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The Application of Nicotiana benthamiana as a Transient Expression Host to Clone the Coding Sequences of Plant Genes
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作者 Jianzhong Huang Peng Jia +3 位作者 Xiaoju Zhong Xiuying Guan Hongbin Zhang Honglei Ruan 《American Journal of Molecular Biology》 CAS 2024年第2期54-65,共12页
Coding sequences (CDS) are commonly used for transient gene expression, in yeast two-hybrid screening, to verify protein interactions and in prokaryotic gene expression studies. CDS are most commonly obtained using co... Coding sequences (CDS) are commonly used for transient gene expression, in yeast two-hybrid screening, to verify protein interactions and in prokaryotic gene expression studies. CDS are most commonly obtained using complementary DNA (cDNA) derived from messenger RNA (mRNA) extracted from plant tissues and generated by reverse transcription. However, some CDS are difficult to acquire through this process as they are expressed at extremely low levels or have specific spatial and/or temporal expression patterns in vivo. These challenges require the development of alternative CDS cloning technologies. In this study, we found that the genomic intron-containing gene coding sequences (gDNA) from Arabidopsis thaliana, Oryza sativa, Brassica napus, and Glycine max can be correctly transcribed and spliced into mRNA in Nicotiana benthamiana. In contrast, gDNAs from Triticum aestivum and Sorghum bicolor did not function correctly. In transient expression experiments, the target DNA sequence is driven by a constitutive promoter. Theoretically, a sufficient amount of mRNA can be extracted from the N. benthamiana leaves, making it conducive to the cloning of CDS target genes. Our data demonstrate that N. benthamiana can be used as an effective host for the cloning CDS of plant genes. 展开更多
关键词 Coding sequence Genomic sequence Nicotiana benthamiana Plant Genes
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Pig pangenome graph reveals functional features of non‑reference sequences
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作者 Jian Miao Xingyu Wei +6 位作者 Caiyun Cao Jiabao Sun Yuejin Xu Zhe Zhang Qishan Wang Yuchun Pan Zhen Wang 《Journal of Animal Science and Biotechnology》 SCIE CAS CSCD 2024年第3期956-970,共15页
Background The reliance on a solitary linear reference genome has imposed a significant constraint on our compre-hensive understanding of genetic variation in animals.This constraint is particularly pronounced for non... Background The reliance on a solitary linear reference genome has imposed a significant constraint on our compre-hensive understanding of genetic variation in animals.This constraint is particularly pronounced for non-reference sequences(NRSs),which have not been extensively studied.Results In this study,we constructed a pig pangenome graph using 21 pig assemblies and identified 23,831 NRSs with a total length of 105 Mb.Our findings revealed that NRSs were more prevalent in breeds exhibiting greater genetic divergence from the reference genome.Furthermore,we observed that NRSs were rarely found within coding sequences,while NRS insertions were enriched in immune-related Gene Ontology terms.Notably,our investigation also unveiled a close association between novel genes and the immune capacity of pigs.We observed substantial differences in terms of frequencies of NRSs between Eastern and Western pigs,and the heat-resistant pigs exhibited a substantial number of NRS insertions in an 11.6 Mb interval on chromosome X.Additionally,we discovered a 665 bp insertion in the fourth intron of the TNFRSF19 gene that may be associated with the ability of heat tolerance in South-ern Chinese pigs.Conclusions Our findings demonstrate the potential of a graph genome approach to reveal important functional features of NRSs in pig populations. 展开更多
关键词 Heat tolerance Immune ability Non-reference sequences Pig pangenome
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Phylogenetic, phylogeographic and divergence time analysis of Anopheles subpictus species complex using ITS2 and COI sequences
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作者 Lihini Sandaleka Muthukumarana Methsala Madurangi Wedage +1 位作者 Samanthika Rathnayake Nissanka Kolitha De Silva 《Asian Pacific Journal of Tropical Medicine》 SCIE CAS 2024年第5期214-225,I0004-I0038,共47页
Objective:To address the phylogenetic and phylogeographic relationship between different lineages of Anopheles(An.)subpictus species complex in most parts of the Asian continent by maximum utilization of Internal Tran... Objective:To address the phylogenetic and phylogeographic relationship between different lineages of Anopheles(An.)subpictus species complex in most parts of the Asian continent by maximum utilization of Internal Transcriber Spacer 2(ITS2)and cytochrome C oxidase I(COI)sequences deposited at the GenBank.Methods:Seventy-five ITS2,210 COI and 26 concatenated sequences available in the NCBI database were used.Phylogenetic analysis was performed using Bayesian likelihood trees,whereas median-joining haplotype networks and time-scale divergence trees were generated for phylogeographic analysis.Genetic diversity