Identification of long non-coding RNAs in insects genomes

International audienceThe development of high throughput sequencing technologies (HTS) has allowed researchers to better assess the complexity and diversity of the transcriptome. Among the many classes of non-coding RNAs (ncRNAs) identified the last decade, long non-coding RNAs (lncRNAs) represent a diverse and numerous repertoire of important ncRNAs, reinforcing the view that they are of central importance to the cell machinery in all branches of life. Although lncRNAs have been involved in essential biological processes such as imprinting, gene regulation or dosage compensation especially in mammals, the repertoire of lncRNAs is poorly characterized for many non-model organisms. In this review, we first focus on what is known about experimentally validated lncRNAs in insects and then review bioinformatic methods to annotate lncRNAs in the genomes of hexapods

Probing the energy levels of organic bulk heterojunctions by varying the donor content

The performance of organic solar cells is strongly governed by the properties of the photovoltaic active layer. In particular, the energetics at the donor (D)–acceptor (A) interface dictate the properties of charge transfer (CT) states and limit the open-circuit voltage. More generally, energetic landscapes in thin films are affected by intermolecular, e.g., van der Waals, dipole, and quadrupole, interactions that vary with D:A mixing ratio and impact energy levels of free charges (ionization energy, electron affinity) and excitons (singlet, CT states). Disentangling how different intermolecular interactions impact energy levels and support or hinder free charge generation is still a major challenge. In this work, we investigate interface energetics of bulk heterojunctions via sensitive external quantum efficiency measurements and by varying the D:A mixing ratios of ZnPc or its fluorinated derivatives and C60. With increasing donor fluorination, the energetic offset between FxZnPc and C60 reduces. Moving from large to low offset systems, we find qualitatively different trends in device performances with D:C60 mixing ratios. We rationalize the performance trends via changes in the energy levels that govern exciton separation and voltage losses. We do so by carefully analyzing shifts and broadening sEQE spectra on a linear and logarithmic scale. Linking this analysis with molecular properties and device performance, we comment on the impact of charge–quadrupole interactions for CT dissociation and free charge generation in our D:C60 blends. With this, our work (1) demonstrates how relatively accessible characterization techniques can be used to probe energy levels and (2) addresses ongoing discussions on future molecular design and optimal D–A pairing for efficient CT formation and dissociation

Insights into palaeobotany

Copyright © 2023 Société botanique de France. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. The attached file is the published version of the article

Revisiting the missing protein-coding gene catalog of the domestic dog

<p>Abstract</p> <p>Background</p> <p>Among mammals for which there is a high sequence coverage, the whole genome assembly of the dog is unique in that it predicts a low number of protein-coding genes, ~19,000, compared to the over 20,000 reported for other mammalian species. Of particular interest are the more than 400 of genes annotated in primates and rodent genomes, but missing in dog.</p> <p>Results</p> <p>Using over 14,000 orthologous genes between human, chimpanzee, mouse rat and dog, we built multiple pairwise synteny maps to infer short orthologous intervals that were targeted for characterizing the canine missing genes. Based on gene prediction and a functionality test using the ratio of replacement to silent nucleotide substitution rates (<it>d</it>_N/<it>d</it>_S), we provide compelling structural and functional evidence for the identification of 232 new protein-coding genes in the canine genome and 69 gene losses, characterized as undetected gene or pseudogenes. Gene loss phyletic pattern analysis using ten species from chicken to human allowed us to characterize 28 canine-specific gene losses that have functional orthologs continuously from chicken or marsupials through human, and 10 genes that arose specifically in the evolutionary lineage leading to rodent and primates.</p> <p>Conclusion</p> <p>This study demonstrates the central role of comparative genomics for refining gene catalogs and exploring the evolutionary history of gene repertoires, particularly as applied for the characterization of species-specific gene gains and losses.</p

Structure and stimuli-responsiveness of all-DNA dendrimers: theory and experiment

