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Decomposition of dynamic transcriptomic responses during effector-triggered immunity reveals conserved responses in two distinct plant cell populations

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Plant Communications 2024年第8期5卷 1-17页

作者： Xiaotong Liu Daisuke Igarashi Rachel A.Hillmer thomas stoddard You Lu Kenichi Tsuda Chad L.Myers Fumiaki Katagiri Department of Plant and Microbial Biology University of Minnesota-Twin CitiesSt PaulMN 55108USA Department of Computer science and Engineering University of Minnesota-Twin CitiesMinneapolisMN 55455USA Bioinformatics and Computational Biology Graduate Program University of Minnesota-Twin CitiesMinneapolisMN 55455USA Institute for Innovation Ajinomoto Co.Inc.KawasakiJapan state Key Laboratory of Agricultural Microbiology Hubei Hongshan LaboratoryHubei Key Lab of Plant PathologyCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan 430070China present address:225 s 6th st MinneapolisMN 55402USA present address:Biotalys Inc.2520 Meridian Parkway Suite 480DurhamNC 27713USA present address:Life sciences Institute and Department of Cell and Developmental Biology University of Michigan Medical SchoolAnn ArborMI 48109USA

Rapid plant immune responses in the appropriate cells are needed for effective defense against *** transcriptome analysis is often used to describe overall immune responses,collection of transcriptome data with sufficient resolution in both space and time is *** reanalyzed public Arabidopsis time-course transcriptome data obtained after low-dose inoculation with a Pseudomonas syringae strain expressing the effector AvrRpt2,which induces effector-triggered immunity in ***-peak time-course patterns are prevalent among thousands of upregulated *** implemented a multicompartment modeling approach to decompose the double-peak pattern into two single-peak patterns for each *** decomposed peaks reveal an“echoing”pattern:the peak times of the first and second peaks correlate well across most upregulated *** demonstrated that the two peaks likely represent responses of two distinct cell populations that respond either cell autonomously or indirectly to ***,the peak decomposition has extracted spatial information from the time-course *** echoing pattern also indicates a conserved transcriptome response with different initiation times between the two cell populations despite different elicitor types.A gene set highly overlapping with the conserved gene set is also upregulated with similar kinetics during pattern-triggered *** of a WRKY network via different entry-point WRKYs can explain the similar but not identical transcriptome responses elicited by different elicitor *** discuss potential benefits of the properties of the WRKY activation network as an immune signaling network in light of pressure from rapidly evolving pathogens.

关键词： Arabidopsis Pseudomonas syringae plant immune response multi-compartment model WRKY transcription factors resilient immune signaling network

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Occupancy of avian foraging guilds in soybean fields and borders in Entre Ríos, Argentina: responses to vegetation structure and prey resources

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Avian Research 2020年第4期11卷 398-411页

作者： Andrea P.Goijman Michael J.Conroy Vanina D.Varni Jeffrey J.thompson María Elena Zaccagnini Instituto de Recursos Biológicos CIRNInstituto Nacional de Tecnología Agropecuaria(CNIA-INTA)HurlinghamBuenos AiresArgentina D.B.Warnell school of Forestry and Natural Resources University of GeorgiaAthensGA 30602USA present address:Athens GAUSA present address:Laboratorio de Genómica Ecológica y Evolutiva IrapuatoGtoMéxico present address:Guyra Paraguay-CONACYT Av.Cnel.Carlos BóvedaParque Ecológico Capital-Viñas CuéAsunciónParaguay present address:Instituto saite AsunciónParaguay present address:the Ronin Institute MontclairNJUSA present address:Instituto Nacional de Tecnología Agropecuaria(INTA) CABAArgentina

Background:Reconciling agriculture and biodiversity conservation is a challenge given the growing demand for agricultural *** recent decades,Argentina has witnessed agricultural expansion and intensification affecting biodiversity and associated ecosystem *** agroecosystems,the level of habitat quality is critical for birds,and may depend on vegetation structure,availability of invertebrate prey,and the use of *** the relationship between vegetation structure and avian occurrence has been widely studied,to our knowledge,there are no studies that also incorporate prey availability throughout the cycle of soybean crops in *** estimated and predicted the effects of land cover and temporal variation on the occurrence of avian foraging guilds in Entre Ríos,Argentina,in order to guide management related to potential ecosystem services provided by *** also estimated temporal effects of vegetation structure and insecticides on the main arthropod orders consumed by birds to evaluate prey ***:We conducted bird and arthropod surveys for 2 years along transects located in 20 randomly selected soybean fields(N=60)and their adjacent borders(N=78)throughout the crop growing season,in four *** estimated avian occupancy,accounting for imperfect detection,and arthropod counts fitting generalized linear mixed ***:the number of native trees in field borders positively influenced the occurrence of most bird species,mainly *** foliage gleaners,also were positively affected by grass *** and aerial foragers were weakly affected by distance to forest and native *** general,the availability of invertebrates to birds was highest during the third *** counts in borders were greater during the last three crop stages than during the pre-sowing ***:We found that with 10 to 15 native tree species in borders,coupled with a complex vegetation structure w

