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Utilizing resequencing big data to facilitate Brassica vegetable breeding:tracing introgression pedigree and developing highly specific markers for clubroot resistance
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作者 Zhiyong Ren Jinquan Li +5 位作者 Xingyu zhang Xingxu Li junhong zhang Zhibiao Ye Yuyang zhang Qijun Nie 《Horticultural Plant Journal》 SCIE CAS CSCD 2024年第3期771-783,共13页
Clubroot caused by Plasmodiophora brassicae is a devastating disease of Cruciferous crops.Developing cultivars with clubroot resistance(CR)is the most effective control measure.For the two major Brassica vegetable spe... Clubroot caused by Plasmodiophora brassicae is a devastating disease of Cruciferous crops.Developing cultivars with clubroot resistance(CR)is the most effective control measure.For the two major Brassica vegetable species B.rapa and B.oleracea,several commercial cultivars with unclear CR pedigrees have been intensively used as CR donors in breeding.However,the continuous occurrence of CR-breaking makes the CR pedigree underlying these cultivars one of the breeders'most urgent concerns.The complex intraspecific diversity of these two major Brassica vegetables has also limited the applicability of CR markers in different breeding programs.Here we first traced the pedigree underlying two kinds of CR that have been widely applied in breeding by linkage and introgression analyses based on public resequencing data.In B.rapa,a major locus CRzi8 underlying the CR of the commercial CR donor‘DegaoCR117’was identified.CRzi8 was further shown to have been introgressed from turnip(B.rapa ssp.rapifera)and that it carried a potential functional allele of Crr1a.The turnip introgression carried CRb^(c),sharing the same coding sequence with the CRb that was also identified from chromosome C07 of B.oleracea CR cultivars with different morphotypes.Within natural populations,variation analysis of linkage intervals of CRzi8,PbBa8.1,CRb,and CRb^(c)yielded easily resolved InDel markers(>20 bp)for these fundamental CR genes.The specificity of these markers was tested in diverse cultivars panels,and each exhibited high reliability in breeding.Our research demonstrates the value of the practice of applying resequencing big data to solve urgent concerns in breeding programs. 展开更多
关键词 BRASSICA Clubroot resistance RESEQUENCING Introgression analysis Molecular marker
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VG,encoding a thylakoid formation protein,regulates the formation of variegated leaves in tomato
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作者 Jianwen Song Lijie Guo +4 位作者 Lele Shang Wenqian Wang Chuying Yu Zhibiao Ye junhong zhang 《Horticultural Plant Journal》 SCIE CAS CSCD 2023年第1期98-108,共11页
Leaf-color mutations have been studied extensively in plants.However,to better understand the complex mechanisms underlying the formation of leaf color,it is essential to continue discover novel genes involved in the ... Leaf-color mutations have been studied extensively in plants.However,to better understand the complex mechanisms underlying the formation of leaf color,it is essential to continue discover novel genes involved in the process of leaf color development.In this study,we identified a variegated-leaf(vg)mutant in tomato that exhibited defective phenotypes in thylakoids and photosynthesis.To clone the vg locus,an F2population was constructed from the cross between the vg mutant(Solanum lycopersicum)and the wild tomato LA1589(S.pimpinellifolium).Using the map-based cloning approach,the vg locus was mapped on chromosome 7 and narrowed down to a 128 kb region that contained 21 open reading frames(ORFs).The expression levels of ORF9,ORF10,and ORF13 were significantly lower in vg than in the wild-type plants,while the ORF11 transcript level was elevated in vg.We then mutagenized ORF9,ORF10,and ORF13 by the CRISPR/Cas9 system in the wild-type tomato background and found that only the ORF10 mutation reproduced the phenotype of variegated leaves,indicating that ORF10 represents VG and its down-regulated expression was responsible for the variegated leaf phenotype.ORF10 encodes a thylakoid formation protein and its mutant lines showed reduced levels of chlorophyll synthesis and photosynthesis.Taken together,these results suggest that VG is necessary for chloroplast development,chlorophyll synthesis,and photosynthesis in tomato. 展开更多
关键词 CHLOROPLAST Genetic mapping MUTATION TOMATO Variegated leaves
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Biological soil crust distribution in Artemisia ordosica communities along a grazing pressure gradient in Mu Us Sandy Land, Northern China 被引量:11
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作者 junhong zhang Bo WU +4 位作者 YongHua LI WenBin YANG YaKai LEI HaiYan HAN Ji HE 《Journal of Arid Land》 SCIE CSCD 2013年第2期172-179,共8页
