High-Frequency Linear Array (20 MHz) Based on Lead-Free BCTZ Crystal.

Centimeter-sized BaTiO3-based crystals grown by top-seeded solution growth from the BaTiO3-CaTiO3-BaZrO3 system were used to process a high-frequency (HF) lead-free linear array. Piezoelectric plates with (110)pc cut within 1° accuracy were used to manufacture two 1-3 piezo-composites with thicknesses of 270 and [Formula: see text] for resonant frequencies in air of 10 and 30 MHz, respectively. The electromechanical characterization of the BCTZ crystal plates and the 10-MHz piezocomposite yielded the thickness coupling factors of 40% and 50%, respectively. We quantified the electromechanical performance of the second piezocomposite (30 MHz) according to the reduction in the pillar sizes during the fabrication process. The dimensions of the piezocomposite at 30 MHz were sufficient for a 128-element array with a 70- [Formula: see text] element pitch and a 1.5-mm elevation aperture. The transducer stack (backing, matching layers, lens, and electrical components) was tuned with the characteristics of the lead-free materials to deliver optimal bandwidth and sensitivity. The probe was connected to a real-time HF 128-channel echographic system for acoustic characterization (electroacoustic response and radiation pattern) and to acquire high-resolution in vivo images of human skin. The center frequency of the experimental probe was 20 MHz, and the fractional bandwidth at -6 dB was 41%. Skin images were compared against those obtained with a lead-based 20-MHz commercial imaging probe. Despite significant differences in sensitivity between elements, in vivo images obtained with a BCTZ-based probe convincingly demonstrated the potential of integrating this piezoelectric material in an imaging probe.

A Quantitative, Genome-Wide Analysis in Drosophila Reveals Transposable Elements' Influence on Gene Expression Is Species-Specific.

Transposable elements (TEs) are parasite DNA sequences that are able to move and multiply along the chromosomes of all genomes. They can be controlled by the host through the targeting of silencing epigenetic marks, which may affect the chromatin structure of neighboring sequences, including genes. In this study, we used transcriptomic and epigenomic high-throughput data produced from ovarian samples of several Drosophila melanogaster and Drosophila simulans wild-type strains, in order to finely quantify the influence of TE insertions on gene RNA levels and histone marks (H3K9me3 and H3K4me3). Our results reveal a stronger epigenetic effect of TEs on ortholog genes in D. simulans compared with D. melanogaster. At the same time, we uncover a larger contribution of TEs to gene H3K9me3 variance within genomes in D. melanogaster, which is evidenced by a stronger correlation of TE numbers around genes with the levels of this chromatin mark in D. melanogaster. Overall, this work contributes to the understanding of species-specific influence of TEs within genomes. It provides a new light on the considerable natural variability provided by TEs, which may be associated with contrasted adaptive and evolutionary potentials.

Evaluation of Methods to Detect Shifts in Directional Selection at the Genome Scale.

Identifying the footprints of selection in coding sequences can inform about the importance and function of individual sites. Analyses of the ratio of nonsynonymous to synonymous substitutions (dN/dS) have been widely used to pinpoint changes in the intensity of selection, but cannot distinguish them from changes in the direction of selection, that is, changes in the fitness of specific amino acids at a given position. A few methods that rely on amino-acid profiles to detect changes in directional selection have been designed, but their performances have not been well characterized. In this paper, we investigate the performance of six of these methods. We evaluate them on simulations along empirical phylogenies in which transition events have been annotated and compare their ability to detect sites that have undergone changes in the direction or intensity of selection to that of a widely used dN/dS approach, codeml's branch-site model A. We show that all methods have reduced performance in the presence of biased gene conversion but not CpG hypermutability. The best profile method, Pelican, a new implementation of Tamuri AU, Hay AJ, Goldstein RA. (2009. Identifying changes in selective constraints: host shifts in influenza. PLoS Comput Biol. 5(11):e1000564), performs as well as codeml in a range of conditions except for detecting relaxations of selection, and performs better when tree length increases, or in the presence of persistent positive selection. It is fast, enabling genome-scale searches for site-wise changes in the direction of selection associated with phenotypic changes.

