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Spatiotemporal oxygen dynamics in young leaves reveal cyclic hypoxia in plants

Molecular Plant 2024年第3期17卷 377-394页

作者： Paolo M.Triozzi Luca Brunello Giacomo Novi Gianmarco Ferri Francesco Cardarelli Elena Loreti Mariano Perales Pierdomenico Perata PlantLab Center of Plant SciencesSant'Anna School of Advanced Studies56010 PisaItaly Centro de Biotecnologia y Genomica de Plantas Universidad Politecnica de Madrid(UPM)-Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria(INIA-CSIC)Campus de Montegancedo UPMPozuelo de Alarcon28223 MadridSpain Fondazione Pisana per la Scienza 56017 PisaItaly Laboratorio NEST Scuola Normale SuperioreIstituto Nanoscienze-CNRPiazza S.Silvestro1256127 PisaItaly institute of Agricultural Biology and Biotechnology National Research Council56124 PisaItaly departamento de Biotecnologia-Biologia Vegetal Escuela Tecnica Superior de Ingenieria AgronomicaAlimentaria y de BiosistemasUniversidad Politecnica de Madrid(UPM)28040 Madrid.Spain

Oxygen is essential for plant growth and *** occurs in plants due to limited oxygen avail-abilityfollowing adverse environmental conditions as well inhypoxic niches in otherwisenormoxic ***,the existence and functional integration of spatiotemporal oxygen dynamics with plant development remains *** animal systems dynamic fluctuations in oxygen availability are known as cyclic *** this study,we demonstrate that cyclic fluctuations in internal oxygen levels occur in young emerging leaves of Arabidopsis *** hypoxia in plants is based on a mechanism requiring the ETHyLENE RESPONSE FACTORS type VII(ERFVII)that are central components of the oxygen-sensing machinery in *** ERFVll-dependent mechanism allows precise adjustment of leaf growth in response to carbon status and oxygen availability within plant *** study thus establishes a functional connection between internal spatiotemporal oxygen dynamics and developmental processes of plants.

关键词： Arabidopsis hypoxia cyclic hypoxia leaf development oxygen-sensing mechanism ERFVII

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Dynamics of canopy-dwelling arthropods under different weed management options,including glyphosate,in conventional and genetically modified insect-resistant maize

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Insect Science 2021年第4期28卷 1121-1138页

作者： Esteban García-Ruiz Guillermo Cobos Ismael Sánchez-Ramos Susana Pascual María-Cristina Chueca María-Concepción Escorial Inés Santín-Montanyá Íñigo Loureiro Manuel González-Núñez Plant Protection department Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria(INIA)MadridSpain

The use of genetically modified varieties tolerant to herbicides(HT varieties)and resistant to insects(Bt varieties)in combination with application of a broad-spectrum herbicide such as glyphosate could be an effective option for the simultaneous control of weeds and pests in ***,the possible impact of these tools on nontarget arthropods still needs to be *** a field study in central Spain,potential changes in populations of canopy-dwelling arthropods in Bt maize under different weed management options,including glyphosate application,were ***-dwelling arthropods were sampled by visual inspection and yellow sticky *** Bt variety had no effect on any group of studied arthropods,except for the expected case of corn borers—the target pests of Bt *** the effects of herbicide regimes,the only observed difference was a lower abundance of Cicadellidae and Mymaridae on yellow sticky traps in plots not treated with pre-emergence *** effect was especially pronounced in a treatment involving two glyphosate *** decrease in Cicadellidae and Mymaridae populations was associated with a higher density of weeds in plots,which may have hindered colonization of the crop by *** differences,however,were only significant in the last year of the *** low likelihood of the use of glyphosate-and herbicide-tolerant varieties for weed control triggering important effects on the nontarget arthropod fauna of the maize canopy is discussed.

