Assessment of resolution and intercenter reproducibility of results of genotyping Staphylococcus aureus by pulsed-field gel electrophoresis of SmaI macrorestriction fragments: a multicenter study

Twenty well-characterized isolates of methicillin-resistant Staphylococcus aureus were used to study the optimal resolution and interlaboratory reproducibility of pulsed-field gel electrophoresis (PFGE) of DNA macrorestriction fragments. Five identical isolates (one PFGE type), 5 isolates that produced related PFGE subtypes, and 10 isolates with unique PFGE patterns were analyzed blindly in 12 different laboratories by in-house protocols. In several laboratories a standardized PFGE protocol with a commercial kit was applied successfully as well. Eight of the centers correctly identified the genetic homogeneity of the identical isolates by both the in-house and standard protocols. Four of 12 laboratories failed to produce interpretable data by the standardized protocol, due to technical problems (primarily plug preparation). With the five rel

A cross-disease meta-GWAS identifies four new susceptibility loci shared between systemic sclerosis and Crohn’s disease

Abstract: Genome-wide association studies (GWASs) have identified a number of genetic risk loci associated with systemic sclerosis (SSc) and Crohn’s disease (CD), some of which confer susceptibility to both diseases. In order to identify new risk loci shared between these two immune-mediated disorders, we performed a cross-disease meta-analysis including GWAS data from 5,734 SSc patients, 4,588 CD patients and 14,568 controls of European origin. We identified 4 new loci shared between SSc and CD, IL12RB2, IRF1/SLC22A5, STAT3 and an intergenic locus at 6p21.31. Pleiotropic variants within these loci showed opposite allelic effects in the two analysed diseases and all of them showed a significant effect on gene expression. In addition, an enrichment in the IL-12 family and type I interferon signaling pathways was observed among the set of SSc-CD common genetic risk loci. In conclusion, through the first cross-disease meta-analysis of SSc and CD, we identified genetic variants with pleiotropic effects on two clinically distinct immune-mediated disorders. The fact that all these pleiotropic SNPs have opposite allelic effects in SSc and CD reveals the complexity of the molecular mechanisms by which polymorphisms affect diseases

Spatial extrapolation of lysimeter results using thermal infrared imaging

Measuring evaporation (E) with lysimeters is costly and prone to numerous errors. By comparing the energy balance and the remotely sensed surface temperature of lysimeters with those of the undisturbed surroundings, we were able to assess the representativeness of lysimeter measurements and to quantify differences in evaporation caused by spatial variations in soil moisture content. We used an algorithm (the so called 3T model) to spatially extrapolate the measured E of a reference lysimeter based on differences in surface temperature, net radiation and soil heat flux. We tested the performance of the 3T model on measurements with multiple lysimeters (47.5 cm inner diameter) and micro lysimeters (19.2 cm inner diameter) installed in bare sand, moss and natural dry grass. We developed different scaling procedures using in situ measurements and remotely sensed surface temperatures to derive spatially distributed estimates of

Diversity and abundance of ammonia-oxidizing <i>Archaea</i> and <i>Bacteria</i> in tropical and cold-water coral reef sponges

We analysed the diversity and abundance of ammonia-oxidizing Archaea (AOA) and Bacteria (AOB) in the shallow warm-water sponge Halisarca caerulea and the deep cold-water sponges Higginsia thielei and Nodastrella nodastrella. The abundance of AOA and AOB was analysed using catalyzed reporter deposition-fluorescence in situ hybridization and (real-time) quantitative PCR (Q-PCR) targeting archaeal and bacterial amoA genes. Archaeal abundance was similar between sponge species, while bacterial abundance was higher in H. caerulea than in N. nodastrella and H. thielei. Q-PCR showed that AOA outnumbered AOB by a factor of 2 to 35, suggesting a larger role of AOA than of AOB in ammonia oxidation in sponges. PCR-denaturing gradient gel electrophoresis was performed to analyse the taxonomic affiliation of the microbial community associated with these sponges. Archaeal and bacterial amoA genes were found in all 3 sponges. The structure of the phylogenetic trees in relation to temperature and sponge species was analysed using all published amoA sequences retrieved from sponges. Temperature was an important factor influencing the distribution of nitrifiers in sponges. Both archaeal and bacterial amoA sponge sequences tended to cluster with sequences retrieved from habitats of similar temperature. This is the first time that similarity in AOB diversity is described between distantly related species (H. thielei belonging to the class Demospongiae, and N. nodastrella to Hexactinellida). The results described here support the idea of a relatively uniform microbial community between distantly related sponges and suggest that temperature (rather than phylogenetic distance) is determining the diversity of AOA and AOB in sponges

Recovery patterns of the coral microbiome after relief of algal contact

Interactions between macroalgae and corals are omnipresent on eutrophied and overfished reefs worldwide. Contact with macroalgae can disrupt corals and their microbiomes through diverse mechanisms, including shading, abrasion, and the release of algal exudates. However, changes in the coral microbiome after algal contact ceases have not been studied. Weinvestigated the recovery of the microbiome of massive reef-building Porites corals following experimental removal of the overgrowing green macroalga Halimeda macrophysa. We followed changes in the microbiome of macroalgal-removed and adjacent healthy-looking tissue of coral colonies over 40 days. Coral tissue was predominantly bleached underneath the macroalgae but regained almost its full pigmentation by day 40. Despite this recovery in pigmentation, the bacterial microbiome of macroalgal-removed coral tissue did not return to that of adjacent healthy-looking tissue (control). Overall, macroalgal contact led to the suppression of Gammaproteobacteria and increased diversity and dominance of Alphaproteobacteria, a shift that persevered for 40 days after algal removal. Causal effect analysis showed a positive effect of influential OTUs in healthy-looking tissue assigned to Gammaproteobacteria and Bacteroidia on the relative abundance of other OTUs within these classes. The effect of influential OTUs assigned to Alphaproteobacteria in macroalgal-removed tissue on the relative abundance of other OTUs was more diverse. Despite the high heterogeneity of coral microbiomes, differences in the relative abundance of main bacterial classes and orders between control/healthy and macroalgal-removed tissue showed temporal patterns. Differences in the Alpha-, Gamma-, Deltaproteobacteria and Bacteroidia between control/healthy and macroalgal-removed tissue increased after cessation of macroalga contact and stabilized or declined towards day 40. Acidimicrobiia, Deltaproteobacteria, Rhodospirillales and Rhodovibrionales returned to average relative abundances in the adjacent control/healthy tissue after 40 days. Nevertheless, Rhizobiales and Rhodobacterales (Alphaproteobacteria) still dominated the macroalgal-removed microbiome on day 40. We conclude that macroalgal overgrowth induces changes in the coral microbiome, and that algal removal did not lead to full recovery of the microbiome in 40 days. Return of pigmentation and distinct shifts in bacterial groups over time appear a possible pathway to the recovery of the coral microbiome after macroalgal removal.</p

Data presented in the paper “Occurrence and life history characteristics of tropical flatfishes at the coral reefs of Curaçao, Dutch Caribbean"

Research objective: the collection of life history characteristics of tropical flatfishes occurring at the fringing reefs of Curaçao. Type of research: field work on coral reefs. Method of data collection: multiple scuba dives year round by two divers. Type of data: various body parameters on individual flatfishes of various specie