Staff Publications

Staff Publications

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    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

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The Antimicrobial Activity of the Essential Oil of Pistacia lentiscus var. Chia
Gkogka, E. ; Hazeleger, W.C. ; Posthumus, M.A. ; Beumer, R.R. - \ 2013
Journal of Essential Oil Bearing Plants 16 (2013)6. - ISSN 0972-060X - p. 714 - 729.
plant essential oils - tea tree oil - escherichia-coli o157-h7 - helicobacter-pylori - mastic gum - listeria-monocytogenes - chemical-composition - in-vitro - antibacterial activity - staphylococcus-aureus
The essential oil of the resin of Pistacia lentiscus var. Chia (mastic oil) was studied in vitro against a wide range of foodborne pathogenic and spoilage microorganisms with a diffusion and a dilution method. Furthermore its chemical composition was analyzed by means of Gas Chromatography-Mass Spectrometry (GC-MS) and the possibility of using the essential oil in food preservation was discussed. The Minimal Inhibitory Concentrations (MICs) of mastic oil were estimated for 6 species of bacteria (Bacillus cereus, Campylobacter jejuni, Clostridium perfringens, Escherichia coli, Salmonella Typhimurium, Staphylococcus aureus), 2 species of yeasts (Saccharomyces cerevisiae and Zygosaccharomyces bailii) and 3 species of fungi (Penicillium roquefortii, Aspergillus flavus and Eurotium amstelodami). GC-MS analysis revealed a chemotype dominated by monoterpenes, principally alpha-pinene and beta-myrcene comprising more than 90 % of the mastic oil. Both methods showed Cl. perfringens as the most susceptible microorganism followed by S. cerevisiae and Z. bailii. With the exception of C. jejuni, Gram-positive were found to be more susceptible to the essential oil than Gram-negative microorganisms and all fungi appeared very resistant to mastic oil. Based on the observed MICs, the contribution of mastic oil to the preservation of bakery/confectionary products at the amounts currently used for flavoring purposes is likely to be negligible.
Transcriptome signatures of class I and III stress response deregulation in Lactobacillus plantarum reveal pleiotropic adaptation
Bokhorst-van de Veen, H. van; Bongers, R.S. ; Wels, M. ; Bron, P.A. ; Kleerebezem, M. - \ 2013
Microbial Cell Factories 12 (2013)1. - ISSN 1475-2859 - 15 p.
gram-positive bacteria - heat-shock response - lactic-acid bacteria - bacillus-subtilis - listeria-monocytogenes - gastrointestinal-tract - low gc - streptococcus-pneumoniae - comparative genomics - helicobacter-pylori
Background - To cope with environmental challenges bacteria possess sophisticated defense mechanisms that involve stress-induced adaptive responses. The canonical stress regulators CtsR and HrcA play a central role in the adaptations to a plethora of stresses in a variety of organisms. Here, we determined the CtsR and HrcA regulons of the lactic acid bacterium Lactobacillus plantarum WCFS1 grown under reference (28°C) and elevated (40°C) temperatures, using ctsR, hrcA, and ctsR-hrcA deletion mutants. Results - While the maximum specific growth rates of the mutants and the parental strain were similar at both temperatures (0.33¿±¿0.02 h-1 and 0.34¿±¿0.03 h-1, respectively), DNA microarray analyses revealed that the CtsR or HrcA deficient strains displayed altered transcription patterns of genes encoding functions involved in transport and binding of sugars and other compounds, primary metabolism, transcription regulation, capsular polysaccharide biosynthesis, as well as fatty acid metabolism. These transcriptional signatures enabled the refinement of the gene repertoire that is directly or indirectly controlled by CtsR and HrcA of L. plantarum. Deletion of both regulators, elicited transcriptional changes of a large variety of additional genes in a temperature-dependent manner, including genes encoding functions involved in cell-envelope remodeling. Moreover, phenotypic assays revealed that both transcription regulators contribute to regulation of resistance to hydrogen peroxide stress. The integration of these results allowed the reconstruction of CtsR and HrcA regulatory networks in L. plantarum, highlighting the significant intertwinement of class I and III stress regulons. Conclusions - Taken together, our results enabled the refinement of the CtsR and HrcA regulatory networks in L. plantarum, illustrating the complex nature of adaptive stress responses in this bacterium
Promoting health and advancing development through improved housing in low-income settings
Haines, A. ; Bruce, N. ; Cairncross, S. ; Davies, M. ; Greenland, K. ; Hiscox, A.F. ; Lindsay, S. ; Lindsay, T. ; Satterthwaite, D. ; Wilkinson, P. - \ 2013
Journal of Urban Health 90 (2013)5. - ISSN 1099-3460 - p. 810 - 831.
