Olivier Thas

Butyrate-producing Clostridium cluster XIVa species specifically colonize mucins in an in vitro gut model

The human gut is colonized by a complex microbiota with multiple benefits. Although the surface-attached, mucosal microbiota has a unique composition and potential to influence human health, it remains difficult to study in vivo. Therefore, we performed an in-depth microbial characterization (human intestinal tract chip (HITChip)) of a recently developed dynamic in vitro gut model, which simulates both luminal and mucosal gut microbes (mucosal-simulator of human intestinal microbial ecosystem (M-SHIME)). Inter-individual differences among human subjects were confirmed and microbial patterns unique for each individual were preserved in vitro. Furthermore, in correspondence with in vivo studies, Bacteroidetes and Proteobacteria were enriched in the luminal content while Firmicutes rather colonized the mucin layer, with Clostridium cluster XIVa accounting for almost 60% of the mucin-adhered microbiota. Of the many acetate and/or lactate-converting butyrate producers within this cluster, Roseburia intestinalis and Eubacterium rectale most specifically colonized mucins. These 16S rRNA gene-based results were confirmed at a functional level as butyryl-CoA:acetate-CoA transferase gene sequences belonged to different species in the luminal as opposed to the mucin-adhered microbiota, with Roseburia species governing the mucosal butyrate production. Correspondingly, the simulated mucosal environment induced a shift from acetate towards butyrate. As not only inter-individual differences were preserved but also because compared with conventional models, washout of relevant mucin-adhered microbes was avoided, simulating the mucosal gut microbiota represents a breakthrough in modeling and mechanistically studying the human intestinal microbiome in health and disease. Finally, as mucosal butyrate producers produce butyrate close to the epithelium, they may enhance butyrate bioavailability, which could be useful in treating diseases, such as inflammatory bowel disease.

Multiple putative oncogenes at the chromosome 20q amplicon contribute to colorectal adenoma to carcinoma progression

Objective: This study aimed to identify the oncogenes at 20q involved in colorectal adenoma to carcinoma progression by measuring the effect of 20q gain on mRNA expression of genes in this amplicon. Methods: Segmentation of DNA copy number changes on 20q was performed by array CGH (comparative genomic hybridisation) in 34 non-progressed colorectal adenomas, 41 progressed adenomas (ie, adenomas that present a focus of cancer) and 33 adenocarcinomas. Moreover, a robust analysis of altered expression of genes in these segments was performed by microarray analysis in 37 adenomas and 31 adenocarcinomas. Protein expression was evaluated by immunohistochemistry on tissue microarrays. Results: The genes C20orf24, AURKA, RNPC1, TH1L, ADRM1, C20orf20 and TCFL5, mapping at 20q, were significantly overexpressed in carcinomas compared with adenomas as a consequence of copy number gain of 20q. Conclusion: This approach revealed C20orf24, AURKA, RNPC1, TH1L, ADRM1, C20orf20 and TCFL5 genes to be important in chromosomal instability-related adenoma to carcinoma progression. These genes therefore may serve as highly specific biomarkers for colorectal cancer with potential clinical applications.

MicroRNA Expression in Induced Sputum of Smokers and Patients with Chronic Obstructive Pulmonary Disease

RATIONALE Chronic obstructive pulmonary disease (COPD) is characterized by progressive inflammation in the airways and lungs combined with disturbed homeostatic functions of pulmonary cells. MicroRNAs (miRNAs) have the ability to regulate these processes by interfering with gene transcription and translation. OBJECTIVES We aimed to identify miRNA expression in induced sputum and examined whether the expression of miRNAs differed between patients with COPD and subjects without airflow limitation. METHODS Expression of 627 miRNAs was evaluated in induced sputum supernatant of 32 subjects by stem-loop reverse transcription-quantitative polymerase chain reaction. Differentially expressed miRNAs were validated in an independent replication cohort of 41 subjects. Enrichment of miRNA target genes was identified by in silico analysis. Protein expression of target genes was determined by ELISA. MEASUREMENTS AND MAIN RESULTS Thirty-four miRNAs were differentially expressed between never-smokers and current smokers without airflow limitation in the screening cohort. Eight miRNAs were expressed at a significantly lower level in current-smoking patients with COPD compared with never-smokers without airflow limitation. Reduced expression of let-7c and miR-125b in patients with COPD compared with healthy subjects was confirmed in the validation cohort. Target genes of let-7c were significantly enriched in the sputum of patients with severe COPD. The concentration of tumor necrosis factor receptor type II (TNFR-II, implicated in COPD pathogenesis and a predicted target gene of let-7c) was inversely correlated with the sputum levels of let-7c . CONCLUSIONS let-7c is significantly reduced in the sputum of currently smoking patients with COPD and is associated with increased expression of TNFR-II.

