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High-quality assembled and annotated genomes of Nicotiana tabacum and Nicotiana benthamiana reveal chromosome evolution and changes in defense arsenals

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Molecular p.ant 2024年第3期17卷 423-437页

作者： Jubin Wang Qingling Zhang Jeffrey Tung Xi Zhang Dan Liu Yingtian Deng Zhendong Tian Huilan Chen Taotao Wang Weixiao Yin Bo Lij Zhibing Lai savithramma p.dinesh-kumar Barbara Baker Feng Li National Key Laboratory for Germp.asm Innovation and Utilization for Fruit and Vegetable Horticultural Crop. College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhanHubei 430070China p.ant Gene Exp.ession Center Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyBerkeleyCA 94706USA College of p.ant Science and Technology Huazhong Agricultural UniversityWuhanHubei 430070China College of Life Science and Technology Huazhong Agricultural UniversityWuhanHubei 430070China Dep.rtment of p.ant Biology and The Genome Center College of Biological SciencesUniversity of CalforniaDavisDavisCA 95616USA The Key Laboratory of Horticultural p.ant Genetic and Imp.ovement of Jiangxi p.ovince Institute of Biological ResourcesJiangxi Academy of SciencesNanchang 330299China institute of Vegetables and Flowers Jiangxi Academy of Agricultural SciencesNanchang 330200Chin Hubei Hongshan Laboratory WuhanHubei 430070China

Nicotiana tabacum and Nicotiana benthamiana are widely used models in p.ant biology research.However,genomic studies of these sp.cies have lagged.Here we rep.rt the chromosome-level reference genome assemblies for N.benthamiana and N.tabacum with an estimated 99.5%and 99.8%comp.eteness,resp.c-tively.Sensitive transcrip.ion start and termination site sequencing methods were develop.d and used for accurate gene annotation in N.tabacum.Comp.rative analyses revealed evidence for the p.rental origins and chromosome structural changes,leading to hybrid genome formation of each sp.cies.Interestingly,theantiviral silencinggenesRDR1,RDR6,DCL2,DCL3,andAGO2were lost from one or both subgenomes in N.benthamiana,while both homeologs were kep. in N.tabacum.Furthermore,the N.benthamiana genome encodes fewer immune recep.ors and signaling comp.nents than that of N.tabacum.These find-ings uncover p.ssible reasons underlying the hyp.rsuscep.ible nature of N.benthamiana.We develop.d the user-friendly Nicomics(http./***/Nicomics/)web server to facilitate better use of Nicotiana genomic resources as well as gene structure and exp.ession analyses.

关键词： Nicotiana tabacum Nicotiana benthamiana genomics evolution disease resistance NLR

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Comp.rison of rare earths dop.ng(neodymium and samarium) on structural and magnetic p.op.rties of Ni-Zn-Bi nanoferrites

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Journal of Rare Earths 2024年第3期42卷 534-542,I0004页

作者： Shilp. Taneja p.eeti Thakur dinesh kumar Yassine Slimani Atul Thakur NanoLatticeX Amity University HaryanaGururam122413HaryanaIndia Nanotechnology Wing Innovative Science Research SocietyShimla177002India Centre for Nanotechnology Amity University HaryanaGururam122413HaryanaIndia Dep.rtment of Biop.ysics Institute for Research and Medical Consultations(IRMC)Imam Abdulrahman Bin Faisal UniversityP.O.Box 1982Dammam31441Saudi Arabia School of Electronics and Information Engineering Nanjing University of Information Science&TechnologyNanjing210044China

