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鸢尾属分子系统发育学研究进展 认领
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作者 程琳 奉树成 +3 位作者 肖月娥 于凤扬 朱淑霞 王贤荣 《广西植物》 CAS CSCD 北大核心 2021年第1期31-39,共9页
鸢尾属植物具有重要的观赏价值和经济价值,研究该属属内系统演化关系对该属种质保存、利用和遗传育种具有重要意义。目前,有关鸢尾属各分类单元的系统学关系长期处于争议状态。因此,该文以经典分类系统主要观点为基础,从不同分类单元的... 鸢尾属植物具有重要的观赏价值和经济价值,研究该属属内系统演化关系对该属种质保存、利用和遗传育种具有重要意义。目前,有关鸢尾属各分类单元的系统学关系长期处于争议状态。因此,该文以经典分类系统主要观点为基础,从不同分类单元的系统关系总结了鸢尾属分子系统发育学研究进展。结果表明:现有分子系统发育学研究结果大多支持鸢尾属为并系,且该属存在多个起源,属下的有髯鸢尾亚属、无髯鸢尾亚属均为多系,朱诺鸢尾亚属可分为5个分支,其中朱诺鸢尾组为多系。有髯鸢尾亚属和无髯鸢尾亚属下多个组的分类地位尚未确立。同时,该研究结果显示无髯鸢尾组下的加利福尼亚鸢尾系和金脉鸢尾亚系可能为复合种类群,从而导致近缘种种间形态特征界限模糊。此外,还确立了经典分类系统中部分存疑种的分类地位,如将射干和野鸢尾并入鸢尾属、将蛇头鸢尾和中甸鸢尾分别归入网脉鸢尾亚属和尼泊尔鸢尾亚属等。该文还对鸢尾属起源分布和进化历史等进行了展望,为今后鸢尾属的进一步研究提供了参考。 展开更多
关键词 鸢尾属 分类 分子系统发育 进化 基因组
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Bioinformatic analysis of cytokine expression in the proximal and distal nerve stumps after peripheral nerve injury 认领
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作者 Xiao-Qing Cheng Wen-Jing Xu +7 位作者 Xiao Ding Gong-Hai Han Shuai Wei Ping Liu Hao-Ye Meng Ai-Jia Shang Yu Wang Ai-Yuan Wang 《中国神经再生研究:英文版》 SCIE CAS CSCD 2021年第5期878-884,共7页
In our previous study,we investigated the dynamic expression of cytokines in the distal nerve stumps after peripheral nerve injury using microarray analysis,which can characterize the dynamic expression of proteins.In... In our previous study,we investigated the dynamic expression of cytokines in the distal nerve stumps after peripheral nerve injury using microarray analysis,which can characterize the dynamic expression of proteins.In the present study,we used a rat model of right sciatic nerve transection to examine changes in the expression of cytokines at 1,7,14 and 28 days after injury using protein microarray analysis.Interleukins were increased in the distal nerve stumps at 1–14 days post nerve transection.However,growth factors and growth factor-related proteins were mainly upregulated in the proximal nerve stumps.The P-values of the inflammatory response,apoptotic response and cell-cell adhesion in the distal stumps were higher than those in the proximal nerve stumps,but the opposite was observed for angiogenesis.The number of cytokines related to axons in the distal stumps was greater than that in the proximal stumps,while the percentage of cytokines related to axons in the distal stumps was lower than that in the proximal nerve stumps.Visualization of the results revealed the specific expression patterns and differences in cytokines in and between the proximal and distal nerve stumps.Our findings offer potential therapeutic targets and should help advance the development of clinical treatments for peripheral nerve injury.Approval for animal use in this study was obtained from the Animal Ethics Committee of the Chinese PLA General Hospital on September 7,2016(approval No.2016-x9-07). 展开更多
关键词 cytokine distal stumps Gene Ontology Kyoto Encyclopedia of Genes and Genomes Pathway microarray microenvironment peripheral nerve injury proximal stumps
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Unraveling the puzzle of the origin and evolution of cotton A-genome 认领
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作者 MA Zhiying 《棉花研究(英文)》 2020年第2期146-148,共3页
Gossypium hirsutum,the most widely planted cotton species,its evolution has long been an unsolved puzzle because of its hybrid origin from D-genome and A-genome species.To better understand the genetic component of co... Gossypium hirsutum,the most widely planted cotton species,its evolution has long been an unsolved puzzle because of its hybrid origin from D-genome and A-genome species.To better understand the genetic component of cotton,Huang et al.recently sequenced and assembled the first A1-genome G.herbaceum,and updated the A2-genome G.arboreum and(AD)1-genome G.hirsutum.On the basis of the three reference genomes,they resolved existing controversial concepts and provided novel evolutionary insights surrounding the A-genome. 展开更多
关键词 Cotton genomes Gossypium herbaceum Origins EVOLUTION Structural variations
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真菌基因组de novo测序组装的方法与实践 认领
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作者 李丽翠 曲积彬 +2 位作者 曾昭清 Tom Hsiang 余知和 《基因组学与应用生物学》 CAS CSCD 北大核心 2020年第1期173-180,共8页
真菌基因组较其他真核生物基因组结构简单,长度短,易于测序、组装与注释,因此真菌基因组是研究真核生物基因组的模型。为研究真菌基因组组装策略,本研究基于Illumina HiSeq测序平台对烟曲霉菌株An16007基因组测序,分别使用5种de novo组... 真菌基因组较其他真核生物基因组结构简单,长度短,易于测序、组装与注释,因此真菌基因组是研究真核生物基因组的模型。为研究真菌基因组组装策略,本研究基于Illumina HiSeq测序平台对烟曲霉菌株An16007基因组测序,分别使用5种de novo组装软件ABySS、SOAP-denovo、Velvet、MaSuRCA和IDBA-UD组装基因组,然后通过Augustus软件进行基因预测,BUSCO软件评估组装结果。研究发现,5种组装软件对基因组组装结果不同,ABySS组装的基因组较其他4种组装软件具有更高的完整性和准确性,且预测的基因数量较高,因此,ABySS更适合本研究基因组的组装。本研究提供了真菌de novo测序、组装及组装质量评估的技术流程,为基因组<100 Mb的真菌或其他生物基因组的研究提供参考。 展开更多
关键词 基因组 N50 K-mer 生物信息学软件 UBUNTU LINUX 组装
