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Sequence Analysis of Transcription Factor AtWRKY35 and Construction of Prokaryotic Expression Vector
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作者 伍林涛 康公平 +4 位作者 奉斌 韩宏仕 杜才富 曾章丽 张敏琴 《Agricultural Science & Technology》 CAS 2014年第10期1649-1650,1718,共3页
As members of a super gene family, WRKY transcription factors are widely distributed in higher plants. ln this study, bioinformatic analysis of WRKY35, a member of the WRKY gene family, was carried out. Results indica... As members of a super gene family, WRKY transcription factors are widely distributed in higher plants. ln this study, bioinformatic analysis of WRKY35, a member of the WRKY gene family, was carried out. Results indicated that tran-scription factor WRKY35 harbors a WRKYGQK core domain and a Cys2His2 or Cys2His/Cys zinc finger in the 5’ end without transmembrane domain. After PCR amplification and restriction digestion, WRKY35 gene fragment was ligated to prokaryotic expression vector PET28. This study provided basis for expression anal-ysis of WRKY35 protein and subsequent functional identification of WRKY35 gene. 展开更多
关键词 WRKY transcription factor sequence analysis Prokaryotic expression vector
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Cloning and Sequence Analysis of PBF Encoding Genes from Hexaploid Common Wheat Chinese Spring (Triticum aestivum L.)
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作者 郭丽娜 高翔 《Agricultural Science & Technology》 CAS 2013年第5期722-726,731,共6页
[Objective] This study aimed to investigate the polymorphism of PBF en- coding genes from common wheat Chinese Spring (Triticum aestivum L.). [Method] Using common wheat Chinese Spring as the experimental material, ... [Objective] This study aimed to investigate the polymorphism of PBF en- coding genes from common wheat Chinese Spring (Triticum aestivum L.). [Method] Using common wheat Chinese Spring as the experimental material, gene-specific primers were designed and applied to amplify the genomic DNA of Chinese Spring. PCR products were isolated, purified and ligated into the cloning vector. Positive clones were randomly selected for sequencing. A series of softwares including DNAMAN, Signalp, PSIPRED, Nuc_PLoc and MEGA were employed for sequence assembly and alignment, signal peptide prediction, primary and secondary structure prediction, as well as analyses of subcellular location and phylogenetic relationships between the PBF family members in Poaceae. [Result] Twenty-five target sequences were obtained from the genome of hexaploid common wheat Chinese Spring, which were classified into three clusters based on the sequence similarity. SNPs exist at two loci of the subunit, resulting in the change of encoded amino acid residues and affecting the secondary structure of final product encoded. [Conclusion] PBF encoding sequences are extremely conservative in Chinese Spring with certain variations. This study provides theoretical reference to evaluate the expression efficiency of wheat storage proteins. 展开更多
关键词 Common wheat PBF transcription factor CLONING sequence analysis
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Cloning and Sequence Analysis of IGFBP-7 Gene in Sheep