关键词： Bt maize canopy-dwelling arthropods GMHT maize glyphosate herbicide management parasitoids

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Building Expertise on FAIR Through Evolving Bring your Own Data(ByOD) Workshops: describing the Data, Software, and Management-focused Approaches and Their Evolution

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Data Intelligence 2024年第2期6卷 429-456页

作者： César H.Bernabé Lieze Thielemans Rajaram Kaliyaperumal Claudio Carta Shuxin Zhang Celia W.G.van Gelder Nirupama Benis Luiz Olavo Bonino da Silva Santos Ronald Cornet Bruna dos Santos Vieira Nawel Lalout Ines Henriques Alberto Camara Ballesteros Kees Burger Martijn G.Kersloot Friederike Ehrhart Esther van Enckevort Chris T.Evelo Alasdair J.G.Gray Marc Hanauer Kristina Hettne Joep de Ligt Arnaldo Pereira Nuria Queralt-Rosinach Erik Schultes Domenica Taruscio Andra Waagmeester Mark D.Wilkinson Egon L.Willighagen Mascha Jansen Barend Mons Marco Roos Annika Jacobsen Biosemantics Group Department of Human GeneticsLeiden University Medical CentreLeidenThe Netherlands NIHR Academic Fellow in General Practice University College London and The Royal Free NHS Foundation Trust national Centre for Rare Diseases Istituto Superiore di SanitaRomeItaly department of Medical Informatics Amsterdam UMC location University of AmsterdamMeibergdreef 9AmsterdamThe Netherlands Amsterdam Public Health Methodology&Digital HealthAmsterdamThe Netherlands Health-Rl UtrechtThe Netherlands Semantics Services and Cybersecurity groupUniversity of TwenteEnschedeThe Netherlands department of Medical Imaging Radboud Institute for Health SciencesRadboud University Medical CenterNijmegenThe Netherlands department of Medical BioSciences Radboud University Medical CenterNijmegenThe Netherlands The Duchenne Parent Project VeneendaalThe Netherlands departamento de Biotecnologia-Biologia Vegetal Escuela Tecnica Superior de Ingenieria AgronomicaAlimentaria y de BiosistemasCentro de Biotecnologia y Genomica de PlantasUniversidad Politecnica de Madrid(UPM)-Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria-CSIC(INIA-CSIC).Campus MontegancedoPozuelo de Alarcon(Madrid)Spain Castor AmsterdamThe Netherlands department of Bioinformatics-BiGCaT Maastricht UniversityMaastrichtThe Netherlands University Medical Center Groningen University of GroningenGroningenThe Netherlands Maastricht Centre for Systems Biology(MaCSBio) Maastricht UniversityMaastrichtThe Netherlands department of Computer Science Heriot-Watt UniversityEdinburghUK INSERM US14-OrphanetPlateforme Maladies RaresParisFrance Centre for Digital Scholarship Leiden University LibrariesThe Netherlands Center for Molecular Medicine Cancer Genomics NetherlandsDepartment of GeneticsUniversity Medical Center UtrechtUniversity UtrechtThe Netherlands University of Aveiro DETI/IEETAAveiroPortugal GO FAIR Foundation LeidenThe Netherlands The Leiden Academic Center for Drug Research LeidenThe Netherlands Micel

Since 2014,"Bring your Own Data"workshops(ByODs)have been organised to inform people about the process and benefits of making resources Findable,Accessible,Interoperable,and Reusable(FAIR,and the FAIRification process).The ByOD workshops'content and format differ depending on their goal,context,and the background and needs of ***-focused ByODs educate domain experts on how to make their data FAIR to find new answers to research ***-focused ByODs promote the benefits of making data FAIR and instruct project managers and policy-makers on the characteristics of FAIRification ***-focused ByODs gather software developers and experts on FAIR to implement or improve software resources that are used to support ***,these ByODs intend to foster collaboration between different types of stakeholders involved in data management,curation,and reuse(*** experts,trainers,developers,data owners,data analysts,FAIR experts).The ByODs also serve as an opportunity to learn what kind of support for FAIRification is needed from different communities and to develop teaching materials based on practical examples and *** this paper,we detail the three different structures of the ByODs and describe examples of early ByODs related to plant breeding data,and rare disease registries and biobanks,which have shaped the structure of the *** discuss the latest insights into making ByODs more productive by leveraging our almost ten years of training experience in these workshops,including successes and encountered ***,we examine how the participants'feedback has motivated the research on FAIR,including the development of workflows and software.

