Divergent selection in a Mediterranean pine on local spatial scales

1. The effects of selection on an organism's genome are hard to detect on small spatial scales, as gene flow can swamp signatures of local adaptation. Therefore, most genome scans to detect signatures of environmental selection are performed on large spatial scales; however, divergent selection on the local scale (e.g. between contrasting soil conditions) has also been demonstrated, in particular for herbaceous plants. 2. Here, we hypothesised that in topographically complex landscapes, microenvironment variability is strong enough to leave a selective footprint in the genomes of long-lived organisms. To test this, we investigated paired south- versus north-facing Pinus pinaster stands on the local scale, with trees growing in close vicinity (≤820 m distance between paired south- and north-facing stands), in a Mediterranean mountain area. While trees on north-facing slopes experience less radiation, trees on south-facing slopes suffer from especially harsh conditions, particularly during the dry summer season. 3. Two outlier analyses consistently revealed five putatively adaptive loci (out of 4034), in candidate genes two of which encoded non-synonymous substitutions. Additionally, one locus showed consistent allele frequency differences in all three stand pairs indicating divergent selection despite high gene flow on the local scale. Permutation tests demonstrated that our findings were robust. 4. Functional annotation of these candidate genes revealed biological functions related to abiotic stress response, such as water availability, in other plant species. 5. Synthesis. Our study highlights how divergent selection in heterogeneous microenvironments shapes and maintains the functional genetic variation within populations of long-lived forest tree species, being the first to focus on adaptive genetic divergence between south- and north-facing slopes within continuous forest stands. This is especially relevant in the current context of climate change, as this variation is at the base of plant population responses to future climate.European Commission http://dx.doi.org/10.13039/501100000780European Science Foundation http://dx.doi.org/10.13039/501100000782Spanish Ministry of Science and Innovation http://dx.doi.org/10.13039/501100004837University of BrodeauxPeer Reviewe

Completion of Hepatitis C Virus Replication Cycle in Heterokaryons Excludes Dominant Restrictions in Human Non-liver and Mouse Liver Cell Lines

Hepatitis C virus (HCV) is hepatotropic and only infects humans and chimpanzees. Consequently, an immunocompetent small animal model is lacking. The restricted tropism of HCV likely reflects specific host factor requirements. We investigated if dominant restriction factors expressed in non-liver or non-human cell lines inhibit HCV propagation thus rendering these cells non-permissive. To this end we explored if HCV completes its replication cycle in heterokaryons between human liver cell lines and non-permissive cell lines from human non-liver or mouse liver origin. Despite functional viral pattern recognition pathways and responsiveness to interferon, virus production was observed in all fused cells and was only ablated when cells were treated with exogenous interferon. These results exclude that constitutive or virus-induced expression of dominant restriction factors prevents propagation of HCV in these cell types, which has important implications for HCV tissue and species tropism. In turn, these data strongly advocate transgenic approaches of crucial human HCV cofactors to establish an immunocompetent small animal model

