Jan Roelof van der Meer

Summary

Affiliation: University of Lausanne
Country: Switzerland

Publications

  1. pmc Characterisation of the putative effector interaction site of the regulatory HbpR protein from Pseudomonas azelaica by site-directed mutagenesis
    Christelle Vogne
    Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
    PLoS ONE 6:e16539. 2011
  2. pmc Cellular variability of RpoS expression underlies subpopulation activation of an integrative and conjugative element
    Ryo Miyazaki
    Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
    PLoS Genet 8:e1002818. 2012
  3. pmc Genome-Wide Analysis of Salicylate and Dibenzofuran Metabolism in Sphingomonas Wittichii RW1
    Edith Coronado
    Department of Fundamental Microbiology, University of Lausanne Lausanne, Switzerland
    Front Microbiol 3:300. 2012
  4. pmc Improved statistical analysis of low abundance phenomena in bimodal bacterial populations
    Friedrich Reinhard
    Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
    PLoS ONE 8:e78288. 2013
  5. pmc Mutant HbpR transcription activator isolation for 2-chlorobiphenyl via green fluorescent protein-based flow cytometry and cell sorting
    Siham Beggah
    Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, Quartier UNIL Sorge, 1015 Lausanne, Switzerland
    Microb Biotechnol 1:68-78. 2008
  6. pmc Tunable reporter signal production in feedback-uncoupled arsenic bioreporters
    Davide Merulla
    Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
    Microb Biotechnol 6:503-14. 2013
  7. pmc Community-wide plasmid gene mobilization and selection
    Vladimir Sentchilo
    Department of Fundamental Microbiology, University of Lausanne, Biophore, Quartier UNIL Sorge, Lausanne, Switzerland
    ISME J 7:1173-86. 2013
  8. doi request reprint Where microbiology meets microengineering: design and applications of reporter bacteria
    Jan Roelof van der Meer
    University of Lausanne, Department of Fundamental Microbiology, 1015 Lausanne, Switzerland
    Nat Rev Microbiol 8:511-22. 2010
  9. pmc Transcriptome analysis of the mobile genome ICEclc in Pseudomonas knackmussii B13
    Muriel Gaillard
    Department of Fundamental Microbiology, University of Lausanne, Switzerland
    BMC Microbiol 10:153. 2010
  10. pmc Stochasticity and bistability in horizontal transfer control of a genomic island in Pseudomonas
    Marco Minoia
    Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
    Proc Natl Acad Sci U S A 105:20792-7. 2008