indices and genetic differentiation were also calculated.Results:Two genetically divergent molecular forms of An.subpictus species complex corresponding to sibling species A and B are established.Species A evolved around 37-82 million years ago in Sri Lanka,India,and the Netherlands,and species B evolved around 22-79 million years ago in Sri Lanka,India,and Myanmar.Vietnam,Thailand,and Cambodia have two molecular forms:one is phylogenetically similar to species B.Other forms differ from species A and B and evolved recently in the above mentioned countries,Indonesia and the Philippines.Genetic subdivision among Sri Lanka,India,and the Netherlands is almost absent.A substantial genetic differentiation was obtained for some populations due to isolation by large geographical distances.Genetic diversity indices reveal the presence of a long-established stable mosquito population,at mutation-drift equilibrium,regardless of population fluctuations.Conclusions:An.subpictus species complex consists of more than two genetically divergent molecular forms.Species A is highly divergent from the rest.Sri Lanka and India contain only species A and B. 展开更多
关键词 Molecular systematics ITS2 COI DNA sequences Phylogeny PHYLOGEOGRAPHY
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On power series statistical convergence and new uniform integrability of double sequences
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作者 Sevda Y■ld■z Kamil Demirci 《Applied Mathematics(A Journal of Chinese Universities)》 SCIE CSCD 2024年第3期519-532,共14页
In the present paper,we mostly focus on P_(p)^(2)-statistical convergence.We will look into the uniform integrability via the power series method and its characterizations for double sequences.Also,the notions of P_(p... In the present paper,we mostly focus on P_(p)^(2)-statistical convergence.We will look into the uniform integrability via the power series method and its characterizations for double sequences.Also,the notions of P_(p)^(2)-statistically Cauchy sequence,P_(p)^(2)-statistical boundedness and core for double sequences will be described in addition to these findings. 展开更多
关键词 power series methods statistical convergence uniform integrability double sequences
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Adaptive Successive POI Recommendation via Trajectory Sequences Processing and Long Short-Term Preference Learning
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作者 Yali Si Feng Li +3 位作者 Shan Zhong Chenghang Huo Jing Chen Jinglian Liu 《Computers, Materials & Continua》 SCIE EI 2024年第10期685-706,共22页
Point-of-interest(POI)recommendations in location-based social networks(LBSNs)have developed rapidly by incorporating feature information and deep learning methods.However,most studies have failed to accurately reflec... Point-of-interest(POI)recommendations in location-based social networks(LBSNs)have developed rapidly by incorporating feature information and deep learning methods.However,most studies have failed to accurately reflect different users’preferences,in particular,the short-term preferences of inactive users.To better learn user preferences,in this study,we propose a long-short-term-preference-based adaptive successive POI recommendation(LSTP-ASR)method by combining trajectory sequence processing,long short-term preference learning,and spatiotemporal context.First,the check-in trajectory sequences are adaptively divided into recent and historical sequences according to a dynamic time window.Subsequently,an adaptive filling strategy is used to expand the recent check-in sequences of users with inactive check-in behavior using those of similar active users.We further propose an adaptive learning model to accurately extract long short-term preferences of users to establish an efficient successive POI recommendation system.A spatiotemporal-context-based recurrent neural network and temporal-context-based long short-term memory network are used to model the users’recent and historical checkin trajectory sequences,respectively.Extensive experiments on the Foursquare and Gowalla datasets reveal that the proposed method outperforms several other baseline methods in terms of three evaluation metrics.More specifically,LSTP-ASR outperforms the previously best baseline method(RTPM)with a 17.15%and 20.62%average improvement on the Foursquare and Gowalla datasets in terms of the Fβmetric,respectively. 展开更多
关键词 Location-based social networks adaptive successive point-of-interest recommendation long short-term preference trajectory sequences
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Secure Transmission of Compressed Medical Image Sequences on Communication Networks Using Motion Vector Watermarking
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作者 Rafi Ullah Mohd Hilmi bin Hasan +1 位作者 Sultan Daud Khan Mussadiq Abdul Rahim 《Computers, Materials & Continua》 SCIE EI 2024年第3期3283-3301,共19页
