinformatics and systems biology: bridging the gap between heterogeneous student backgrounds

scientific article published on 19 April 2013

Characteristics and osmoregulatory roles of uptake systems for proline and glycine betaine in Lactococcus lactis.

scientific article published on September 1993

Complete genome sequence of Lactococcus lactis subsp. lactis KF147, a plant-associated lactic acid bacterium.

scientific article published on 26 March 2010

Continuous measurement of the cytoplasmic pH in Lactococcus lactis with a fluorescent pH indicator

scientific article published in November 1991

Convergence in probiotic Lactobacillus gut-adaptive responses in humans and mice

scientific article published on 27 May 2010

DNA micro-array-based identification of bile-responsive genes in Lactobacillus plantarum

scientific article published on 01 April 2006

DNA supercoiling depends on the phosphorylation potential in Escherichia coli.

scientific article

Defining control coefficients in non-ideal metabolic pathways

article

Development and application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adults

scientific article

Dichotomy in post-genomic microbiology.

scientific article published in August 2007

Effect of amino acid availability on vitamin B12 production in Lactobacillus reuteri

scientific article

Exploring metabolic pathway reconstruction and genome-wide expression profiling in Lactobacillus reuteri to define functional probiotic features

scientific article (publication date: 29 April 2011)

Expression of plant flavor genes in Lactococcus lactis.

scientific article published on 5 January 2007

Functional analysis of the role of CggR (central glycolytic gene regulator) in Lactobacillus plantarum by transcriptome analysis ⬇️

scientific article published on October 29, 2010

Functional identification in Lactobacillus reuteri of a PocR-like transcription factor regulating glycerol utilization and vitamin B12 synthesis

scientific article

Functions of the membrane-associated and cytoplasmic malate dehydrogenases in the citric acid cycle of Corynebacterium glutamicum.

scientific article

Gene expression analysis reveals a gene set discriminatory to different metals in soil

scientific article published on 4 February 2010

Genome instability in Lactobacillus rhamnosus GG.

scientific article

Genome-scale diversity and niche adaptation analysis of Lactococcus lactis by comparative genome hybridization using multi-strain arrays.

scientific article published on 21 February 2011

Genome-scale genotype-phenotype matching of two Lactococcus lactis isolates from plants identifies mechanisms of adaptation to the plant niche

scientific article

Genome-wide transposon mutagenesis indicates that Mycobacterium marinum customizes its virulence mechanisms for survival and replication in different hosts

scientific article published on 17 February 2015

Glutathione protects Lactococcus lactis against oxidative stress.

scientific article

High biodiversity in a benzene-degrading nitrate-reducing culture is sustained by a few primary consumers

scientific article published on 05 May 2021

High local substrate availability stabilizes a cooperative trait. ⬇️

scientific article published on 9 December 2010

How biochemical constraints of cellular growth shape evolutionary adaptations in metabolism.

scientific article

How fast-growing bacteria robustly tune their ribosome concentration to approximate growth-rate maximization

scientific article published on 26 March 2015

How to determine control of growth rate in a chemostat. Using metabolic control analysis to resolve the paradox

scientific article published on 01 August 1994

Identification of Lactobacillus plantarum genes modulating the cytokine response of human peripheral blood mononuclear cells.

scientific article

Identification of the sigmaB regulon of Bacillus cereus and conservation of sigmaB-regulated genes in low-GC-content gram-positive bacteria.

scientific article published on 6 April 2007

Improvement of Lactobacillus plantarum aerobic growth as directed by comprehensive transcriptome analysis

scientific article published on 6 June 2008

Introducing glutathione biosynthetic capability into Lactococcus lactis subsp. cremoris NZ9000 improves the oxidative-stress resistance of the host

scientific article published on 4 August 2006

Involvement of the mannose phosphotransferase system of Lactobacillus plantarum WCFS1 in peroxide stress tolerance.