We present a comprehensive theoretical and experimental study of the solution phase properties of DNA-based family of nanoparticles - dendrimer-like DNA molecules (DL-DNA). These charged DNA dendrimers are novel macromolecular aggregates, which hold high promise in targeted self-assembly of soft matter systems in the bulk and at interfaces. To describe the behavior of this family of dendrimers (with generations ranging from G1 to G7), we use a theoretical model in which base-pairs of a single DL-DNA molecule are modeled by charged monomers, whose interactions are chosen to mimic the equilibrium properties of DNA correctly. Experimental results on the sizes and conformations of DL-DNA are based on static and 1dynamic light scattering; at the same time, Molecular Dynamics simulations are employed to model the equilibrium properties of DL-DNA, which compare favorably with the findings from experiments while at the same time providing a host of additional information and insight into the molecular structure of the nanostructures. We also examine the salt-responsiveness of these macromolecules, finding that despite the strong screening of electrostatic interactions, brought about by the added salt, the macromolecules shrink only slightly, their size robustness stemming from the high bending rigidity of the DNA-segments. The study of these charged dendrimer systems is an important field of research in the area of soft matter due to their potential role for various interdisciplinary applications, ranging from molecular cages and carriers for drug delivery in a living organism to the development of dendrimer- and dendron-based ultra-thin films in the area of nanotechnology. These findings are essential to determine if DL-DNA is a viable candidate for the experimental realization of cluster crystals in the bulk, a novel form of solids with multiple site occupancy.Comment: 38 pages, 17 figure

Evaluation of Luminosity Reduction in the ILC Head-on Scheme from Parasitic Collisions

online : http://cern.ch/AccelConf/p07/PAPERS/THPMN008.PDFInternational audienceAn interaction region with head-on collisions is being developed for the ILC as an alternative to the base line 14 mrad crossing angle design, motivated by simpler beam manipulations upstream of the interaction point (IP) and a more favourable configuration for the detector and physics analysis. The design of the post-collision beam line in this scheme involves however a number of technological challenges, one of which is the strength requirement for the electrostatic separators (ES) placed immediately after the final doublet to extract the spent beam. In this paper, we examine in detail the main mechanism behind this requirement, the multi-beam kink instability, which results from the long-range beam-beam forces at the parasitic crossings after the bunches have been extracted. Our analysis uses realistic bunch distributions, the Guinea-Pig program to treat beam-beam effects at the interaction point and the DIMAD program to track the disrupted beam distributions in the postcollision beam line

Coat colour in dogs: identification of the Merle locus in the Australian shepherd breed

BACKGROUND: Coat colours in canines have many natural phenotypic variants. Some of the genes and alleles involved also cause genetic developmental defects, which are also observed in humans and mice. We studied the genetic bases of the merle phenotype in dogs to shed light on the pigmentation mechanisms and to identify genes involved in these complex pathways. The merle phenotype includes a lack of eumelanic pigmentation and developmental defects, hearing impairments and microphthalmia. It is similar to that observed in microphthalmia mouse mutants. RESULTS: Taking advantage of the dog as a powerful genetic model and using recently available genomic resources, we investigated the segregation of the merle phenotype in a five-generation pedigree, comprising 96 sampled Australian shepherd dogs. Genetic linkage analysis allowed us to identify a locus for the merle phenotype, spanning 5.5 megabases, at the centromeric tip of canine chromosome 10 (CFA10). This locus was supported by a Lod score of 15.65 at a recombination fraction θ = 0. Linkage analysis in three other breeds revealed that the same region is linked to the merle phenotype. This region, which is orthologous to human chromosome 12 (HSA12 q13-q14), belongs to a conserved ordered segment in the human and mouse genome and comprises several genes potentially involved in pigmentation and development. CONCLUSION: This study has identified the locus for the merle coat colour in dogs to be at the centromeric end of CFA10. Genetic studies on other breeds segregating the merle phenotype should allow the locus to be defined more accurately with the aim of identifying the gene. This work shows the power of the canine system to search for the genetic bases of mammalian pigmentation and developmental pathways

