Increased susceptibility of 129SvEvBrd mice to IgE-Mast cell mediated anaphylaxis

<p>Abstract</p> <p>Background</p> <p>Experimental analyses have identified strain-dependent factors that regulate susceptibility to anaphylaxis in mice. We assessed the susceptibility of the widely used 129SvEvBrd (also known as 129S5) mouse strain to IgE/mast cell-mediated anaphylaxis as compared to BALB/c. Mice were subjected to passive and oral Ovalbumin [OVA]-induced active anaphylaxis. Tissue mast cell, plasma histamine, total IgE and OVA-specific IgE levels and susceptibility to histamine i.v infusion were assessed. Bone marrow mast cell (BMMC)s were examined for Fc_εRI, c-kit, degranulation efficiency, proliferation, apoptosis and cytokine profile.</p> <p>Results</p> <p>129S5 mice had significantly increased susceptibility to passive and oral OVA-induced active anaphylaxis. Increased susceptibility to anaphylaxis was associated with increased homeostatic mast cell levels but not OVA-specific IgE or IgG₁levels. <it>In vitro </it>analyses of BMMCs revealed no difference in Fc_εRI and c-Kit expression, however, 129S5 BMMCs possessed greater proliferative capacity and reduced caspase-3-mediated apoptosis. IgE-BMMC degranulation assays demonstrated no difference in degranulation efficiency. Furthermore, 129S5 mice possessed increased sensitivity to histamine-induced hypothermia.</p> <p>Conclusions</p> <p>We conclude that 129S5 mice have increased susceptibility to anaphylaxis as compared to BALB/c strain and their increased susceptibility was associated with altered mast cell proliferation and homeostatic tissue levels and responsiveness to histamine. Given the wide spread usage of the 129SvEvBrd strain of mice in experimental gene targeting methodology, these data have important implications for studying IgE-reactions in mouse systems.</p

Quality of Computationally Inferred Gene Ontology Annotations

Gene Ontology (GO) has established itself as the undisputed standard for protein function annotation. Most annotations are inferred electronically, i.e. without individual curator supervision, but they are widely considered unreliable. At the same time, we crucially depend on those automated annotations, as most newly sequenced genomes are non-model organisms. Here, we introduce a methodology to systematically and quantitatively evaluate electronic annotations. By exploiting changes in successive releases of the UniProt Gene Ontology Annotation database, we assessed the quality of electronic annotations in terms of specificity, reliability, and coverage. Overall, we not only found that electronic annotations have significantly improved in recent years, but also that their reliability now rivals that of annotations inferred by curators when they use evidence other than experiments from primary literature. This work provides the means to identify the subset of electronic annotations that can be relied upon—an important outcome given that >98% of all annotations are inferred without direct curation

Prisutnost vrsta roda Legionella u vodoopskrbnom sustavu u objektima koji su stalno otvoreni i objektima sezonskog tipa

