Identification of Restricted Subsets of Mature microRNA Abnormally Expressed in Inactive Colonic Mucosa of Patients with Inflammatory Bowel Disease

Background

Ulcerative Colitis (UC) and Crohn''s Disease (CD) are two chronic Inflammatory Bowel Diseases (IBD) affecting the intestinal mucosa. Current understanding of IBD pathogenesis points out the interplay of genetic events and environmental cues in the dysregulated immune response. We hypothesized that dysregulated microRNA (miRNA) expression may contribute to IBD pathogenesis. miRNAs are small, non-coding RNAs which prevent protein synthesis through translational suppression or mRNAs degradation, and regulate several physiological processes.

Methodology/Findings

Expression of mature miRNAs was studied by Q-PCR in inactive colonic mucosa of patients with UC (8), CD (8) and expressed relative to that observed in healthy controls (10). Only miRNAs with highly altered expression (>5 or <0.2 -fold relative to control) were considered when Q-PCR data were analyzed. Two subsets of 14 (UC) and 23 (CD) miRNAs with highly altered expression (5.2->100 -fold and 0.05–0.19 -fold for over- and under- expression, respectively; 0.001<p≤0.05) were identified in quiescent colonic mucosa, 8 being commonly dysregulated in non-inflamed UC and CD (mir-26a,-29a,-29b,-30c,-126*,-127-3p,-196a,-324-3p). Several miRNA genes with dysregulated expression co-localize with acknowledged IBD-susceptibility loci while others, (eg. clustered on 14q32.31), map on chromosomal regions not previously recognized as IBD-susceptibility loci. In addition, in silico clustering analysis identified 5 miRNAs (mir-26a,-29b,-126*,-127-3p,-324-3p) that share coordinated dysregulation of expression both in quiescent and in inflamed colonic mucosa of IBD patients. Six miRNAs displayed significantly distinct alteration of expression in non-inflamed colonic biopsies of UC and CD patients (mir-196b,-199a-3p,-199b-5p,-320a,-150,-223).

Conclusions/Significance

Our study supports miRNAs as crucial players in the onset and/or relapse of inflammation from quiescent mucosal tissues in IBD patients. It allows speculating a role for miRNAs as contributors to IBD susceptibility and suggests that some of the miRNA with altered expression in the quiescent mucosa of IBD patients may define miRNA signatures for UC and CD and help develop new diagnostic biomarkers.     

Cross-scale analysis of the region effect on vascular plant species diversity in southern and northern European mountain ranges

Background

The divergent glacial histories of southern and northern Europe affect present-day species diversity at coarse-grained scales in these two regions, but do these effects also penetrate to the more fine-grained scales of local communities?

Methodology/Principal Findings

We carried out a cross-scale analysis to address this question for vascular plants in two mountain regions, the Alps in southern Europe and the Scandes in northern Europe, using environmentally paired vegetation plots in the two regions (n = 403 in each region) to quantify four diversity components: (i) total number of species occurring in a region (total γ-diversity), (ii) number of species that could occur in a target plot after environmental filtering (habitat-specific γ-diversity), (iii) pair-wise species compositional turnover between plots (plot-to-plot β-diversity) and (iv) number of species present per plot (plot α-diversity). We found strong region effects on total γ-diversity, habitat-specific γ-diversity and plot-to-plot β-diversity, with a greater diversity in the Alps even towards distances smaller than 50 m between plots. In contrast, there was a slightly greater plot α-diversity in the Scandes, but with a tendency towards contrasting region effects on high and low soil-acidity plots.

Conclusions/Significance

We conclude that there are strong regional differences between coarse-grained (landscape- to regional-scale) diversity components of the flora in the Alps and the Scandes mountain ranges, but that these differences do not necessarily penetrate to the finest-grained (plot-scale) diversity component, at least not on acidic soils. Our findings are consistent with the contrasting regional Quaternary histories, but we also consider alternative explanatory models. Notably, ecological sorting and habitat connectivity may play a role in the unexpected limited or reversed region effect on plot α-diversity, and may also affect the larger-scale diversity components. For instance, plot connectivity and/or selection for high dispersal ability may increase plot α-diversity and compensate for low total γ-diversity.     

Cellular HIV-1 DNA Levels in Drug Sensitive Strains Are Equivalent to Those in Drug Resistant Strains in Newly-Diagnosed Patients in Europe

Background

HIV-1 genotypic drug resistance is an important threat to the success of antiretroviral therapy and transmitted resistance has reached 9% prevalence in Europe. Studies have demonstrated that HIV-1 DNA load in peripheral blood mononuclear cells (PBMC) have a predictive value for disease progression, independently of CD4 counts and plasma viral load.

