De novo transcriptome assembly data of the marine bioluminescent dinoflagellate Pyrocystis lunula

Pyrocystis lunula is a unicellular bioluminescing dinoflagellates. While the mechanisms and genes underlying bioluminescence and luciferase synthesis are understood in many bioluminescing clades, it remains unknown in dinoflagellates. We took advantage of merging long and short reads to provide here a de novo assembly of P. lunula transcriptome. A total of 975 million filtered paired-end reads were obtained and assembled into 155,716 contigs corresponding to putative transcripts that were functionally annotated. This dataset will be valuable for improving our understanding of protist's biology and is accessible via NCBI BioProject (PRJNA727555)

Stay-green protein, defective in Mendel's green cotyledon mutant, acts independent and upstream of pheophorbide a oxygenase in the chlorophyll catabolic pathway

Type C stay-green mutants are defined as being defective in the pathway of chlorophyll breakdown, which involves pheophorbide a oxygenase (PAO), required for loss of green color. By analyzing senescence parameters, such as protein degradation, expression of senescence-associated genes and loss of photosynthetic capacity, we demonstrate that JI2775, the green cotyledon (i) pea line used by Gregor Mendel to establish the law of genetics, is a true type C stay-green mutant. STAY-GREEN (SGR) had earlier been shown to map to the I locus. The defect in JI2775 is due to both reduced expression of SGR and loss of SGR protein function. Regulation of PAO through SGR had been proposed. By determining PAO protein abundance and activity, we show that PAO is unaffected in JI2775. Furthermore we show that pheophorbide a accumulation in the mutant is independent of PAO. When silencing SGR expression in Arabidopsis pao1 mutant, both pheophorbide a accumulation and cell death phenotype, typical features of pao1, are lost. These results confirm that SGR function within the chlorophyll catabolic pathway is independent and upstream of PA

Exploiting the Time-Reversal Operator for Adaptive Optics, Selective Focusing and Scattering Pattern Analysis

We report on the experimental measurement of the backscattering matrix of a weakly scattering medium in optics, composed of a few dispersed gold nanobeads. The DORT method (Decomposition of the Time Reversal Operator) is applied to this matrix and we demonstrate selective and efficient focusing on individual scatterers, even through an aberrating layer. Moreover, we show that this approach provides the decomposition of the scattering pattern of a single nanoparticle. These results open important perspectives for optical imaging, characterization and selective excitation of nanoparticles.Comment: 10 page

Post-transcriptional regulation of photosynthetic genes is a key driver of C4 leaf ontogeny.

C4 photosynthesis allows highly efficient carbon fixation that originates from tightly regulated anatomical and biochemical modifications of leaf architecture. Recent studies showed that leaf transcriptome modifications during leaf ontogeny of closely related C3 (Tarenaya hassleriana) and C4 (Gynandropsis gynandra) species within the Cleomaceae family existed but they did not identify any dedicated transcriptional networks or factors specifically driving C4 leaf ontogeny. RNAseq analysis provides a steady-state quantification of whole-cell mRNAs but does not allow any discrimination between transcriptional and post-transcriptional processes that may occur simultaneously during leaf ontogeny. Here we use exon-intron split analysis (EISA) to determine the extent to which transcriptional and post-transcriptional processes are involved in the regulation of gene expression between young and expanded leaves in both species. C4-specific changes in post-transcriptional regulation were observed for genes involved in the Calvin-Benson cycle and some photosystem components but not for C4 core-cycle genes. Overall, this study provides an unbiased genome-wide insight into the post-transcriptional mechanisms that regulate gene expression through the control of mRNA levels and could be central to the onset of C4 photosynthesis. This mechanism is cytosolic which implies cell-specific modifications of mRNA stability. Understanding this mechanism may be crucial when aiming to transform C3 crops into C4 crops

Fast Local Laplacian Filters: Theory and Applications

International audienceMulti-scale manipulations are central to image editing but they are also prone to halos. Achieving artifact-free results requires sophisticated edge- aware techniques and careful parameter tuning. These shortcomings were recently addressed by the local Laplacian filters, which can achieve a broad range of effects using standard Laplacian pyramids. However, these filters are slow to evaluate and their relationship to other approaches is unclear. In this paper, we show that they are closely related to anisotropic diffusion and to bilateral filtering. Our study also leads to a variant of the bilateral filter that produces cleaner edges while retaining its speed. Building upon this result, we describe an acceleration scheme for local Laplacian filters on gray-scale images that yields speed-ups on the order of 50×. Finally, we demonstrate how to use local Laplacian filters to alter the distribution of gradients in an image. We illustrate this property with a robust algorithm for photographic style transfer

