Genetic evidence supporting the association of protease and protease inhibitor genes with inflammatory bowel disease: a systematic review

As part of the European research consortium IBDase, we addressed the role of proteases and protease inhibitors (P/PIs) in inflammatory bowel disease (IBD), characterized by chronic mucosal inflammation of the gastrointestinal tract, which affects 2.2 million people in Europe and 1.4 million people in North America. We systematically reviewed all published genetic studies on populations of European ancestry (67 studies on Crohn's disease [CD] and 37 studies on ulcerative colitis [UC]) to identify critical genomic regions associated with IBD. We developed a computer algorithm to map the 807 P/PI genes with exact genomic locations listed in the MEROPS database of peptidases onto these critical regions and to rank P/PI genes according to the accumulated evidence for their association with CD and UC. 82 P/PI genes (75 coding for proteases and 7 coding for protease inhibitors) were retained for CD based on the accumulated evidence. The cylindromatosis/turban tumor syndrome gene (CYLD) on chromosome 16 ranked highest, followed by acylaminoacyl-peptidase (APEH), dystroglycan (DAG1), macrophage-stimulating protein (MST1) and ubiquitin-specific peptidase 4 (USP4), all located on chromosome 3. For UC, 18 P/PI genes were retained (14 proteases and 4 protease inhibitors), with a considerably lower amount of accumulated evidence. The ranking of P/PI genes as established in this systematic review is currently used to guide validation studies of candidate P/PI genes, and their functional characterization in interdisciplinary mechanistic studies in vitro and in vivo as part of IBDase. The approach used here overcomes some of the problems encountered when subjectively selecting genes for further evaluation and could be applied to any complex disease and gene family.     

Mosses modify effects of warmer and wetter conditions on tree seedlings at the alpine treeline

Climate warming enables tree seedling establishment beyond the current alpine treeline, but to achieve this, seedlings have to establish within existing tundra vegetation. In tundra, mosses are a prominent feature, known to regulate soil temperature and moisture through their physical structure and associated water retention capacity. Moss presence and species identity might therefore modify the impact of increases in temperature and precipitation on tree seedling establishment at the arctic‐alpine treeline. We followed Betula pubescens and Pinus sylvestris seedling survival and growth during three growing seasons in the field. Tree seedlings were transplanted along a natural precipitation gradient at the subarctic‐alpine treeline in northern Sweden, into plots dominated by each of three common moss species and exposed to combinations of moss removal and experimental warming by open‐top chambers (OTCs). Independent of climate, the presence of feather moss, but not Sphagnum, strongly supressed survival of both tree species. Positive effects of warming and precipitation on survival and growth of B. pubescens seedlings occurred in the absence of mosses and as expected, this was partly dependent on moss species. P. sylvestris survival was greatest at high precipitation, and this effect was more pronounced in Sphagnum than in feather moss plots irrespective of whether the mosses had been removed or not. Moss presence did not reduce the effects of OTCs on soil temperature. Mosses therefore modified seedling response to climate through other mechanisms, such as altered competition or nutrient availability. We conclude that both moss presence and species identity pose a strong control on seedling establishment at the alpine treeline, and that in some cases mosses weaken climate‐change effects on seedling establishment. Changes in moss abundance and species composition therefore have the potential to hamper treeline expansion induced by climate warming.     

Inter-epidemic Transmission of Rift Valley Fever in Livestock in the Kilombero River Valley,Tanzania: A Cross-Sectional Survey

Background

In recent years, evidence of Rift Valley fever (RVF) transmission during inter-epidemic periods in parts of Africa has increasingly been reported. The inter-epidemic transmissions generally pass undetected where there is no surveillance in the livestock or human populations. We studied the presence of and the determinants for inter-epidemic RVF transmission in an area experiencing annual flooding in southern Tanzania.

Methodology

A cross-sectional sero-survey was conducted in randomly selected cattle, sheep and goats in the Kilombero river valley from May to August 2011, approximately four years after the 2006/07 RVF outbreak in Tanzania. The exposure status to RVF virus (RVFV) was determined using two commercial ELISA kits, detecting IgM and IgG antibodies in serum. Information about determinants was obtained through structured interviews with herd owners.

