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Single-cell transcriptome atlases of soybean root and mature nodule reveal new regulatory programs that control the nodulation process

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Plant Communications 2024年第8期5卷 69-91页

作者： Sergio Alan Cervantes-Perez Prince Zogli Sahand Amini Sandra Thibivilliers Sutton Tennant Md Sabbir Hossain Hengping Xu Ian Meyer Akash Nooka Pengchong Ma Qiuming Yao Michael J.Naldrett Andrew Farmer olivier martin Samik Bhattacharya Jasper Klaver Marc Libault Department of Agronomy and Horticulture University of Nebraska-LincolnLincolnNE 68503USA Division of Plant Science and Technology College of AgricultureFoodand Natural ResourcesUniversity of Missouri-ColumbiaColumbiaMO 65211USA Interdisciplinary Plant Group of Missouri-Columbia ColumbiaMO 65211USA School of Computing University of Nebraska-LincolnLincolnNE 68503USA Proteomics and Metabolomics Facility Center for BiotechnologyUniversity of Nebraska-LincolnLincolnNE 68588USA National Center for Genome Resources Santa FeNM 87505USA INRAE UniversiteParis-SaclayInstitut des Sciences des Plantes de Paris SaclayIPS2Batiment 630 Plateau du MoulonRue Noetzlin91192 Gif sur Yvette CedexFrance Resolve Biosciences Monheim am RheinGermany Present address:The School of Plant Sciences University of ArizonaTucsonAZ 85721USA Present address:GALY Co. 100 Hood Park Dr.BostonMA 02126USA

The soybean root system is *** addition to being composed of various cell types,the soybean root system includes the primary root,the lateral roots,and the nodule,an organ in which mutualistic symbiosis with N-fixing rhizobia occurs.A mature soybean root nodule is characterized by a central infection zone where atmospheric nitrogen is fixed and assimilated by the symbiont,resulting from the close cooperation between the plant cell and the *** date,the transcriptome of individual cells isolated from developing soybean nodules has been established,but the transcriptomic signatures of cells from the mature soybean nodule have not yet been *** single-nucleus RNA-seq and Molecular Cartography technologies,we precisely characterized the transcriptomic signature of soybean root and mature nodule cell types and revealed the co-existence of different sub-populations of ***-infected cells in the mature soybean nodule,including those actively involved in nitrogen fixation and those engaged in *** of the single-cell-resolution nodule transcriptome atlas and the associated gene co-expression network confirmed the role of known nodulation-related genes and identified new genes that control the nodulation *** instance,we functionally characterized the role of GmFWL3,a plasma membrane microdomain-associated protein that controls rhizobial *** study reveals the unique cellular complexity of the mature soybean nodule and helps redefine the concept of cell types when considering the infection zone of the soybean nodule.

关键词： soybean root nodule single-cell RNA-seq nanodomains

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Individual tree extraction from terrestrial laser scanning data via graph pathing

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Forest Ecosystems 2021年第4期8卷 903-913页

作者： Di Wang Xinlian Liang Gislain II Mofack olivier martin-Ducup Department of Remote Sensing Science and Technology School of Electronic EngineeringXidian University710077 Xi’anChina State Key Laboratory of Information Engineering in Surveying Mapping and Remote Sensing Wuhan University430079 WuhanChina Department of Remote Sensing and Photogrammetry Finnish Geospatial Research Institute02430 MasalaFinland Plant Systematics and Ecology Laboratory Higher Teacher’s Training CollegeUniversity of Yaounde IBP 337 YaoundeCameroon AMAP Univ MontpellierIRDCNRSCIRADINRAEF-34000 MontpellierFrance

Background:Individual tree extraction from terrestrial laser scanning(TLS)data is a prerequisite for tree-scale estimations of forest biophysical *** task currently is undertaken through laborious and time-consuming manual assistance and quality *** study presents a new fully automatic approach to extract single trees from large-area TLS *** data-driven method operates exclusively on a point cloud graph by path finding,which makes our method computationally efficient and universally applicable to data from various forest ***:We demonstrated the proposed method on two openly available ***,we achieved state-of-the-art performance on locating single trees on a benchmark dataset by significantly improving the mean accuracy by over 10% especially for difficult forest ***,we successfully extracted 270 trees from one hectare temperate *** validation resulted in a mean Intersection over Union(mIoU)of 0.82 for single crown segmentation,which further led to a relative root mean square error(RMSE%)of 21.2% and 23.5% for crown area and tree volume estimations,***:Our method allows automated access to individual tree level information from TLS point *** proposed method is free from restricted assumptions of forest *** is also computationally efficient with an average processing time of several seconds for one million *** is expected and hoped that our method would contribute to TLS-enabled wide-area forest qualifications,ranging from stand volume and carbon stocks modelling to derivation of tree functional traits as part of the global ecosystem understanding.

