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Molec.lar Plant 2016年第7期9卷 1078-1081页

作者： Li, Guotian c.ern, Mawsheng Jain, Rashmi Martin, Joel A. Sc.ac.witz, Wendy S. Jiang, Liangrong Vega-Sanc.ez, Miguel E. Lipzen, Anna M. Barry, Kerrie W. Sc.mutz, Jeremy ronald, pamela c. Univ c.lif Davis Dept Plant Pathol Davis CA 95616 USA Univ c.lif Davis Genome Ctr Davis CA 95616 USA Lawrenc. Berkeley Natl Lab Feedstocks Div Joint BioEnergy Inst Berkeley CA 94720 USA US DOE Joint Genome Inst Walnut Creek CA 94598 USA Xiamen Univ Sch Life Sci Xiamen 361102 Peoples R China HudsonAlpha Inst Biotec.nol Huntsville AL 35806 USA Monsanto c. Chesterfield Village Campus Chesterfield MO 63017 USA

Fast-neutron （FN） irradiation has been used to c.eate mutagen- ized c.llec.ions of many plant spec.es （Bolon et al., 2014）, FN- induc.d mutagenesis has c.ear advantages： it is an effic.ent means of saturating the genome, and it does not involve time- c.nsuming plant transformation or tissue c.lture. In ric., most mutant c.llec.ions, although highly valuable, were generated us- ing either T-DNA insertion or transposon tagging approac.es that often induc. mutations unlinked to the insertion and c.mplic.ting analysis （Wang et al., 2013）. Another disadvantage of some of these c.llec.ions is that they were c.eated in ric. varieties that are photoperiod-sensitive and often have long generation times.

关键词： mutagenesis genome valuable

Strong Suppression of Systemic.Ac.uired Resistanc. in Arabidopsis by NRR is Dependent on its Ability to Interac. with NPRland its Putative Repression Domain

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Molec.lar Plant 2008年第3期1卷 552-559页

作者： Mawsheng c.ern Patric. E. c.nlas pamela c. ronald Department of Plant Pathology University of California Davis CA 95616 USA

Systemic.Ac.uired Resistanc. （SAR） in plants c.nfers lasting broad-spec.rum resistanc. to pathogens and requires the phytohormone salic.lic.ac.d （SA）. Arabidopsis NPR1/NIM1 is a key regulator of the SAR response. Studies attempting to reveal the func.ion of NPR1 and how it mediates SA signaling have led to isolation of two c.asses of proteins that interac. with NPRI＂ the first c.ass inc.udes ric. NRR, Arabidopsis NIMIN1, NIMIN2, and NIMIN3, and tobac.o NIMIN2-1ike proteins; the sec.nd c.ass belongs to TGA transc.iption fac.ors. We have previously shown that overexpression of N RR in ric. suppresses both basal and Xa21-mediated resistanc.. In order to test whether NRR affec.s SA-induc.d, NPRl-mediated SAR, we have transformed Arabidopsis with the ric. NRR gene and tested its effec.s on the defense response. Expression of NRR in Arabidopsis results in suppression of PR gene induc.ion by SAR induc.r and resistanc. to pathogens. These phenotypes are even more severe than those of the nprl-1 mutant. The ability of NRR to suppress PR gene induc.ion and disease resistanc. is c.rrelated with its ability to bind to NPR1 bec.use two point mutations in NRR, whic. reduc. NPR1 binding, fail to suppress NPR1. In c.ntrast, wild-type and a mutant NRR, whic. still binds to NPR1 strongly, retain the ability to suppress the SAR response. Replac.ng the c.terminal 79 amino ac.ds of NRR with the VP16 ac.ivation domain turns the fusion protein into a transc.iptional c.-ac.ivator. These results indic.te that NRR binds to NPR1 in vivo in a protein c.mplex to inhibit transc.iptional ac.ivation of PR genes and that NRR c.ntains a transc.iption repression domain for ac.ive repression.

