Changes of the bacterial composition in duodenal fluid from patients with liver cirrhosis and molecular bacterascites.

Small intestinal bacterial overgrowth and compositional changes of intestinal microbiota are pathomechanistic factors in liver cirrhosis leading to bacterial translocation and infectious complications. We analyzed the quantity and composition of duodenal bacterial DNA (bactDNA) in relation to bactDNA in blood and ascites of patients with liver cirrhosis. Duodenal fluid and corresponding blood and ascites samples from 103 patients with liver cirrhosis were collected. Non-liver disease patients (n = 22) served as controls. BactDNA was quantified by 16S-rRNA gene-based PCR. T-RFLP and 16S-rRNA amplicon sequencing were used to analyze bacterial composition. Duodenal bacterial diversity in cirrhosis was distinct to controls showing significantly higher abundances of Streptococcus, Enterococcus and Veillonella. Patients with bactDNA positive ascites revealed reduced spectrum of core microbiota with Streptococcus as key player of duodenal community and higher prevalence of Granulicatella proving presence of cirrhosis related intestinal dysbiosis. Regarding duodenal fluid bactDNA quantification, no significant differences were found between patients with cirrhosis and controls. Additionally, percentage of subjects with detectable bactDNA in blood did not differ between patients and controls. This study evaluated the diversity of bacterial DNA in different body specimens with potential implications on understanding how intestinal bacterial translocation may affect infectious complications in cirrhosis.

Detection of Inflammatory and Homeostasis Biomarkers after Selective Removal of Carious Dentin-An In Vivo Feasibility Study.

Deep carious dentin lesions induce an immune reaction within the pulp-dentin complex, leading to the release of cytokines, which might be suitable biomarkers in pulp diagnostics. This in vivo feasibility study determines the concentration of different cytokines after selective removal of carious infected dentin (SCR). In our methodology, paired samples are obtained from 21 patients-each of them with two deep carious lesions at posterior teeth without clinical symptoms. After SCR, lesions are randomly assigned to treatment strategy: Group 1 (11 patients): Carious dentin is covered either with BiodentineTM (n = 11) or gutta-percha (n = 11) before using the adhesive OptibondTM FL. Group 2 (10 patients): The adhesives ClearfilTM SE Protect Bond (n = 10) or ClearfilTM SE Bond 2 (n = 10) are directly applied. Prepared cavities are rinsed with phosphate buffered saline containing 0.05% Tween 20 (10X) for five minutes immediately after SCR (visit 1) and eight weeks later (visit 2). Rinsing liquid is regained. Concentrations of IL-1ß, IL-6, IL-10, C-reactive protein (CRP), TNF-α, IFN-γ, TIMP-1, -2, and MMP-7, -8, -9 are assessed by customized multiplex assays, evaluated with fluorescence analyzer. Non-parametric statistical analysis (Wilcoxon, Mann-Whitney U Test, p < 0.05) is performed (SPSS 25). Our results show that concentrations of CRP, IL-1ß, IL-6, TIMP-1, -2, and MMPs were detectable. Median concentrations of CRP, IL-1ß und IL-6 were significantly higher in visit 1 (304.9, 107.4, 3.8 pg/mL), compared to visit 2 (67.8, 2.3, 0.0 pg/mL; pi < 0.001). The study revealed that the non-invasive determination of cytokines from prepared dental cavities is possible.

Antibacterial effect of a brominated self-etch adhesive on carious dentin - An in vivo study.

OBJECTIVES: This in vivo study compared the antibacterial effect of a self-etch adhesive with and without the brominated monomer 12-methacryloyloxydodecyl-pyridinium bromide (MDPB) on carious dentin after selective caries removal. METHODS: 10 patients showing deep primary carious lesions at two posterior teeth without pulpal symptoms were included. At visit I, carious tissue was selectively removed and carious dentin was sampled with a sterile roundbur (Komet No. 18). One cavity was restored with composite (SDR, Ceram X; DENTSPLY DeTrey) using an MDPB-containing self-etch adhesive (Clearfil Protect Bond, Kuraray Noritake; PB). The other restoration served as a control (Clearfil SE Bond II, Kuraray Noritake; SE). At visit II after 8 weeks, carious dentin was sampled again. Bacterial growth in carious dentin was differentiated using microbial cultivation. Bacterial DNA from intact cells and cell-free DNA were quantified using 16S rRNA gene-based real-time PCR and the microbial community composition was analyzed by amplicon deep-sequencing. Wilcoxon test was applied for statistical analysis. RESULTS: Both treatments showed a decrease of intact bacterial cells in carious dentin at visit II compared to visit I (PB: visit I: 1.1*106, visit II: 1.7*105 (p = 0.03); SE: visit I: 1.1*107, visit II = 2.4*105 (p = 0.002)). No statistically significant reduction of cell-free bacterial DNA was detected (PB: visit I: 6.1*105, visit II: 1.6*105 (p = 0.08); SE: visit I: 5.3*105, visit II: 2.9*105 (p = 0.10)). The decrease of intact cell-derived (p = 0.371) and cell-free DNA (p = 0.455) did not differ significantly between PB and SE. Lactobacillus was most abundant within the microbial community at both visits. Alpha-diversity was not affected by treatment and samples showed high intra- and interindividual diversity. CONCLUSION AND CLINICAL SIGNIFICANCE: Both self-etch adhesives have an antibacterial effect due to a decrease of bacterial DNA after selective caries removal. However, the results do not reveal any additional antibacterial effect by MDPB. The study is registered with the German Clinical Trials Register (DRKS00011532).

