Browsing by Subject "TRACT"

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  • Strobbe, Floortje; Benard, Melanie; Rossen, Noortje G.; de Vos, Willem M.; Kumar, Nitin; Lawley, Trevor D.; Zoetendal, Erwin G.; Hugenholtz, Floor; Ponsioen, Cyriel Y. (2021)
    We evaluated a novel 'protected' biopsy method to reliably ascertain the spatial distribution of the mucosa-adherent colonic microbiota. Apart from minor differences at genus level, overall similarities along the colon were high between the various areas, irrespective of protected or unprotected sampling.
  • Rooijers, Koos; Kolmeder, Carolin; Juste, Catherine; Dore, Joel; de Been, Mark; Boeren, Sjef; Galan, Pilar; Beauvallet, Christian; de Vos, Willem M.; Schaap, Peter J. (2011)
  • Ali, Abir Salwa; Gronberg, Malin; Federspiel, Birgitte; Scoazec, Jean-Yves; Hjortland, Geir Olav; Gronbaek, Henning; Ladekarl, Morten; Langer, Seppo W.; Welin, Staffan; Vestermark, Lene Weber; Arola, Johanna; Osterlund, Pia; Knigge, Ulrich; Sorbye, Halfdan; Grimelius, Lars; Janson, Eva Tiensuu (2017)
    Background Gastroenteropancreatic neuroendocrine carcinomas (GEP-NECs) are aggressive, rapidly proliferating tumors. Therapeutic response to current chemotherapy regimens is usually short lasting. The aim of this study was to examine the expression and potential clinical importance of immunoreactive p53 protein in GEP-NEC. Materials and methods Tumor tissues from 124 GEP-NEC patients with locally advanced or metastatic disease treated with platinum-based chemotherapy were collected from Nordic centers and clinical data were obtained from the Nordic NEC register. Tumor proliferation rate and differentiation were re-evaluated. All specimens were immunostained for p53 protein using a commercially available monoclonal antibody. Kaplan-Meier curves and cox regression analyses were used to assess progression-free survival (PFS) and overall survival (OS). Results All tumor tissues were immunoreactive for either one or both neuroendocrine biomarkers (chromogranin A and synaptophysin) and Ki67 index was >20% in all cases. p53 immunoreactivity was only shown in 39% of the cases and was not found to be a prognostic marker for the whole cohort. However, p53 immunoreactivity was correlated with shorter PFS in patients with colorectal tumors (HR = 2.1, p = 0.03) in a univariate analysis as well as to poorer PFS (HR = 2.6, p = 0.03) and OS (HR = 3.4, p = 0.02) in patients with colorectal tumors with distant metastases, a correlation which remained significant in the multivariate analyses. Conclusion In this cohort of GEP-NEC patients, p53 expression could not be correlated with clinical outcome. However, in patients with colorectal NECs, p53 expression was correlated with shorter PFS and OS. Further studies are needed to establish the role of immunoreactive p53 as a prognostic marker for GEP-NEC patients.
  • Kolmeder, Carolin A.; Salojarvi, Jarkko; Ritari, Jarmo; de Been, Mark; Raes, Jeroen; Falony, Gwen; Vieira-Silva, Sara; Kekkonen, Riina A.; Corthals, Garry L.; Palva, Airi; Salonen, Anne; de Vos, Willem M. (2016)
    Recent metagenomic studies have demonstrated that the overall functional potential of the intestinal microbiome is rather conserved between healthy individuals. Here we assessed the biological processes undertaken in-vivo by microbes and the host in the intestinal tract by conducting a metaproteome analysis from a total of 48 faecal samples of 16 healthy adults participating in a placebo-controlled probiotic intervention trial. Half of the subjects received placebo and the other half consumed Lactobacillus rhamnosus GG for three weeks (10(10) cfu per day). Faecal samples were collected just before and at the end of the consumption phase as well as after a three-week follow-up period, and were processed for microbial composition and metaproteome analysis. A common core of shared microbial protein functions could be identified in all subjects. Furthermore, we observed marked differences in expressed proteins between subjects that resulted in the definition of a stable and personalized microbiome both at the mass-spectrometry-based proteome level and the functional level based on the KEGG pathway analysis. No significant changes in the metaproteome were attributable to the probiotic intervention. A detailed taxonomic assignment of peptides and comparison to phylogenetic microarray data made it possible to evaluate the activity of the main phyla as well as key species, including Faecalibacterium prausnitzii. Several correlations were identified between human and bacterial proteins. Proteins of the human host accounted for approximately 14% of the identified metaproteome and displayed variations both between and within individuals. The individually different human intestinal proteomes point to personalized host-microbiota interactions. Our findings indicate that analysis of the intestinal metaproteome can complement gene-based analysis and contributes to a thorough understanding of the activities of the microbiome and the relevant pathways in health and disease.
  • Pensar, Johan; Puranen, Santeri; Arnold, Brian; MacAlasdair, Neil; Kuronen, Juri; Tonkin-Hill, Gerry; Pesonen, Maiju; Xu, Yingying; Sipola, Aleksi; Sanchez-Buso, Leonor; Lees, John A.; Chewapreechi, Claire; Bentley, Stephen D.; Harris, Simon R.; Parkhill, Julian; Croucher, Nicholas J.; Corander, Jukka (2019)
    Covariance-based discovery of polymorphisms under co-selective pressure or epistasis has received considerable recent attention in population genomics. Both statistical modeling of the population level covariation of alleles across the chromosome and model-free testing of dependencies between pairs of polymorphisms have been shown to successfully uncover patterns of selection in bacterial populations. Here we introduce a model-free method, SpydrPick, whose computational efficiency enables analysis at the scale of pan-genomes of many bacteria. SpydrPick incorporates an efficient correction for population structure, which adjusts for the phylogenetic signal in the data without requiring an explicit phylogenetic tree. We also introduce a new type of visualization of the results similar to the Manhattan plots used in genome-wide association studies, which enables rapid exploration of the identified signals of co-evolution. Simulations demonstrate the usefulness of our method and give some insight to when this type of analysis is most likely to be successful. Application of the method to large population genomic datasets of two major human pathogens, Streptococcus pneumoniae and Neisseria meningitidis, revealed both previously identified and novel putative targets of co-selection related to virulence and antibiotic resistance, highlighting the potential of this approach to drive molecular discoveries, even in the absence of phenotypic data.