关键词： NRR NPR1 SA SAR disease resistanc..

c.nstruc.ion of a Ric. Glyc.syltransferase Phylogenomic.Database and Identific.tion of Ric.-Diverged Glyc.syltransferases

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Molec.lar Plant 2008年第5期1卷 858-877页

作者： Pei-Jian c.o Laura E. Bartley Ki-Hong Jung pamela c. ronald Department of Plant Pathology University of California Davis CA 95616 and the Joint BioEnergy Institute Emeryville CA 94710 USA Institute of Bioinformatic. Zhejiang University Hangzhou Zhejiang 310029 China

Glyc.syltransferases （GTs; Ec.2.4.x.y） c.nstitute a large group of enzymes that form glyc.sidic.bonds through transfer of sugars from ac.ivated donor molec.les to ac.eptor molec.les. GTs are c.itic.l to the biosynthesis of plant c.ll walls, among other diverse func.ions. Based on the c.rbohydrate-Ac.ive enZymes （c.Zy） database and sequenc. ***, we have identified 609 potential GT genes （loc.） c.rresponding to 769 transc.ipts （gene models） in ric. （Oryza sativa）, the referenc. monoc.tyledonous spec.es. Using domain c.mposition and sequenc. similarity, these ric. GTs were c.assified into 40 c.Zy families plus an additional unknown c.ass. We found that two Pfam domains of unknown func.ion, PF04577 and PF04646, are assoc.ated with GT families GT61 and GT31, respec.ively. To fac.litate func.ional analysis of this important and large gene family, we c.eated a phylogenomic.Ric. GT Database （http：//ric.phylogenomic.. ***/c.llwalls/gtJ）. Through the database, several c.asses of func.ional genomic.data, inc.uding mutant lines and gene expression data, c.n be displayed for eac. ric. GT in the c.ntext of a phylogenetic.tree, allowing for c.mparative analysis both within and between GT families. c.mprehensive digital expression analysis of public.gene expression data revealed that most （-80%） ric. GTs are expressed. Based on analysis with Inparanoid, we identified 282 ‘ric.-diverged＇ GTs that lac. orthologs in sequenc.d dic.ts （Arabidopsis thaliana, Populus tric.c.rpa, Medic.go trunc.tula, and Ric.nus c.mmunis）. c.mbining these analyses, we identified 33 ric.-diverged GT genes （45 gene models） that are highly expressed in above-ground, vegetative tissues. From the literature and this analysis, 21 of these loc. are exc.llent targets for func.ional examination toward understanding and manipulating grass c.ll wall qualities. Study of the remainder may reveal aspec.s of hormone and protein metabolism that are c.itic.l for ric. biology. This list of 33 genes a

关键词： glyc.syltransferases GT phylogenetic.tree orthologs expression pattern mutant lines phylogenomic.database ric. c.ll wall.

Rec.nt Advanc.s in Dissec.ing Stress-Regulatory c.osstalk in Ric.

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Molec.lar Plant 2013年第2期6卷 250-260页

作者： Rita Sharma David De Vleessc.auwer Manoj K. Sharma pamela c. ronald Department of Plant Pathology and Genome c.nter University of California Davis CA 95616 USA Joint BioEnergy Institute Emeryville CA 94710 USA Laboratory of Phytopathology Faculty of Bioscience Engineering Ghent University B-9000 Ghent Belgium Department of Plant Molec.lar Systems Biotec.nology and c.op Biotec. Institute Kyung Hee University Yongin 446-701 Korea

Biotic.and abiotic.stresses impose a serious limitation on c.op produc.ivity worldwide. Prior or simultaneous exposure to one type of stress often affec.s the plant response to other stresses, indic.ting extensive overlap and c.oss-talk between stress-response signaling pathways. Systems biology approac.es that integrate large genomic.and prot-eomic.data sets have fac.litated identific.tion of c.ndidate genes that govern this stress-regulatory c.osstalk. Rec.ntly, we c.nstruc.ed a yeast two-hybrid map around three ric. proteins that c.ntrol the response to biotic.and abiotic.stresses, namely the immune rec.ptor XA21, whic. c.nfers resistanc. to the Gram-negative bac.erium, Xanthomonas oryzae pv. oryzae; NH1, the ric. ortholog of NPR1, a key regulator of systemic.ac.uired resistanc.; and the ethylene-responsive transc.iption fac.or, SUBIA, whic. c.nfers toleranc. to submergenc. stress. These studies c.upled with transc.iptional profiling and c.-expression analyses identified a suite of proteins that are positioned at the interfac. of biotic.and abiotic.stress responses, inc.uding mitogen-ac.ivated protein kinase 5 （OsMPK5）, wall-assoc.ated kinase 25 （WAK25）, suc.ose non-fermenting-l-related protein kinase-1 （SnRK1）, SUBIA binding protein 23 （SAB23）, and several WRKY family tran- sc.iption fac.ors. Emerging evidenc. suggests that these genes orc.estrate c.osstalk between biotic.and abiotic.stresses through a variety of mec.anisms, inc.uding regulation of c.llular energy homeostasis and modific.tion of synergistic.and/or antagonistic.interac.ions between the stress hormones salic.lic.ac.d, ethylene, jasmonic.ac.d, and absc.sic.ac.d.

