Transcriptome of the deep-sea black scabbardfish, Aphanopus carbo (Perciformes: Trichiuridae) : tissue-specific expression patterns and candidate genes associated to depth adaptation

Deep-sea fishes provide a unique opportunity to study the physiology and evolutionary adaptation to extreme environments. We carried out a high throughput sequencing analysis on a 454 GS-FLX titanium plate using unnormalized cDNA libraries from six tissues of A. carbo. Assemblage and annotations were performed by Newbler and InterPro/Pfam analyses, respectively. The assembly of 544,491 high quality reads provided 8,319 contigs, 55.6% of which retrieved blast hits against the NCBI nonredundant database or were annotated with ESTscan. Comparison of functional genes at both the protein sequences and protein stability levels, associated with adaptations to depth, revealed similarities between A. carbo and other bathypelagic fishes. A selection of putative genes was standardized to evaluate the correlation between number of contigs and their normalized expression, as determined by qPCR amplification. The screening of the libraries contributed to the identification of new EST simple-sequence repeats (SSRs) and to the design of primer pairs suitable for population genetic studies as well as for tagging and mapping of genes. The characterization of the deep-sea fish A. carbo first transcriptome is expected to provide abundant resources for genetic, evolutionary, and ecological studies of this species and the basis for further investigation of depth-related adaptation processes in fishes.Publisher PDFPeer reviewe

Locking-free curved elements with refined kinematics for the analysis of composite structures

A new class of refined curved beam elements is proposed for the accurate stress analysis of composite structures. The element possesses three-dimensional capabilities and it is suited for the study of curved laminates and fiber-reinforced composites at the microscopic scale. The numerical issues associated with membrane and shear lockings are overcome by means of assumed interpolations of the strain components based on the mixed interpolation of tensorial components method (MITC). Higher-order expansions with only displacement unknowns are employed for the cross-section assumptions at the component level, enabling the computation of component-wise stress fields. For this purpose, a hierarchical set of Legendre functions is implemented, which allows the user to tune the kinematics of the element through the polynomial order input. The detrimental effects of locking in composite modeling are investigated and the robustness and efficiency of the beam element is assessed through comparison against solutions from the literature and refined solid models

A comparative study of experimental configurations in synchrotron pair distribution function

The identification and quantification of amorphous components and nanocrystalline phases with very small crystal sizes, smaller than ~3 nm, within samples containing crystalline phases is very challenging. However, this is important as there are several types of systems that contain these matrices: building materials, glass-ceramics, some alloys, etc. The total scattering synchrotron pair distribution function (PDF) can be used to characterize the local atomic order of the nanocrystalline components and to carry out quantitative analyses in complex mixtures. Although the resolution in momentum transfer space has been widely discussed, the resolution in the interatomic distance space has not been discussed to the best of our knowledge. Here, we report synchrotron PDF data collected at three beamlines in different experimental configurations and X-ray detectors. We not only discuss the effect of the resolution in Q-space, Qmax ins of the recorded data and Qmax of the processed data, but we also discuss the resolution in the interatomic distance (real) space. A thorough study of single-phase crystalline nickel used as standard was carried out. Then, selected cement-related samples including anhydrous tricalcium and dicalcium silicates, and pastes derived from the hydration of tricalcium silicate and ye’elimite with bassanite were analyzed.This work is part of the PhD of Mr. Jesus D. Zea-Garcia. This work was supported by Spanish MINECO and FEDER [BIA2017-82391-R research project and I3 [IEDI-2016-0079] program]