DNA damage in Gammarus fossarum sperm as a biomarker of genotoxic pressure: intrinsic variability and reference level

In the perspective of a biomonitoring application for assessing genotoxicity of freshwater ecosystems, the Comet assay has recently been developed on spermatozoa in the amphipod Gammarus fossarum, in order to propose a sensitive and reliable genotoxicity biomarker in an ecologically relevant freshwater species. The appropriate use of a genotoxicity biomarker requires good knowledge of its basal level and its natural variability related to intrinsic biotic and environmental abiotic factors. We propose a procedure for which the lowest biomarker variability related to methodological and intrinsic biotic factors is obtained and a reference value of biomarker basal response taking into account its spatio-temporal changes has been defined. A strong impact of spermatogenesis status and exposure time on the response to genotoxicant pressure was observed. These reports led us to select a standard organism, i.e., the mature male gammarid in precopula. No effect of temperature and conductivity on baseline DNA damage was observed in the laboratory for the tested range (6-24 °C and 300/600 μS cm⁻¹). Similarly, no spatio-temporal change relative to season or the physico-chemical characteristics of the water was recorded during the field survey. On the basis of these results, a reference level with maximal threshold values has been proposed for the standard gammarid.     

Conformational Insights into the Control of CNF1 Toxin Activity by Peptidyl-Prolyl Isomerization: A Molecular Dynamics Perspective

The cytotoxic necrotizing factor 1 (CNF1) toxin from uropathogenic Escherichia coli constitutively activates Rho GTPases by catalyzing the deamidation of a critical glutamine residue located in the switch II (SWII). In crystallographic structures of the CNF1 catalytic domain (CNF1^CD), surface-exposed P768 and P968 peptidyl-prolyl imide bonds (X-Pro) adopt an unusual cis conformation. Here, we show that mutation of each proline residue into glycine abrogates CNF1^CD in vitro deamidase activity, while mutant forms of CNF1 remain functional on RhoA in cells. Using molecular dynamics simulations coupled to protein-peptide docking, we highlight the long-distance impact of peptidyl-prolyl cis-trans isomerization on the network of interactions between the loops bordering the entrance of the catalytic cleft. The energetically favorable isomerization of P768 compared with P968, induces an enlargement of loop L1 that fosters the invasion of CNF1^CD catalytic cleft by a peptide encompassing SWII of RhoA. The connection of the P968 cis isomer to the catalytic cysteine C866 via a ladder of stacking interactions is alleviated along the cis-trans isomerization. Finally, the cis-trans conversion of P768 favors a switch of the thiol side chain of C866 from a resting to an active orientation. The long-distance impact of peptidyl-prolyl cis-trans isomerizations is expected to have implications for target modification.     

Short communication: Variation in the composition and properties of Swedish raw milk for ultra-high-temperature processing

The composition and properties of raw milk are of great importance for the quality and shelf life of the final dairy product, especially in products with a long shelf life [e.g., ultra-high-temperature (UHT)-treated milk]. The objective of this study was to investigate the compositional variation in raw milk samples before processing at the dairy plant. Moreover, we wanted to investigate the effect of the UHT process on this variation (i.e., if the same variation could be observed in the corresponding UHT milk). The quality traits analyzed included detailed milk composition, counts of total and psychrotrophic bacteria, proteolytic activity, and color, as well as predictive measures of stability (i.e., ethanol stability and heat coagulating time). Samples of raw milk and the corresponding produced UHT milk were collected and analyzed on a monthly basis during 1 yr. Principal component analysis was used to identify months showing similarities and differences with respect to total variation. In contrast to previous studies, we observed only small variations between months and no clear effect of season for the raw milk. For the UHT milk, July and the winter months (December, January, and February) tended to separate from the other months. Quality traits showing significant variation were only to some extent identical in raw milk and UHT-processed milk. A better understanding of the natural variation in raw milk quality will provide opportunities to improve the shelf life of UHT-treated milk products.     

