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.

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.

OUP accepted manuscript

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.

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.

Highly textured lead-free piezoelectric polycrystals grown by the micro-pulling down freezing technique in the BaTiO3–CaTiO3 system

Growth of highly textured lead-free piezoelectric polycrystals in the BaTiO₃–CaTiO₃ system by the micro-pulling down technique.

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.

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'.

Lead-free piezoelectric crystals grown by the micro-pulling down technique in the BaTiO3–CaTiO3–BaZrO3 system

Growth of lead-free piezoelectric single crystal fibres in the BaTiO₃–CaTiO₃–BaZrO₃ system by the micro-pulling down technique.

Single crystal growth of BaZrO3 from the melt at 2700 °C using optical floating zone technique and growth prospects from BaB2O4 flux at 1350 °C

Growth of BaZrO₃ crystals at 2700 °C in a mirror furnace and growth prospects at 1350 °C using BaB₂O₄ flux are reported.

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.

Influence of Ta5+ content on the crystallographic structure and electrical properties of [001]PC-oriented (Li,Na,K)(Nb,Ta)O3 single crystals

A series of centimeter-sized lead-free piezoelectric Li⁺- and Ta⁵⁺-modified (Na,K)NbO₃ single crystals with an ABO₃ perovskite structure was successfully grown by the top-seeded solution growth method.

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 (K_0.5Na_0.5)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.

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.

MOSAIC_SSD: a new web tool for species sensitivity distribution to include censored data by maximum likelihood

Censored data are seldom taken into account in species sensitivity distribution (SSD) analysis. However, they are found in virtually every dataset and sometimes represent the better part of the data. Stringent recommendations on data quality often entail discarding a lot of these meaningful data, resulting in datasets of reduced size which lack representativeness of any realistic community. However, it is reasonably simple to include censored data in SSD by using an extension of the standard maximum likelihood method. The authors detail this approach based on the use of the R-package fitdistrplus, dedicated to the fit of parametric probability distributions. The authors present the new Web tool MOSAIC_SSD, that can fit an SSD on datasets containing any type of data, censored or not. The MOSAIC_SSD Web tool predicts any hazardous concentration and provides bootstrap confidence intervals on the predictions. Finally, the authors illustrate the added value of including censored data in SSD, taking examples from published data.

Statistical handling of reproduction data for exposure-response modeling

Reproduction data collected through standard bioassays are classically analyzed by regression in order to fit exposure-response curves and estimate ECx values (x% effective concentration). But regression is often misused on such data, ignoring statistical issues related to (i) the special nature of reproduction data (count data), (ii) a potential inter-replicate variability, and (iii) a possible concomitant mortality. This paper offers new insights in dealing with those issues. Concerning mortality, particular attention was paid not to waste any valuable data-by dropping all the replicates with mortality-or to bias ECx values. For that purpose we defined a new covariate summing the observation periods during which each individual contributes to the reproduction process. This covariate was then used to quantify reproduction-for each replicate at each concentration-as a number of offspring per individual-day. We formulated three exposure-response models differing by their stochastic part. Those models were fitted to four data sets and compared using a Bayesian framework. The individual-day unit proved to be a suitable approach to use all the available data and prevent bias in the estimation of ECx values. Furthermore, a nonclassical negative-binomial model was shown to correctly describe the inter-replicate variability observed in the studied data sets.

T-cell factor 4 and β-catenin chromatin occupancies pattern zonal liver metabolism in mice

β-catenin signaling can be both a physiological and oncogenic pathway in the liver. It controls compartmentalized gene expression, allowing the liver to ensure its essential metabolic function. It is activated by mutations in 20%-40% of hepatocellular carcinomas (HCCs) with specific metabolic features. We decipher the molecular determinants of β-catenin-dependent zonal transcription using mice with β-catenin-activated or -inactivated hepatocytes, characterizing in vivo their chromatin occupancy by T-cell factor (Tcf)-4 and β-catenin, transcriptome, and metabolome. We find that Tcf-4 DNA bindings depend on β-catenin. Tcf-4/β-catenin binds Wnt-responsive elements preferentially around β-catenin-induced genes. In contrast, genes repressed by β-catenin bind Tcf-4 on hepatocyte nuclear factor 4 (Hnf-4)-responsive elements. β-Catenin, Tcf-4, and Hnf-4α interact, dictating β-catenin transcription, which is antagonistic to that elicited by Hnf-4α. Finally, we find the drug/bile metabolism pathway to be the one most heavily targeted by β-catenin, partly through xenobiotic nuclear receptors.

