Variation at interleukin-6 receptor gene is associated to joint damage in rheumatoid arthritis

IntroductionInterleukin-6 (IL-6) cytokine signaling is key in Rheumatoid Arthritis (RA) pathophysiology. Blocking IL-6 receptor (IL6R) has proven to be a highly effective treatment to prevent joint damage. This study was performed to investigate the association between the genetic variation at IL6R gene and the severity of joint damage in RA.MethodsIL6R gene tagging SNPs (n = 5) were genotyped in a discovery group of 527 RA patients from 5 different university hospitals from Spain. For each marker, a linear regression analysis was performed using an additive model and adjusting for the years of evolution of the disease, autoantibody status, gender and age. Haplotypes combining the SNPs were also estimated and tested for association with the level of joint destruction. Using an independent cohort of 705 RA patients from 6 university hospitals we performed a validation study of the SNPs associated in the discovery phase.ResultsIn the discovery group we found a highly significant association between IL6R SNP rs4845618 and the level of joint destruction in RA (P = 0.0058, P_corrected = 0.026), and a moderate association with SNP rs4453032 (P = 0.02, P_corrected = 0.05). The resulting haplotype from both SNPs was more significantly associated with joint damage (P = 0.0037, P_corrected = 0.011). Using the validation cohort, we replicated the association between the two IL-6R SNPs with the degree of joint destruction in RA (P = 0.007 and P = 0.04, meta-analysis P = 0.00011 and P = 0.0021, respectively), and the haplotype association (P = 0.0058, meta-analysis P = 6.64 e-5).ConclusionsGenetic variation at IL6R gene is associated with joint damage in RA.

Electronic supplementary material

The online version of this article (doi:10.1186/s13075-015-0737-8) contains supplementary material, which is available to authorized users.     

Comparative field study to evaluate the performance of three different traps for collecting sand flies in northeastern Italy

Three standard methods for collecting sand flies (sticky trap, CDC light trap, and CO₂ trap) were compared in a field study conducted from June to October, 2012, at a site located in the center of a newly established autochthonous focus of canine leishmaniasis in northeastern Italy. Six traps (two sticky traps, two CDC light traps, and two CO₂ traps) were activated at the same time for a single night every two weeks during the season of sand fly activity. A total of 5,667 sand flies were collected and 2,213 identified, of which 82.1% were Phlebotomus perniciosus, 17.4% P. neglectus, 0.3% Sergentomya minuta, and 0.2% P. mascitti. The performances of all traps were influenced by their position inside the site, increasing with proximity to the animal shelters. CO₂ traps were more attractive for females of P. perniciosus and P. neglectus. CDC light traps showed an intermediate efficiency and were more attractive for P. neglectus, compared to other two traps. Results suggest that in northern Italy the CO₂ trap is a suitable sampling method for sand fly monitoring programs that include transmitted pathogen surveillance.     

CNstream: A method for the identification and genotyping of copy number polymorphisms using Illumina microarrays

Background  

Understanding the genetic basis of disease risk in depth requires an exhaustive knowledge of the types of genetic variation. Very recently, Copy Number Variants (CNVs) have received much attention because of their potential implication in common disease susceptibility. Copy Number Polymorphisms (CNPs) are of interest as they segregate at an appreciable frequency in the general population (i.e. > 1%) and are potentially implicated in the genetic basis of common diseases.     

AStream: an R package for annotating LC/MS metabolomic data

AStream, an R-statistical software package for the curation and identification of feature peaks extracted from liquid chromatography mass spectrometry (LC/MS) metabolomics data, is described. AStream detects isotopic, fragment and adduct patterns by identifying feature pairs that fulfill expected relational patterns. Data reduction by AStream allows compounds to be identified reliably and subsequently linked to metabolite databases. AStream provides researchers with a fast, reliable tool for summarizing metabolomic data, notably reducing curation time and increasing consistency of results. AVAILABILITY: The AStream R package and a study example can be freely accessed at http://www.urr.cat/AStream/AStream.html.     

Allergy to pollen of urban cultivated plants

Pollens of many plants located in public or privategardens may cause pollinosis in predisposedindividuals. There is evidence that the prevalence ofsensitization to ``new' tree pollens (Betulaceae,Corylaceae, Cupressaceae, Taxodiaceae, and otherfamilies) is increasing in the recent years in Italy.Allergenic plants are often imported from foreigncountries, therefore low-allergenic species must berecognized in order to prevent new pollensensitizations. In this study we suggest a list ofrecommended and notrecommended plants for public andprivate green.     

Unravelling plant diversification: Intraspecific genetic differentiation in hybridizing Anacyclus species in the western Mediterranean Basin

Premise

The interfertile species Anacyclus clavatus, A. homogamos, and A. valentinus represent a plant complex coexisting in large anthropic areas of the western Mediterranean Basin with phenotypically mixed populations exhibiting a great floral variation. The goal of this study was to estimate the genetic identity of each species, to infer the role of hybridization in the observed phenotypic diversity, and to explore the effect of climate on the geographic distribution of species and genetic clusters.

