Modeling non coding background sequences appropriately is important for the detection of regulatory elements from DNA sequences. Based on the chi square statistic test, some explanations about why to choose higher ...Modeling non coding background sequences appropriately is important for the detection of regulatory elements from DNA sequences. Based on the chi square statistic test, some explanations about why to choose higher order Markov chain model and how to automatically select the proper order are given in this paper. The chi square test is first run on synthetic data sets to show that it can efficiently find the proper order of Markov chain. Using chi square test, distinct higher order context dependences inherent in ten sets of sequences of yeast S.cerevisiae from other literature have been found. So the Markov chain with higher order would be more suitable for modeling the non coding background sequences than an independent model.展开更多
Hepatocellular carcinoma(HCC) is one of the most common malignancies leading to high mortality rates in the general population and the sixth most common cancer worldwide. HCC is characterized by deregulation of multip...Hepatocellular carcinoma(HCC) is one of the most common malignancies leading to high mortality rates in the general population and the sixth most common cancer worldwide. HCC is characterized by deregulation of multiple genes and signalling pathways. These genetic effects can involve both protein coding genes as well as non-coding RNA genes. Long noncoding RNAs(lnc RNAs) are transcripts longer than 200 nt, constituting a subpopulation of nc RNAs. Their biological effects are not well understood comparedto small non-coding RNA(micro RNAs), but they have been recently recognized to exert a crucial role in the regulation of gene expression and modulation of signalling pathways. Notably, several studies indicated that lnc RNAs contribute to the pathogenesis and progression of HCC. Investigating the molecular mechanisms underlying lnc RNAs expression opens potential applications in diagnosis and treatment of liver disease. This editorial provides three examples(MALAT-1 metastasis associated lung adenocarcinoma transcript, HULC highly upregulated in liver cancer and HOTAIR HOX transcript antisense intergenic RNA) of well-known lnc RNAs upregulated in HCC, whose mechanisms of action are known, and for which therapeutic applications are delineated. Targeting of lnc RNAs using several approaches(siR NA-mediated silencing or changing their secondary structure) offers new possibility to treat HCC.展开更多
In this paper , through the discrim ination of Farey sequence in the forced Brusselator withweak coupling , it is proved that there is a topological translation fro m a nonlinear differen tial system ( limit cycle)...In this paper , through the discrim ination of Farey sequence in the forced Brusselator withweak coupling , it is proved that there is a topological translation fro m a nonlinear differen tial system ( limit cycle) to the circle m ap .展开更多
Long non-coding RNAs(lncRNAs)are abundantly expressed in the central nervous system and exert a critical role in gene regulation via multiple biological processes.To uncover the functional significance and molecular m...Long non-coding RNAs(lncRNAs)are abundantly expressed in the central nervous system and exert a critical role in gene regulation via multiple biological processes.To uncover the functional significance and molecular mechanisms of lncRNAs in spinal cord injury(SCI),the expression signatures of lncRNAs were profiled using RNA sequencing(RNA-seq)technology