Collaborators

Detail Information

Publications37

  1. pmc Characterisation of the putative effector interaction site of the regulatory HbpR protein from Pseudomonas azelaica by site-directed mutagenesis
    Christelle Vogne
    Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
    PLoS ONE 6:e16539. 2011
    ..This suggests that they are important for the process of effector activation, but not necessarily for effector specificity recognition...
  2. pmc Cellular variability of RpoS expression underlies subpopulation activation of an integrative and conjugative element
    Ryo Miyazaki
    Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
    PLoS Genet 8:e1002818. 2012
    ..Our results demonstrate how stochastic noise levels of global transcription factors can be transduced to a precise signaling cascade in a subpopulation of cells leading to ICE activation...
  3. pmc Genome-Wide Analysis of Salicylate and Dibenzofuran Metabolism in Sphingomonas Wittichii RW1
    Edith Coronado
    Department of Fundamental Microbiology, University of Lausanne Lausanne, Switzerland
    Front Microbiol 3:300. 2012
    ..wittichii RW1 perceives DBF as a stressor, whereas after longer exposure, the compound is recognized as a carbon source and metabolized using several pathways in parallel...
  4. pmc Improved statistical analysis of low abundance phenomena in bimodal bacterial populations
    Friedrich Reinhard
    Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
    PLoS ONE 8:e78288. 2013
    ..This study proposes a number of rational approximations to quantifying small subpopulations and offers an easy-to-use protocol for their implementation in the open source statistical software environment R. ..
  5. pmc Mutant HbpR transcription activator isolation for 2-chlorobiphenyl via green fluorescent protein-based flow cytometry and cell sorting
    Siham Beggah
    Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, Quartier UNIL Sorge, 1015 Lausanne, Switzerland
    Microb Biotechnol 1:68-78. 2008
    ..Our data thus demonstrate that a one-step in vitro 'evolutionary' adaptation of the HbpR protein can result in both enhancement and reduction of the native effector recognition...
  6. pmc Tunable reporter signal production in feedback-uncoupled arsenic bioreporters
    Davide Merulla
    Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
    Microb Biotechnol 6:503-14. 2013
    ..The higher expression levels and sensitivities of the response curves in the uncoupled circuits may be useful for improving field-test assays using arsenic bioreporters. ..
  7. pmc Community-wide plasmid gene mobilization and selection
    Vladimir Sentchilo
    Department of Fundamental Microbiology, University of Lausanne, Biophore, Quartier UNIL Sorge, Lausanne, Switzerland
    ISME J 7:1173-86. 2013
    ..This suggests that plasmids not only contribute to the adaptation of single individual prokaryotic species, but of the prokaryotic community as a whole under local selective conditions...
  8. doi request reprint Where microbiology meets microengineering: design and applications of reporter bacteria
    Jan Roelof van der Meer
    University of Lausanne, Department of Fundamental Microbiology, 1015 Lausanne, Switzerland
    Nat Rev Microbiol 8:511-22. 2010
    ..New trends for integrating synthetic biology and microengineering into the design of bacterial bioreporter platforms are also highlighted...
  9. pmc Transcriptome analysis of the mobile genome ICEclc in Pseudomonas knackmussii B13
    Muriel Gaillard
    Department of Fundamental Microbiology, University of Lausanne, Switzerland
    BMC Microbiol 10:153. 2010
    ..It provides the host with the capacity to degrade chloroaromatics and 2-aminophenol...
  10. pmc Stochasticity and bistability in horizontal transfer control of a genomic island in Pseudomonas
    Marco Minoia
    Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
    Proc Natl Acad Sci U S A 105:20792-7. 2008
    ..The finding that, despite apparent stochasticity, HGT rates can be modulated by external environmental conditions provides an explanation as to why selective conditions can promote DNA exchange...
  11. doi request reprint Intracellular excision and reintegration dynamics of the ICEclc genomic island of Pseudomonas knackmussii sp. strain B13
    Vladimir Sentchilo
    Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, Quartier UNIL Sorge, 1015 Lausanne, Switzerland
    Mol Microbiol 72:1293-306. 2009
    ..Recombination site analysis provided evidence to explain the characteristics of a larger number of genomic island insertions observed in a variety of strains, including Bordetella petri, Pseudomonas aeruginosa and Burkholderia...
  12. doi request reprint Bioreporters and biosensors for arsenic detection. Biotechnological solutions for a world-wide pollution problem
    Davide Merulla
    Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
    Curr Opin Biotechnol 24:534-41. 2013
    ..New emerging trends focus on genetic rewiring of reporter cells and/or integration into microdevices for more optimal detection. A number of case studies have shown realistic field applicability of bioreporter assays...