Effect of a bioactive cement on the microbial community in carious dentin after selective caries removal - An in-vivo study.

OBJECTIVES: Selective caries removal in deep lesions means that soft carious affected dentin is left in the center of the cavity. Thus, using a tricalcium silicate cement Biodentine™ (Septodont, Paris) to seal the remaining soft dentin could have an antibacterial effect. This in-vivo study aimed to do quantitative and qualitative analyses on the bacterial composition within carious dentin before and after selective caries removal when applying Biodentine. METHODS: Eleven patients with deep primary carious lesions at two posterior teeth without pulpal symptoms were included. Carious dentin was selectively removed and sampled with a sterile round bur (Komet No. 18) at baseline visit and eight weeks later. On the first visit, one lesion per patient, the remaining carious dentin was covered with Biodentine before adhesive restoration. Caries samples were investigated by microbial cultivation, molecular analysis and amplicon deep-sequencing of 16S rRNA genes. Bacterial DNA from intact cells was differentiated from cell-free DNA by DNase degradation prior to DNA isolation. RESULTS: Reduction of cell-derived as well as cell-free bacterial DNA eight weeks after selective caries removal was significantly higher when Biodentine was applied. Lactobacillus was most abundant within the microbial community of deep carious dentin lesions at the first visit. After intervention with Biodentine application, Lactobacillus was diminished to a high degree. In general, the diversity in samples, as well as bacterial composition differed interindividually as well as intraindividually. CONCLUSION AND CLINICAL SIGNIFICANCE: Despite the heterogenous and diversity of microbial composition in patients, Biodentine can have beneficial antibacterial effects when applied to residual carious dentin, offering an alternative and safe treatment option. The study is officially registered with German Clinical Trials Register (DRKS00011067).

The role of ADGRE5/CD97 in human retinal pigment epithelial cell growth and survival.

Cell surface molecules of retinal pigment epithelial (RPE) cells participate in the pathogenesis of retinal diseases. In an attempt to identify cell surface proteins that play a role in RPE cell-cell interactions, we have considered studying the expression, regulation, and signaling of ADGRE5/CD97, an adhesion G protein-coupled receptor family member, based on its known adhesive function in other cell types such as leukocytes. We showed that RPE cells express three isoforms of CD97 and identified inflammation-related cytokines as important mediators regulating CD97 expression. Whereas TNF-α and IFN-γ upregulated CD97, TGF-ß decreased CD97 expression. Due to interaction with CD55, ARPE-19 cells firmly adhered to monocytes and T lymphocytes when overexpressing CD97, suggesting a role for CD97 in controlling leukocyte infiltration across the RPE-based blood-retinal barrier. CD97-mediated signaling acted synergistically with PDGF-BB and IFN-γ to regulate cell growth and survival, ensuring a cellular balance under inflammatory conditions. These findings suggest that CD97 on RPE cells serves to control leukocyte activation and trafficking in uveoretinal inflammation while at the same time regulating second messenger-mediated gene expression, cell growth, and survival.

Molecular characterization of intact cell-derived and cell-free bacterial DNA from carious dentine samples.