scientific article published on 2 April 2010

Kinetic mechanism and specificity of the arginine-ornithine antiporter of Lactococcus lactis

scientific article published on 01 June 1989

Lactobacillus plantarum gene clusters encoding putative cell-surface protein complexes for carbohydrate utilization are conserved in specific gram-positive bacteria

scientific article published on 24 May 2006

Large intergenic cruciform-like supermotifs in the Lactobacillus plantarum genome.

scientific article published on 13 March 2009

Light-driven amino acid uptake in Streptococcus cremoris or Clostridium acetobutylicum membrane vesicles fused with liposomes containing bacterial reaction centers.

scientific article

Mechanism and energetics of a citrate-transport system of Klebsiella pneumoniae

scientific article published in January 1991

Mechanism of Na(+)-dependent citrate transport in Klebsiella pneumoniae ⬇️

scientific article published on August 1, 1992

Metabolic models for rational improvement of lactic acid bacteria as cell factories.

scientific article

Metabolic shifts: a fitness perspective for microbial cell factories

scientific article published on 31 August 2012

Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution.

scientific article

Mixed-culture transcriptome analysis reveals the molecular basis of mixed-culture growth in Streptococcus thermophilus and Lactobacillus bulgaricus

scientific article

Molecular assessment of bacterial vaginosis by Lactobacillus abundance and species diversity

scientific article

Molecular biology for flux control.

scientific article

Multidrug resistance in Lactococcus lactis: evidence for ATP-dependent drug extrusion from the inner leaflet of the cytoplasmic membrane.

scientific article

NarK is a nitrite-extrusion system involved in anaerobic nitrate respiration by Escherichia coli.

scientific article

Natural diversity and adaptive responses of Lactococcus lactis.

scientific article

Nonhierarchical Flux Regulation Exposes the Fitness Burden Associated with Lactate Production in Synechocystis sp. PCC6803.

scientific article

PanCGH: a genotype-calling algorithm for pangenome CGH data

scientific article

PhenoLink--a web-tool for linking phenotype to ~omics data for bacteria: application to gene-trait matching for Lactobacillus plantarum strains

scientific article

Phenotypic and genomic diversity of Lactobacillus plantarum strains isolated from various environmental niches

scientific article

Physiological responses to folate overproduction in Lactobacillus plantarum WCFS1.

scientific article

Protein costs do not explain evolution of metabolic strategies and regulation of ribosomal content: does protein investment explain an anaerobic bacterial Crabtree effect?

scientific article published on 9 May 2015

Proteome constraints reveal targets for improving microbial fitness in nutrient-rich environments

scientific article published on 01 April 2021

Proteome constraints reveal targets for improving microbial fitness in nutrient-rich environments

scientific article published on 16 October 2020

Proton motive force-driven and ATP-dependent drug extrusion systems in multidrug-resistant Lactococcus lactis.

scientific article

Public goods and metabolic strategies

scientific article

Regulatory phenotyping reveals important diversity within the species Lactococcus lactis.

scientific article published on 10 July 2009

Shifts in growth strategies reflect tradeoffs in cellular economics

scientific article published on 3 November 2009

Standardized assay medium to measure Lactococcus lactis enzyme activities while mimicking intracellular conditions

scientific article published on 21 October 2011

Systems biology of lactic acid bacteria: a critical review.

scientific article published on 30 August 2011

The SOS response of Listeria monocytogenes is involved in stress resistance and mutagenesis

scientific article

The efflux of a fluorescent probe is catalyzed by an ATP-driven extrusion system in Lactococcus lactis ⬇️

scientific article published on May 1, 1992

The pivotal regulator GlnB of Escherichia coli is engaged in subtle and context-dependent control

scientific article published on 7 May 2009

Thioredoxin reductase is a key factor in the oxidative stress response of Lactobacillus plantarum WCFS1.

scientific article published on 28 August 2007

Trehalose degradation and glucose efflux precede cell ejection during germination of heat-resistant ascospores of Talaromyces macrosporus

scientific article

Two homologous Agr-like quorum-sensing systems cooperatively control adherence, cell morphology, and cell viability properties in Lactobacillus plantarum WCFS1.

