Relevance of cell subcompartmentalization techniques to predict adverse effects of metals in bivalves and fish

Subcellular fractionation is an interesting technique to study metal cell compartmentalization and helps on evaluating the impact of a contaminant in an organism. It provides a better understanding about the fate and behaviour of metals within cell compartments, being then able to identify if metals experience a detoxification process or, on the contrary, they are trophically available. Having this information about metals and metalloids is crucial in the context of risk assessment, as it provides valuable information about their behaviour throughout the food chain at different trophic levels. Coastal and marine environments are often affected by dangerous spillages. Pollutants tend to accumulate in water, soils and sediments, where they can become readily available to species, such as bivalves and fish. These species are often used as bioindicators as they can provide information about the trophic transfer and/or the accumulation and of different pollutants. After a bibliographic search, the protocols used to study the subcellular fractionation on bivalves and fish exposed to metals have been highlighted. This literature mini review focuses on the different protocols used for studying this issue and the improvements that subcellular fractionation has brought to the topic. Nonetheless, future research needs and perspectives are pointed out as they can improve the robustness of using such techniques for risk assessment

Large-Eddy Simulations of Fluid and Magnetohydrodynamic Turbulence Using Renormalized Parameters

In this paper a procedure for large-eddy simulation (LES) has been devised for fluid and magnetohydrodynamic turbulence in Fourier space using the renormalized parameters. The parameters calculated using field theory have been taken from recent papers by Verma [Phys. Rev. E, 2001; Phys. Plasmas, 2001]. We have carried out LES on $64^3$ grid. These results match quite well with direct numerical simulations of $128^3$. We show that proper choice of parameter is necessary in LES.Comment: 12 pages, 4 figures: Proper figures inserte

Forced Stratified Turbulence: Successive Transitions with Reynolds Number

Numerical simulations are made for forced turbulence at a sequence of increasing values of Reynolds number, R, keeping fixed a strongly stable, volume-mean density stratification. At smaller values of R, the turbulent velocity is mainly horizontal, and the momentum balance is approximately cyclostrophic and hydrostatic. This is a regime dominated by so-called pancake vortices, with only a weak excitation of internal gravity waves and large values of the local Richardson number, Ri, everywhere. At higher values of R there are successive transitions to (a) overturning motions with local reversals in the density stratification and small or negative values of Ri; (b) growth of a horizontally uniform vertical shear flow component; and (c) growth of a large-scale vertical flow component. Throughout these transitions, pancake vortices continue to dominate the large-scale part of the turbulence, and the gravity wave component remains weak except at small scales.Comment: 8 pages, 5 figures (submitted to Phys. Rev. E

Collision Chronology Along the İzmir‐Ankara‐Erzincan Suture Zone: Insights From the Sarıcakaya Basin, Western Anatolia

An edited version of this paper was published by AGU. Copyright 2019 American Geophysical Union.Debate persists concerning the timing and geodynamics of intercontinental collision, style of syncollisional deformation, and development of topography and fold‐and‐thrust belts along the >1,700‐km‐long İzmir‐Ankara‐Erzincan suture zone (İAESZ) in Turkey. Resolving this debate is a necessary precursor to evaluating the integrity of convergent margin models and kinematic, topographic, and biogeographic reconstructions of the Mediterranean domain. Geodynamic models argue either for a synchronous or diachronous collision during either the Late Cretaceous and/or Eocene, followed by Eocene slab breakoff and postcollisional magmatism. We investigate the collision chronology in western Anatolia as recorded in the sedimentary archives of the 90‐km‐long Sarıcakaya Basin perched at shallow structural levels along the İAESZ. Based on new zircon U‐Pb geochronology and depositional environment and sedimentary provenance results, we demonstrate that the Sarıcakaya Basin is an Eocene sedimentary basin with sediment sourced from both the İAESZ and Söğüt Thrust fault to the south and north, respectively, and formed primarily by flexural loading from north‐south shortening along the syncollisional Söğüt Thrust. Our results refine the timing of collision between the Anatolides and Pontide terranes in western Anatolia to Maastrichtian‐Middle Paleocene and Early Eocene crustal shortening and basin formation. Furthermore, we demonstrate contemporaneous collision, deformation, and magmatism across the İAESZ, supporting synchronous collision models. We show that regional postcollisional magmatism can be explained by renewed underthrusting instead of slab breakoff. This new İAESZ chronology provides additional constraints for kinematic, geodynamic, and biogeographic reconstructions of the Mediterranean domain

