Genome-wide analysis of AGO, DCL and RDR gene families reveals RNA-directed DNA methylation is involved in fruit abscission in Citrus sinensis

Background: Small RNAs regulate a wide variety of processes in plants, from organ development to both biotic and abiotic stress response. Being master regulators in genetic networks, their biogenesis and action is a fundamental aspect to characterize in order to understand plant growth and development. Three main gene families are critical components of RNA silencing: DICER-LIKE (DCL), ARGONAUTE (AGO) and RNA-DEPENDENT RNA POLYMERASE (RDR). Even though they have been characterized in other plant species, there is no information about these gene families in Citrus sinensis, one of the most important fruit species from both economical and nutritional reasons. While small RNAs have been implicated in the regulation of multiple aspects of plant growth and development, their role in the abscission process has not been characterized yet. Results: Using genome-wide analysis and a phylogenetic approach, we identified a total of 13 AGO, 5 DCL and 7 RDR genes. We characterized their expression patterns in root, leaf, flesh, peel and embryo samples using RNA-seq data. Moreover, we studied their role in fruit abscission through gene expression analysis in fruit rind compared to abscission zone from samples obtained by laser capture microdissection. Interestingly, we determined that the expression of several RNA silencing factors are down-regulated in fruit abscission zone, being particularly represented gene components of the RNA-dependent DNA Methylation pathway, indicating that repression of this process is necessary for fruit abscission to take place in Citrus sinensis. Conclusions: The members of these 3 families present characteristic conserved domains and distinct expression patterns. We provide a detailed analysis of the members of these families and improved the annotation of some of these genes based on RNA-seq data. Our data suggests that the RNA-dependent DNA Methylation pathway is involved in the important fruit abscission process in C. sinensis.Fil: Sabbione, Agustín Andrés. Universidad Nacional del Litoral. Facultad de Ciencias Agrarias; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe; ArgentinaFil: Daurelio, Lucas Damian. Universidad Nacional del Litoral. Facultad de Ciencias Agrarias; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe; ArgentinaFil: Veggeti, A.. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe; Argentina. Universidad Nacional del Litoral. Facultad de Ciencias Agrarias; ArgentinaFil: Talón, Manuel. Institut Valencià Dinvestigacions Agràries; EspañaFil: Tadeo, Francisco. Institut Valencià Dinvestigacions Agràries; EspañaFil: Dotto, Marcela Claudia. Universidad Nacional del Litoral. Facultad de Ciencias Agrarias; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Santa Fe; Argentin

Neutrophil extracellular traps stimulate proinflammatory responses in human airway epithelial cells

Tissue injury leads to the release of uric acid (UA). At high local concentrations, UA can form monosodium urate crystals (MSU). MSU and UA stimulate neutrophils to release extracellular traps (NET). Here, we investigated whether these NET could be involved in the development of inflammation by stimulating cytokine release by airway epithelial cells. We found that NET significantly increased the secretion of CXCL8/IL-8 and IL-6 by alveolar and bronchial epithelial cells. These effects were not observed when NETosis was inhibited by Diphenyleneiodonium, elastase inhibitor, or Cl-amidine. Similar findings were made with NET induced by cigarette smoke extract, suggesting that NET proinflammatory capacity is independent of the inducing stimulus. Furthermore, NET affected neither the viability and morphology of epithelial cells nor the barrier integrity of polarized cells. The epithelial stimulatory capacity of NET was not affected by degradation of DNA with micrococcal nuclease, treatment with heparin, or inhibition of the elastase immobilized to DNA, but it was significantly reduced by pretreatment with an anti-HMGB-1 blocking antibody. Altogether, our findings indicate that NET exert direct proinflammatory effects on airway epithelial cells that might contribute in vivo to the further recruitment of neutrophils and the perpetuation of inflammation upon lung tissue damage.Instituto de Estudios Inmunológicos y Fisiopatológico

Neutrophil extracellular traps stimulate proinflammatory responses in human airway epithelial cells

Tissue injury leads to the release of uric acid (UA). At high local concentrations, UA can form monosodium urate crystals (MSU). MSU and UA stimulate neutrophils to release extracellular traps (NET). Here, we investigated whether these NET could be involved in the development of inflammation by stimulating cytokine release by airway epithelial cells. We found that NET significantly increased the secretion of CXCL8/IL-8 and IL-6 by alveolar and bronchial epithelial cells. These effects were not observed when NETosis was inhibited by Diphenyleneiodonium, elastase inhibitor, or Cl-amidine. Similar findings were made with NET induced by cigarette smoke extract, suggesting that NET proinflammatory capacity is independent of the inducing stimulus. Furthermore, NET affected neither the viability and morphology of epithelial cells nor the barrier integrity of polarized cells. The epithelial stimulatory capacity of NET was not affected by degradation of DNA with micrococcal nuclease, treatment with heparin, or inhibition of the elastase immobilized to DNA, but it was significantly reduced by pretreatment with an anti-HMGB-1 blocking antibody. Altogether, our findings indicate that NET exert direct proinflammatory effects on airway epithelial cells that might contribute in vivo to the further recruitment of neutrophils and the perpetuation of inflammation upon lung tissue damage.Instituto de Estudios Inmunológicos y Fisiopatológico