Fast and Robust Pyramid-based Image Processing

Multi-scale manipulations are central to image editing but they are also prone to halos. Achieving artifact-free results requires sophisticated edgeaware techniques and careful parameter tuning. These shortcomings were recently addressed by the local Laplacian filters, which can achieve a broad range of effects using standard Laplacian pyramids. However, these filters are slow to evaluate and their relationship to other approaches is unclear. In this paper, we show that they are closely related to anisotropic diffusion and to bilateral filtering. Our study also leads to a variant of the bilateral filter that produces cleaner edges while retaining its speed. Building upon this result, we describe an acceleration scheme for local Laplacian filters that yields speed-ups on the order of 50x. Finally, we demonstrate how to use local Laplacian filters to alter the distribution of gradients in an image. We illustrate this property with a robust algorithm for photographic style transfer

Genetically modified crops in Switzerland: implications for agrosystem sustainability evidenced by multi-criteria model

International audienceAbstractIn Switzerland, genetically modified (GM) crops have been banned in 2005 and have never been used in agriculture. The relevance and sustainability of genetically modified crops for agrosystems have been assessed following a mandate from the Swiss Parliament defined by the Federal Act on Agriculture (187d al.1). For that, an ex ante study based on a multi-criteria decision analysis model that summarises literature and the opinion of experts has been done.The impacts of genetically modified crops on both environmental and socio-economical sustainability in Switzerland have been assessed. Here, we review four model crops for Swiss agriculture: maize, sugar beet, potato and apple. Each crop was compared for both conventional and genetically modified farming systems that contain a specific trait, namely insecticide production (Bacillus thuringiensis (Bt)), herbicide tolerance (HT), fungal resistance (FR), or bacterial resistance (BR). Results show that six out of seven scenarios showed a lower socio-economical sustainability for genetically modified compared to the conventional systems, whereas a slight improvement in the environmental component, mostly resources use, was observed in all scenarios. In conclusion, our work indicates that only carefully tailored and designed genetically modified crops would meet the high standard of requirements of Swiss agrosystems. Our model has thus allowed a quick diagnostic on the impact of genetically modified cultivation on sustainability

An evergreen mind and a heart for the colors of fall

With the finest biochemical and molecular approaches, convincing explorative strategies, and long-term vision, Stefan Hörtensteiner succeeded in elucidating the biochemical pathway responsible for chlorophyll degradation. After having contributed to the identification of key chlorophyll degradation products in the course of the past 25 years, he gradually identified and characterized most of the crucial players in the PAO/phyllobilin degradation pathway of chlorophyll. He was one of the brightest plant biochemists of his generation, and his work opened doors to a better understanding of plant senescence, tetrapyrrole homeostasis, and their complex regulation. He sadly passed away on 5 December 2020, aged 57

Non-specific activities of the major herbicide-resistance gene BAR

Bialaphos resistance (BAR) and phosphinothricin acetyltransferase (PAT) genes, which convey resistance to the broad-spectrum herbicide phosphinothricin (also known as glufosinate) via N-acetylation, have been globally used in basic plant research and genetically engineered crops1-4. Although early in vitro enzyme assays showed that recombinant BAR and PAT exhibit substrate preference toward phosphinothricin over the 20 proteinogenic amino acids1, indirect effects of BAR-containing transgenes in planta, including modified amino acid levels, have been seen but without the identification of their direct causes5,6. Combining metabolomics, plant genetics and biochemical approaches, we show that transgenic BAR indeed converts two plant endogenous amino acids, aminoadipate and tryptophan, to their respective N-acetylated products in several plant species. We report the crystal structures of BAR, and further delineate structural basis for its substrate selectivity and catalytic mechanism. Through structure-guided protein engineering, we generated several BAR variants that display significantly reduced non-specific activities compared with its wild-type counterpart in vivo. The transgenic expression of enzymes can result in unintended off-target metabolism arising from enzyme promiscuity. Understanding such phenomena at the mechanistic level can facilitate the design of maximally insulated systems featuring heterologously expressed enzymes.Searle Scholars Progra

Alizay, Igoville – Le Fort (tranche 3 nord)

La poursuite des fouilles sur les communes d’Alizay et Igoville a permis d’étudier, sur cette portion de la Seine, les dynamiques de comblement de la vallée et le rythme des occupations humaines sur un peu moins de 5 ha. Ces résultats viennent compléter les travaux présentés dans le cadre du Bilan scientifique 2011 (2013, p. 19-21). Cette année, les fouilles ont principalement porté sur la lecture des dynamiques sédimentaires et des restitutions paléoenvironnementales afférentes dans un secte..