CONCLUSIONS

β-catenin patterns the zonal liver together with Tcf-4, Hnf-4α, and xenobiotic nuclear receptors. This network represses lipid metabolism and exacerbates glutamine, drug, and bile metabolism, mirroring HCCs with β-catenin mutational activation.

Epidemiology of asexuality induced by the endosymbiotic Wolbachia across phytophagous wasp species: host plant specialization matters

Among eukaryotes, sexual reproduction is by far the most predominant mode of reproduction. However, some systems maintaining sexuality appear particularly labile and raise intriguing questions on the evolutionary routes to asexuality. Thelytokous parthenogenesis is a form of spontaneous loss of sexuality leading to strong distortion of sex ratio towards females and resulting from mutation, hybridization or infection by bacterial endosymbionts. We investigated whether ecological specialization is a likely mechanism of spread of thelytoky within insect communities. Focusing on the highly specialized genus Megastigmus (Hymenoptera: Torymidae), we first performed a large literature survey to examine the distribution of thelytoky in these wasps across their respective obligate host plant families. Second, we tested for thelytoky caused by endosymbionts by screening in 15 arrhenotokous and 10 thelytokous species for Wolbachia, Cardinium, Arsenophonus and Rickettsia endosymbionts and by performing antibiotic treatments. Finally, we performed phylogenetic reconstructions using multilocus sequence typing (MLST) to examine the evolution of endosymbiont-mediated thelytoky in Megastigmus and its possible connections to host plant specialization. We demonstrate that thelytoky evolved from ancestral arrhenotoky through the horizontal transmission and the fixation of the parthenogenesis-inducing Wolbachia. We find that ecological specialization in Wolbachia's hosts was probably a critical driving force for Wolbachia infection and spread of thelytoky, but also a constraint. Our work further reinforces the hypothesis that community structure of insects is a major driver of the epidemiology of endosymbionts and that competitive interactions among closely related species may facilitate their horizontal transmission.

Laser demonstration with highly doped Yb:Gd2O3 and Yb:Y2O3 crystals grown by an original flux method

We present, to the best of our knowledge, the first laser demonstration of an Yb-doped Gd(2)O(3) cubic crystal. This crystal was obtained by the flux method using an original borate-based solvent, which was particularly well suited to the growth of rare earth sesquioxide crystals at half the working temperature of classical growth techniques. This flux method is a very interesting alternative for the production of laser sesquioxide crystals, not only because it provides access to new matrices of the cubic polymorph, but also because it permits high Yb(3+)-doping levels for these crystals. The first laser results of two highly Yb(3+)-doped sesquioxides, namely Gd(2)O(3) and Y(2)O(3), grown by this flux method are presented here, including the Ti:sapphire and diode pumping configurations. Laser efficiencies and emission spectra for these two crystals were studied and compared.

Two-photon excited fluorescence in the LYB:Eu monoclinic crystal: towards a new scheme of single-beam dual-voxel direct laser writing in crystals

We report on two-photon excited fluorescence in the oriented Eu(3+)doped LYB monoclinic crystal under femtosecond laser tight focusing. Due to spatial walk-off, the two polarization modes of the incident femtosecond beam simultaneously provide the independent excitation of two distinct focuses, leading to a single-beam dual-voxel nonlinear excitation of fluorescence below material modification threshold. These observations emphasize on the anisotropy of both two-photon absorption as well as fluorescence emission. They demonstrate the localized control of the nonlinear energy deposit, thanks to the adjustment of both the input power and polarization, by properly balancing the injected energy in each voxel. Such approach should be considered for future direct laser writing of waveguides in propagation directions out of the dielectric axes, so as to optimally cope with the highly probable anisotropy of laser-induced material modification thresholds in these crystals. These results open new ways for further potential developments in direct laser writing as the simultaneous inscription of double-line structures for original waveguides processes.