Quantifying nitrogen in GeSbTe:N alloys

We have calibrated on-site WD-XRF (wavelength-dispersive X-ray fluorescence) measurements of GeSbTe:N (GST:N) stoichiometry with off-site accurate ion beam analysis (IBA). N is determined by elastic backscattering spectrometry (EBS) using the resonance at 3.7 MeV in the 14N(a, a)14N reaction. Ge and Sb+Te are determined by Rutherford backscattering spectrometry (RBS) separately but self-consistently with the resonant EBS: the Sb/Te ratio can be determined by RBS but not with useful precision. The XRF instrumental function is determined using pure metal standards and the spectra are quantified using Fundamental Parameters code. We find that, as expected, for both Ge and (Sb+Te) the heavy elements are determined accurately by XRF (within the uncertainties), but for N the standardless XRF has non-linear errors around 10%. Using the absolute N content determined by IBA a calibration curve is obtained allowing N determination by WD-XRF at a precision of about 1% and an absolute accuracy (traceable through IBA) of about 4 % for GST films with N content between 4-20 at%. The IBA measurement precision of the N content of the GST-N XRF calibration samples is 0.4 at% (that is, a relative precision ranging from 10 % to 2 % for N contents between 4-20 at%)

Quantifying nitrogen in GeSbTe:N alloys

We have calibrated on-site WD-XRF (wavelength-dispersive X-ray fluorescence) measurements of GeSbTe:N (GST:N) stoichiometry with off-site accurate ion beam analysis (IBA). N is determined by elastic backscattering spectrometry (EBS) using the resonance at 3.7 MeV in the 14N(a, a)14N reaction. Ge and Sb+Te are determined by Rutherford backscattering spectrometry (RBS) separately but self-consistently with the resonant EBS: the Sb/Te ratio can be determined by RBS but not with useful precision. The XRF instrumental function is determined using pure metal standards and the spectra are quantified using Fundamental Parameters code. We find that, as expected, for both Ge and (Sb+Te) the heavy elements are determined accurately by XRF (within the uncertainties), but for N the standardless XRF has non-linear errors around 10%. Using the absolute N content determined by IBA a calibration curve is obtained allowing N determination by WD-XRF at a precision of about 1% and an absolute accuracy (traceable through IBA) of about 4 % for GST films with N content between 4-20 at%. The IBA measurement precision of the N content of the GST-N XRF calibration samples is 0.4 at% (that is, a relative precision ranging from 10 % to 2 % for N contents between 4-20 at%)

Role of vacancy defects in Al doped ZnO thin films for optoelectronic devices

International audienceWe report on the electrical, optical and photoluminescence properties of industry-ready Al doped ZnO thin films grown by physical vapor deposition, and their evolution after annealing under vacuum. Doping ZnO with Al atoms increases the carrier density but also favors the formation of Zn vacancies, thereby inducing a saturation of the conductivity mechanism at high aluminum content. The electrical and optical properties of these thin layered materials are both improved by annealing process which creates oxygen vacancies that releases charge carriers thus improving the conductivity. This study underlines the effect of the formation of extrinsic and intrinsic defects in Al doped ZnO compound during the fabrication process. The quality and the optoelectronic response of the produced films are increased (up to 1.52 m Omega.cm and 3.73 eV) and consistent with the industrial device requirements

Ge–Sb–S–Se–Te amorphous chalcogenide thin films towards on-chip nonlinear photonic devices

International audienceThanks to their unique optical properties Ge–Sb–S–Se–Te amorphous chalcogenide materials andcompounds ofer tremendous opportunities of applications, in particular in near and mid-infraredrange. This spectral range is for instance of high interest for photonics or optical sensors. Usingco-sputtering technique of chalcogenide compound targets in a 200 mm industrial deposition tool,we show how by modifying the amorphous structure of GeSb$_w$S$_x$Se$_y$Te$_z$ chalcogenide thin flmsone can signifcantly tailor their linear and nonlinear optical properties. Modelling of spectroscopicellipsometry data collected on the as-deposited chalcogenide thin flms is used to evaluate their linearand nonlinear properties. Moreover, Raman and Fourier-transform infrared spectroscopies permittedto get a description of their amorphous structure. For the purpose of applications, their thermalstability upon annealing is also evaluated. We demonstrate that depending on the GeSb$_w$S$_x$Se$_y$Te$_z$flm composition a trade-of between a high transparency in near- or mid-infrared ranges, strongnonlinearity and good thermal stability can be found in order to use such materials for applicationscompatible with the standard CMOS integration processes of microelectronics and photonics