Introduction: HIV infection represents a major public health problem for both developing and developed countries as it has grown to global pandemic. Spectrum of clinical presentation of HIV can greatly vary with geopo...Introduction: HIV infection represents a major public health problem for both developing and developed countries as it has grown to global pandemic. Spectrum of clinical presentation of HIV can greatly vary with geopolitical, socioeconomic and cultural environment. Aims: The aim of this study was to estimate the prevalence, socio-demographic conditions, clinical presentations, opportunistic infections and the possible associated risk factors for acquiring HIV infection. Materials and Methods: An observational prospective study was conducted from January 2010 to December 2014 at our centre situated in north India. As per the strategy and policy prescribed by NACO, tests were performed on the serum samples. Results: Out of the total 35369 clients tested for HIV infection, 292 were found to be HIV-1 seropositive. Two HIV-2 cases were found among the studied population. The seroprevalence of HIV was found to be 0.83% (294/35369). Mean age of the study group was 30 ± 5.65 (range: 02 - 80) years. Overall positivity rates among attendees were found to be 0.97% (138/14098), 0.96% (35/3610), 0.82% (7/850), 0.78% (22/2810) and 0.65% (92/14001) in the years 2010, 2011, 2012, 2013 and 2014 respectively. Heterosexual route of transmission was the major route of infection in 78.2 % patients. At the time of presentation, it was observed that Tuberculosis (14.9%) was the most common opportunistic infection. Conclusion: The study shows that there is a decreasing trend in the HIV prevalence in North India. However, the number of HIV cases is still significant and suggests the need for focused prevention efforts in high-risk groups.展开更多
In this manuscript, we are reporting structural, bonding, optical, dielectric, and electrical properties of Gd-doped ZnO composite samples (Zn<sub>1</sub><sub>−</sub><sub>x</sub>Gd&...In this manuscript, we are reporting structural, bonding, optical, dielectric, and electrical properties of Gd-doped ZnO composite samples (Zn<sub>1</sub><sub>−</sub><sub>x</sub>Gd<sub>x</sub>O, x = 0, 0.05, 0.10) prepared by solid-state reaction method. XRD spectra confirm the wurtzite hexagonal phase with a grain size distribution of 42 - 47 nm. The FT-IR spectra confirm bonding behavior like Zn-O, O=C=O, and O-H stretching modes. FESEM micrographs show that the grains of crystallites possess nearly spherical morphology. Optical absorption spectra confirm that the optical band gap decreases systematically from 3.19 eV to 3.15 eV for x = 0.0 to x = 0.10 samples. For all samples, PL spectra exhibited near-band emission, blue emission, and green emission peaks. The dielectric constant decreases as the applied frequency increases. Hall effect results show that with increasing doping concentration of Gd, mobility and resistivity increase while bulk concentration decreases. Current-Voltage study shows that current increases when temperature is increased. Rare earth-doped ZnO is potential material used for optoelectronics and spintronics device applications. Properties of Gd-doped ZnO are studied by various research groups, but dielectric studies are limitedly reported. Therefore, the present research work aims to study the change of electrical, optical, and dielectric properties of Gd-doped ZnO for device applications.展开更多
In this manuscript a comparative study on Bi<sub>2</sub>O<sub>3</sub>/polystyrene and Bi<sub>2</sub>O<sub>3</sub>/PVDF composites has been executed via analysis of struc...In this manuscript a comparative study on Bi<sub>2</sub>O<sub>3</sub>/polystyrene and Bi<sub>2</sub>O<sub>3</sub>/PVDF composites has been executed via analysis of structural, bonding, surface morphology and dielectric response of composites for energy storage. The composites have been synthesized using solution cast method by varying concentrations of Bi<sub>2</sub>O<sub>3</sub> (BO = 1 - 5 mw%) into polystyrene (PS) and polyvinylidene fluoride (PVDF) polymers respectively. X-ray diffraction confirms the generation of crystallinity, Fourier transform infrared (FT-IR) spectroscopy confirms bonding behavior and scanning electron microscopy (SEM) confirms uniform distribution of Bi<sub>2</sub>O<sub>3</sub> (BO) in PS and PVDF polymers. Impedance spectroscopy has been employed for determination of dielectric response of the fabricated composites. The dielectric constant has been found to be increased as 1.4 times of pristine PS to BO<sub>5%</sub>PS<sub>95%</sub> composites and 1.8 times of pristine PVDF to BO<sub>5%</sub>PVDF<sub>95%</sub> composites respectively. These high dielectric composite electrodes are useful for flexible energy storage devices.展开更多