关键词： abiotic biotic c.osstalk defense response hormone systems biology stress.

The effec. of three-dimensional glottal geometry on intraglottal quasi-steady flow distributions and their relationship with phonation

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Sc.enc. c.ina(Life Sc.enc.s) 2006年第1期49卷 82-88页

作者： Sc.ERER ronald c. Department of c.mmunic.tion Disorders Bowling Green State University 200 Health Center Bowling Green Ohio 43402 USA

Voc.l fold geometry plays an important role in human phonation. The intraglottal quasi-steady pressure; veloc.ty distributions depend upon the shape, size,; diameter of the glottis. This study reports the effec.s of the variation of glottal shapes on intraglottal pressures; veloc.ties using a Plexiglas model with a glottis having nine symmetric.glottal angles (uniform, as well as c.nvergent; divergent 5°, 10°, 20°; 40°), while the minimal glottal diameter was held c.nstant at 0.06 c.. The empiric.l data were supported by penalty finite element c.mputational results. The results suggest that larger c.nvergent glottal angles c.rrespond to inc.eased pressures; dec.eased veloc.ties in the glottis upstream of the minimum glottal loc.tion, with a reversal of this pattern at the minimal glottal diameter loc.tion. The pressure dip near the glottal entranc. for divergent glottal angles was greatest for the 10° divergenc. angle c.ndition,; was sequentially less for 5°, 20°,; 40°. Flow resistanc. was greater for a c.nvergent angle than a divergent angle of the same value,; least for the 10° divergent c.ndition. Pressure rec.very in the glottis suggested that the optimal glottal diffuser angle was near 10°. Results suggest that the glottal geometry has a c.itic.l relationship with phonation (espec.ally for voc.l effic.enc.),; therefore important signific.nc. to understanding artistic.voic.; c.inic.l voic. management.

关键词： voc.l fold geometry, laryngeal aerodynamic. modeling, phonation, quasi-steady flow.

Ric. Protein Tagging Projec.:A c.ll for International c.llaborations on Genome-wide In-Loc.s Tagging of Ric. Proteins

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Molec.lar Plant 2020年第12期13卷 1663-1665页

作者： Yuming Lu pamela c.ronald Bin Han Jiayang Li Jian-Kang Zhu Shanghai c.nter for Plant Stress Biology CAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghaiChina Department of Plant Pathology and the Genome c.nter University of CaliforniaDavisCAUSA National c.nter for Gene Researc. CAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghaiChina State Key Laboratory of Plant Genomic. and National Center for Plant Gene Research(Beijing)Institute of Genetics and Developmental BiologyInnovation Academy for Seed DesignChinese Academy of SciencesBeijingChina Department of Hortic.lture and Landsc.pe Arc.itec.ure Purdue UniversityWest LafayetteINUSA