Protein microarray analysis of cytokine expression changes in distal stumps after sciatic nerve transection 认领 被引量:1
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作者 Xiao-Qing Cheng Xue-Zhen Liang +9 位作者 Shuai Wei Xiao Ding Gong-Hai Han Ping Liu Xun Sun Qi Quan He Tang Qing Zhao Ai-Jia Shang Jiang Peng 《中国神经再生研究:英文版》 SCIE CAS CSCD 2020年第3期503-511,共9页
A large number of chemokines,cytokines,other trophic factors and the extracellular matrix molecules form a favorable microenvironment for peripheral nerve regeneration.This microenvironment is one of the major factors... A large number of chemokines,cytokines,other trophic factors and the extracellular matrix molecules form a favorable microenvironment for peripheral nerve regeneration.This microenvironment is one of the major factors for regenerative success.Therefore,it is important to investigate the key molecules and regulators affecting nerve regeneration after peripheral nerve injury.However,the identities of specific cytokines at various time points after sciatic nerve injury have not been determined.The study was performed by transecting the sciatic nerve to establish a model of peripheral nerve injury and to analyze,by protein microarray,the expression of different cytokines in the distal nerve after injury.Results showed a large number of cytokines were up-regulated at different time points post injury and several cytokines,e.g.,ciliary neurotrophic factor,were downregulated.The construction of a protein-protein interaction network was used to screen how the proteins interacted with differentially expressed cytokines.Kyoto Encyclopedia of Genes and Genomes pathway and Gene ontology analyses indicated that the differentially expressed cytokines were significantly associated with chemokine signaling pathways,Janus kinase/signal transducers and activators of transcription,phosphoinositide 3-kinase/protein kinase B,and notch signaling pathway.The cytokines involved in inflammation,immune response and cell chemotaxis were up-regulated initially and the cytokines involved in neuronal apoptotic processes,cell-cell adhesion,and cell proliferation were up-regulated at 28 days after injury.Western blot analysis showed that the expression and changes of hepatocyte growth factor,glial cell line-derived neurotrophic factor and ciliary neurotrophic factor were consistent with the results of protein microarray analysis.The results provide a comprehensive understanding of changes in cytokine expression and changes in these cytokines and classical signaling pathways and biological functions during Wallerian degeneration,as well as a bas 展开更多
关键词 cytokines DISTAL stump gene ontology KYOTO ENCYCLOPEDIA of Genes and Genomes pathway peripheral nerve injury protein microarray PROTEIN-PROTEIN interaction network Wallerian degeneration
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Different protein expression patterns in rat spinal nerves during wallerian degeneration assessed using isobaric tags for relative and absolute quantitation proteomics profiling 认领 被引量:2
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作者 Shuai Wei Xue-Zhen Liang +12 位作者 Qian Hu Wei-Shan Wang Wen-Jing Xu Xiao-Qing Cheng Jiang Peng Quan-Yi Guo Shu-Yun Liu Wen Jiang Xiao Ding Gong-Hai Han Ping Liu Chen-Hui Shi Yu Wang 《中国神经再生研究:英文版》 SCIE CAS CSCD 2020年第2期315-323,共9页
Sensory and motor nerve fibers of peripheral nerves have different anatomies and regeneration functions after injury. To gain a clear understanding of the biological processes behind these differences, we used a label... Sensory and motor nerve fibers of peripheral nerves have different anatomies and regeneration functions after injury. To gain a clear understanding of the biological processes behind these differences, we used a labeling technique termed isobaric tags for relative and absolute quantitation to investigate the protein profiles of spinal nerve tissues from Sprague-Dawley rats. In response to Wallerian degeneration, a total of 626 proteins were screened in sensory nerves, of which 368 were upregulated and 258 were downregulated. In addition, 637 proteins were screened in motor nerves, of which 372 were upregulated and 265 were downregulated. All identified proteins were analyzed using the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis of bioinformatics, and the presence of several key proteins closely related to Wallerian degeneration were tested and verified using quantitative real-time polymerase chain reaction analyses. The differentially expressed proteins only identified in the sensory nerves were mainly relevant to various biological processes that included cell-cell adhesion, carbohydrate metabolic processes and cell adhesion, whereas differentially expressed proteins only identified in the motor nerves were mainly relevant to biological processes associated with the glycolytic process, cell redox homeostasis, and protein folding. In the aspect of the cellular component, the differentially expressed proteins in the sensory and motor nerves were commonly related to extracellular exosomes, the myelin sheath, and focal adhesion. According to the Kyoto Encyclopedia of Genes and Genomes, the differentially expressed proteins identified are primarily related to various types of metabolic pathways. In conclusion, the present study screened differentially expressed proteins to reveal more about the differences and similarities between sensory and motor nerves during Wallerian degeneration. The present findings could provide a reference point for a future investigation into the differences between s 展开更多