<span style="font-family:Verdana;">The new coronavirus called SARS-CoV-2 is a new type of virus named as COVID-19. Although, </span><span style="font-family:Verdana;">it has </...<span style="font-family:Verdana;">The new coronavirus called SARS-CoV-2 is a new type of virus named as COVID-19. Although, </span><span style="font-family:Verdana;">it has </span><span style="font-family:Verdana;">few similarities with pandemic flu viruses</span><span style="font-family:Verdana;">,</span><span style="font-family:Verdana;"> the respiratory system and immune system are damaged through the viruses infected the population wh</span><span style="font-family:Verdana;">o</span><span style="font-family:Verdana;"> has weakened immunity. SARS-CoV-2 spread</span><span style="font-family:Verdana;">s</span><span style="font-family:Verdana;"> when people don’t have the sign and symptoms. This virus COVID-19 appears to spread more easily than the flu, and asymptomatic transmission may account for a greater proportion of COVID-19’s spreader over the World. In inundation of the current understanding</span><span style="font-family:Verdana;">,</span><span style="font-family:Verdana;"> the roles of insect vectors are helping in the transmission of viral pathogens as well and the possible roles of some newly joined insects in the mechanical transmission of COVID-19.</span><span style="font-family:Verdana;"> We also specifically provide the prevention and control methods related to contamination, disease burden, risk pattern in the family, near and dear to maintain the precision of social distancing and development of the immune system to fight against SARS-CoV-2.展开更多
We used our collection of Arabidopsis transcription factor (TF) ORFeome clones to construct protein microarrays containing as many as 802 TF proteins. These protein microarrays were used for both protein-DNA and pro...We used our collection of Arabidopsis transcription factor (TF) ORFeome clones to construct protein microarrays containing as many as 802 TF proteins. These protein microarrays were used for both protein-DNA and proteinprotein interaction analyses. For protein-DNA interaction studies, we examined AP2/ERF family TFs and their cognate cis-elements. By careful comparison of the DNA-binding specificity of 13 TFs on the protein microarray with previous non-microarray data, we showed that protein microarrays provide an efficient and high throughput tool for genome-wide analysis of TF-DNA interactions. This microarray protein-DNA interaction analysis allowed us to derive a comprehensive view of DNA-binding profiles of AP2/ERF family proteins in Arabidopsis. It also revealed four TFs that bound the EE (evening element) and had the expected phased gene expression under clock-regulation, thus providing a basis for further functional analysis of their roles in clock regulation of gene expression. We also developed procedures for detecting protein interactions using this TF protein microarray and discovered four novel partners that interact with HY5, which can be validated by yeast two-hybrid assays. Thus, plant TF protein microarrays offer an attractive high-throughput alternative to traditional techniques for TF functional characterization on a global scale.展开更多
Virus-induced gene silencing (VIGS) is a powerful genetic tool for rapid assessment of plant gene functions in the post-genomic era. Here, we successfully implemented a Tobacco Rattle Virus (TRV)-based VlGS system...Virus-induced gene silencing (VIGS) is a powerful genetic tool for rapid assessment of plant gene functions in the post-genomic era. Here, we successfully implemented a Tobacco Rattle Virus (TRV)-based VlGS system to study functions of genes involved in either primary or secondary cell wall formation in Nicotiana benthamiana plants. A 3-week post- VIGS time frame is sufficient to observe phenotypic alterations in the anatomical structure of stems and chemical composition of the primary and secondary cell walls. We used cell wall glycan-directed monoclonal antibodies to demonstrate that alteration of cell wall polymer synthesis during the secondary growth phase of VIGS plants has profound effects on the extractability of components from woody stem cell walls. Therefore, TRV-based VlGS together with cell wall component profiling methods provide a high-throughput gene discovery platform for studying plant cell wall formation from a bioenergy perspective.展开更多