Dietary Long-Chain n-3 Polyunsaturated Fatty Acid Supplementation Alters Electrophysiological Properties in the Nucleus Accumbens and Emotional Behavior in Naïve and Chronically Stressed Mice

Long-chain (LC) n-3 polyunsaturated fatty acids (PUFAs) have drawn attention in the field of neuropsychiatric disorders, in particular depression. However, whether dietary supplementation with LC n-3 PUFA protects from the development of mood disorders is still a matter of debate. In the present study, we studied the effect of a two-month exposure to isocaloric diets containing n-3 PUFAs in the form of relatively short-chain (SC) (6% of rapeseed oil, enriched in α-linolenic acid (ALA)) or LC (6% of tuna oil, enriched in eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA)) PUFAs on behavior and synaptic plasticity of mice submitted or not to a chronic social defeat stress (CSDS), previously reported to alter emotional and social behavior, as well as synaptic plasticity in the nucleus accumbens (NAc). First, fatty acid content and lipid metabolism gene expression were measured in the NAc of mice fed a SC (control) or LC n-3 (supplemented) PUFA diet. Our results indicate that LC n-3 supplementation significantly increased some n-3 PUFAs, while decreasing some n-6 PUFAs. Then, in another cohort, control and n-3 PUFA-supplemented mice were subjected to CSDS, and social and emotional behaviors were assessed, together with long-term depression plasticity in accumbal medium spiny neurons. Overall, mice fed with n-3 PUFA supplementation displayed an emotional behavior profile and electrophysiological properties of medium spiny neurons which was distinct from the ones displayed by mice fed with the control diet, and this, independently of CSDS. Using the social interaction index to discriminate resilient and susceptible mice in the CSDS groups, n-3 supplementation promoted resiliency. Altogether, our results pinpoint that exposure to a diet rich in LC n-3 PUFA, as compared to a diet rich in SC n-3 PUFA, influences the NAc fatty acid profile. In addition, electrophysiological properties and emotional behavior were altered in LC n-3 PUFA mice, independently of CSDS. Our results bring new insights about the effect of LC n-3 PUFA on emotional behavior and synaptic plasticity.     

Examples of landslides associated with the Natal Group and pietermaritzburg formation in the greater Durban area of Natal,South Africa

If the incidence of landslides in the greater Durban area is related to geological formation, then most landslides have been associated with the shales of the Pietermaritzburg Formation. However, in the last eight years, most landslides have been associated with the Natal Group Sandstone and occurred during the very heavy rains of September, 1987, and March, 1988. In fact, prior to 1987 the Natal Group Sandstone was considered relatively stable. On the other hand, many areas in the greater Durban area underlain by shale have long been regarded as unsuitable for development as they were considered potentially unstable. Two types of instability occur on these formations, that is, sliding blocks of rock along bedding planes, and sliding of the weathered and colluvial soil material on top of bedrock. Illustrations of both types of slides on both formations are presented.     

Targeted online liquid chromatography electron capture dissociation mass spectrometry for the localization of sites of in vivo phosphorylation in human Sprouty2

We demonstrate a strategy employing collision-induced dissociation for phosphopeptide discovery, followed by targeted electron capture dissociation (ECD) for site localization. The high mass accuracy and low background noise of the ECD mass spectra allow facile sequencing of coeluting isobaric phosphopeptides, with up to two isobaric phosphopeptides sequenced from a single mass spectrum. In contrast to the previously described neutral loss dependent ECD method, targeted ECD allows analysis of both phosphotyrosine peptides and lower abundance phosphopeptides. The approach was applied to phosphorylation analysis of human Sprouty2, a regulator of receptor tyrosine kinase signaling. Fifteen sites of phosphorylation were identified, 11 of which are novel.     

Wax morphology in bitumen

Wax crystallisation and melting in bitumen is usually considered detrimental to bitumen quality and asphalt performance. The objectives of this paper are to study wax morphology in bitumen and to investigate effects of time, temperature, and thermal cycling on wax crystallisation. Various samples were selected, including eight waxy bitumens of different sources and three laboratory blends prepared by adding a slack wax and two isolated bitumen waxes to the non-waxy bitumen. Test methods used were differential scanning calorimetry (DSC), polarised light microscopy (PLM), confocal laser scanning microscopy (CLSM), and freeze etching (fracture) in combination with transmission electron microscopy (FF-TEM). The DSC results indicated that the selected bitumen samples differ widely in wax content and wax crystallisation starting and melting out temperatures. It was found that non-waxy bitumen displayed no structure or crystals neither in PLM, CLSM or FF-TEM, while waxy bitumens from different crude origins showed a large variation of structures. The morphology of wax crystals was highly dependent on crystallisation temperature as well as temperature history. The wax which has been isolated from waxy bitumen and mixed into non-waxy bitumen displayed similar morphology as the wax in the original bitumen. It was also found that bitumen wax usually melted at temperatures lower than 60°C although in one case a temperature of 80°C was needed until complete melting of the wax.     