Findings

An overall seroprevalence of 11.3% (n = 1680) was recorded; 5.5% in animals born after the 2006/07 RVF outbreak and 22.7% in animals present during the outbreak. There was a linear increase in prevalence in the post-epidemic annual cohorts. Nine inhibition-ELISA positive samples were also positive for RVFV IgM antibodies indicating a recent infection. The spatial distribution of seroprevalence exhibited a few hotspots. The sex difference in seroprevalence in animals born after the previous epidemic was not significant (6.1% vs. 4.6% for females and males respectively, p = 0.158) whereas it was significant in animals present during the outbreak (26.0% vs. 7.8% for females and males respectively, p<0.001). Animals living >15 km from the flood plain were more likely to have antibodies than those living <5 km (OR 1.92; 95% CI 1.04–3.56). Species, breed, herd composition, grazing practices and altitude were not associated with seropositivity.

Conclusion

These findings indicate post-epidemic transmission of RVFV in the study area. The linear increase in seroprevalence in the post-epidemic annual cohorts implies a constant exposure and presence of active foci transmission preceding the survey.     

ICEA of Mycoplasma agalactiae: a new family of self‐transmissible integrative elements that confers conjugative properties to the recipient strain

Horizontal gene transfer (HGT) is a major force of microbial evolution but was long thought to be marginal in mycoplasmas. In silico detection of exchanged regions and of loci encoding putative Integrative Conjugative Elements (ICE) in several mycoplasma genomes challenged this view, raising the prospect of these simple bacteria being able to conjugate. Using the model pathogen Mycoplasma agalactiae, we demonstrated for the first time that one of these elements, ICEA, is indeed self‐transmissible. As a hallmark of conjugative processes, ICEA transfers were DNase resistant and required viable cells. ICEA acquisition conferred ICE‐negative strains with the new ability to conjugate, allowing the spread of ICEA. Analysis of transfer‐deficient mutants indicated that this process requires an ICEA‐encoded lipoprotein of unknown function, CDS14. Formation of a circular extrachromosomal intermediate and the subsequent chromosomal integration of ICEA involved CDS22, an ICEA‐encoded product distantly related to the ISLre2 transposase family. Remarkably, ICEA has no specific or no preferential integration site, often resulting in gene disruptions. Occurrence of functional mycoplasma ICE offers these bacteria with a means for HGT, a phenomenon with far‐reaching implications given their minute‐size genome and the number of species that are pathogenic for a broad host‐range.     

Bone overgrowth-associated mutations in the LRP4 gene impair sclerostin facilitator function

Humans lacking sclerostin display progressive bone overgrowth due to increased bone formation. Although it is well established that sclerostin is an osteocyte-secreted bone formation inhibitor, the underlying molecular mechanisms are not fully elucidated. We identified in tandem affinity purification proteomics screens LRP4 (low density lipoprotein-related protein 4) as a sclerostin interaction partner. Biochemical assays with recombinant proteins confirmed that sclerostin LRP4 interaction is direct. Interestingly, in vitro overexpression and RNAi-mediated knockdown experiments revealed that LRP4 specifically facilitates the previously described inhibitory action of sclerostin on Wnt1/β-catenin signaling. We found the extracellular β-propeller structured domain of LRP4 to be required for this sclerostin facilitator activity. Immunohistochemistry demonstrated that LRP4 protein is present in human and rodent osteoblasts and osteocytes, both presumed target cells of sclerostin action. Silencing of LRP4 by lentivirus-mediated shRNA delivery blocked sclerostin inhibitory action on in vitro bone mineralization. Notably, we identified two mutations in LRP4 (R1170W and W1186S) in patients suffering from bone overgrowth. We found that these mutations impair LRP4 interaction with sclerostin and its concomitant sclerostin facilitator effect. Together these data indicate that the interaction of sclerostin with LRP4 is required to mediate the inhibitory function of sclerostin on bone formation, thus identifying a novel role for LRP4 in bone.     