Plant intracellular nucleotide binding leucine-rich repeat (NLR) immune receptors play critical roles in pathoge n surveillance. Most plant NLRs characterized so far were found to use a single domain/sensor to recogni...Plant intracellular nucleotide binding leucine-rich repeat (NLR) immune receptors play critical roles in pathoge n surveillance. Most plant NLRs characterized so far were found to use a single domain/sensor to recognize pathogen effectors. Here we report that the Sw-5b NLR immune receptor uses two distinct domains to detect the viral movement protein NSm encoded by tospovirus. In addition to its leucine-rich repeat (LRR) domain that has been previously reported, 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 specific 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 response. An Sw-5b SD mutant that is disrupted 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 adopts a two-step recog nition mechanism to enhance viral effector perception.展开更多
Gene co-expression networks provide an important tool for systems biology studies. Using microarray data from the Array Express database, we constructed an Arabidopsis gene co-expression network, termed At GGM2014, ba...Gene co-expression networks provide an important tool for systems biology studies. Using microarray data from the Array Express database, we constructed an Arabidopsis gene co-expression network, termed At GGM2014, based on the graphical Gaussian model, which contains 102,644 co-expression gene pairs among 18,068 genes. The network was grouped into 622 gene co-expression modules. These modules function in diverse house-keeping, cell cycle, development, hormone response, metabolism, and stress response pathways. We developed a tool to facilitate easy visualization of the expression patterns 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-specific expression pattern failed to record modular regulation under various stress conditions. This discrepancy could be best explained by the fact that experiments to study plant stress responses focused mainly on leaves and less on roots, and thus failed to recover specific regulation pattern in other tissues. Overall, the modular structures revealed by our network provide extensive information to generate testable hypotheses about diverse plant signaling pathways. At GGM2014 offers a constructive tool for plant systems biology studies.展开更多
Nicotiana tabacum and Nicotiana benthamiana are widely used models in plant biology research.However,genomic studies of these species have lagged.Here we report the chromosome-level reference genome assemblies for N.b...Nicotiana tabacum and Nicotiana benthamiana are widely used models in plant biology research.However,genomic studies of these species have lagged.Here we report the chromosome-level reference genome assemblies for N.benthamiana and N.tabacum with an estimated 99.5%and 99.8%completeness,respec-tively.Sensitive transcription start and termination site sequencing methods were developed and used for accurate gene annotation in N.tabacum.Comparative analyses revealed evidence for the parental origins and chromosome structural changes,leading to hybrid genome formation of each species.Interestingly,theantiviral silencinggenesRDR1,RDR6,DCL2,DCL3,andAGO2were lost from one or both subgenomes in N.benthamiana,while both homeologs were kept in N.tabacum.Furthermore,the N.benthamiana genome encodes fewer immune receptors and signaling components than that of N.tabacum.These find-ings uncover possible reasons underlying the hypersusceptible nature of N.benthamiana.We developed the user-friendly Nicomics(http:/lifenglab.hzau.edu.cn/Nicomics/)web server to facilitate better use of Nicotiana genomic resources as well as gene structure and expression analyses.展开更多
Suppressor of G2 allele of skp1(SGT1)is a highly conserved eukaryotic protein that plays a vital role in growth,development,and immunity in both animals and plants.Although some SGT1 interactors have been identified,t...Suppressor of G2 allele of skp1(SGT1)is a highly conserved eukaryotic protein that plays a vital role in growth,development,and immunity in both animals and plants.Although some SGT1 interactors have been identified,the molecular regulatory network of SGT1 remains unclear.SGT1 serves as a co-chaperone to stabilize protein complexes such as the nucleotide-binding leucine-rich repeat(NLR)class of immune receptors,thereby positively regulating plant immunity.SGT1 has also been found to be asso-ciated with the SKP1-Cullin-F-box(SCF)E3 ubiquitin ligase complex.However,whether SGT1 targets im-mune repressors to coordinate plant immune activation remains elusive.In this study,we constructed a toolbox for TurbolD-and split-TurbolD-based proximity labeling(PL)assays in Nicotiana benthamiana and used the PL toolbox to explore the SGT1 interactome during pre-and post-immune activation.The comprehensive SGT1 interactome network we identified highlights a dynamic shift from proteins associ-ated with plant development to those linked with plant immune responses.We found that SGT1 interacts with Necrotic Spotted Lesion1(NSL1),which negatively regulates salicylic acid-mediated defenseby inter-fering with the nucleocytoplasmic trafficking of non-expressor of pathogenesis-related genes 1(NPR1)during N NLR-mediated response to tobacco mosaic virus.SGT1 promotes the SCF-dependent degrada-tion of NSL1 to facilitate immune activation,while salicylate-induced protein kinase-mediated phosphory-lation of SGT1further potentiates this process.Besides NNLR,NSL1also functions in several other NLR-mediated immunity.Collectively,our study unveils the regulatory landscape of SGT1 and reveals a novel SGT1-NSL1 signaling module that orchestrates plant innate immunity.展开更多