indoor air-pollution - solid-fuel use - flying mosquitos diptera - risk-factors - vertical-distribution - cardiovascular-disease - meningococcal disease - developing-countries - helicobacter-pylori - mortality
There is major untapped potential to improve health in low-income communities through improved housing design, fittings, materials and construction. Adverse effects on health from inadequate housing can occur through a range of mechanisms, both direct and indirect, including as a result of extreme weather, household air pollution, injuries or burns, the ingress of disease vectors and lack of clean water and sanitation. Collaborative action between public health professionals and those involved in developing formal and informal housing could advance both health and development by addressing risk factors for a range of adverse health outcomes. Potential trade-offs between design features which may reduce the risk of some adverse outcomes whilst increasing the risk of others must be explicitly considered.
Detection of bacterial DNA in bile of cats with lymphocytic cholangitis
Otte, C.M.A. ; Pérez, O.N. ; Favier, R.P. ; Rothuizen, J. ; Penning, L.C. - \ 2012
Veterinary Microbiology 156 (2012)1-2. - ISSN 0378-1135 - p. 217 - 221.
16s ribosomal-rna - gradient gel-electrophoresis - polymerase-chain-reaction - helicobacter-pylori - pcr amplification - sp-nov. - jeotgalicoccus - disease - liver - populations
In this study, we have successfully used molecular methods based on the amplification of the 16S ribosomal RNA gene on feline bile samples to show that bile of cats with LC is not sterile. This is probably due to the fact that the inflammatory process in the biliary tree causes dilatations. As a result, bacteria can easily migrate from the intestines via the common bile duct. The diversity of species identified and the presence of Helicobacter spp. DNA in both patients and controls suggests that bacteriobilia is secondary to the disease and is not the cause of LC.
Structure, dynamics and domain organization of the repeat protein Cin1 from the apple scab fungus
Mesarich, C.H. ; Schmitz, M. ; Tremouilhac, P. ; McGillivray, D.J. ; Templeton, M.D. ; Dingley, A.J. - \ 2012
Biochimica et Biophysica Acta. Proteins & Proteomics 1824 (2012)10. - ISSN 1570-9639 - p. 1118 - 1128.
model-free approach - magnetic-resonance relaxation - nmr structure determination - ray solution scattering - torsion angle dynamics - cell-wall protein - venturia-inaequalis - zinc-fingers - helicobacter-pylori - backbone dynamics
Venturia inaequalis is a hemi-biotrophic fungus that causes scab disease of apple. A recently-identified gene from this fungus, cin1 (cellophane-induced 1), is up-regulated over 1000-fold in planta and considerably on cellophane membranes, and encodes a cysteine-rich secreted protein of 523 residues with eight imperfect tandem repeats of ~ 60 amino acids. The Cin1 sequence has no homology to known proteins and appears to be genus-specific; however, Cin1 repeats and other repeat domains may be structurally similar. An NMR-derived structure of the first two repeat domains of Cin1 (Cin1-D1D2) and a low-resolution model of the full-length protein (Cin1-FL) using SAXS data were determined. The structure of Cin1-D1D2 reveals that each domain comprises a core helix–loop–helix (HLH) motif as part of a three-helix bundle, and is stabilized by two intra-domain disulfide bonds. Cin1-D1D2 adopts a unique protein fold as DALI and PDBeFOLD analysis identified no structural homology. A 15N backbone NMR dynamic analysis of Cin1-D1D2 showed that a short stretch of the inter-domain linker has large amplitude motions that give rise to reciprocal domain–domain mobility. This observation was supported by SAXS data modeling, where the scattering length density envelope remains thick at the domain–domain boundary, indicative of inter-domain dynamics. Cin1-FL SAXS data models a loosely-packed arrangement of domains, rather than the canonical parallel packing of adjacent HLH repeats observed in a-solenoid repeat proteins. Together, these data suggest that the repeat domains of Cin1 display a “beads-on-a-string” organization with inherent inter-domain flexibility that is likely to facilitate interactions with target ligands.