Spectral entropy as an electroencephalographic measure of anesthetic drug effect: a comparison with bispectral index and processed midlatency auditory evoked response.

Background:The authors compared the behavior of two calculations of electroencephalographic spectral entropy, state entropy (SE) and response entropy (RE), with the A-Line® ARX Index (AAI) and the Bispectral Index (BIS) and as measures of anesthetic drug effect. They compared the measures for baseline variability, burst suppression, and prediction probability. They also developed pharmacodynamic models relating SE, RE, AAI, and BIS to the calculated propofol effect-site concentration (Ceprop). Methods:With institutional review board approval, the authors studied 10 patients. All patients received 50 mg/min propofol until either burst suppression greater than 80% or mean arterial pressure less than 50 mmHg was observed. SE, RE, AAI, and BIS were continuously recorded. Ceprop was calculated from the propofol infusion profile. Baseline variability, prediction of burst suppression, prediction probability, and Spearman rank correlation were calculated for SE, RE, AAI, and BIS. The relations between Ceprop and the electroencephalographic measures of drug effect were estimated using nonlinear mixed effect modeling. Results:Baseline variability was lowest when using SE and RE. Burst suppression was most accurately detected by spectral entropy. Prediction probability and individualized Spearman rank correlation were highest for BIS and lowest for SE. Nonlinear mixed effect modeling generated reasonable models relating all four measures to Ceprop. Conclusions:Compared with BIS and AAI, both SE and RE seem to be useful electroencephalographic measures of anesthetic drug effect, with low baseline variability and accurate burst suppression prediction. The ability of the measures to predict Ceprop was best for BIS.

Accurate particle size distribution determination by nanoparticle tracking analysis based on 2-D Brownian dynamics simulation

A physical model is presented to simulate the average step length distribution during nanoparticle tracking analysis experiments as a function of the particle size distribution and the distribution of the number of steps within the tracks. Considering only tracks of at least five steps, numerical simulation could be replaced by a normal distribution approximation. Based on this model, simulation of a step length distribution allows obtaining a much more reliable estimation of the particle size distribution, thereby reducing the artificial broadening of the distribution, as is typically observed by direct conversion of step length to particle size data. As this fitting procedure also allowed including data from particles that were followed for a relatively low number of steps, the measurement time could be reduced for particles that are known to be monodisperse. Whereas the inversion is less sensitive towards the particle size distribution width, still similar values were obtained for both the average diameter and standard deviation of a polystyrene latex sample irrespective of the track length, provided that the latter included at least five steps.

Flow cytometry for fast microbial community fingerprinting

Characterizing the microbial community of water is important in different domains, ranging from food and beverage production to wastewater treatment. Conventional methods, such as heterotrophic plate count, selective plating and molecular techniques, are time consuming and labor intensive. A flow cytometry based approach was developed for a fast and objective comparison of microbial communities based on the distribution of cellular features from single cells within these communities. The method consists of two main parts, firstly the generation of fingerprint data by flow cytometry and secondly a novel statistical pipeline for the analysis of flow cytometric data. The combined method was shown to be useful for the discrimination and classification of different brands of drinking water. It was also successfully applied to detect changes in microbial community composition of drinking water caused by changing environmental factors. Generally, the method can be used as a fast fingerprinting method of microbial communities in aquatic samples and as a tool to detect shifts within these communities.

Environmental conditions and community evenness determine the outcome of biological invasion

Biological invasion is widely studied, however, conclusions on the outcome of this process mainly originate from observations in systems that leave a large number of experimental variables uncontrolled. Here using a fully controlled system consisting of assembled bacterial communities, we evaluate the degree of invasion and the effect on the community functionality in relation to the initial community evenness under specific environmental stressors. We show that evenness influences the level of invasion and that the introduced species can promote functionality under stress. The evenness-invasibility relationship is negative in the absence and neutral in the presence of stress. Under these conditions, the introduced species is able to maintain the functionality of uneven communities. These results indicate that communities, initially having the same genetic background, in the presence of the same invader, react in a different way with respect to invasibility and functionality depending on specific environmental conditions and community evenness.