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作者 Mingliang ZHOU Pinggui YANG +1 位作者 Dengjun WU Xiangyu ZHANG 《Agricultural Biotechnology》 CAS 2015年第6期38-42,共5页
In this study, full-length CDS sequence of IGFBP-7 gene was cloned from Liangshan semi-fine wool sheep with RT-PCR method and analyzed with bioinformatics methods. The results showed that the full-length CDS sequence ... In this study, full-length CDS sequence of IGFBP-7 gene was cloned from Liangshan semi-fine wool sheep with RT-PCR method and analyzed with bioinformatics methods. The results showed that the full-length CDS sequence of IGFBP-7 gene in Liangshan semi-fine wool sheep was 846 bp in length, encoding 282 amino acids. The CDS sequence shared 99%, 95% and 90% homology with bovine, human and rat, respectively; the amino acid sequence shared 98%, 93% and 89%, respectively. The GenBank accession number was FJ589640.1. The amino acid molecular weight of IGFBP-7 was 29.0 kD, and the theoretical isoelec- tric point (pl) was 8.25. The result of phylogenetic analysis showed that IGFBP-7 gone in Liangshan semi-fine wool sheep exhibited close phylogenetic relationships with bovine, goat and other mammals, and distant phylogenetic relationships with Danio rerio and Haliotis diversicolor. IGFBP-7 gene had uniformly distributed hy- drophobic and hydrophilic regions, harboring one signal peptide, two transmembrane regions, 16 phosphorylation sites, four N-glycosylation sites and one O-glyco- sylation site. The result of secondary structure analysis showed that the random coil, or-helix and β-sheet regions accounted for 64.89%, 19.86% and 15.25%, respectively. The result of tertiary structure analysis showed that IGFBP-7 harbors an IGFBP_N domain and an Ig-like domain. This study provided scientific basis for further investigating the function of IGFBP-7 gene in sheep. 展开更多
关键词 SHEEP Insulin-like growth factor-binding protein-7 gene (IGFBP-7 gene) CLONING sequence analysis
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Single-nuclei RNA sequencing uncovers heterogenous transcriptional signatures in Parkinson's disease associated with nuclear receptor-related factor 1 defect 被引量:2
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作者 Piniel Alphayo Kambey Wen-Ya Liu +4 位作者 Jiao Wu Bakwatanisa Bosco Iqra Nadeem Kouminin Kanwore Dian-Shuai Gao 《Neural Regeneration Research》 SCIE CAS CSCD 2023年第9期2037-2046,共10页
Previous studies have found that deficiency in nuclear receptor-related factor 1(Nurr1),which participates in the development,differentiation,survival,and degeneration of dopaminergic neurons,is associated with Parkin... Previous studies have found that deficiency in nuclear receptor-related factor 1(Nurr1),which participates in the development,differentiation,survival,and degeneration of dopaminergic neurons,is associated with Parkinson s disease,but the mechanism of action is perplexing.Here,we first asce rtained the repercussion of knocking down Nurr1 by pe rforming liquid chromatography coupled with tandem mass spectrometry.We found that 231 genes were highly expressed in dopaminergic neurons with Nurr1 deficiency,14 of which were linked to the Parkinson’s disease pathway based on Kyoto Encyclopedia of Genes and Genomes analysis.To