Medical imaging plays a key role within modern hospital management systems for diagnostic purposes.Compression methodologies are extensively employed to mitigate storage demands and enhance transmission speed,all whil... Medical imaging plays a key role within modern hospital management systems for diagnostic purposes.Compression methodologies are extensively employed to mitigate storage demands and enhance transmission speed,all while upholding image quality.Moreover,an increasing number of hospitals are embracing cloud computing for patient data storage,necessitating meticulous scrutiny of server security and privacy protocols.Nevertheless,considering the widespread availability of multimedia tools,the preservation of digital data integrity surpasses the significance of compression alone.In response to this concern,we propose a secure storage and transmission solution for compressed medical image sequences,such as ultrasound images,utilizing a motion vector watermarking scheme.The watermark is generated employing an error-correcting code known as Bose-Chaudhuri-Hocquenghem(BCH)and is subsequently embedded into the compressed sequence via block-based motion vectors.In the process of watermark embedding,motion vectors are selected based on their magnitude and phase angle.When embedding watermarks,no specific spatial area,such as a region of interest(ROI),is used in the images.The embedding of watermark bits is dependent on motion vectors.Although reversible watermarking allows the restoration of the original image sequences,we use the irreversible watermarking method.The reason for this is that the use of reversible watermarks may impede the claims of ownership and legal rights.The restoration of original data or images may call into question ownership or other legal claims.The peak signal-to-noise ratio(PSNR)and structural similarity index(SSIM)serve as metrics for evaluating the watermarked image quality.Across all images,the PSNR value exceeds 46 dB,and the SSIM value exceeds 0.92.Experimental results substantiate the efficacy of the proposed technique in preserving data integrity. 展开更多
关键词 Block matching algorithm(BMA) compression full-search algorithm motion vectors ultrasound image sequence WATERMARKING
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A study of sequence stratigraphy of the Early Cretaceous coal-bearing series in the southeastern Songliao Basin, NE China 被引量:1
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作者 Kai Shao Longyi Shao +3 位作者 Dongmin Ma Dongdong Wang Shuai Wang Di Gao 《International Journal of Coal Science & Technology》 EI 2020年第2期263-272,共10页
The Early Cretaceous is an important coal accumulation period in China.Abundant coal resources were formed in the southeastern margin of Songliao Basin.Sequence stratigraphy and coal accumulation of the Early Cretaceo... The Early Cretaceous is an important coal accumulation period in China.Abundant coal resources were formed in the southeastern margin of Songliao Basin.Sequence stratigraphy and coal accumulation of the Early Cretaceous in the southeastern margin of Songliao Basin have been studied on the basis of extensive outcrop and borehole data.Based on regional unconformity,basal erosional surfaces of incised valley fills,and abrupt depositional facies-reversal surface,six sequence boundaries have been identified,which subdivide the Early Cretaceous coal-bearing series into 5 third-order sequences.Sequence I corresponds to Huoshiling Formation,sequences II and III correspond to member I and member II of Shahezi Formation.Sequences IV and V correspond to member I and member II of Yingcheng Formation.Sequence I developed at the initial subsiding stage,sequence II and III developed during the stable subsiding stage,while sequence IV and V developed during the basin shrinkage stage.The major coal seams were developed in the sequence II and III,which ensured the relative balance between the increase rate of the accommodation space and the rate of peat accumulation for a longer period,thus forming a thick coal seam. 展开更多
关键词 Songliao Basin sequence stratigraphy Depositional system Coal accumulation
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Graded and Quantitative Technology and Application of Coal-Bearing Reservoir Based on Seismic Reflection Characteristics
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作者 Hao Zhang Huan Wan +7 位作者 Liming Lin Wenjun Xing Tiemei Yang Longgang Zhou Lijun Gao Guangchao Zhi Xin Liu Xiaowen Song 《Journal of Geoscience and Environment Protection》 2024年第6期279-290,共12页
Taiyuan formation is the main exploration strata in Ordos Basin, and coals are widely developed. Due to the interference of strong reflection of coals, we cannot completely identify the effective reservoir information... Taiyuan formation is the main exploration strata in Ordos Basin, and coals are widely developed. Due to the interference of strong reflection of coals, we cannot completely identify the effective reservoir information of coal-bearing reservoir on seismic data. Previous researchers have studied the reservoir by stripping or weakening the strong reflection, but it is difficult to determine the effectiveness of the remaining reflection seismic data. In this paper, through the establishment of 2D forward model of coal-bearing strata, the corresponding geophysical characteristics of different reflection types of coal-bearing strata are analyzed, and then the favorable sedimentary facies zones for reservoir development are predicted. On this basis, combined