Variety in vegetable and fruit consumption and the risk of gastric and esophageal cancer in the European prospective investigation into cancer and nutrition
Jeurnink, S.M. ; Büchner, F.L. ; Bueno-de Mesquita, H.B. ; Siersema, P.D. ; Boshuizen, H.C. ; Numans, M.E. ; Dahm, C.C. ; Overvad, K. ; Tjonneland, A. ; Roswall, N. ; Clavel-Chapelon, F. ; Boutron-Ruault, M.C. ; Morois, S. ; Kaaks, R. ; Teucher, B. ; Boeing, H. ; Buijsse, B. ; Trichopoulou, A. ; Benetou, V. ; Zylis, D. ; Palli, D. ; Sieri, S. ; Vineis, P. ; Tumino, R. ; Panico, S. ; Ocké, M.C. ; Peeters, P.H. ; Skeie, G. ; Brustad, M. ; Lund, E. ; Sanchez-Cantalejo, E. ; Navarro, C. ; Amiano, P. ; Ardanaz, E. ; Ramón Quirós, J. ; Hallmans, G. ; Johansson, I. ; Lindkvist, B. ; Regnér, S. ; Khaw, K.T. ; Wareham, N. ; Key, T.J. ; Slimani, N. ; Norat, T. ; Vergnaud, A.C. ; Romaguera, D. ; Gonzalez, C.A. - \ 2012
International Journal of Cancer 131 (2012)6. - ISSN 0020-7136 - p. E963 - E973.
epic-eurgast - epidemiologic evidence - helicobacter-pylori - physical-activity - diet diversity - cereal fiber - vitamin-c - stomach - adenocarcinomas - metaanalysis
Diets high in vegetables and fruits have been suggested to be inversely associated with risk of gastric cancer. However, the evidence of the effect of variety of consumption is limited. We therefore investigated whether consumption of a variety of vegetables and fruit is associated with gastric and esophageal cancer in the European Prospective Investigation into Cancer and Nutrition study. Data on food consumption and follow-up on cancer incidence were available for 452,269 participants from 10 European countries. After a mean follow-up of 8.4 years, 475 cases of gastric and esophageal adenocarcinomas (180 noncardia, 185 cardia, gastric esophageal junction and esophagus, 110 not specified) and 98 esophageal squamous cell carcinomas were observed. Diet Diversity Scores were used to quantify the variety in vegetable and fruit consumption. We used multivariable Cox proportional hazard models to calculate risk ratios. Independent from quantity of consumption, variety in the consumption of vegetables and fruit combined and of fruit consumption alone were statistically significantly inversely associated with the risk of esophageal squamous cell carcinoma (continuous hazard ratio per 2 products increment 0.88; 95% CI 0.79–0.97 and 0.76; 95% CI 0.62–0.94, respectively) with the latter particularly seen in ever smokers. Variety in vegetable and/or fruit consumption was not associated with risk of gastric and esophageal adenocarcinomas. Independent from quantity of consumption, more variety in vegetable and fruit consumption combined and in fruit consumption alone may decrease the risk of esophageal squamous cell carcinoma. However, residual confounding by lifestyle factors cannot be excluded
Protection against diarrhea associated with Giardia intestinalis is lost with Multi-Nutrient Supplementation: A Study in Tanzanian Children
Veenemans, J. ; Mank, T. ; Ottenhof, M. ; Baidjoe, A.Y. ; Mbugi, E.V. ; Demir, A.Y. ; Wielders, J.P.M. ; Savelkoul, H.F.J. ; Verhoef, J.C.M. - \ 2011
PLoS Neglected Tropical Diseases 5 (2011)6. - ISSN 1935-2727 - 10 p.