关键词： Agriculture Birds Ecosystem services Insecticide Insectivores Invertebrates Management Native trees Occurrence

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Variational Calculation of Lattice sU(N) Gauge system

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Chinese Physics Letters 1996年第5期13卷 337-339页

作者： ZHENG Xi-te shahram Alavian Department of Applied Physics Sichuan Union University(Chengdu University of Science and Technology)Chengdu 610065 saskatchewan Accelerator Laboratory University of SaskatchewanSaskatoonSaskatchewanCanadaS7N5C6(present address)

A general method for an analytical calculation of sU(N)lattice gauge theories with finite N≥3 *** an example,the order parameter(E)of lattice sU(4)gauge systetn is *** result is in good agree^nent with Monte Carlo si... 详细信息

关键词： gauge lattice finite

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Past,present and future of indium phosphide quantum dots

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Nano Research 2022年第5期15卷 4468-4489页

作者： Houman Bahmani Jalali sadra sadeghi Itir Bakis Dogru Yuksel Asim Onal sedat Nizamoglu Graduate school of Biomedical science and Engineering KoçUniversityIstanbul 34450Turkey Department of Electric and Electronics Engineering KoçUniversityIstanbul 34450Turkey Department of Material science and Engineering KoçUniversityIstanbul 34450Turkey present address:Photonic Nanomaterials Group Istituto Italiano di TecnologiaGenova 16124Italy present address:Department of Electrical and Computer Engineering Queen's UniversityKingston K7L 3N6Canada present address:Nanophotonics Group Debye Institute for Nanomaterials ScienceUtrecht UniversityUtrecht 3508 TAThe Netherlands

Indium phosphide(InP)colloidal quantum dots(QDs)have been drawn significant attention as a potentially less toxic alternative to cadmium-based QDs over the past two *** advances in their colloidal synthesis methods have allowed for the synthesis of a wide variety of compositions,heterojunctions,dopants,and ligands that enabled spectral tunability from blue to near-infrared,narrow emission linewidths,and perfect quantum yields approaching ***,it has higher covalency compared to cadmium chalcogenides leading to improved optical *** state-of-the-art InP QDs with appealing optical and electronic properties have excelled in many applications such as light-emitting diodes,luminescent solar concentrators(LsCs),and solar cells with high potential for *** review focuses on the history,recent development,and future aspect of synthesis and application of colloidal InP QDs.

关键词： indium phosphide InP quantum dot nanocrystal synthesis colloidal doping

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Optical actuation of a micromechanical photodiode via the photovoltaic-piezoelectric effect

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Microsystems & Nanoengineering 2021年第2期7卷 167-175页

作者： A.Rampal R.N.Kleiman Department of Engineering Physics McMaster UniversityHamiltonONL8S 4L7Canada present address:CircuitMind Inc 185 Spadina AvenueTorontoONM5T 2C6Canada

Radiation pressure and photothermal forces have been previously used to optically actuate micro/nanomechanical structures fabricated from semiconductor piezoelectric materials such as gallium arsenide(GaAs).In these materials,coupling of the photovoltaic and piezoelectric properties has not been fully explored and leads to a new type of optical actuation that we call the photovoltaic-piezoelectric effect(PVPZ).We demonstrate this effect by electrically measuring,via the direct piezoelectric effect,the optically induced strain in a novel torsional *** micron-scale torsional resonator is fabricated from a lattice-matched single-crystal molecular beam epitaxy(MBE)-grown GaAs photodiode *** find that the strain depends on the product of the electro-optic responsivity and piezoelectric constant of *** photovoltaic-piezoelectric effect has important potential applications,such as in the development of configurable optical circuits,which can be used in neuromorphic photonic chips,processing of big data with deep learning and the development of quantum circuits.