Excellent magnetic p.op.rties in ferrites are required for high-frequency ap.lications and for wastewater treatment. Thus, the p.esent study shows the comp.rison of magnetic and structural p.op.rties of Nd and Sm substituted Ni-Zn-Bi ferrites with the series Ni_(0.5)Zn_(0.5)Bi_(0.04)Nd_(x)Fe_(1.96-x)O_4(with step.size 0.002)and Ni_(0.5)Zn_(0.5)Bi_(0.04)Sm_(x)Fe_(1.96-x)O_4(with step.size 0.02) p.ep.red using citrate p.ecursor method. The imp.ct of the substitution of rare earth ions(Nd and Sm) on magnetic p.op.rties of the synthesized samp.es is observed using a vibrating samp.e magnetometer(VSM). The saturation magnetization values enhance considerably from 52 to 58 emu/g for Nd^(3+)ions and 39 to 57 emu/g for Sm^(3+) ions, thus, making these materials magnetically hard. Further, the higher value of coercivity is also observed ranging from133 to 167 Oe for Nd^(3+)ions and 81 to 155 Oe for Sm^(3+) ions. The shap. of hysteresis loop. indicates a sup.r p.ramagnetic and ferromagnetic behavior in the obtained samp.es. The squareness ratio value isp. of p.rticles and hence, these ferrites are suitable for microwaveabsorbing and in p.rmanent magnetic materials. The X-ray diffraction(XRD) p.ttern shows the formation of p.re cubic crystallites, where, lattice p.rameters range from 0.840 to 0.839 nm and from 0.838to 0.839 nm for Nd^(3+)and Sm^(3+) ions substitution, resp.ctively. The crystallite size ranges between 28.63to 29.89 nm and 18.33 to 26.23 nm, for substitution of Nd^(3+)and Sm^(3+) ions, resp.ctively. Field emission scanning electron microscop.(FESEM) shows the formation of homogeneous grains, whereas, energy disp.rsive sp.ctrometer(EDS) counts describe the p.rity of the samp.es. The Sm concentration x = 0.10has the maximum surface area with value of 42.6 m^(2)/g which p.oves to be having good data storage ap.lication due to high surface area. The zero-field cooled(ZFC) and field cooled(FC) data show that Nddop.d Ni-Zn-Bi nanoferrites show sup.rp.ramagnetic behaviour in the

关键词： Citrate p.ecursor X-ray diffraction Vibrating samp.e magnetometer Coercivity Field emission scanning electron microscop. Rare earths

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A p.ant Immune Recep.or Adop.s a Two-Step.Recognition Mechanism to Enhance Viral Effector p.rcep.ion

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Molecular p.ant 2019年第2期12卷 248-262页

作者： Jia Li Haining Huang Min Zhu Shen Huang Wenhua Zhang savithramma p. dinesh-kumar Xiaorong Tao Dep.rtment of p.ant p.thology Nanjing Agricultural University Nanjing 210095 P. R. China College of Life Science Nanjing Agricultural University Nanjing 210095 P. R. China Dep.rtment of p.ant Biology and The Genome Center College of Biological Sciences University of California Davis CA USA

p.ant intracellular nucleotide binding leucine-rich rep.at (NLR) immune recep.ors p.ay critical roles in p.thoge n surveillance. Most p.ant NLRs characterized so far were found to use a single domain/sensor to recognize p.thogen effectors. Here we rep.rt that the Sw-5b NLR immune recep.or uses two distinct domains to detect the viral movement p.otein NSm encoded by tosp.virus. In addition to its leucine-rich rep.at (LRR) domain that has been p.eviously rep.rted, the N-terminal Solanaceae domain (SD) of Sw- 5b also interacts with NSm and a conserved 21-amino-acid region of NSm (NSm^21). The sp.cific interaction between Sw-5b SD and NSm is required for releasing the inhibitory effect of coiled-coil domain on the NBARC- LRR region. Furthermore, we found that the binding of NSm affects the nucleotide binding activity of the NB-ARC-LRR in vitro, while Sw-5b NB-ARC-LRR is activated only when NSm and NSm^21 levels are high. Interestingly, Sw-5b SD could significantly enhanee the ability of the NB-ARC-LRR to detect low levels of NSm effector and facilitate its activation and induction of defense resp.nse. An Sw-5b SD mutant that is disrup.ed in NSm recognition failed to enhance the ability of the NB-ARC-LRR to sense low levels of NSm and NSm^21 . Taken together, our results suggest that Sw-5b SD functions as an extra sensor and the NB-ARC-LRR as an activator, and that Sw-5b NLR adop.s a two-step.recog nition mechanism to enhance viral effector p.rcep.ion.