关键词： Point cloud Segmentation Tree extraction Graph pathing

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Solving surface plasmon resonances and near field in metallic nanostructures:Green’s matrix method and its applications

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Chinese Science Bulletin 2010年第24期55卷 2608-2617页

作者： GU Ying LI Jia martin olivier J F GONG QiHuang State Key Laboratory for Mesoscopic Physics Department of Physics Peking University Beijing 100871 China Nanophotonics and Metrology Laboratory Swiss Federal Institute of Technology Lausanne (EPFL) CH-1015 Lausanne Switzerland

With the development of nanotechnology,many new optical phenomena in nanoscale have been *** the coupling of optical waves and collective oscillations of free electrons in metallic nanostructures,surface plasmon polaritons can be excited accompanying a strong near field enhancement that decays in a subwavelength scale,which have potential applications in the surface-enhanced Raman scattering,biosensor,optical communication,solar cells,and nonlinear optical frequency *** the present article,we review the Green's matrix method for solving the surface plasmon resonances and near field in arbitrarily shaped nanostructures and in binary metallic *** this method,we design the plasmonic nanostructures whose resonances are tunable from the visible to near-infrared,study the interplay of plasmon resonances,and propose a new way to control plasmonic resonances in binary metallic nanostructures.

关键词：表面等离子体共振纳米结构二元金属矩阵方法近场应用表面增强拉曼散射表面等离子激元

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Fano-resonance-assisted metasurface for color routing

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Light(Science & Applications) 2017年第1期6卷 700-707页

作者： Chen Yan Kuang-Yu Yang olivier JF martin Institute of Microengineering Nanophotonics and Metrology LaboratorySwiss Federal Institute of Technology(EPFL)CH-1015 LausanneSwitzerland

Controlling the phase of an electromagnetic field using plasmonic nanostructures provides a versatile way to manipulate light at the *** phase modulation has been demonstrated using inhomogeneous metasurfaces with different geometries;however,for many applications such as filtering,hyperspectral imaging and color holography,narrowband frequency selectivity is a key *** this work,we demonstrate,both theoretically and experimentally,a narrowband metasurface that relies on Fano resonances to control the propagation of *** geometrically tuning the sub-radiant modes with respect to a fixed super-radiant resonance,we can create a phase modulation along the surface within a narrow spectral *** resulting anomalous reflection measured for such a Fano-resonant metasurface exhibits a 100 nm bandwidth and a color routing efficiency of up to 81%at a central wavelength ofλ=750 *** design flexibility provided by this Fano-assisted metasurface for colorselective light manipulation is further illustrated by demonstrating a highly directional color-routing effect between two channels,atλ=532 and 660 nm,without any crosstalk.

关键词： color filtering Fourier imaging metasurfaces plasmonic Fano resonance wavefront manipulation

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Revisiting Newton’s rings with a plasmonic optical flat for high-accuracy surface inspection

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Light(Science & Applications) 2016年第1期5卷 459-464页

作者： Yun Zheng Jie Bian Xiao-Long Wang Ju-Xiu Liu Peng Feng Hai-Xiong Ge olivier JF martin Wei-Hua Zhang College of Engineering and Applied Sciences National Laboratory of Solid State Microstructures and Collaborative Innovation Center of Advanced MicrostructuresNanjing UniversityNanjing 210093China Nanophotonics and Metrology Laboratory Swiss Federal Institute of Technology Lausanne(EPFL)Lausanne 1015Switzerland

Two parallel optical surfaces often exhibit colorful fringes along the lines of equal thickness because of the interference of *** simple phenomenon allows one to observe subwavelength corrugations on a reflective surface by simply placing on it a flat reference dielectric surface,a so-called optical flat,and inspecting the resultant interference *** this work,we extend this principle from dielectric surfaces to two-dimensional plasmonic *** couplings between an Au nanodisk array and an Au thin film were measured quantitatively using two different techniques,namely,the classical Newton’s rings method and a closed-loop nano-positioning *** high spectral sensitivity to the inter-surface distance was observed in the near-field coupling regime,where a 1-nm change in distance could alter the resonance wavelength by almost 10 nm,440 times greater than the variation in the case without near-field *** the help of a numerical fitting technique,the resonance wavelength could be determined with a precision of 0.03 nm,corresponding to a distance precision as high as 0.003 *** this effect,we demonstrated that a plasmonic nanodisk array can be utilized as a plasmonic optical flat,with which nanometer-deep grooves can be directly visualized using a low-cost microscope.

关键词： near-field optical coupling optical flat plasmonics

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Application of near-infrared spectroscopy for fast germplasm analysis and classification in multi-environment using intact-seed peanut(Arachis hypogaea L.)