with seismic properties, the coal-bearing reservoir is quantitatively characterized by seismic inversion. The above research shows that the Taiyuan formation in LS block of Ordos Basin is affected by coals and forms three or two peaks in different locations. The reservoir plane sedimentary facies zone is effectively characterized by seismic reflection structure. Based on the characteristics of sedimentary facies belt and petrophysical analysis, the reservoir is semi quantitatively characterized by attribute analysis and waveform indication, and quantitatively characterized by pre stack geostatistical inversion. Based on the forward analysis of coal measure strata, this technology characterizes the reservoir facies belt through seismic reflection characteristics, and describes coal measure reservoirs step by step. It effectively guides the exploration of LS block in Ordos Basin, and has achieved good practical application effect. 展开更多
关键词 coal-bearing Reservoir Seismic Reflection Characteristics Waveform Indication Inversion Geostatistics Inversion
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Targeted gene sequencing and bioinformatics analysis of patients with gallbladder neuroendocrine carcinoma:A case report
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作者 Yun-Chuan Yang Zhi-Tao Chen +2 位作者 Da-Long Wan Hui Tang Mu-Lin Liu 《World Journal of Gastrointestinal Oncology》 SCIE 2025年第1期239-251,共13页
BACKGROUND Gallbladder neuroendocrine carcinoma(NEC)represents a subtype of gallbladder malignancies characterized by a low incidence,aggressive nature,and poor prognosis.Despite its clinical severity,the genetic alte... BACKGROUND Gallbladder neuroendocrine carcinoma(NEC)represents a subtype of gallbladder malignancies characterized by a low incidence,aggressive nature,and poor prognosis.Despite its clinical severity,the genetic alterations,mechanisms,and signaling pathways underlying gallbladder NEC remain unclear.CASE SUMMARY This case study presents a rare instance of primary gallbladder NEC in a 73-year-old female patient,who underwent a radical cholecystectomy with hepatic hilar lymphadenectomy and resection of liver segments IV-B and V.Targeted gene sequencing and bioinformatics analysis tools,including STRING,GeneMANIA,Metascape,TRRUST,Sangerbox,cBioPortal and GSCA,were used to analyze the biological functions and features of mutated genes in gallbladder NEC.Twelve mutations(APC,ARID2,IFNA6,KEAP1,RB1,SMAD4,TP53,BTK,GATA1,GNAS,and PRDM3)were identified,and the tumor mutation burden was determined to be 9.52 muts/Mb via targeted gene sequencing.A protein-protein interaction network showed significant interactions among the twelve mutated genes.Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses were used to assess mutation functions and pathways.The results revealed 40 tumor-related pathways.A key regulatory factor for gallbladder NEC-related genes was identified,and its biological functions and features were compared with those of gallbladder carcinoma.CONCLUSION Gallbladder NEC requires standardized treatment.Comparisons with other gallbladder carcinomas revealed clinical phenotypes,molecular alterations,functional characteristics,and enriched pathways. 展开更多
关键词 Gallbladder neuroendocrine carcinoma Targeted-gene sequencing Bioinformatics analysis case report IMMUNOCYTOCHEMISTRY Case report
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Spatial transcriptomics combined with single-nucleus RNA sequencing reveals glial cell heterogeneity in the human spinal cord
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作者 Yali Chen Yiyong Wei +3 位作者 Jin Liu Tao Zhu Cheng Zhou Donghang Zhang 《Neural Regeneration Research》 SCIE CAS 2025年第11期3302-3316,共15页
Glial cells play crucial roles in regulating physiological and pathological functions,including sensation,the response to infection and acute injury,and chronic neurodegenerative disorders.Glial cells include astrocyt... Glial cells play crucial roles in regulating physiological and pathological functions,including sensation,the response to infection and acute injury,and chronic neurodegenerative disorders.Glial cells include astrocytes,microglia,and oligodendrocytes in the central nervous system,and satellite glial cells and Schwann cells in the peripheral nervous system.Despite the greater understanding of glial cell types and functional heterogeneity achieved through single-cell and single-nucleus RNA sequencing in animal models,few studies have investigated the transcriptomic profiles of glial cells in the human spinal cord.Here,we used high-throughput single-nucleus RNA sequencing and spatial transcriptomics to map the cellular and molecular heterogeneity of astrocytes,microglia,and oligodendrocytes in the human spinal cord.To explore the conservation and divergence across species,we compared these findings with those from mice.In the human spinal cord,astrocytes,microglia,and oligodendrocytes were each divided into six distinct transcriptomic subclusters.In the mouse spinal cord,astrocytes,microglia,and oligodendrocytes were divided into five,four,and five distinct transcriptomic subclusters,respectively.The comparative results revealed substantial heterogeneity in all glial