BioNLP Shared Task--The Bacteria Track

BACKGROUND

We present the BioNLP 2011 Shared Task Bacteria Track, the first Information Extraction challenge entirely dedicated to bacteria. It includes three tasks that cover different levels of biological knowledge. The Bacteria Gene Renaming supporting task is aimed at extracting gene renaming and gene name synonymy in PubMed abstracts. The Bacteria Gene Interaction is a gene/protein interaction extraction task from individual sentences. The interactions have been categorized into ten different sub-types, thus giving a detailed account of genetic regulations at the molecular level. Finally, the Bacteria Biotopes task focuses on the localization and environment of bacteria mentioned in textbook articles. We describe the process of creation for the three corpora, including document acquisition and manual annotation, as well as the metrics used to evaluate the participants' submissions.

RESULTS

Three teams submitted to the Bacteria Gene Renaming task; the best team achieved an F-score of 87%. For the Bacteria Gene Interaction task, the only participant's score had reached a global F-score of 77%, although the system efficiency varies significantly from one sub-type to another. Three teams submitted to the Bacteria Biotopes task with very different approaches; the best team achieved an F-score of 45%. However, the detailed study of the participating systems efficiency reveals the strengths and weaknesses of each participating system.

CONCLUSIONS

The three tasks of the Bacteria Track offer participants a chance to address a wide range of issues in Information Extraction, including entity recognition, semantic typing and coreference resolution. We found common trends in the most efficient systems: the systematic use of syntactic dependencies and machine learning. Nevertheless, the originality of the Bacteria Biotopes task encouraged the use of interesting novel methods and techniques, such as term compositionality, scopes wider than the sentence.

Cation ordering in the double tungstate LiFe(WO4)2

Single crystals of lithium iron tungstate, LiFe(WO(4))(2), were obtained using a high-temperature solution growth method. The analysis was conducted using the monoclinic space group C2/c, with β = 90.597 (2)°, giving R1 = 0.0177. The Li and Fe atoms lie on twofold axes. The structure can also be refined using the orthorhombic space group Cmcm, giving slightly higher residuals. The experimental value of β and the residuals mitigate in favour of the monoclinic description of the structure. Calculated bond-valence sums for the present results are closer to expected values than those obtained using the results of a previously reported analysis of this structure.

The transforming growth factor-α and cyclin D1 genes are direct targets of β-catenin signaling in hepatocyte proliferation

BACKGROUND & AIMS

β-Catenin is an oncogene frequently mutated in hepatocellular carcinoma. In this study, we investigated target genes of β-catenin signaling in hepatocyte proliferation.

METHODS

We studied transgenic mice displaying either inactivation or activation of the β-catenin pathway, focusing on analysis of liver proliferation due to aberrant β-catenin activation, and on the regeneration process during which β-catenin signaling is transiently activated. We localized in situ the various partners involved in proliferation or identified as targets of β-catenin in these transgenic and regenerating livers. We also performed comparative transcriptome analyses, using microarrays. Finally, we extracted, from deep-sequencing data, both the DNA regulatory elements bound to the β-catenin/Tcf nuclear complex and the expression levels of critical targets identified in microarrays.

RESULTS

β-Catenin activation during liver regeneration occurred during G1/S cell cycle progression and allowed zonal extension of the normal territory of active β-catenin and panlobular proliferation. We found that β-catenin controlled both cell-autonomous and non-cell-autonomous hepatocyte proliferation, through direct transcriptional and complex control of cyclin D1 gene expression and of the expression of a new target gene, Tgfα.

CONCLUSIONS

We propose that β-catenin controls panlobular hepatocyte proliferation partly by controlling, together with its Tcf4 nuclear partner, expression of the pro-proliferation cyclin D1 and Tgfα genes. This study constitutes a first step toward understanding the oncogenic properties of this prominent signaling pathway in the liver.

Inferring the role of transcription factors in regulatory networks

BACKGROUND

Expression profiles obtained from multiple perturbation experiments are increasingly used to reconstruct transcriptional regulatory networks, from well studied, simple organisms up to higher eukaryotes. Admittedly, a key ingredient in developing a reconstruction method is its ability to integrate heterogeneous sources of information, as well as to comply with practical observability issues: measurements can be scarce or noisy. In this work, we show how to combine a network of genetic regulations with a set of expression profiles, in order to infer the functional effect of the regulations, as inducer or repressor. Our approach is based on a consistency rule between a network and the signs of variation given by expression arrays.