better understand how Nurr1 deficiency autonomously invokes the decline of dopaminergic neurons and elicits Parkinson’s disease symptoms,we performed single-nuclei RNA sequencing in a Nurr1 LV-shRNA mouse model.The results revealed cellular heterogeneity in the substantia nigra and a number of activated genes,the preponderance of which encode components of the major histocompatibility Ⅱ complex.Cd74,H2-Ab1,H2-Aα,H2-Eb1,Lyz2,Mrc1,Slc6α3,Slc47α1,Ms4α4b,and Ptprc2 were the top 10 diffe rentially expressed genes.Immunofluorescence staining showed that,after Nurr1knockdown,the number of CD74-immunoreactive cells in mouse brain tissue was markedly increased.In addition,Cd74 expression was increased in a mouse model of Parkinson’s disease induced by treatment with 6-hydroxydopamine.Ta ken togethe r,our res ults suggest that Nurr1 deficiency results in an increase in Cd74 expression,thereby leading to the destruction of dopaminergic neuro ns.These findings provide a potential therapeutic target for the treatment of Parkinson’s disease. 展开更多
关键词 6-HYDROXYDOPAMINE dopaminergic neurons dopamine transporter nuclear receptor-related factor 1 Parkinson’s disease proteomics analysis Seurat clustering single-nuclei RNA sequencing substantia nigra tyrosine hydroxylase
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Alterative Expression and Sequence of Human Elongation Factor-1δ during Malignant Transformation of Human Bronchial Epithelial Cells Induced by Cadmium Chloride 被引量:2
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作者 YI-XIONG LEI MIN WANG +2 位作者 LIAN WEI XI LU HUA-ZHAO LIN 《Biomedical and Environmental Sciences》 SCIE CAS CSCD 2010年第2期151-157,共7页
Objective To study the alternative expression and sequence of human elongation factor-1δ (human EF-1δ p31) during malignant transformation of human bronchial epithelial cells induced by cadmium chloride (CdCl2) ... Objective To study the alternative expression and sequence of human elongation factor-1δ (human EF-1δ p31) during malignant transformation of human bronchial epithelial cells induced by cadmium chloride (CdCl2) and its possible mechanism. Methods Total RNA was isolated at different stages of transformed human bronchial epithelial cells (16HBE) induced by CdCl2 at a concentration of 5.0 μM. Special primers and probe for human EF-1δ p31 were designed and expression of human EF-18 mRNA from different cell lines was detected with fluorescent quantitative PCR technique. EF-18 cDNA from different cell lines was purified and cloned into pMD 18-T vector followed by confirming and sequencing analysis. Results The expressions of human EF-1δ p31 at different stages of 16HBE cells transformed by CdCl2 was elevated (P〈0.01 or P〈0.05). Compared with their corresponding non-transformed ceils, the overexpression level of EF-15 p31 was averagely increased 2.9 folds in Cd-pretransformed cells, 4.3 folds in Cd-transformed ceils and 7.2 folds in Cd-tumorigenic cells. No change was found in the sequence of overexpressed EF-1δ p31 at different stages of 16HBE cells transformed by CdCl2. Conclusion Overexpression of human EF-1δ p31 is positively correlated with malignant transformation of 16HBE cells induced by CdCl2, but is not correlated with DNA mutations. 展开更多