关键词： FAIR FAIRification FAIR expertise Bring your Own Data Workshop ByOD

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Soil carbon characterization along the profile of two forest soils under Quercus pyrenaica

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Journal of Forestry Research 2020年第2期31卷 591-600页

作者： A.P.Fernandez-Getino J.L.Alonso-Prados M.I.Santin-Montanya UPF-DTEVPF Instituto Nacional de Investigacion y Tecnologia Agraria y AlimentariaINIACtra.A Corunakm 7.528040 MadridSpain Dpto.Proteccion Vegetal Instituto Nacional de Investigacion y Tecnologia Agraria y AlimentariaINIACtra.A Corun akm 7.528040 MadridSpain

In light of concerns over climate change and increasing levels of CO2 in the atmosphere,it is of importance to investigate soil organic matter in Mediterranean forests at a profile ***-depth studies of the organic fraction are also of interest to improve understanding of carbon balance and to facilitate modelling of carbon fixation in forest *** research evaluates the relationships between diverse parameters such as colour,content,and form of soil organic matter(SOM).Two Quercus pyrenica ecosystems with soils classified as inceptisols with a xeric or dry moisture regime,and developed under a Mediterranean climate in Spain,were used to characterize SOM through the complete sequence of layers of the soil *** differentiating factor between the two ecosystems was slope *** was done using characteristics of humic substances(HS)as indicators of SOM turnover in *** analysis was used to further characterize the humic *** soil colour measurements are a tool for soil type classification and soil organic carbon prediction,the relation between HS colour measured by reflection and by transmission was determined in order to establish a relationship between measurement *** analysis and colour provided evidence of a different level of stabilization of HS from both soils,and between the different *** of humic acids was found to be greater in deeper horizons than in the surface *** inverse relationship between HS colour measured by reflection and by transmission was *** soils showed a clear trend in which horizons presenting lower absorbance numbers showed higher figures of hue and value.A more marked accumulation of humified compounds was found in pedons,(the smallest unit or volume of soil that contains all the soil types),in the less steep *** might be explained in terms of the physiographic position affecting infiltration behavior and exposure to runoff.

关键词： Organic matter turnover Colour humic substance(HS)by reflection Colour HS by transmission Humification index Mediterranean Quercus species

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development of cork oak (Quercus suber L.) seedlings in response to tree shelters and mulching in northwestern Tunisia

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Journal of Forestry Research 2013年第2期24卷 193-204页

作者： Taher Mechergui Marta Pardos Naceur Boussaidi Brahim Hasnaoui Douglass F. Jacobs Faculté des Sciences de Bizerte (FSB) instituto Nacional de investigacion y Tecnologia agraria y alimentaria (inia). Centro de investigacion Forestal. Ctra. de La Coruňa Institut Sylvo-Pastoral de Tabarka department of Forestry and Natural Resources Purdue University

The need for reforestation in cork oak （Quercus suber L.） areas is challenged by difficulties. Principal among these is herbivory of young plants, vegetative competition, and slow growth rates of cork oak seedlings. We evaluated the early development of cork oak seedlings treated using tree shelters and mulching in northwestern Tunisia. We tested three tree shelter treatments （non-vented, vented, and control） to shield seedlings from animal damage and five mulch types to control competing vegetation （Italian Stone Pine, Lentisk, combination of Italian Stone Pine and Lentisk （organic mulches）, gravel （inorganic mulch） and no mulch）. At the end of the two-year experiment, sheltered seedlings were 89-99% taller than unshelteredseedlings and had higher numbers and lengths of shoot growth flushes. In contrast, both stem diameter growth and dry weight biomass （from samples extracted after two years） were significantly reduced inside tree shelters. Root-to-shoot ratio was not significantly different in sheltered vs. unsheltered seedlings, suggesting that tree shelters do not adversely affect this parameter. Mulching alone did not favour growth, but could be beneficial when combined with tree shelters. The combination of vented tree shelters and gravel mulch was the most effective treatment for promoting diameter, height and stem volume growth.