cell types between humans and mice.Additionally,we detected sex differences in gene expression in human spinal cord glial cells.Specifically,in all astrocyte subtypes,the levels of NEAT1 and CHI3L1 were higher in males than in females,whereas the levels of CST3 were lower in males than in females.In all microglial subtypes,all differentially expressed genes were located on the sex chromosomes.In addition to sex-specific gene differences,the levels of MT-ND4,MT2A,MT-ATP6,MT-CO3,MT-ND2,MT-ND3,and MT-CO_(2) in all spinal cord oligodendrocyte subtypes were higher in females than in males.Collectively,the present dataset extensively characterizes glial cell heterogeneity and offers a valuable resource for exploring the cellular basis of spinal cordrelated illnesses,including chronic pain,amyotrophic lateral sclerosis,and multiple sclerosis. 展开更多
关键词 astrocyte glial cell HUMAN microglia oligodendrocyte sex differentiation single-nucleus RNA sequencing spatial transcriptomics species variation spinal cord
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Coal-bearing strata sequence stratigraphy of Paleogene Meihe Formation,Meihe Basin,NE China
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作者 Yueyue Bai Qingtian Lii +3 位作者 Zhaojun Liu Pingchang Sun Rong Liu Shuqing Yao 《International Journal of Coal Science & Technology》 EI CAS CSCD 2021年第4期547-561,共15页
The Meihe Basin is an important Paleogene coal-bearing basin located in the Dunhua-Mishan Fault Zone,northeastern China.Based on a comprehensive study of well logs,seismic profiles,cores and rock geochemical propertie... The Meihe Basin is an important Paleogene coal-bearing basin located in the Dunhua-Mishan Fault Zone,northeastern China.Based on a comprehensive study of well logs,seismic profiles,cores and rock geochemical properties,the coal distribution,paleoenvironment evolution within a sequence stratigraphic framework and the accumulation model to explain how coal seams developed in small fault basin were discussed in detail.Three-third-order sequences were identified in the Paleogene Meihe Formation of Meihe Basin and the two coal-bearing sequences are the Lower Coalbearing Member of Sequence I and the Upper Coal-bearing Member of Sequence III.All three types of system tracts are developed in both sequences,i.e.,the lowstand systems tract(LST),the transgressive systems tract(TST),and the highstand systems tract(HST).In LST of Sequence I,fan delta plain marsh is the main coal accumulating environment where coal seams are thin,discontinuous and therefore uneconomic for mining,and it is the same with all coal seams developed in Sequence III.While in TST and HST of Sequence I,lake swamp is the main sedimentary environment where coal seams are thick,continuous,widely distributed,and thus economically attractive for mining.In the study area,the nice thick economical coal seams are usually developed in an ideal stable depositional environment where organic matter accommodation space grows at a balanced rate with peat,in other words,free of sediment input or channel migration.The key findings of this study could provide guidance for the exploration of coal seams in the Meihe Basin and other similar basins. 展开更多
关键词 Coal seam sequence stratigraphy Fan delta SWAMP Meihe Basin
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Single-cell sequencing reveals the features of adaptive immune responses in the liver of a mouse model of dengue fever
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作者 Yizhen Yuan Qian Chen +3 位作者 Zhe Li Fangzhou Cai Dan Li Wei Wang 《Animal Models and Experimental Medicine》 2025年第1期30-43,共14页
Background:Dengue fever,an acute insect-borne infectious disease caused by the dengue virus(DENV),poses a great challenge to global public health.Hepatic involve-ment is the most common complication of severe dengue a... Background:Dengue fever,an acute insect-borne infectious disease caused by the dengue virus(DENV),poses a great challenge to global public health.Hepatic involve-ment is the most common complication of severe dengue and is closely related to the occurrence and development of disease.However,the features of adaptive immune responses associated with liver injury in severe dengue are not clear.Methods:We used single-cell sequencing to examine the liver tissues of mild or se-vere dengue mice model to analyze the changes in immune response of T cells in the liver after dengue virus infection,and the immune interaction between macrophages and T cells.Flow cytometry was used to detect T cells and macrophages in mouse liver and blood to verify the single-cell sequencing results.Results:Our result showed CTLs were significantly activated in the severe liver injury group but the immune function-related signal pathway was down-regulated.The rea-son may be that the excessive immune response in the severe group at the late stage of DENV infection induces the polarization of macrophages into M2 type,and the macrophages then inhibit T cell immunity through the TGF-βsignaling pathway.In ad-dition,the increased proportion of Treg cells suggested that Th17/Treg homeostasis was disrupted in the livers of severe liver injury mice.Conclusions:In this study,single-cell sequencing and flow cytometry revealed the characteristic changes of T cell immune response and the role of macrophages in the liver of severe dengue fever mice.Our study provides a better understanding of the pathogenesis of liver injury in dengue fever patients. 展开更多