Genetic diversity analysis in the section Caulorrhizae (genus Arachis) using microsatellite markers

Diversity in 26 microsatellite loci from section Caulorrhizae germplasm was evaluated by using 33 accessions of A. pintoi Krapov. & W.C. Gregory and ten accessions of Arachis repens Handro. Twenty loci proved to be polymorphic and a total of 196 alleles were detected with an average of 9.8 alleles per locus. The variability found in those loci was greater than the variability found using morphological characters, seed storage proteins and RAPD markers previously used in this germplasm. The high potential of these markers to detect species-specific alleles and discriminate among accessions was demonstrated. The set of microsatellite primer pairs developed by our group for A. pintoi are useful molecular tools for evaluating Section Caulorrhizae germplasm, as well as that of species belonging to other Arachis sections

Development of a Mesoamerican intra-genepool genetic map for quantitative trait loci detection in a drought tolerant × susceptible common bean (Phaseolus vulgaris L.) cross

Drought is a major constraint to common bean (Phaseolus vulgaris L.) production, especially in developing countries where irrigation for the crop is infrequent. The Mesoamerican genepool is the most widely grown subdivision of common beans that include small red, small cream and black seeded varieties. The objective of this study was to develop a reliable genetic map for a Mesoamerican × Mesoamerican drought tolerant × susceptible cross and to use this map to analyze the inheritance of yield traits under drought and fully irrigated conditions over 3 years of experiments. The source of drought tolerance used in the cross was the cream-seeded advanced line BAT477 crossed with the small red variety DOR364 and the population was made up of recombinant inbred lines in the F5 generation. Quantitative trait loci were detected by composite interval mapping for the traits of overall seed yield, yield per day, 100 seed weight, days to flowering and days to maturity for each field environment consisting of two treatments (irrigated and rainfed) and lattice design experiments with three repetitions for a total of six environments. The genetic map based on amplified fragment length polymorphism and random amplified polymorphic DNA markers was anchored with 60 simple sequence repeat (SSR) markers and had a total map length of 1,087.5 cM across 11 linkage groups covering the whole common bean genome with saturation of one marker every 5.9 cM. Gaps for the genetic map existed on linkage groups b03, b09 and b11 but overall there were only nine gaps larger than 15 cM. All traits were inherited quantitatively, with the greatest number for seed weight followed by yield per day, yield per se, days to flowering and days to maturity. The relevance of these results for breeding common beans is discussed in particular in the light of crop improvement for drought tolerance in the Mesoamerican genepool

Strong and weak constraint variational assimilations for reduced order fluid flow modeling

International audienceIn this work we propose and evaluate two variational data assimilation techniques for the estimation of low order surrogate experimental dynamical models for fluid flows. Both methods are built from optimal control recipes and rely on proper orthogonal decomposition and a Galerkin projection of the Navier Stokes equation. The techniques proposed di er in the control variables they involve. The first one introduces a weak dynamical model defined only up to an additional uncertainty time-dependent function whereas the second one, handles a strong dynamical constraint in which the dynamical system's coe cients constitute the control variables. Both choices correspond to di erent approximations of the relation between the reduced basis on which is expressed the motion field and the basis components that have been neglected in the reduced order model construction. The techniques have been assessed on numerical data and for real experimental conditions with noisy Image Velocimetry data

Genetic diversity in cultivated carioca common beans based on molecular marker analysis