The purpose of this study was to compare the quality of hot water between eleven hotels in the Split-Dalmatia County, Croatia that are open year round and 10 summer season hotels and retirement homes with irregular use of water. We took 122 samples between May and December 2009. Water temperature and free residual chlorine were measured in situ. Physical and chemical analysis included pH, electrical conductivity, and concentrations of iron, manganese, copper, zinc, calcium, and magnesium that were measured using atomic absorption spectrophotometry, while the Legionella species were determined using a cultivation method on buffered charcoal yeast extract agar. Differences in metal concentrations between the seasonal and year-round accommodation facilities were negligible, save for zinc that was higher in year-round (0.341 mg L-1) than in seasonal facilities (0.130 mg L-1). Samples from all year-round and six summer season hotels were negative to the Legionella species, but four seasonal facilities turned up with positive samples to Legionella pneumophila. Our study has demonstrated that water quality differs between year-round and seasonal accommodation facilities. These findings suggest that metal plumbing components and associated corrosion products are important factors in the survival and growth of Legionella species in water distribution systems.Svrha ovog istraživanja bila je procijeniti kakvoću tople vode s pomoću određenih fi zikalnih, kemijskih i mikrobioloških parametara, analizirajući uzorke vode na prisutnost vrsta roda Legionella, u ustanovama koje su otvorene tijekom cijele godine i onih koje su otvorene samo tijekom ljetnih mjeseci u Splitskodalmatinskoj županiji, Hrvatska. U istraživanju su određene koncentracije željeza, mangana, bakra, cinka, kalcija i magnezija u toploj vodi u 122 uzorka iz 21 ustanove u razdoblju od svibnja 2009. do prosinca 2009. Deset ustanova bilo je otvoreno tijekom ljetnih mjeseci, dok je 11 ostalo otvoreno tijekom godine. Temperatura i slobodni rezidualni klor mjereni su in situ prijenosnim digitalnim termometrom i prijenosnim digitalnim aparatom za mjerenje slobodnoga rezidualnog klora. Koncentracije željeza, mangana, bakra, cinka, kalcija i magnezija određene su metodom atomske apsorpcijske spektrofotometrije. Legionele su određivane u istim uzorcima metodom kultivacije na BCYE-agaru 72 h pri 36 °C. Nalaz vrste Legionella pneumophila bio je negativan u 11 ustanova koje rade kroz cijelu godinu i u šest ustanova koje su otvorene sezonski. Rezultati su bili pozitivni u 4 ustanove koje su otvorene sezonski. U ustanovama koje su otvorene tijekom cijele godine određene su koncentracije u vodi: željeza 0,039 mg L-1, magnezija 0,791 mg L-1, kalcija 52,94 mg L-1, cinka 0,341 mg L-1, bakra 0,012 mg L-1 te mangana 5,08 μg L-1. U ustanovama otvorenim sezonski također su u vodiodređene koncentracije: željeza 0,052 mg L-1, magnezija 0,867 mg L-1, kalcija 54,87 mg L-1, cinka 0,130 mg L-1, bakra 0,008 mg L-1 i mangana 5,64 μg L-1. Samo je koncentracija cinka bila povišena u hotelima koji su radili tijekom cijele godine. Naše je istraživanje pokazalo da se kvaliteta vode razlikuje u vodovodnim sustavima koji se trajno rabe u odnosu prema sustavima sezonskog tipa. Ovo saznanje ima veliko značenje za kontrolu kakvoće vode u turističkim područjima

Translational Selection Is Ubiquitous in Prokaryotes

Codon usage bias in prokaryotic genomes is largely a consequence of background substitution patterns in DNA, but highly expressed genes may show a preference towards codons that enable more efficient and/or accurate translation. We introduce a novel approach based on supervised machine learning that detects effects of translational selection on genes, while controlling for local variation in nucleotide substitution patterns represented as sequence composition of intergenic DNA. A cornerstone of our method is a Random Forest classifier that outperformed previous distance measure-based approaches, such as the codon adaptation index, in the task of discerning the (highly expressed) ribosomal protein genes by their codon frequencies. Unlike previous reports, we show evidence that translational selection in prokaryotes is practically universal: in 460 of 461 examined microbial genomes, we find that a subset of genes shows a higher codon usage similarity to the ribosomal proteins than would be expected from the local sequence composition. These genes constitute a substantial part of the genome—between 5% and 33%, depending on genome size—while also exhibiting higher experimentally measured mRNA abundances and tending toward codons that match tRNA anticodons by canonical base pairing. Certain gene functional categories are generally enriched with, or depleted of codon-optimized genes, the trends of enrichment/depletion being conserved between Archaea and Bacteria. Prominent exceptions from these trends might indicate genes with alternative physiological roles; we speculate on specific examples related to detoxication of oxygen radicals and ammonia and to possible misannotations of asparaginyl–tRNA synthetases. Since the presence of codon optimizations on genes is a valid proxy for expression levels in fully sequenced genomes, we provide an example of an “adaptome” by highlighting gene functions with expression levels elevated specifically in thermophilic Bacteria and Archaea