关键词 adaptive immunity dengue fever model liver injury single-cell sequencing
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Expanding Viral Diversity in Rice Fields by Next-Generation Sequencing
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作者 WANG Haoran CHEN Guoqing FENG Guozhong 《Rice science》 2025年第1期44-51,I0024-I0040,共25页
In rice fields,rice plants usually grow alongside wild weeds and are attacked by various invertebrate species.Viruses are abundant in plants and invertebrates,playing crucial ecological roles in controlling microbial ... In rice fields,rice plants usually grow alongside wild weeds and are attacked by various invertebrate species.Viruses are abundant in plants and invertebrates,playing crucial ecological roles in controlling microbial abundance and maintaining community structures.To date,only 16 rice viruses have been documented in rice-growing regions.These viruses pose serious threats to rice production and have traditionally been identified only from rice plants and insect vectors by isolation techniques.Advances in next-generation sequencing(NGS)have made it feasible to discover viruses on a global scale.Recently,numerous viruses have been identified in plants and invertebrates using NGS technologies.In this review,we discuss viral studies in rice plants,invertebrate species,and weeds in rice fields.Many novel viruses have been discovered in rice ecosystems through NGS technologies,with some also detected using metatranscriptomic and small RNA sequencing.These analyses greatly expand our understanding of viruses in rice fields and provide valuable insights for developing efficient strategies to manage insect pests and virus-mediated rice diseases. 展开更多
关键词 next-generation sequencing virus rice plant invertebrate species wild weed ECOSYSTEM viral transmission
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Improving cutoff frequency estimation via optimized π-pulse sequence
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作者 Wang-Sheng Zheng Chen-Xia Zhang Bei-Li Gong 《Chinese Physics B》 2025年第1期273-278,共6页
The cutoff frequency is one of the crucial parameters that characterize the environment. In this paper, we estimate the cutoff frequency of the Ohmic spectral density by applying the π-pulse sequences(both equidistan... The cutoff frequency is one of the crucial parameters that characterize the environment. In this paper, we estimate the cutoff frequency of the Ohmic spectral density by applying the π-pulse sequences(both equidistant and optimized)to a quantum probe coupled to a bosonic environment. To demonstrate the precision of cutoff frequency estimation, we theoretically derive the quantum Fisher information(QFI) and quantum signal-to-noise ratio(QSNR) across sub-Ohmic,Ohmic, and super-Ohmic environments, and investigate their behaviors through numerical examples. The results indicate that, compared to the equidistant π-pulse sequence, the optimized π-pulse sequence significantly shortens the time to reach maximum QFI while enhancing the precision of cutoff frequency estimation, particularly in deep sub-Ohmic and deep super-Ohmic environments. 展开更多
关键词 environment parameters estimation quantum Fisher information optimized p-pulse sequence
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Managing virus diseases in citrus:Leveraging high-throughput sequencing for versatile applications
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作者 Hongming Chen Zhiyou Xuan +2 位作者 Lu Yang Song Zhang Mengji Cao 《Horticultural Plant Journal》 2025年第1期57-68,共12页
In this review,the advantages and advances in applying high-throughput sequencing(HTS)in the management of viral diseases in citrus,along with some challenges,are discussed to provide perspectives on future prospects.... In this review,the advantages and advances in applying high-throughput sequencing(HTS)in the management of viral diseases in citrus,along with some challenges,are discussed to provide perspectives on future prospects.Since the initial implementation of HTS in citrus virology,a substantial number of citrus viruses have been identified,with a notable increase in the last 7 years.The acquisition of viral genomes and various HTS-based omics analyses serve as crucial pillars for advancing research in the etiology,epidemiology,pathology,evolution,ecology,and biotechnology of citrus viruses.HTS has notably contributed to disease diagnosis,such as the diagnoses of concave gum and impietratura,as well as to the surveillance of new virus risks and the preparation of virus-free materials.However,certain inherent defects in HTS and coupled bioinformatics analysis,such as challenges with sequence assembly and the detection of viral dark matter,require improvement to enhance practical efficiency.In addition,the utilization of HTS for the systematic management of citrus viral diseases remains limited,and drawing insights from other virus-plant pathosystems while integrating emerging compatible techniques and ideas may broaden its specific applications. 展开更多