Protein–protein interaction(PPI)networks are key to nearly all aspects of cellular activity.Therefore,the identification of PPIs is important for understanding a specific biological process in an organism.Compared wi...Protein–protein interaction(PPI)networks are key to nearly all aspects of cellular activity.Therefore,the identification of PPIs is important for understanding a specific biological process in an organism.Compared with conventional methods for probing PPIs,the recently described proximity labeling(PL)approach combined with mass spectrometry(MS)-based quantitative proteomics hasemerged as apowerful approach for characterizing PPIs.However,the application of PL in planta remains in its infancy.Here,we summarize recent progress in PL and its potential utilization in plant biology.We specifically summarize advances in PL,including the development and comparison of different PL enzymes and the application of PL for deciphering various molecular interactions in different organisms with an emphasis on plant systems.展开更多
文摘Introduction: HIV infection represents a major public health problem for both developing and developed countries as it has grown to global pandemic. Spectrum of clinical presentation of HIV can greatly vary with geopolitical, socioeconomic and cultural environment. Aims: The aim of this study was to estimate the prevalence, socio-demographic conditions, clinical presentations, opportunistic infections and the possible associated risk factors for acquiring HIV infection. Materials and Methods: An observational prospective study was conducted from January 2010 to December 2014 at our centre situated in north India. As per the strategy and policy prescribed by NACO, tests were performed on the serum samples. Results: Out of the total 35369 clients tested for HIV infection, 292 were found to be HIV-1 seropositive. Two HIV-2 cases were found among the studied population. The seroprevalence of HIV was found to be 0.83% (294/35369). Mean age of the study group was 30 ± 5.65 (range: 02 - 80) years. Overall positivity rates among attendees were found to be 0.97% (138/14098), 0.96% (35/3610), 0.82% (7/850), 0.78% (22/2810) and 0.65% (92/14001) in the years 2010, 2011, 2012, 2013 and 2014 respectively. Heterosexual route of transmission was the major route of infection in 78.2 % patients. At the time of presentation, it was observed that Tuberculosis (14.9%) was the most common opportunistic infection. Conclusion: The study shows that there is a decreasing trend in the HIV prevalence in North India. However, the number of HIV cases is still significant and suggests the need for focused prevention efforts in high-risk groups.
文摘In this manuscript, we are reporting structural, bonding, optical, dielectric, and electrical properties of Gd-doped ZnO composite samples (Zn<sub>1</sub><sub>−</sub><sub>x</sub>Gd<sub>x</sub>O, x = 0, 0.05, 0.10) prepared by solid-state reaction method. XRD spectra confirm the wurtzite hexagonal phase with a grain size distribution of 42 - 47 nm. The FT-IR spectra confirm bonding behavior like Zn-O, O=C=O, and O-H stretching modes. FESEM micrographs show that the grains of crystallites possess nearly spherical morphology. Optical absorption spectra confirm that the optical band gap decreases systematically from 3.19 eV to 3.15 eV for x = 0.0 to x = 0.10 samples. For all samples, PL spectra exhibited near-band emission, blue emission, and green emission peaks. The dielectric constant decreases as the applied frequency increases. Hall effect results show that with increasing doping concentration of Gd, mobility and resistivity increase while bulk concentration decreases. Current-Voltage study shows that current increases when temperature is increased. Rare earth-doped ZnO is potential material used for optoelectronics and spintronics device applications. Properties of Gd-doped ZnO are studied by various research groups, but dielectric studies are limitedly reported. Therefore, the present research work aims to study the change of electrical, optical, and dielectric properties of Gd-doped ZnO for device applications.