关键词： resonator piezoelectric effect

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Universal switching of plasmonic signals using optical resonator modes

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Light(science & Applications) 2016年第1期5卷 135-142页

作者： Cillian PT McPolin Nicolas Olivier Jean-sebastien Bouillard Daniel O’Connor Alexey V Krasavin Wayne Dickson Gregory A Wurtz Anatoly V Zayats Department of Physics King’s College LondonStrandLondon WC2R 2LSUK present address:University of sheffield Hounsfield RoadSheffield S37RHUK present address:University of Hull Cottingham RoadHull HU67RXUK present address:National Physical Laboratory Hampton RoadTeddingtonMiddlesex TW110LWUK University of North Florida 1 UNF DriveJacksonvilleFL 32224USA

We propose and investigate,both experimentally and theoretically,a novel mechanism for switching and modulating plasmonic signals based on a Fano interference process,which arises from the coupling between a narrow-band optical Fabry–Pérot cavity and a surface plasmon polariton(sPP)*** sPP wave emitted from the cavity is actively modulated in the vicinity of the cavity resonances by altering the cavity Q-factor and/or resonant *** experimentally demonstrate dynamic sPP modulation both by mechanical control of the cavity length and all-optically by harnessing the ultrafast nonlinearity of the Au mirrors that form the *** electro-optical modulation scheme is also proposed and numerically *** operation of the switch via mechanical means yields a modulation in the sPP coupling efficiency of~80%,while the all-optical control provides an ultrafast modulation with an efficiency of 30%at a rate of~0.6 *** experimental observations are supported by both analytical and numerical calculations of the mechanical,all-optical and electro-optical modulation methods.

关键词： Fano resonances optical signal processing plasmonics ultrafast switching

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Electronic properties of wurtzite GaAs： A correlated structural, optical, and theoretical analysis of the same polytypic GaAs nanowire

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Nano Research 2018年第9期11卷 4708-4721页

作者： Alexander senichev Pierre Corfdir Oliver Brandt Manfred Ramsteiner steffen Breuer Jorg schilling Lutz Geelhaar Peter Werner Max-Planck-lnstitut fur Mikrostrukturl)hysik Halle 06120 Germany PauI-Drude-lnstitut for Festkorperelektronik Berlin 10117 Germany Centre for Innovation Competence siLi-nano Martin-Luther-Universitat Halle 06120 Germany present address: Birck Nanotechnology Center Purdue University West Lafayette Indiana 47907 USA present address: Fraunhofer HHI Berlin 10587 Germany present address: ABB Corporate Research Baden-Dattwi15405 Switzerland

III-V compound semiconductor nanowires are generally characterized by the coexistence of zincblende and wurtzite structures. so far, this polytypism has impeded the determination of the electronic properties of the metastable wurtzite phase of GaAs, which thus remain highly controversial. In an effort to obtain new insights into this topic, we cross-correlate nanoscale spectral imaging by near-field scanning optical microscopy with a transmission electron microscopy analysis of the very same polytypic GaAs nanowire dispersed onto a si wafer. thus, spatially resolved photoluminescence spectra could be unambiguously assigned to nanowire segments whose structure is known with lattice-resolved accuracy. An emission energy of 1.528 eV was observed from extended zincblende segments, revealing that the dispersed nanowire was under uniaxial strain presumably due to interaction with its supporting substrate. these crucial information and the emission energy obtained for extended pure wurtzite segments were used to perform envelope function calculations of zincblende quantum disks in a wurtzite matrix as well as the inverse structure. In these calculations, we varied the fundamental bandgap, the electron mass, and the band offset between zincblende and wurtzite GaAs. From this multi-parameter comparison with the experimental data, we deduced that the bandgap between the F8 conduction and A valence band ranges from 1.532 to 1.539 eV in strain-free wurtzite GaAs, and estimated values of 1.507 to 1.514 eV for the F7-A bandgap.

关键词： nanowires crystal-phase quantumstructures wurtzite GaAs strain near-field scanning optical microscopy photoluminescence

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Ecological succession following forest decline in a xeric oak forest of south-central United states

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Journal of Plant Ecology 2016年第4期9卷 402-409页

作者： Devin P.Bendixsen stephen W.Hallgren Jesse A.Burton Department of Natural Resource Ecology and Management Oklahoma State University008 Ag HallStillwaterOK 74074USA present address:Department of Biomolecular sciences Boise State University1357 S.Brady St.BoiseID 83725USA present address:National Park service 2680 Natchez Trace PkwyTupeloMS 38804USA

Aims the loss of canopy trees associated with forest decline can greatly influence the species composition and structure of a forest and have major impacts on the *** studied the changes in forest composition and structure 1 and 5 years following nearly total canopy mortality on several hundreds of hectares of xeric oak forests in south-central United *** the forests were within an ecotonal vegetation type composed of a mosaic of forest,savanna and grassland,we sought to learn whether forest decline areas would recover to forest or change to more open savanna and grassland conditions in the landscape pattern of *** low intensity fire shaped the vegetation type,we sought to learn whether fire would keep the decline areas *** the study was conducted in a xeric oak forest in east-central Oklahoma,*** located vegetation and regeneration surveys were conducted in decline and non-decline stands 1 and 5 years following nearly total canopy *** at breast height(DBH),regeneration and sprout origin were recorded for all woody *** Findingsthe major canopy species post oak(Quercus stellata Wangenh.),blackjack oak(Quercus marilandica Muenchh.)and black hickory(Carya texana Buckl.)suffered 85-92%mortality;however,minor canopy components experienced limited *** affected all size classes of canopy trees except those below 5 cm breast height *** was abundant regeneration of all species and fire seemed to maintain a high level of *** appeared to decrease the relative importance of stump sprouting and increase other types including root *** areas had abundant true seedlings,with stem origin from a root with the same diameter as the stem,which is very unusual for xeric oak *** height in decline areas was twice that of non-decline *** findings suggest that forest decline may lead to:(i)reduced oak dominance and species change in t