关键词： Quercus suber L. afforestation tree shelter mulching seedling growth polycyclism

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Influence of mulching and tree shelters on 4-year survival and growth of zeen oak (Quercus canariensis) seedlings

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Journal of Forestry Research 2019年第1期30卷 129-141页

作者： Taher Mechergui Marta Pardos Douglass F.Jacobs Facultédes Sciences de Bizerte Laboratoire des Ressources Sylvo-Pastorales (Institut Sylvo-Pastoral de Tabarka) instituto Nacional de investigacion y Tecnologia agraria y alimentaria (inia) Centro de Investigacion Forestal department of Forestry and Natural Resources Hardwood Tree Improvement and Regeneration Center Purdue University

We assessed the effect of mulching and tree shelters on the establishment and early growth of zeen oak(Quercus canariensis Willd.) during the first 4 years after planting in Northwestern Tunisia. Five mulch types(Italian Stone Pine(Pinus pinea L.), Lentisk(Pistacia lentiscus L.),and a combination of Italian Stone Pine and Lentisk(organic mulches), gravel(inorganic mulch) and control), and three tree shelter types(non-vented and vented tree shelters, and control) were tested. An increase in the number of internodes occurred under the gravel mulch, while a reduction in survival was found for the lentisk mulch. Tree shelters had no effect on survival, but increased mean height growth and reduced mean diameter growth during the 4 years(excepting a non-significant effect for vented tree shelter at year four). Comparison of the annual shoots and growth units(GU) between sheltered and unsheltered plants according to year of formation revealed two growth phases. In first phase, shoots were totally or partially inside the shelters; mean length of annual shoots and GU were greater for sheltered plants. The second phase was characterized by shoots emerging from shelters; mean length of annual shoots and GU were similar for all plants, with or without tree shelters. Results suggest that the use of tree shelters, particularly vented shelters, could contribute to the improvement of the artificial regeneration of zeen *** use of mulching alone or in combination with tree shelters did not improve zeen oak performance in the field.

关键词： Zeen oak Mulching Tree shelters Plantation Survival rate Growth

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OsDMI3,a Ca^(2+)/calmodulin kinase,integrates and amplifies H_(2)O_(2) and Ca^(2+) signaling in ABA-mediated responses

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Molecular Plant 2023年第6期16卷 968-970页

作者： Miguel-Angel Torres Diego Jose Berlanga Centro de Biotecnologia y Genomica de Plantas Universidad Politecnica de Madrid(UPM)-Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria(INIA/CSIC)Campus de Montegancedo UPM28223 Pozuelo de AlarconMadridSpain departamento de Biotecnologia-Biologia Vegetal Escuela Técnica Superior de Ingenieria AgronomicaAlimentaria y de BiosistemasUPM28040 MadridSpain

Abscisic acid(ABA)is an important hormone that regulates both plant development and stress responses(Chen et al.,2020).In the absence of ABA,group A PROTEIN PHOSPHATASE 2Cs(PP2Cs)interact with and inhibit SUCROSE-NON-FERMENTING 1-RELATED KINASES 2(SnRK2s).When ABA is present,ABA receptor PyRABACTIN RESISTANCE 1 and PyRABACTIN RESISTANCE 1-LIKE PROTEINS bind to and inhibit PP2Cs,allowing phosphorylation and activation of SnRK2s that,in turn,phosphorylate downstream targets,such as transcription factors,ion channels,and transporters(Figure 1).

关键词： SnRK2 Figure

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The FAIR Data Point:Interfaces and Tooling

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Data Intelligence 2023年第1期5卷 184-201页

作者： Oussama Mohammed Benhamed Kees Burger Rajaram Kaliyaperumal Luiz Olavo Bonino da Silva Santos Marek Suchánek Jan Slifka Mark D.Wilkinsoni departamento de Biotecnologia-Biologia Vegetal Escuela Tecnica Superior de Ingenieria AgronomicaAlimentaria y de BiosistemasCentro de Biotecnologia y Genomica de Plantas UPM-INIAUniversidad Politecnica de Madrid(UPM)-Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria(INIA)MadridES 28223Spain Leiden University Medical Center Leiden2333 ZCthe Netherlands University of Twente Enschede7513 GBthe Netherlands Czech Technical University in Prague PragueCZ 15000Czech Republic