基金UGCCAS and DST-FIST (PURSE) funded Department of Zoology, Banaras Hindu University,Varanasi for laboratory facilities and the UGC and University’s start-up grants for partial financial assistance
文摘In this manuscript a comparative study on Bi<sub>2</sub>O<sub>3</sub>/polystyrene and Bi<sub>2</sub>O<sub>3</sub>/PVDF composites has been executed via analysis of structural, bonding, surface morphology and dielectric response of composites for energy storage. The composites have been synthesized using solution cast method by varying concentrations of Bi<sub>2</sub>O<sub>3</sub> (BO = 1 - 5 mw%) into polystyrene (PS) and polyvinylidene fluoride (PVDF) polymers respectively. X-ray diffraction confirms the generation of crystallinity, Fourier transform infrared (FT-IR) spectroscopy confirms bonding behavior and scanning electron microscopy (SEM) confirms uniform distribution of Bi<sub>2</sub>O<sub>3</sub> (BO) in PS and PVDF polymers. Impedance spectroscopy has been employed for determination of dielectric response of the fabricated composites. The dielectric constant has been found to be increased as 1.4 times of pristine PS to BO<sub>5%</sub>PS<sub>95%</sub> composites and 1.8 times of pristine PVDF to BO<sub>5%</sub>PVDF<sub>95%</sub> composites respectively. These high dielectric composite electrodes are useful for flexible energy storage devices.
基金supported Department of Zoology,Banaras Hindu University,Varanasi for laboratory facilities and the University’s start-up-grant and UGC-BSR research start-up-grant for financial assistance
文摘<span style="font-family:Verdana;">The new coronavirus called SARS-CoV-2 is a new type of virus named as COVID-19. Although, </span><span style="font-family:Verdana;">it has </span><span style="font-family:Verdana;">few similarities with pandemic flu viruses</span><span style="font-family:Verdana;">,</span><span style="font-family:Verdana;"> the respiratory system and immune system are damaged through the viruses infected the population wh</span><span style="font-family:Verdana;">o</span><span style="font-family:Verdana;"> has weakened immunity. SARS-CoV-2 spread</span><span style="font-family:Verdana;">s</span><span style="font-family:Verdana;"> when people don’t have the sign and symptoms. This virus COVID-19 appears to spread more easily than the flu, and asymptomatic transmission may account for a greater proportion of COVID-19’s spreader over the World. In inundation of the current understanding</span><span style="font-family:Verdana;">,</span><span style="font-family:Verdana;"> the roles of insect vectors are helping in the transmission of viral pathogens as well and the possible roles of some newly joined insects in the mechanical transmission of COVID-19.</span><span style="font-family:Verdana;"> We also specifically provide the prevention and control methods related to contamination, disease burden, risk pattern in the family, near and dear to maintain the precision of social distancing and development of the immune system to fight against SARS-CoV-2.
基金We thank William Terzaghi for reading and commenting on this manuscript. This work was supported by the Chinese National Natural Science Foundation and in part by The National Science Foundation 2010 Program (US) and by the National Institutes of Health grant number GM069418 to SLH.