Methodology/Principal Findings

Molecular-beacon-based real-time PCR was used to measure HIV-1 second template switch (STS) DNA in PBMC in newly-diagnosed HIV-1 patients across Europe. These patients were representative for the HIV-1 epidemic in the participating countries and were carrying either drug-resistant or sensitive viral strains. The assay design was improved from a previous version to specifically detect M-group HIV-1 and human CCR5 alleles. The findings resulted in a median of 3.32 log₁₀ HIV-1 copies/10⁶ PBMC and demonstrated for the first time no correlation between cellular HIV-1 DNA load and transmitted drug-resistance. A weak association between cellular HIV-1 DNA levels with plasma viral RNA load and CD4⁺ T-cell counts was also reconfirmed. Co-receptor tropism for 91% of samples, whether or not they conferred resistance, was CCR5. A comparison of pol sequences derived from RNA and DNA, resulted in a high similarity between the two.

Conclusions/Significance

An improved molecular-beacon-based real-time PCR assay is reported for the measurement of HIV-1 DNA in PBMC and has investigated the association between cellular HIV-1 DNA levels and transmitted resistance to antiretroviral therapy in newly-diagnosed patients from across Europe. The findings show no correlation between these two parameters, suggesting that transmitted resistance does not impact disease progression in HIV-1 infected individuals. The CCR5 co-receptor tropism predominance implies that both resistant and non-resistant strains behave similarly in early infection. Furthermore, a correlation found between RNA- and DNA-derived sequences in the pol region suggests that genotypic drug-resistance testing could be carried out on either template.     

Linking In Vitro and In Vivo Survival of Clinical Leishmania donovani Strains

Background

Leishmania donovani is an intracellular protozoan parasite that causes a lethal systemic disease, visceral leishmaniasis (VL), and is transmitted between mammalian hosts by phlebotomine sandflies. Leishmania expertly survives in these ‘hostile’ environments with a unique redox system protecting against oxidative damage, and host manipulation skills suppressing oxidative outbursts of the mammalian host. Treating patients imposes an additional stress on the parasite and sodium stibogluconate (SSG) was used for over 70 years in the Indian subcontinent.

Methodology/Principal Findings

We evaluated whether the survival capacity of clinical L. donovani isolates varies significantly at different stages of their life cycle by comparing proliferation, oxidative stress tolerance and infection capacity of 3 Nepalese L. donovani strains in several in vitro and in vivo models. In general, the two strains that were resistant to SSG, a stress encountered in patients, attained stationary phase at a higher parasite density, contained a higher amount of metacyclic parasites and had a greater capacity to cause in vivo infection in mice compared to the SSG-sensitive strain.

Conclusions/Significance

The 2 SSG-resistant strains had superior survival skills as promastigotes and as amastigotes compared to the SSG-sensitive strain. These results could indicate that Leishmania parasites adapting successfully to antimonial drug pressure acquire an overall increased fitness, which stands in contrast to what is found for other organisms, where drug resistance is usually linked to a fitness cost. Further validation experiments are under way to verify this hypothesis.     

Nouvelles données sur l’évolution paléoclimatique de l’époque magdalénienne,d’après l’étude lithostratigraphique du Roc-aux-Sorciers (Angles-sur-l’Anglin,Vienne, France)

Situated a few kilometres from Angles-sur-Anglin (Vienne, France), the Roc-aux-Sorciers cave has yielded in 1927 and 1950 industry of the Middle and Upper Magdalenian periods. Our analyses of the sedimentary filling, dated from isotope stage 2, demonstrate the existence of two climatic sequences in the six ensembles defined during the excavations. A first sequence, at the base of the cave filling, corresponds to the occupation levels of the Middle Magdalenian and of the early Upper Magdalenian. At that time, the climate was globally cold and particularly humid, a conclusion that does not support Bastin's 1975 hypothesis on the oscillation of Angles-sur-Anglin, which postulates a mild and humid climate. In fact, the climate evolved progressively towards a slight warming from the base to the top of the stratigraphy. During the second sequence, corresponding to the occupation period of the Upper Magdalenian, the relatively stable climate was slightly warmer and quite humid. Stratigraphical and sedimentological data thus provide new information on the conditions under which the filling was deposited and on the palaeoclimatology of the Poitou-Charentes region during Magdalenian occupation.     

Multiple Escherichia coli RecQ Helicase Monomers Cooperate to Unwind Long DNA Substrates: A FLUORESCENCE CROSS-CORRELATION SPECTROSCOPY STUDY*

