Background Transgenic research in crops involves using genetic engineering techniques to introduce specific genes of interest from other organisms,or even entirely new genes into plant genomes to create crops with des...Background Transgenic research in crops involves using genetic engineering techniques to introduce specific genes of interest from other organisms,or even entirely new genes into plant genomes to create crops with desirable traits that wouldn’t be possible through conventional breeding methods.Transgenic crops have been developed for various traits globally.Whitefly,Bemisia tabaci(Gennadius)is one of the major sucking pests of cotton that cause significant damage to the cotton production.To combat whitefly infestations,researchers have developed four transgenic cotton lines expressing the fern protein.And those transgenic lines need to be evaluated for their performance against the target pest—whitefly.The evaluation was designed as controlled trials in polyhouse or muslin cloth cages under open-choice and no-choice conditions by comparing four transgenic cotton lines(A,B,C,and D)with three control groups,including untransformed cotton plants with a same genetic background of the transgenic line,conventionally bred whitefly-resistant cotton,and whitefly-susceptible cotton.In order to study the generational effect,the evaluation also involved studies on whitefly development in laboratory,muslin cloth cage,and polyhouse conditions.Results Both open-choice and no-choice experiments had shown that all the four transgenic cotton lines(A,B,C,and D)expressing the fern protein reduced adult whitefly numbers significantly compared with the control lines,except for the no-choice conditions in 2021,where the transgenic line C was non-significant different from the resistant control line.Notably,the nymphal population on the resistant control line was relatively low and nonsignificant different from the transgenic line C in 2021;and the transgenic lines A and C in 2022 under open-choice conditions.Under no-choice condition,the nymphal counts in the resistant control line was non-significant different from transgenic lines C and D in 2021;and transgenic line D in 2022.All transgenic lines showed significant decrease in egg hatching in 2021 and nymphal development in 2022,except for the transgenic line C which had no significant different in the nymphal development comparing with non-transgenic control lines in 2022.Adult emergence rates in both years of evaluation showed significant decrease in transgenic lines A and B comparing with the control lines.Additionally,the results showed a significant reduction in cotton leaf curl disease and sooty mold development in all the four transgenic lines compared with susceptible control under open-choice conditions,indicating potential benefits of transgenic lines beyond direct effect on whitefly control.Furthermore,the research explored the generational effects of the fern protein on whitefly which revealed the lowest fecundity in the transgenic line C across F0,F1 and F3 generations,lower egg hatching in F1 and F2 generations in transgenic lines A and B,shorter nymphal duration in F1 and F2 generations in transgenic line B,and the least total adult emergence in the transgenic line C in F0 and F3 generations.Conclusions These findings suggest that the transgenic cotton lines expressing fern protein disrupts whitefly populations and the life cycle to a certain extent.However,results are not consistent over generations and years of study,indicating these transgenic lines were not superior over control lines and need to be improved in future breeding.展开更多