in a Sprague-Dawley rat model of the 10th thoracic vertebra complete transection SCI.Results showed that 116 of 14,802 detected lncRNAs were differentially expressed,among which 16—including eight up-regulated(H19,Vof16,Hmox2-ps1,LOC100910973,Ybx1-ps3,Nnat,Gcgr,LOC680254)and eight down-regulated(Rmrp,Terc,Ngrn,Ppp2r2b,Cox6a2,Rpl37a-ps1,LOC360231,Rpph1)—demonstrated fold changes>2 in response to transection SCI.A subset of these RNA-seq results was validated by quantitative real-time PCR.The levels of 821 mRNAs were also significantly altered post-SCI;592 mRNAs were up-regulated and 229 mRNAs were down-regulated by more than 2-fold.Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)analyses showed that differentially expressed mRNAs were related to GO biological processes and molecular functions such as injury and inflammation response,wound repair,and apoptosis,and were significantly enriched in 15 KEGG pathways,including cell phagocytosis,tumor necrosis factor alpha pathway,and leukocyte migration.Our results reveal the expression profiles of lncRNAs and mRNAs in the rat spinal cord of a complete transection model,and these differentially expressed lncRNAs and mRNAs represent potential novel targets for SCI treatment.We suggest that lncRNAs may play an important role in the early immuno-inflammatory response after spinal cord injury.This study was approved by the Administration Committee of Experimental Animals,Guangdong Province,China.展开更多
Small non-coding RNAs with important regulatory roles are not confined to eukaryotes. Recent work has uncovered a growing number of bacterial small RNAs （sRNAs）, some of which have been shown to regulate critical ce...Small non-coding RNAs with important regulatory roles are not confined to eukaryotes. Recent work has uncovered a growing number of bacterial small RNAs （sRNAs）, some of which have been shown to regulate critical cellular processes. Computational approaches, in combination with molecular experiments, have played an important role in the identification of these sRNAs. At present, there is no information on the presence of small non-coding RNAs and their genes in the Agrobacterium tumefaciens genome. To identify potential sRNAs in this important bacterium, deep sequencing of the short RNA populations isolated from Agrobacterium tumefaciens C58 was carried out. From a data set of more than 10,000 short sequences, 16 candidate sRNAs have been tentatively identified based on computational analysis. All of these candidates can form stem-loop structures by RNA folding predictions and the majority of the secondary structures are rich in GC base-pairs：：Some are followed by a short stretch of U residues, indicative of a rho-independent transcription terminator, whereas some of the short RNAs are found in the stem region of the hairpin, indicative of eukaryotic-like sRNAs. Experimental strategies will need to be used to verify these candidates. The study of an expanded list of candidate sRNAs in Agrobacterium will allow a more complete understanding of the range of roles played by regulatory RNAs in prokaryotes.展开更多
目的通过对不明原因复发性流产(URSA)孕妇绒毛组织的lncRNA比对参考基因组进行注释,探究URSA中潜在的lncRNA生物学靶点。方法收集4例URSA(实验组)和4例选择性终止妊娠(ETP)孕妇(对照组)的绒毛组织样本,使用StringTie处理并预测各转录本,...目的通过对不明原因复发性流产(URSA)孕妇绒毛组织的lncRNA比对参考基因组进行注释,探究URSA中潜在的lncRNA生物学靶点。方法收集4例URSA(实验组)和4例选择性终止妊娠(ETP)孕妇(对照组)的绒毛组织样本,使用StringTie处理并预测各转录本,DESeq2获得差异表达lncRNA,Kyoto Encyclopedia of Genes and Genomes(KEGG)富集分析对lncRNA反式调控及lncRNA顺式调控潜在通路进行探索。结果使用4种编码潜能分析方法对候选lncRNA进行进一步的筛选,共有474个共表达转录本,接着DESeq2获得差异表达lncRNA,有705个显著上调lncRNA数目和107个显著下调表达lncRNA数目,对差异表达的lncRNA和所有差异表达的基因进行共表达分析,其中lncRNA反式调控分子功能主要作用在蛋白结合,生物过程发生在细胞外基质组织,存在于细胞表面。KEGG结果显示其主要是作用于lncRNA HLA-DQA2进而富集在金黄色葡萄球菌感染通路。lncRNA顺式调控分子功能主要作用在蛋白结合,生物过程发生在RNA聚合酶对转录的调节,存在于核染色质。KEGG富集结果显示其主要是作用于lncRNA HLA-DQA2以及BIRCT进而富集在弓形体病感染通路。结论lncRNA HLA-DQA2可能通过调控炎症感染信号通路导致不明原因复发性流产,其可能成为潜在的治疗靶点。展开更多