Interfacial rearrangements and strain evolution in the thin film growth of ZnPc on glass

We report on the characterization of the growth of vacuum-deposited zinc phthalocyanine (ZnPc) thin films on glass through a combination of in situ grazing incidence x-ray scattering, x-ray reflectivity, and atomic force microscopy. We found that the growth at room temperature proceeds via the formation of two structurally unique substrate-induced interfacial layers, followed by the growth of the γ-ZnPc polymorph thereafter (thickness ≈1.0 nm). As the growth of the bulk γ-ZnPc progresses, a substantial out-of-plane lattice strain (≈15% relative to γ-ZnPc powder) is continually relaxed during the thin film growth. The rate of strain relaxation was slowed after a thickness of ≈13 nm, corresponding to the transition from layer growth to island growth. The findings reveal the real-time microstructural evolution of ZnPc and highlight the importance of substrate-induced strain on thin film growth

Modeling soil organic carbon dynamics in temperate forests with Yasso07

In a context of global changes, modeling and predicting the dynamics of soil carbon stocks (CSs) in forest ecosystems are vital but challenging. Yasso07 is considered to be one of the most promising models for such a purpose. We examine the accuracy of its prediction of soil carbon dynamics over the whole French metropolitan territory at a decennial timescale. We used data from 101 sites in the RENECOFOR network, which encompasses most of the French temperate forests. These data include (i) the quantity of above-ground litterfall from 1994 to 2008, measured yearly, and (ii) the soil CSs measured twice at an interval of approximately 15 years (once in the early 1990s and around 2010). We used Yasso07 to simulate the annual changes in carbon stocks (ACCs; in tC ha−1 yr−1) for each site and then compared the estimates with actual recorded data. We carried out meta-analyses to reveal the variability in litter biochemistry in different tree organs for conifers and broadleaves. We also performed sensitivity analyses to explore Yasso07's sensitivity to annual litter inputs and model initialization settings. At the national level, the simulated ACCs (+0.00±0.07 tC ha−1 yr−1, mean ± SE) were of the same order of magnitude as the observed ones (+0.34±0.06 tC ha−1 yr−1). However, the correlation between predicted and measured ACCs remained weak (R2<0.1). There was significant overestimation for broadleaved stands and underestimation for coniferous sites. Sensitivity analyses showed that the final estimated CS was strongly affected by settings in the model initialization, including litter and soil carbon quantity and quality and also by simulation length. Carbon quality set with the partial steady-state assumption gave a better fit than the model with the complete steady-state assumption. With Yasso07 as the support model, we showed that there is currently a bottleneck in soil carbon modeling and prediction due to a lack of knowledge or data on soil carbon quality and fine-root quantity in the litter

Limiting factors for charge generation in low-offset fullerene-based organic solar cells

Free charge generation after photoexcitation of donor or acceptor molecules in organic solar cells generally proceeds via (1) formation of charge transfer states and (2) their dissociation into charge separated states. Research often either focuses on the first component or the combined effect of both processes. Here, we provide evidence that charge transfer state dissociation rather than formation presents a major bottleneck for free charge generation in fullerene-based blends with low energetic offsets between singlet and charge transfer states. We investigate devices based on dilute donor content blends of (fluorinated) ZnPc:C60 and perform density functional theory calculations, device characterization, transient absorption spectroscopy and time-resolved electron paramagnetic resonance measurements. We draw a comprehensive picture of how energies and transitions between singlet, charge transfer, and charge separated states change upon ZnPc fluorination. We find that a significant reduction in photocurrent can be attributed to increasingly inefficient charge transfer state dissociation. With this, our work highlights potential reasons why low offset fullerene systems do not show the high performance of non-fullerene acceptors