RSSsite: a reference database and prediction tool for the identification of cryptic Recombination Signal Sequences in human and murine genomes

Recombination signal sequences (RSSs) flanking V, D and J gene segments are recognized and cut by the VDJ recombinase during development of B and T lymphocytes. All RSSs are composed of seven conserved nucleotides, followed by a spacer (containing either 12 ± 1 or 23 ± 1 poorly conserved nucleotides) and a conserved nonamer. Errors in V(D)J recombination, including cleavage of cryptic RSS outside the immunoglobulin and T cell receptor loci, are associated with oncogenic translocations observed in some lymphoid malignancies. We present in this paper the RSSsite web server, which is available from the address http://www.itb.cnr.it/rss. RSSsite consists of a web-accessible database, RSSdb, for the identification of pre-computed potential RSSs, and of the related search tool, DnaGrab, which allows the scoring of potential RSSs in user-supplied sequences. This latter algorithm makes use of probability models, which can be recasted to Bayesian network, taking into account correlations between groups of positions of a sequence, developed starting from specific reference sets of RSSs. In validation laboratory experiments, we selected 33 predicted cryptic RSSs (cRSSs) from 11 chromosomal regions outside the immunoglobulin and TCR loci for functional testing

Clinical impact of subclonal EGFR T790M mutations in advanced-stage EGFR-mutant non-small-cell lung cancers.

Advanced non-small-cell lung cancer (NSCLC) patients with EGFR T790M-positive tumours benefit from osimertinib, an epidermal growth factor receptor-tyrosine kinase inhibitor (EGFR-TKI). Here we show that the size of the EGFR T790M-positive clone impacts response to osimertinib. T790M subclonality, as assessed by a retrospective NGS analysis of 289 baseline plasma ctDNA samples from T790M-positive advanced NSCLC patients from the AURA3 phase III trial, is associated with shorter progression-free survival (PFS), both in the osimertinib and the chemotherapy-treated patients. Both baseline and longitudinal ctDNA profiling indicate that the T790M subclonal tumours are enriched for PIK3CA alterations, which we demonstrate to confer resistance to osimertinib in vitro that can be partially reversed by PI3K pathway inhibitors. Overall, our results elucidate the impact of tumour heterogeneity on response to osimertinib in advanced stage NSCLC patients and could help define appropriate combination therapies in these patients

Alimentação na escola como forma de atender às recomendações nutricionais de alunos dos Centros Integrados de Educação Pública (CIEPS) School meal programs as a means to meet nutritional requirements for students in the Integrated Public School Centers (CIEPS)

Avalia-se o consumo alimentar de 244 crianças amostradas utilizando-se o registro dos alimentos por elas ingeridos, durante três dias não consecutivos da semana. Analisa-se a adequação de energia e nutrientes de acordo com o padrão definido para a população brasileira. Observa-se que a dieta dos escolares revela-se, em média, deficiente em energia: as refeições consumidas no âmbito dos CIEPs não alcançam 70% de adequação. Verifica-se que, inversamente, o conteúdo protéico das dietas apresenta-se muito acima do preconizado. Ressalta-se a satisfatória adequação das refeições consumidas no âmbito dos CIEPs quanto às vitaminas A, tiamina, riboflavina e niacina. Merece destaque a surpreendente adequação das dietas dos escolares em relação ao ácido ascórbico. Contribui para esse resultado a presença freqüente de frutas cítricas nas refeições da escola. Com relação ao ferro, constata-se que, com exceção dos escolares mais velhos, todos os demais exibem dietas que ultrapassam 90% de adequação. Quanto ao cálcio, nota-se que as dietas da maioria (exceto a dos alunos de maior idade) alcançam 100% de adequação. Resultados do estudo mostram necessidade de corrigir falhas do conteúdo nutricional das refeições distribuídas na escola, pois as mesmas constituem parte fundamental do consumo alimentar dos alunos dos CIEPs.<br>This study evaluates food intake of 244 children between ages 7-13 years using records of ingested foods on three non-consecutive days. The study analyzes energy and nutrient adequacy based on standards for the Brazilian population. Diet was generally found to be energy-deficient: meals consumed at the CIEPs met less than 70% of the requirement. On the other hand, protein was well above recommended levels. Worthy of note was the adequacy of meals in the CIEPs as to vitamin A, thiamin, riboflavin, and niacin, as well as the surprising adequacy of ascorbic acid, resulting from the frequent presence of citrus fruits in school meals. Except for older students, all schoolchildren studied had greater than 90% minimum iron intake. As for calcium, again except for older ones, consumption was 100% or more of minimum required levels. Results showed the need to correct flaws in the nutritional content of school meals, which are central to dietary intake for CIEP students

The PHD Domain of Np95 (mUHRF1) Is Involved in Large-Scale Reorganization of Pericentromeric Heterochromatin

Heterochromatic chromosomal regions undergo large-scale reorganization and progressively aggregate, forming chromocenters. These are dynamic structures that rapidly adapt to various stimuli that influence gene expression patterns, cell cycle progression, and differentiation. Np95-ICBP90 (m- and h-UHRF1) is a histone-binding protein expressed only in proliferating cells. During pericentromeric heterochromatin (PH) replication, Np95 specifically relocalizes to chromocenters where it highly concentrates in the replication factories that correspond to less compacted DNA. Np95 recruits HDAC and DNMT1 to PH and depletion of Np95 impairs PH replication. Here we show that Np95 causes large-scale modifications of chromocenters independently from the H3:K9 and H4:K20 trimethylation pathways, from the expression levels of HP1, from DNA methylation and from the cell cycle. The PHD domain is essential to induce this effect. The PHD domain is also required in vitro to increase access of a restriction enzyme to DNA packaged into nucleosomal arrays. We propose that the PHD domain of Np95-ICBP90 contributes to the opening and/or stabilization of dense chromocenter structures to support the recruitment of modifying enzymes, like HDAC and DNMT1, required for the replication and formation of PH