Background Polygalacturonase inhibiting proteins(PGIPs)play a pivotal role in plant defense against plant patho-gens by inhibiting polygalacturonase(PG),an enzyme produced by pathogens to degrade plant cell wall pecti...Background Polygalacturonase inhibiting proteins(PGIPs)play a pivotal role in plant defense against plant patho-gens by inhibiting polygalacturonase(PG),an enzyme produced by pathogens to degrade plant cell wall pectin.PGIPs,also known as leucine-rich repeat pathogenesis-related(PR)proteins,activate the host’s defense response upon interaction with PG,thereby reinforcing the host defense against plant pathogens attacks.In Egyptian or extra-long staple cotton(Gossypium barbadense),the interaction between PGIP and PG is one of the crucial steps in the defense mechanism against major pathogens such as Xanthomonas citri pv.malvacearum and Alternaria mac-rospora,which are responsible for bacterial leaf blight and leaf spot diseases,respectively.Results To unravel the molecular mechanisms underlying these PR proteins,we conducted a comprehensive study involving molecular modeling,protein-protein docking,site-specific double mutation(E169G and F242K),and molec-ular dynamics simulations.Both wild-type and mutated cotton PGIPs were examined in the interaction with the PG enzyme of a bacterial and fungal pathogen.Our findings revealed that changes in conformations of double-mutated residues in the active site of PGIP lead to the inhibition of PG binding.The molecular dynamics simulation studies provide insights into the dynamic behaviour and stability of the PGIP-PG complexes,shedding light on the intricate details of the inhibitory and exhibitory mechanism against the major fungal and bacterial pathogens of G.barbadense,respectively.Conclusions The findings of this study not only enhance our understanding of the molecular interactions between PGs of Xanthomonas citri pv.malvacearum and Alternaria macrospora and PGIP of G.barbadense but also pre-sent a potential strategy for developing the disease-resistant cotton varieties.By variations in the binding affinities of PGs through specific mutations in PGIP,this research offers promising avenues for the development of enhanced resistance to cotton plants against bacterial leaf blight and leaf spot diseases.展开更多
Creutzfeldt-Jakob disease(CJD)is a rare neurodegenerative disorder characterized by abnormalities in the prion protein(PrP),the most common form of human prion disease.Although Genome-Wide Association Studies(GWAS)hav...Creutzfeldt-Jakob disease(CJD)is a rare neurodegenerative disorder characterized by abnormalities in the prion protein(PrP),the most common form of human prion disease.Although Genome-Wide Association Studies(GWAS)have identified numerous risk genes for CJD,the mechanisms underlying these risk loci remain poorly understood.This study aims to elucidate novel genetically prioritized candidate proteins associated with CJD in the human brain through an integrative analytical pipeline.Utilizing datasets from Protein Quantitative Trait Loci(pQTL)(NpQTL1=152,NpQTL2=376),expression QTL(eQTL)(N=452),and the CJD GWAS(NCJD=4110,NControls=13569),we implemented a systematic analytical pipeline.This pipeline included Proteome-Wide Association Study(PWAS),Mendelian randomization(MR),Bayesian colocalization,and Transcriptome-Wide Association Study(TWAS)to identify novel genetically prioritized candidate proteins implicated in CJD pathogenesis within the brain.Through PWAS,we identified that the altered abundance of six brain proteins was significantly associated with CJD.Two genes,STX6 and PDIA4,were established as lead causal genes for CJD,supported by robust evidence(False Discovery Rate<0.05 in MR analysis;PP4/(PP3+PP4)≥0.75 in Bayesian colocalization).Specifically,elevated levels of STX6 and PDIA4 were associated with an increased risk of CJD.Additionally,TWAS demonstrated that STX6 and PDIA4 were associated with CJD at the transcriptional level.展开更多