This study investigated the distribution pattern of biological soil crust (BSC) in Artemisia ordosica communities in Mu Us Sandy Land. Three experimental sites were selected according to grazing pressure gradient. I... This study investigated the distribution pattern of biological soil crust (BSC) in Artemisia ordosica communities in Mu Us Sandy Land. Three experimental sites were selected according to grazing pressure gradient. In each experimental site, the total vegetation cover, A. ordosica cover, BSC cover, litter-fall cover, BSC degree of fragmentation, BSC thickness and soil properties were investigated in both fixed and semi-fixed sand dunes and simultaneously analyzed in the laboratory. The results showed that at the same grazing pressure, BSC cover and composition were significantly affected by the fixation degree of sand dunes. In addition, BSC cover in the fixed sand dunes was 83.74% on average, whereas it is proportionally dominated by 28% mosses, 21% lichens, and 51% algae. Meanwhile, BSC cover in the semi-fixed sand dunes was 23.54% on average, which is proportionally domi- nated by 6.3% mosses, 2.5% lichens, and 91.2% algae. Fine sand, organic matter, and total nitrogen (N) contents in the fixed sand dunes were all significantly higher than those in the semi-fixed sand dunes. Litter-fall cover de- creased along the grazing pressure gradient, whereas BSC fragmentation degree increased. Fine sand content decreased along with the increase of grazing pressure, whereas medium sand content increased in both fixed and semi-fixed dunes. The organic matter and total N contents in the no grazing site were significantly higher than those in light and normal grazing sites. However, there were no significant differences between the light and normal grazing sites. In addition, there were also no significant differences in BSC thickness between the light and normal grazing sites in the fixed sand dunes. However, a significant decrease was observed in both BSC cover and thick- ness in the normal grazing site. The BSC in the semi-fixed dunes was more sensitive to disturbance. 展开更多
关键词 Artemisia ordosica community biological soil crust grazing pressure soil properties Mu Us Sandy Land
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SlBBX20 interacts with the COP9 signalosome subunit SlCSN5-2 to regulate anthocyanin biosynthesis by activating SlDFR expression in tomato 被引量:4
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作者 Dan Luo Cheng Xiong +9 位作者 Aihua Lin Chunli zhang Wenhui Sun junhong zhang Changxian Yang Yongen Lu Hanxia Li Zhibiao Ye Ping He Taotao Wang 《Horticulture Research》 SCIE 2021年第1期2121-2132,共12页
Anthocyanins play vital roles in plant stress tolerance and growth regulation.Previously,we reported that the photomorphogenesis-related transcription factor SlBBX20 regulates anthocyanin accumulation in tomato.Howeve... Anthocyanins play vital roles in plant stress tolerance and growth regulation.Previously,we reported that the photomorphogenesis-related transcription factor SlBBX20 regulates anthocyanin accumulation in tomato.However,the underlying mechanism remains unclear.Here,we showed that SlBBX20 promotes anthocyanin biosynthesis by binding the promoter of the anthocyanin biosynthesis gene SlDFR,suggesting that SlBBX20 directly activates anthocyanin biosynthesis genes.Furthermore,we found by yeast two-hybrid screening that SlBBX20 interacts with the COP9 signalosome subunit SlCSN5-2,and the interaction was confirmed by bimolecular fluorescence complementation and coimmunoprecipitation assays.SlCSN5 gene silencing led to anthocyanin hyperaccumulation in the transgenic tomato calli and shoots,and SlCSN5-2 overexpression decreased anthocyanin accumulation,suggesting thSlCSN5-2 enhanced the ubiquitination of SlBBX20 and promoted the degradation of SlBBX20 in vivo.Consistently,silencing the SlCSN5-2 homolog in tobacco significantly increased the accumulation of the SlBBX20 protein.Since SlBBX20 is a vital regulator of photomorphogenesis,the SlBBX20-SlCSN5-2 module may represent a novel regulatory pathway in light-induced anthocyanin biosynthesis. 展开更多
关键词 some ANTHOCYANIN VITAL
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S14G-humanin restored cellular homeostasis disturbed by amyloid-beta protein 被引量:1
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作者 Xue Li Wencong Zhao +2 位作者 Hongqi Yang junhong zhang Jianjun Ma 《Neural Regeneration Research》 SCIE CAS CSCD 2013年第27期2573-2580,共8页
Humanin is a potential therapeutic agent for Alzheimer’s disease, and its derivative, S14G-humanin, is 1 000-fold stronger in its neuroprotective effect against Alzheimer’s disease-relevant insults. Alt-hough effect... Humanin is a potential therapeutic agent for Alzheimer’s disease, and its derivative, S14G-humanin, is 1 000-fold stronger in its neuroprotective effect against Alzheimer’s disease-relevant insults. Alt-hough effective, the detailed molecular mechanism through which S14G-humanin exerts its effects remains unclear. Data from this study showed that fibril ar amyloid-beta 40 disturbed cel ular ho-meostasis through the cel membrane, increasing intracel ular calcium, generating reactive oxygen species, and decreasing the mitochondrial membrane potential. S14G-humanin restored these re-sponses. The results suggested that S14G-humanin blocked the effects of amyloid-beta 40 on the neuronal cel membrane, and restored the disturbed cel ular homeostasis, thereby exerting a neuroprotective effect on hippocampal neurons. 展开更多
关键词 neural regeneration Alzheimer's disease amyloid-beta protein wild type humanin S14G-humanin re-active oxygen species mitochondrial membrane potential grants-supported paper NEURODEGENERATION NEUROREGENERATION
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Interactions between ShPP2-1, an F-box family gene, and ACR11A regulate cold toleranee of tomato 被引量:2