An Expanded Evaluation of Protein Function Prediction Methods Shows an Improvement In Accuracy

Background: A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their relatively low throughput and restricted purview have led to an increasing role for computational function prediction. However, assessing methods for protein function prediction and tracking progress in the field remain challenging. Results: We conducted the second critical assessment of functional annotation (CAFA), a timed challenge to assess computational methods that automatically assign protein function. We evaluated 126 methods from 56 research groups for their ability to predict biological functions using Gene Ontology and gene-disease associations using Human Phenotype Ontology on a set of 3681 proteins from 18 species. CAFA2 featured expanded analysis compared with CAFA1, with regards to data set size, variety, and assessment metrics. To review progress in the field, the analysis compared the best methods from CAFA1 to those of CAFA2. Conclusions: The top-performing methods in CAFA2 outperformed those from CAFA1. This increased accuracy can be attributed to a combination of the growing number of experimental annotations and improved methods for function prediction. The assessment also revealed that the definition of top-performing algorithms is ontology specific, that different performance metrics can be used to probe the nature of accurate predictions, and the relative diversity of predictions in the biological process and human phenotype ontologies. While there was methodological improvement between CAFA1 and CAFA2, the interpretation of results and usefulness of individual methods remain context-dependent

An expanded evaluation of protein function prediction methods shows an improvement in accuracy

Background: A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their relatively low throughput and restricted purview have led to an increasing role for computational function prediction. However, assessing methods for protein function prediction and tracking progress in the field remain challenging. Results: We conducted the second critical assessment of functional annotation (CAFA), a timed challenge to assess computational methods that automatically assign protein function. We evaluated 126 methods from 56 research groups for their ability to predict biological functions using Gene Ontology and gene-disease associations using Human Phenotype Ontology on a set of 3681 proteins from 18 species. CAFA2 featured expanded analysis compared with CAFA1, with regards to data set size, variety, and assessment metrics. To review progress in the field, the analysis compared the best methods from CAFA1 to those of CAFA2. Conclusions: The top-performing methods in CAFA2 outperformed those from CAFA1. This increased accuracy can be attributed to a combination of the growing number of experimental annotations and improved methods for function prediction. The assessment also revealed that the definition of top-performing algorithms is ontology specific, that different performance metrics can be used to probe the nature of accurate predictions, and the relative diversity of predictions in the biological process and human phenotype ontologies. While there was methodological improvement between CAFA1 and CAFA2, the interpretation of results and usefulness of individual methods remain context-dependent. Keywords: Protein function prediction, Disease gene prioritizationpublishedVersio

Meningiomas exhibit loss of heterozygosity of the APC gene

The molecular mechanisms and candidate genes involved in development of meningiomas still need investigation and elucidation. In the present study 33 meningiomas were analyzed regarding genetic changes of tumor suppressor gene Adenomatous polyposis coli (APC), a component of the wnt signaling. Gene instability was tested by polymerase chain reaction/loss of heterozygosity (LOH) using Restriction Fragment Length Polymorphism (RFLP) method. RFLP was performed by two genetic markers, Rsa I in APC's exon 11 and Msp I in its exon 15. The results of our analysis showed altogether 15 samples with LOH of the APC gene out of 32 heterozygous patients (47%). Seven patients had LOHs at both exons, while four LOHs were exclusive for exon 11 and four for exon 15. The changes were distributed according to pathohistological grade as follows: 46% of meningothelial meningioma showed LOH; 33% of fibrous; 75% of mixed (transitional); 75% of angiomatous, and one LOH was found in a single case of psammomatous meningioma. None of the LOHs were found in atypical and anaplastic cases. Immunostaining showed that samples with LOHs were accompanied with the absence of APC protein expression or presence of mutant APC proteins (chi(2 )= 13.81, df = 2, P < 0.001). We also showed that nuclear localization of beta-catenin correlates to APC genetic changes (chi(2 )= 21.96, df = 2, P < 0.0001). The results of this investigation suggest that genetic changes of APC gene play a role in meningioma formation