关键词 Deep sequencing Virus epidemics Functional genomics CRISPR/Cas Virus-host interactions
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Predicting Diabetic Retinopathy Using a Machine Learning Approach Informed by Whole-Exome Sequencing Studies
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作者 Chongyang She Wenying Fan +2 位作者 Yunyun Li Yong Tao Zufei Li 《Biomedical and Environmental Sciences》 2025年第1期67-78,共12页
Objective To establish and validate a novel diabetic retinopathy(DR)risk-prediction model using a whole-exome sequencing(WES)-based machine learning(ML)method.Methods WES was performed to identify potential single nuc... Objective To establish and validate a novel diabetic retinopathy(DR)risk-prediction model using a whole-exome sequencing(WES)-based machine learning(ML)method.Methods WES was performed to identify potential single nucleotide polymorphism(SNP)or mutation sites in a DR pedigree comprising 10 members.A prediction model was established and validated in a cohort of 420 type 2 diabetic patients based on both genetic and demographic features.The contribution of each feature was assessed using Shapley Additive explanation analysis.The efficacies of the models with and without SNP were compared.Results WES revealed that seven SNPs/mutations(rs116911833 in TRIM7,1997T>C in LRBA,1643T>C in PRMT10,rs117858678 in C9orf152,rs201922794 in CLDN25,rs146694895 in SH3GLB2,and rs201407189 in FANCC)were associated with DR.Notably,the model including rs146694895 and rs201407189 achieved better performance in predicting DR(accuracy:80.2%;sensitivity:83.3%;specificity:76.7%;area under the receiver operating characteristic curve[AUC]:80.0%)than the model without these SNPs(accuracy:79.4%;sensitivity:80.3%;specificity:78.3%;AUC:79.3%).Conclusion Novel SNP sites associated with DR were identified in the DR pedigree.Inclusion of rs146694895 and rs201407189 significantly enhanced the performance of the ML-based DR prediction model. 展开更多
关键词 Machine learning Diabetic retinopathy Whole exome sequencing Type 2 diabetes mellitus
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Landscape of four different stages of human gastric cancer revealed by single-cell sequencing
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作者 Xu-Shan Tang Chun-Lei Xu +2 位作者 Na Li Jian-Qing Zhang Yong Tang 《World Journal of Gastrointestinal Oncology》 2025年第2期179-197,共19页
BACKGROUND Gastric cancer(GC)poses a substantial risk to human health due to its high prevalence and mortality rates.Nevertheless,current therapeutic strategies remain insufficient.Single-cell RNA sequencing(scRNA-seq... BACKGROUND Gastric cancer(GC)poses a substantial risk to human health due to its high prevalence and mortality rates.Nevertheless,current therapeutic strategies remain insufficient.Single-cell RNA sequencing(scRNA-seq)offers the potential to provide comprehensive insights into GC pathogenesis.AIM To explore the distribution and dynamic changes of cell populations in the GC tumor microenvironment using scRNA-seq techniques.METHODS Cancerous tissues and paracancerous tissues were obtained from patients diagnosed with GC at various stages(I,II,III,and IV).Single-cell suspensions were prepared and analyzed using scRNA-seq to examine transcriptome profiles and cell-cell interactions.Additionally,quantitative real-time polymerase chain reaction(qRT-PCR)and flow cytometry were applied for measuring the expression of cluster of differentiation(CD)2,CD3D,CD3E,cytokeratin 19,cytokeratin 8,and epithelial cell adhesion molecules.RESULTS Transcriptome data from 73645 single cells across eight tissues of four patients were categorized into 25 distinct cell clusters,representing 10 different cell types.Variations were observed in these cell type distribution.The adjacent epithelial cells in stages II and III exhibited a degenerative trend.Additionally,the quantity of CD4 T cells and CD8 T cells were evidently elevated in cancerous tissues.Interaction analysis displayed a remarkable increase in interaction between B cells and other mast cells in stages II,III,and IV of GC.These findings were further validated through qRT-PCR and flow cytometry,demonstrating elevated T cells and declined epithelial cells within the cancerous tissues.CONCLUSION This study provides a comprehensive analysis of cell dynamics across GC stages,highlighting key interactions within the tumor microenvironment.These findings offer valuable insights for developing novel therapeutic strategies. 展开更多
关键词 Gastric cancer Single-cell RNA sequencing Tumor microenvironment Cancer progression Cell-cell interactions
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Molecular Phylogeny of the Lardizabalaceae Based on TrnL-F Sequences and Combined Chloroplast Data 被引量:5
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作者 王峰 李德铢 杨俊波 《Acta Botanica Sinica》 CSCD 2002年第8期971-977,共7页
