This paper discusses the design of the queue for DNA-based computer on the point view of data structure. The nucleotide encodings for all components of the queue are given out formally. The linear double-stranded DNA ...This paper discusses the design of the queue for DNA-based computer on the point view of data structure. The nucleotide encodings for all components of the queue are given out formally. The linear double-stranded DNA molecules are used as the storage structure of the queue, and the basic bio-operations over the queue are described. Furthermore, the comparison between the queue of the electronic computer and that of DNA-based computer are elucidated. To prove the feasibility of our work, nucleotide encodings for an instance of queue are given out. All the biological technology mentioned in this paper can be practically implemented in the laboratory. Based on this work, other data structures could be developed in DNA-based computer.展开更多
目的检测膀胱癌中长链非编码RNA(long non-coding RNA,lncRNA)烟酰胺核苷酸转氢酶反义RNA1(nicotinamide nucleotide transhydrogenase antisense RNA 1,NNT-AS1)表达情况,研究其对膀胱癌细胞增殖、迁移、侵袭及肿瘤干细胞干性的影响及...目的检测膀胱癌中长链非编码RNA(long non-coding RNA,lncRNA)烟酰胺核苷酸转氢酶反义RNA1(nicotinamide nucleotide transhydrogenase antisense RNA 1,NNT-AS1)表达情况,研究其对膀胱癌细胞增殖、迁移、侵袭及肿瘤干细胞干性的影响及可能分子机制。方法实时荧光定量PCR(quantitative real-time PCR,qRT-PCR)法检测膀胱癌组织标本及细胞中LncRNA NNT-AS1表达情况;将膀胱癌细胞转染分为sh-NC组,sh-NNT-AS1组,sh-NNT-AS1+inh-582-5p组和sh-NNT-AS1+inh-582-5p+si-NCKAP1组。采用CCK-8法检测细胞增殖吸光度值(A值);Transwell实验检测细胞迁移、侵袭穿膜数;细胞成球实验检测干细胞干性。检索starBase和TargetScan数据库,并通过双荧光素酶报告基因实验预测验证LncRNA NNT-AS1和miR-582-5p,miR-582-5p与NCKAP1的靶向结合关系。Western blot检测膀胱癌干细胞标志蛋白(CD44,ALDH1A1,Oct4,Nanog)及Hippo-YAP/TAZ信号通路相关蛋白表达灰度值。结果与癌旁组织相比,膀胱癌组织中LncRNA NNT-AS1表达水平(0.34±0.07 vs 1.15±0.21)明显升高,差异有统计学意义(t=16.364,P<0.001)。与人正常膀胱上皮SV-HUC-1细胞(1.00±0.01)相比,膀胱癌细胞T24,5637,UM-UC-3和TCC-SUP中LncRNA NNT-AS1表达(6.03±0.17,4.66±0.36,5.47±0.26,3.02±0.20)明显升高,差异有统计学意义(t=17.472~51.160,均P<0.001)。与sh-NC组相比,在24,48和72 h时sh-NNT-AS1组细胞增值能力(A值)均显著降低(0.80±0.01 vs 1.07±0.06,1.18±0..07 vs 1.83±0.03,1.89±0.07 vs 2.53±0.06),差异有统计学意义(t=7.688,14.783,12.024,均P<0.05);sh-NNT-AS1组细胞迁移穿膜数(55.00±2.65个vs 354.30±7.84个)、细胞侵袭穿膜数(45.67±2.33个vs 303.00±9.07个)及膀胱癌干细胞成球数(20.85±2.17个vs 41.35±3.67个)显著降低,差异具有统计学意义(t=-62.641,-47.596,8.328,均P<0.001)。与sh-NC组相比,sh-NNT-AS1组细胞中CD44(0.04±0.01 vs 1.12±0.02),ALDH1A1(0.23±0.01 vs 1.16±0.05),Oct4(0.17±0.02 vs 1.10±0.04),Nanog(0.49±0.03 vs 1.24±0.03)的蛋白表达灰度值显著降低,差异具有统计学意义(t=83.656,31.591,36.019,30.619,均P<0.001)。与si-NC组相比,sh-NNT-AS1组CD44+CD133+细胞比例(9.30%±0.79%vs 88.50%±2.77%)明显降低,差异有统计学意义(t=-47.624,P<0.001)。双荧光素酶报告基因检测结果显示miR-582-5p为LncRNANNT-AS1靶基因,NCKAP1为miR-582-5p靶基因;LncRNA NNT-AS1靶向调控miR-582-5p/NCKAP1轴。与sh-NNT-AS1组相比,在24,48,72 h时sh-NNT-AS1+inh-582-5p组细胞增值能力(A值)均明显升高(0.98±0.03 vs 0.73±0.06,1.74±0.04 vs 1.22±0.05,2.33±0.16 vs 1.69±0.14),差异有统计学意义(t=5.977~11.628,均P<0.001)。与sh-NNT-AS1+inh-582-5p组相比,在24,48,72 h时sh-NNT-AS1+inh-582-5p+si-NCKAP1组细胞增值能力(A值)显著降低(0.69±0.04,1.01±0.07,1.39±0.08),差异有统计学意义(t=7.877~16.323,均P<0.001)。与sh-NNT-AS1组相比,sh-NNT-AS1+inh-582-5p组细胞迁移穿膜数(322.31±28.45个vs 81.42±13.22个)、细胞侵袭穿膜数(316.07±30.21个vs 92.13±12.65个)及膀胱癌干细胞成球数(38.55±2.20个vs 18.98±1.16个)显著增加,差异具有统计学意义(t=15.115,13.158,14.592,均P<0.001)。与sh-NNT-AS1组相比,sh-NNT-AS1+inh-582-5p组细胞CD44(1.05±0.08 vs 0.10±0.01),ALDH1A1(1.20±0.16 vs 0.22±0.02),Oct4(1.32±0.14 vs 0.19±0.03),Nanog(0.97±0.12 vs 0.15±0.04),YAP(1.29±0.11 vs 0.42±0.07)和TAZ(1.41±0.16 vs 0.35±0.05)蛋白表达灰度值均显著增加,差异具有统计学意义(t=10.650~21.243,均P<0.001)。与sh-NNT-AS1+inh-582-5p组相比,sh-NNT-AS1+inh-582-5p+si-NCKAP1组细胞迁移穿膜数(65.33±12.60个)、细胞侵袭穿膜数(71.08±15.19个)、膀胱癌干细胞成球数(11.36±1.05个)均显著降低,差异具有统计学意义(t=16.125,14.395,21.365,均P<0.001)。与sh-NNT-AS1+inh-582-5p组相比,sh-NNT-AS1+inh-582-5p+si-NCKAP1组细胞CD44(0.25±0.05),ALDH1A1(0.61±0.11),Oct4(0.22±0.08),Nanog(0.44±0.07),YAP(0.25±0.09)和TAZ(0.30±0.04)蛋白表达灰度值显著降低,差异具有统计学意义(t=6.412~17.889,均P<0.001)。结论膀胱癌中LncRNA NNT-AS1表达上调,其对膀胱癌细胞增殖、侵袭及肿瘤干细胞干性的影响,可能是通过调控miR-582-5p/NCKAP1分子轴,激活Hippo-YAP/TAZ信号通路完成。展开更多