The current study comprehensively evaluates four different protein extraction methods based on urea,sodium dodecyl sulfate(SDS),anionic surfactants(BT),and total RNA extractor(Trizol),aiming to optimize the sample pre...The current study comprehensively evaluates four different protein extraction methods based on urea,sodium dodecyl sulfate(SDS),anionic surfactants(BT),and total RNA extractor(Trizol),aiming to optimize the sample preparation workflow for mass spectrometry-based proteomics.Using HeLa cells as an example,we found that the method employing the mass spectrometry-compatible surfactant BT reagent significantly reduces the total time consumed for protein extraction and minimizes protein losses during the sample preparation process.Further integrating the four protein extraction methods,we identified over 7000 proteins from HeLa cells without relying on pre-fractionation techniques,and 2990 of them were quantified using label-free quantification.It is worth noting that the BT and SDS methods demonstrate higher efficiency in extracting membrane proteins,while the Urea and Trizol methods are more effective in extracting proteins from nuclear and cytoplasmic fractions.In summary,this study provides a novel solution for deep proteome coverage,particularly in the context of cellular protein extraction,by integrating mass spectrometry-compatible surfactants with traditional extraction methods to effectively enhance protein identification numbers.展开更多
Profiling the protein composition of bacteria is essential for understanding their biology,physiology and interaction with environment.Mass spectrometry has become a pivotal tool for protein analysis,facilitating the ...Profiling the protein composition of bacteria is essential for understanding their biology,physiology and interaction with environment.Mass spectrometry has become a pivotal tool for protein analysis,facilitating the examination of expression levels,molecular masses and structural modifications.In this study,we compared the performance of three widely-used mass spectrometry methods,i.e.,matrix-assisted laser desorption/ionization(MALDI)protein fingerprinting,top-down proteomics and bottom-up proteomics,in the profiling of bacterial protein composition.It was revealed that bottom-up proteomics provided the highest protein coverage and exhibited the greatest protein profile overlap between bacterial species.In contrast,MALDI protein fingerprinting demonstrated superior detection reproducibility and effectiveness in distinguishing between bacterial species.Although top-down proteomics identified fewer proteins than bottom-up approach,it complemented MALDI fingerprinting in the discovery of bacterial protein markers,both favoring abundant,stable,and hydrophilic bacterial ribosomal proteins.This study represents the most systematic and comprehensive comparison of mass spectrometry-based protein profiling methodologies to date.It provides valuable guidelines for the selection of appropriate profiling strategies for specific analytical purposes.This will facilitate studies across various fields,including infection diagnosis,antimicrobial resistance detection and pharmaceutical target discovery.展开更多
The assembly of a protein complex is very important for its biological function,which can be investigated by determining the order of assembly/disassembly of its protein subunits.Although static structures of many pro...The assembly of a protein complex is very important for its biological function,which can be investigated by determining the order of assembly/disassembly of its protein subunits.Although static structures of many protein com-plexes are available in the protein data bank,their assembly/disassembly orders of subunits are largely unknown.In addition to experimental techniques for studying subcomplexes in the assembly/disassembly of a protein complex,computational methods can be used to predict the assembly/disassembly order.Since sampling is a nontrivial issue in simulating the assembly/disassembly process,coarse-grained simulations are more efficient than atomic simulations are.In this work,we developed computational protocols for predicting the assembly/disassembly orders of protein complexes via coarse-grained simulations.The protocols were illustrated via two protein complexes,and the predicted assembly/disassembly orders were consistent with the available experimental data.展开更多
