Transcript profiling of chitosan-treated Arabidopsis seedlings

In nature, plants can recognize potential pathogens, thus activating intricate networks of defense signals and reactions. Inducible defense is often mediated by the detection of microbe or pathogen associated molecular pattern elicitors, such as flagellin and chitin. Chitosan, the deacetylated form of chitin, plays a role in inducing protection against pathogens in many plant species. We evaluated the ability of chitosan to confer resistance to Botrytis cinerea in Arabidopsis leaves. We subsequently treated Arabidopsis seedlings with chitosan and carried out a transcript profiling analysis using both ATH1 GeneChip microarrays and quantitative RT-PCR. The results showed that defense response genes, including camalexin biosynthesis genes, were up-regulated by chitosan, both in wild-type and in the chitin-insensitive cerk1 mutant, indicating that chitosan is perceived through a CERK1-independent pathway

Quantifying the ecological effects of water abstraction in Alpine streams through flume simulations

4openNoWater abstraction by small hydropower plants is a growing human pressure on Alpine stream ecosystems. Using a set of seminatural streamside flumes, we investigated the response of benthic invertebrate communities to a 50% experimental reduction of the natural discharge. We collected EPT taxa from upstream (control) and downstream (flow reduction) sections of the flumes before starting the simulations, and after 1 and 3 weeks of simulated flow reduction, while also collecting invertebrates drifting from each section every 24–48 h. Despite an initial (i.e., before simulation) difference in benthic densities and diversity between controls and treatments, these metrics changed and differed over time, with the reduced flow section becoming more diverse and with less individuals. Taxonomic composition differed between flow types, with a short-term (1 week after the beginning of flow reduction) increase of taxonomic heterogeneity. There was no evidence that flow reduction affected functional diversity and homogenized functional composition of the communities. Drift composition differed between flow types with drift rates and richness lower under reduced flow. Functional dispersion was always significantly lower in the drift collected in low-flow conditions where drift propensity was significantly higher for animals preferring medium to fast currents, living temporarily attached to the substrate and feeding as passive filterers; drift propensity was slightly lower for organisms moving as crawlers. Hence, short-term taxonomic and functional changes in benthic invertebrate communities with reduction in flow are likely related to behavioural responses such as drift, thus providing insight on the potential mechanisms underlying community-level effects of water abstraction.Italian Ministry of Education, University and Research (MIUR) in the frame of the ‘Departments of Excellence’ Grant. Open Access Funding provided by Fondazione Edmund Mach Istituto Agrario di San Michele all'Adige within the CRUI-CARE Agreement.Vallefuoco, Francesca; Bruno, Maria Cristina; Zolezzi, Guido; Larsen, StefanoVallefuoco, F.; Bruno, M.C.; Zolezzi, G.; Larsen, S

Moving waters to mitigate hydropeaking: a case study from the Italian Alps

We assessed the effect of a hydropeaking diversion mitigation measure that allows for additional hydropower production, which markedly reduced hydropeaking on a 10-km stream reach in the north-eastern Italian Alps. Hydropeaking, caused by a storage hydropower plant, affected the study reach from the 1920s to 2015, when a cascade of three small run-of-the-river plants was installed to divert the hydropeaks from the plant outlet directly into the intake of the RoRs plants, and hydropeaking was released downstream the confluence with a major free-flowing tributary. The flow regime in the mitigated reach shifted from a hydropeaking-dominated to a baseflow-dominated regime in winter, with flow variability represented only by snowmelt and rainfall in late spring and summer. The application of two recently proposed sets of hydropeaking indicators, the hydraulic analysis of the hydropeaking wave, together with the assessment of biotic changes, allowed quantifying the changes in ecohydraulic processes associated with hydropeaking mitigation. The flow regime in the mitigated reach changed to a residual flow type, with much less frequent residual hydropeaks; although an average two-fold increase in downramping rates were recorded downstream the junction with the tributary, these changes did not represent an ecological concern. The functional composition of the macrobenthic communities shifted slightly in response to flow mitigation, but the taxonomic composition did not recover to conditions typical of more natural flow regimes. This was likely due to the reduced dilution of pollutants and resulting slight worsening in water quality. Conversely, the hyporheic communities showed an increase in diversity and abundance of interstitial taxa, especially in the sites most affected by hydropeaking. This effect was likely due to changes in the interstitial space availability, brought by a reduction of fine sediments clogging. Besides illustrating a feasible hydropeaking mitigation option for Alpine streams, our work suggests the importance of monitoring both benthic and hyporheic communities, together with the flow and sediment supply regimes, and physico-chemical water quality parameters