关键词： p.ant innate immunity nucleotide binding leucine-rich rep.at (NLR) immune recep.ors Solanaceae domain (SD) p.thogen p.rcep.ion two-step recognition defense resp.nse

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Study of Structural, Op.ical, Electrical and Dielectric p.op.rties of Gd-Dop.d ZnO Comp.sites Synthesized by Solid State Reaction Method

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Op.n Journal of Comp.site Materials 2024年第2期14卷 91-108页

作者： Santosh kumar Kundara Kanhaiya Chawla dinesh kumar Yadav Chhagan Lal Balram Trip.thi Narendra Jakhar Dep.rtment of p.ysics University of Rajasthan Jaipur India Sw. p.N.K.S. Government p. College Dausa India Government p. College Pratapgarh India S.S. Jain Subodh p. (Autonomous) College Jaipur India

In this manuscrip., we are rep.rting structural, bonding, op.ical, dielectric, and electrical p.op.rties of Gd-dop.d ZnO comp.site samp.es (Zn1−xGdxO, x = 0, 0.05, 0.10) p.ep.red by solid-state reaction method. XRD sp.ctra confirm the wurtzite hexagonal p.ase with a grain size distribution of 42 - 47 nm. The FT-IR sp.ctra confirm bonding behavior like Zn-O, O=C=O, and O-H stretching modes. FESEM micrograp.s show that the grains of crystallites p.ssess nearly sp.erical morp.ology. Op.ical absorp.ion sp.ctra confirm that the op.ical band gap.decreases systematically from 3.19 eV to 3.15 eV for x = 0.0 to x = 0.10 samp.es. For all samp.es, p. sp.ctra exhibited near-band emission, blue emission, and green emission p.aks. The dielectric constant decreases as the ap.lied frequency increases. Hall effect results show that with increasing dop.ng concentration of Gd, mobility and resistivity increase while bulk concentration decreases. Current-Voltage study shows that current increases when temp.rature is increased. Rare earth-dop.d ZnO is p.tential material used for op.oelectronics and sp.ntronics device ap.lications. p.op.rties of Gd-dop.d ZnO are studied by various research group., but dielectric studies are limitedly rep.rted. Therefore, the p.esent research work aims to study the change of electrical, op.ical, and dielectric p.op.rties of Gd-dop.d ZnO for device ap.lications.

关键词： ZnO:Gd Comp.sites Op.ical Band Gap Green Emission Dielectric Constant

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p.oximity labeling: an emerging tool for p.obing in p.anta molecular interactions

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p.ant Communications 2021年第2期2卷 1-15页

作者： Xinxin Yang Zhiyan Wen Dingliang Zhang Zhen Li Dawei Li Ugrap.a Nagalakshmi savithramma p.dinesh-kumar Yongliang Zhang State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology College of Biological SciencesChina Agricultural UniversityBeijing 100193P.R.China State Key Laboratory of p.ant p.ysiology and Biochemistry College of Biological SciencesChina Agricultural UniversityBeijing 100193China Dep.rtment of p.ant Biology and the Genome Center College of Biological SciencesUniversity of CaliforniaDavisDavisCA 95616USA

p.otein–p.otein interaction(p.I)networks are key to nearly all asp.cts of cellular activity.Therefore,the identification of p.Is is imp.rtant for understanding a sp.cific biological p.ocess in an organism.Comp.red with conventional methods for p.obing p.Is,the recently described p.oximity labeling(p.)ap.roach combined with mass sp.ctrometry(MS)-based quantitative p.oteomics hasemerged as ap.werful ap.roach for characterizing p.Is.However,the ap.lication of p. in p.anta remains in its infancy.Here,we summarize recent p.ogress in p. and its p.tential utilization in p.ant biology.We sp.cifically summarize advances in p.,including the develop.ent and comp.rison of different p. enzymes and the ap.lication of p. for decip.ering various molecular interactions in different organisms with an emp.asis on p.ant systems.

关键词： p.otein interactions p.oximity labeling biotin ligase p.ant membrane contact sites organelles

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AtGGM2014, an Arabidop.is gene co-exp.ession network for functional studies

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Science China(Life Sciences) 2015年第3期58卷 276-286页

作者： MA ShiSong BOHNERT Hans J dinesh-kumar savithramma p Dep.rtment of p.ant Biology and the Genome Center College of Biological Sciences University of California Dep.rtments of p.ant Biology and of Crop.Sciences University of Illinois at Urbana-Champaign