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作者 Jianwen Song Lele Shang +5 位作者 Shiwei Chen Yongen Lu Yuyang zhang Bo Ouyang Zhibiao Ye junhong zhang 《Horticulture Research》 SCIE 2021年第1期1986-1996,共11页
There is a critical need to identify germplasm resources and genes that promote cold tolerance of tomato because global tomato production is threatened by cold stress.We found that the expression of an F-box gene fami... There is a critical need to identify germplasm resources and genes that promote cold tolerance of tomato because global tomato production is threatened by cold stress.We found that the expression of an F-box gene family member named ShPP2-1 from Solanum habrochaites is cold inducible and studied its contribution to cold tolerance.Overexpression of ShPP2-1 in cultivated tomato(AC)reduced cold tolerance by intensifying damage to cell membranes.To explore the underlying molecular mechanism,we conducted a yeast two-hybrid library screen and found that a protein containing ACT domain repeats named ACR11A interacts with PP2-1.Overexpression of SIACR11A in AC enhanced the cold tolerance of seedlings and germinating seeds.Cold tolerance decreased in tomato plants that overexpressed both of these genes.Additionally,we performed seed germination experiments in the cold with 177 tomato accessions and identified two alleles of SlACR11A that differ in one single-nucleotide polymorphism.We found that one of these alleles,SlACR11A G,is significantly enriched in cold-tolerant tomato plants.Taken together,our fi ndings indicate that the combination of low expression levels of PP2-1 and high expression levels of ACR11A can promote cold tolerance.These genes may therefore serve as direct targets for both genetic engineering and improvement projects that aim to enhance the cold tolerance of tomato. 展开更多
关键词 CULTIVATED GERMPLASM TOLERANCE
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The loss of function of HEL,which encodes a cellulose synthase interactive protein,causes helical and vine-like growth of tomato 被引量:2
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作者 Qihong Yang Xiaoshuai Wan +5 位作者 Jiaying Wang Yuyang zhang junhong zhang Taotao Wang Changxian Yang Zhibiao Ye 《Horticulture Research》 SCIE 2020年第1期493-502,共10页
Helical growth is an economical way for plant to obtain resources.The classic microtubule–microfibril alignment model of Arabidopsis helical growth involves restriction of the appropriate orientation of cellulose mic... Helical growth is an economical way for plant to obtain resources.The classic microtubule–microfibril alignment model of Arabidopsis helical growth involves restriction of the appropriate orientation of cellulose microfibrils appropriately in the cell walls.However,the molecular mechanism underlying tomato helical growth remains unknown.Here,we identified a spontaneous tomato helical(hel)mutant with right-handed helical cotyledons and petals but left-handed helical stems and true leaves.Genetic analysis revealed that the hel phenotype was controlled by a single recessive gene.Using map-based cloning,we cloned the HEL gene,which encodes a cellulose interacting protein homologous to CSI1 of Arabidopsis.We identified a 27 bp fragment replacement that generated a premature stop codon.Transgenic experiments showed that the helical growth phenotype could be restored by the allele of this gene from wild-type Pyriforme.In contrast,the knockout mutation of HEL in Pyriforme via CRISPR/Cas9 resulted in helical growth.These findings shed light on the molecular control of the helical growth of tomato. 展开更多
关键词 HELICAL CELLULOSE walls
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SIRCM1,which encodes tomato Lutescent1,is required for chlorophyll synthesis and chloroplast development in fruits 被引量:1
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作者 Genzhong Liu Huiyang Yu +8 位作者 Lei Yuan Changxing Li Jie Ye Weifang Chen Ying Wang Pingfei Ge junhong zhang Zhibiao Ye Yuyang zhang 《Horticulture Research》 SCIE 2021年第1期1643-1656,共14页
In plants,chloroplasts are the sites at which photosynthesis occurs,and an increased abundance of chloroplasts increases the nutritional quality of plants and the resultant color of fruits.However,the molecular mechan... In plants,chloroplasts are the sites at which photosynthesis occurs,and an increased abundance of chloroplasts increases the nutritional quality of plants and the resultant color of fruits.However,the molecular mechanisms underlying chlorophyll synthesis and chloroplast development in tomato fruits remain unknown.In this study,we isolated a chlorophyll-de fi cient mutant,reduced chlorophyll mutant 1(rcml),by ethylmethanesulfonate mutagenesis;this mutant produced yellowish fruits with altered chloroplast development.MutMap revealed that Solyc08g005010 is the causal gene underlying the rcm1 mutant phenotype.A single-nucleotide base substitution in the second exon of SIRCM1 results in premature termination of its translated protein.SIRCM1 encodes a chloroplast-targeted metalloendopeptidase that is orthologous to the BCM1 protein of Arabidopsis and the stay-green G protein of soybean(Glycine max L.Merr.).Notably,the yellowish phenotype of the lutescent1 mutant can be restored with the allele of SlRCM1 from wild-type tomato.In contrast,knockout of SlRCM1 by the CRISPR/Cas9 system in Alisa Craig yielded yellowish fruits at the mature green stage,as was the case for lutescent1.Amino acid sequence alignment and functional complementation assays showed that SlRCM1 is indeed Lutescent1.These fi ndings provide new insights into the regulation of chloroplast development in tomato fruits. 展开更多