关键词 gene ontology Kyoto ENCYCLOPEDIA of Genes and Genomes ISOBARIC tags for RELATIVE and absolute quantitation motor NERVE PROTEOMICS sensory NERVE spinal NERVE Wallerian degeneration
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The Battle to Sequence the Bread Wheat Genome:A Tale of the Three Kingdoms 认领
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作者 Jiantao Guan Diego F.Garcia +3 位作者 Yun Zhou Rudi Appels Aili Li Long Mao 《基因组蛋白质组与生物信息学报:英文版》 SCIE CAS CSCD 2020年第3期221-229,共9页
In the year 2018,the world witnessed the finale of the race to sequence the genome of the world’s most widely grown crop,the common wheat.Wheat has been known to bear a notoriously large and complicated genome of a p... In the year 2018,the world witnessed the finale of the race to sequence the genome of the world’s most widely grown crop,the common wheat.Wheat has been known to bear a notoriously large and complicated genome of a polyploidy nature.A decade competition to sequence the wheat genome initiated with a single consortium of multiple countries,taking a conventional strategy similar to that for sequencing Arabidopsis and rice,became ferocious over time as both sequencing technologies and genome assembling methodologies advanced.At different stages,multiple versions of genome sequences of the same variety(e.g.,Chinese Spring)were produced by several groups with their special strategies.Finally,16 years after the rice genome was finished and 9 years after that of maize,the wheat research community now possesses its own reference genome.Armed with these genomics tools,wheat will reestablish itself as a model for polyploid plants in studying the mechanisms of polyploidy evolution,domestication,genetic and epigenetic regulation of homoeolog expression,as well as defining its genetic diversity and breeding on the genome level.The enhanced resolution of the wheat genome should also help accelerate development of wheat cultivars that are more tolerant to biotic and/or abiotic stresses with better quality and higher yield. 展开更多
关键词 Common wheat Homoeologous genomes POLYPLOID SEQUENCING Triticum aestivum
Bioinformatic identification of key candidate genes and pathways in axon regeneration after spinal cord injury in zebrafish 认领
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作者 Jia-He Li Zhong-Ju Shi +6 位作者 Yan Li Bin Pan Shi-Yang Yuan Lin-Lin Shi Yan Hao Fu-Jiang Cao Shi-Qing Feng 《中国神经再生研究:英文版》 SCIE CAS CSCD 2020年第1期103-111,共9页
Zebrafish and human genomes are highly homologous;however,despite this genomic similarity,adult zebrafish can achieve neuronal proliferation,regeneration and functional restoration within 6–8 weeks after spinal cord ... Zebrafish and human genomes are highly homologous;however,despite this genomic similarity,adult zebrafish can achieve neuronal proliferation,regeneration and functional restoration within 6–8 weeks after spinal cord injury,whereas humans cannot.To analyze differentially expressed zebrafish genes between axon-regenerated neurons and axon-non-regenerated neurons after spinal cord injury,and to explore the key genes and pathways of axonal regeneration after spinal cord injury,microarray GSE56842 was analyzed using the online tool,GEO2R,in the Gene Expression Omnibus database.Gene ontology and protein-protein interaction networks were used to analyze the identified differentially expressed genes.Finally,we screened for genes and pathways that may play a role in spinal cord injury repair in zebrafish and mammals.A total of 636 differentially expressed genes were obtained,including 255 up-regulated and 381 down-regulated differentially expressed genes in axon-regenerated neurons.Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment results were also obtained.A protein-protein interaction network contained 480 node genes and 1976 node connections.We also obtained the 10 hub genes with the highest correlation and the two modules with the highest score.The results showed that spectrin may promote axonal regeneration after spinal cord injury in zebrafish.Transforming growth factor beta signaling may inhibit repair after spinal cord injury in zebrafish.Focal adhesion or tight junctions may play an important role in the migration and proliferation of some cells,such as Schwann cells or neural progenitor cells,after spinal cord injury in zebrafish.Bioinformatic analysis identified key candidate genes and pathways in axonal regeneration after spinal cord injury in zebrafish,providing targets for treatment of spinal cord injury in mammals. 展开更多