关键词 Human elongation factor-1δ Cadmium chloride Human bronchial epithelial cells Cell transformation sequencing analysis
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Biological characteristics of dynamic expression of nerve regeneration related growth factors in dorsal root ganglia after peripheral nerve injury 被引量:5
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作者 Yin-Ying Shen Xiao-Kun Gu +3 位作者 Rui-Rui Zhang Tian-Mei Qian Shi-Ying Li Sheng Yi 《Neural Regeneration Research》 SCIE CAS CSCD 2020年第8期1502-1509,共8页
The regenerative capacity of peripheral nerves is limited after nerve injury.A number of growth factors modulate many cellular behaviors,such as proliferation and migration,and may contribute to nerve repair and regen... The regenerative capacity of peripheral nerves is limited after nerve injury.A number of growth factors modulate many cellular behaviors,such as proliferation and migration,and may contribute to nerve repair and regeneration.Our previous study observed the dynamic changes of genes in L4–6 dorsal root ganglion after rat sciatic nerve crush using transcriptome sequencing.Our current study focused on upstream growth factors and found that a total of 19 upstream growth factors were dysregulated in dorsal root ganglions at 3,9 hours,1,4,or 7 days after nerve crush,compared with the 0 hour control.Thirty-six rat models of sciatic nerve crush injury were prepared as described previously.Then,they were divided into six groups to measure the expression changes of representative genes at 0,3,9 hours,1,4 or 7 days post crush.Our current study measured the expression levels of representative upstream growth factors,including nerve growth factor,brain-derived neurotrophic factor,fibroblast growth factor 2 and amphiregulin genes,and explored critical signaling pathways and biological process through bioinformatic analysis.Our data revealed that many of these dysregulated upstream growth factors,including nerve growth factor,brain-derived neurotrophic factor,fibroblast growth factor 2 and amphiregulin,participated in tissue remodeling and axon growth-related biological processes Therefore,the experiment described the expression pattern of upstream growth factors in the dorsal root ganglia after peripheral nerve injury.Bioinformatic analysis revealed growth factors that may promote repair and regeneration of damaged peripheral nerves.All animal surgery procedures were performed in accordance with Institutional Animal Care Guidelines of Nantong University and ethically approved by the Administration Committee of Experimental Animals,China(approval No.20170302-017)on March 2,2017. 展开更多
关键词 axon growth bioinformatic analysis dorsal root ganglia growth factors Ingenuity Pathway analysis nerve regeneration peripheral nerve injury rat sciatic nerve crush injury transcriptome sequencing upstream regulators
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Cloning and sequencing of the fourth exon of transforming growth factor α gene
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作者 惠宏襄 金明 +1 位作者 韩骅 王成济 《Journal of Medical Colleges of PLA(China)》 CAS 1994年第3期199-201,共3页