关键词 synthesis FRUITS ALIGNMENT
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Combustion and Sulfur-fixing Performance of Pulping Black Liquor Coal-water Slurry 被引量:2
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作者 BaoNong Tian LianQing Huang +1 位作者 junhong zhang FuShan Chen 《Paper And Biomaterials》 2017年第2期33-41,共9页
The effects of adding pulping black liquor and other additives to coal-water slurry(CWS) on the sulfur-fixing performance of the resultant mixture(pulping black liquor coal-water slurry) were evaluated. The experiment... The effects of adding pulping black liquor and other additives to coal-water slurry(CWS) on the sulfur-fixing performance of the resultant mixture(pulping black liquor coal-water slurry) were evaluated. The experimental results demonstrated that the ash content of the black liquor coalwater slurry decreased as the addition of pulping black liquor in the mixture increased. Nevertheless, the addition amount should be appropriately selected to ensure that the black liquor coal-water slurry had a moderate calorific value. Addition of black liquor improved the combustion performance of CWS by lowering the ignition point and stabilizing the combustion process; moreover, the sulfur-fixation ratio after combustion increased by 12 to 16 percentage points than that of CWS, and the content of high-melting-point salt in the ash from CWS after adding black liquor was low. The sulfur-fixing ratio of CWS after adding a sulfur-fixing agent was effectively increased by 25 to 30 percenatge points, but with compromise of the fluidity and stability of the CWS; thus, the addition amount of a sulfur-fixing agent should be optimized. 展开更多
关键词 pulping black liquor coal-water slurry combustion performance sulfur-fixing performance
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Identification and evaluation of reference genes for normalization in quantitative real-time PCR analysis in the premodel tree Betula luminifera 被引量:1
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作者 Jun Wu junhong zhang +3 位作者 Ying Pan Huahong Huang Xiongzhen Lou Zaikang Tong 《Journal of Forestry Research》 SCIE CAS CSCD 2017年第2期273-282,共10页
Betula luminifera is a commercial tree species that is emerging as a new model system for tree genomics research. A draft genomic sequence is expected to be publicly available in the near future, which means that an e... Betula luminifera is a commercial tree species that is emerging as a new model system for tree genomics research. A draft genomic sequence is expected to be publicly available in the near future, which means that an explosion of gene expression studies awaits. Thus, the work of selecting appropriate reference genes for q PCR normalization in different tissues or under various experimental conditions is extremely valuable. In this study, ten candidate genes were analyzed in B. luminifera subjected to different abiotic stresses and at various flowering stages.The expression stability of these genes was evaluated using three distinct algorithms implemented using ge Norm,Norm Finder and Best Keeper. The best-ranked reference genes varied across different sample sets, though RPL39,MDH and EF1 a were determined as the most stable by the three programs among all tested samples. RPL39 and EF1 a should be appropriate for normalization in N-starved roots,while the combination of RPL39 and MDH should be appropriate for N-starved stems and EF1 a and MDH should be appropriate in N-starved leaves. In PEG-treated(osmotic) roots, MDH was the most suitable, whereas EF1 a was suitable for PEG-treated stems and leaves. TUA was also stably expressed levels in PEG-treated plants. The combination of RPL39 and TUB should be appropriate for heat-stressed leaves and flowering stage. For reference gene validation, the expression levels of SOD and NFYA-3were investigated. This work will be beneficial to future studies on gene expression under different abiotic stress conditions and flowering status in B. luminifera. 展开更多
关键词 flowering abiotic Betula normalization osmotic varied roots programs valuable stressed
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Cyclin gene SlCycB1 alters plant architecture in association with histone H3.2 in tomato
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作者 Tingyan zhang Yaru Wang +4 位作者 Shoaib Munir Taotao Wang Zhibiao Ye junhong zhang Yuyang zhang 《Horticultural Plant Journal》 SCIE CSCD 2022年第3期341-350,共10页
Cell cycle regulation plays a critical role in plant growth and development.In this study,the role of a tomato cell cycle gene SlCycB1 has been characterized.Expression analysis revealed that SlCycB1 was mostly expres... Cell cycle regulation plays a critical role in plant growth and development.In this study,the role of a tomato cell cycle gene SlCycB1 has been characterized.Expression analysis revealed that SlCycB1 was mostly expressed in stem,root,and leaves,with relative lower expression in flower and fruit.Tomato plants overexpressing SlCycB1 exhibited a reduction in cell number and increased cell size leading to the growth retardation.Furthermore,yeast two-hybrid analysis and bimolecular fluorescence complementation revealed that SlCycB1 interacted with histone H3.2,an essential component of the nucleosome.Histone H3.2 was transcriptionally up-regulated in the SlCycB1 overexpressing tomato lines.Furthermore,the overexpression of histone H3.2 in transgenic plants showed similar phenotypes to SlCycB1 overexpressing lines.Based on these findings,we concluded that SlCycB1 overexpression altered tomato architecture in association with histone H3.2. 展开更多