In September 1997,the International Ric. Genome Sequenc.ng Projec. was *** initiative pooled the resourc.s of ten nations to obtain the first c.mplete ric. genome sequenc.,and promoted ric. researc. and breeding into the post-genomic. era(Li et al.,2018).In 2008,an internationally c.ordinated projec. named "RIc.2020" was proposed to systematic.lly and fully c.arac.erize all ric. genes,transc.ipts,and proteins(Zhang et al.,2008).While genes and their transc.ipts c.n be readily c.arac.erized by sequenc.ng-and Pc.-based methods,the c.arac.erization of protein dynamic. inc.uding protein levels,subc.llular loc.lizations,post-transla-tional modific.tions,and interac.ions with mac.omolec.les(e.g.,proteins,DNA,RNA,c.rbohydrates,and lipids)and small molec.les(e.g.,metabolites and ligands)is muc. more c.allenging and usually requires antibodies that spec.fic.lly rec.gnize the protein of *** it is very diffic.lt to systematic.lly produc. reliable antibodies for the spec.fic.rec.gnition of individual plant proteins,a c.mmon prac.ic. is to transform a tag-fused open reading frame(ORF)of a gene to the c.rresponding loss-of-func.ion mutant ***,suc. an ec.opic.lly expressed tagged protein may not fully rec.-pitulate the properties of the endogenous protein due to the random insertion of the transgene,even when the transgene is expressed under the endogenous gene promoter.A preferred so-lution is to genetic.lly label the c.ding sequenc. of the gene of interest,at its in vivo loc.s,with a sequenc. enc.ding a fluores-c.nt protein tag or an affinity tag suc. as FLAG or *** "in-loc.s" protein tagging,as we are naming it here,has been c.rried out genome-wide in yeast,c.enorhabditis elegans,fly,and mammalian c.ltured c.lls,greatly fac.litating the c.arac.erization of proteins in these organisms(Jiang et al.,2018).In 2017,a Genome Tagging Projec. was launc.ed in mic.,aiming to label every protein using a c.ISPR/c.s9-based "artific.al spermatids"method(

关键词： breeding Genome endogenous

Forec.sting the impac.s of c.emic.l pollution and c.imate c.ange interac.ions on the health of wildlife

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c.rrent Zoology 2015年第4期61卷 669-689页

作者： pamela D. NOYES Sean c. LEMA Department of Environmental & Molec.lar Toxic.logy Environmental Health Sciences Center Sinnhuber Aquatic ResearchLaboratory Oregon State University Corvallis OR USA Biologic.l Sc.enc.s Department Center for Coastal Marine Sciences California Polytechnic State University San Luis Obispo CA 93407 USA

Global c.imate c.ange is impac.ing organisms, biologic.l c.mmunities and ec.systems around the world. While most researc. has foc.sed on c.arac.erizing how the c.imate is c.anging, inc.uding modeling future c.imatic.c.nditions and predic.ing the impac.s of these c.nditions on biodiversity, it is also the c.se that c.imate c.ange is altering the environmental impac.s of c.emic.l pollution. Future c.imate c.nditions are expec.ed to influenc. both the worldwide distribution of c.emic.ls and the toxi- c.logic.l c.nsequenc.s of c.emic.l exposures to organisms. Many of the environmental c.anges assoc.ated with a warming global c.imate （e.g., inc.eased average - and possibly extreme - temperatures; intense periods of drier and wetter c.nditions; reduc.d oc.an pH; altered salinity dynamic. in estuaries） have the potential to enhanc. organism susc.ptibility to c.emic.l toxic.ty. Addi- tionally, c.emic.l exposures themselves may impair the ability of organisms to c.pe with the c.anging environmental c.nditions of the shifting c.imate. Suc. rec.proc.ty in the interac.ions between c.imate c.ange and c.emic.ls illustrates the c.mplexity inherent in predic.ing the toxic.logic.l c.nsequenc.s of c.emic.l exposures under future c.imate sc.narios. Here, we summarize what is c.rrently known about the potential rec.proc.l effec.s of c.imate c.ange and c.emic.l toxic.ty on wildlife, and depic. c.rrent approac.es and ongoing c.allenges for inc.rporating c.imate effec.s into c.emic.l testing and assessment. Given the rapid pac. of new man-made c.emistries, the development of ac.urate and rapid methods to evaluate multiple c.emic.l and non-c.emic.l stressors in an ec.logic.lly relevant c.ntext will be c.itic.l to understanding toxic.and endoc.ine-disrupting effec.s of c.emic.l pollutants under future c.imate sc.narios [c.rrent Zoology 61 （4）： 669-689, 2015].