Microbial analyzes of carious dentine samples, especially in terms of interventions, represent a challenge due to difficulties in carious dentine sampling particularly with small bacterial DNA contents. Therefore, information about the quantitative reduction of bacterial DNA as well as microbial shifts and differences in diversity correlating with treatment interventions are scarce. In this study, carious dentine samples were collected in a first step in the course of a selective caries excavation at two different deep dentine caries lesions in three patients. Second, after selective caries excavation and sampling of carious dentine, an intervention was performed by applying dental materials onto the remaining carious dentine followed by a restoration of the study teeth with composite fillings. After 8 weeks, remaining carious dentine was sampled and analyzed as described above. The microbial community before and after therapy was analyzed by conventional culture compared to bacterial DNA analyses using 16S rRNA gene based real-time PCR and terminal restriction fragment length polymorphism (T-RFLP) for fingerprinting community changes within carious dentine samples. An ultra-pure workflow allowed the valid comparison of even small carious dentine samples with low DNA contents and the differentiation between intact cell-derived and cell-free bacterial DNA. Intra- and inter-subject related differences in the bacterial DNA content and its composition in deep dentine caries were determined considering the first visits. The ratio of cell-free bacterial DNA and DNA from intact cells decreased in two of three subjects included in the current study from visit 1 to visit 2 with the test substance (1:200 to 1:17) and the control substance (1:82 to 1:7). T-RFLP revealed changes in the bacterial diversity and composition shifts after treatment as well as between cell-free bacterial DNA and DNA derived from intact cells. The approach of differentiation and quantification of cell-free and intact cell-derived bacterial DNA is reasonable within the investigation of carious dentine samples, especially when considering the effect of an intervention. T-RFLP is principally suitable for the analysis of microbial shifts within carious dentine samples.

Loss of paraspinal muscle mass is a gender-specific consequence of cirrhosis that predicts complications and death.

BACKGROUND: Loss of skeletal muscle mass is a recognised complication with a prognostic impact in patients with cirrhosis. AIM: To explore in a retrospective analysis which muscle compartment most reliably predicts the occurrence of cirrhosis-associated complications and if there are gender-related differences. METHODS: 795 patients with cirrhosis listed for liver transplantation between 2001 and 2014 met the inclusion and exclusion criteria including an abdominal CT scan (±200). Controls were 109 patients who underwent a CT scan after polytrauma. The paraspinal muscles index (PSMI), the abdominal wall muscles index (AWMI) and its combination skeletal muscle index (SMI) were assessed at L3/L4, normalised to the height (cm2 /m2 ). RESULTS: 62.0% of patients with cirrhosis had alcoholic liver disease, and 70.6% were male. As compared to controls, a reduction in PSMI and SMI but not AWMI was associated with high model of end-stage liver disease (MELD) score, high Child-Pugh class, and the presence or history of cirrhosis-associated complications in males but not females. PSMI independently predicted the occurrence of bacterial infections (HR 0.932), spontaneous bacterial peritonitis (HR 0.901), hepatic encephalopathy (HR 0.961), and hepatorenal syndrome (HR 0.946) by multivariate Cox regression analysis in a gender-independent manner. Post-transplant survival was not associated with the PSMI; neither AWMI nor SMI predicted any clinical endpoints. CONCLUSIONS: This study links muscle wasting in patients with cirrhosis predominantly to males. However, the presence of a low PSMI mass is a gender-independent predictor of developing cirrhosis-associated complications and death. Scores combining the MELD with muscle parameters should be re-validated by utilizing the PSMI.

Molecular quantification and differentiation of Candida species in biological specimens of patients with liver cirrhosis.

Patients with liver cirrhosis are susceptible to fungal infections. Due to low sensitivity of culture-based methods, we applied a real-time PCR assay targeting the 18S rRNA gene in combination with direct sequencing and terminal-restriction fragment length polymorphism (T-RFLP) in order to establish a novel tool to detect fungal DNA and to quantify and differentiate Candida DNA, also in polyfungal specimens. In total, 281 samples (blood n = 135, ascites n = 92, duodenal fluid n = 54) from 135 patients with liver cirrhosis and 52 samples (blood n = 26, duodenal fluid n = 26) from 26 control patients were collected prospectively. Candida DNA was quantified in all samples. Standard microbiological culture was performed for comparison. Blood and ascites samples, irrespective of the patient cohort, showed a method-independent low fungal detection rate of approximately 1%, and the Candida DNA content level did not exceed 3.0x10(1) copies ml-1 in any sample. In contrast, in duodenal fluid of patients with liver cirrhosis high fungal detection rates were discovered by using both PCR- and culture-based techniques (81.5% vs. 66.7%; p = 0.123) and the median level of Candida DNA was 3.8x10(5) copies ml-1 (2.3x10(2)-6.3x10(9)). In cirrhosis and controls, fungal positive culture results were confirmed by PCR in 96% and an additional amount of 44% of culture negative duodenal samples were PCR positive. Using T-RFLP analysis in duodenal samples, overall 85% of results from microbial culture were confirmed and in 75% of culture-negative but PCR-positive samples additional Candida species could be identified. In conclusion, PCR-based methods and subsequent differentiation of Candida DNA might offer a quick approach to identifying Candida species without prior cultivation.