israeli bedouin infants - lamblia infection - protozoal parasites - helicobacter-pylori - natural-history - young-children - bangladesh - childhood - disease - consequences
Background - Asymptomatic carriage of Giardia intestinalis is highly prevalent among children in developing countries, and evidence regarding its role as a diarrhea-causing agent in these settings is controversial. Impaired linear growth and cognition have been associated with giardiasis, presumably mediated by malabsorption of nutrients. In a prospective cohort study, we aim to compare diarrhea rates in pre-school children with and without Giardia infection. Because the study was conducted in the context of an intervention trial assessing the effects of multi-nutrients on morbidity, we also assessed how supplementation influenced the relationship between Giardia and diarrhoea rates, and to what extent Giardia modifies the intervention effect on nutritional status. Methods and Findings - Data were collected in the context of a randomized placebo-controlled efficacy trial with 2×2 factorial design assessing the effects of zinc and/or multi-micronutrients on morbidity (n = 612; height-for-age z-score
AI-2 does not function as a quorum sensing molecule in Campylobacter jejuni during exponential growth in vitro
Holmes, K. ; Tavender, T.J. ; Winzer, K. ; Wells, J. ; Hardie, K. - \ 2009
BMC Microbiology 9 (2009). - ISSN 1471-2180 - 12 p.
guillain-barre-syndrome - to-cell communication - escherichia-coli - salmonella-typhimurium - vibrio-harveyi - helicobacter-pylori - gene-expression - neisseria-meningitidis - signaling molecule - reactive arthritis
Background - Campylobacter jejuni contains a homologue of the luxS gene shown to be responsible for the production of the signalling molecule autoinducer-2 (AI-2) in Vibrio harveyi and Vibrio cholerae. The aim of this study was to determine whether AI-2 acted as a diffusible quorum sensing signal controlling C. jejuni gene expression when it is produced at high levels during mid exponential growth phase. Results - AI-2 activity was produced by the parental strain NCTC 11168 when grown in rich Mueller-Hinton broth (MHB) as expected, but interestingly was not present in defined Modified Eagles Medium (MEM-a). Consistent with previous studies, the luxS mutant showed comparable growth rates to the parental strain and exhibited decreased motility halos in both MEM-a and MHB. Microarray analysis of genes differentially expressed in wild type and luxS mutant strains showed that many effects on mRNA transcript abundance were dependent on the growth medium and linked to metabolic functions including methionine metabolism. Addition of exogenously produced AI-2 to the wild type and the luxS mutant, growing exponentially in either MHB or MEM-a did not induce any transcriptional changes as analysed by microarray. Conclusion - Taken together these results led us to conclude that there is no evidence for the role of AI-2 in cell-to-cell communication in C. jejuni strain NCTC 11168 under the growth conditions used, and that the effects of the luxS mutation on the transcriptome are related to the consequential loss of function in the activated methyl cycle
Functional Characterization of Excision Repair and RecA-Dependent Recombinational DNA Repair in Campylobacter jejuni
Gaasbeek, E.J. ; Wal, F.J. van der; Putten, J.P.M. van; Boer, P. ; Graaf-van Bloois, L. van der; Boer, A.G. de; Vermaning, B.J. ; Wagenaar, J.A. - \ 2009
Journal of Bacteriology 191 (2009)12. - ISSN 0021-9193 - p. 3785 - 3793.