关键词 TOMATO CYCLIN SlCycB1 HISTONE Growth and development
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Improved deep residual shrinkage network for a multi-cylinder heavy-duty engine fault detection with single channel surface vibration
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作者 Xiaolong Zhu junhong zhang +6 位作者 Xinwei Wang Hui Wang Yedong Song Guobin Pei Xin Gou Linlong Deng Jiewei Lin 《Energy and AI》 EI 2024年第2期277-288,共12页
The health monitoring and fault diagnosis of heavy-duty engines are increasingly important for energy storage ecosystem. During operation, vibration characters corresponding to the specific fault need to be extracted ... The health monitoring and fault diagnosis of heavy-duty engines are increasingly important for energy storage ecosystem. During operation, vibration characters corresponding to the specific fault need to be extracted from the overall system vibration. Faulty characteristics emanating from one single cylinder are also mixed with those from other cylinders. Besides, the change of working condition brings strong nonlinearities in surface vibration. To solve these problems, an improved deep residual shrinkage network (IDRSN) is developed for detecting diverse engine faults at various degrees using single channel surface vibration signal. Within IDRSN, a wide convolution kernel is utilized in first convolution layer to capture the long-term fault-related impacts and eliminate the short-time random impact. The residual network module is adopted to enhance the focus the relevant components of vibration signals. Mini-batch training strategy is used to improve the model stability. Meanwhile, Gradient-weighted class activation map is adopted to assess the consistency between the learned knowledge and the fault-related information. The IDRSN is implemented to diagnosing a diesel engine under various faults, faulty degrees and operating speeds. Comparisons with existing models are analyzed in terms of hyper-parameters, training samples, noise resistance, and visualization. Results demonstrate the proposed IDRSN's superior performance on fault diagnosis accuracy, stability, anti-noise performance, and anti-interference performance. An average accuracy rate of 98.38 % was achieved by the proposed IDRSN, in comparison to 96.64 % and 93.56 % achieved by the DRSN and the wide-kernel deep convolutional neural network respectively. These results highlight the proposed IDRSN's superiority in diagnosing multiple faults under various working conditions, offering a low-cost, highly effective, and applicable approach for complex fault diagnosis tasks. 展开更多
关键词 Improved deep residual shrinkage network Fault diagnosis ENGINE Vibration signal Multiple working conditions Deep learning
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Reinforcement learning based UAV formation control in GPS-denied environment 被引量:1
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作者 Bodi MA Zhenbao LIU +5 位作者 Feihong JIANG Wen ZHAO Qingqing DANG Xiao WANG junhong zhang Lina WANG 《Chinese Journal of Aeronautics》 SCIE EI CAS CSCD 2023年第11期281-296,共16页
Highly accurate positioning is a crucial prerequisite of multi Unmanned Aerial Vehicle close-formation flight for target tracking,formation keeping,and collision avoidance.Although the position of a UAV can be obtaine... Highly accurate positioning is a crucial prerequisite of multi Unmanned Aerial Vehicle close-formation flight for target tracking,formation keeping,and collision avoidance.Although the position of a UAV can be obtained through the Global Positioning System(GPS),it is difficult for a UAV to obtain highly accurate positioning data in a GPS-denied environment(e.g.,a GPS jamming area,suburb,urban canyon,or mountain area);this may cause it to miss a tracking target or collide with another UAV.In particular,UAV close-formation control in GPS-denied environments faces difficulties owing to the low-accuracy position,close distance between vehicles,and nonholonomic dynamics of a UAV.In this paper,on the one hand,we develop an innovative UAV formation localization method to address the formation localization issues in GPS-denied environments;on the other hand,we design a novel reinforcement learning based algorithm to achieve the high-efficiency and robust performance of the controller.First,a novel Lidar-based localization algorithm is developed to measure the localization of each aircraft in the formation flight.In our solution,each UAV is equipped with Lidar as the position measurement sensor instead of the GPS module.The k-means algorithm is implemented to calculate the center point position of UAV.A novel formation position vector matching method is proposed to match center points with UAVs in the formation and estimate their position information.Second,a reinforcement learning based UAV formation control algorithm is developed by selecting the optimal policy to control UAV swarm to start and keep flying in a close formation of a specific geometry.Third,the innovative collision risk evaluation module is proposed to address the collision-free issues in the formation group.Finally,a novel experience replay method is also provided in this paper to enhance the learning efficiency.Experimental results validate the accuracy,effectiveness,and robustness of the proposed scheme. 展开更多