Rather than random degradation products, the 18 to 40 nucleotides(nt) transfer RNA-derived small RNAs(tsRNAs) are RNA species generated specifically from pre-RNAs or mature tRNAs in archaea, bacteria and eukaryotes. R...Rather than random degradation products, the 18 to 40 nucleotides(nt) transfer RNA-derived small RNAs(tsRNAs) are RNA species generated specifically from pre-RNAs or mature tRNAs in archaea, bacteria and eukaryotes. Recent studies from animal systems have shown that tsRNAs are important non-coding RNAs that regulate gene expression at the transcriptional and/or post-transcriptional levels. They are involved in various biological processes, such as cell proliferation, tumor genesis, stress response and intergenerational epigenetic inheritance. In this review, we will summarize the discovery, biogenesis, and function of tsRNAs in higher plants. In addition, analysis on tsRNAs from lower plants is shown.展开更多
A growing number of genes responsible for reproductive incompatibilities between species （barrier loci） exhibit the signals of positive selection. However, the possibility that genes experiencing positive selection ...A growing number of genes responsible for reproductive incompatibilities between species （barrier loci） exhibit the signals of positive selection. However, the possibility that genes experiencing positive selection diverge early in speciation and commonly cause reproductive incompatibilities has not been systematically investigated on a genome-wide scale. Here, I outline a research program for studying the genetic basis of speciation in broadcast spawning marine invertebrates that uses a priori genome-wide information on a large, unbiased sample of genes tested for positive selection. A targeted sequence capture approach is proposed that scores single-nucleotide polymorphisms （SNPs） in widely separated species populations at an early stage of allopatric divergence. The targeted capture of both coding and non-coding sequences enables SNPs to be characterized at known locations across the genome and at genes with known selective or neutral histories. The neutral coding and non-coding SNPs provide robust background distributions for identifying Fsm-outliers within genes that can, in principle, identify specific mutations experiencing diversifying selection. If natural hybridization occurs between species, the neutral coding and noncoding SNPs can provide a neutral admixture model for genomic clines analyses aimed at finding genes exhibiting strong blocks to introgression. Strongylocentrotid sea urchins are used as a model system to outline the approach but it can be used for any group that has a complete reference genome available.展开更多
基金This work was supportedin part by the National Nature Science Foundation of China (No.60474037and60004006) Programfor NewCentury Excellent Talents in University (NCET04 415) +1 种基金Specialized Research Fund for the Doctoral Programof Higher Educationfrom Educational Committee of China (No.20030255009) the Youth Foundation fromEducational Committee of Anhui Province(No.2005jql043) .