The RecQ family helicases catalyze the DNA unwinding reaction in an ATP hydrolysis-dependent manner. We investigated the mechanism of DNA unwinding by the Escherichia coli RecQ helicase using a new sensitive helicase assay based on fluorescence cross-correlation spectroscopy (FCCS) with two-photon excitation. The FCCS-based assay can be used to measure the unwinding activity under both single and multiple turnover conditions with no limitation related to the size of the DNA strands constituting the DNA substrate. We found that the monomeric helicase was sufficient to perform the unwinding of short DNA substrates. However, a significant increase in the activity was observed using longer DNA substrates, under single turnover conditions, originating from the simultaneous binding of multiple helicase monomers to the same DNA molecule. This functional cooperativity was strongly dependent on several factors, including DNA substrate length, the number and size of single-stranded 3′-tails, and the temperature. Regarding the latter parameter, a strong cooperativity was observed at 37 °C, whereas only modest or no cooperativity was observed at 25 °C regardless of the nature of the DNA substrate. Consistently, the functional cooperativity was found to be tightly associated with a cooperative DNA binding mode. We also showed that the cooperative binding of helicase to the DNA substrate indirectly accounts for the sigmoidal dependence of unwinding activity on ATP concentration, which also occurs only at 37 °C but not at 25 °C. Finally, we further examined the influences of spontaneous DNA rehybridization (after helicase translocation) and the single-stranded DNA binding property of helicase on the unwinding activity as detected in the FCCS assay.     

Oxidized low-density lipoprotein increases osteopontin expression by generation of oxidative stress

Osteopontin (OPN) is an important mediator of inflammation and is involved in the generation of atherosclerotic lesions. Oxidized LDL (OxLDL) increased the intracellular and secreted levels of OPN in rat smooth muscle cells in a dose- and time-dependent manner. Experiments with kinase inhibitors demonstrated that this effect was mediated by ERK and JNK, but not p38. OxLDL induced oxidative stress, measured by the intracellular levels of reactive oxygen species (ROS) and lipid peroxidation products. The increase in OPN levels was reproduced by the lipid extract of the particle and prevented by the antioxidant vitamin E. Furthermore, ROS generated by UVA irradiation or treatment with pro-oxidant compounds such as buthionine sulfoximine or H₂O₂ also enhanced intracellular and secreted OPN. Finally, OxLDL also augmented OPN levels in other cell types such as fibroblasts, keratinocytes, and endothelial cells. This work demonstrates the role of OxLDL in the expression of the OPN gene and further highlights the role of oxidative stress in the regulation of this cytokine. This might be related to the proinflammatory effects of OxLDL in the initiation and progression of atherosclerotic plaque.     

Effects of high-altitude hypoxia on the hormonal response to hypothalamic factors

Acute and chronic exposure to high altitude induces various physiological changes, including activation or inhibition of various hormonal systems. In response to activation processes, a desensitization of several pathways has been described, especially in the adrenergic system. In the present study, we aimed to assess whether the hypophyseal hormones are also subjected to a hypoxia-induced decrease in their response to hypothalamic factors. Basal levels of hormones and the responses of TSH, thyroid hormones, prolactin, sex hormones, and growth hormone to the injection of TRH, gonadotropin-releasing hormone, and growth hormone-releasing hormone (GHRH) were studied in eight men in normoxia and on prolonged exposure (3-4 days) to an altitude of 4,350 m. Thyroid hormones were elevated at altitude (+16 to +21%), while TSH levels were unchanged, and follicle-stimulating hormone and prolactin decreased, while leutinizing hormone was unchanged. Norepinephrine and cortisol levels were elevated, while no change was observed in levels of epinephrine, dopamine, growth hormone (GH), IGF-1, and IGFBP-3. The mean response to hypothalamic factors was similar in both altitudes for all studied hormones, although total T4 was lower in hypoxia during 45 to 60 min after injection. The effect of hypoxia on the hypophyseal response to hypothalamic factors was similar among subjects, except for the GH response to GHRH administration. We conclude that prolonged exposure to high-altitude hypoxia induces contrasted changes in hormonal levels, but the hypophyseal response to hypothalamic factors does not appear to be blunted.     

Relating mechanical strength at the stem level to values obtained from defect-free wood samples

Stem or branch failure is a recurrent problem in silviculture and arboriculture. The risk of rupture varies with species in relation to the inherent mechanical properties of the species and the presence of defects. In general, calculations of critical loads for breakage are based on mechanical properties determined from defect-free samples and adjustment factors that try to scale up to full trees that include defects. This study aims at developing an objective method to scale up mechanical resistance to breakage from defect-free samples to full trees, including different types of defects. It combines two approaches. In the first one, a correction factor is determined from a meta-analysis of various tree-pulling studies involving balsam fir [Abies balsamea (L.) Mill.], white spruce [Picea glauca (Moench) Voss], jack pine [Pinus banksiana Lamb.], and black spruce [Picea mariana (Mill.) B.S.P.]. The second approach consists in obtaining empirical data from three-point bending tests using 8-foot (2.44 m) logs with various amounts of decay. Results show that the correction required varies according to the species and the presence of some defects. For balsam fir, which was the species showing the most important difference between whole log and small sample values, differences in correction factors were found between tree-pulling tests and three-point bending tests. Data from winching tests tend to underestimate the stem’s resistance to breakage since they likely represent the weakest trees among those tested. No relationship was found between the adjustment factors and different indices used in arboriculture to account for decay, showing the complexity of mechanical resistance at the stem level.