Cotton (Gossypium spp.) is the most important natural textile fiber crop in the world.The ideal plant architecture of cotton is suitable for mechanical harvesting and productivity in modern agricultural production.How...Cotton (Gossypium spp.) is the most important natural textile fiber crop in the world.The ideal plant architecture of cotton is suitable for mechanical harvesting and productivity in modern agricultural production.However,cotton genes regulating plant development and architecture have not been fully identified.We identified a basic helix-loop-helix (b HLH) transcription factor,GhPAS1 (PAGODA1 SUPPRESSOR1) in G.hirsutum (Upland cotton).GhPAS1 was located in the nucleus and showed a strong transcription activation effect.Tissue-specific expression patterns showed that GhPAS1 was highly expressed in floral organs,followed by high expression in early stages of ovule development and rapid fiber elongation.GhPAS1 overexpression in Arabidopsis and BRZ (brassinazole,BR biosynthesis inhibitor) treatment indicated that GhPAS1 positively regulates and responds to the BR (brassinosteroid) signaling pathway and promotes cell elongation.GhPAS1 overexpression in Arabidopsis mediated plant development in addition to increasing plant biomass.Virus-induced gene silencing of GhPAS1 indicated that down-regulation of GhPAS1 inhibited cotton growth and development,as plant height,fruit branch length,and boll size of silenced plants were lower than in control plants.Fiber length and seed yield were also lower in silenced plants.We conclude that GhPAS1,a b HLH transcription factor,regulates plant development and architecture in cotton.These findings may help breeders and researchers develop cotton cultivars with desirable agronomic characteristics.展开更多
Brassinosteroid(BR), a steroid phytohormone, whose signaling transduction pathways include a series of phosphorylation and dephosphorylation events, and GSK3 s are the main negative regulator kinases. BRs have been sh...Brassinosteroid(BR), a steroid phytohormone, whose signaling transduction pathways include a series of phosphorylation and dephosphorylation events, and GSK3 s are the main negative regulator kinases. BRs have been shown to play vital roles in cotton fiber elongation. However, the underlying mechanism is still elusive. In this study, fibers of a BR-defective mutant Pagoda 1(pag1), and its corresponding wild-type(ZM24) were selected for a comparative global phosphoproteome analysis at critical developmental time points: fast-growing stage(10 days after pollination(DPA)) and secondary cell wall synthesis stage(20DPA). Based on the substrate characteristics of GSK3, 900 potential substrates were identified. Their GO and KEGG annotation results suggest that BR functions in fiber development by regulating GhSKs(GSK3s of Gossypium hirsutum L.) involved microtubule cytoskeleton organization, and pathways of glucose, sucrose and lipid metabolism. Further experimental results revealed that among the GhSK members identified, GhSK13 not only plays a role in BR signaling pathway, but also functions in developing fiber by respectively interacting with an AP2-like ethylene-responsive factor GhAP2L, a nuclear transcription factor GhDNFYB19, and a homeodomain zipper member GhHDZ5. Overall, our phosphoproteomic research advances the understanding of fiber development controlled by BR signal pathways especially through GhSKs, and also offers numbers of target proteins for improving cotton fiber quality.展开更多
Accurate knowledge of species distributions and population dynamics is the basis for conservation biology.However, for certain species with unique life histories and very small populations, monitoring species distribu...Accurate knowledge of species distributions and population dynamics is the basis for conservation biology.However, for certain species with unique life histories and very small populations, monitoring species distributions and population dynamics is extremely difficult. Recently, newly developed eDNA technology has been widely used in species monitoring, biodiversity assessments, and biomass assessments. In this research, we studied Fenneropenaeus chinensis in the Bohai Sea. We used a 0.45 μm glass fiber filter combined with a vacuum to filter 2 L seawater samples for eDNA enrichment from 54 stations in June and 60 stations in August. A DNeasy Blood and Tissue kit was used to extract the eDNA. After DNA extraction, the specific primers and probes of the mitochondrial DNA COI gene of F. chinensis were designed. Real-time quantitative PCR was used to qualitatively and quantitatively analyze the eDNA in the Bohai Sea. The temporal and spatial distribution of F. chinensis was detected by the eDNA technique. The relationship between the eDNA copy number and trawl-netted F. chinensis biomass was explored. The applicability and sensitivity of eDNA technology in marine crustacean research were verified. The results showed that the mtDNA COI gene of F. chinensis was successfully amplified in the 54 water samples collected in June, and the detection rate reached 100%. Detections occurred in only 23 of the 60 stations sampled in August. F. chinensis had a detection rate of only 38%. The copy number of eDNA obtained by realtime PCR was fitted to the density of F. chinensis captured by bottom trawling. There was not a significant positive correlation between copy number and biomass. The results obtained through this research will provide a method and theoretical basis for the application of eDNA technology in marine crustacean research.展开更多