Using normal brain cell geneomic DNA as a template,transforming growth factor(TGFa)-IV exon gene was amplified by polymerase chain reaction(PCR). The sequence of amplified fragment was analysed with a DNA sequencing k... Using normal brain cell geneomic DNA as a template,transforming growth factor(TGFa)-IV exon gene was amplified by polymerase chain reaction(PCR). The sequence of amplified fragment was analysed with a DNA sequencing kit.The results showed that the cloned fragment is proved to be the TGFa-IV exon gene. 展开更多
关键词 TRANSFORMING GROWTH factor GENE EXON polymerase chain reaction clone sequence analysis
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一测多评法测定法制半夏曲中11种成分含量及其GRA、EW-TOPSIS质量评价
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作者 舒波 雷果平 袁斌 《医药导报》 CAS 北大核心 2024年第7期1120-1126,共7页
目的采用一测多评(QAMS)法同时测定法制半夏曲中肌苷、鸟苷、腺苷等11种成分含量,并建立其灰色关联度分析(GRA)联合熵权逼近理想解排序分析法(EW-TOPSIS)综合质量评价方法。方法采用Shimadzu C 18色谱柱;乙腈-0.5%醋酸为流动相,梯度洗脱... 目的采用一测多评(QAMS)法同时测定法制半夏曲中肌苷、鸟苷、腺苷等11种成分含量,并建立其灰色关联度分析(GRA)联合熵权逼近理想解排序分析法(EW-TOPSIS)综合质量评价方法。方法采用Shimadzu C 18色谱柱;乙腈-0.5%醋酸为流动相,梯度洗脱,流速1.0 mL·min-1;检测波长254和290 nm。以对甲氧基肉桂酸乙酯为内参比物质,计算其他10个成分的相对校正因子(RCF),测定各成分含量。采用GRA联合EW-TOPSIS模型对法制半夏曲进行综合质量评价。结果法制半夏曲中11种成分在一定浓度范围内线性关系良好,相关系数均>0.999;平均加样回收率96.94%~100.12%(RSD<2.0%,n=9);QAMS与外标法(ESM)实测值无明显差异。GRA模型相对关联度0.2903~0.6187,EW-TOPSIS模型相对接近度0.2114~0.6343;GRA和EW-TOPSIS模型综合评价结果基本一致。结论QAMS法便捷、准确,可用于法制半夏曲多指标成分定量控制,GRA联合EW-TOPSIS模型可用于法制半夏曲综合质量评价。 展开更多
关键词 法制半夏曲 一测多评法 多指标成分 相对校正因子 灰色关联度分析 熵权-逼近理想解排序法 质量评价
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CNV结合STR分型技术检测孕早期流产组织潜在葡萄胎效果及风险因素分析
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作者 孙艳 文晓燕 +1 位作者 刘风藏 王桂琦 《中国计划生育学杂志》 2024年第1期222-226,共5页
目的:评估基因组拷贝数变异测序(CNV-seq)结合短串联重复序列(STR)多态性分析技术在检测孕早期(≤9周)流产物组织中潜在葡萄胎病例的应用效果.方法:收集2021年1月-2022年12月行孕早期流产组织CNV-seq结合STR多态性检测病例114例,其中部... 目的:评估基因组拷贝数变异测序(CNV-seq)结合短串联重复序列(STR)多态性分析技术在检测孕早期(≤9周)流产物组织中潜在葡萄胎病例的应用效果.方法:收集2021年1月-2022年12月行孕早期流产组织CNV-seq结合STR多态性检测病例114例,其中部分新鲜绒毛组织进行CNV-seq结合STR多态性检测,部分组织行病理学检测.比较两种检测方法结果,并分析潜在葡萄胎病例的临床特征和影响因素.结果:CNV-seq结合STR多态性检测共检出染色体异常病例28例,阳性率为24.6%,其中单亲二倍体(UPD)8例,占阳性病例28.6%;病理学检出葡萄胎病例12例,阳性率为10.5%,其中完全性葡萄胎(CHM)10例,占阳性病例的83.3%.两种检测方法的结果一致率为89.5%,Kappa值为0.75,两种方法具较好一致性.潜在葡萄胎病例与非葡萄胎病例在年龄、孕次、流产次、β-hCG水平、超声表现等方面有差异,其中年龄、β-hCG水平和超声表现是潜在葡萄胎危险因素(均P<0.05).结论:CNV-seq结合STR多态性分析技术能有效检测孕早期流产物组织中潜在葡萄胎病例,有助于指导临床治疗和避免再次流产. 展开更多
关键词 孕早期流产 葡萄胎 基因组拷贝数变异测序 短串联重复序列多态性分析技术 危险因素
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Molecular cloning, pathologically-correlated expression and functional characterization of the colony- stimulating factor 1 receptor (CSF-1R) gene from a teleost, Plecoglossus altivelis 被引量:4
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作者 Qiang CHEN Xin-Jiang LU +1 位作者 Ming-Yun LI Jiong CHEN 《Zoological Research》 CAS CSCD 2016年第2期96-102,共7页
Colony-stimulating factor 1 receptor (CSF-1R) is an important regulator of monocytes/macrophages (MO/MФ). Although several CSF-1R genes have been identified in teleosts, the precise role of CSF- 1R in ayu (Pleco... Colony-stimulating factor 1 receptor (CSF-1R) is an important regulator of monocytes/macrophages (MO/MФ). Although several CSF-1R genes have been identified in teleosts, the precise role of CSF- 1R in ayu (Plecoglossus altivelis) remains unclear. In this study, we characterized the CSF-1R homologue from P. altivelis, and named it PaCSF-1R. Multiple sequence