Methylome sequencing for fibrolamellar hepatocellular carcinoma depicts distinctive features

With the goal of studying epigenetic alterations in fibrolamellar hepatocellular carcinoma (FLC) and establish an associated DNA methylation signature, we analyzed LINE-1 methylation in a cohort of FLC and performed next-generation sequencing of DNA methylation in a training set of pure-FLCs and non-cirrhotic hepatocellular carcinomas (nc-HCC). DNA methylation was correlated with gene expression. Furthermore, we established and validated an epigenetic signature differentiating pure-FLC from other HCCs. LINE-1 methylation correlated with shorter recurrence-free survival and overall survival in resected pure-FLC patients. Unsupervised clustering using CG sites located in islands distinguished pure-FLC from nc-HCC. Major DNA methylation changes occurred outside promoters, mainly in gene bodies and intergenic regions located in the vicinity of liver developmental genes (i.e., SMARCA4 and RXRA). Partially methylated domains were more prone to DNA methylation changes. Furthermore, we identified several putative tumor suppressor genes (e.g., DLEU7) and oncogenes (e.g., DUSP4). While ∼70% of identified gene promoters gaining methylation were marked by bivalent histone marks (H3K4me3/H3K27me3) in embryonic stem cells, ∼70% of those losing methylation were marked by H3K4me3. Finally, we established a pure FLC DNA methylation signature and validated it in an independent dataset. Our analysis reveals a distinct epigenetic signature of pure FLC as compared to nc-HCC, with DNA methylation changes occurring in the vicinity of liver developmental genes. These data suggest new options for targeting FLC based on cancer epigenome aberrations.     

Density and productivity of breeding Skylarks Alauda arvensis in relation to crop type on agricultural lands in western France

Capsule Small field size and the maintenance of set-aside and lucerne are important to ensure high breeding pair densities and productivity.

Aims To investigate the effects of crop types and their attributes on density and productivity of breeding Skylark.

Methods At each of four selected study sites in western France, territory density, vegetation height, vegetation cover and field size was estimated by field and attempts were made to find nests. Crop types included winter and spring cereals, oilseed rape, sunflower, maize, grass, lucerne, set-aside, and bare ground.

Results About 80% of Skylark territories included more than one crop type. Birds preferred small fields and territory density decreased with increasing field size. Density was highest in crops with low vegetation height and cover. Set-aside, lucerne and grass supported highest territory density. Fledging productivity was highest in set-aside and lucerne, and was zero on bare ground. Skylark density decreased throughout the breeding season (-26% in 1999 and -29% in 2000), suggesting an instability in territory distribution or activity in intensive farmland.

Conclusions Farming systems that decrease field size and increase set-aside and lucerne instead of oilseed rape, maize and sunflower will benefit Skylark and other declining farmland species.     

Bifurcation analysis applied to a model of motion integration with a multistable stimulus

A computational study into the motion perception dynamics of a multistable psychophysics stimulus is presented. A diagonally drifting grating viewed through a square aperture is perceived as moving in the actual grating direction or in line with the aperture edges (horizontally or vertically). The different percepts are the product of interplay between ambiguous contour cues and specific terminator cues. We present a dynamical model of motion integration that performs direction selection for such a stimulus and link the different percepts to coexisting steady states of the underlying equations. We apply the powerful tools of bifurcation analysis and numerical continuation to study changes to the model’s solution structure under the variation of parameters. Indeed, we apply these tools in a systematic way, taking into account biological and mathematical constraints, in order to fix model parameters. A region of parameter space is identified for which the model reproduces the qualitative behaviour observed in experiments. The temporal dynamics of motion integration are studied within this region; specifically, the effect of varying the stimulus gain is studied, which allows for qualitative predictions to be made.     

Cyclic GMP modulates store-operated calcium entry inducing phosphatidylserine translocation at the surface of megakaryocytic cells

When subjected to stimulation, cells from the vascular compartment show a spontaneous collapse of the plasma membrane phospholipid asymmetry and phosphatidylserine is exposed at the external leaflet. Thus, phosphatidylserine externalization is essential for normal hemostasis and phagocytosis. The mechanism governing the migration of phosphatidylserine to the exoplasmic leaflet is not yet fully understood. We have proposed that store-operated calcium entry (SOCE) constitutes a key step of this process. Here, interaction of [Ca(2+)](i), cAMP and cGMP pathways and phosphatidylserine exposure was examined in human megakaryocytic cells. The membrane permeable cAMP and cGMP analogues, pCPT-cAMP and pCPT-cGMP, enhanced the Ca(2+) signal induced by ionophore and SOCE. Responses to pCPT-cAMP and pCPT-cGMP were independent of protein kinase A, protein kinase G (PKG) or ERK pathways. Inhibition of small G-proteins reduced or abolished the increase of [Ca(2+)](i) induced by pCPT-cAMP or pCPT-cGMP, respectively. pCPT-cGMP but not pCPT-cAMP enhanced the ability of cells to expose phosphatidylserine. This effect was not prevented by the inhibition of PKG or small G-proteins. These results show the differential role of cyclic nucleotides in the Ca(2+)-dependent membrane remodeling. Hence, pCPT-cGMP is another regulatory element for the completion of SOCE-induced phosphatidylserine transmembrane redistribution in HEL cells through a mechanism implicating small G-proteins.     