Deep neural network(DNN)models have been widely used in e-commerce,games,auto-mobiles,manufacturing,and so on.Improper structure,parameters,activation function,or incorrect loss function of the DNN models may cause de...Deep neural network(DNN)models have been widely used in e-commerce,games,auto-mobiles,manufacturing,and so on.Improper structure,parameters,activation function,or incorrect loss function of the DNN models may cause defects in performance or secu-rity.As a result,there are some researches that focus on repairing DNN such as MODE and Apricot.However,the cost of repairing is high or the repair may lead to overfit-ting.In order to solve this problem,we propose GenMuNN,which is a Mutation-Based Approach to Repair Deep Neural Network Models.First,it analyzes the importance of the weights of the neurons in each layer of the DNN model to the correctness of the final prediction results,and ranks the weights according to the influence on the prediction results of the DNN model.Second,mutation is performed to generate mutants based on the rank of weights,and genetic algorithms are used to select mutants for the next round of mutation until the stop condition is touched.Experiments are carried on a set of DNN models which are trained with the MNIST dataset.The experimental results show that GenMuNN can improve the accuracy of the DNN models.展开更多
Drought stress results in significant losses in agricultural production, and especially that of cotton. The molecular mechanisms that coordinate drought tolerance remain elusive in cotton. Here, we isolated a drought-...Drought stress results in significant losses in agricultural production, and especially that of cotton. The molecular mechanisms that coordinate drought tolerance remain elusive in cotton. Here, we isolated a drought-response gene GhKLCR1, which is a close homolog of AtKLCR1, which encodes a kinesin light chain-related protein enriched with a tetratrico peptide-repeat region.A subcellular localization assay showed that GhKLCR1 is associated with the cell membrane. A tissue-specific expression profile analysis demonstrated that GhKLCR1 is a cotton root-specific gene. Further abiotic and hormonal stress treatments showed that GhKLCR1 was upregulated during abiotic stresses, especially after polyethylene glycol treatments. In addition, the glucuronidase(GUS) staining activity increased as the increment of mannitol concentration in transgenic Arabidopsis plants harboring the fusion construct PGhKLCR1::GUS. The root lengths of 35 S::GhKLCR1 lines were significantly reduced compared with that of wild type. Additionally, seed germination was strongly inhibited in 35 S::GhKLCR1 lines after 300-mmol L^(-1) mannitol treatments as compared with Columbia-0, indicating the sensitivity of GhKLCR1 to drought. These findings provide a better understanding of the structural, physiological and functional mechanisms of kinesin light chain-related proteins.展开更多
基金supported by the Funds for Creative Research Groups of China (31621005)the National Transgenic Major Project of China (2018ZX0800921B)。
文摘Cotton (Gossypium spp.) is the most important natural textile fiber crop in the world.The ideal plant architecture of cotton is suitable for mechanical harvesting and productivity in modern agricultural production.However,cotton genes regulating plant development and architecture have not been fully identified.We identified a basic helix-loop-helix (b HLH) transcription factor,GhPAS1 (PAGODA1 SUPPRESSOR1) in G.hirsutum (Upland cotton).GhPAS1 was located in the nucleus and showed a strong transcription activation effect.Tissue-specific expression patterns showed that GhPAS1 was highly expressed in floral organs,followed by high expression in early stages of ovule development and rapid fiber elongation.GhPAS1 overexpression in Arabidopsis and BRZ (brassinazole,BR biosynthesis inhibitor) treatment indicated that GhPAS1 positively regulates and responds to the BR (brassinosteroid) signaling pathway and promotes cell elongation.GhPAS1 overexpression in Arabidopsis mediated plant development in addition to increasing plant biomass.Virus-induced gene silencing of GhPAS1 indicated that down-regulation of GhPAS1 inhibited cotton growth and development,as plant height,fruit branch length,and boll size of silenced plants were lower than in control plants.Fiber length and seed yield were also lower in silenced plants.We conclude that GhPAS1,a b HLH transcription factor,regulates plant development and architecture in cotton.These findings may help breeders and researchers develop cotton cultivars with desirable agronomic characteristics.
基金supported by the National Natural Science Foundation of China(31971987 and 31601067)。
文摘Brassinosteroid(BR), a steroid phytohormone, whose signaling transduction pathways include a series of phosphorylation and dephosphorylation events, and GSK3 s are the main negative regulator kinases. BRs have been shown to play vital roles in cotton fiber elongation. However, the underlying mechanism is still elusive. In this study, fibers of a BR-defective mutant Pagoda 1(pag1), and its corresponding wild-type(ZM24) were selected for a comparative global phosphoproteome analysis at critical developmental time points: fast-growing stage(10 days after pollination(DPA)) and secondary cell wall synthesis stage(20DPA). Based on the substrate characteristics of GSK3, 900 potential substrates were identified. Their GO and KEGG annotation results suggest that BR functions in fiber development by regulating GhSKs(GSK3s of Gossypium hirsutum L.) involved microtubule cytoskeleton organization, and pathways of glucose, sucrose and lipid metabolism. Further experimental results revealed that among the GhSK members identified, GhSK13 not only plays a role in BR signaling pathway, but also functions in developing fiber by respectively interacting with an AP2-like ethylene-responsive factor GhAP2L, a nuclear transcription factor GhDNFYB19, and a homeodomain zipper member GhHDZ5. Overall, our phosphoproteomic research advances the understanding of fiber development controlled by BR signal pathways especially through GhSKs, and also offers numbers of target proteins for improving cotton fiber quality.