  • Hyvärinen, I.; Hukkinen, M.; Kivisaari, R.; Parviainen, H.; Nordin, A.; Pakarinen, M. P. (2019)
    Aim: The incidence of pancreaticobiliary maljunction is thought to approximate 1:100,000 within Western populations. We aimed to study the significance of pancreaticobiliary maljunction in biliary tract malignancies. Methods: Medical records and magnetic resonance cholangiopancreatography images of 252 consecutive patients treated for biliary malignancies during 2005-2016 were reviewed. Patients with other known risk factors for biliary cancers (n = 27) were excluded. A common pancreaticobiliary channel measuring > 10 mm outside the duodenal wall was defined as pancreaticobiliary maljunction. Main Results: Of the 225 patients, a reliably interpretable preoperative magnetic resonance cholangiopancreatography was available for 73 (32%). Sex (47% vs 57% females) and age at diagnosis (67 vs 66 years) were similar among patients with or without an magnetic resonance cholangiopancreatography (p = ns for both). In magnetic resonance cholangiopancreatography, a pancreaticobiliary maljunction with a median length of 20 mm (range 10-23 mm) was identified in four patients (5.5%, 95% confidence interval 1.6-14), while none had evident accompanying biliary tree dilatation. Pancreaticobiliary maljunction patients were significantly more often females (100% vs 43%, p = 0.043), less likely to have intrahepatic bile duct cancer (0% vs 65%, p = 0.019) while more likely to have gallbladder cancer (75% vs 22%, p = 0.044) compared to the others. Age at diagnosis (66 vs 67 years, p = 0.898), extrahepatic bile duct cancer incidence (25% vs 13%, p = 0.453), and survival status at last follow-up (50% vs 42% alive, p = 1.000) were comparable between the subgroups. Conclusion: The prevalence of pancreaticobiliary maljunction is substantially higher in adults with biliary malignancies than one would expect based on its incidence, reinforcing the etiologic role of pancreaticobiliary maljunction especially in females with gallbladder cancer.
  • Murtola, Tiina; Alku, Paavo; Malinen, Jarmo; Geneid, Ahmed (2018)
    High-speed videoendoscopy, glottal inverse filtering, and physical modeling can be used to obtain complementary information about speech production. In this study, the three methodologies are combined to pursue a better understanding of the relationship between the glottal air flow and glottal area. Simultaneously acquired high-speed video and glottal inverse filtering data from three male and three female speakers were used. Significant correlations were found between the quasi-open and quasi-speed quotients of the glottal area (extracted from the high-speed videos) and glottal flow (estimated using glottal inverse filtering), but only the quasi-open quotient relationship could be represented as a linear model. A simple physical glottal flow model with three different glottal geometries was optimized to match the data. The results indicate that glottal flow skewing can be modeled using an inertial vocal/subglottal tract load and that estimated inertia within the glottis is sensitive to the quality of the data. Parameter optimisation also appears to favour combining the simplest glottal geometry with viscous losses and the more complex glottal geometries with entrance/exit effects in the glottis.
  • van Passel, Mark W. J.; Kant, Ravi; Zoetendal, Erwin G.; Plugge, Caroline M.; Derrien, Muriel; Malfatti, Stephanie A.; Chain, Patrick S. G.; Woyke, Tanja; Palva, Airi; de Vos, Willem M.; Smidt, Hauke (2011)
  • Buntin, Nirunya; de Vos, Willem M.; Hongpattarakere, Tipparat (2017)
    The adhesion ability to mucin varied greatly among 18 Lactobacillus plantarum isolates depending on their isolation habitats. Such ability remained at high level even though they were sequentially exposed to the gastrointestinal (GI) stresses. The majority of L. plantarum isolated from shrimp intestine and about half of food isolates exhibited adhesion ability (51.06-55.04%) about the same as the well-known adhesive L. plantarum 299v. Interestingly, five infant isolates of CIF17A2, CIF17A4, CIF17A5, CIF17AN2, and CIF17AN8 exhibited extremely high adhesion ranging from 62.69 to 72.06%. Such highly adhesive property correlating to distinctively high cell surface hydrophobicity was significantly weaken after pretreatment with LiCl and guanidine-HCl confirming the entailment of protein moiety. Regarding the draft genome information, all molecular structures of major cell wall-anchored proteins involved in the adhesion based on L. plantarum WCSF1, including lp_0964, lp_1643, lp_3114, lp_2486, lp_3127, and lp_3059 orthologues were detected in all isolates. Exceptionally, the gene-trait matching between yeast agglutination assay and the relevant mannose-specific adhesin (lp_1229) encoding gene confirmed the Msa absence in five infant isolates expressed distinctively high adhesion. Interestingly, the predicted flagellin encoding genes (fliC) firstly revealed in lp_1643, lp_2486, and lp_3114 orthologues may potentially contribute to such highly adhesive property of these isolates.