RESULTS

We evaluate our approach in several settings of increasing complexity. First, we generate artificial expression data on a transcriptional network of E. coli extracted from the literature (1529 nodes and 3802 edges), and we estimate that 30% of the regulations can be annotated with about 30 profiles. We additionally prove that at most 40.8% of the network can be inferred using our approach. Second, we use this network in order to validate the predictions obtained with a compendium of real expression profiles. We describe a filtering algorithm that generates particularly reliable predictions. Finally, we apply our inference approach to S. cerevisiae transcriptional network (2419 nodes and 4344 interactions), by combining ChIP-chip data and 15 expression profiles. We are able to detect and isolate inconsistencies between the expression profiles and a significant portion of the model (15% of all the interactions). In addition, we report predictions for 14.5% of all interactions.

CONCLUSION

Our approach does not require accurate expression levels nor times series. Nevertheless, we show on both data, real and artificial, that a relatively small number of perturbation experiments are enough to determine a significant portion of regulatory effects. This is a key practical asset compared to statistical methods for network reconstruction. We demonstrate that our approach is able to provide accurate predictions, even when the network is incomplete and the data is noisy.

Topology and static response of interaction networks in molecular biology

We introduce a mathematical framework describing static response of networks occurring in molecular biology. This formalism has many similarities with the Laplace-Kirchhoff equations for electrical networks. We introduce the concept of graph boundary and we show how the response of the biological networks to external perturbations can be related to the Dirichlet or Neumann problems for the corresponding equations on the interaction graph. Solutions to these two problems are given in terms of path moduli (measuring path rigidity with respect to the propagation of interaction along the graph). Path moduli are related to loop products in the interaction graph via generalized Mason-Coates formulae. We apply our results to two specific biological examples: the lactose operon and the genetic regulation of lipogenesis. Our applications show consistency with experimental results and in the case of lipogenesis check some hypothesis on the behaviour of hepatic fatty acids on fasting.

Qualitative analysis of the relation between DNA microarray data and behavioral models of regulation networks

We introduce a mathematical framework that allows to test the compatibility between differential data and knowledge on genetic and metabolic interactions. Within this framework, a behavioral model is represented by a labeled oriented interaction graph; its predictions can be compared to experimental data. The comparison is qualitative and relies on a system of linear qualitative equations derived from the interaction graph. We show how to partially solve the qualitative system, how to identify incompatibilities between the model and the data, and how to detect competitions in the biological processes that are modeled. This approach can be used for the analysis of transcriptomic, metabolic or proteomic data.

GenoFrag: software to design primers optimized for whole genome scanning by long-range PCR amplification

Genome sequence data can be used to analyze genome plasticity by whole genome PCR scanning. Small sized chromosomes can indeed be fully amplified by long-range PCR with a set of primers designed using a reference strain and applied to several other strains. Analysis of the resulting patterns can reveal the genome plasticity. To facilitate such analysis, we have developed GenoFrag, a software package for the design of primers optimized for whole genome scanning by long-range PCR. GenoFrag was developed for the analysis of Staphylococcus aureus genome plasticity by whole genome amplification in approximately 10 kb-long fragments. A set of primers was generated from the genome sequence of S.aureus N315, employed here as a reference strain. Two subsets of primers were successfully used to amplify two portions of the N315 chromosome. This experimental validation demonstrates that GenoFrag is a robust and reliable tool for primer design and that whole genome PCR scanning can be envisaged for the analysis of genome diversity in S.aureus, one of the major public health concerns worldwide.

Canine distemper virus replication in cells on microcarriers

Chick embryo and Vero cells were grown on Gelaspher M gelatin microcarriers in suspension culture. The microcarriers had no adverse effects on cell morphology and growth. Microcarrier cell cultures were used for large-scale production of canine distemper virus. Virus yields (TCID50 per ml) were more than 10-times higher as compared to stationary cell culture.