High gas pressure: an innovative method for the inactivation of dried bacterial spores

In this article, an original non-thermal process to inactivate dehydrated bacterial spores is described. The use of gases such as nitrogen or argon as transmission media under high isostatic pressure led to an inactivation of over 2 logs CFU/g of Bacillus subtilis spores at 430 MPa, room temperature, for a 1 min treatment. A major requirement for the effectiveness of the process resided in the highly dehydrated state of the spores. Only a water activity below 0.3 led to substantial inactivation. The solubility of the gas in the lipid components of the spore and its diffusion properties was essential to inactivation. The main phenomenon involved seems to be the sorption of the gas under pressure by the spores' structures such as residual pores and plasma membranes, followed by a sudden drop in pressure. Observation by phase-contrast microscopy suggests that internal structures have been affected by the treatment. Some parallels with polymer permeability to gas and rigidity at various water activities offer a few clues about the behavior of the outer layers of spores in response to this parameter and provide a good explanation for the sensitivity of spores to high gas pressure discharge at low hydration levels. Specificity of microorganisms such as size, organization, and composition could help in understanding the differences between spores and yeast regarding the parameters required for inactivation, such as pressure or maintenance time.     

Ventricle equilibrium position in healthy and normal pressure hydrocephalus brains using an analytical model

The driving force that causes enlargement of the ventricles remains unclear in case of normal pressure hydrocephalus (NPH). Both healthy and NPH brain conditions are characterized by a low transparenchymal pressure drop, typically 1 mm Hg. The present paper proposes an analytical model for normal and NPH brains using Darcy's and Biot's equations and simplifying the brain geometry to a hollow sphere with an internal and external radius. Self-consistent solutions for the large deformation problem that is associated with large ventricle dilation are presented and the notion of equilibrium or stable ventricle position is highlighted for both healthy and NPH conditions. The influence of different biomechanical parameters on the stable ventricle geometry is assessed and it is shown that both CSF seepage through the ependyma and parenchymal permeability play a key role. Although very simple, the present model is able to predict the onset and development of NPH conditions as a deviation from healthy conditions.     

Comparison of the genetic determinism of two key phenological traits,flowering and maturity dates,in three Prunus species: peach,apricot and sweet cherry

The present study investigates the genetic determinism of flowering and maturity dates, two traits highly affected by global climate change. Flowering and maturity dates were evaluated on five progenies from three Prunus species, peach, apricot and sweet cherry, during 3–8 years. Quantitative trait locus (QTL) detection was performed separately for each year and also by integrating data from all years together. High heritability estimates were obtained for flowering and maturity dates. Several QTLs for flowering and maturity dates were highly stable, detected each year of evaluation, suggesting that they were not affected by climatic variations. For flowering date, major QTLs were detected on linkage groups (LG) 4 for apricot and sweet cherry and on LG6 for peach. QTLs were identified on LG2, LG3, LG4 and LG7 for the three species. For maturity date, a major QTL was detected on LG4 in the three species. Using the peach genome sequence data, candidate genes underlying the major QTLs on LG4 and LG6 were investigated and key genes were identified. Our results provide a basis for the identification of genes involved in flowering and maturity dates that could be used to develop cultivar ideotypes adapted to future climatic conditions.     

Unusual sterolic mixture,and 24‐isopropylcholesterol,from the sponge Ciocalypta sp. reduce cholesterol uptake and basolateral secretion in Caco‐2 cells

An unusual sterolic mixture (82.3% of 24‐isopropylated sterols) and its major component, 24‐isopropylcholesterol, isolated from a marine sponge, Ciocalypta sp. (Halichondriidae), reduce cholesterol uptake, basolateral secretion and ACAT‐2 mRNA expression and increase the expression of ABCA1 mRNA in Caco‐2 cells. The decreases of cholesterol uptake and secretion induced by 24‐isopropylcholesterol alone were more than that of both the sterolic mixture and β‐sitosterol. These data add a new sterol, 24‐isopropylcholesterol, to sterols that may reduce intestinal cholesterol absorption. J. Cell. Biochem. 106: 659–665, 2009. © 2009 Wiley‐Liss, Inc.     

Contrasted patterns of age-specific reproduction in long-lived seabirds

While the number of studies providing evidence of actuarial senescence is increasing, and covers a wide range of taxa, the process of reproductive senescence remains poorly understood. In fact, quite high reproductive output until the last years of life has been reported in several vertebrate species, so that whether or not reproductive senescence is widespread remains unknown. We compared age-specific changes of reproductive parameters between two closely related species of long-lived seabirds: the small-sized snow petrel Pagodroma nivea, and the medium-sized southern fulmar Fulmarus glacialoides. Both are sympatric in Antarctica. We used an exceptional dataset collected over more than 40 years to assess age-specific variations of both breeding probability and breeding success. We found contrasted age-specific reproductive patterns between the two species. Reproductive senescence clearly occurred from 21 years of age onwards in the southern fulmar, in both breeding probability and success, whereas we did not report any decline in the breeding success of the snow petrel, although a very late decrease in the proportion of breeders occurred at 34 years. Such a contrasted age-specific reproductive pattern was rather unexpected. Differences in life history including size or migratory behaviour are the most likely candidates to account for the difference we reported in reproductive senescence between these sympatric seabird species.