Occludin S408 phosphorylation regulates tight junction protein interactions and barrier function

Although the C-terminal cytoplasmic tail of the tight junction protein occludin is heavily phosphorylated, the functional impact of most individual sites is undefined. Here, we show that inhibition of CK2-mediated occludin S408 phosphorylation elevates transepithelial resistance by reducing paracellular cation flux. This regulation requires occludin, claudin-1, claudin-2, and ZO-1. S408 dephosphorylation reduces occludin exchange, but increases exchange of ZO-1, claudin-1, and claudin-2, thereby causing the mobile fractions of these proteins to converge. Claudin-4 exchange is not affected. ZO-1 domains that mediate interactions with occludin and claudins are required for increases in claudin-2 exchange, suggesting assembly of a phosphorylation-sensitive protein complex. Consistent with this, binding of claudin-1 and claudin-2, but not claudin-4, to S408A occludin tail is increased relative to S408D. Finally, CK2 inhibition reversed IL-13-induced, claudin-2-dependent barrier loss. Thus, occludin S408 dephosphorylation regulates paracellular permeability by remodeling tight junction protein dynamic behavior and intermolecular interactions between occludin, ZO-1, and select claudins, and may have therapeutic potential in inflammation-associated barrier dysfunction.     

Long-term in vitro culture affects phenotypic plasticity of Neoregelia johannis plants

Plant Cell, Tissue and Organ Culture (PCTOC) - We carried out immunoassay of plant hormones [indoleacetic acid (IAA), cytokinins and abscisic acid (ABA)] in the extracts from explants...     

Evaluation of Lignans from Piper cubeba against Schistosoma mansoni Adult Worms: A Combined Experimental and Theoretical Study

Six dibenzylbutyrolactonic lignans ((?)‐hinokinin ( 1 ), (?)‐cubebin ( 2 ), (?)‐yatein ( 3 ), (?)‐5‐methoxyyatein ( 4 ), dihydrocubebin ( 5 ) and dihydroclusin ( 6 )) were isolated from Piper cubeba seed extract and evaluated against Schistosoma mansoni. All lignans, except 5 , were able to separate the adult worm pairs and reduce the egg numbers during 24 h of incubation. Lignans 1 , 3 and 4 (containing a lactone ring) were the most efficient concerning antiparasitary activity. Comparing structures 3 and 4 , the presence of the methoxy group at position 5 appears to be important for this activity. Considering 1 and 3 , it is possible to see that the substitution pattern change (methylenedioxy or methoxy groups) in positions 3′ and 4′ alter the biological response, with 1 being the second most active compound. Computational calculations suggest that the activity of compound 4 can be correlated with the largest lipophilicity value.     

Long-term microbial community dynamics at two full-scale biotrickling filters treating pig house exhaust air

In this study, the microbial community structure of two full-scale biotrickling filters treating exhaust air from a pig housing facility were evaluated using 16S metabarcoding. The effect of inoculation with activated sludge of a nearby domestic waste water treatment plant was investigated, which is a cheap procedure and easy to apply in practice. The study was performed at a three-stage and a two-stage full-scale biotrickling filter; of which, only the latter was inoculated. Both biotrickling filters evolved towards a rather similar community over time, which differed from the one in the activated sludge used for inoculation. However, the bacterial population at both biotrickling filters showed small differences on the family level. A large population of heterotrophic bacteria, including denitrifying bacteria, was present in both biotrickling filters. In the non-inoculated biotrickling filter, nitrite-oxidizing bacteria (NOB) could not be detected, which corresponded with the incomplete nitrification leading to high nitrite accumulation observed in this system. Inoculation with the wide spectrum inoculum activated sludge had in this study a positive effect on the biotrickling filter performance (higher ammonia removal and lower nitrous oxide production). It could thus be beneficial to inoculate biotrickling filters in order to enrich NOB at the start-up, making it easier to keep the free nitrous acid concentration low enough to not be inhibited by it.