关键词 axonal REGENERATION differentially expressed GENES focal ADHESIONS Gene Ontology Kyoto Encyclopedia of GENES and Genomes neural REGENERATION protein-protein interaction network SIGNALING PATHWAY SPECTRIN tight junctions transforming growth factor beta Wnt SIGNALING PATHWAY
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Genome of a thermophilic bacterium Geobacillus sp. TFV3 from Deception Island, Antarctica 认领
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作者 Xin Jie CHING Chui Peng TEOH +5 位作者 Dexter J.H.LEE Marcelo GONZáLEZ-ARAVENA Nazalan NAJIMUDIN Yoke Kqueen CHEAH Paris LAVIN Clemente Michael Vui Ling WONG 《极地科学进展:英文版》 CSCD 2020年第2期146-152,共7页
Thermophilic microorganisms have always been an important part of the ecosystem,particularly in a hot environment,as they play a key role in nutrient recycling at high temperatures where most microorganisms cannot cop... Thermophilic microorganisms have always been an important part of the ecosystem,particularly in a hot environment,as they play a key role in nutrient recycling at high temperatures where most microorganisms cannot cope.While most of the thermophiles are archaea,thermophiles can also be found among some species of bacteria.These bacteria are very useful in the fundamental study of heat adaptation,and they are also important as potential sources of thermostable enzymes and metabolites.Recently,we have isolated a Gram-positive thermophilic bacterium,Geobacillus sp.TFV3 from a volcanic soil sample from Deception Island,Antarctica.This project was undertaken to analyze the genes of this thermophilic Antarctic bacterium and to determine the presence of thermal-stress adaptation proteins in its genome.The genome of Geobacillus sp.TFV3 was first purified,sequenced,assembled,and annotated.The complete genome was found to harbor genes encoding for useful thermal-stress adaptation proteins.The majority of these proteins were categorized under the family of molecular chaperone and heat shock protein.This genomic information could eventually provide insights on how the bacterium adapts itself towards high growth temperatures. 展开更多
关键词 temperature 16SrDNA GENOMES GEOBACILLUS Deception Island
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Identification of microRNA-mRNA regulatory networks and pathways related to retinoblastoma across human and mouse 认领
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作者 Rui Tian He Zou +3 位作者 Lu-Fei Wang Mei-Jiao Song Lu Liu Hui Zhang 《国际眼科杂志:英文版》 SCIE CAS 2020年第4期535-544,共10页
AIM: To explore the m RNA and pathways related to retinoblastoma(RB) genesis and development.METHODS: Microarray datasets GSE29683(human) and GSE29685(mouse) were downloaded from NCBI GEO database. Homologous genes be... AIM: To explore the m RNA and pathways related to retinoblastoma(RB) genesis and development.METHODS: Microarray datasets GSE29683(human) and GSE29685(mouse) were downloaded from NCBI GEO database. Homologous genes between the two species were identified using WGCNA, followed by protein-protein interaction(PPI) network construction and gene enrichment analysis. Disease-related mi RNAs and pathways were retrieved from mi R2 Disease database and Comparative Toxicogenomics Database(CTD), respectively.RESULTS: A total of 352 homologous genes were identified. Two pathways including "cell cycle" and "pathway in cancer" in CTD and enrichment analysis were identified and seven mi RNAs(including hsa-mi R-373, hsa-mi R-34 a, hsami R-129, hsa-mi R-494, hsa-mi R-503, hsa-let-7 and hsami R-518 c) were associated with RB. mi RNAs modulate "cell cycle" and "pathway in cancer" pathways via regulating 13 genes(including CCND1, CDC25 C, E2 F2, CDKN2 D and TGFB2).CONCLUSION: These results suggest that these mi RNAs play crucial roles in RB genesis through "cell cycle" and "pathway in cancer" pathways by regulating their targets including CCND1, CDC25 C, E2 F2 and CDKN2 D. 展开更多
关键词 KYOTO ENCYCLOPEDIA of Genes and GENOMES pathway micro RNA RETINOBLASTOMA weighted gene CO-EXPRESSION network analysis
Hub genes and key pathways of traumatic brain injury: bioinformatics analysis and in vivo validation 认领 被引量:2
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作者 Yun-Liang Tang Long-Jun Fang +3 位作者 Ling-Yang Zhong Jian Jiang Xiao-Yang Dong Zhen Feng 《中国神经再生研究:英文版》 SCIE CAS CSCD 2020年第12期2262-2269,共8页