Phase Transitions and Physical Properties of the Mixed Valence Iron Phosphate Fe3(PO3OH)4(H2O)4.

Iron phosphate materials have attracted a lot of attention due to their potential as cathode materials for lithium-ion rechargeable batteries. It has been shown that lithium insertion or extraction depends on the Fe mixed valence and reduction or oxidation of the Fe ions' valences. In this paper, we report a new synthesis method for the Fe3(PO3OH)4(H2O)4 mixed valence iron phosphate. In addition, we perform temperature-dependent measurements of structural and physical properties in order to obtain an understanding of electronic-structural interplay in this compound. Scanning electron microscope images show needle-like single crystals of 50 µm to 200 µm length which are stable up to approximately 200 °C, as revealed by thermogravimetric analysis. The crystal structure of Fe3(PO3OH)4(H2O)4 single crystals has been determined in the temperature range of 90 K to 470 K. A monoclinic isostructural phase transition was found at ~213 K, with unit cell volume doubling in the low temperature phase. While the local environment of the Fe2+ ions does not change significantly across the structural phase transition, small antiphase rotations occur for the Fe3+ octahedra, implying some kind of electronic order. These results are corroborated by first principle calculations within density functional theory, which also point to ordering of the electronic degrees of freedom across the transition. The structural phase transition is confirmed by specific heat measurements. Moreover, hints of 3D antiferromagnetic ordering appear below ~11 K in the magnetic susceptibility measurements. Room temperature visible light absorption is consistent with the Fe2+/Fe3+ mixed valence.

High Stability of the Epigenome in Drosophila Interspecific Hybrids.

Interspecific hybridization is often seen as a genomic stress that may lead to new gene expression patterns and deregulation of transposable elements (TEs). The understanding of expression changes in hybrids compared with parental species is essential to disentangle their putative role in speciation processes. However, to date we ignore the detailed mechanisms involved in genomic deregulation in hybrids. We studied the ovarian transcriptome and epigenome of the Drosophila buzzatii and Drosophila koepferae species together with their F1 hybrid females. We found a trend toward underexpression of genes and TE families in hybrids. The epigenome in hybrids was highly similar to the parental epigenomes and showed intermediate histone enrichments between parental species in most cases. Differential gene expression in hybrids was often associated only with changes in H3K4me3 enrichments, whereas differential TE family expression in hybrids may be associated with changes in H3K4me3, H3K9me3, or H3K27me3 enrichments. We identified specific genes and TE families, which their differential expression in comparison with the parental species was explained by their differential chromatin mark combination enrichment. Finally, cis-trans compensatory regulation could also contribute in some way to the hybrid deregulation. This work provides the first study of histone content in Drosophila interspecific hybrids and their effect on gene and TE expression deregulation.

Transcriptome-wide deregulation of gene expression by artificial light at night in tadpoles of common toads.

Artificial light at night (ALAN) affects numerous physiological and behavioural mechanisms in various species by potentially disturbing circadian timekeeping systems and modifying melatonin levels. However, given the multiple direct and indirect effects of ALAN on organisms, large-scale transcriptomic approaches are essential to assess the global effect of ALAN on biological processes. Moreover, although studies have focused mainly on variations in gene expression during the night in the presence of ALAN, it is necessary to investigate the effect of ALAN on gene expression during the day. In this study, we combined de novo transcriptome sequencing and assembly, and a controlled laboratory experiment to evaluate the transcriptome-wide gene expression response using high-throughput (RNA-seq) in Bufo bufo tadpoles exposed to ecologically relevant light levels. Here, we demonstrated for the first time that ALAN affected gene expression at night (3.5% and 11% of differentially expressed genes when exposed to 0.1 and 5 lx compared to controls, respectively), but also during the day (11.2% of differentially expressed genes when exposed to 5 lx compared to controls) with a dose-dependent effect. ALAN globally induced a downregulation of genes (during the night, 58% and 62% of the genes were downregulated when exposed to 0.1 and 5 lx compared to controls, respectively, and during the day, 61.2% of the genes were downregulated when exposed to 5 lx compared to controls). ALAN effects were detected at very low levels of illuminance (0.1 lx) and affected mainly genes related to the innate immune system and, to a lesser extend to lipid metabolism. These results provide new insights into understanding the effects of ALAN on organism. ALAN impacted the expression of genes linked to a broad range of physiological pathways at very low levels of ALAN during night-time and during daytime, potentially resulting in reduced immune capacity under environmental immune challenges.