文摘This paper discusses the design of the queue for DNA-based computer on the point view of data structure. The nucleotide encodings for all components of the queue are given out formally. The linear double-stranded DNA molecules are used as the storage structure of the queue, and the basic bio-operations over the queue are described. Furthermore, the comparison between the queue of the electronic computer and that of DNA-based computer are elucidated. To prove the feasibility of our work, nucleotide encodings for an instance of queue are given out. All the biological technology mentioned in this paper can be practically implemented in the laboratory. Based on this work, other data structures could be developed in DNA-based computer.
文摘目的检测膀胱癌中长链非编码RNA(long non-coding RNA,lncRNA)烟酰胺核苷酸转氢酶反义RNA1(nicotinamide nucleotide transhydrogenase antisense RNA 1,NNT-AS1)表达情况,研究其对膀胱癌细胞增殖、迁移、侵袭及肿瘤干细胞干性的影响及可能分子机制。方法实时荧光定量PCR(quantitative real-time PCR,qRT-PCR)法检测膀胱癌组织标本及细胞中LncRNA NNT-AS1表达情况;将膀胱癌细胞转染分为sh-NC组,sh-NNT-AS1组,sh-NNT-AS1+inh-582-5p组和sh-NNT-AS1+inh-582-5p+si-NCKAP1组。采用CCK-8法检测细胞增殖吸光度值(A值);Transwell实验检测细胞迁移、侵袭穿膜数;细胞成球实验检测干细胞干性。检索starBase和TargetScan数据库,并通过双荧光素酶报告基因实验预测验证LncRNA NNT-AS1和miR-582-5p,miR-582-5p与NCKAP1的靶向结合关系。Western blot检测膀胱癌干细胞标志蛋白(CD44,ALDH1A1,Oct4,Nanog)及Hippo-YAP/TAZ信号通路相关蛋白表达灰度值。结果与癌旁组织相比,膀胱癌组织中LncRNA NNT-AS1表达水平(0.34±0.07 vs 1.15±0.21)明显升高,差异有统计学意义(t=16.364,P<0.001)。与人正常膀胱上皮SV-HUC-1细胞(1.00±0.01)相比,膀胱癌细胞T24,5637,UM-UC-3和TCC-SUP中LncRNA NNT-AS1表达(6.03±0.17,4.66±0.36,5.47±0.26,3.02±0.20)明显升高,差异有统计学意义(t=17.472~51.160,均P<0.001)。与sh-NC组相比,在24,48和72 h时sh-NNT-AS1组细胞增值能力(A值)均显著降低(0.80±0.01 vs 1.07±0.06,1.18±0..07 vs 1.83±0.03,1.89±0.07 vs 2.53±0.06),差异有统计学意义(t=7.688,14.783,12.024,均P<0.05);sh-NNT-AS1组细胞迁移穿膜数(55.00±2.65个vs 354.30±7.84个)、细胞侵袭穿膜数(45.67±2.33个vs 303.00±9.07个)及膀胱癌干细胞成球数(20.85±2.17个vs 41.35±3.67个)显著降低,差异具有统计学意义(t=-62.641,-47.596,8.328,均P<0.001)。与sh-NC组相比,sh-NNT-AS1组细胞中CD44(0.04±0.01 vs 1.12±0.02),ALDH1A1(0.23±0.01 vs 1.16±0.05),Oct4(0.17±0.02 vs 1.10±0.04),Nanog(0.49±0.03 vs 1.24±0.03)的蛋白表达灰度值显著降低,差异具有统计学意义(t=83.656,31.591,36.019,30.619,均P<0.001)。与si-NC组相比,sh-NNT-AS1组CD44+CD133+细胞比例(9.30%±0.79%vs 88.50%±2.77%)明显降低,差异有统计学意义(t=-47.624,P<0.001)。双荧光素酶报告基因检测结果显示miR-582-5p为LncRNANNT-AS1靶基因,NCKAP1为miR-582-5p靶基因;LncRNA NNT-AS1靶向调控miR-582-5p/NCKAP1轴。与sh-NNT-AS1组相比,在24,48,72 h时sh-NNT-AS1+inh-582-5p组细胞增值能力(A值)均明显升高(0.98±0.03 vs 0.73±0.06,1.74±0.04 vs 1.22±0.05,2.33±0.16 vs 1.69±0.14),差异有统计学意义(t=5.977~11.628,均P<0.001)。与sh-NNT-AS1+inh-582-5p组相比,在24,48,72 h时sh-NNT-AS1+inh-582-5p+si-NCKAP1组细胞增值能力(A值)显著降低(0.69±0.04,1.01±0.07,1.39±0.08),差异有统计学意义(t=7.877~16.323,均P<0.001)。与sh-NNT-AS1组相比,sh-NNT-AS1+inh-582-5p组细胞迁移穿膜数(322.31±28.45个vs 81.42±13.22个)、细胞侵袭穿膜数(316.07±30.21个vs 92.13±12.65个)及膀胱癌干细胞成球数(38.55±2.20个vs 18.98±1.16个)显著增加,差异具有统计学意义(t=15.115,13.158,14.592,均P<0.001)。与sh-NNT-AS1组相比,sh-NNT-AS1+inh-582-5p组细胞CD44(1.05±0.08 vs 0.10±0.01),ALDH1A1(1.20±0.16 vs 0.22±0.02),Oct4(1.32±0.14 vs 0.19±0.03),Nanog(0.97±0.12 vs 0.15±0.04),YAP(1.29±0.11 vs 0.42±0.07)和TAZ(1.41±0.16 vs 0.35±0.05)蛋白表达灰度值均显著增加,差异具有统计学意义(t=10.650~21.243,均P<0.001)。与sh-NNT-AS1+inh-582-5p组相比,sh-NNT-AS1+inh-582-5p+si-NCKAP1组细胞迁移穿膜数(65.33±12.60个)、细胞侵袭穿膜数(71.08±15.19个)、膀胱癌干细胞成球数(11.36±1.05个)均显著降低,差异具有统计学意义(t=16.125,14.395,21.365,均P<0.001)。与sh-NNT-AS1+inh-582-5p组相比,sh-NNT-AS1+inh-582-5p+si-NCKAP1组细胞CD44(0.25±0.05),ALDH1A1(0.61±0.11),Oct4(0.22±0.08),Nanog(0.44±0.07),YAP(0.25±0.09)和TAZ(0.30±0.04)蛋白表达灰度值显著降低,差异具有统计学意义(t=6.412~17.889,均P<0.001)。结论膀胱癌中LncRNA NNT-AS1表达上调,其对膀胱癌细胞增殖、侵袭及肿瘤干细胞干性的影响,可能是通过调控miR-582-5p/NCKAP1分子轴,激活Hippo-YAP/TAZ信号通路完成。