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Oil Crop Science 2024年第2期9卷 132-141页

作者： Fentanesh Chekole Kassie Gilles Chaix Hermine Bille Ngalle Maguette Seye Coura Fall Hodo-Abalo Tossim Aissatou Sambou olivier Gibert Fabrice Davrieux Joseph martin Bell Jean-Francois Rami Daniel Fonceka Joel Romaric Nguepjop Department of Plant Biology and Physiology Faculty of SciencesUniversity of Yaounde IYaoundeP.O.Box 337Cameroon Department of Plant Science College of AgricultureWolaita Sodo UniversitySodoP.O.Box 138Ethiopia CIRAD UMR AGAP InstitutMontpellierFrance AGAP Institut Univ MontpellierCIRADINRAEInstitut AgroMontpellierFrance ChemHouse Research Group MontpellierFrance Centre D’Etudes Regional Pour L’Amelioration de L’Adaptation a La Secheresse(CERAAS/ISRA) Route de KhomboleThiesBP 3320Senegal Dispositif de Recherche et de Formation en Partenariat Innovation et Amelioration Varietale en Afrique de L’Ouest(IAVAO)CERAASRoute de KhomboleThiesBP 3320Senegal CIRAD UMR QUALISUDSaint PierreFrance

Peanut is a worldwide oilseed crop and the need to assess germplasm in a non-destructive manner is important for seed nutritional *** this study,Near Infrared Spectroscopy(NIRS)was applied to rapidly assess germplasm variability from whole seed of 699 samples,field-collected and assembled in four genetic and environmentbased sets:one set of 300 varieties of a core-collection and three sets of 133 genotypes of an interspecific population,evaluated in three environments in a large spatial scale of two countries,Mbalmayo and Bafia in Cameroon and Nioro in Senegal,under rainfed *** elemental spectra were gathered on six subsets of seeds of each sample,after three rotation scans,with a spectral resolution of 16 cm-1over the spectral range of867 nm to 2530 *** were then processed by principal component analysis(PCA)coupled with Partial least squares-discriminant analysis(PLS-DA).As results,a huge variability was found between varieties and genotypes for all NIR wavelength within and between *** magnitude of genetic variation was particularly observed at 11 relevant wavelengths such as 1723 nm,usually related to oil content and fatty acid *** yielded the most chemical attributes in three significant PCs(i.e.,eigenvalues>10),which together captured 93%of the total variation,revealing genetic and environment structure of varieties and genotypes into four clusters,corresponding to the four samples *** pattern of genetic variability of the interspecific population covers,remarkably half of spectrum of the core-collection,turning out to be the ***,a PLS-DA model was developed and a strong accuracy of 99.6%was achieved for the four sets,aiming to classify each seed sample according to environment *** confusion matrix achieved for the two sets of Bafia and Nioro showed 100%of instances classified correctly with 100%at both sensitivity and specificity,confirming that their seed quality was different f

关键词： Groundnut Oilseed Near infrared spectroscopy Germplasm analysis Environment Nutritional Breeding

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Hierarchical networks of food exchange in the black garden ant Lasius niger

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Insect Science 2021年第3期28卷 825-838页

作者： martin Quque olivier Bles Annaelle Benard Amelie Heraud Bastien Meunier Frangois Criscuolo Jean-Louis Deneubourg Cedric Sueur CA/RS IPHCUniversite de StrasbourgStrasbourgUMR718France Centre for Nonlinear Phenomena and Complex Systems(Cenoli)-CP 231 Universite libre de Bruxelles(ULB)BruxellesBelgium Universite de Bourgogne Franche-Comte DijonFrance Universite de Rennes 1 RennesFrance Institut Universitaire de France ParisFrance

In most eusocial insects,the division of labor results in relatively few individuals foraging for the entire ***,the survival of the colony depends on its efficiency in meeting the nutritional needs of all its ***,we characterize the network topology of a eusocial insect to understand the role and centrality of each caste in this network during the process of food *** constructed trophallaxis networks from 34 food-exchange experiments in black garden ants(Lasius niger).We tested the influence of brood and colony size on(i)global indices at the network level(i.e.,efficiency,resilience,centralization,and modularity)and(ii)individual values(i.e.,degree,strength,betweenness,and the clustering coefficient).Network resilience,the ratio between global efficiency and centralization,was stable with colony size but increased in the presence of broods,presumably in response to the nutritional needs of *** metrics highlighted the major role of foragers in food *** addition,a hierarchical clustering analysis suggested that some domestics acted as intermediaries between foragers and other *** appeared to be hierarchical rather than random or centralized exclusively around ***,our results suggested that networks emerging from social insect interactions can improve group performance and thus colony fitness.