alignment and phylogenetic tree analysis showed that PaCSF-1R was most closely related to that of Japanese ricefish (Oryzias latipes). Tissue distribution and expression analysis showed that the PaCSF-1R transcript was mainly expressed in the head kidney-derived MO/MФ, spleen, and head kidney, and its expression was significantly altered in various tissues upon Vibrio anguillarum infection. After PaCSF-1R neutralization for 48 h, the phagocytic activity of MO/MФ was significantly decreased, suggesting that PaCSF-1R plays a role in regulating the phagocytic function of ayu MO/M(P. 展开更多
关键词 Colony-stimulating factor 1 receptor Pathologically-correlated expression Monocytes/macrophages PHAGOCYTOSIS sequence analysis
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蟾蜍TNFRSF11b、TNFRSF9基因克隆及生物信息学分析
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作者 苏岩 褚涵 +5 位作者 余坤 潘瑞 叶陈娟 李军德 黄晓 张恬 《中国现代中药》 CAS 2023年第8期1655-1667,共13页
目的:克隆中华蟾蜍肿瘤坏死因子受体超家族(TNFRSF)BbgTNFRSF11b、BbgTNFRSF9基因的全长序列,并分析其序列特征。方法:根据转录组测序所得的TNFRSF11b、TNFRSF9基因片段设计特异性引物,以中华蟾蜍蟾皮为材料,利用逆转录聚合酶链式反应(P... 目的:克隆中华蟾蜍肿瘤坏死因子受体超家族(TNFRSF)BbgTNFRSF11b、BbgTNFRSF9基因的全长序列,并分析其序列特征。方法:根据转录组测序所得的TNFRSF11b、TNFRSF9基因片段设计特异性引物,以中华蟾蜍蟾皮为材料,利用逆转录聚合酶链式反应(PCR)技术获得BbgTNFRSF11b、BbgTNFRSF9基因全长互补脱氧核糖核酸(cDNA)序列,并采用生物信息学手段分析其序列特征,通过实时荧光定量PCR方法检测BbgTNFRSF11b、BbgTNFRSF9基因在中华蟾蜍7种组织/器官中的表达情况。结果:克隆获得蟾蜍BbgTNFRSF11b基因的全长cDNA序列为1233bp,编码410个氨基酸,理论相对分子质量为46.97kDa,等电点为8.64,不存在跨膜区及信号肽,为亲水性蛋白,具有多个磷酸化位点。BbgTNFRSF9基因的全长cDNA序列为829bp,编码247个氨基酸,理论相对分子质量为67.874kDa,理论等电点为5.12,存在信号肽,为疏水性蛋白,具有多个磷酸化位点,进化树分析发现BbgTNFRSF11b、BbgTNFRSF9基因与其他动物TNFRSF11b、TNFRSF9基因相似度不高,表明该基因虽有特殊结构域但不同物种间差异较大。组织表达分析显示,BbgTNFRSF11b、BbgTNFRSF9基因在耳后腺中表达显著高于其他部位。结论:成功获得蟾蜍BbgTNFRSF11b、BbgTNFRSF9基因序列,掌握其序列特征,为后续深入研究该蛋白的功能提供参考。 展开更多
关键词 蟾蜍 基因克隆 序列分析 肿瘤坏死因子受体超家族
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全面性发育迟缓患儿的染色体分析及预后危险因素研究
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作者 陈玲 崔玲玉 +2 位作者 王泽熙 檀晓娜 岳玲 《西部医学》 2023年第12期1817-1821,共5页
目的探讨全面性发育迟缓(GDD)患儿染色体特征,并分析患儿预后的影响因素。方法选取2018年1月—2021年5月河北省儿童医院收治的181例GDD患儿作为观察对象,全部患儿均接受全外显子测序+拷贝数变异(CNVs)检测,对患儿染色体进行分析。全部... 目的探讨全面性发育迟缓(GDD)患儿染色体特征,并分析患儿预后的影响因素。方法选取2018年1月—2021年5月河北省儿童医院收治的181例GDD患儿作为观察对象,全部患儿均接受全外显子测序+拷贝数变异(CNVs)检测,对患儿染色体进行分析。全部患儿随访1年,依据患儿预后将其分为预后不良组与预后良好组,比较两组患儿基线资料,分析GDD患儿预后的影响因素。结果181例GDD患儿中检出非良性CNVs 59例,检出率为32.60%(其中致病性CNVs为25.41%,可能致病性CNVs为5.52%,临床意义不明CNVs为1.66%);良性CNVs为67.40%。随访1年,181例患儿经治疗后预后不良142例(78.45%)。预后不良组患儿首诊年龄高于预后良好组,新生儿黄疸、早产、新生儿缺血缺氧性脑病(HIE)、致病性CNVs占比高于预后良好组,差异有统计学意义(P<0.05);两组性别、出生方式、宫内感染等基线资料比较,差异无统计学意义(P>0.05)。经Logistic回归分析结果显示,首诊年龄高、新生儿黄疸、早产、HIE、致病性CNVs是GDD患儿预后不良的危险因素(OR>1,P<0.05)。结论经全外显子测序+CNVs进行染色体分析可明确GDD患儿遗传学病因,且GDD患儿预后的可能危险因素为首诊年龄、新生儿黄疸、早产、HIE及致病性CNVs。 展开更多
关键词 全面性发育迟缓 全外显子测序 拷贝数变异 染色体分析 预后 影响因素
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马铃薯低氮肥胁迫响应TCP转录因子的鉴定与分析 被引量:2
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作者 牛苏燕 梁芳 +5 位作者 张珍华 蒋素华 武思 王默霏 袁秀云 崔波 《广西植物》 CAS CSCD 北大核心 2023年第2期293-302,共10页
TCP转录因子是植物特有的一类转录因子,参与植物生物学过程的多个方面。为研究马铃薯TCP转录因子在响应低氮肥胁迫中的作用,该研究以氮肥供应不足(0.05 mmol·L^(-1))和氮肥供应充足(7.5 mmol·L^(-1))条件下马铃薯的根和叶片构... TCP转录因子是植物特有的一类转录因子,参与植物生物学过程的多个方面。为研究马铃薯TCP转录因子在响应低氮肥胁迫中的作用,该研究以氮肥供应不足(0.05 mmol·L^(-1))和氮肥供应充足(7.5 mmol·L^(-1))条件下马铃薯的根和叶片构建4个转录组文库进行测序,并对差异表达的TCP转录因子进行分析。结果表明:(1)在4个转录组文库中共鉴定TCP转录因子24个,它们主要分布在2号、3号、6号染色体上。(2)经结构域分析显示,24个TCP转录因子均具有典型的basic-Helix-Loop-Helix结构域。(3)经系统进化分析显示,马铃薯与拟南芥TCP蛋白可聚集在一起,分属于10个亚类。(4)转录组测序结果显示,在低氮肥胁迫下,大多数TCP转录因子被抑制表达,有3个TCP转录因子在根中显著性差异表达,5个TCP转录因子在叶中特异性表达。(5)根据GO功能注释分析和马铃薯TCP转录因子与拟南芥TCP转录因子的亲缘关系分析推测,这些TCP转录因子参与了马铃薯对低氮肥胁迫的响应。该研究结果为进一步研究马铃薯与其他粮食作物TCP转录因子响应低氮肥胁迫的分子功能奠定了基础。 展开更多