escherichia-coli - mismatch-repair - natural transformation - helicobacter-pylori - genome sequence - haemophilus-influenzae - replication forks - ultraviolet-light - genetic diversity - clinical isolate
The presence and functionality of DNA repair mechanisms in Campylobacter jejuni are largely unknown. In silico analysis of the complete translated genome of C. jejuni NCTC 11168 suggests the presence of genes involved in methyl-directed mismatch repair (MMR), nucleotide excision repair, base excision repair (BER), and recombinational repair. To assess the functionality of these putative repair mechanisms in C. jejuni, mutS, uvrB, ung, and recA knockout mutants were constructed and analyzed for their ability to repair spontaneous point mutations, UV irradiation-induced DNA damage, and nicked DNA. Inactivation of the different putative DNA repair genes did not alter the spontaneous mutation frequency. Disruption of the UvrB and RecA orthologues, but not the putative MutS or Ung proteins, resulted in a significant reduction in viability after exposure to UV irradiation. Assays performed with uracil-containing plasmid DNA showed that the putative uracil-DNA glycosylase (Ung) protein, important for initiation of the BER pathway, is also functional in C. jejuni. Inactivation of recA also resulted in a loss of natural transformation. Overall, the data indicate that C. jejuni has multiple functional DNA repair systems that may protect against DNA damage and limit the generation of genetic diversity. On the other hand, the apparent absence of a functional MMR pathway may enhance the frequency of on-and-off switching of phase variable genes typical for C. jejuni and may contribute to the genetic heterogeneity of the C. jejuni population.
Glycosyltransferase-catalyzed synthesis of bioactive oligosaccharides
Weijers, C.A.G.M. ; Franssen, M.C.R. ; Visser, G.M. - \ 2008
Biotechnology Advances 26 (2008)5. - ISSN 0734-9750 - p. 436 - 456.
engineered escherichia-coli - active natural-products - one-pot strategies - helicobacter-pylori - cholera-toxin - chemoenzymatic synthesis - campylobacter-jejuni - fucosyl-transferase - crystal-structure - cyclodextrin glucanotransferase
Mammalian cell surfaces are all covered with bioactive oligosaccharides which play an important role in molecular recognition events such as immune recognition, cell¿cell communication and initiation of microbial pathogenesis. Consequently, bioactive oligosaccharides have been recognized as a medicinally relevant class of biomolecules for which the interest is growing. For the preparation of complex and highly pure oligosaccharides, methods based on the application of glycosyltransferases are currently recognized as being the most effective. The present paper reviews the potential of glycosyltransferases as synthetic tools in oligosaccharide synthesis. Reaction mechanisms and selected characteristics of these enzymes are described in relation to the stereochemistry of the transfer reaction and the requirements of sugar nucleotide donors. For the application of glycosyltransferases, accepted substrate profiles are summarized and the whole-cell approach versus isolated enzyme methodology is compared. Sialyltransferase-catalyzed syntheses of gangliosides and other sialylated oligosaccharides are described in more detail in view of the prominent role of these compounds in biological recognition.
Role of ureolytic activity in Bacillus cereus nitrogen metabolism and acid survival
Mols, J.M. ; Abee, T. - \ 2008
Applied and Environmental Microbiology 74 (2008)8. - ISSN 0099-2240 - p. 2370 - 2378.
subtilis ureabc operon - emetic toxin - helicobacter-pylori - streptococcus-salivarius - yersinia-enterocolitica - anthracis pxo1 - low ph - expression - strains - growth
The presence and activities of urease genes were investigated in 49 clinical, food, and environmental Bacillus cereus isolates. Ten strains were shown to have urease genes, with eight of these strains showing growth on urea as the sole nitrogen source. Two of the urease-positive strains, including the sequenced strain ATCC 10987, could not use urea for growth, despite their capacities to produce active urease. These observations can be explained by the inability of the two strains to use ammonium as a nitrogen source. The impact of urea hydrolysis on acid stress resistance was subsequently assessed among the ureolytic B. cereus strains. However, none of the strains displayed increased fitness under acidic conditions or showed enhanced acid shock survival in the presence of urea. Expression analysis of urease genes in B. cereus ATCC 10987 revealed a low level of expression of these genes and a lack of pH-, nitrogen-, urea-, oxygen-, and growth phase-dependent modulation of mRNA transcription. This is in agreement with the low urease activity observed in strain ATCC 10987 and the other nine strains tested. Although a role for B. cereus ureolytic activity in acid survival cannot be excluded, its main role appears to be in nitrogen metabolism, where ammonium may be provided to the cells in nitrogen-limited, urea-containing environments
Riboflavin Biosynthesis Is Associated with Assimilatory Ferric Reduction and Iron Acquisition by Campylobacter Jejuni.