While the FAIR Principles do not specify a technical solution for'FAIRness',it was clear from the outset of the FAIR initiative that it would be useful to have commodity software and tooling that would simplify the creation of FAIR-compliant *** FAIR Data Point is a metadata repository that follows the DCAT(2)schema,and utilizes the Linked Data Platform to manage the hierarchical metadata layers as LDP *** has been a recent flurry of development activity around the FAIR Data Point that has significantly improved its power and *** we describe five specific tools—an installer,a loader,two Webbased interfaces,and an indexer-aimed at maximizing the uptake and utility of the FAIR Data Point.

关键词： FAIR Data Linked data Semantic Web Metadata User interfaces Tooling Semantic query

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development of ecoregion-based merchantable volume systems for Pinus brutia Ten. and Pinus nigra Arnold. in southern Turkey

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Journal of Forestry Research 2016年第1期27卷 101-117页

作者： Ramazan Ozcelik yasin Karatepe Nevzat Gurlevik Isabel Canellas Felipe Crecente-Campo Faculty of Forestry Suleyman Demirel UniversityEast Campus32260 IspartaTurkey Centro de investigacion Forestal(CIFOR) Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria(INIA)Crta.de la Corufia km 7.528040 MadridSpain CERNA ingeniería Medioambiental S.L.P.c/Ourense 541°B27004 LugoSpain

Estimating individual tree volume is one of the essential building blocks in forest growth and yield models. Ecologically based taper equations provide accurate vol- ume predictions and allow classification by mer- chantable sizes, assisting in sustainable forest management. In the present study, ecoregion-based compatible volume systems for brutian pine and black pine in the three ecoregions of southern Turkey were developed. Several well-known taper functions were evaluated. A second- order continuous-time autoregressive error structure was used to correct the inherent autocorrelation in the hierar- chical data, allowing the model to be applied to irregularly spaced and unbalanced data. The compatible segmented model of Fang et al. （For Sci 46：1-12, 2000） best described the experimental data. It is therefore recommended for estimating diameter at a specific height, height to a specific diameter, merchantable volume, and total volume for the three ecoregions and two species analyzed. The nonlinearextra sum of squares method indicated differences in ecoregion and tree-specific taper functions. A different taper function should therefore be used for each pine spe- cies and ecoregion in southern Turkey. Using ecoregion- specific taper equations allows making more robust esti- mations and, therefore, will enhance the accuracy of diameter at different heights and volume predictions.

关键词： Taper function Segmented model Brutianpine Black pine. Ecoregion Pinaceae

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FAIR Data Point:A FAIR-Oriented Approach for Metadata Publication

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Data Intelligence 2023年第1期5卷 163-183页

作者： Luiz Olavo Bonino da Silva Santos Kees Burger Rajaram Kaliyaperumal Mark D.Wilkinson Services and Cybersecurity group Faculty of Electrical EngineeringMathematics and Computer ScienceUniversity of Twente-Enschede7513GBthe Netherlands Biosemantics group Department of Human GeneticsLeiden University Medical Center-LeidenNL 2333 ZCthe Netherlands Escuela Técnica Superior de Ingenieria Agronomica Alimentaria y de BiosistemasCentro de Biotecnologia y Genomica de Plantas UPM-INIAUniversidad Politecnica de Madrid(UPM)-Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria(INIA)MadridES 28223Spain

Metadata,data about other digital objects,play an important role in FAIR with a direct relation to all FAIR *** this paper we present and discuss the FAIR Data Point(FDP),a software architecture aiming to define a common approach to publish semantically-rich and machine-actionable metadata according to the FAIR *** present the core components and features of the FDP,its approach to metadata provision,the criteria to evaluate whether an application adheres to the FDP specifications and the service to register,index and allow users to search for metadata content of available FDPs.

关键词： FAIR FAIR data point FAIR principles Metadata Interoperability Linked data Semantic interoperability

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