文摘We used our collection of Arabidopsis transcription factor (TF) ORFeome clones to construct protein microarrays containing as many as 802 TF proteins. These protein microarrays were used for both protein-DNA and proteinprotein interaction analyses. For protein-DNA interaction studies, we examined AP2/ERF family TFs and their cognate cis-elements. By careful comparison of the DNA-binding specificity of 13 TFs on the protein microarray with previous non-microarray data, we showed that protein microarrays provide an efficient and high throughput tool for genome-wide analysis of TF-DNA interactions. This microarray protein-DNA interaction analysis allowed us to derive a comprehensive view of DNA-binding profiles of AP2/ERF family proteins in Arabidopsis. It also revealed four TFs that bound the EE (evening element) and had the expected phased gene expression under clock-regulation, thus providing a basis for further functional analysis of their roles in clock regulation of gene expression. We also developed procedures for detecting protein interactions using this TF protein microarray and discovered four novel partners that interact with HY5, which can be validated by yeast two-hybrid assays. Thus, plant TF protein microarrays offer an attractive high-throughput alternative to traditional techniques for TF functional characterization on a global scale.
文摘Virus-induced gene silencing (VIGS) is a powerful genetic tool for rapid assessment of plant gene functions in the post-genomic era. Here, we successfully implemented a Tobacco Rattle Virus (TRV)-based VlGS system to study functions of genes involved in either primary or secondary cell wall formation in Nicotiana benthamiana plants. A 3-week post- VIGS time frame is sufficient to observe phenotypic alterations in the anatomical structure of stems and chemical composition of the primary and secondary cell walls. We used cell wall glycan-directed monoclonal antibodies to demonstrate that alteration of cell wall polymer synthesis during the secondary growth phase of VIGS plants has profound effects on the extractability of components from woody stem cell walls. Therefore, TRV-based VlGS together with cell wall component profiling methods provide a high-throughput gene discovery platform for studying plant cell wall formation from a bioenergy perspective.
基金the National Natural Science Foundation, China (31630062, 31801705 and 31870143)the National Program on Key Basic Research Project, China (973 Program, 2014CB138400)+4 种基金the Youth Talent Support Program, China and Distinguished Professor of Jiangsu Province, China to X.T.the Natural Science Foundation of Jiangsu Province, China (BK20180532)the Postdoctoral Science Foundation, China (2018M642269) to J.L.the National Science Foundation grants, United States (NSF-IOS-1354434 and NSF-IOS-1339185) to S.P.D.-K. The materials of tomato wild species were obtained from the UC Davis/C.Mmaintained by the Department of Plant Sciences, University of California, Davis, CA.
文摘Plant intracellular nucleotide binding leucine-rich repeat (NLR) immune receptors play critical roles in pathoge n surveillance. Most plant NLRs characterized so far were found to use a single domain/sensor to recognize pathogen effectors. Here we report that the Sw-5b NLR immune receptor uses two distinct domains to detect the viral movement protein NSm encoded by tospovirus. In addition to its leucine-rich repeat (LRR) domain that has been previously reported, 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 specific 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 response. An Sw-5b SD mutant that is disrupted 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 adopts a two-step recog nition mechanism to enhance viral effector perception.
基金supported by US National Science Foundation grants DBI-0723722 and DBI-1042344 to SPDKUC Davis funds to SPDK
文摘Gene co-expression networks provide an important tool for systems biology studies. Using microarray data from the Array Express database, we constructed an Arabidopsis gene co-expression network, termed At GGM2014, based on the graphical Gaussian model, which contains 102,644 co-expression gene pairs among 18,068 genes. The network was grouped into 622 gene co-expression modules. These modules function in diverse house-keeping, cell cycle, development, hormone response, metabolism, and stress response pathways. We developed a tool to facilitate easy visualization of the expression patterns 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-specific expression pattern failed to record modular regulation under various stress conditions. This discrepancy could be best explained by the fact that experiments to study plant stress responses focused mainly on leaves and less on roots, and thus failed to recover specific regulation pattern in other tissues. Overall, the modular structures revealed by our network provide extensive information to generate testable hypotheses about diverse plant signaling pathways. At GGM2014 offers a constructive tool for plant systems biology studies.
基金supported by grants from the National Natural Science Foundation of China(32272491,32061143022,32202250)Work in Barbara Baker's laboratory is supported by USDA ARS CRIS 2030-22000-009-00D and 2030-22000-034-00Dby an Innovative Genomics Institute(2017)Aaward.