  13. doi request reprint Genome-wide transposon insertion scanning of environmental survival functions in the polycyclic aromatic hydrocarbon degrading bacterium Sphingomonas wittichii RW1
    Clémence Roggo
    Department of Fundamental Microbiology, University of Lausanne, 1015, Lausanne, Switzerland
    Environ Microbiol 15:2681-95. 2013
    ..Our results demonstrate the power of genome-wide transposon scanning approaches for analysis of complex traits...
  14. doi request reprint Development of bioreporter assays for the detection of bioavailability of long-chain alkanes based on the marine bacterium Alcanivorax borkumensis strain SK2
    Rekha Kumari
    Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
    Environ Microbiol 13:2808-19. 2011
    ..borkumensis. The fluorescence signal from flask assays could easily be captured with a normal digital camera, making such tests feasible to be carried out on, e.g. marine oil responder vessels in case of oil accidents...
  15. doi request reprint Development of a microfluidics biosensor for agarose-bead immobilized Escherichia coli bioreporter cells for arsenite detection in aqueous samples
    Nina Buffi
    Laboratory of Microsystems Engineering, École Polytechnique Fédérale Lausanne, EPFL STI LMIS, Lausanne, Switzerland
    Lab Chip 11:2369-77. 2011
    ..The time needed to reliably and reproducibly detect a concentration of 50 μg L(-1) was 75-120 minutes, and 120-180 minutes for a concentration of 10 μg L(-1)...
  16. doi request reprint A dual functional origin of transfer in the ICEclc genomic island of Pseudomonas knackmussii B13
    Ryo Miyazaki
    Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, Quartier UNIL Sorge, 1015 Lausanne, Switzerland
    Mol Microbiol 79:743-58. 2011
    ..This unique dual origin of transfer system might have provided an evolutionary advantage for distribution of ICE, a hypothesis that is supported by the fact that both oriT regions are conserved in several GEIs related to ICEclc...
  17. doi request reprint Development of a multistrain bacterial bioreporter platform for the monitoring of hydrocarbon contaminants in marine environments
    Robin Tecon
    Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
    Environ Sci Technol 44:1049-55. 2010
    ..We conclude that bacterium-based bioassays can be a suitable alternative for rapid on-site quantitative measurement of hydrocarbons in seawater...
  18. pmc A new large-DNA-fragment delivery system based on integrase activity from an integrative and conjugative element
    Ryo Miyazaki
    Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
    Appl Environ Microbiol 79:4440-7. 2013
    ..The integrase delivery system works in concert with existing vector systems and could thus be a powerful tool for synthetic constructions of new metabolic pathways in a variety of host bacteria. ..
  19. ncbi request reprint Examining chemical compound biodegradation at low concentrations through bacterial cell proliferation
    Kamila Czechowska
    Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, Quartier UNIL Sorge, 1015 Lausanne, Switzerland
    Environ Sci Technol 47:1913-21. 2013
    ..Yield approximations from the observed community growth was to some extent in agreement with standard OECD biodegradation test results for all, except one of the examined compounds...
  20. ncbi request reprint A new green fluorescent protein-based bacterial biosensor for analysing phenanthrene fluxes
    Robin Tecon
    Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
    Environ Microbiol 8:697-708. 2006
    ..A relationship between GFP production and phenanthrene mass transfer is proposed...
  21. pmc Host and invader impact of transfer of the clc genomic island into Pseudomonas aeruginosa PAO1
    Muriel Gaillard
    Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
    Proc Natl Acad Sci U S A 105:7058-63. 2008
    ..Absence of immediate detriment to the host may have contributed to the wide distribution of genomic islands like clc in bacterial genomes...
  22. pmc The clc element of Pseudomonas sp. strain B13, a genomic island with various catabolic properties
    Muriel Gaillard
    Department of Fundamental Microbiology, Bâtiment Biophore, University of Lausanne, CH 1015 Lausanne, Switzerland
    J Bacteriol 188:1999-2013. 2006
    ..This indicates the dynamic evolution of this type of element and the continued transition between elements with a more pathogenic character and those with catabolic properties...
  23. doi request reprint Use of flow cytometric methods for single-cell analysis in environmental microbiology
    Kamila Czechowska
    Department of Fundamental Microbiology, Bâtiment Biophore, University of Lausanne, 1015 Lausanne, Switzerland
    Curr Opin Microbiol 11:205-12. 2008
    ....
  24. doi request reprint Toxicity of triclosan, penconazole and metalaxyl on Caulobacter crescentus and a freshwater microbial community as assessed by flow cytometry
    David R Johnson
    Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
    Environ Microbiol 11:1682-91. 2009
    ..Because 10 nM of triclosan is within the range of concentrations observed in freshwater systems, these results also raise concerns about the risk of introducing triclosan into the environment...
