Joint segmentation, calling, and normalization of multiple CGH profiles

The statistical analysis of array comparative genomic hybridization (CGH) data has now shifted to the joint assessment of copy number variations at the cohort level. Considering multiple profiles gives the opportunity to correct for systematic biases observed on single profiles, such as probe GC content or the so-called "wave effect." In this article, we extend the segmentation model developed in the univariate case to the joint analysis of multiple CGH profiles. Our contribution is multiple: we propose an integrated model to perform joint segmentation, normalization, and calling for multiple array CGH profiles. This model shows great flexibility, especially in the modeling of the wave effect that gives a likelihood framework to approaches proposed by others. We propose a new dynamic programming algorithm for break point positioning, as well as a model selection criterion based on a modified bayesian information criterion proposed in the univariate case. The performance of our method is assessed using simulated and real data sets. Our method is implemented in the R package cghseg.     

Crystal structure of the Psb27 assembly factor at 1.6??: implications for binding to Photosystem II

The biogenesis and oxygen-evolving activity of cyanobacterial Photosystem II (PSII) is dependent on a number of accessory proteins not found in the crystallised dimeric complex. These include Psb27, a small lipoprotein attached to the lumenal side of PSII, which has been assigned a role in regulating the assembly of the Mn(4)Ca cluster catalysing water oxidation. To gain a better understanding of Psb27, we have determined in this study the crystal structure of the soluble domain of Psb27 from Thermosynechococcus elongatus to a resolution of 1.6??. The structure is a four-helix bundle, similar to the recently published solution structures of Psb27 from Synechocystis PCC 6803 obtained by nuclear magnetic resonance (NMR) spectroscopy. Importantly, the crystal structure presented here helps us resolve the differences between the NMR-derived structural models. Potential binding sites for Psb27 within PSII are discussed in light of recent biochemical data in the literature.     

Traits émotionnels, intelligence émotionnelle: intÉrêt de ces concepts et Étude de leurs interrelations

Studies on personality traits conducted during the past decade indicate that there is a set of emotion-related traits on which individuals differ. Moreover, other studies showed that there are some abilities related to the processing of both emotions and emotional information, referred to as the concept of emotional intelligence. The authors of the article evaluated one hundred adults (ranging in age from 20–50) using the French version of a series of scales to measure stable emotionrelated traits and emotional intelligence. The results showed that these instruments provide accurate internal consistency and reliability, and that there are significant relationships between the individual emotional characteristics observed. A factorial analysis conducted with varimax rotation underlined five primary factors identified as: Clear-sightedness of emotions, Emotional richness, Identification, Understanding and Emotional control. The average emotional profiles based on these five primary factors depend on gender and age. In particular, the female and the oldest participants showed a greater emotional richness. The examination of these five factors should lead to a better understanding of the relationships which exist between these emotional characteristics and cognitive performances, and their involvement in clinical syndromes.     

Implanting Glass Spinal Cord Windows in Adult Mice with Experimental Autoimmune Encephalomyelitis

Experimental autoimmune encephalomyelitis (EAE) in adult rodents is the standard experimental model for studying autonomic demyelinating diseases such as multiple sclerosis. Here we present a low-cost and reproducible glass window implantation protocol that is suitable for intravital microscopy and studying the dynamics of spinal cord cytoarchitecture with subcellular resolution in live adult mice with EAE. Briefly, we surgically expose the vertebrae T12-L2 and construct a chamber around the exposed vertebrae using a combination of cyanoacrylate and dental cement. A laminectomy is performed from T13 to L1, and a thin layer of transparent silicone elastomer is applied to the dorsal surface of the exposed spinal cord. A modified glass cover slip is implanted over the exposed spinal cord taking care that the glass does not directly contact the spinal cord. To reduce the infiltration of inflammatory cells between the window and spinal cord, anti-inflammatory treatment is administered every 2 days (as recommended by ethics committee) for the first 10 days after implantation. EAE is induced only 2-3 weeks after the cessation of anti-inflammatory treatment.Using this approach we successfully induced EAE in 87% of animals with implanted windows and, using Thy1-CFP-23 mice (blue axons in dorsal spinal cord), quantified axonal loss throughout EAE progression. Taken together, this protocol may be useful for studying the recruitment of various cell populations as well as their interaction dynamics, with subcellular resolution and for extended periods of time. This intravital imaging modality represents a valuable tool for developing therapeutic strategies to treat autoimmune demyelinating diseases such as EAE.     