文摘Nicotiana tabacum and Nicotiana benthamiana are widely used models in plant biology research.However,genomic studies of these species have lagged.Here we report the chromosome-level reference genome assemblies for N.benthamiana and N.tabacum with an estimated 99.5%and 99.8%completeness,respec-tively.Sensitive transcription start and termination site sequencing methods were developed and used for accurate gene annotation in N.tabacum.Comparative analyses revealed evidence for the parental origins and chromosome structural changes,leading to hybrid genome formation of each species.Interestingly,theantiviral silencinggenesRDR1,RDR6,DCL2,DCL3,andAGO2were lost from one or both subgenomes in N.benthamiana,while both homeologs were kept in N.tabacum.Furthermore,the N.benthamiana genome encodes fewer immune receptors and signaling components than that of N.tabacum.These find-ings uncover possible reasons underlying the hypersusceptible nature of N.benthamiana.We developed the user-friendly Nicomics(http:/lifenglab.hzau.edu.cn/Nicomics/)web server to facilitate better use of Nicotiana genomic resources as well as gene structure and expression analyses.
基金supported by grants from the National Natural Science Foundation of China(32320103003 and 32122070)the“High-end Foreign Experts Recruitment Plan”of Ministry of Science and Technology(G2023108007L)+3 种基金Chinese Universities Scientific Fund(2023TC074)Pinduoduo-China Agricultural University Research Fund(PC2023B02012)China National Postdoctoral Program for Innovative Talents(BX20240421)2115 Talent Development Program of China Agricultural University.
文摘Suppressor of G2 allele of skp1(SGT1)is a highly conserved eukaryotic protein that plays a vital role in growth,development,and immunity in both animals and plants.Although some SGT1 interactors have been identified,the molecular regulatory network of SGT1 remains unclear.SGT1 serves as a co-chaperone to stabilize protein complexes such as the nucleotide-binding leucine-rich repeat(NLR)class of immune receptors,thereby positively regulating plant immunity.SGT1 has also been found to be asso-ciated with the SKP1-Cullin-F-box(SCF)E3 ubiquitin ligase complex.However,whether SGT1 targets im-mune repressors to coordinate plant immune activation remains elusive.In this study,we constructed a toolbox for TurbolD-and split-TurbolD-based proximity labeling(PL)assays in Nicotiana benthamiana and used the PL toolbox to explore the SGT1 interactome during pre-and post-immune activation.The comprehensive SGT1 interactome network we identified highlights a dynamic shift from proteins associ-ated with plant development to those linked with plant immune responses.We found that SGT1 interacts with Necrotic Spotted Lesion1(NSL1),which negatively regulates salicylic acid-mediated defenseby inter-fering with the nucleocytoplasmic trafficking of non-expressor of pathogenesis-related genes 1(NPR1)during N NLR-mediated response to tobacco mosaic virus.SGT1 promotes the SCF-dependent degrada-tion of NSL1 to facilitate immune activation,while salicylate-induced protein kinase-mediated phosphory-lation of SGT1further potentiates this process.Besides NNLR,NSL1also functions in several other NLR-mediated immunity.Collectively,our study unveils the regulatory landscape of SGT1 and reveals a novel SGT1-NSL1 signaling module that orchestrates plant innate immunity.
基金supported by grants from the National Natural Science Foundation of China(31872637 to Y.Z.and 31830106 to D.L.)NSF-IOS-1354434+1 种基金NSF-IOS-1339185NIH-GM132582 to S.P.D.-K.
文摘Protein–protein interaction(PPI)networks are key to nearly all aspects of cellular activity.Therefore,the identification of PPIs is important for understanding a specific biological process in an organism.Compared with conventional methods for probing PPIs,the recently described proximity labeling(PL)approach combined with mass spectrometry(MS)-based quantitative proteomics hasemerged as apowerful approach for characterizing PPIs.However,the application of PL in planta remains in its infancy.Here,we summarize recent progress in PL and its potential utilization in plant biology.We specifically summarize advances in PL,including the development and comparison of different PL enzymes and the application of PL for deciphering various molecular interactions in different organisms with an emphasis on plant systems.