The molecular phylogeny of the Lardizabalaceae is reconstructed based on chloroplast trn L_F sequences alone and combined trn L_F and rbc L sequences. The phylogenetic topologies agree well with Qin's and... The molecular phylogeny of the Lardizabalaceae is reconstructed based on chloroplast trn L_F sequences alone and combined trn L_F and rbc L sequences. The phylogenetic topologies agree well with Qin's and Takhtajan's tribal classification in both analyses. Decaisneae and Sinofranchetieae are basal clades in the phylogenetic trees and external to all other taxa in the family. Lardizabaleae consisting of Boquila and Lardizabala are well supported in both trn L_F (100%) analysis and trn L_F and rbc L combined analysis (99%). Tribe Akebieae are strongly supported by a bootstrap value of 100% in both trn L_F analysis and trn L_F and rbc L combined analysis. However, the new genus Archakebia is nested within the genus Akebia in the trn L_F trees. In the combined trees, Archakebia is sister to Akebia with high bootstrap support. The inter_relationships among three closely related genera Parvatia , Holboellia and Stauntonia are still problematic. P. brunoniana ssp. elliptica is sister to H. latifolia in both analyses with low bootstrap support. H. parviflora is nested within the Stauntonia and sister to S. cavalerieana . Therefore, these three genera of tribe Akebieae may not be monophylytic and their generic boundary and delimitation need to be further studied, by exploring more molecular data, together with more morphological characters. 展开更多
关键词 LARDIZABALACEAE molecular phylogeny trn L_F sequences rbc L sequences
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ITS1 SEQUENCES OF NUCLEAR RIBOSOMAL DNA IN WILD RICES AND CULTIVATED RICES OF CHINA AND THEIR PHYLOGENETIC IMPLICATIONS 被引量:22
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作者 周毅 邹喻苹 +2 位作者 洪德元 周骏马 陈受宜 《Acta Botanica Sinica》 CSCD 1996年第10期785-791,共7页
The first internal transcribed spacer(ITS1) of nuclear ribosomal DNA of three wild rice species and two subspecies of cultivated rice, which are distributed in China, was amplified using PCR technique and sequenced wi... The first internal transcribed spacer(ITS1) of nuclear ribosomal DNA of three wild rice species and two subspecies of cultivated rice, which are distributed in China, was amplified using PCR technique and sequenced with automated fluorescent sequencing. The sequences of ITS1 ranged from 193 bp to 218 bp in size and G/C content varied from 69.3% to 72.7%. In pairwise comparisons among the five taxa, sequence site divergence ranged from 1.5% to 10.6%. Phylogenetic analysis of ITS1 sequences using Wagner parsimony generated a single well resolved tree, which revealed that Oryza rufipogon was much more closely related to cultivated rice species than to the other two wild species. Oryza granulata was less closely related to either cultivated rice species or the other two wild species, and might be a unique and isolated taxon in the genus Oryza. The phylogenetic relationships of the three wild rice species and two cultivated rice subspecies inferred from ITS1 sequences is highly concordant with those based on the molecular evidence from isozyme, chloroplast DNA (cpDNA), mitochondrial DNA(mtDNA) and nuclear DNA (nDNA) of the genus Oryza . 展开更多
关键词 Wild rice Cultivated rice ITS1 of rDNA sequence analysis PHYLOGENY
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Characterization of Two Groups of Low_copy and Specific DNA Sequences Isolated from Chromosome 7B of Common Wheat 被引量:2
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作者 刘振兰 董玉柱 刘宝 《Acta Botanica Sinica》 CSCD 2002年第8期946-950,共5页
Recent work revealed that, in the genomes of polyploid wheat, there exists a class of low_copy and chromosome_specific sequences that are labile upon polyploid formation. This class of sequences was proposed to play ... Recent work revealed that, in the genomes of polyploid wheat, there exists a class of low_copy and chromosome_specific sequences that are labile upon polyploid formation. This class of sequences was proposed to play a critical role in the stabilization and establishment of nascent plant polyploids as new species. To further study this issue, five wheat chromosome 7B_specific sequences, isolated from common wheat (Triticum aestivum L.) by chromosome microdissection, were characterized. The sequences were studied by genomic Southern hybridizations on a collection of polyploid wheats and their diploid progenitors. Four sequences hybridized to all polyploid species, but at the diploid level to only species closely related to the B_genome of polyploid wheat. This indicates that these sequences originated with the divergence of the diploid species, and was then vertically transmitted to polyploids. One sequence hybridized to all species at both the diploid and polyploid levels, suggesting its elimination after the polyploid wheat formation. The hybridization of this sequence to two synthetic polyploid wheats indicated that sequence elimination is a rapid event and probably related to methylation status of the sequence. Based on the above results, we suggest that selective changes of low_copy sequences occur rapidly after polyploid formation, which may contribute to the differentiation of chromosomes in newly formed allopolyploid wheats. 展开更多
关键词 polyploid wheat chromosome_specific DNA sequences sequence elimination DNA methylation genome evolution
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