为研究不同比例明胶/马铃薯淀粉对大豆分离蛋白(soybean protein isolate,SPI)凝胶性能及3D打印性能的影响,该文以SPI、明胶和马铃薯淀粉为原料,通过热诱导的方式制备SPI复合凝胶,并对复合凝胶的水分分布、质构、流变特性、结构、微观...为研究不同比例明胶/马铃薯淀粉对大豆分离蛋白(soybean protein isolate,SPI)凝胶性能及3D打印性能的影响,该文以SPI、明胶和马铃薯淀粉为原料,通过热诱导的方式制备SPI复合凝胶,并对复合凝胶的水分分布、质构、流变特性、结构、微观结构以及3D打印特性等进行了表征。结果表明,明胶与马铃薯淀粉比例在1∶8~6∶8(质量比,下同)范围内,随着比例增加,自由水比例降低,不易流动水比例升高,明胶与马铃薯淀粉比例为6∶8时,不易流动水比例最高,占比为2.48%。复配凝胶的硬度、内聚性和咀嚼性随着明胶与马铃薯淀粉比例的增加逐渐降低,6∶8时达到最低,质地最为柔软。随着剪切速率升高,凝胶的黏度均下降,样品的G′和G″随着明胶与马铃薯淀粉比例的增加也均呈升高趋势。傅里叶红外光谱结果显示,添加了明胶和马铃薯淀粉的样品在波长3295.44 cm-1处的—OH振动发生红移,氢键作用增强。随着明胶与马铃薯淀粉比例的增加,复配凝胶孔径逐渐减小,明胶与马铃薯淀粉比例为6∶8时,凝胶孔隙分布呈现出最高的均匀性,打印精度最好,高度打印精确度99.60%,直径打印精确度99.92%,且在1 h内未出现明显塌陷。综上所述,明胶/马铃薯淀粉比例为6∶8时,对大豆分离蛋白凝胶3D打印性能的改善最为显著,这为开发蛋白基3D打印油墨提供理论依据。展开更多
文摘Background Transgenic research in crops involves using genetic engineering techniques to introduce specific genes of interest from other organisms,or even entirely new genes into plant genomes to create crops with desirable traits that wouldn’t be possible through conventional breeding methods.Transgenic crops have been developed for various traits globally.Whitefly,Bemisia tabaci(Gennadius)is one of the major sucking pests of cotton that cause significant damage to the cotton production.To combat whitefly infestations,researchers have developed four transgenic cotton lines expressing the fern protein.And those transgenic lines need to be evaluated for their performance against the target pest—whitefly.The evaluation was designed as controlled trials in polyhouse or muslin cloth cages under open-choice and no-choice conditions by comparing four transgenic cotton lines(A,B,C,and D)with three control groups,including untransformed cotton plants with a same genetic background of the transgenic line,conventionally bred whitefly-resistant cotton,and whitefly-susceptible cotton.In order to study the generational effect,the evaluation also involved studies on whitefly development in laboratory,muslin cloth cage,and polyhouse conditions.Results Both open-choice and no-choice experiments had shown that all the four transgenic cotton lines(A,B,C,and D)expressing the fern protein reduced adult whitefly numbers significantly compared with the control lines,except for the no-choice conditions in 2021,where the transgenic line C was non-significant different from the resistant control line.Notably,the nymphal population on the resistant control line was relatively low and nonsignificant different from the transgenic line C in 2021;and the transgenic lines A and C in 2022 under open-choice conditions.Under no-choice condition,the nymphal counts in the resistant control line was non-significant different from transgenic lines C and D in 2021;and transgenic line D in 2022.All transgenic lines showed significant decrease in egg hatching in 2021 and nymphal development in 2022,except for the transgenic line C which had no significant different in the nymphal development comparing with non-transgenic control lines in 2022.Adult emergence rates in both years of evaluation showed significant decrease in transgenic lines A and B comparing with the control lines.Additionally,the results showed a significant reduction in cotton leaf curl disease and sooty mold development in all the four transgenic lines compared with susceptible control under open-choice conditions,indicating potential benefits of transgenic lines beyond direct effect on whitefly control.Furthermore,the research explored the generational effects of the fern protein on whitefly which revealed the lowest fecundity in the transgenic line C across F0,F1 and F3 generations,lower egg hatching in F1 and F2 generations in transgenic lines A and B,shorter nymphal duration in F1 and F2 generations in transgenic line B,and the least total adult emergence in the transgenic line C in F0 and F3 generations.Conclusions These findings suggest that the transgenic cotton lines expressing fern protein disrupts whitefly populations and the life cycle to a certain extent.However,results are not consistent over generations and years of study,indicating these transgenic lines were not superior over control lines and need to be improved in future breeding.