A wide array of molecular markers has been used to investigate the genetic diversity among common bean species. However, the best combination of markers for studying such diversity among common bean cultivars has yet to be determined. Few reports have examined the genetic diversity of the carioca bean, commercially one of the most important common beans in Brazil. In this study, we examined the usefulness of two molecular marker systems (simple sequence repeats – SSRs and amplified fragment length polymorphisms – AFLPs) for assessing the genetic diversity of carioca beans. The amount of information provided by Roger’s modified genetic distance was used to analyze SSR data and Jaccards similarity coefficient was used for AFLP data. Seventy SSRs were polymorphic and 20 AFLP primer combinations produced 635 polymorphic bands. Molecular analysis showed that carioca genotypes were quite diverse. AFLPs revealed greater genetic differentiation and variation within the carioca genotypes (Gst = 98% and Fst = 0.83, respectively) than SSRs and provided better resolution for clustering the carioca genotypes. SSRs and AFLPs were both suitable for assessing the genetic diversity of Brazilian carioca genotypes since the number of markers used in each system provided a low coefficient of variation. However, fingerprint profiles were generated faster with AFLPs, making them a better choice for assessing genetic diversity in the carioca germplasm

Skeleton of an unusual cat-sized marsupial relative (Metatheria: Marsupialiformes) from the middle Eocene (Lutetian: 44-43 million years ago) of Turkey

We describe a near-complete, three-dimensionally preserved skeleton of a metatherian (relative of modern marsupials) from the middle Eocene (Lutetian: 44–43 million years ago) Lülük member of the Uzunçarşıdere Formation, central Turkey. With an estimated body mass of 3–4 kg, about the size of a domestic cat (Felis catus) or spotted quoll (Dasyurus maculatus), it is an order of magnitude larger than the largest fossil metatherians previously known from the Cenozoic of the northern hemisphere. This new taxon is characterised by large, broad third premolars that probably represent adaptations for hard object feeding (durophagy), and its craniodental morphology suggests the capacity to generate high bite forces. Qualitative and quantitative functional analyses of its postcranial skeleton indicate that it was probably scansorial and relatively agile, perhaps broadly similar in locomotor mode to the spotted quoll, but with a greater capacity for climbing and grasping. Bayesian phylogenetic analysis of a total evidence dataset comprising 259 morphological characters and 9kb of DNA sequence data from five nuclear protein-coding genes, using both undated and “tip-and-node dating” approaches, place the new taxon outside the marsupial crown-clade, but within the clade Marsupialiformes. It demonstrates that at least one metatherian lineage evolved to occupy the small-medium, meso- or hypo-carnivore niche in the northern hemisphere during the early Cenozoic, at a time when there were numerous eutherians (placentals and their fossil relatives) filling similar niches. However, the known mammal fauna from Uzunçarşıdere Formation appears highly endemic, and geological evidence suggests that this region of Turkey was an island for at least part of the early Cenozoic, and so the new taxon may have evolved in isolation from potential eutherian competitors. Nevertheless, the new taxon reveals previously unsuspected ecomorphological disparity among northern hemisphere metatherians during the first half of the Cenozoic

Pediatric-type high-grade neuroepithelial tumors with CIC gene fusion share a common DNA methylation signature

Pediatric neoplasms in the central nervous system (CNS) show extensive clinical and molecular heterogeneity and are fundamentally different from those occurring in adults. Molecular genetic testing contributes to accurate diagnosis and enables an optimal clinical management of affected children. Here, we investigated a rare, molecularly distinct type of pediatric high-grade neuroepithelial tumor (n = 18), that was identified through unsupervised visualization of genome-wide DNA methylation array data, together with copy number profiling, targeted next-generation DNA sequencing, and RNA transcriptome sequencing. DNA and/or RNA sequencing revealed recurrent fusions involving the capicua transcriptional repressor (CIC) gene in 10/10 tumor samples analyzed, with the most common fusion being CIC::LEUTX (n = 9). In addition, a CIC::NUTM1 fusion was detected in one of the tumors. Apart from the detected fusion events, no additional oncogenic alteration was identified in these tumors. The histopathological review demonstrated a morphologically heterogeneous group of high-grade neuroepithelial tumors with positive immunostaining for markers of glial differentiation in combination with weak and focal expression of synaptophysin, CD56 and CD99. All tumors were located in the supratentorial compartment, occurred during childhood (median age 8.5 years) and typically showed early relapses. In summary, we expand the spectrum of pediatric-type tumors of the CNS by reporting a previously uncharacterized group of rare high-grade neuroepithelial tumors that share a common DNA methylation signature and recurrent gene fusions involving the transcriptional repressor CIC. Downstream functional consequences of the fusion protein CIC::LEUTX and potential therapeutic implications need to be further investigated