Gaskin, D.J.H. ; Holmes, K. ; Mulholland, F. ; Wells, J. - \ 2007
Applied and Environmental Microbiology 73 (2007)24. - ISSN 0099-2240 - p. 7819 - 7825.
gtp-cyclohydrolase ii - helicobacter-pylori - escherichia-coli - transporter ribu - gene-expression - genome sequence - major role - reductases - feob - metabolism
One of the pathways involved in the acquisition of the essential metal iron by bacteria involves the reduction of insoluble Fe3+ to soluble Fe2+, followed by transport of Fe2+ to the cytoplasm. Flavins have been implicated as electron donors in this poorly understood process. Ferrous iron uptake is essential for intestinal colonization by the important pathogen Campylobacter jejuni and may be of particular importance under low-oxygen conditions. In this study, the links among riboflavin biosynthesis, ferric reduction, and iron acquisition in C. jejuni NCTC11168 have been investigated. A riboflavin auxotroph was generated by inactivation of the ribB riboflavin biosynthesis gene (Cj0572), and the resulting isogenic ribB mutant only grew in the presence of exogenous riboflavin or the riboflavin precursor diacetyl but not in the presence of the downstream products flavin adenine dinucleotide and flavin mononucleotide. Riboflavin uptake was unaffected in the ribB mutant under iron-limited conditions but was lower in both the wild-type strain and the ribB mutant under iron-replete conditions. Mutation of the fur gene, which encodes an iron uptake regulator of C. jejuni, resulted in an increase in riboflavin uptake which was independent of the iron content of the medium, suggesting a role for Fur in the regulation of the as-yet-unknown riboflavin transport system. Finally, ferric reduction activity was independent of iron availability in the growth medium but was lowered in the ribB mutant compared to the wild-type strain and, conversely, increased in the fur mutant. Taken together, the findings confirm close relationships among iron acquisition, riboflavin production, and riboflavin uptake in C. jejuni
The FlgS/FlgR two-component signal transduction system regulates the fla regulon in Campylobacter jejuni
Wosten, M. ; Wagenaar, J.A. ; Putten, J.P.M. van - \ 2004
Journal of Biological Chemistry 279 (2004)16. - ISSN 0021-9258 - p. 16214 - 16222.
pseudomonas-aeruginosa - helicobacter-pylori - functional-characterization - molecular characterization - salmonella-typhimurium - transposon mutagenesis - flagellin expression - viscous environment - housekeeping genes - escherichia-coli
The human pathogen Campylobacter jejuni is a highly motile organism that carries a flagellum on each pole. The flagellar motility is regarded as an important trait in C. jejuni colonization of the intestinal tract, however, the knowledge of the regulation of this important colonization factor is rudimentary. We demonstrate by phosphorylation assays that the sensor FlgS and the response regulator FlgR form a two-component system that is on the top of the Campylobacter flagellum hierarchy. Phosphorylated FlgR is needed to activate RpoN-dependent genes of which the products form the hook-basal body filament complex. By real-time reverse transcriptase-PCR we identified that FlgS, FlgR, RpoN, and FliA belong to the early flagellar genes and are regulated by 70. FliD and the putative anti--factor FlgM are regulated by a 54- and 28-dependent promoters. Activation of the fla regulon is growth phase-dependent, a 100-fold rpoN mRNA reduction is seen in the early stationary phase compared with the early logarithmic phase. Whereas flaB transcription decreases, flaA transcription increases in early stationary phase. Our data show that the C. jejuni flagellar hierarchy largely differs from that of other bacteria. Phenotypical analysis revealed that unflagellated C. jejuni mutants grow three times faster in broth medium compared with wild-type bacteria. In vivo the C. jejuni flagella are needed to pass the gastrointestinal tract of chickens, but not to colonize the ceaca of the chicken.
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