关键词 Close formation control GPS-denied environment Reinforcement learning Unmanned aerial vehicles(UAVs) Intelligent flight control
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Genome-wide Analysis of Plant-specific Dof Transcription Factor Family in Tomato 被引量:29
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作者 Xiaofeng Cai Yuyang zhang +7 位作者 Chanjuan zhang Tingyan zhang Tixu Hu Jie Ye junhong zhang Taotao Wang Hanxia Li Zhibiao Ye 《Journal of Integrative Plant Biology》 SCIE CAS CSCD 2013年第6期552-566,共15页
The Dof (DNA binding with One Finger) family encoding single zinc finger proteins has been known as a family of plant-specific transcription factors. These transcription factors are involved in a variety of function... The Dof (DNA binding with One Finger) family encoding single zinc finger proteins has been known as a family of plant-specific transcription factors. These transcription factors are involved in a variety of functions of importance for different biological processes in plants. In the current study, we identified 34 Dof family genes in tomato (Solanum lycopersicum L.), distributed on 11 chromosomes. A complete overview of SlDof genes in tomato is presented, including the gene structures, chromosome locations, phylogeny, protein motifs and evolution pattern. Phylogenetic analysis of 34 SlDof proteins resulted in four classes constituting six clusters. In addition, a comparative analysis between these genes in tomato, Arabidopsis (Arabidopsis thaliana L.) and rice (Oryza sativa L.) was also performed. The tomato Dof family expansion has been dated to recent duplication events, and segmental duplication is predominant for the SlDof genes. Furthermore, the SlDof genes displayed differential expression either in their transcript abundance or in their expression patterns under normal growth conditions. This is the first step towards genome-wide analyses of the Dof genes in tomato. Our study provides a very useful reference for cloning and functional analysis of the members of this gene family in tomato and other species. 展开更多
关键词 DOF TOMATO DUPLICATION gene expression MOTIF phylogenetic analysis.
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A comprehensive review of integrative pharmacology-based investigation:A paradigm shift in traditional Chinese medicine 被引量:27
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作者 Haiyu Xu Yanqiong zhang +9 位作者 Ping Wang junhong zhang Hong Chen Luoqi zhang Xia Du Chunhui Zhao Dan Wu Feng Liu Hongjun Yang Changxiao Liu 《Acta Pharmaceutica Sinica B》 SCIE CAS CSCD 2021年第6期1379-1399,共21页
Over the past decade,traditional Chinese medicine(TCM) has widely embraced systems biology and its various data integration approaches to promote its modernization.Thus,integrative pharmacology-based traditional Chine... Over the past decade,traditional Chinese medicine(TCM) has widely embraced systems biology and its various data integration approaches to promote its modernization.Thus,integrative pharmacology-based traditional Chinese medicine(TCMIP) was proposed as a paradigm shift in TCM.This review focuses on the presentation of this novel concept and the main research contents,methodologies and applications of TCMIP.First,TCMIP is an interdisciplinary science that can establish qualitative and quantitative pharmacokinetics-pharmacodynamics(PK-PD) correlations through the integration of knowledge from multiple disciplines and techniques and from different PK-PD processes in vivo.Then,the main research contents of TCMIP are introduced as follows:chemical and ADME/PK profiles of TCM formulas;confirming the three forms of active substances and the three action modes;establishing the qualitative PK-PD correlation;and building the quantitative PK-PD correlations,etc.After that,we summarize the existing data resources,computational models and experimental methods of TCMIP and highlight the urgent establishment of mathematical modeling and experimental methods.Finally,we further discuss the applications of TCMIP for the improvement of TCM quality control,clarification of the molecular mechanisms underlying the actions of TCMs and discovery of potential new drugs,especially TCM-related combination drug disco very. 展开更多
关键词 Integrative pharmacology-based traditional Chinese medicine PK-PD correlations Big data Mathematical modeling Multidimensional association network
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Bevacizumab biosimilar LY01008 compared with bevacizumab(Avastin)as first-line treatment for Chinese patients with unresectable,metastatic,or recurrent non-squamous non-small-cell lung cancer:A multicenter,randomized,double-blinded,phase Ⅲ trial 被引量:8
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作者 Yuankai Shi Kaijian Lei +73 位作者 Yuming Jia Bingqiang Ni Zhiyong He Minghong Bi Xicheng Wang Jianhua Shi Ming Zhou Qian Sun Guolei Wang Dongji Chen Yongqian Shu Lianke Liu Zhongliang Guo Yong Liu Junquan Yang Ke Wang Ke Xiao LinWu Tienan Yi Debin Sun Mafei Kang Tianjiang Ma Yimin Mao Jinsheng Shi Tiegang Tang Yan Wang Puyuan Xing Dongqing Lv Wangjun Liao Zhiguo Luo Bin Wang Xiaohong Wu Xiaoli Zhu Shuhua Han Qisen Guo Rongyu Liu Zhiwei Lu Jianyong zhang Jian Fang Changlu Hu Yinghua Ji Guolong Liu Hong Lu Dedong Wu junhong zhang Shuyang Zhu Zheng Liu Wensheng Qiu Feng Ye Yan Yu Yanqiu Zhao Qinhong Zheng Jun Chen Zhanyu Pan Yiping zhang Wenjuan Lian Bo Jiang Bo Qiu Guojun zhang Hua zhang Yanju Chen Yuan Chen Hongbing Duan Manxiang Li Shengming Liu Lijun Ma Hongming Pan Xia Yuan Xueli Yuan Yulong Zheng Emei Gao Li Zhao Shumin Wang Can Wu 《Cancer Communications》 SCIE 2021年第9期889-903,共15页