基金CABin grant(F.no.Agril.Edn.4-1/2013-A&P)Indian Council of Agricul-tural Research,Ministry of Agriculture and Farmers’Welfare,Govt.of India and Department of Biotechnology,Govt.of India for BIC project grant(BT/PR40161/BTIS/137/32/2021)。
文摘Background Polygalacturonase inhibiting proteins(PGIPs)play a pivotal role in plant defense against plant patho-gens by inhibiting polygalacturonase(PG),an enzyme produced by pathogens to degrade plant cell wall pectin.PGIPs,also known as leucine-rich repeat pathogenesis-related(PR)proteins,activate the host’s defense response upon interaction with PG,thereby reinforcing the host defense against plant pathogens attacks.In Egyptian or extra-long staple cotton(Gossypium barbadense),the interaction between PGIP and PG is one of the crucial steps in the defense mechanism against major pathogens such as Xanthomonas citri pv.malvacearum and Alternaria mac-rospora,which are responsible for bacterial leaf blight and leaf spot diseases,respectively.Results To unravel the molecular mechanisms underlying these PR proteins,we conducted a comprehensive study involving molecular modeling,protein-protein docking,site-specific double mutation(E169G and F242K),and molec-ular dynamics simulations.Both wild-type and mutated cotton PGIPs were examined in the interaction with the PG enzyme of a bacterial and fungal pathogen.Our findings revealed that changes in conformations of double-mutated residues in the active site of PGIP lead to the inhibition of PG binding.The molecular dynamics simulation studies provide insights into the dynamic behaviour and stability of the PGIP-PG complexes,shedding light on the intricate details of the inhibitory and exhibitory mechanism against the major fungal and bacterial pathogens of G.barbadense,respectively.Conclusions The findings of this study not only enhance our understanding of the molecular interactions between PGs of Xanthomonas citri pv.malvacearum and Alternaria macrospora and PGIP of G.barbadense but also pre-sent a potential strategy for developing the disease-resistant cotton varieties.By variations in the binding affinities of PGs through specific mutations in PGIP,this research offers promising avenues for the development of enhanced resistance to cotton plants against bacterial leaf blight and leaf spot diseases.
文摘Creutzfeldt-Jakob disease(CJD)is a rare neurodegenerative disorder characterized by abnormalities in the prion protein(PrP),the most common form of human prion disease.Although Genome-Wide Association Studies(GWAS)have identified numerous risk genes for CJD,the mechanisms underlying these risk loci remain poorly understood.This study aims to elucidate novel genetically prioritized candidate proteins associated with CJD in the human brain through an integrative analytical pipeline.Utilizing datasets from Protein Quantitative Trait Loci(pQTL)(NpQTL1=152,NpQTL2=376),expression QTL(eQTL)(N=452),and the CJD GWAS(NCJD=4110,NControls=13569),we implemented a systematic analytical pipeline.This pipeline included Proteome-Wide Association Study(PWAS),Mendelian randomization(MR),Bayesian colocalization,and Transcriptome-Wide Association Study(TWAS)to identify novel genetically prioritized candidate proteins implicated in CJD pathogenesis within the brain.Through PWAS,we identified that the altered abundance of six brain proteins was significantly associated with CJD.Two genes,STX6 and PDIA4,were established as lead causal genes for CJD,supported by robust evidence(False Discovery Rate<0.05 in MR analysis;PP4/(PP3+PP4)≥0.75 in Bayesian colocalization).Specifically,elevated levels of STX6 and PDIA4 were associated with an increased risk of CJD.Additionally,TWAS demonstrated that STX6 and PDIA4 were associated with CJD at the transcriptional level.
文摘The current study comprehensively evaluates four different protein extraction methods based on urea,sodium dodecyl sulfate(SDS),anionic surfactants(BT),and total RNA extractor(Trizol),aiming to optimize the sample preparation workflow for mass spectrometry-based proteomics.Using HeLa cells as an example,we found that the method employing the mass spectrometry-compatible surfactant BT reagent significantly reduces the total time consumed for protein extraction and minimizes protein losses during the sample preparation process.Further integrating the four protein extraction methods,we identified over 7000 proteins from HeLa cells without relying on pre-fractionation techniques,and 2990 of them were quantified using label-free quantification.It is worth noting that the BT and SDS methods demonstrate higher efficiency in extracting membrane proteins,while the Urea and Trizol methods are more effective in extracting proteins from nuclear and cytoplasmic fractions.In summary,this study provides a novel solution for deep proteome coverage,particularly in the context of cellular protein extraction,by integrating mass spectrometry-compatible surfactants with traditional extraction methods to effectively enhance protein identification numbers.