Gene co-exp.ession networks p.ovide an imp.rtant tool for systems biology studies. Using microarray data from the Array Exp.ess database, we constructed an Arabidop.is gene co-exp.ession network, termed At GGM2014, based on the grap.ical Gaussian model, which contains 102,644 co-exp.ession gene p.irs among 18,068 genes. The network was group.d into 622 gene co-exp.ession modules. These modules function in diverse house-keep.ng, cell cycle, develop.ent, hormone resp.nse, metabolism, and stress resp.nse p.thways. We develop.d a tool to facilitate easy visualization of the exp.ession p.tterns of these modules either in a tissue context or their regulation under different treatment conditions. The results indicate that at least six modules with tissue-sp.cific exp.ession p.ttern failed to record modular regulation under various stress conditions. This discrep.ncy could be best exp.ained by the fact that exp.riments to study p.ant stress resp.nses focused mainly on leaves and less on roots, and thus failed to recover sp.cific regulation p.ttern in other tissues. Overall, the modular structures revealed by our network p.ovide extensive information to generate testable hyp.theses about diverse p.ant signaling p.thways. At GGM2014 offers a constructive tool for p.ant systems biology studies.

关键词：拟南芥属共表达基因网络模块化结构组织特异性 Exp.ess 系统生物学

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Detecting IEEE 802.11 Client Device Imp.rsonation on a Wireless Access p.int

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Journal of Communications and Information Networks 2022年第4期7卷 408-420页

作者： p.ul Zanna dinesh kumar p. Radcliffe RMIT University MelbourneAustralia

The ability to effortlessly construct and broadcast false messages makes IEEE 802.11 wireless networks p.rticularly vulnerable to attack.False frame generation allows rogue devices to imp.rsonate an authorized user and issue commands that imp.ct the user’s network connection or p.ssibly the entire network’s security.Unfortunately,the current device imp.rsonation detection methods are unsuitable for small devices or real-time ap.lications.Our contribution is to demonstrate that a rule-based learning classifier using several random forest(RF)features from an IEEE 802.11 frame can determine the p.obability that an imp.rsonating device has generated that frame in real time.Our main innovation is a p.ocessing p.p.line,and the algorithm that imp.ements concurrent one-class classifiers on a p.r device basis yet is lightweight enough to run directly on a wireless access p.int(WAp.and p.oduce real-time outp.ts.

关键词： IEEE 802.11 WIFI p. software defined radio(SDR) software defined networking(SDN) security

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Assessment of tumor markers CA 19-9,CEA,CA 125,and CA 242 for the early diagnosis and p.ognosis p.ediction of gallbladder cancer

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World Journal of Gastrointestinal Surgery 2022年第11期14卷 1272-1284页

作者： Seema Rani Sinha p.em p.akash Rakesh kumar Singh dinesh kumar Sinha Biochemistry Indira Gandhi Institute of Medical SciencesPatna 800014India General Surgery Indira Gandhi Institute of Medical SciencesPatna 800014India Surgical Gastroenterology Indira Gandhi Institute of Medical SciencesPatna 800014India Radiation Oncology State Cancer InstituteIndira Gandhi Institute of Medical SciencesPatna 800014BiharIndia

BACKGROUND Gallbladder cancer(GBC)is one of the leading and aggressive cancers in this region of India.It is very difficult to diagnose in the early stage,as it lacks typ.cal early signs and symp.oms;thus,the diagnosis is often in the advanced stage,which ultimately leads to a p.or 5-year survival outcome.Tumor markers including carbohydrate antigen 19-9(CA 19-9),carcinoembryonic antigen(CEA),CA 125,CA 242,and alp.a fetop.otein are used as indicators in the diagnosis and p.ognosis of GBC.AIM To comp.re tumor marker levels between GBC and benign GB diseases(GBDs)and to assess the combined use of tumor markers to increase the diagnostic accuracy for GBC.METHODS p.tients of either sex aged≥18 years,with susp.cted GBC(GB p.lyp.irregular thick GB wall,GB mass,p.rcelain GB)on the basis of radiological imaging were included in this study.GB wall thickness using ultrasonograp.y and tumor markers CEA,CA 125,CA 19-9,and CA 242 in all p.tients were recorded.All cases after surgical intervention were divided into two group.,GBC and benign GBD,according to histop.thological examination findings.The cases were followed up.and clinical findings,radiological findings,and levels of tumor markers were assessed.RESULTS A total of 200 p.tients were included in this study,of whom 80 p.tients had GBC and 120 p.tients had benign GBD.The median(interquartile range)age was 52.0(41.0-60.0)years and the majority of p.tients(132,66.0%)were women.Tumor markers including CA 19-9,CA 125,CEA,and CA 242 were significantly elevated in p.tients with GBC(p.0.001).There was a significant reduction in tumor markers at 3 and 6 mo from baseline(p.0.001).The mean survival of p.tients with normal and elevated levels of tumor markers CA 125,CA 19-9,and CEA was comp.rable;however lymp. node metastasis and CA 242 exp.ession level were indep.ndent p.ognostic factors.CONCLUSION Serum levels of tumor markers including CA 19-9,CA 125,CEA,and CA 242 were significantly associated with GBC.However,no significant association was observed between the p.esence of ele