The exact mechanisms associated with secondary brain damage following traumatic brain injury(TBI)remain unclear;therefore,identifying the critical molecular mechanisms involved in TBI is essential.The m RNA expression... The exact mechanisms associated with secondary brain damage following traumatic brain injury(TBI)remain unclear;therefore,identifying the critical molecular mechanisms involved in TBI is essential.The m RNA expression microarray GSE2871 was downloaded from the Gene Expression Omnibus(GEO)repository.GSE2871 comprises a total of 31 cerebral cortex samples,including two post-TBI time points.The microarray features eight control and seven TBI samples,from 4 hours post-TBI,and eight control and eight TBI samples from 24 hours post-TBI.In this bioinformatics-based study,109 and 66 differentially expressed genes(DEGs)were identified in a Sprague-Dawley(SD)rat TBI model,4 and 24 hours post-TBI,respectively.Functional enrichment analysis showed that the identified DEGs were significantly enriched in several terms,such as positive regulation of nuclear factor-κB transcription factor activity,mitogen-activated protein kinase signaling pathway,negative regulation of apoptotic process,and tumor necrosis factor signaling pathway.Moreover,the hub genes with high connectivity degrees were primarily related to inflammatory mediators.To validate the top five hub genes,a rat model of TBI was established using the weight-drop method,and real-time quantitative polymerase chain reaction analysis of the cerebral cortex was performed.The results showed that compared with control rats,Tnf-α,c-Myc,Spp1,Cxcl10,Ptprc,Egf,Mmp9,and Lcn2 were upregulated,and Fn1 was downregulated in TBI rats.Among these hub genes,Fn1,c-Myc,and Ptprc may represent novel biomarkers or therapeutic targets for TBI.These identified pathways and key genes may provide insights into the molecular mechanisms of TBI and provide potential treatment targets for patients with TBI.This study was approved by the Experimental Animal Ethics Committee of the First Affiliated Hospital of Nanchang University,China(approval No.003)in January 2016. 展开更多
关键词 bioinformatics DEGs differentially expressed genes Gene Ontology hub genes inflammation Kyoto Encyclopedia of Genes and Genomes molecular mechanism traumatic brain injury
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Analysis of the autophagy gene expression profile of pancreatic cancer based on autophagy-related protein microtubule-associated protein 1A/1B-light chain 3 认领 被引量:1
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作者 Yan-Hui Yang Yu-Xiang Zhang +3 位作者 Yang Gui Jiang-Bo Liu Jun-Jun Sun Hua Fan 《世界胃肠病学杂志:英文版》 SCIE CAS 2019年第17期2086-2098,共13页
BACKGROUND Pancreatic cancer is a highly invasive malignant tumor. Expression levels of the autophagy-related protein microtubule-associated protein 1A/1B-light chain 3 (LC3) and perineural invasion (PNI) are closely ... BACKGROUND Pancreatic cancer is a highly invasive malignant tumor. Expression levels of the autophagy-related protein microtubule-associated protein 1A/1B-light chain 3 (LC3) and perineural invasion (PNI) are closely related to its occurrence and development. Our previous results showed that the high expression of LC3 was positively correlated with PNI in the patients with pancreatic cancer. In this study, we further searched for differential genes involved in autophagy of pancreatic cancer by gene expression profiling and analyzed their biological functions in pancreatic cancer, which provides a theoretical basis for elucidating the pathophysiological mechanism of autophagy in pancreatic cancer and PNI. AIM To identify differentially expressed genes involved in pancreatic cancer autophagy and explore the pathogenesis at the molecular level. METHODS Two sets of gene expression profiles of pancreatic cancer/normal tissue (GSE16515 and GSE15471) were collected from the Gene Expression Omnibus. Significance analysis of microarrays algorithm was used to screen differentially expressed genes related to pancreatic cancer. Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were used to analyze the functional enrichment of the differentially expressed genes. Protein interaction data containing only differentially expressed genes was downloaded from String database and screened. Module mining was carried out by Cytoscape software and ClusterOne plug-in. The interaction relationship between the modules was analyzed and the pivot nodes between the functional modules were determined according to the information of the functional modules and the data of reliable protein interaction network.RESULTS Based on the above two data sets of pancreatic tissue total gene expression, 6098 and 12928 differentially expressed genes were obtained by analysis of genes with higher phenotypic correlation. After extracting the intersection of the two differential gene sets, 4870 genes were determined 展开更多