文摘Profiling the protein composition of bacteria is essential for understanding their biology,physiology and interaction with environment.Mass spectrometry has become a pivotal tool for protein analysis,facilitating the examination of expression levels,molecular masses and structural modifications.In this study,we compared the performance of three widely-used mass spectrometry methods,i.e.,matrix-assisted laser desorption/ionization(MALDI)protein fingerprinting,top-down proteomics and bottom-up proteomics,in the profiling of bacterial protein composition.It was revealed that bottom-up proteomics provided the highest protein coverage and exhibited the greatest protein profile overlap between bacterial species.In contrast,MALDI protein fingerprinting demonstrated superior detection reproducibility and effectiveness in distinguishing between bacterial species.Although top-down proteomics identified fewer proteins than bottom-up approach,it complemented MALDI fingerprinting in the discovery of bacterial protein markers,both favoring abundant,stable,and hydrophilic bacterial ribosomal proteins.This study represents the most systematic and comprehensive comparison of mass spectrometry-based protein profiling methodologies to date.It provides valuable guidelines for the selection of appropriate profiling strategies for specific analytical purposes.This will facilitate studies across various fields,including infection diagnosis,antimicrobial resistance detection and pharmaceutical target discovery.
基金This work was supported by the National Key Research and Development Program of China(2021YFA1301504)the Chinese Academy of Sciences Strategic Priority Research Program(XDB37040202)the National Natural Science Foundation of China(91953101).
文摘The assembly of a protein complex is very important for its biological function,which can be investigated by determining the order of assembly/disassembly of its protein subunits.Although static structures of many protein com-plexes are available in the protein data bank,their assembly/disassembly orders of subunits are largely unknown.In addition to experimental techniques for studying subcomplexes in the assembly/disassembly of a protein complex,computational methods can be used to predict the assembly/disassembly order.Since sampling is a nontrivial issue in simulating the assembly/disassembly process,coarse-grained simulations are more efficient than atomic simulations are.In this work,we developed computational protocols for predicting the assembly/disassembly orders of protein complexes via coarse-grained simulations.The protocols were illustrated via two protein complexes,and the predicted assembly/disassembly orders were consistent with the available experimental data.
文摘为研究不同比例明胶/马铃薯淀粉对大豆分离蛋白(soybean protein isolate,SPI)凝胶性能及3D打印性能的影响,该文以SPI、明胶和马铃薯淀粉为原料,通过热诱导的方式制备SPI复合凝胶,并对复合凝胶的水分分布、质构、流变特性、结构、微观结构以及3D打印特性等进行了表征。结果表明,明胶与马铃薯淀粉比例在1∶8~6∶8(质量比,下同)范围内,随着比例增加,自由水比例降低,不易流动水比例升高,明胶与马铃薯淀粉比例为6∶8时,不易流动水比例最高,占比为2.48%。复配凝胶的硬度、内聚性和咀嚼性随着明胶与马铃薯淀粉比例的增加逐渐降低,6∶8时达到最低,质地最为柔软。随着剪切速率升高,凝胶的黏度均下降,样品的G′和G″随着明胶与马铃薯淀粉比例的增加也均呈升高趋势。傅里叶红外光谱结果显示,添加了明胶和马铃薯淀粉的样品在波长3295.44 cm-1处的—OH振动发生红移,氢键作用增强。随着明胶与马铃薯淀粉比例的增加,复配凝胶孔径逐渐减小,明胶与马铃薯淀粉比例为6∶8时,凝胶孔隙分布呈现出最高的均匀性,打印精度最好,高度打印精确度99.60%,直径打印精确度99.92%,且在1 h内未出现明显塌陷。综上所述,明胶/马铃薯淀粉比例为6∶8时,对大豆分离蛋白凝胶3D打印性能的改善最为显著,这为开发蛋白基3D打印油墨提供理论依据。