A Transposon Story: From TE Content to TE Dynamic Invasion of Drosophila Genomes Using the Single-Molecule Sequencing Technology from Oxford Nanopore.

Transposable elements (TEs) are the main components of genomes. However, due to their repetitive nature, they are very difficult to study using data obtained with short-read sequencing technologies. Here, we describe an efficient pipeline to accurately recover TE insertion (TEI) sites and sequences from long reads obtained by Oxford Nanopore Technology (ONT) sequencing. With this pipeline, we could precisely describe the landscapes of the most recent TEIs in wild-type strains of Drosophila melanogaster and Drosophila simulans. Their comparison suggests that this subset of TE sequences is more similar than previously thought in these two species. The chromosome assemblies obtained using this pipeline also allowed recovering piRNA cluster sequences, which was impossible using short-read sequencing. Finally, we used our pipeline to analyze ONT sequencing data from a D. melanogaster unstable line in which LTR transposition was derepressed for 73 successive generations. We could rely on single reads to identify new insertions with intact target site duplications. Moreover, the detailed analysis of TEIs in the wild-type strains and the unstable line did not support the trap model claiming that piRNA clusters are hotspots of TE insertions.

Structural and Lattice-Dynamical Properties of Tb2O3 under Compression: A Comparative Study with Rare Earth and Related Sesquioxides.

We report a joint experimental and theoretical investigation of the high pressure structural and vibrational properties of terbium sesquioxide (Tb2O3). Powder X-ray diffraction and Raman scattering measurements show that cubic Ia3̅ (C-type) Tb2O3 undergoes two phase transitions up to 25 GPa. We observe a first irreversible reconstructive transition to the monoclinic C2/m (B-type) phase at ∼7 GPa and a subsequent reversible displacive transition from the monoclinic to the trigonal P3̅m1 (A-type) phase at ∼12 GPa. Thus, Tb2O3 is found to follow the well-known C → B → A phase transition sequence found in other cubic rare earth sesquioxides with cations of larger atomic mass than Tb. Our ab initio theoretical calculations predict phase transition pressures and bulk moduli for the three phases in rather good agreement with experimental results. Moreover, Raman-active modes of the three phases have been monitored as a function of pressure, while lattice-dynamics calculations have allowed us to confirm the assignment of the experimental phonon modes in the C- and A-type phases as well as to make a tentative assignment of the symmetry of most vibrational modes in the B-type phase. Finally, we extract the bulk moduli and the Raman-active mode frequencies together with their pressure coefficients for the three phases of Tb2O3. These results are thoroughly compared and discussed in relation to those reported for rare earth and other related sesquioxides as well as with new calculations for selected sesquioxides. It is concluded that the evolution of the volume and bulk modulus of all the three phases of these technologically relevant compounds exhibit a nearly linear trend with respect to the third power of the ionic radii of the cations and that the values of the bulk moduli for the three phases depend on the filling of the f orbitals.

Detecting adaptive convergent amino acid evolution.