关键词 Pancreatic cancer Autophagy-related PROTEIN microtubule-associated PROTEIN 1A/1B-light chain 3 Perineural invasion Gene Ontology ANALYSIS KYOTO ENCYCLOPEDIA of Genes and Genomes pathway ANALYSIS Ubiquitin C
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Investigating loss of heterozygosity in a SCRaMbLEd yeast genome 认领
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作者 Junbiao Dai 《中国科学:生命科学英文版》 SCIE CAS CSCD 2019年第6期868-869,共2页
Loss of heterozygosity (LOH) is a phenomenon in which elimination of one parental genomic region occurs in interspecific hybrids. LOH is common in cancer (Deng et al., 1996;Koufos et al., 1985). However, genetic analy... Loss of heterozygosity (LOH) is a phenomenon in which elimination of one parental genomic region occurs in interspecific hybrids. LOH is common in cancer (Deng et al., 1996;Koufos et al., 1985). However, genetic analysis of LOH has been mainly conducted based on predetermined features of individual genomes. 展开更多
关键词 LOSS of HETEROZYGOSITY ELIMINATION INDIVIDUAL GENOMES
Opportunities to Use DNA Methylation to Distil Functional Elements in Large Crop Genomes 认领
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作者 Peter A.Crisp Jaclyn M.Noshay +1 位作者 Sarah N.Anderson Nathan M.Springer 《分子植物:英文版》 SCIE CAS CSCD 2019年第3期282-284,共3页
DNA methylation is a chromatin modification that is often associated with the exciti ng and sometimes unpredictable patter ns of inheritanee that can unfold with epigenetic phenomena. The stability and heritability of... DNA methylation is a chromatin modification that is often associated with the exciti ng and sometimes unpredictable patter ns of inheritanee that can unfold with epigenetic phenomena. The stability and heritability of DNA methylati on patter ns perhaps allow us to utilize DNA methylation profiles to distil the suite of potentially functional elements in large crop genomes. Here, we discuss the potential and possible ways to use the absence of DNA methylation to identify potential regulatory regions within intergenic sequences and the presence of DNA methylation to identify pseudogenes. 展开更多
关键词 DNA METHYLATION LARGE CROP GENOMES
Diagnostic and prognostic value of lncRNA cancer susceptibility candidate 9 in hepatocellular carcinoma 认领 被引量:2
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作者 Yong-Lian Zeng Zhen-Ya Guo +3 位作者 Hui-Zhao Su Fu-Di Zhong Ke-Qing Jiang Guan-Dou Yuan 《世界胃肠病学杂志:英文版》 SCIE CAS 2019年第48期6902-6915,共14页
BACKGROUND Hepatocellular carcinoma (HCC) is a common malignant gastrointestinal tumor There are currently few clinical diagnostic and prognostic markers for HCC.LncRNA cancer susceptibility candidate 9 (CASC9) is a l... BACKGROUND Hepatocellular carcinoma (HCC) is a common malignant gastrointestinal tumor There are currently few clinical diagnostic and prognostic markers for HCC.LncRNA cancer susceptibility candidate 9 (CASC9) is a long-chain non-coding RNA discovered in recent years,and previous studies have found that IncRNA CASC9 participates in the occurrence and development of HCC,but its clinical value remains unclear.AIM To determine the expression of IncRNA CASC9 in HCC and its diagnostic and prognostic value.METHODS Data on CASC9 expression in patients with HCC were collected from the Cancer Genome Atlas (TCGA) database to analyze the relationship between CASC9 and patient survival.A total of 80 HCC patients treated in The First Affiliated Hospital of Guangxi Medical University from May 2012 to January 2014 were enrolled in the patient group,and 50 healthy subjects were enrolled in the control group during the same period.CASC9 expression in the two groups was determined using quantitative real-time polymerase chain reaction,and its diagnostic and prognostic value was analyzed based on the CASC9 data and pathological data in these HCC patients.The relationship between CASC9 and patient survival was assessed during the 5-year follow-up period.RESULTS Analysis of data from TCGA database revealed that control samples showed significantly lower CASC9 expression than carcinoma tissue samples (P <0.001);the low CASC9 expression group had a higher survival rate than the high CASC9expression group (P=0.011),and the patient group showed significantly increased expression of serum CASC9,with the area under the curve (AUC) of0.933.CASC9 expression was related to tumor size,combined hepatitis,tumor,node,metastasis (TNM) staging,lymph node metastasis,differentiation and alpha fetoprotein,and the high CASC9 expression group showed lower 1-year,3-year and 5-year survival rates than the low CASC9 expression group (all aP <0.05).Multivariate Cox regression analysis revealed that TNM staging,lymph node metastasis,differentiation,alpha fe 展开更多
关键词 LncRNA cancer SUSCEPTIBILITY CANDIDATE 9 Hepatocellular carcinoma Prognosis KYOTO ENCYCLOPEDIA of Genes and GENOMES Gene Ontology Competing ENDOGENOUS RNA