Absolute quantification of microparticles by flow cytometry in ascites of patients with decompensated cirrhosis: a cohort study.

BACKGROUND: Microparticles (MPs) are small (<1 µm) cell membrane-derived vesicles that are formed in response to cellular activation or early stages of apoptosis. Increased plasma MP levels have been associated with liver disease severity. Here we investigated the clinical impact of ascites MPs in patients with decompensated liver cirrhosis. METHODS: Ascites and blood samples of 163 patients with cirrhosis (ascites n = 163, blood n = 31) were collected between February 2011 and December 2012. MPs were obtained from ascites and from blood by two-step ultracentrifugation and quantified by flow cytometry. Quantitative absolute MP levels were correlated with clinical and laboratory baseline parameters as well as patient outcomes. Ascites microparticles were stained with antibodies against CD66b (neutrophils) and CD3 (lymphocytes) in a subgroup of 60 matched patients. RESULTS: MPs were detected in all ascites and blood samples. Absolute ascites MP levels correlated with blood levels (r = 0.444, p = 0.011). Low ascites MP levels (<488.4 MP/µL) were associated with a poor 30-day survival probability (<488.4 MP/µL 71.1% vs. >488.4 MP/µL 94.7%, log rank p = 0.001) and such patients had a higher relative amount of ascites microparticles derived from neutrophils and lymphocytes. Low levels of ascites MPs, high MELD score and antibiotic treatment were independent risk factors for death within 30 days. CONCLUSIONS: Ascites MP levels predict short-term survival along with the liver function in patients with decompensated cirrhosis. Further studies which evaluate ascites MPs as disease specific biomarker with a validation cohort and which investigate its underlying mechanisms are needed. Neutrophils and lymphocytes contributed more frequently to the release of microparticles in patients with low ascites levels, possibly indicating an immune activation in this cohort.

Ascites' neutrophil function is significantly impaired in patients with decompensated cirrhosis but can be restored by autologous plasma incubation.

Systemic immune cell dysfunction is a typical feature of liver diseases and increases the risk of bacterial infection, especially spontaneous bacterial peritonitis. We evaluated functional properties of neutrophil granulocytes in blood and ascites of patients both with and without decompensated cirrhosis. We collected blood and ascites samples from 63 patients with cirrhosis and eight without cirrhosis. Phagocytosis activity (PA) and oxidative burst activity (OBA) were evaluated after ex vivo stimulation with E. coli, while fluorescence signals were measured by flow cytometry. Ascites' neutrophil function tests were repeated after incubation with autologous plasma. Ascites' neutrophils showed an impaired PA and OBA (median blood PA 98.1% (86.8-99.8) vs. ascites' PA 50.5% (0.4-97.3), p < 0.0001; median blood OBA 98.7% (27.5-100) vs. ascites' OBA 27.5% (0.3-96.7), p < 0.0001). Patients with non-cirrhotic ascites showed higher PA but equally suppressed OBA. Ascites' neutrophil function could be partially restored after incubation with autologous plasma (median increase PA: 22.5% (-49.7 - +93.2), p = 0.002; OBA: 22.8% (-10.4 - +48.8), p = 0.002). Ascites' neutrophils of patients with cirrhosis are functionally impaired, but could be partially restored after incubation with plasma. Further investigations are needed to identify the factors in ascites that are associated with neutrophils' function.

Detection of molecular bacterascites in decompensated cirrhosis defines a risk with decreased survival.

BACKGROUND: The prognostic relevance of bacterial DNA (bactDNA) detection in ascitic fluid of patients with cirrhosis is still under debate. Using quantitative real-time PCR with broad-range primers targeting the V3 and V4 variable region of the 16S rRNA gene, we measured bactDNA concentrations in patients with and without leukocytic ascites and evaluated the impact on short-term survival. PATIENTS AND METHODS: Ascites samples from 173 patients with decompensated cirrhosis were consecutively collected between February 2011 and December 2012. BactDNA-positive ascites samples were sequenced and chromatograms were identified using RipSeq. Clinical data collection and survival analyses were carried out retrospectively and correlated with ascites bactDNA levels. RESULTS: BactDNA was detected qualitatively with a similar frequency in both nonleukocytic and leukocytic ascites [40% (57/144) and 43.5% (10/23), respectively; P=0.724]. However, the median bactDNA level was significantly higher in leukocytic ascites than in nonleukocytic ascites (1.2×10 vs. 5.7×10 copies/ml; P=0.008). Patients' survival was associated significantly with bactDNA level. The 30-day and 180-day survival was reduced if bactDNA was above the quantification limit of 520 copies/ml (84 and 63% vs. 72 and 43%, respectively; P<0.05) and worst if bactDNA was above 5000 copies/ml. The bacterial spectrum was dominated by Gram-positive strains as shown by direct sequencing. CONCLUSION: BactDNA quantification in ascitic fluid samples using culture-independent 16S rRNA gene-based methods seems to be an interesting approach to identify patients at risk of reduced survival. Our study warrants further evaluation of antibiotic treatment in patients with molecular bacterascites.