The more, the merrier: heterotroph richness stimulates methanotrophic activity

Although microorganisms coexist in the same environment, it is still unclear how their interaction regulates ecosystem functioning. Using a methanotroph as a model microorganism, we determined how methane oxidation responds to heterotroph diversity. Artificial communities comprising of a methanotroph and increasing heterotroph richness, while holding equal starting cell numbers were assembled. We considered methane oxidation rate as a functional response variable. Our results showed a significant increase of methane oxidation with increasing heterotroph richness, suggesting a complex interaction in the cocultures leading to a stimulation of methanotrophic activity. Therefore, not only is the methanotroph diversity directly correlated to methanotrophic activity for some methanotroph groups as shown before, but also the richness of heterotroph interacting partners is relevant to enhance methane oxidation too. In this unprecedented study, we provide direct evidence showing how heterotroph richness exerts a response in methanotroph–heterotroph interaction, resulting in increased methanotrophic activity. Our study has broad implications in how methanotroph and heterotroph interact to regulate methane oxidation, and is particularly relevant in methane-driven ecosystems.

Interaction between Podisus maculiventris and Harmonia axyridis two predators used in augmentative biological control in greenhouse crops

Intraguild predation (IGP) betweenthe pentatomid Podisus maculiventris(Say) and the coccinellid Harmoniaaxyridis (Pallas) in the absence or presenceof the extraguild prey Spodopteralittoralis (Boisduval) and Myzuspersicae (Sulzer) was studied in thelaboratory. Interactions were asymmetric infavor of the pentatomid. Podisusmaculiventris readily fed upon eggs and larvaeof H. axyridis, but adult beetles wererarely attacked. Success of attacks by P.maculiventris was stage dependent, fourthinstars and adults being more successful inkilling ladybeetle larvae than second instars.Attacks by H. axyridis on the pentatomidwere rare and none of them were successful. Theeffect of introducing extraguild prey on thelevel of IGP was tested both in petri dishesand on caged sweet pepper plants. Whensufficient numbers of S. littoralislarvae were present to satiate the pentatomid,predation on H. axyridis larvae decreasedsignificantly, indicating that the coccinellidis a less preferred or less vulnerable prey.When the aphid M. persicae was presentedas extraguild prey, levels of IGP were notaltered. Nymphs of P. maculiventrissuccessfully completed development whenexclusively fed on larvae of H. axyridis,but developmental time was longer than onlepidopteran prey. No pentatomid nymphs reachedadulthood on aphids alone. IGP by P.maculiventris on H. axyridis may be ofsome importance in greenhouse crops, where bothpredators are being used increasingly inaugmentative biological control programs.Nonetheless, it is expected that in practicelarger larvae and adults of H. axyridiswill escape most attacks by the pentatomid.

Comparison of computer-controlled administration of propofol with two manually controlled infusion techniques

Ninety women were studied in order to compare dose requirements and quality of anaesthesia between target‐controlled infusion and two manually controlled infusion schemes for propofol administration: group I received target‐controlled infusion for induction (4 μg.ml−1 target blood concentration, increased by 2 μg.ml−1 after 3 min if consciousness not lost), groups II and III received an induction bolus of propofol at infusion rates of 1200 or 600 ml.h−1, respectively, until loss of consciousness. Anaesthesia was maintained with propofol target‐controlled infusion in group I or by constant rate infusion in the other two groups. Computer simulations were used to calculate blood and effect‐site propofol concentrations. Mean induction times (SD) were 78 (65) s in group I versus 51 (10) s and 62 (12) s in groups II and III, respectively (p < 0.05 between groups II and III). Mean induction doses were: 1.31 (0.44), 2.74 (0.56) and 1.77 (0.43) mg.kg−1 and mean maintenance doses were 13.4 (3.55), 9.32 (1.71) and 9.97 (1.53) mg.kg−1.h−1 in groups I, II and III, respectively (p < 0.05 between all groups). There was a lower incidence of apnoea in group I than in groups II and III. There were no significant differences between the groups in other objective parameters of anaesthetic quality studied. Computer simulations showed an ‘overshoot’ in propofol blood and effect‐site concentration with manual induction and significantly higher maintenance levels with target‐controlled infusion.