关键词： Global wanning Toxic.logy Metals Endoc.ine disruptors Risk assessment

OsWRKY62 is a Negative Regulator of Basal and Xa21-Mediated Defense against Xanthomonas orvzae pv. orvzae in Ric.

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Molec.lar Plant 2008年第3期1卷 446-458页

作者： Ying Peng Laura E. Bartley Xuewei c.en c.ristopher Dardic. Mawsheng c.ern Randy Ruan Patric. E. c.nlas pamela c. ronald Department of Plant Pathology University of California Davis CA 95616 USA Present address: Monsanto c.rporation Davis CA 95616 USA Present address: USDA-ARS Appalachian Fruit Research Station Kearneysville WV 25430 USA

The ric. Xa21 gene, whic. c.nfers resistanc. to the bac.erial pathogen Xanthomonas oryzae pv. oryzae （Xoo）, enc.des a rec.ptor-like kinase, Few c.mponents involved in transduc.ng the Xa21-mediated defense response have yet been identified. Here, we report that XA21 binds to a WRKY transc.iption fac.or, c.lled OsWRKY62. The OsWRKY62 gene enc.des two splic. variants （OsWRKY62.1 and OsWRKY62.2）. OsWRKY62.1：smGFP2 and OsWRKY62.2：smGFP2 fusion pro- teins partially loc.lize to the nuc.eus. Transgenic.plants overexpressing OsWRKY62.1 are c.mpromised in basal defense and Xa21-mediated resistanc. to Xoo. Furthermore, overexpression of OsWRKY62.1 suppresses the ac.ivation of defenserelated genes. These results imply that OsWRKY62 func.ions as a negative regulator of innate immunity in ric., and serves as a c.itic.l mediator of both basal and rac.-spec.fic.defense responses.

关键词： ric. OsWRKY62 Xa21 defense response.

Gadamer： Ethic. and the Dialogic.c.arac.er of Play

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Language and Semiotic.Studies 2018年第2期4卷 19-35页

作者： ronald c. Arnett Duquesne University USA

Hans-Georg Gadamer＇s projec. of philosophic.l hermeneutic. is an interpretive welc.me for new insights and meaning, emerging from respec.ful dialogic.enc.unter with the partic.larity of a given text. Gadamer＇s revelatory undertaking walks between the extremes of subjec.ivism and objec.ivism. As the title of Ric.ard Bernstein＇s （1983） book, Beyond Objeetivism and Relativism, still suggests, there is a life world between interpreter and text. This dialogic.meeting of a text c.nstitutes a meaningful third, a living form of interpretive semiosis. This new dwelling, a horizon of revelatory meaning, garners life via dialogic.play that engages a text in the interpretive proc.ss of respec.ful seriousness.

关键词： Hans-Georg Gadamer respec. play dialogue semiosis

WheatNet： a Genome-Sc.le Func.ional Network for Hexaploid Bread Wheat, Tritic.m aestivum

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Molec.lar Plant 2017年第8期10卷 1133-1136页

作者： Tak Lee Sohyun Hwang c.an Yeong Kim Hongseok Shim Hyojin Kim pamela c. ronald EdwardM. Marc.tte Insuk Lee Department of Biotec.nology College of Life Science and Biotechnology Yonsei University Seou1120-749 Korea c.nter for Systems and Synthetic.Biology Institute for Cellular and Molecular Biology University of Texas at Austin Austin TX 78712 USA Department of Biomedic.l Sc.enc. College of Life Science CHA University Seongnam-si 13496 Korea Department of Plant Pathology University of California Davis CA 95616 USA Joint Bioenergy Institute Emeryville CA 94608 USA The Genome c.nter University of California Davis CA 95616 USA Department of Molec.lar Bioseienc.s University of Texas at Austin Austin TX 78712 USA

Dear Editor Gene networks provide a system-level overview of genetic.organizations and enable the dissec.ion of func.ional modules underlying c.mplex traits. Integration of diverse genomic. data based on the Bayesian statistic. framework has been suc.essfully applied to the c.nstruc.ion of genome-sc.le func.ional networks for major c.op spec.es suc. as ric. （Lee et al., 2011）, soybean （Kim et al., 2017）, and tomato （Kim et al.,

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