Application of qualitative and quantitative real-time PCR, direct sequencing, and terminal restriction fragment length polymorphism analysis for detection and identification of polymicrobial 16S rRNA genes in ascites.

Qualitative and quantitative 16S rRNA gene-based real-time PCR and direct sequencing were applied for rapid detection and identification of bacterial DNA (bactDNA) in 356 ascites samples. bactDNA was detected in 35% of samples, with a mean of 3.24 log copies ml(-1). Direct sequencing of PCR products revealed 62% mixed chromatograms predominantly belonging to Gram-positive bacteria. Terminal restriction fragment length polymorphism (T-RFLP) results of a sample subset confirmed sequence data showing polymicrobial DNA contents in 67% of bactDNA-positive ascites samples.

Primer pairs for the specific environmental detection and T-RFLP analysis of the ubiquitous flagellate taxa Chrysophyceae and Kinetoplastea.

Bacterivorous protists play a key role in microbial soil food webs, however due to the lack of specific PCR protocols targeting selected protist taxa, knowledge on the diversity and dynamics of these groups is scarce. We developed specific PCR primers in combination with a T-RFLP protocol for the cultivation-independent analysis of two important taxa of bacterivorous flagellates, the Chrysophyceae and Kinetoplastea, in soil samples. Sequence analysis of clone libraries originating from two soils in temperate regions demonstrated the specificity of the respective primer pairs. Clone sequences affiliating to the Chrysophyceae mainly clustered within the clade C2, which has been known so far for its presence mainly in cold climatic regions, whereas Kinetoplastea sequences were mainly related to the Neobodonid clade. Based on an in silico restriction analysis of database sequence entries, suitable restriction enzymes for a T-RFLP approach were selected. This in silico approach revealed the necessity to use a combination of two restriction enzymes for T-RFLP analysis of the Chrysophyceae. Soil T-RFLP profiles reflected all T-RFs of the clone library sequences obtained from the same soils and allowed to distinguish flagellate communities from different sites. We propose to use these primer pairs for PCR detection and rapid fingerprint screening in environmental samples and envisage their use also for quantitative PCR or next generation sequencing approaches.

The axon guidance molecule Netrin-4 is expressed by Müller cells and contributes to angiogenesis in the retina.

Retinal glial (Müller) cells are involved in a wide range of developmental mechanisms, including axon guidance and angiogenesis. This study was undertaken to explore whether Netrin-4, an axonal guidance molecule, is expressed by Müller cells and promotes angiogenesis-related activities. Netrin-4 was found through all retinal layers, and its expression was demonstrated in Müller cells, retinal pigment epithelium cells and bovine retinal endothelial cells (BRECs). Co-localization of Netrin-4 with Müller cell-specific molecules [cellular retinaldehyde-binding protein (cRALBP), vimentin] was observed in the ganglion cell layer, nerve fiber layer, and at the outer limiting membrane. Under hypoxic conditions, the release of Netrin-4 from Müller cells was increased, with mRNA levels upregulated in a hypoxia-inducible factor-1-dependent manner and dependent on the concomitantly induced release of vascular endothelial growth factor. These findings were consistent with an intensified immunofluorescence of Netrin-4 labeling in the postischemic retinas after ischemia-reperfusion. Netrin-4 stimulated BRECs to increase phosphorylation of the mitogen-activated protein (MAP) kinases, extracellular signal-regulated kinase (ERK)-1/-2, and p38, in a dose-dependent manner. Synthetic inhibitors of the MAP kinases were able to suppress Netrin-4-induced migration and proliferation of BRECs suggesting that both MAP kinases are differentially involved in Netrin-4-induced angiogenesis. Two receptors for Netrins, i.e., deleted in colorectal cancer (DCC) and uncoordinated-5-homolog 1 (Unc5H1), were detected in BRECs. DCC is at least partially required for Netrin-4-induced activation of ERK-1/-2. These data suggest that Müller glial cells contribute to, and may modulate, retinal Netrin-4 levels. This may be a novel pathway of Müller cell-mediated control of retinal angiogenesis, particularly under hypoxic/ischemic conditions when the cells upregulate Netrin-4 expression.