Methods

We used eight nuclear microsatellites to genotype 585 individuals from 31 populations of three Anacyclus species for population genetic analyses by using clustering algorithms based on Bayesian models and ordination methods. In addition, we used ecological niche models and niche overlap analyses for both the species and genetic clusters. We used an expanded data set, including 721 individuals from 129 populations for ecological niche models of the genetic clusters.

Results

We found a clear correspondence between species and genetic clusters, except for A. clavatus that included up to three genetic clusters. We detected individuals with admixed genetic ancestry in A. clavatus and in mixed populations. Ecological niche models predicted similar distributions for species and genetic clusters. For the two specific genetic clusters of A. clavatus, ecological niche models predicted remarkably different areas.

Conclusions

Gene flow between Anacyclus species likely explains phenotypic diversity in contact areas. In addition, we suggest that introgression could be involved in the origin of one of the two A. clavatus genetic clusters, which also showed ecological differentiation.     

GStream: Improving SNP and CNV Coverage on Genome-Wide Association Studies

We present GStream, a method that combines genome-wide SNP and CNV genotyping in the Illumina microarray platform with unprecedented accuracy. This new method outperforms previous well-established SNP genotyping software. More importantly, the CNV calling algorithm of GStream dramatically improves the results obtained by previous state-of-the-art methods and yields an accuracy that is close to that obtained by purely CNV-oriented technologies like Comparative Genomic Hybridization (CGH). We demonstrate the superior performance of GStream using microarray data generated from HapMap samples. Using the reference CNV calls generated by the 1000 Genomes Project (1KGP) and well-known studies on whole genome CNV characterization based either on CGH or genotyping microarray technologies, we show that GStream can increase the number of reliably detected variants up to 25% compared to previously developed methods. Furthermore, the increased genome coverage provided by GStream allows the discovery of CNVs in close linkage disequilibrium with SNPs, previously associated with disease risk in published Genome-Wide Association Studies (GWAS). These results could provide important insights into the biological mechanism underlying the detected disease risk association. With GStream, large-scale GWAS will not only benefit from the combined genotyping of SNPs and CNVs at an unprecedented accuracy, but will also take advantage of the computational efficiency of the method.     

Modelling invasive alien species distributions from digital biodiversity atlases. Model upscaling as a means of reconciling data at different scales

Aim

There is a wealth of information on species occurrences in biodiversity data banks, albeit presence‐only, biased and scarce at fine resolutions. Moreover, fine‐resolution species maps are required in biodiversity conservation. New techniques for dealing with this kind of data have been reported to perform well. These fine‐resolution maps would be more robust if they could explain data at coarser resolutions at which species distributions are well represented. We present a new methodology for testing this hypothesis and apply it to invasive alien species (IAS).

Location

Catalonia, Spain.

Methods

We used species presence records from the Biodiversity data bank of Catalonia to model the distribution of ten IAS which, according to some recent studies, achieve their maximum distribution in the study area. To overcome problems inherent with the data, we prepared different correction treatments: three for dealing with bias and five for autocorrelation. We used the MaxEnt algorithm to generate models at 1‐km resolution for each species and treatment. Acceptable models were upscaled to 10 km and validated against independent 10 km occurrence data.

Results

Of a total of 150 models, 20 gave acceptable results at 1‐km resolution and 12 passed the cross‐scale validation test. No apparent pattern emerged, which could serve as a guide on modelling. Only four species gave models that also explained the distribution at the coarser scale.

Main conclusions

Although some techniques may apparently deliver good distribution maps for species with scarce and biased data, they need to be taken with caution. When good independent data at a coarser scale are available, cross‐scale validation can help to produce more reliable and robust maps. When no independent data are available for validation, however, new data gathering field surveys may be the only option if reliable fine‐scale resolution maps are needed.     

Post-mortem investigations on a leatherback turtle Dermochelys coriacea stranded along the Northern Adriatic coastline

Leatherback sea turtles Dermochelys coriacea are regularly reported in the Mediterranean Sea but rarely reach the northern Adriatic Sea. In the summer of 2009, a well-preserved carcass of an adult female of this species was found dead along the coast of Lido di Venezia. A complete necropsy was carried out, along with evaluation of levels of tissue trace elements. The the post-mortem revealed acute severe bacterial gastroenteritis caused by Photobacterium damselae ssp. piscicida, an opportunistic agent that infected an apparently debilitated animal weakened by ingested plastic debris. High levels of heavy metals (Hg, Pb, Cd and As) found in the liver and kidneys might have contributed to the animal's demise. These findings support previous indications that marine debris is one of the major threats to marine animals, particularly for critically endangered species such as the leatherback turtle.