基金This work was supported by the National Key R&D Program of China(2017YFE0104400)the National Basic Research Program of China(2015CB453303)+1 种基金Special Funds for Taishan Scholar Project of Shandong ProvinceSpecial Funds for Taishan Scholar Project of Shandong Provincethe Aoshan Talents Cultivation Program supported by the Pilot National Laboratory for Marine Science and Technology(Qingdao)(2017ASTCP-ES07).
文摘Accurate knowledge of species distributions and population dynamics is the basis for conservation biology.However, for certain species with unique life histories and very small populations, monitoring species distributions and population dynamics is extremely difficult. Recently, newly developed eDNA technology has been widely used in species monitoring, biodiversity assessments, and biomass assessments. In this research, we studied Fenneropenaeus chinensis in the Bohai Sea. We used a 0.45 μm glass fiber filter combined with a vacuum to filter 2 L seawater samples for eDNA enrichment from 54 stations in June and 60 stations in August. A DNeasy Blood and Tissue kit was used to extract the eDNA. After DNA extraction, the specific primers and probes of the mitochondrial DNA COI gene of F. chinensis were designed. Real-time quantitative PCR was used to qualitatively and quantitatively analyze the eDNA in the Bohai Sea. The temporal and spatial distribution of F. chinensis was detected by the eDNA technique. The relationship between the eDNA copy number and trawl-netted F. chinensis biomass was explored. The applicability and sensitivity of eDNA technology in marine crustacean research were verified. The results showed that the mtDNA COI gene of F. chinensis was successfully amplified in the 54 water samples collected in June, and the detection rate reached 100%. Detections occurred in only 23 of the 60 stations sampled in August. F. chinensis had a detection rate of only 38%. The copy number of eDNA obtained by realtime PCR was fitted to the density of F. chinensis captured by bottom trawling. There was not a significant positive correlation between copy number and biomass. The results obtained through this research will provide a method and theoretical basis for the application of eDNA technology in marine crustacean research.
基金This work was supported by the Beijing Information Science and Technology Uni-versity“Qin-Xin Talent”Cultivation Project(No.QXTCP C201906)the Bei-jing Information Science and Technology University Research Level Improvement Project(No.2020KYNH214)the Science and Technology Project of the Bei-jing Municipal Education Commission(No.KM201811232016)。
文摘Deep neural network(DNN)models have been widely used in e-commerce,games,auto-mobiles,manufacturing,and so on.Improper structure,parameters,activation function,or incorrect loss function of the DNN models may cause defects in performance or secu-rity.As a result,there are some researches that focus on repairing DNN such as MODE and Apricot.However,the cost of repairing is high or the repair may lead to overfit-ting.In order to solve this problem,we propose GenMuNN,which is a Mutation-Based Approach to Repair Deep Neural Network Models.First,it analyzes the importance of the weights of the neurons in each layer of the DNN model to the correctness of the final prediction results,and ranks the weights according to the influence on the prediction results of the DNN model.Second,mutation is performed to generate mutants based on the rank of weights,and genetic algorithms are used to select mutants for the next round of mutation until the stop condition is touched.Experiments are carried on a set of DNN models which are trained with the MNIST dataset.The experimental results show that GenMuNN can improve the accuracy of the DNN models.
基金supported by the National Natural Science Foundation of China (31501345)
文摘Drought stress results in significant losses in agricultural production, and especially that of cotton. The molecular mechanisms that coordinate drought tolerance remain elusive in cotton. Here, we isolated a drought-response gene GhKLCR1, which is a close homolog of AtKLCR1, which encodes a kinesin light chain-related protein enriched with a tetratrico peptide-repeat region.A subcellular localization assay showed that GhKLCR1 is associated with the cell membrane. A tissue-specific expression profile analysis demonstrated that GhKLCR1 is a cotton root-specific gene. Further abiotic and hormonal stress treatments showed that GhKLCR1 was upregulated during abiotic stresses, especially after polyethylene glycol treatments. In addition, the glucuronidase(GUS) staining activity increased as the increment of mannitol concentration in transgenic Arabidopsis plants harboring the fusion construct PGhKLCR1::GUS. The root lengths of 35 S::GhKLCR1 lines were significantly reduced compared with that of wild type. Additionally, seed germination was strongly inhibited in 35 S::GhKLCR1 lines after 300-mmol L^(-1) mannitol treatments as compared with Columbia-0, indicating the sensitivity of GhKLCR1 to drought. These findings provide a better understanding of the structural, physiological and functional mechanisms of kinesin light chain-related proteins.