Amphiphilic gradient poly(styrene-co-acrylic acid) copolymer prepared via nitroxide-mediated solution polymerization. Synthesis, characterization in aqueous solution and evaluation as emulsion polymerization stabilizer

A well-defined, amphiphilic poly(styrene-co-acrylic acid) copolymer was synthesized in a single step by nitroxide-mediated controlled free-radical copolymerization of styrene and acrylic acid, without protection of the acid groups: M_n=6500 g mol⁻¹, M_w/M_n=1.5 and a composition of F_AA=0.70±0.03 in acrylic acid. In addition to the good control over molar mass and molar mass distribution, the copolymer exhibited a narrow composition distribution with a slight gradient. Such copolymer was an efficient stabilizer for the emulsion polymerizations of styrene and of mixtures of methyl methacrylate and n-butyl acrylate, until 45 wt% solids. A low amount (typically 3-4 wt% based on the monomer(s)) was needed for a good stabilization. This is approximately a decade lower than the required amount of random, amphiphilic copolymers prepared via conventional free-radical polymerization. The performances were, however, below those of analogous diblock copolymers, but the great advantage is the very easy synthetic procedure.     

Interactive Meso-scale Simulation of Skyscapes

Although an important component of natural scenes, the representation of skyscapes is often relatively simplistic. This can be largely attributed to the complexity of the thermodynamics underpinning cloud evolution and wind dynamics, which make interactive simulation challenging. We address this problem by introducing a novel layered model that encompasses both terrain and atmosphere, and supports efficient meteorological simulations. The vertical and horizontal layer resolutions can be tuned independently, while maintaining crucial inter-layer thermodynamics, such as convective circulation and land-air transfers of heat and moisture. In addition, we introduce a cloud-form taxonomy for clustering, classifying and upsampling simulation cells to enable visually plausible, finely-sampled volumetric rendering. As our results demonstrate, this pipeline allows interactive simulation followed by up-sampled rendering of extensive skyscapes with dynamic clouds driven by consistent wind patterns. We validate our method by reproducing characteristic phenomena such as diurnal shore breezes, convective cells that contribute to cumulus cloud formation, and orographic effects from moist air driven upslope.     

High Order Spatial Generalization of 2D and 3D Isotropic Discrete Gradient Operators with Fast Evaluation on GPUs

Based on the concept of isotropic centered finite differences, this work generalizes the spatial order of accuracy of the 2D and 3D isotropic discrete gradient operators to a higher order. A suitable methodology is used to obtain a set of equations from which it is possible to deduce stencil weights to achieve numerical approximations of both high order spatial and high order isotropic gradients. We consider that the suggested discretization will be useful for enhancing the quality of the results in various scientific fields. The spatial order ( $S$ ) controls the spatial order of accuracy of the gradient norm and direction, while the isotropic order ( $I$ ) controls, in some situations, the spatial order of accuracy of the gradient direction. A useful list of the stencil weights needed to construct different high order spatial and isotropic gradients is given. Numerical tests show that the numerical spatial orders of accuracy of the gradient approximation are the same as those predicted theoretically. Also, to illustrate the benefit of the new discretizations, some simulations with a multiphase lattice Boltzmann model are presented. Then, a series of benchmarks comparing various efficient convolution algorithms used to compute function or image gradients is presented. Different platforms implemented on CPUs and GPUs are studied, namely: plain MATLAB; the Jacket plugin for MATLAB; and CUDA. The results show situations in which substantial computational speedup can be obtained with CUDA and the Jacket plugin for MATLAB versus MATLAB on a CPU. Examples of 2D and 3D gradient computations using convolution products performed with our code are available for download as electronic supplementary material.