Whole Genome Gene Expression Meta-Analysis of Inflammatory Bowel Disease Colon Mucosa Demonstrates Lack of Major Differences between Crohn's Disease and Ulcerative Colitis

Background

In inflammatory bowel disease (IBD), genetic susceptibility together with environmental factors disturbs gut homeostasis producing chronic inflammation. The two main IBD subtypes are Ulcerative colitis (UC) and Crohn’s disease (CD). We present the to-date largest microarray gene expression study on IBD encompassing both inflamed and un-inflamed colonic tissue. A meta-analysis including all available, comparable data was used to explore important aspects of IBD inflammation, thereby validating consistent gene expression patterns.

Methods

Colon pinch biopsies from IBD patients were analysed using Illumina whole genome gene expression technology. Differential expression (DE) was identified using LIMMA linear model in the R statistical computing environment. Results were enriched for gene ontology (GO) categories. Sets of genes encoding antimicrobial proteins (AMP) and proteins involved in T helper (Th) cell differentiation were used in the interpretation of the results. All available data sets were analysed using the same methods, and results were compared on a global and focused level as t-scores.

Results

Gene expression in inflamed mucosa from UC and CD are remarkably similar. The meta-analysis confirmed this. The patterns of AMP and Th cell-related gene expression were also very similar, except for IL23A which was consistently higher expressed in UC than in CD. Un-inflamed tissue from patients demonstrated minimal differences from healthy controls.

Conclusions

There is no difference in the Th subgroup involvement between UC and CD. Th1/Th17 related expression, with little Th2 differentiation, dominated both diseases. The different IL23A expression between UC and CD suggests an IBD subtype specific role. AMPs, previously little studied, are strongly overexpressed in IBD. The presented meta-analysis provides a sound background for further research on IBD pathobiology.     

Development of a multi-assay approach for monitoring coral diversity using eDNA metabarcoding

Coral Reefs - Cumulative anthropogenic pressures have triggered a global decline in the health of marine ecosystems, and coral reefs, in particular, are in crisis. With climate and...     

Pharmacological Characterization of a Betaine/GABA Transporter 1 (BGT1) Inhibitor Displaying an Unusual Biphasic Inhibition Profile and Anti-seizure Effects

Neurochemical Research - Focal epileptic seizures can in some patients be managed by inhibiting γ-aminobutyric acid (GABA) uptake via the GABA transporter 1 (GAT1) using tiagabine...     

Complex Actions of Ionomycin in Cultured Cerebellar Astrocytes Affecting Both Calcium-Induced Calcium Release and Store-Operated Calcium Entry

The polyether antibiotic ionomycin is a common research tool employed to raise cytosolic Ca²⁺ in almost any cell type. Although initially thought to directly cause physicochemical translocation of extracellular Ca²⁺ into the cytosol, a number of studies have demonstrated that the mechanism of action is likely to be more complex, involving modulation of intrinsic Ca²⁺ signaling pathways. In the present study we assessed the effect of ionomycin on primary cultures of murine cerebellar astrocytes. Ionomycin concentrations ranging from 0.1 to 10 μM triggered a biphasic increase in cytosolic Ca²⁺, consisting of an initial peak and a subsequent sustained plateau. The response was dependent on concentration and exposure time. While the plateau phase was abolished in the absence of extracellular Ca²⁺, the peak phase persisted. The peak amplitude could be lowered significantly by application of dantrolene, demonstrating involvement of Ca²⁺-induced Ca²⁺-release (CICR). The plateau phase was markedly reduced when store-operated Ca²⁺-entry (SOCE) was blocked with 2-aminoethoxydiphenyl borate. Our results show that ionomycin directly affects internal Ca²⁺ stores in astrocytes, causing release of Ca²⁺ into the cytosol, which in turn triggers further depletion of the stores through CICR and subsequently activates SOCE. This mechanistic action of ionomycin is important to keep in mind when employing it as a pharmacological tool.     

Recovery after Shift Work: Relation to Coronary Risk Factors in Women

Shift work increases the risk for developing cardiovascular disease. There is, however, little knowledge of what aspects of shift scheduling that are detrimental and what characteristics promote good health. The aim of the present study was to evaluate whether coronary risk factors deteriorate after a hard work period and whether recovery, in the form of a week off, was sufficient to improve them. A total of 19 women worked an extremely rapidly rotating and clockwise shift schedule at a paper and pulp factory. They underwent two health examinations, one at the end of the work period and one after the week off. In addition, the women were divided into a tolerant and a vulnerable group, depending on their satisfaction with their work hours. Most risk factors did not change, but total cholesterol and low‐density lipoprotein (LDL)‐cholesterol were lower after the working period than after the week‐off. In addition, vulnerable women had higher levels of total cholesterol and a higher ratio of total cholesterol/high‐density lipoprotein (HDL) than tolerant ones. In conclusion, the finding that a week‐off worsens cholesterol levels was against our hypothesis and suggests further studies on how activities/responsibilities outside the workplace affect shift‐working women. It was also shown that susceptible shift workers had worse lipid profiles.     