Background:Previous studies have demonstrated the preclinical pharmacological and toxicological consistency,and clinical pharmacokinetic equivalence of bevacizumab biosimilar LY01008 with reference bevacizumab(Avastin... Background:Previous studies have demonstrated the preclinical pharmacological and toxicological consistency,and clinical pharmacokinetic equivalence of bevacizumab biosimilar LY01008 with reference bevacizumab(Avastin).This randomized controlled trial aimed to compare the efficacy and safety of LY01008 with Avastin in first-line treatment of Chinese patients with advanced or recurrent non-squamous non-small cell lung cancer(NSCLC).Methods:StageⅢB-ⅣNSCLC patients with evaluable lesions,good physical status,and adequate organ functions from 67 centers across China were randomized in a ratio of 1:1 to receive LY01008 or Avastin 15 mg/kg intravenously in combination with paclitaxel/carboplatin(combined treatment)for 4-6 cycles,followed by maintenance monotherapy with LY01008 until disease progression,intolerable toxicity,or death.The primary endpoint was objective response rate(ORR)in accordance with Response Evaluation Criteria in Solid Tumors(RECIST)version 1.1 confirmed by independent radiological review committees(IRRC).Secondary endpoints included disease control rate(DCR),duration of response(DoR),progression-free survival(PFS),overall survival(OS),and safety.This study was registered in Clinical Trials.gov(NCT03533127).Results:Between December 15^(th),2017,and May 15^(th),2019,a total of 649 patients were randomized to the LY01008(n=324)or Avastin(n=325)group.As of September 25th,2019 for primary endpoint analysis,589 patients received ORR evaluation,with a median number of combined treatment cycles of 5(range 1-6)andmedian duration of treatment of 3.0(range 0.0-5.1)months.ORRof responseevaluable patients in the LY01008 and Avastin groups were 48.5% and 53.0%,respectively.The stratified ORR ratio was 0.91(90%CI 0.80-1.04,within the prespecified equivalence margin of 0.75-1.33).Up to May 15^(th),2020,with a median follow-up of 13.6(range 0.8-28.4)months,no notable differences in DCR,median DoR,median PFS,median OS,and 1-year OS rate were observed between the LY01008 and Avastin groups.There were no clinically meaningful differences in safety and immunogenicity across treatment groups.Conclusions:LY01008 demonstrated similarity to Avastin in terms of efficacy and safety in Chinese patients with advanced or recurrent non-squamous NSCLC.LY01008 combined with paclitaxel/carboplatin is expected to become a new treatment option for unresectable,metastatic,LY01008 and Avastin groups.There were no clinically meaningful differences in safety and immunogenicity across treatment groups.Conclusions:LY01008 demonstrated similarity to Avastin in terms of efficacy and safety in Chinese patients with advanced or recurrent non-squamous NSCLC.LY01008 combined with paclitaxel/carboplatin is expected to become a new treatment option for unresectable,metastatic,or recurrent non-squamous NSCLC patients in the first-line setting. 展开更多
关键词 ANTI-ANGIOGENESIS anti-VEGF monoclonal antibody AVASTIN BEVACIZUMAB BIOSIMILAR nonsmall cell lung cancer LY01008 vascular endothelial growth factor
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The chromosome-scale genome of Phoebe bournei reveals contrasting fates of terpene synthase (TPS)-a and TPS-b subfamilies 被引量:7
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作者 Xiao Han junhong zhang +13 位作者 Shuang Han Sun Li Chong Guanliang Meng Minyan Song Yang Wang Shengcai Zhou Chengcheng Liu Luhuan Lou Xiongzhen Lou Longjun Cheng Erpei Lin Huahong Huang Qi Yang Zaikang Tong 《Plant Communications》 SCIE 2022年第6期26-42,共17页
Terpenoids,including aromatic volatile monoterpenoids and sesquiterpenoids,function in defense against pathogens and herbivores.Phoebe trees are remarkable for their scented wood and decay resistance.Unlike other Laur... Terpenoids,including aromatic volatile monoterpenoids and sesquiterpenoids,function in defense against pathogens and herbivores.Phoebe trees are remarkable for their scented wood and decay resistance.Unlike other Lauraceae species investigated to date,Phoebe species predominantly accumulate sesquiterpenoids instead of monoterpenoids.Limited genomic data restrict the elucidation of terpenoid variation and functions.Here,we present a chromosome-scale genome assembly of a Lauraceae tree,Phoebe bournei,and identify 72 full-length terpene synthase(TPS)genes.Genome-level comparison shows pervasive lineage-specific duplication and contraction of TPS subfamilies,which have contributed to the extreme terpenoid variation within Lauraceae species.Although the TPS-a and TPS-b subfamilies were both expanded via tandem duplication in P.bournei,more TPS-a copies were retained and constitutively expressed,whereas more TPS-b copies were lost.The TPS-a genes on chromosome 8 functionally diverged to synthesize eight highly accumulated sesquiterpenes in P.bournei.The essential oil of P.bournei and its main component,b-caryophyllene,exhibited antifungal activities against the three most widespread canker pathogens of trees.The TPS-a and TPS-b subfamilies have experienced contrasting fates over the evolution of P.bournei.The abundant sesquiterpenoids produced by TPS-a proteins contribute to the excellent pathogen resistance of P.bournei trees.Overall,this study sheds light on the evolution and adaptation of terpenoids in Lauraceae and provides valuable resources for boosting plant immunity against pathogens in various trees and crops. 展开更多