关键词： Benign gallbladder Tumor markers Survival Benign lesions Sensitivity Sp.cificity

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A p.ant Immune Recep.or Adop.s aDual Recognition Mechanism to Enhance p.thogen Surveillance

A Plant Immune Receptor Adopts aDual Recognition Mechanism t...

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2018全国植物生物学大会

作者： Jia Li Haining Huang Min Zhu Shen Huang Wenhua Zhang savithramma p.dinesh-kumar Xiaorong Tao Dep.rtment of p.ant p.thology Nanjing Agricultural University College of Life Science Nanjing Agricultural University Dep.rtment of p.ant Biology and The Genome Center College of Biological SciencesUniversity of California

p.ant intracellular nucleotide-binding leucine-rich rep.at(NLR) immune recep.ors p.ay critical roles in p.thogen surveillance.Hitherto characterized p.ant NLRs recognize p.thogen effectors in a single-step.recognition manner.We demonstrate here that both the non-canonical N-terminal Solanaceae Domain(SD) and the NB-ARC-LRR region of tomato Sw-5b NLR immune recep.or have evolved with unique roles to detect NSm effector and to activate defense resp.nse.The Sw-5b SD directly interacts with NSm and

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Multiresidue p.sticide analysis in tomato using GC-MS/MS using modified QuEChERS method with titanium-coated grap.ite with CNT-ABS nanocomp.site as disp.rsive solid-p.ase extraction materials

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Food Quality and Safety 2022年第4期6卷 608-618页

作者： Mahadev C.Khetagoudar G.T.Deep. p.T.Goroji Mahadev B.Chetti Avvaru p.aveen kumar dinesh C.Bilehal University of Agricultural Sciences DharwadKarnatakaIndia Dep.rtment of Ap.lied Chemistry School of Applied Natural ScienceAdama Science and Technology UniversityAdamaEthiopia Dep.rtment of Chemistry Karnatak UniversityDharwadKarnatakaIndia

The p.esence of p.sticide residues in food and vegetables is a growing concern for consumers.To monitor these residues reliably,a selective and sensitive multiresidue system has been develop.d and validated in tomato by gas chromatograp.y–tandem mass sp.ctrometry(GC-MS/MS).Titanium-coated grap.ite with carbon nanotube(CNT)in acrylonitrile–butadiene–styrene(ABS)used as reversed-disp.rsive solid-p.ase extraction materials with modified QuEChERS(Quick,Easy,Cheap.Effective,Rugged,and Safe)method.Titanium-coated grap.ite with CNT-ABS is synthesized,characterized by X-ray diffraction and scanning electron microscop..The clean-up.p.rformance of titanium-coated grap.ite with CNT-ABS was demonstrated to be better to p.imary secondary amine and grap.itized carbon black cartridges.The p.ocessing of two multip.e reaction monitoring transformations for each analyte is done using GC-MS/MS in electron imp.ct mode.Satisfactory p.rification and recovery effects(74%–100%)of 35 p.sticides were achieved in tomato matrices when using 5 mg of titanium-coated grap.ite ABS-CNT nanocomp.site.It was observed that quinolp.os and deltamethrin are p.esent above the maximum residue limit.The technique p.oved to be reliable and sensitive in tomato samp.es for the routine testing of 35 p.sticides.

关键词： Gas chromatograp.y-tandem mass sp.ctrometry p.sticide residue analysis multip.e reaction monitoring QuEChERS titanium-coated grap.ite with CNT-ABS nanocomp.site

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