关键词 马铃薯 TCP转录因子 氮肥胁迫 转录组测序 生物信息学分析
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不同窖龄及位置浓香型白酒窖泥微生物群落多样性与理化因子的比较分析 被引量:6
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作者 肖琴 何平 +3 位作者 周瑞平 刘超 袁思棋 赵金松 《食品科学》 EI CAS CSCD 北大核心 2023年第20期165-174,共10页
采用高通量测序技术、线性判别分析效应量(linear discriminant analysis effect size,LEfSe)和冗余分析(redundancy analysis,RDA)等方法,分别对5、10 a和20 a窖龄及不同空间位置窖泥的原核和真核微生物群落结构、差异微生物和微生物... 采用高通量测序技术、线性判别分析效应量(linear discriminant analysis effect size,LEfSe)和冗余分析(redundancy analysis,RDA)等方法,分别对5、10 a和20 a窖龄及不同空间位置窖泥的原核和真核微生物群落结构、差异微生物和微生物与理化因子之间的关系进行研究。结果表明:5 a的窖泥原核微生物和真核微生物多样性均高于10 a和20 a窖龄的窖泥;所有样品中,原核微生物共检出37个门、83个纲、176个目、306个科、629个属,其中优势菌门5个;真核微生物共检出12个门、37个纲、74个目、160个科、282个属,其中优势菌门3个,优势菌属15个;经LEfSe差异微生物分析,原核差异微生物12种(属水平),真核差异微生物共15种,各样品的差异微生物是在白酒酿造过程中发挥重要作用的物种;窖泥理化因子的测定结果表明,样品pH值变化范围为3.66~5.20,不同位置的窖泥有效磷含量均具有显著差异;RDA结果显示,Lactobacillus、unclassified_f__Aspergillaceae、Thermomyces与水分、氨态氮和有效磷呈负相关,Methanobacterium、Clostridium_sensu_stricto_12、Caproiciproducens、Methanobrevibacter、Cryptococcus_f__Tremellaceae、Apiotrichum与水分、pH值、氨态氮、有效磷呈正相关。本研究系统研究不同窖龄、不同空间位置的窖泥原核、真核微生物群落结构,借助微生物与理化性质相关性分析揭示了不同窖龄及位置浓香型窖泥微生物群落结构与理化因子的差异及两者的联系,为建立日常窖泥养护和优质窖泥驯化、制作提供了理论支撑。 展开更多
关键词 窖泥 高通量测序 原核和真核微生物 理化因子 相关性分析
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小湾库区微生物群落结构多样性与水质状况分析
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作者 吴嘉伟 谭凤霞 +5 位作者 祁梅 张潇峮 何杰秋 吴泽成 张峰 柴毅 《水生态学杂志》 CSCD 北大核心 2023年第6期122-127,共6页
为了解小湾库区不同水域的微生物多样性及微生物群落与生态环境的关系,2019年在库区选取6个采样点(W1~W6),通过16SrDNA基因扩增和高通量测序,分析库区微生物群落结构组成与多样性差异及水质状况。结果显示,小湾库区水体整体呈偏碱性,CO... 为了解小湾库区不同水域的微生物多样性及微生物群落与生态环境的关系,2019年在库区选取6个采样点(W1~W6),通过16SrDNA基因扩增和高通量测序,分析库区微生物群落结构组成与多样性差异及水质状况。结果显示,小湾库区水体整体呈偏碱性,COD含量为14.79~24.47 mg/L,TN浓度为0.53~2.39 mg/L,TP浓度为0.14~1.17 mg/L。不同采样点的微生物Chao1指数、覆盖率均较高,Shannon指数为3.42~4.48,Simpson指数为0.030~0.092,反映出各采样点微生物群落多样性丰富,其中群落丰富度以W6区域最高。各采样点的微生物主要有变形菌门(Pro-teobacteria)、蓝细菌门(Cyanobacteria)、放线菌门(Actinobacteria)、拟杆菌门(Bacteroidetes)和绿弯菌门(Chloroflexi),丰度之和达90%以上,以变形菌门为优势菌;在属水平上,以不动杆菌属(Acinetobacter)为第一优势菌属。PCoA分析发现,W5和W6聚为一类,W1~W4聚为另一类,并具有显著差异。研究表明,小湾库区水质整体良好,但部分区域已出现富营养化现象,且有扩散趋势,需采取环境治理措施。建议通过合理放养、适度捕捞的方式充分利用水域天然饵料资源,在保证小湾库区正常水力发电的前提下,适度开发库区渔业资源。 展开更多
关键词 微生物群落 高通量测序 多样性分析 环境因子 小湾库区
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牛分枝杆菌CVCC68002全基因组测序与功能分析
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作者 王霞 马伟超 +2 位作者 雒林通 裴芳 王廷璞 《甘肃农业大学学报》 CAS CSCD 2023年第5期11-24,共14页
【目的】为进一步深入研究牛分枝杆菌CVCC68002基因组特征,致病性和遗传进化关系,为牛分支杆菌感染疾病的预防和深入研究提供参考。【方法】利用Illumina和Pacbio测序技术平台对CVCC68002菌株进行全基因组测序建库,采用生物信息学和系... 【目的】为进一步深入研究牛分枝杆菌CVCC68002基因组特征,致病性和遗传进化关系,为牛分支杆菌感染疾病的预防和深入研究提供参考。【方法】利用Illumina和Pacbio测序技术平台对CVCC68002菌株进行全基因组测序建库,采用生物信息学和系统进化树等方法,对该菌株基因组功能注释、致病性和遗传进化关系进行了分析。【结果】通过分析发现该菌株基因组全长4357100 bp,GC含量为65.64%,编码基因达4145个;在GO、KEGG、COG、NR数据库基因组特征显示其具有高氨基酸和碳水化合物代谢能力。通过PHI,VFDB,ARDC和CARD数据库对其致病性进行相关分析,得到456个毒力基因注释,主要涉及细菌黏附与定殖、细菌逃避宿主免疫防御系统、分泌系统蛋白和转录因子等。并找到相关包括万古霉素,青霉素,多胺类抗生素、异烟肼、吡嗪酰胺、氟喹诺酮等的抗药性基因,另外,外排泵的抗性蛋白注释量显著,推测牛分枝杆菌通过外排抗性蛋白从而达到抗药自我保护的目的。【结论】获得牛分枝杆菌CVCC68002株完整基因组信息,完善系统进化信息,明确了其毒力因子和有效地靶标抗药基因,为后续对该菌株分子生物学特征、致病性和耐药基因筛选研究奠定了理论基础。 展开更多
