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Background Interferon-regulatory factors ( IRFs) play a crucial role in immunity, not only influencing interferon expression but also T cell differentiation. IRF-4 was only recently recognized as a further major player in T cell differentiation. Objective As IRF-1 polymorphisms were shown to be associated with atopy and allergy, we comprehensively investigated effects of IRF-4 variants on allergy, asthma and related phenotypes in German children. Methods Fifteen tagging single nucleotide polymorphisms (SNPs) in the IRF-4 gene were genotyped by MALDI- TOF MS in the cross-sectional ISAAC phase II study population from Munich and Dresden (age 9-11; N = 3099). Replication was performed in our previously established genome-wide association study ( GWAS) data set ( N = 1303) consisting of asthma cases from the Multicenter Asthma Genetic in Childhood ( MAGIC) study and reference children from the ISAAC II study. Results SNPs were not significantly associated with asthma but with bronchial hyperresponsiveness, atopy and, most interestingly, with recurrent bronchitis in the first data set. The IRF-4 variant rs9378805 was associated with recurrent bronchitis in the ISAAC population and replicated in the GWAS data set where further SNPs showed associations with recurrent bronchitis and asthma. Conclusions We found genetic associations in IRF-4 to be associated with recurrent bronchitis in our two study populations. Associated polymorphisms are localized in a putative regulatory element in the 3′ UTR region of IRF-4. These findings suggest a putative role of IRF-4 in the development of bronchitis. [ABSTRACT FROM AUTHOR]

Aims: To analyse the occurrence of faecal carriage of vancomycin-resistant enterococci (VRE) in Buteo buteo and to study the associated resistance and virulence genes. Methods and Results: The presence of VRE was investigated in 33 faecal samples of B. buteo. Samples were seeded in Slanetz–Bartley agar plates supplemented with vancomycin for VRE recovery. Genes encoding antimicrobial resistance and virulence were studied by polymerase chain reaction. Vancomycin-resistant Enterococcus faecium isolates were characterized by multilocus sequence typing. VRE with an acquired mechanism of resistance ( vanA genotype) were detected in 9% of samples analysed ( Ent. faecium and Enterococcus durans). In addition, 27% of samples contained VRE with an intrinsic mechanism of resistance ( Enterococcus gallinarum, vanC1). All vanA-containing isolates showed resistance to tetracycline and erythromycin and harboured the tet(M) and/or tet(L) genes, in addition to the ermB gene. The vat(E) and/or vat(D), cat(A) and aph(3′)-IIIa genes were identified in quinupristin–dalfopristin-, chloramphenicol-, and kanamycin-resistant vanA-containing strains, respectively. The sequence types ST273 and ST5 were identified in two vanA-positive Ent. faecium isolates, and the presence of hyl, gelE, cylA, cylL and cylM virulence genes and gelatinase activity were identified in Ent. faecium ST5 strain. Conclusions: The intestinal tract of B. buteo could be a reservoir of vanA-positive enterococci. Significance and Impact of the Study: First study focused to define the occurrence of vanA-containing Enterococcus strains in B. buteo. [ABSTRACT FROM AUTHOR]

Background: Interleukin 15 (IL15) promotes activation and proliferation of CD8+ T cells and enhances the differentiation into Th2 cells. A previous study described five polymorphisms in the IL15 gene to be associated with asthma in a haplotype analysis. Aim: We selected HapMap tagging single nucleotide polymorphisms (SNPs) from IL15 to systematically investigate these IL15 associations in a large population-based sample. Methods: Genotyping of seven IL15 SNPs was performed using MALDI-TOF MS in a cross-sectional study population of 3099 children from Dresden or Munich (age 9–11 years). All children were phenotyped by standardized and validated protocols for atopic phenotypes. Effects of single SNPs and haplotypes were studied usingsas 9.1.3 andhaploview. Equivalence tests were performed to prove the significance of negative results. Results: Neither single IL15 polymorphisms nor haplotype analyses showed associations with asthma or atopy after correction for multiple testing. Conclusion: These results do not confirm previous case–control studies and suggest that IL15 gene variants do not play an important role in the development for asthma or other atopic disorders. [ABSTRACT FROM AUTHOR]