关键词 Phoebe bournei genome sequence terpene synthases SESQUITERPENOIDS positive selection pathogen resistance
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Silencing GRAS2 reduces fruit weight in tomato 被引量:2
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作者 Miao Li Xin Wang +3 位作者 Changxing Li Hanxia Li junhong zhang Zhibiao Ye 《Journal of Integrative Plant Biology》 SCIE CAS CSCD 2018年第6期498-513,共16页
GRAS family transcription factors are involved in multiple biological processes in plants. Here, we report that GRAS2 plays a vital role in regulating fruit weight in tomato (Solanum lycopersicum). We establish that... GRAS family transcription factors are involved in multiple biological processes in plants. Here, we report that GRAS2 plays a vital role in regulating fruit weight in tomato (Solanum lycopersicum). We establish that the expression of GRAS2 was elevated in ovaries and maintained at a constant level in fertilized ovules. Reduction of GRAS2 expression in transgenic plants reduced fruit weight through modulating ovary growth and cell size. At the metabolic level, downregulation of GRAS2 decreased activities of the gibberellic acid biosyn- thesis and signal transduction pathways, leading to insufficient levels of active gibberellic acid during the initial ovary development of tomato. Moreover, genotypic diversity of GRAS2 was consistent with the molecular basis of fruit weight evolution, suggesting that GRAS2 contributes to the molecular basis of the evolution of fruit weight in tomato. Collectively, these findings enhance our understanding of GRAS2 functions, in fruit development of tomato, and demonstrate a strong association between the GRAS gene family and fruit development. 展开更多
关键词 Philip W. Becraft Iowa State University USA
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Nanosized zinc oxides-based materials for electrochemical energy storage and conversion: Batteries and supercapacitors 被引量:1
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作者 Tingting Wei Nan zhang +3 位作者 Yurui Ji junhong zhang Yanrong Zhu Tingfeng Yi 《Chinese Chemical Letters》 SCIE CAS CSCD 2022年第2期714-729,共16页
Transition metal oxides(TMO) bring a novel direction for the development of energy store materials due to their excellent stability. They not only have high capacity and good cycle performance, but also are cheap and ... Transition metal oxides(TMO) bring a novel direction for the development of energy store materials due to their excellent stability. They not only have high capacity and good cycle performance, but also are cheap and easily available. Zinc oxide(Zn O) as an important part of TMO have gradually attracted attention in the research of electrochemistry. Zn O, as a metal semiconductor with the advantages of wide band gap, possesses high ion migration rate, good chemical stability, simple preparation and low cost, and is widely used in various fields. However, poor conductivity, low permittivity and quick capacity decays quickly impede the commercial application of these electrodes. In recent years, in order to improve the structural stability, ion diffusion and conductivity of zinc oxides-based anodes, various strategies have been raised, such as structural design, surface modification and composition control. In this paper, the recent advances of zinc oxides-based materials for batteries and hybrid supercapacitors(SCs) were introduced. We comprehensively reviewed the prepared process, reaction mechanism and electrochemical performance and discussed the shortcoming of zinc oxides-based nanomaterials. In particular, several insights toward the future research development, practical applications and commercialization of energy storage devices are also proposed for improving the performance of zinc oxides-based materials. 展开更多
关键词 Zinc oxides-based materials Battery SUPERCAPACITORS Nanomaterials Hierarchical structure
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Spinal Cord Mapping of Respiratory Intercostal Motoneurons in Adult Mice
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作者 junhong zhang Fenlan Luo +8 位作者 Shuancheng Ren Yaling Wang Wu Li Kan Xu Ziyi Zheng Chao He Jianxia Xia Wei Xiong Zhi-An Hu 《Neuroscience Bulletin》 SCIE CAS CSCD 2022年第12期1588-1592,共5页
Dear Editor,Respiration is a vital and continuous physiological process depending on the output from spinal respiratory motoneurons to excite the inspiratory pump muscles[1-3].In mammals,phrenic motoneurons and interc... Dear Editor,Respiration is a vital and continuous physiological process depending on the output from spinal respiratory motoneurons to excite the inspiratory pump muscles[1-3].In mammals,phrenic motoneurons and intercostal motoneurons are the main spinal respiratory motoneurons,which innervate the diaphragm and intercostal muscles(IMs),respectively[4]. 展开更多
关键词 pump MAPPING VITAL
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