关键词： insects network evolution self-organization social evolution social network analyses

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Spatial symmetries in nonlocal multipolar metasurfaces

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Advanced Photonics 2023年第4期5卷 9-22页

作者： Karim Achouri Ville Tiukuvaara olivier J.F.martin Institute of Electrical and Microengineering École Polytechnique Fédérale de LausanneNanophotonics and Metrology LaboratoryLausanneSwitzerland

We propose a framework that connects the spatial symmetries of a metasurface to its material parameter tensors and its scattering *** provides a simple and universal way to effortlessly determine the properties of a metasurface scattering response,such as chirality or asymmetric transmission,and which of its effective material parameters should be taken into account in the prospect of a homogenization *** contrast to existing techniques,this approach does not require any a priori knowledge of group theory or complicated numerical simulation schemes,hence making it fast,easy to use and *** working principle consists in recursively solving symmetry-invariance conditions that apply to dipolar and quadrupolar material parameters,which include nonlocal interactions,as well as the metasurface scattering *** overall process thus only requires listing the spatial symmetries of the *** the proposed framework,we demonstrate the existence of multipolar extrinsic chirality,which is a form of chiral response that is achieved in geometrically achiral structures sensitive to field gradients,even at normal incidence.

关键词： spatial symmetries metamaterials bianisotropy multipoles chirality

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Molecular Evolution of the Substrate Specificity of Chloroplastic Aldolases/Rubisco Lysine Methyltransferases in Plants

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Molecular Plant 2016年第4期9卷 569-581页

作者： Sheng Ma Jacqueline martin-Laffon Morgane Mininno Oceane Gigarel Sabine Brugiere olivier Bastien Marianne Tardift Stephane Ravanel Claude Alban Universite Grenoble Alpes Laboratoire de Physiologie Cellulaire & Vegetale 38041 Grenoble France CNRS UMR5168 38054 Grenoble France CEA iRTSV Laboratoire de Physiologie Cellulaire & Vegetale 38054 Grenoble France INRA USC1359 38054 Grenoble France Universite Grenoble Alpes 38041 Grenoble France CEA iRTSV Biologie & Grande Echelle 38054 Grenoble France INSERM U1038 38054 Grenoble France

Rubisco and fructose-1,6-bisphosphate aldolases （FBAs） are involved in CO2 fixation in chloroplasts. Both enzymes are trimethylated at a specific lysine residue by the chloroplastic protein methyltransferase LSMT. Genes coding LSMT are present in all plant genomes but the methylation status of the substrates varies in a species-specific manner. For example, chloroplastic FBAs are naturally trimethylated in both Pisum sati- vum and Arabidopsis thaliana, whereas the Rubisco large subunit is trimethylated only in the former spe- cies. The in vivo methylation status of aldolases and Rubisco matches the catalytic properties of AtLSMT and PsLSMT, which are able to trimethylate FBAs or FBAs and Rubisco, respectively. Here, we created chimera and site-directed mutants of monofunctional AtLSMT and bifunctional PsLSMT to identify the molecular determinants responsible for substrate specificity. Our results indicate that the His-Ala/Pro- Trp triad located in the central part of LSMT enzymes is the key motif to confer the capacity to trimethylate Rubisco. Two of the critical residues are located on a surface loop outside the methyltransferase catalytic site. We observed a strict correlation between the presence of the triad motif and the in vivo methylation status of Rubisco. The distribution of the motif into a phylogenetic tree further suggests that the ancestral function of LSMT was FBA trimethylation. In a recent event during higher plant evolution, this function evolved in ancestors of Fabaceae, Cucurbitaceae, and Rosaceae to include Rubisco as an additional substrate to the archetypal enzyme. Our study provides insight into mechanisms by which SET-domain protein methyltransferases evolve new substrate specificity.

关键词： SET-domain protein methyltransferase site-directed mutagenesis chimeric enzyme methylation,molecular evolution green lineage

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Neoadjuvant sorafenib combined with gemcitabine plus oxaliplatin in advanced hepatocellular carcinoma

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World Journal of Gastroenterology 2011年第17期17卷 2255-2258页

作者： Nicolas Williet olivier Dubreuil Tarek Boussaha Isabelle Trouilloud Bruno Landi martin Housset Muriel Botti Philippe Rougier Jacques Belghiti Julien Taieb Department of Gastroenterology Europeen Georges Pompidou HospitalMedical University75908 ParisFrance Department of Radiotherapy Europeen Georges Pompidou HospitalMedical University75908 ParisFrance Beaujon Hspital Medical University100boulevard du Général Leclerc92110 ClichyFrance

This paper reports the first case of a patient with hepatocellular carcinoma with lymph node metastasis treated by sorafenib combined with gemcitabine plus oxaliplatin,with a partial response and normalization of α fetoprotein,which allowed curative *** potential synergy between these three drugs needs to be confirmed,and is currently being investigated in a randomized phase Ⅱ trial.

关键词： Hepatocellular carcinoma Gemcitabine Oxaliplatin Sorafenib Neoadjuvant therapy

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