关键词 牛分枝杆菌 基因组测序 致病性分析 毒力因子 耐药性分析
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烟草转录因子bHLH93基因的克隆及表达分析 被引量:9
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作者 武明珠 李锋 +5 位作者 王燃 罗朝鹏 魏春阳 魏攀 林福呈 杨军 《烟草科技》 EI CAS CSCD 北大核心 2015年第3期1-7,共7页
碱性/螺旋-环-螺旋(basic/helix-loop-helix,b HLH)转录因子是一类广泛存在于真核生物体内的重要转录因子,能够参与调控植物体多种生理途径。为了明确b HLH转录因子在烟草中的功能和调控机制,通过同源克隆技术从烟草中克隆到一个b HLH... 碱性/螺旋-环-螺旋(basic/helix-loop-helix,b HLH)转录因子是一类广泛存在于真核生物体内的重要转录因子,能够参与调控植物体多种生理途径。为了明确b HLH转录因子在烟草中的功能和调控机制,通过同源克隆技术从烟草中克隆到一个b HLH转录因子基因(Ntb HLH93),并结合生物信息学和基因表达模式分析进一步预测其生物学功能。结果表明:Ntb HLH93 c DNA序列长1 254 bp,包含一个长度为1 047 bp的开放阅读框,编码349个氨基酸。Ntb HLH93属于疏水性蛋白,其二级结构中的主要结构元件是α-螺旋和无规则卷曲,三级结构中具有b HLH家族典型的螺旋-环-螺旋结构特征。Ntb HLH93基因表达具有明显的组织特异性,主要在烟草不同生育期侧根和盛花期子房组织中高表达,这与植物甾醇集中在生长分裂旺盛组织中合成的特征相吻合。 展开更多
关键词 烟草 NtbHLH93 转录因子 序列分析
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白羊草NAC转录因子基因的克隆及表达分析 被引量:12
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作者 方志红 王学敏 +3 位作者 李俊 董洁 高洪文 董宽虎 《草地学报》 CAS CSCD 北大核心 2013年第3期590-597,共8页
NAC转录因子是植物特有的转录因子并在植物的生长发育过程中发挥重要的作用,根据其他植物NAC转录因子基因的氨基酸保守序列设计简并引物,通过RT-PCR和RACE技术从白羊草(Bothriochloa ischaemum)中获得了全长cDNA,命名为BiNAC。序列分析... NAC转录因子是植物特有的转录因子并在植物的生长发育过程中发挥重要的作用,根据其他植物NAC转录因子基因的氨基酸保守序列设计简并引物,通过RT-PCR和RACE技术从白羊草(Bothriochloa ischaemum)中获得了全长cDNA,命名为BiNAC。序列分析表明,该cDNA片段全长为1549bp,开放阅读框1125bp,编码374个氨基酸,具有典型的NAC类蛋白的结构特征。进化树分析表明,该蛋白属于ATAF亚族,与高粱(Sorghum bi-color)亲缘关系最近,同源性达到94%。Real-time PCR检测结果表明,BiNAC基因在茎中的表达量最高,根中表达量最少,并且受NaCl胁迫表达上调。同时成功构建了植物表达载体pBI121-BiNAC-GUS,为进一步开展NAC基因的功能研究创造了条件。 展开更多
关键词 白羊草 NAC转录因子 表达分析 基因序列
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厚叶悬蒴苣苔BcWRKY1转录因子基因的克隆及初步的功能分析 被引量:9
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作者 刘戈宇 胡鸢雷 +2 位作者 赵锋 祝建波 林忠平 《北京大学学报(自然科学版)》 EI CAS CSCD 北大核心 2007年第4期446-452,共7页
通过RT-PCR程序,从经过SA诱导的厚叶悬蒴苣苔中获得含WRKY家族保守序列的一条cDNA片段。运用RACE(Rapid Amplification of cDNA Ends)技术获得全长1803bp的cDNA克隆,名之为BcWRKY1。序列分析表明:BcWRKY1与甘薯SPF1[D30038]相似性最高,... 通过RT-PCR程序,从经过SA诱导的厚叶悬蒴苣苔中获得含WRKY家族保守序列的一条cDNA片段。运用RACE(Rapid Amplification of cDNA Ends)技术获得全长1803bp的cDNA克隆,名之为BcWRKY1。序列分析表明:BcWRKY1与甘薯SPF1[D30038]相似性最高,保守区同源性达到84%。初步的Northern杂交分析表明:干旱、低温、高盐等逆境胁迫和外加SA、MeJA、JA、ABA等信号分子的诱导均能提高BcWRKY1基因的表达。但是表达情况各不相同。150mmol/L NaCl对BcWRKY1的诱导作用尤为明显和迅速。2168bp的BcWRKY1的基因组DNA克隆亦已获得,序列分析表明它含有4个内含子。 展开更多
关键词 厚叶悬蒴苣苔 WRKY转录因子 功能分析
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小麦NAC转录因子的基因克隆与序列分析 被引量:6
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作者 史红飞 高翔 +6 位作者 陈其皎 董剑 赵万春 李晓燕 王延鹏 臧闻 李志业 《麦类作物学报》 CAS CSCD 北大核心 2011年第3期395-401,共7页
为了深入研究小麦中NAC家族转录因子基因,针对NAC基因家族成员,设计了覆盖其全长编码区的1对特异引物,从陕253小麦品种中克隆了2条大小分别为1 463、1549 bp的片段,命名为TaNAC2、TaNAC4(GenBank登录号为HQ872050-HQ872051)。序列分析表... 为了深入研究小麦中NAC家族转录因子基因,针对NAC基因家族成员,设计了覆盖其全长编码区的1对特异引物,从陕253小麦品种中克隆了2条大小分别为1 463、1549 bp的片段,命名为TaNAC2、TaNAC4(GenBank登录号为HQ872050-HQ872051)。序列分析表明,这2个序列包含典型NAC的完整编码序列,包括两个内含子,具有完整的开放阅读框;推导的氨基酸序列分别为383、405个,这2个基因在N-端均具有NAC基因的典型DNA结合结构域,即NAC结构域,且氨基酸序列在该结构域的A、B、C、D、E5个亚区高度保守,仅在C亚区出现一个氨基酸的差异L-M,而且在C-D区出现罕见的半胱氨酸变异,此发现对于小麦品质的研究非常重要。同时发现这2个NAC类转录因子都不含有核定位信号(NLS),但是有相关的转录调控功能区域。通过系统进化树分析,证实克隆序列属于NAC基因家族成员,并且发现的TaNAC4属于NAC转录因子家族的NAM亚组,TaNAC2属于NAC转录因子家族的CUC亚组。 展开更多
关键词 小麦 陕253 NAC转录因子 基因克隆 序列分析
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