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.     

An experimental evaluation of the critical potential difference inducing cell membrane electropermeabilization.

When applied on intact cell suspension, electric field pulses are known to induce membrane permeabilization (electropermeabilization) and fusion (electrofusion). These effects are triggered through a modulation of the membrane potential difference. Due to the vectorial character of the electric field effects, this modulation, which is superimposed on the resting membrane potential difference, is position-dependent on the cell surface. This explains the difference between the experimentally observed critical field strengths requested to trigger the processes of permeabilization and fusion. The critical membrane potential difference which induces membrane permeabilization can be calculated from these experimental observations. It is observed that its value is always about 200 mV for many different cell systems as we previously reported in the case of pure lipid vesicles. This is much less than assumed in most previous studies.     

MacStylet, software to analyse electrical penetration graph data on the Macintosh

Conclusion Since the EPG method is increasingly utilized in the investigation of plant-Homoptera interactions, this software has been developed to enable fast processing of abundant data. The objective seems to have been achieved and, with a little practice, a 2-hour experiment may be analysed in about 10–15 minutes. Mac-Stylet is stand-alone shareware, freely distributed to all persons interested (request to G. Febvay, email: febvay@jouy.inra.fr).     

Continuous production of N-carbamyl-D-alanine byPeptococcus anaerobius adsorbed on activated charcoal

Summary The strict anaerobic bacteriumPeptococcus anderobius produced a D-hydantoinase which was used to catalyse the formation of N-carbamyl-D-alanine from DL-5-methylhydantoin. Whole cells ofP. anaerobius adsorbed on granular activated charcoal were stable for up to seven days when used in two bioreactor systems (percolation and fluidization) operated continuously under aerobic conditions at 50°C.     

Fusing VE-Cadherin to α-Catenin Impairs Fetal Liver Hematopoiesis and Lymph but Not Blood Vessel Formation

We have recently shown that genetic replacement of VE-cadherin by a VE-cadherin–α-catenin fusion construct strongly impairs opening of endothelial cell contacts during leukocyte extravasation and induction of vascular permeability in adult mice. Here we show that this mutation leads to lethality at midgestation on a clean C57BL/6 background. Investigating the reasons for embryonic lethality, we observed a lack of fetal liver hematopoiesis and severe lymphedema but no detectable defects in blood vessel formation and remodeling. As for the hematopoiesis defect, VE-cadherin–α-catenin affected neither the generation of hematopoietic stem and progenitor cells (HSPCs) from hemogenic endothelium nor their differentiation into multiple hematopoietic lineages. Instead, HSPCs accumulated in the fetal circulation, suggesting that their entry into the fetal liver was blocked. Edema formation was caused by disturbed lymphatic vessel development. Lymphatic progenitor cells of VE-cadherin–α-catenin-expressing embryos were able to leave the cardinal vein and migrate to the site of the first lymphatic vessel formation, yet subsequently, these cells failed to form large lumenized lymphatic vessels. Thus, stabilizing endothelial cell contacts by a covalent link between VE-cadherin and α-catenin affects recruitment of hematopoietic progenitors into the fetal liver and the development of lymph but not blood vessels.     

Functional morphology of the sperm-containing chambers of the sea slug Okenia polycerelloides in the context of sexual selection

Sea slugs are interesting models to study post-copulatory sexual selection in simultaneous hermaphrodites due to the enormous variation of their reproductive systems. However, the knowledge of the functional morphology of their reproductive system is limited to few species, and it is rarely discussed in the context of sexual selection theory. In this study, we investigated the functional morphology of the sperm-containing chambers (i.e., ampulla, seminal receptacle, and bursa copulatrix) of the reproductive system of Okenia polycerelloides (Ortea & Bouchet, 1983), based on light, confocal, and electron microscopy. Although the morphology of the ampulla is similar to other species, indicating that it is a site for autosperm storage, we found some sperm facing the ampullar epithelium, a feature commonly regarded as characteristic of the seminal receptacle of sea slugs. The seminal receptacle of O. polycerelloides showed secretory activity and contained sperm with distribution and orientation suggestive of stratification of allosperm from distinct mating events, a feature that would affect sperm competition. The bursa copulatrix had epithelial cells with secretory and absorptive characteristics, and contained degraded sperm and yolk granules within its lumen. Comparative analyses of the contents of each organ demonstrated that sperm digestion occurs in the bursa copulatrix and affects sperm heads first, changing their morphology from slender and curved to shorter and ellipsoid before complete lysis. Although digestion and absorption of surplus sperm are currently the main hypothesized functions for the bursa copulatrix, its role in cryptic female choice should not be ruled out. The close structural connection between the seminal receptacle and bursa copulatrix, as well as their muscular walls, would enable control over the fate of the sperm received in each mating event, that is, storage or digestion.     

The Effect of Dolphin-Assisted Therapy on the Cognitive and Social Development of Children with Down Syndrome

Cognitive and speech development are delayed in children with Down syndrome (DS). We investigated the effect of dolphin-assisted therapy (DAT), a form of animal-assisted intervention, on the development of speech/language and social behavior in children with DS. We hypothesized that DAT would improve the social and cognitive functions with respect to verbalization and thereby promote task performance. A semi-crossover design was used to study 45 children with DS: 18 received a weekly one-hour session of DAT for 6 weeks (group A), 12 children (group B) started with swimming pool sessions (control period of 6 weeks) and thereafter received DAT, and 17 children (group C) were put on a waiting list (control period of 6 weeks) before receiving DAT. The parameters “verbalization,” “impulsiveness,” “proper understanding of rules,” “recognition of persons,” and “establishing contacts” were measured using the Matson Evaluation of Social Skills for Individuals with Severe Retardation (MESSIER) before and after DAT, as well as before and after each of the control periods. Repeated measures ANOVA revealed no significant changes for any of the variables during the control periods (swimming pool, waiting list). Following the period of DAT there was a significant improvement in “verbalization” and “recognition of persons,” while “impulsiveness” decreased. No significant changes were found for the other parameters. “Verbalization” continued to increase during the follow-up period of 6 months, while “recognition of persons” slightly decreased. The results of this study provide support for our hypothesis. Through improvements in verbalization and the recognition of persons, the execution of tasks among children with DS receiving DAT improved. Additional studies are needed to determine if these positive effects of DAT are long-term.