  25. pmc Transcriptome and membrane fatty acid analyses reveal different strategies for responding to permeating and non-permeating solutes in the bacterium Sphingomonas wittichii
    David R Johnson
    Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
    BMC Microbiol 11:250. 2011
    ..The responses to these perturbations were then assessed and compared using a combination of growth assays, transcriptome profiling, and membrane fatty acid analyses...
  26. doi request reprint Cell differentiation to "mating bodies" induced by an integrating and conjugative element in free-living bacteria
    Friedrich Reinhard
    Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
    Curr Biol 23:255-9. 2013
    ..Given the low transfer frequencies of most ICE, we anticipate regulation by subpopulation differentiation to be widespread...
  27. doi request reprint Reversible and irreversible pollutant-induced bacterial cellular stress effects measured by ethidium bromide uptake and efflux
    Kamila Czechowska
    Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, Quartier UNIL Sorge, 1015 Lausanne, Switzerland
    Environ Sci Technol 46:1201-8. 2012
    ..The procedure developed here using bacterial ethidium bromide efflux pump activity may be a useful complement to screen sublethal toxicity effects of chemicals...
  28. doi request reprint Effect of two types of biosurfactants on phenanthrene availability to the bacterial bioreporter Burkholderia sartisoli strain RP037
    Robin Tecon
    Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
    Appl Microbiol Biotechnol 85:1131-9. 2010
    ..Our data therefore suggest that biosurfactant effects may be strongly dependent on the strain and type of biosurfactant...
  29. ncbi request reprint Information from single-cell bacterial biosensors: what is it good for?
    Robin Tecon
    Department of Fundamental Microbiology, Bâtiment Biophore, Quartier UNIL Sorge, University of Lausanne, CH 1015 Lausanne, Switzerland
    Curr Opin Biotechnol 17:4-10. 2006
    ..Serious attempts have been made to measure and interpret single-cell reporter gene expression and to understand variability in reporter expression among individuals in a population...
  30. pmc An operon of three transcriptional regulators controls horizontal gene transfer of the integrative and conjugative element ICEclc in Pseudomonas knackmussii B13
    Nicolas Pradervand
    Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
    PLoS Genet 10:e1004441. 2014
    ..Bioinformatic analysis showed that the mfsR-marR-tciR operon is unique for ICEclc and a few highly related ICE, whereas tciR orthologues occur more widely in a large variety of suspected ICE among Proteobacteria. ..
  31. pmc Life history analysis of integrative and conjugative element activation in growing microcolonies of Pseudomonas
    Friedrich Reinhard
    Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, Quartier UNIL Sorge, Lausanne, Switzerland
    J Bacteriol 196:1425-34. 2014
    ..Finally, we find that ICEclc active cells appear spatially at random in a microcolony, which may have been a selective advantage for maximizing ICEclc horizontal transmission to new recipient species. ..
  32. ncbi request reprint Analysis of bioavailable arsenic in rice with whole cell living bioreporter bacteria
    Barbara Baumann
    Department of Fundamental Microbiology, University of Lausanne, CH 1015 Lausanne, Switzerland
    J Agric Food Chem 55:2115-20. 2007
    ..Detection of mainly inorganic arsenic by the bacterial cells may have important advantages for toxicity assessment of rice consumption and would form a good complement to total chemical arsenic determination...
  33. doi request reprint A flow cytometry based oligotrophic pollutant exposure test to detect bacterial growth inhibition and cell injury
    Kamila Czechowska
    Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, Quartier UNIL Sorge, 1015 Lausanne, Switzerland
    Environ Sci Technol 45:5820-7. 2011
    ....
  34. doi request reprint Characterisation of microbial communities colonising the hyphal surfaces of arbuscular mycorrhizal fungi
    Tanja R Scheublin
    Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
    ISME J 4:752-63. 2010
    ..Analysis of amplified 16S rRNA genes indicated that in particular bacteria from the family of Oxalobacteraceae were highly abundant on AMF hyphae, suggesting that they may have developed specific interactions with the fungi...
  35. ncbi request reprint Ultrasensitive reporter protein detection in genetically engineered bacteria
    Mona Wells
    Laboratory of Soil Science, Swiss Federal Institute of Technology EPFL, CH 1015, Lausanne, Switzerland
    Anal Chem 77:2683-9. 2005
    ..Although we use arsenic inducible bioreporters here, the method is extensible to gfp/egfp bioreporters that are responsive to other substances...
  36. pmc Escherchia coli ribose binding protein based bioreporters revisited
    Artur Reimer
    Department of Fundamental Microbiology, University of Lausanne, Bâtiment Biophore, Quartier UNIL Sorge 1015 Lausanne, Switzerland
    Sci Rep 4:5626. 2014
    ..In contrast, the purified published TNT-binding variant did not bind TNT nor did TNT cause induction of the E. coli reporter system. ..