基金supported by the General Program of National Natural Science Foundation of China (31471165 to Zhicheng Dong)
文摘Rather than random degradation products, the 18 to 40 nucleotides(nt) transfer RNA-derived small RNAs(tsRNAs) are RNA species generated specifically from pre-RNAs or mature tRNAs in archaea, bacteria and eukaryotes. Recent studies from animal systems have shown that tsRNAs are important non-coding RNAs that regulate gene expression at the transcriptional and/or post-transcriptional levels. They are involved in various biological processes, such as cell proliferation, tumor genesis, stress response and intergenerational epigenetic inheritance. In this review, we will summarize the discovery, biogenesis, and function of tsRNAs in higher plants. In addition, analysis on tsRNAs from lower plants is shown.
基金Acknowledgments I would like to thank Nicolas Bierne for the opportunity of contributing to the Special Column： Population Genomics in the Sea. Helpful comments on the manuscript were provided by Nicolas Bierne and two anonymous reviewers.Partial funding for the work described on strongylocentrotid sea urchins was provided by the Natinal Science Foundation （DEB-1011061 ）.
文摘A growing number of genes responsible for reproductive incompatibilities between species （barrier loci） exhibit the signals of positive selection. However, the possibility that genes experiencing positive selection diverge early in speciation and commonly cause reproductive incompatibilities has not been systematically investigated on a genome-wide scale. Here, I outline a research program for studying the genetic basis of speciation in broadcast spawning marine invertebrates that uses a priori genome-wide information on a large, unbiased sample of genes tested for positive selection. A targeted sequence capture approach is proposed that scores single-nucleotide polymorphisms （SNPs） in widely separated species populations at an early stage of allopatric divergence. The targeted capture of both coding and non-coding sequences enables SNPs to be characterized at known locations across the genome and at genes with known selective or neutral histories. The neutral coding and non-coding SNPs provide robust background distributions for identifying Fsm-outliers within genes that can, in principle, identify specific mutations experiencing diversifying selection. If natural hybridization occurs between species, the neutral coding and noncoding SNPs can provide a neutral admixture model for genomic clines analyses aimed at finding genes exhibiting strong blocks to introgression. Strongylocentrotid sea urchins are used as a model system to outline the approach but it can be used for any group that has a complete reference genome available.