Expressed sequence tags (ESTs) offer the opportunity to exploit single, low-copy, conserved sequence motifs for the development of simple sequence repeats (SSRs). The authors have examined the Sugarcane Expressed Sequence Tag database for the presence of SSRs. To test the utility of EST-derived SSR markers, a total of 342 EST-SSRs, which represent a subset of over 2005 SSR-containing sequences that were located in the sugarcane EST database, could be designed from the nonredundant SSR-positive ESTs for possible use as potential genic markers. These EST-SSR markers were used to screen 18 sugarcane (Saccharum spp.) varieties. A high proportion (65.5%) of the above EST-SSRs, which gave amplified fragments of foreseen size, detected polymorphism. The number of alleles ranged from 2 to 24 with an average of 7.55 alleles per locus, while polymorphism information content values ranged from 0.16 to 0.94, with an average of 0.73. The ability of each set of EST-SSR markers to discriminate between varieties was generally higher than the polymorphism information content analysis. When tested for functionality, 82.1% of these 224 EST-SSRs were found to be functional, showing homology to known genes. As the EST-SSRs are within the expressed portion of the genome, they are likely to be associated to a particular gene of interest, improving their utility for genetic mapping; identification of quantitative trait loci, and comparative genomics studies of sugarcane. The development of new EST-SSR markers will have important implications for the genetic analysis and exploitation of the genetic resources of sugarcane and related species and will provide a more direct estimate of functional diversity. Les étiquettes de séquences exprimées (EST) offrent une opportunité d’exploiter des motifs conservés présents en simple ou peu de copies pour le développement de microsatellites (SSR). Les auteurs ont inspecté la base de données d’EST de la canne à sucre pour la présence de SSR. Pour vérifier l’utilité des SSR dérivés d’EST, 342 EST-SSR, lesquels représentent un sous-ensemble des 2 005 séquences contenant des SSR qui ont été trouvées au sein de cette banque d’EST de la canne à sucre, étaient propices au développement de marqueurs génétiques parmi les EST non-redondants contenant des EST. Ces marqueurs EST-SSR ont été employés pour cribler 18 variétés de canne à sucre (Saccharum spp.). Une proportion élevée (65,5%) de ces EST-SSR qui ont amplifié des produits de la taille attendue étaient polymorphes. Le nombre d’allèles variait entre 2 et 24, pour une moyenne de 7,55 allèles par locus, et les valeurs de contenu d’information de polymorphisme variaient entre 0,16 et 0,94, pour une moyenne de 0,73. La capacité de tels jeux de marqueurs à discriminer entre les variétés était généralement plus élevée que l’analyse de contenu d’information de polymorphisme. Lorsque testés pour leur fonction, 82,1% de ces 224 marqueurs EST-SSR se sont avérés fonctionnels en montrant de l’homologie avec des gènes connus. Puisque ces EST-SSR font partie de la portion exprimée du génome, ils sont vraisemblablement associés à des gènes d’intérêt, ce qui augmente leur utilité pour des fins de cartographie génétique, pour l’identification de locus de caractères quantitatifs et pour des études de génomique comparative chez la canne à sucre. Le développement de nouveaux marqueurs EST-SSR aura d’importantes retombées en matière d’analyse génétique et d’exploitation des ressources génétiques chez la canne à sucre et des espèces apparentées en plus de fournir un estimé plus direct de la diversité fonctionnelle. [ABSTRACT FROM AUTHOR]

Background: Signal transducer and activator of transcription 1 (STAT1), an intracellular signal transducer and activator of transcription centrally involved in many inflammatory pathways, was recently suggested to play an important role in allergy related immune responses. Aim: Thus, we investigated the effect of polymorphisms in the STAT1 gene on the development of atopic sensitization and allergic diseases. Methods: Haplotype tagging single nucleotide polymorphisms (SNPs) previously described in the STAT1 gene were genotyped by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry technology in a cross-sectional study population of 3099 German children recruited and phenotyped by the International Study of Asthma and Allergy in Childhood, phase II (ISAAC II). Effects of single SNPs and haplotypes were studied using SAS/Genetics and Haploview. Results: The polymorphism C39134A (rs3771300), located in a potentially cis acting regulatory element in STAT1 intron 24, was inversely related to atopy measured by skin prick test, total and specific serum IgE levels while no effect on atopic disease risk was observed. Conclusion: Our results indicate that STAT1 SNP C39134A may protect from atopic sensitization. Because of its location in a highly conserved noncoding sequence near a putative GATA3 binding site, this polymorphism represents an interesting target for further studies. [ABSTRACT FROM AUTHOR]

Microsatellites or simple sequence repeats (SSRs) are one of the most suitable markers for genome analysis as they have great potential to aid breeders to develop new improved sugarcane varieties. The development of SSR derived from expressed sequence tags (EST) opens new opportunities for genetic investigations at a functional level. In the present work, the polymorphism obtained with a subset of 51 EST–SSRs derived fromsucest was compared with those generated by 50 genomic SSRs (gSSR) in terms of number of alleles, polymorphism information content, discrimination power and their ability to establish genetic relationships among 18 sugarcane clones including three Saccharum species ( S. officinarum, S. barberi, S. sinense). The majority of EST–SSRs loci had four to six alleles in contrast to the seven to nine observed for the gSSRs loci. Approximately, 35% of the gSSRs had PIC values around 0.90 in contrast to 15% of the EST–SSRs. However, the mean discrimination power of the two types of SSR did not differ significantly as much as the average genetic similarity (GS) based on Dice coefficient. The correlation between GS of the two types of SSRs was high ( r = 0.71/P = 0.99) and significant. Although differences were observed between dendrograms obtained with each SSR type, both were in good agreement with pedigree information. The S. officinarum clone IJ76-314 was grouped apart from the other clones evaluated. The results here demonstrate that EST–SSRs can be successfully used for genetic relationship analysis, extending the knowledge of genetic diversity of sugarcane to a functional level. [ABSTRACT FROM AUTHOR]