Toksikološka svojstva citrinina

Citrinin (CTN) is a nephrotoxic mycotoxin produced by several fungal strains belonging to the genera Penicillium, Aspergillus, and Monascus. It contaminates various commodities of plant origin, cereals in particular, and is usually found together with another nephrotoxic mycotoxin, ochratoxin A (OTA). These two mycotoxins are believed to be involved in the aetiology of endemic nephropathy. In addition to nephrotoxicity, CTN is also embryocidal and fetotoxic. The genotoxic properties of CTN have been demonstrated with the micronuleus test (MN), but not with single-cell gel electrophoresis. The mechanism of CTN toxicity is not fully understood, especially not whether CTN toxicity and genotoxicity are the consequence of oxidative stress or of increased permeability of mitochondrial membranes. CTN requires complex cellular biotransformation to exert mutagenicity. Compared with other mycotoxins, CTN contamination of food and feed is rather scarce. However, it is reasonable to believe that humans are much more frequently exposed to CTN than generally accepted, because it is produced by the same moulds as OTA, which is a common contaminant of human food all over the world. At present, there are no specifi c regulations either in Croatia or in the European Union concerning CTN in any kind of commodity.Citrinin (CTN) nefrotoksičan je mikotoksin koji proizvode različiti sojevi plijesni iz rodova Penicillium, Aspergillus i Monascus. CTN se može naći u različitim namirnicama biljnog podrijetla, osobito u žitaricama i obično se nalazi zajedno s drugim nefrotoksičnim mikotoksinom, okratoksinom A (OTA). Pretpostavlja se da je izloženost ovim mikotoksinima povezana s nastankom endemske nefropatije. Osim što je nefrotoksičan, CTN je još i embricidan i fetotoksičan. Na genotoksičnost citrinina upućuje pozitivan mikronukleusni test na različitim vrstama staničnih kultura, iako je kometski test negativan. Mutagenost CTN-a očituje se na različitim vrstama stanica samo ako se pridodaju stanični aktivatori kao npr. S9-mix. Mehanizam toksičnosti CTN-a nije potpuno razjašnjen pa još uvijek traje znanstvena rasprava je li njegova toksičnost i genotoksičnost posljedica oksidacijskog stresa ili povećane permeabilnosti mitohondrijskih membrana. U dostupnoj literaturi podaci o kontaminiranosti hrane i krmiva ovim mikotoksinom mnogo su rjeđi od onih za druge mikotoksine. Može se pretpostaviti da su ljudi često izloženi ovom mikotoksinu zato što ga proizvode iste plijesni koje proizvode i OTA, a one kontaminiraju hranu po cijelom svijetu. U Hrvatskoj i u zemljama Europske Unije ne postoje zakonske odredbe o dopuštenim granicama CTN-a u bilo kojoj vrsti hrane

Autothermal reforming of palm empty fruit bunch bio-oil: thermodynamic modelling

This work focuses on thermodynamic analysis of the autothermal reforming of palm empty fruit bunch (PEFB) bio-oil for the production of hydrogen and syngas. PEFB bio-oil composition was simulated using bio-oil surrogates generated from a mixture of acetic acid, phenol, levoglucosan, palmitic acid and furfural. A sensitivity analysis revealed that the hydrogen and syngas yields were not sensitive to actual bio-oil composition, but were determined by a good match of molar elemental composition between real bio-oil and surrogate mixture. The maximum hydrogen yield obtained under constant reaction enthalpy and pressure was about 12 wt% at S/C = 1 and increased to about 18 wt% at S/C = 4; both yields occurring at equivalence ratio Φ of 0.31. The possibility of generating syngas with varying H2 and CO content using autothermal reforming was analysed and application of this process to fuel cells and Fischer-Tropsch synthesis is discussed. Using a novel simple modelling methodology, reaction mechanisms were proposed which were able to account for equilibrium product distribution. It was evident that different combinations of reactions could be used to obtain the same equilibrium product concentrations. One proposed reaction mechanism, referred to as the ‘partial oxidation based mechanism’ involved the partial oxidation reaction of the bio-oil to produce hydrogen, with the extent of steam reforming and water gas shift reactions varying depending on the amount of oxygen used. Another proposed mechanism, referred to as the ‘complete oxidation based mechanism’ was represented by thermal decomposition of about 30% of bio-oil and hydrogen production obtained by decomposition, steam reforming, water gas shift and carbon gasification reactions. The importance of these mechanisms in assisting in the eventual choice of catalyst to be used in a real ATR of PEFB bio-oil process was discussed