In evolutionary genomics, researchers have taken an interest in identifying substitutions that subtend convergent phenotypic adaptations. This is a difficult question that requires distinguishing foreground convergent substitutions that are involved in the convergent phenotype from background convergent substitutions. Those may be linked to other adaptations, may be neutral or may be the consequence of mutational biases. Furthermore, there is no generally accepted definition of convergent substitutions. Various methods that use different definitions have been proposed in the literature, resulting in different sets of candidate foreground convergent substitutions. In this article, we first describe the processes that can generate foreground convergent substitutions in coding sequences, separating adaptive from non-adaptive processes. Second, we review methods that have been proposed to detect foreground convergent substitutions in coding sequences and expose the assumptions that underlie them. Finally, we examine their power on simulations of convergent changes-including in the presence of a change in the efficacy of selection-and on empirical alignments. This article is part of the theme issue 'Convergent evolution in the genomics era: new insights and directions'.

CAARS: comparative assembly and annotation of RNA-Seq data.

MOTIVATION: RNA sequencing (RNA-Seq) is a widely used approach to obtain transcript sequences in non-model organisms, notably for performing comparative analyses. However, current bioinformatic pipelines do not take full advantage of pre-existing reference data in related species for improving RNA-Seq assembly, annotation and gene family reconstruction. RESULTS: We built an automated pipeline named CAARS to combine novel data from RNA-Seq experiments with existing multi-species gene family alignments. RNA-Seq reads are assembled into transcripts by both de novo and assisted assemblies. Then, CAARS incorporates transcripts into gene families, builds gene alignments and trees and uses phylogenetic information to classify the genes as orthologs and paralogs of existing genes. We used CAARS to assemble and annotate RNA-Seq data in rodents and fishes using distantly related genomes as reference, a difficult case for this kind of analysis. We showed CAARS assemblies are more complete and accurate than those assembled by a standard pipeline consisting of de novo assembly coupled with annotation by sequence similarity on a guide species. In addition to annotated transcripts, CAARS provides gene family alignments and trees, annotated with orthology relationships, directly usable for downstream comparative analyses. AVAILABILITY AND IMPLEMENTATION: CAARS is implemented in Python and Ocaml and is freely available at https://github.com/carinerey/caars. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Temperature-Dependent Evolution of Crystallographic and Domain Structures in (K,Na,Li)(Ta,Nb)O3 Piezoelectric Single Crystals.

(K,Na)NbO3-based ferroelectric single crystals have recently undergone a substantial development, resulting in improved crystal quality and large piezoelectric coefficients, exceeding 700 pC/N, over a broad temperature range. However, further development necessitates a detailed understanding of the mechanisms defining the domain structure and its temperature evolution. This paper presents the investigation into the crystallographic structure and domain configurations of a (K,Na,Li)(Ta,Nb)O3 single crystal over a broad temperature range. The crystal was grown by the submerged-seed solution growth technique and investigated using in situ transmission electron microscopy, X-ray diffraction, dielectric measurements, and polarized light microscopy. The lattice distortion, structural phase transitions, and domain configurations are reported. A transition from the lamellar orthorhombic to the rectangular tetragonal domain structure is observed upon heating. Moreover, the milky optical appearance of the crystal was investigated and found to result from the presence of regions with different domain configurations and domain sizes. The formation of these regions is related to the growth defects, which govern the domain formation when cooling below the Curie temperature.

Fit Reduced GUTS Models Online: From Theory to Practice.

Mechanistic modeling approaches, such as the toxicokinetic-toxicodynamic (TKTD) framework, are promoted by international institutions such as the European Food Safety Authority and the Organization for Economic Cooperation and Development to assess the environmental risk of chemical products generated by human activities. TKTD models can encompass a large set of mechanisms describing the kinetics of compounds inside organisms (e.g., uptake and elimination) and their effect at the level of individuals (e.g., damage accrual, recovery, and death mechanism). Compared to classical dose-response models, TKTD approaches have many advantages, including accounting for temporal aspects of exposure and toxicity, considering data points all along the experiment and not only at the end, and making predictions for untested situations as realistic exposure scenarios. Among TKTD models, the general unified threshold model of survival (GUTS) is within the most recent and innovative framework but is still underused in practice, especially by risk assessors, because specialist programming and statistical skills are necessary to run it. Making GUTS models easier to use through a new module freely available from the web platform MOSAIC (standing for MOdeling and StAtistical tools for ecotoxIClogy) should promote GUTS operability in support of the daily work of environmental risk assessors. This paper presents the main features of MOSAIC_GUTS: uploading of the experimental data, GUTS fitting analysis, and LCx estimates with their uncertainty. These features will be exemplified from literature data. Integr Environ Assess Manag 2018;14:625-630. © 2018 SETAC.