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Bioinformatics analyses of differentially expressed genes associated with spinal cord injury:a microarray-based analysis in a mouse model 认领 被引量:1
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作者 Lei Guo Jing Lv +2 位作者 Yun-Fei Huang Ding-Jun Hao Ji-Jun Liu 《中国神经再生研究:英文版》 SCIE CAS CSCD 2019年第7期1262-1270,共9页
Gene spectrum analysis has shown that gene expression and signaling pathways change dramatically after spinal cord injury,which may affect the microenvironment of the damaged site.Microarray analysis provides a new op... Gene spectrum analysis has shown that gene expression and signaling pathways change dramatically after spinal cord injury,which may affect the microenvironment of the damaged site.Microarray analysis provides a new opportunity for investigating diagnosis,treatment,and prognosis of spinal cord injury.However,differentially expressed genes are not consistent among studies,and many key genes and signaling pathways have not yet been accurately studied.GSE5296 was retrieved from the Gene Expression Omnibus DataSet.Differentially expressed genes were obtained using R/Bioconductor software(expression changed at least two-fold;P<0.05).Database for Annotation,Visualization and Integrated Discovery was used for functional annotation of differentially expressed genes and Animal Transcription Factor Database for predicting potential transcription factors.The resulting transcription regulatory protein interaction network was mapped to screen representative genes and investigate their diagnostic and therapeutic value for disease.In total,this study identified 109 genes that were upregulated and 30 that were downregulated at 0.5,4,and 24 hours,and 3,7,and 28 days after spinal cord injury.The number of downregulated genes was smaller than the number of upregulated genes at each time point.Database for Annotation,Visualization and Integrated Discovery analysis found that many inflammation-related pathways were upregulated in injured spinal cord.Additionally,expression levels of these inflammation-related genes were maintained for at least 28 days.Moreover,399 regulation modes and 77 nodes were shown in the protein-protein interaction network of upregulated differentially expressed genes.Among the 10 upregulated differentially expressed genes with the highest degrees of distribution,six genes were transcription factors.Among these transcription factors,ATF3 showed the greatest change.ATF3 was upregulated within 30 minutes,and its expression levels remained high at 28 days after spinal cord injury.These key genes screened by bioinf 展开更多
关键词 nerve REGENERATION spinal cord injury differentially expressed GENES BIOINFORMATICS ANALYSES Database for Annotation Visualization and Integrated Discovery ANALYSIS inflammation Kyoto Encyclopedia of GENES and Genomes pathway MICROARRAY transcription factors neural REGENERATION
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Neolithic millet farmers contributed to the permanent settlement of the Tibetan Plateau by adopting barley agriculture 认领 被引量:1
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作者 Yu-Chun Li Jiao-Yang Tian +7 位作者 Feng-Wen Liu Bin-Yu Yang Kang-Shu-Yun Gu Zia Ur Rahman Li-Qin Yang Fa-Hu Chen Guang-Hui Dong Qing-Peng Kong 《国家科学评论:英文版》 SCIE EI CSCD 2019年第5期1005-1013,共9页
The permanent human settlement of the Tibetan Plateau(TP)has been suggested to have been facilitated by the introduction of barley agriculture~3.6 kilo-years ago(ka).However,how barley agriculture spread onto the TP r... The permanent human settlement of the Tibetan Plateau(TP)has been suggested to have been facilitated by the introduction of barley agriculture~3.6 kilo-years ago(ka).However,how barley agriculture spread onto the TP remains unknown.Given that the lower altitudes in the northeastern TP were occupied by millet cultivators from 5.2 ka,who also adopted barley farming~4 ka,it is highly possible that it was millet farmers who brought barley agriculture onto the TP~3.6 ka.To test this hypothesis,we analyzed mitochondrial DNA(mt DNA)from 8277 Tibetans and 58514 individuals from surrounding populations,including 682 newly sequenced whole mitogenomes.Multiple lines of evidence,together with radiocarbon dating of cereal remains at different elevations,supports the scenario that two haplogroups(M9a1a1c1b1a and A11a1a),which are common in contemporary Tibetans(20.9%)and were probably even more common(40–50%)in early Tibetans prior to historical immigrations to the TP,represent the genetic legacy of the Neolithic millet farmers.Both haplogroups originated in northern China between 10.0–6.0 ka and differentiated in the ancestors of modern Tibetans~5.2–4.0 ka,matching the dispersal history of millet farming.By showing that substantial genetic components in contemporary Tibetans can trace their ancestry back to the Neolithic millet farmers,our study reveals that millet farmers adopted and brought barley agriculture to the TP~3.6–3.3 ka,and made an important contribution to the Tibetan gene pool. 展开更多