关键词： oak decline prescribed fire seedling stump sprouts drought

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In situ TEM Observation of the Gasification and Growth of Carbon Nanotubes Using Iron Catalysts

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Nano Research 2011年第8期4卷 767-779页

作者： Xiaofeng Feng see Wee Chee Renu sharma Kai Liu Xu Xie Qunqing Li shoushan Fan Kaili Jiang Department of Physics and Tsinghua-Foxconn Nanotechnology Research Center Tsinghua University Beijing 100084 China Leroy Eyring Center for solid state science Arizona State University Tempe AZ 85287 USA present address： Department of Materials science and Engineering University of California Berkeley CA 94720 USA present address： Department of Materials science and Engineerig Rensselaer Polytechnic Institute Troy NY 12180 USA present address： National Institute of science and Technology Gaithersburg MD 20899 USA present address： Department of Materials science and Engineering University of Illinois at Urbana-Champaign Urbana IL 61801 USA

We report the in situ transmission electron microscope (TEM) observation of the catalytic gasification and growth of carbon nanotubes (CNTs). It was found that iron catalysts can consume the CNTs when pumping out the precursor gas, acetylene, at the growth temperature, and reinitiate the growth when acetylene is re-introduced. the switching between gasification and growth of CNTs can be repeated many times with the same catalyst. To understand the phenomenon, thermogravimetric analysis (TGA) coupled with mass spectroscopy was used to study the mechanism involved. It was shown that the residual water molecules in the growth chamber of the TEM react with and remove carbon atoms of CNTs as carbon monoxide vapor under the action of the catalyst, when the precursor gas is pumped out. this result contributes to a better understanding of the water-assisted and oxygen-assisted synthesis of CNT arrays, and provides useful clues on how to extend the lifetime and improve the activity of the catalysts.

关键词： Carbon nanotubes gasification growth iron catalyst environmental transmission electron microscopy (ETEM),thermogravimetric analysis (TGA)

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Responses of an old-field plant community to interacting factors of elevated[CO_(2)],warming,and soil moisture

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Journal of Plant Ecology 2009年第1期2卷 1-11页

作者： E.Cayenne Engel Jake F.Weltzin Richard J.Norby Aimee T.Classen Department of Ecology and Evolutionary Biology University of Tennessee569 Dabney HallKnoxvilleTN 37996-1610USA Environmental sciences Division Oak Ridge National LaboratoryOne Bethel Valley RoadBuilding 1062Oak RidgeTN 37831-6422USA present address:UsA National Phenology Network National Coordinating Office1955 East 6th StreetTucsonAZ 85721USA

Aims the direct effects of atmospheric and climatic change factors—atmospheric[CO_(2)],air temperature and changes in precipitation—can shape plant community composition and alter ecosystem *** is essential to understand how these factors interact to make better predictions about how ecosystems may respond to *** investigated the direct and interactive effects of[CO_(2)],warming and altered soil moisture in open-top chambers(OTCs)enclosing a constructed old-field community to test how these factors shape plant *** and methods the experimental facility in Oak Ridge,TN,UsA,made use of 4-m diameter OTCs and rain shelters to manipulate[CO_(2)](ambient,ambient+300 ppm),air temperature(ambient,ambient+3.5C)and soil moisture(wet,dry).the plant communities within the chambers comprised seven common old-field species,including grasses,forbs and *** tracked foliar cover for each species and calculated community richness,evenness and diversity from 2003 to *** findings this work resulted in three main findings:(1)warming had speciesspecific effects on foliar cover that varied through time and were altered by soil moisture treatments;(2)[CO_(2)]had little effect on individual species or the community;(3)diversity,evenness and richness were influenced most by soil moisture,primarily reflecting the response of one dominant *** conclude that individualistic species responses to atmospheric and climatic change can alter community composition and that plant populations and communities should be considered as part of analyses of terrestrial ecosystem response to climate ***,prediction of plant community responses may be difficult given interactions between factors and changes in response through time.

关键词： climate change foliar cover multi-factor interactions diversity richness

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