MOSAIC: a web-interface for statistical analyses in ecotoxicology.

In ecotoxicology, bioassays are standardly conducted in order to measure acute or chronic effects of potentially toxic substances on reproduction, growth, and/or survival of living animals. MOSAIC, standing for MOdeling and StAtistical tools for ecotoxICology, is a user-friendly web interface dedicated to the mathematical and statistical modelling of such standard bioassay data. Its simple use makes MOSAIC a turnkey decision-making tool for ecotoxicologists and regulators. Without wasting time on extensive mathematical and statistical technicalities, users are provided with advanced and innovative methods for a valuable quantitative environmental risk assessment. MOSAIC is available at http://pbil.univ-lyon1.fr/software/mosaic/ .

Robust Fit of Toxicokinetic-Toxicodynamic Models Using Prior Knowledge Contained in the Design of Survival Toxicity Tests.

Toxicokinetics-toxicodynamic (TKTD) models have emerged as a powerful means to describe survival as a function of time and concentration in ecotoxicology. They are especially powerful to extrapolate survival observed under constant exposure conditions to survival predicted under realistic fluctuating exposure conditions. But despite their obvious benefits, these models have not yet been adopted as a standard to analyze data of survival toxicity tests. Instead simple dose-response models are still often used although they only exploit data observed at the end of the experiment. We believe a reason precluding a wider adoption of TKTD models is that available software still requires strong expertise in model fitting. In this work, we propose a fully automated fitting procedure that extracts prior knowledge on parameters of the model from the design of the toxicity test (tested concentrations and observation times). We evaluated our procedure on three experimental and 300 simulated data sets and showed that it provides robust fits of the model, both in the frequentist and the Bayesian framework, with a better robustness of the Bayesian approach for the sparsest data sets.

Quantitative Molecular Detection of 19 Major Pathogens in the Interdental Biofilm of Periodontally Healthy Young Adults.

In oral health, the interdental spaces are a real ecological niche for which the body has few or no alternative defenses and where the traditional daily methods for control by disrupting biofilm are not adequate. The interdental spaces are the source of many hypotheses regarding their potential associations with and/or causes of cardiovascular disease, diabetes, chronic kidney disease, degenerative disease, and depression. This PCR study is the first to describe the interdental microbiota in healthy adults aged 18-35 years-old with reference to the Socransky complexes. The complexes tended to reflect microbial succession events in developing dental biofilms. Early colonizers included members of the yellow, green, and purple complexes. The orange complex bacteria generally appear after the early colonizers and include many putative periodontal pathogens, such as Fusobacterium nucleatum. The red complex (Porphyromonas gingivalis, Tannerella forsythia, and Treponema denticola) was considered the climax community and is on the list of putative periodontal pathogens. The 19 major periodontal pathogens tested were expressed at various levels. F. nucleatum was the most abundant species, and the least abundant were Actinomyces viscosus, P. gingivalis, and Aggregatibacter actinomycetemcomitans. The genome counts for Eikenella corrodens, Campylobacter concisus, Campylobacter rectus, T. denticola, and Tannerella forsythensis increased significantly with subject age. The study highlights the observation that bacteria from the yellow complex (Streptococcus spp., S. mitis), the green complex (E. corrodens, Campylobacter gracilis, Capnocytophaga ochracea, Capnocytophaga sputigena, A. actinomycetemcomitans), the purple complex (Veillonella parvula, Actinomyces odontolyticus) and the blue complex (A. viscosus) are correlated. Concerning the orange complex, F. nucleatum is the most abundant species in interdental biofilm. The red complex, which is recognized as the most important pathogen in adult periodontal disease, represents 8.08% of the 19 bacteria analyzed. P. gingivalis was detected in 19% of healthy subjects and represents 0.02% of the interdental biofilm. T. forsythensis and T. denticola (0.02 and 0.04% of the interdental biofilm) were detected in 93 and 49% of healthy subjects, respectively. The effective presence of periodontal pathogens is a strong indicator of the need to develop new methods for disrupting interdental biofilm in daily oral hygiene.