scientific article published on 19 September 2008

Unity in organisation and regulation of catabolic operons in Lactobacillus plantarum, Lactococcus lactis and Listeria monocytogenes

scientific article published on 01 April 2005

Using Lactococcus lactis for glutathione overproduction

scientific article published on 13 October 2004

Vesicle trafficking via the Spitzenkörper during hyphal tip growth in Rhizoctonia solani.

scientific article

Visualization for genomics: the Microbial Genome Viewer

scientific article published on 26 February 2004

Volatile compound fingerprinting of mixed-culture fermentations.

scientific article

List of works by Douwe Molenaar

A heat shock following electroporation induces highly efficient transformation of Corynebacterium glutamicum with xenogeneic plasmid DNA.

A high-throughput cheese manufacturing model for effective cheese starter culture screening

Amino acid analysis using chromatography-mass spectrometry: An inter platform comparison study

AmtB-mediated NH3 transport in prokaryotes must be active and as a consequence regulation of transport by GlnK is mandatory to limit futile cycling of NH4(+)/NH3.

An additional PII in Escherichia coli: a new regulatory protein in the glutamine synthetase cascade

An agr-like two-component regulatory system in Lactobacillus plantarum is involved in production of a novel cyclic peptide and regulation of adherence

An alternative PII protein in the regulation of glutamine synthetase in Escherichia coli

Analysis of growth of Lactobacillus plantarum WCFS1 on a complex medium using a genome-scale metabolic model

Availability of public goods shapes the evolution of competing metabolic strategies

Binding proteins enhance specific uptake rate by increasing the substrate-transporter encounter rate

Biochemical and genetic characterization of the membrane‐associated malate dehydrogenase (acceptor) from Corynebacterium glutamicum ⬇️

Biodiversity-based identification and functional characterization of the mannose-specific adhesin of Lactobacillus plantarum.

Bioinformatics and systems biology: bridging the gap between heterogeneous student backgrounds

Characteristics and osmoregulatory roles of uptake systems for proline and glycine betaine in Lactococcus lactis.

Complete genome sequence of Lactococcus lactis subsp. lactis KF147, a plant-associated lactic acid bacterium.

Continuous measurement of the cytoplasmic pH in Lactococcus lactis with a fluorescent pH indicator

Convergence in probiotic Lactobacillus gut-adaptive responses in humans and mice

DNA micro-array-based identification of bile-responsive genes in Lactobacillus plantarum

DNA supercoiling depends on the phosphorylation potential in Escherichia coli.

Defining control coefficients in non-ideal metabolic pathways

Development and application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adults

Dichotomy in post-genomic microbiology.

Effect of amino acid availability on vitamin B12 production in Lactobacillus reuteri

Exploring metabolic pathway reconstruction and genome-wide expression profiling in Lactobacillus reuteri to define functional probiotic features

Expression of plant flavor genes in Lactococcus lactis.

Functional analysis of the role of CggR (central glycolytic gene regulator) in Lactobacillus plantarum by transcriptome analysis ⬇️

Functional identification in Lactobacillus reuteri of a PocR-like transcription factor regulating glycerol utilization and vitamin B12 synthesis

Functions of the membrane-associated and cytoplasmic malate dehydrogenases in the citric acid cycle of Corynebacterium glutamicum.

Gene expression analysis reveals a gene set discriminatory to different metals in soil

Genome instability in Lactobacillus rhamnosus GG.

Genome-scale diversity and niche adaptation analysis of Lactococcus lactis by comparative genome hybridization using multi-strain arrays.

Genome-scale genotype-phenotype matching of two Lactococcus lactis isolates from plants identifies mechanisms of adaptation to the plant niche

Genome-wide transposon mutagenesis indicates that Mycobacterium marinum customizes its virulence mechanisms for survival and replication in different hosts

Glutathione protects Lactococcus lactis against oxidative stress.

High biodiversity in a benzene-degrading nitrate-reducing culture is sustained by a few primary consumers

High local substrate availability stabilizes a cooperative trait. ⬇️

How biochemical constraints of cellular growth shape evolutionary adaptations in metabolism.

