The expression of tubulin cofactor A (TBCA) is regulated by a noncoding antisense Tbca RNA during testis maturation

Abstract - Recently, long noncoding RNAs have emerged as pivotal molecules for the regulation of coding genes' expression. These molecules might result from antisense transcription of functional genes originating natural antisense transcripts (NATs) or from transcriptional active pseudogenes. TBCA interacts with β-tubulin and is involved in the folding and dimerization of new tubulin heterodimers, the building blocks of microtubules. Methodology/Principal findings: We found that the mouse genome contains two structurally distinct Tbca genes located in chromosomes 13 (Tbca13) and 16 (Tbca16). Interestingly, the two Tbca genes albeit ubiquitously expressed, present differential expression during mouse testis maturation. In fact, as testis maturation progresses Tbca13 mRNA levels increase progressively, while Tbca16 mRNA levels decrease. This suggests a regulatory mechanism between the two genes and prompted us to investigate the presence of the two proteins. However, using tandem mass spectrometry we were unable to identify the TBCA16 protein in testis extracts even in those corresponding to the maturation step with the highest levels of Tbca16 transcripts. These puzzling results led us to re-analyze the expression of Tbca16. We then detected that Tbca16 transcription produces sense and natural antisense transcripts. Strikingly, the specific depletion by RNAi of these transcripts leads to an increase of Tbca13 transcript levels in a mouse spermatocyte cell line. Conclusions/Significance: Our results demonstrate that Tbca13 mRNA levels are post-transcriptionally regulated by the sense and natural antisense Tbca16 mRNA levels. We propose that this regulatory mechanism operates during spermatogenesis, a process that involves microtubule rearrangements, the assembly of specific microtubule structures and requires critical TBCA levels.

Membrane selectivity versus sensor response in hydrogenated amorphous silicon CHEMFETs using a semi-empirical model

Toxic amides, such as acrylamide, are potentially harmful to Human health, so there is great interest in the fabrication of compact and economical devices to measure their concentration in food products and effluents. The CHEmically Modified Field Effect Transistor (CHEMFET) based onamorphous silicon technology is a candidate for this type of application due to its low fabrication cost. In this article we have used a semi-empirical modelof the device to predict its performance in a solution of interfering ions. The actual semiconductor unit of the sensor was fabricated by the PECVD technique in the top gate configuration. The CHEMFET simulation was performed based on the experimental current voltage curves of the semiconductor unit and on an empirical model of the polymeric membrane. Results presented here are useful for selection and design of CHEMFET membranes and provide an idea of the limitations of the amorphous CHEMFET device. In addition to the economical advantage, the small size of this prototype means it is appropriate for in situ operation and integration in a sensor array.

Arrow Plot: a new graphical tool for selecting up and down regulated genes and genes differentially expressed on samples subgroups

Background: A common task in analyzing microarray data is to determine which genes are differentially expressed across two (or more) kind of tissue samples or samples submitted under experimental conditions. Several statistical methods have been proposed to accomplish this goal, generally based on measures of distance between classes. It is well known that biological samples are heterogeneous because of factors such as molecular subtypes or genetic background that are often unknown to the experimenter. For instance, in experiments which involve molecular classification of tumors it is important to identify significant subtypes of cancer. Bimodal or multimodal distributions often reflect the presence of subsamples mixtures. Consequently, there can be genes differentially expressed on sample subgroups which are missed if usual statistical approaches are used. In this paper we propose a new graphical tool which not only identifies genes with up and down regulations, but also genes with differential expression in different subclasses, that are usually missed if current statistical methods are used. This tool is based on two measures of distance between samples, namely the overlapping coefficient (OVL) between two densities and the area under the receiver operating characteristic (ROC) curve. The methodology proposed here was implemented in the open-source R software. Results: This method was applied to a publicly available dataset, as well as to a simulated dataset. We compared our results with the ones obtained using some of the standard methods for detecting differentially expressed genes, namely Welch t-statistic, fold change (FC), rank products (RP), average difference (AD), weighted average difference (WAD), moderated t-statistic (modT), intensity-based moderated t-statistic (ibmT), significance analysis of microarrays (samT) and area under the ROC curve (AUC). On both datasets all differentially expressed genes with bimodal or multimodal distributions were not selected by all standard selection procedures. We also compared our results with (i) area between ROC curve and rising area (ABCR) and (ii) the test for not proper ROC curves (TNRC). We found our methodology more comprehensive, because it detects both bimodal and multimodal distributions and different variances can be considered on both samples. Another advantage of our method is that we can analyze graphically the behavior of different kinds of differentially expressed genes. Conclusion: Our results indicate that the arrow plot represents a new flexible and useful tool for the analysis of gene expression profiles from microarrays.