A field facility to simulate climate warming and increased nutrient supply in shallow aquatic ecosystems

Global warming and excess nitrogen deposition can exert strong impacts on aquatic populations, communities, and ecosystems. However, experimental data to establish clear cause-and-effect relationships in naturally complex field conditions are scarce in aquatic environments. Here, we describe the design and performance of a unique outdoor enclosure facility used to simulate warming, increased nitrogen supply, and both factors combined in a littoral freshwater wetland dominated by common reed, Phragmites australis. The experimental system effectively simulated a 2.8 °C climate warming scenario over an extended period, capturing the natural temperature variations in the wetland at diel and seasonal scales with only small deviations. Excess nitrogen supply enhanced nitrate concentrations especially in winter when it was associated with increased concentration of ammonium and dissolved organic carbon. Nitrogen also reduced dissolved oxygen concentrations, particularly in the summer. Importantly, by stimulating biological activity, warming enhanced the nitrogen uptake capacity of the wetland during the winter, emphasizing the need for multifactorial global change experiments that examine both warming and nitrogen loading in concert. Establishing similar experiments across broad environmental gradients holds great potential to provide robust assessments of the impacts of climate change on shallow aquatic ecosystems.     

Parasites as prey in aquatic food webs: implications for predator infection and parasite transmission

While the recent inclusion of parasites into food‐web studies has highlighted the role of parasites as consumers, there is accumulating evidence that parasites can also serve as prey for predators. Here we investigated empirical patterns of predation on parasites and their relationships with parasite transmission in eight topological food webs representing marine and freshwater ecosystems. Within each food web, we examined links in the typical predator–prey sub web as well as the predator–parasite sub web, i.e. the quadrant of the food web indicating which predators eat parasites. Most predator– parasite links represented ‘concomitant predation’ (consumption and death of a parasite along with the prey/host; 58–72%), followed by ‘trophic transmission’ (predator feeds on infected prey and becomes infected; 8–32%) and predation on free‐living parasite life‐cycle stages (4–30%). Parasite life‐cycle stages had, on average, between 4.2 and 14.2 predators. Among the food webs, as predator richness increased, the number of links exploited by trophically transmitted parasites increased at about the same rate as did the number of links where these stages serve as prey. On the whole, our analyses suggest that predation on parasites has important consequences for both predators and parasites, and food web structure. Because our analysis is solely based on topological webs, determining the strength of these interactions is a promising avenue for future research.     

Fine root and aboveground carbon stocks in riparian forests: the roles of diking and environmental gradients

Aims

We analysed current carbon (C) stocks in fine root and aboveground biomass of riparian forests and influential environmental parameters on either side of a dike in the Donau-Auen National Park, Austria.

Methods

On both sides of the dike, carbon (C) stock of fine roots (CFR) under four dominant tree species and of aboveground biomass (CAB) were assessed by topsoil cores (0–30 cm) and angle count sampling method respectively (n?=?48). C stocks were modeled, performing boosted regression trees (BRT).

Results

Overall CFR was 2.8 t ha^?1, with significantly higher C stocks in diked (DRF) compared to flooded riparian forests (FRF). In contrast to CFR, mean CAB was 123 t ha^?1 and lower in DRF compared to FRF. However, dike construction was consistently ruled out as a predictor variable in BRT. CFR was influenced by the distance to the Danube River and the dominant tree species. CAB was mainly influenced by the magnitude of fluctuations in the groundwater table and the distances to the river and the low groundwater table.

Conclusions

Despite pronounced differences in FRF and DRF, we conclude that there is only weak support that dikes directly influence C allocation in floodplain forests within the time scale considered (110 years).     

Pollen morphology in the ericoid clade of the order Ericales,with special emphasis on Cyrillaceae

Pollen morphology and pollen wall structure in 23 species representing all families of the ericoid clade of order Ericales, i.e. Actinidiaceae, Sarraceniaceae, Roridulaceae, Clethraceae, Cyrillaceae, and Ericaceae, was investigated by means of light microscopy and SEM. The pollen wall of all taxa was found to consist of two solid strata, a tectum and foot layer, separated by a more or less narrow infratectum with granular elements. The three genera of Cyrillaceae were found to differ from each other. In Cyrilla and Cliftonia the pollen is psilate, often more than 20 mum in diameter, spheroidal with an indistinct colpus rim; in contrast, pollen of Purdiaea are rugulate and slightly different between species, smaller and often less than 20 mum in diameter, oblate with a projecting rim reaching over the colpus. In several characteristic features, pollen of Purdiaea is more similar to pollen of Clethra (Clethraceae), than to pollen of Cyrilla and Cliftonia .