How fast-growing bacteria robustly tune their ribosome concentration to approximate growth-rate maximization

How to determine control of growth rate in a chemostat. Using metabolic control analysis to resolve the paradox

Identification of Lactobacillus plantarum genes modulating the cytokine response of human peripheral blood mononuclear cells.

Identification of the sigmaB regulon of Bacillus cereus and conservation of sigmaB-regulated genes in low-GC-content gram-positive bacteria.

Improvement of Lactobacillus plantarum aerobic growth as directed by comprehensive transcriptome analysis

Introducing glutathione biosynthetic capability into Lactococcus lactis subsp. cremoris NZ9000 improves the oxidative-stress resistance of the host

Involvement of the mannose phosphotransferase system of Lactobacillus plantarum WCFS1 in peroxide stress tolerance.

Kinetic mechanism and specificity of the arginine-ornithine antiporter of Lactococcus lactis

Lactobacillus plantarum gene clusters encoding putative cell-surface protein complexes for carbohydrate utilization are conserved in specific gram-positive bacteria

Large intergenic cruciform-like supermotifs in the Lactobacillus plantarum genome.

Light-driven amino acid uptake in Streptococcus cremoris or Clostridium acetobutylicum membrane vesicles fused with liposomes containing bacterial reaction centers.

Mechanism and energetics of a citrate-transport system of Klebsiella pneumoniae

Mechanism of Na(+)-dependent citrate transport in Klebsiella pneumoniae ⬇️

Metabolic models for rational improvement of lactic acid bacteria as cell factories.

Metabolic shifts: a fitness perspective for microbial cell factories

Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution.

Mixed-culture transcriptome analysis reveals the molecular basis of mixed-culture growth in Streptococcus thermophilus and Lactobacillus bulgaricus

Molecular assessment of bacterial vaginosis by Lactobacillus abundance and species diversity

Molecular biology for flux control.

Multidrug resistance in Lactococcus lactis: evidence for ATP-dependent drug extrusion from the inner leaflet of the cytoplasmic membrane.

NarK is a nitrite-extrusion system involved in anaerobic nitrate respiration by Escherichia coli.

Natural diversity and adaptive responses of Lactococcus lactis.

Nonhierarchical Flux Regulation Exposes the Fitness Burden Associated with Lactate Production in Synechocystis sp. PCC6803.

PanCGH: a genotype-calling algorithm for pangenome CGH data

PhenoLink--a web-tool for linking phenotype to ~omics data for bacteria: application to gene-trait matching for Lactobacillus plantarum strains

Phenotypic and genomic diversity of Lactobacillus plantarum strains isolated from various environmental niches

Physiological responses to folate overproduction in Lactobacillus plantarum WCFS1.

Protein costs do not explain evolution of metabolic strategies and regulation of ribosomal content: does protein investment explain an anaerobic bacterial Crabtree effect?

Proteome constraints reveal targets for improving microbial fitness in nutrient-rich environments

Proteome constraints reveal targets for improving microbial fitness in nutrient-rich environments

Proton motive force-driven and ATP-dependent drug extrusion systems in multidrug-resistant Lactococcus lactis.

Public goods and metabolic strategies

Regulatory phenotyping reveals important diversity within the species Lactococcus lactis.

Shifts in growth strategies reflect tradeoffs in cellular economics

Standardized assay medium to measure Lactococcus lactis enzyme activities while mimicking intracellular conditions

Systems biology of lactic acid bacteria: a critical review.

The SOS response of Listeria monocytogenes is involved in stress resistance and mutagenesis

The efflux of a fluorescent probe is catalyzed by an ATP-driven extrusion system in Lactococcus lactis ⬇️

The pivotal regulator GlnB of Escherichia coli is engaged in subtle and context-dependent control

Thioredoxin reductase is a key factor in the oxidative stress response of Lactobacillus plantarum WCFS1.

Trehalose degradation and glucose efflux precede cell ejection during germination of heat-resistant ascospores of Talaromyces macrosporus

Two homologous Agr-like quorum-sensing systems cooperatively control adherence, cell morphology, and cell viability properties in Lactobacillus plantarum WCFS1.