OsRMC, a negative regulator of salt stress response in rice, is regulated by two AP2/ERF transcription factors

High salinity causes remarkable losses in rice productivity worldwide mainly because it inhibits growth and reduces grain yield. To cope with environmental changes, plants evolved several adaptive mechanisms, which involve the regulation of many stress-responsive genes. Among these, we have chosen OsRMC to study its transcriptional regulation in rice seedlings subjected to high salinity. Its transcription was highly induced by salt treatment and showed a stress-dose-dependent pattern. OsRMC encodes a receptor-like kinase described as a negative regulator of salt stress responses in rice. To investigate how OsRMC is regulated in response to high salinity, a salt-induced rice cDNA expression library was constructed and subsequently screened using the yeast one-hybrid system and the OsRMC promoter as bait. Thereby, two transcription factors (TFs), OsEREBP1 and OsEREBP2, belonging to the AP2/ERF family were identified. Both TFs were shown to bind to the same GCC-like DNA motif in OsRMC promoter and to negatively regulate its gene expression. The identified TFs were characterized regarding their gene expression under different abiotic stress conditions. This study revealed that OsEREBP1 transcript level is not significantly affected by salt, ABA or severe cold (5 °C) and is only slightly regulated by drought and moderate cold. On the other hand, the OsEREBP2 transcript level increased after cold, ABA, drought and high salinity treatments, indicating that OsEREBP2 may play a central role mediating the response to different abiotic stresses. Gene expression analysis in rice varieties with contrasting salt tolerance further suggests that OsEREBP2 is involved in salt stress response in rice.

Endothelial lipase correlated positively with EPA/AA ratio in RBCs membrane

The fatty acid profile of erythrocyte membranes has been considered a good biomarker for several pathologic situations. Dietary intake, digestion, absorption, metabolism, storage and exchange amongst compartments, greatly influence the fatty acids composition of different cells and tissues. Lipoprotein and hepatic lipases were also involved in fatty acid availability. In the present work we examined the correlations between fatty acid in Red Blood Cells (RBCs) membranes, the fatty acid desaturase and elongase activities, glycaemia, blood lipids, lipoproteins and apoproteins, and the endothelial lipase (EL) mass in plasma. Twenty one individuals were considered in the present study, with age >18 y. RBCs membranes were obtained and analysed for fatty acid composition by gas chromatography. The amount of fatty acids (as percentage) were analysed, and the ratios between fatty acid 16:1/16:0; 18:1/18:0; 18:0/16:0; 22:6 n-3/20:5 n-3 and 20:4 n-6/18:2 n-6 were calculated. Bivariate analysis (rs) and partial correlations were determined. SCD16 estimation activity correlated positively with BMI (rs=0.466, p=0.043) and triacylglycerols (TAG) (rs=0.483, p=0.026), and negatively with the ratio ApoA1/ApoB (rs=-0.566, p=0.007). Endothelial lipase (EL) correlated positively with the EPA/AA ratio in RBCs membranes (rs=0.524, p=0.045). After multi-adjustment for BMI, age, hs-CRP and dietary n3/n6 ratio, the correlations remained significant between EL and EPA/AA ratio. At the best of our knowledge this is the first report that correlated EL with the fatty acid profile of RBCs plasma membranes. The association found here can suggest that the enzyme may be involved in the bioavailability and distribution of n-3/n-6 fatty acids, suggesting a major role for EL in the pathophysiological mechanisms involving biomembranes’ fatty acids, such as in inflammatory response and eicosanoids metabolites pathways.

Rate regulated activities: a problemática do relato financeiro e da sua auditoria: o caso da navegação aérea no contexto europeu

A navegação aérea, enquanto atividade regulada, está sujeita a legislação específica, dependendo o seu exercício de autorização própria atribuída por uma entidade supervisora, que também verifica as tarifas a aplicar. O regulamento (CE) N.º 550/2004 identifica os requisitos comuns para a prestação de serviços de navegação aérea na Europa, dando particular importância à transparência do relato financeiro ao exigir a sua elaboração segundo as normas internacionais de contabilidade e a verificação por uma auditoria independente. Adicionalmente, o Regulamento (EU) N.º 1191/2010, que alterou o Regulamento (CE) N.º 1794/2006, estabelece o regime comum de tarifação de tais serviços, nomeadamente a recuperabilidade de desvios relativos ao volume de tráfego e aos gastos controláveis e não controláveis. Ao nível do enquadramento contabilístico, as atividades reguladas não têm uma norma específica. Existem dois projetos do IASB – um de 2009, que foi suspenso, e um de 2013, relativo à implementação de uma norma transitória que incentive a adoção das normas internacionais por entidades que exerçam atividades reguladas. Existe, ainda, uma norma do FASB não aplicável no espaço europeu. Os R&C de várias entidades evidenciam a existência de diferentes referenciais contabilísticos e que a generalidade dos relatórios de auditoria não tem reservas ou ênfases. Enquanto algumas entidades apenas divulgam os montantes dos desvios, outras entidades consideram que tais montantes se qualificam, reconhecendo-os. Tal facto decorre da inexistência de uma norma internacional que põe em causa a comparabilidade da informação financeira e dificulta o julgamento do auditor quanto à adequação ou não dos procedimentos adotados pela entidade.