Optical contrast and cycling of bistable luminescence properties in Rb2KIn(1-x)CexF6 compounds.

Irradiation cycling was performed to evaluate the ageing of the redox process observed on cerium-doped Rb2KInF6 compounds. An on-off switch of monovalent indium luminescence is observed for the lowest cerium doped material, whereas a nice colourimetric contrast between a bluish-green and orange emission is generated for the material with the highest cerium content. Photoluminescent properties combined with X-ray diffraction, chemical analysis and magnetism measurements allowed an accurate characterization of the system. A complete explanation of the optical behaviour is therefore proposed. Finally, printing tests were performed to illustrate the good functionality of the prepared materials for UV sensitivity.

RAR/RXR binding dynamics distinguish pluripotency from differentiation associated cis-regulatory elements.

In mouse embryonic cells, ligand-activated retinoic acid receptors (RARs) play a key role in inhibiting pluripotency-maintaining genes and activating some major actors of cell differentiation. To investigate the mechanism underlying this dual regulation, we performed joint RAR/RXR ChIP-seq and mRNA-seq time series during the first 48 h of the RA-induced Primitive Endoderm (PrE) differentiation process in F9 embryonal carcinoma (EC) cells. We show here that this dual regulation is associated with RAR/RXR genomic redistribution during the differentiation process. In-depth analysis of RAR/RXR binding sites occupancy dynamics and composition show that in undifferentiated cells, RAR/RXR interact with genomic regions characterized by binding of pluripotency-associated factors and high prevalence of the non-canonical DR0-containing RA response element. By contrast, in differentiated cells, RAR/RXR bound regions are enriched in functional Sox17 binding sites and are characterized with a higher frequency of the canonical DR5 motif. Our data offer an unprecedentedly detailed view on the action of RA in triggering pluripotent cell differentiation and demonstrate that RAR/RXR action is mediated via two different sets of regulatory regions tightly associated with cell differentiation status.

Discussion on the structure stability and the luminescence switch under irradiation of a Ce-doped elpasolite compound.

Ce-doped Rb2 KInF6 elpasolite has the potential for tunable luminescence due to an unusual reversible redox process between the cerium and indium cations. Coupled with a deep understanding of the luminescence properties, XRD analysis and DFT calculations are used to locate the doping elements in the host lattice. The origin explanation of the charge-transfer mechanism that causes a decrease or increase in the blue-green cerium emission in opposition to the red indium emission is discussed regarding the crystallographic structure, the connection of the metallic cations and their equilibrium valence. Still detectable after nineteen years, the optical contrast created under irradiation makes this material a good candidate as photosensor for data storage.

Growth and Characterization of Lead-free Piezoelectric Single Crystals.

Lead-free piezoelectric materials attract more and more attention owing to the environmental toxicity of lead-containing materials. In this work, we review our first attempts of single crystal grown by the top-seeded solution growth method of BaTiO3 substituted with zirconium and calcium (BCTZ) and (K0.5Na0.5)NbO3 substituted with lithium, tantalum, and antimony (KNLSTN). The growth methodology is optimized in order to reach the best compositions where enhanced properties are expected. Chemical analysis and electrical characterizations are presented for both kinds of crystals. The compositionally-dependent electrical performance is investigated for a better understanding of the relationship between the composition and electrical properties. A cross-over from relaxor to ferroelectric state in BCTZ solid solution is evidenced similar to the one reported in ceramics. In KNLSTN single crystals, we observed a substantial evolution of the orthorhombic-to-tetragonal phase transition under minute composition changes.