The cationic composition of incubated cerebral cortex slices

1. A new type of cutting table is described. It makes use of the elastic properties of a nylon thread, 0.08 mm thick, in which longitudinal vibrations greatly increase its ability to cut through soft tissue. Two slices of cerebral cortex may thus be obtained within 3-4 min after the death of an animal. 2. The extent of the swelling of a brain slice, as well as the ionic shift, is directly related to the amount of oxygen in the incubating fluid. Under the best conditions of oxygen supply, the swelling of a first slice was close to 12.2 +/- 4.3 per cent after 5 hr of incubation. The corresponding values for the Na+ and K+ contents were respectively 119.3 +/- 6.9 and 70.9 +/- 5.0 microequiv./g of final fresh weight (P2). 3. Incubation in complete anoxia leads to a considerable shift in the cation content of the slice, which acquires a composition close to that of the incubating fluid. This suggests that a large part of the cell population is still metabolically active when oxygen is present. 4. The inulin space represents 47.1 +/- 5.8 per cent of the initial fresh weight. It is independent of the amount of fluid taken up by the slice as well as of anoxia. 5. The cation content of the non-inulin space, calculated by assuming that the inulin space has the same composition as the incubation medium, was 77.7 microequiv./ml and 160.3 microequiv./ml for Na+ and K+ respectively. 6. The meaning of the inulin space, as well as the physico-chemical state of the cations in the slice, are discussed.     

Cloning and expression of soluble epoxide hydrolase from potato

Five cDNAs encoding a putative soluble epoxide hydrolase (sEH) from potato were isolated and characterized. The cDNAs contained open reading frames encoding 36 kDa polypeptides which were highly homologous to the carboxy terminal region of mammalian sEH. When one of the cDNAs was expressed in a baculovirus system a soluble 38 kDa protein with epoxide hydrolase activity was produced. The recombinant enzyme hydrolyzed a commonly used diagnostic substrate for the soluble form of mammalian EH. Inhibitor profiles of the recombinant potato and mammalian sEH were also similar. The expression of sEH in potato was found to be regulated by both developmental and environmental signals. Levels of mRNA for sEH were higher in meristematic tissue than in mature leaves. This mRNA was also observed to accumulate on wounding and application of exogenous methyl jasmonate.     

A stochastic dispersal-limited trait-based model of community dynamics

I present a model of stochastic community dynamics in which death occurs randomly in the community, propagules disperse randomly from a regional pool, and recruitment of new individuals of a species is proportional to the species local abundance multiplied by its local competitive ability. The competitive ability of a species is assumed to be determined by a function of one trait of the species, and I call this function the environmental filtering function. I show that information on local species abundances in a network of plots, together with trait data for each species, enables the inference of both the immigration rate and the environmental filtering function in each plot. I further study how the diversity patterns produced by this model deviate from the neutral predictions, and how this deviation depends on the characteristics of the environmental filtering function. I show that this inference framework is more powerful at detecting trait-based environmental filtering than existing statistical approaches based on trait distributions, and discuss how the predictions of this model could be used to assess environmental heterogeneity in a plot, to detect functionally meaningful trade-offs among species traits, and to test the assumption that there exists a simple relationship between species traits and local competitive ability.     

Larval Dispersal Modeling of Pearl Oyster Pinctada margaritifera following Realistic Environmental and Biological Forcing in Ahe Atoll Lagoon

Studying the larval dispersal of bottom-dwelling species is necessary to understand their population dynamics and optimize their management. The black-lip pearl oyster (Pinctada margaritifera) is cultured extensively to produce black pearls, especially in French Polynesia''s atoll lagoons. This aquaculture relies on spat collection, a process that can be optimized by understanding which factors influence larval dispersal. Here, we investigate the sensitivity of P. margaritifera larval dispersal kernel to both physical and biological factors in the lagoon of Ahe atoll. Specifically, using a validated 3D larval dispersal model, the variability of lagoon-scale connectivity is investigated against wind forcing, depth and location of larval release, destination location, vertical swimming behavior and pelagic larval duration (PLD) factors. The potential connectivity was spatially weighted according to both the natural and cultivated broodstock densities to provide a realistic view of connectivity. We found that the mean pattern of potential connectivity was driven by the southwest and northeast main barotropic circulation structures, with high retention levels in both. Destination locations, spawning sites and PLD were the main drivers of potential connectivity, explaining respectively 26%, 59% and 5% of the variance. Differences between potential and realistic connectivity showed the significant contribution of the pearl oyster broodstock location to its own dynamics. Realistic connectivity showed larger larval supply in the western destination locations, which are preferentially used by farmers for spat collection. In addition, larval supply in the same sectors was enhanced during summer wind conditions. These results provide new cues to understanding the dynamics of bottom-dwelling populations in atoll lagoons, and show how to take advantage of numerical models for pearl oyster management.