Classification of dendritic cell phenotypes from gene expression data

<p>Abstract</p> <p>Background</p> <p>The selection of relevant genes for sample classification is a common task in many gene expression studies. Although a number of tools have been developed to identify optimal gene expression signatures, they often generate gene lists that are too long to be exploited clinically. Consequently, researchers in the field try to identify the smallest set of genes that provide good sample classification. We investigated the genome-wide expression of the inflammatory phenotype in dendritic cells. Dendritic cells are a complex group of cells that play a critical role in vertebrate immunity. Therefore, the prediction of the inflammatory phenotype in these cells may help with the selection of immune-modulating compounds.</p> <p>Results</p> <p>A data mining protocol was applied to microarray data for murine cell lines treated with various inflammatory stimuli. The learning and validation data sets consisted of 155 and 49 samples, respectively. The data mining protocol reduced the number of probe sets from 5,802 to 10, then from 10 to 6 and finally from 6 to 3. The performances of a set of supervised classification models were compared. The best accuracy, when using the six following genes --Il12b, Cd40, Socs3, Irgm1, Plin2 and Lgals3bp-- was obtained by Tree Augmented Naïve Bayes and Nearest Neighbour (91.8%). Using the smallest set of three genes --Il12b, Cd40 and Socs3-- the performance remained satisfactory and the best accuracy was with Support Vector Machine (95.9%). These data mining models, using data for the genes Il12b, Cd40 and Socs3, were validated with a human data set consisting of 27 samples. Support Vector Machines (71.4%) and Nearest Neighbour (92.6%) gave the worst performances, but the remaining models correctly classified all the 27 samples.</p> <p>Conclusions</p> <p>The genes selected by the data mining protocol proposed were shown to be informative for discriminating between inflammatory and steady-state phenotypes in dendritic cells. The robustness of the data mining protocol was confirmed by the accuracy for a human data set, when using only the following three genes: Il12b, Cd40 and Socs3. In summary, we analysed the longitudinal pattern of expression in dendritic cells stimulated with activating agents with the aim of identifying signatures that would predict or explain the dentritic cell response to an inflammatory agent.</p

Assessing the eco-hydraulic effects of a hydropeaking mitigation measure with increased energy production in the Noce River (Italian Alps)

We investigated the ecohydraulic effects of a recently implemented hydropeaking mitigation measure in the Upper Noce Stream (NE Italy, Italian Alps), which also allows for additional hydropower production. The Upper Noce, a 3rd order gravel-bed stream, was affected since the mid-1920s by storage hydropower production and associated hydropeaking. The mitigation measure consisted in the diversion of most of the released hydropeaks into a sequence of three newly-installed, cascading run-of-the-river power plants, fed by a penstock running almost parallel to the former hydropeaking reach. The hydropeaking-diversion mitigation measure markedly reduced hydropeaking on a 10-km stream reach, and hydropeaking is now released immediately upstream the confluence with a major free-flowing tributary, which increases the hydropeaking baseflow. The flow regime in the mitigated reach shifted from hydropeaking-dominated to baseflow-dominated regime in winter, with flow variability represented only by snowmelt and rainfall in late spring and summer. We applied two sets of indicators (the Hydropeaking Indicators HP1, HP2 and the COSH method) and conducted a simplified hydraulic analysis of the hydropeaking wave propagation. We assessed the ecological effects of the mitigation measure using three complementary data sources: the analysis of (a) the benthic and (b) hyporheic invertebrate communities, based on datasets collected before and after the implementation of the diversion measure, and (c) ancillary data monitored by the diversion plant manager for required environmental monitoring, which included the suspended sediment regime and the Extended Biotic Index, measured yearly from the year before to the four subsequent years after the implementation of the mitigation measure. Three main changes in eco-hydraulic processes associated with hydropeaking mitigation were detected. i) The flow regime in the mitigated reach changed to a residual flow type, with much less frequent residual hydropeaks, with an average two-fold increase in downramping rates that were recorded downstream the junction with a major tributary. ii) The functional composition of the macrobenthic communities shifted slightly in response to flow mitigation, but the taxonomic composition did not recover to conditions typical of more natural flow regimes. This was likely due to the reduced dilution of pollutants and resulting slight worsening in water quality. iii) The hyporheic communities conversely showed an increase in diversity and abundance of interstitial taxa, especially in the sites most affected by hydropeaking, and this effect was likely due to changes in the interstitial space availability, brought by an alteration of the previous time-space pattern of fine sediment transport, which eventually resulted in reduction of fine sediments clogging of the gravel bed interstices. Besides illustrating a feasible hydropeaking mitigation option for Alpine streams, this work suggests the importance of monitoring both benthic and hyporheic communities, together with the flow and sediment supply regimes, and physico-chemical water quality parameters, for carefully detecting changes in eco-hydraulic processes associated with hydropeaking mitigation that may not be fully expected in the design phase

Cell Specific eQTL Analysis without Sorting Cells

The functional consequences of trait associated SNPs are often investigated using expression quantitative trait locus (eQTL) mapping. While trait-associated variants may operate in a cell-type specific manner, eQTL datasets for such cell-types may not always be available. We performed a genome-environment interaction (GxE) meta-analysis on data from 5,683 samples to infer the cell type specificity of whole blood cis-eQTLs. We demonstrate that this method is able to predict neutrophil and lymphocyte specific cis-eQTLs and replicate these predictions in independent cell-type specific datasets. Finally, we show that SNPs associated with Crohn’s disease preferentially affect gene expression within neutrophils, including the archetypal NOD2 locus

NLRP10 Enhances CD4+ T-Cell-Mediated IFNγ Response via Regulation of Dendritic Cell-Derived IL-12 Release

NLRP10 is a nucleotide-binding oligomerization domain-like receptor that functions as an intracellular pattern recognition receptor for microbial products. Here, we generated a Nlrp10−/− mouse to delineate the role of NLRP10 in the host immune response and found that Nlrp10−/− dendritic cells (DCs) elicited sub-optimal IFNγ production by antigenspecific CD4+ T cells compared to wild-type (WT) DCs. In response to T-cell encounter, CD40 ligation or Toll-like receptor 9 stimulation, Nlrp10−/− DCs produced low levels of IL-12, due to a substantial decrease in NF-κB activation. Defective IL-12 production was also evident in vivo and affected IFNγ production by CD4+ T cells. Upon Mycobacterium tuberculosis (Mtb) infection, Nlrp10−/− mice displayed diminished T helper 1-cell responses and increased bacterial growth compared to WT mice. These data indicate that NLRP10-mediated IL-12 production by DCs is critical for IFNγ induction in T cells and contributes to promote the host defense against Mtb