Parallel Reyes-style Adaptive Subdivision with Bounded Memory Usage

  Recent advances in graphics hardware have made it a desirable goal to implement the Reyes algorithm on current graphics cards.  One key component in this algorithm is the bound-and-split phase, where surface patches are recursively split until they are smaller than a given screen-space bound.  While this operation has been successfully parallelized for execution on the GPU using a breadth-first traversal, the resulting implementations are limited by their unpredictable worst-case memory consumption and high global memory bandwidth utilization.  In this paper, we propose an alternate strategy that allows limiting the amount of necessary memory by controlling the number of assigned worker threads.  The result is an implementation that scales to the performance of the breadth-first approach while offering three advantages: significantly decreased memory usage, a smooth and predictable tradeoff between memory usage and performance, and increased locality for surface processing.  This allows us to render scenes that would require too much memory to be processed by the breadth-first method

Physically based computer graphics for realistic image formation to simulate optical measurement systems

Physically based image synthesis methods, a research direction in computer graphics (CG), are capable of simulating optical measuring systems in their entirety and thus constitute an interesting approach for the development, simulation, optimization, and validation of such systems. In addition, other CG methods, so-called procedural modeling techniques, can be used to quickly generate large sets of virtual samples and scenes thereof that comprise the same variety as physical testing objects and real scenes (e.g., if digitized sample data are not available or difficult to acquire). Appropriate image synthesis (rendering) techniques result in a realistic image formation for the virtual scenes, considering light sources, material, complex lens systems, and sensor properties, and can be used to evaluate and improve complex measuring systems and automated optical inspection (AOI) systems independent of a physical realization. In this paper, we provide an overview of suitable image synthesis methods and their characteristics, we discuss the challenges for the design and specification of a given measuring situation in order to allow for a reliable simulation and validation, and we describe an image generation pipeline suitable for the evaluation and optimization of measuring and AOI systems

Potential and challenges of using computer graphics for the simulation of optical measurement systems

Physically-based image synthesis methods, a research direction in computer graphics (CG), are capable of simulating optical measuring systems in their entirety and thus constitute an interesting approach for the development, simulation, optimization, and validation of such systems. In addition, other CG methods, so called procedural modeling techniques, can be used to quickly generate large sets of virtual samples and scenes thereof that comprise the same variety as physical testing objects and real scenes (e.g., if digitized sample data is not available or difficult to acquire). Appropriate image synthesis (rendering) techniques result in a realistic image formation for the virtual scenes, considering light sources, material, complex lens systems, and sensor properties, and can be used to evaluate and improve complex measuring systems and automated optical inspection (AOI) systems independent of a physical realization. In this paper, we describe an image generation pipeline for the evaluation and optimization of measuring and AOI systems, we provide an overview over suitable image synthesis methods and their characteristics, and we discuss the challenges for the design and specification of a given measuring situation in order to allow for a reliable simulation and validation

Wide Gamut Spectral Upsampling with Fluorescence

Physically based spectral rendering has become increasingly important in recent years. However, asset textures in such systems are usually still drawn or acquired as RGB tristimulus values. While a number of RGB to spectrum upsampling techniques are available, none of them support upsampling of all colours in the full spectral locus, as it is intrinsically bigger than the gamut of physically valid reflectance spectra. But with display technology moving to increasingly wider gamuts, the ability to achieve highly saturated colours becomes an increasingly important feature. Real materials usually exhibit smooth reflectance spectra, while computationally generated spectra become more blocky as they represent increasingly bright and saturated colours. In print media, plastic or textile design, fluorescent dyes are added to extend the boundaries of the gamut of reflectance spectra. We follow the same approach for rendering: we provide a method which, given an input RGB tristimulus value, automatically provides a mixture of a regular, smooth reflectance spectrum plus a fluorescent part. For highly saturated input colours, the combination yields an improved reconstruction compared to what would be possible relying on a reflectance spectrum alone. At the core of our technique is a simple parametric spectral model for reflectance, excitation, and emission that allows for compact storage and is compatible with texture mapping. The model can then be used as a fluorescent diffuse component in an existing more complex BRDF model. We also provide importance sampling routines for practical application in a path tracer