Exploring the Factor Structure of Neurocognitive Measures in Older Individuals

Here we focus on factor analysis from a best practices point of view, by investigating the factor structure of neuropsychological tests and using the results obtained to illustrate on choosing a reasonable solution. The sample (n=1051 individuals) was randomly divided into two groups: one for exploratory factor analysis (EFA) and principal component analysis (PCA), to investigate the number of factors underlying the neurocognitive variables; the second to test the “best fit” model via confirmatory factor analysis (CFA). For the exploratory step, three extraction (maximum likelihood, principal axis factoring and principal components) and two rotation (orthogonal and oblique) methods were used. The analysis methodology allowed exploring how different cognitive/psychological tests correlated/discriminated between dimensions, indicating that to capture latent structures in similar sample sizes and measures, with approximately normal data distribution, reflective models with oblimin rotation might prove the most adequate.     

Data quality aware analysis of differential expression in RNA-seq with NOISeq R/Bioc package

As the use of RNA-seq has popularized, there is an increasing consciousness of the importance of experimental design, bias removal, accurate quantification and control of false positives for proper data analysis. We introduce the NOISeq R-package for quality control and analysis of count data. We show how the available diagnostic tools can be used to monitor quality issues, make pre-processing decisions and improve analysis. We demonstrate that the non-parametric NOISeqBIO efficiently controls false discoveries in experiments with biological replication and outperforms state-of-the-art methods. NOISeq is a comprehensive resource that meets current needs for robust data-aware analysis of RNA-seq differential expression.     

Vacuolar apical compartment (VAC) in breast carcinoma cell lines (MCF-7 and T47D): failure of the cell-cell regulated exocytosis mechanism of apical membrane

Abstract. We have previously shown that an integral plasma membrane glycoprotein (AP2) is highly polarized to the apical domain in confluent Madin-Darby canine kidney (MDCK) epithelial cells. However, when the monolayers are prevented from forming intercellular contacts, approximately 60% of the AP2 cellular content is stored in the intracellular vacuolar apical compartment (VAC). In the current work we found that AP2 was present in the non-tumorigenic human mammary epithelial cell line MCF-10A. in the breast carcinoma cell lines MCF-7 and T47D, and in breast ductal carcinomas in vivo. By radioimmunoassay, an intracellular Compartment of AP2 was identified in the mammary cell lines in culture. In MCF-10A, this compartment behaved as in MDCK cells; namely it was observed only when the cells cannot form cell-cell contacts. However, in the carcinoma cell lines MCF-7 and T47D, a significant AP2 intracellular compartment was observed also under conditions permissive for the formation of intercellular contacts. These results were confirmed by immunofluorescence and immunoelectron microscopy experiments that showed VACs in MCF-7 and T47D, even in cells with extensive intercellular contacts. In MCF-7 cells, the addition of serum caused a partial decrease of the AP2 intracellular compartment. The exocytosis of VACs occurred towards the center of multi-cellular groups, forming intercellular lumens, similar to those transiently observed in MDCK cells and to structures described by others during embryo development. Altogether, these results suggest that VAC exocytosis is controlled by cell-cell contact signalling, which may be defective in carcinoma cells.     

Initiation of growth in pbpAts and rodAts mutants of Escherichia coli

Escherichia coli strains harbouring pbpAts mutations are particularly sensitive to functional alterations of penicillin-binding protein 2 (PBP 2) at the initiation of growth. Shift-up to 42 degrees C results in the inability of cells to reach a steady rate of growth and division. Furthermore, a very high proportion of cells generate minicell-like structures which are pinched-off through a process requiring the activity of penicillin-binding protein 3 (PBP 3).     

Dispersal ability rather than ecological tolerance drives differences in range size between lentic and lotic water beetles (Coleoptera: Hydrophilidae)

Aim In aquatic ecosystems, standing (lentic) and running (lotic) waters differ fundamentally in their stability and persistence, shaping the comparative population genetic structure, geographical range size and speciation rates of lentic versus lotic lineages. While the drivers of this pattern remain incompletely understood, the suite of traits making up the ability of a species to establish new populations is instrumental in determining such differences. Here we explore the degree to which the association between habitat type and geographical range size results from differences in dispersal ability or fundamental niche breadth in the members of the Enochrus bicolor complex, an aquatic beetle clade with species across the lentic–lotic divide. Location Western Mediterranean, with a special focus on North Africa, the Iberian Peninsula and Sicily. Methods DNA sequences for four loci were obtained from species of the E. bicolor complex and analysed using phylogenetic inference. Dispersal and establishment abilities were assessed in lentic–lotic species pairs of the complex, using flight wing morphometrics and thermal tolerance ranges as surrogates, respectively. Results There were clear differences in range size between the lotic and lentic taxa of the complex, which appears to have had a lotic origin with two transitions to standing waters. Only small differences were observed in temperature tolerance and acclimation ability between the two lotic–lentic sister species studied. By contrast, wing morphometrics revealed clear, consistent differences between lotic and lentic Enochrus species pairs, the latter having a higher dispersal capacity. Main conclusions We hypothesize that there have been two habitat shifts from lotic to lentic waters, which have allowed marked expansions in geographical range size in western Mediterranean species of the E. bicolor complex. Differences in dispersal rather than in establishment ability appear to underlie differences in geographical range extent, as transitions to lentic waters were associated with changes in wing morphology, but not in thermal tolerance range. In this lineage of water beetles, selection for dispersal in geologically short‐lived lentic systems has driven the evolution of larger range sizes in lentic taxa compared with those of their lotic relatives.