关键词 Tibetans MILLET FARMERS BARLEY AGRICULTURE ARCHAEOLOGY mitochondrial genomes
拟穴青蟹两个Crustin新变体的克隆与表达分析 认领
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作者 张财亮 黄贝 +2 位作者 熊静 陈芳奕 黄文树 《厦门大学学报:自然科学版》 CAS CSCD 北大核心 2019年第4期505-515,共11页
Crustins是一类广泛存在于甲壳动物中富含半胱氨酸的阳离子抗菌肽.该研究从拟穴青蟹(Scylla Paramamosain)中克隆获得两个Crustin新变体,分别命名为SpCrus1b和SpCrus2b.分析显示两者的前体肽包含N-端信号肽和C-端成熟肽两部分,成熟肽均... Crustins是一类广泛存在于甲壳动物中富含半胱氨酸的阳离子抗菌肽.该研究从拟穴青蟹(Scylla Paramamosain)中克隆获得两个Crustin新变体,分别命名为SpCrus1b和SpCrus2b.分析显示两者的前体肽包含N-端信号肽和C-端成熟肽两部分,成熟肽均含有12个位置高度保守的半胱氨酸.SpCrus1b在信号肽和乳清酸蛋白(WAP)结构域之间存在一个半胱氨酸富集区,属于典型的Ⅰ型Crustins;SpCrus2b除具有SpCrus1b的结构特征外,在近N-端额外含有一个甘氨酸富集区,属于典型的Ⅱ型Crustins.基因组结构分析显示SpCrus1b的基因组DNA序列为4个外显子/3个内含子结构,而SpCrus2b的基因组DNA序列为2个外显子/1个内含子结构.两者均主要在鳃中表达,且在脂多糖(LPS)刺激24h和聚肌胞苷酸(PolyI:C)刺激12h后表达量均极显著上调(p<0.01),表明SpCrus1b和SpCrus2b参与了拟穴青蟹抗细菌和抗病毒的先天免疫过程. 展开更多
关键词 抗菌肽 CRUSTIN 基因克隆 基因组 表达分析 拟穴青蟹$
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Complete loss of RNA editing from the plastid genome and most highly expressed mitochondrial genes of Welwitschia mirabilis 认领
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作者 Weishu Fan Wenhu Guo +2 位作者 Lexis Funk Jeffrey P.Mower Andan Zhu 《中国科学:生命科学英文版》 SCIE CAS CSCD 2019年第4期498-506,共9页
Comparative genomics among gymnosperms suggested extensive loss of mitochondrial RNA editing sites from Welwitschia mirabilis based on predictive analysis.However,empirical or transcriptome data to confirm this massiv... Comparative genomics among gymnosperms suggested extensive loss of mitochondrial RNA editing sites from Welwitschia mirabilis based on predictive analysis.However,empirical or transcriptome data to confirm this massive loss event are lacking,and the potential mechanisms of RNA site loss are unclear.By comparing genomic sequences with transcriptomic and reversetranscription PCR sequencing data,we performed a comprehensive analysis of the pattern of RNA editing in the mitochondrial and plastid genomes(mitogenome and plastome,respectively)of W.mirabilis and a second gymnosperm,Ginkgo biloba.For W.mirabilis,we found only 99 editing sites located in 13 protein-coding genes in the mitogenome and a complete loss of RNA editing from the plastome.The few genes having high editing frequency in the Welwitschia mitogenome showed a strong negative correlation with gene expression level.Comparative analyses with G.biloba,containing 1,405 mitochondrial and 345 plastid editing sites,revealed that the editing loss from W.mirabilis is mainly due to the substitution of editable cytidines to thymidines at the genomic level,which could be caused by retroprocessing.Our result is the first study to uncover massive editing loss from both the mitogenome and plastome in a single genus.Furthermore,our results suggest that gene expression level and retroprocessing both contributed to the evolution of RNA editing in plant organellar genomes. 展开更多
关键词 RNA EDITING MASSIVE LOSS expression levels ORGANELLE GENOMES Welwitschia
SeqSQC:A Bioconductor Package for Evaluating the Sample Quality of Next-generation Sequencing Data 认领
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作者 Qian Liu Qiang Hu +7 位作者 Song Yao Marilyn L. Kwan Janise M. Roh Hua Zhao Christine B. Ambrosone Lawrence H. Kushi Song Liu Qianqian Zhu 《基因组蛋白质组与生物信息学报:英文版》 SCIE CAS CSCD 2019年第2期211-218,共8页
As next-generation sequencing (NGS) technology has become widely used to identify genetic causal variants for various diseases and traits,a number of packages for checking NGS data quality have sprung up in public dom... As next-generation sequencing (NGS) technology has become widely used to identify genetic causal variants for various diseases and traits,a number of packages for checking NGS data quality have sprung up in public domains. In addition to the quality of sequencing data,sample quality issues,such as gender mismatch,abnormal inbreeding coefficient,cryptic relatedness,and population outliers,can also have fundamental impact on downstream analysis. However,there is a lack of tools specialized in identifying problematic samples from NGS data,often due to the limitation of sample size and variant counts. We developed SeqSQC,a Bioconductor package,to automate and accelerate sample cleaning in NGS data of any scale. SeqSQC is designed for efficient data storage and access,and equipped with interactive plots for intuitive data visualization to expedite the identification of problematic samples. SeqSQC is available at http://bioconductor. org/packages/SeqSQC. 展开更多
关键词 Next-generation SEQUENCING QUALITY assessment 1000 GENOMES Project Whole-exome SEQUENCING BIOCONDUCTOR PACKAGE
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