针对非周期长码直接序列扩频(Non-Periodic Long Code Direct Sequence Spread Spectrum,NPLC-DSSS)信号扩频码盲估计的问题,在已知扩频周期,信息码码元宽度以及码速率的条件下,本文提出了一种基于相似度的伪码序列盲估计方法.该方法通...针对非周期长码直接序列扩频(Non-Periodic Long Code Direct Sequence Spread Spectrum,NPLC-DSSS)信号扩频码盲估计的问题,在已知扩频周期,信息码码元宽度以及码速率的条件下,本文提出了一种基于相似度的伪码序列盲估计方法.该方法通过构造信息码库,利用平均相似度对信息码进行同步,再利用特征值分解对扩频码序列进行估计.仿真实验表明,该算法较现有算法不仅抗噪声性能提高了1 dB,而且能够对信息码同步位置及伪码序列进行联合盲估计.展开更多
针对码索引调制(Code Index Modulation, CIM)相对于直接序列扩频在提升频谱利用率时,造成误比特率性能明显下降的问题,该文提出非正交-码索引调制(Non-orthogonal-Code Index Modulation, N-CIM)。发射端信息比特分割为伪随机(Pseudo N...针对码索引调制(Code Index Modulation, CIM)相对于直接序列扩频在提升频谱利用率时,造成误比特率性能明显下降的问题,该文提出非正交-码索引调制(Non-orthogonal-Code Index Modulation, N-CIM)。发射端信息比特分割为伪随机(Pseudo Noise, PN)码映射块和调制信息块,并分别映射为PN码的索引和调制符号,调制符号的实部与虚部再选择相同的激活的PN码进行扩频。仿真与分析结果表明,在相同频谱效率时,N-CIM的误比特率性能比CIM在加性高斯白噪声信道中当误比特率为10–5时具备约2～3 dB的优势,在瑞利衰落信道中当误比特率为10–2时具备约2 dB的优势。展开更多
文摘Modeling non coding background sequences appropriately is important for the detection of regulatory elements from DNA sequences. Based on the chi square statistic test, some explanations about why to choose higher order Markov chain model and how to automatically select the proper order are given in this paper. The chi square test is first run on synthetic data sets to show that it can efficiently find the proper order of Markov chain. Using chi square test, distinct higher order context dependences inherent in ten sets of sequences of yeast S.cerevisiae from other literature have been found. So the Markov chain with higher order would be more suitable for modeling the non coding background sequences than an independent model.
文摘Hepatocellular carcinoma(HCC) is one of the most common malignancies leading to high mortality rates in the general population and the sixth most common cancer worldwide. HCC is characterized by deregulation of multiple genes and signalling pathways. These genetic effects can involve both protein coding genes as well as non-coding RNA genes. Long noncoding RNAs(lnc RNAs) are transcripts longer than 200 nt, constituting a subpopulation of nc RNAs. Their biological effects are not well understood comparedto small non-coding RNA(micro RNAs), but they have been recently recognized to exert a crucial role in the regulation of gene expression and modulation of signalling pathways. Notably, several studies indicated that lnc RNAs contribute to the pathogenesis and progression of HCC. Investigating the molecular mechanisms underlying lnc RNAs expression opens potential applications in diagnosis and treatment of liver disease. This editorial provides three examples(MALAT-1 metastasis associated lung adenocarcinoma transcript, HULC highly upregulated in liver cancer and HOTAIR HOX transcript antisense intergenic RNA) of well-known lnc RNAs upregulated in HCC, whose mechanisms of action are known, and for which therapeutic applications are delineated. Targeting of lnc RNAs using several approaches(siR NA-mediated silencing or changing their secondary structure) offers new possibility to treat HCC.
文摘In this paper , through the discrim ination of Farey sequence in the forced Brusselator withweak coupling , it is proved that there is a topological translation fro m a nonlinear differen tial system ( limit cycle) to the circle m ap .
基金financially supported by the National Natural Science Foundation of China,No.81371366(to HFW)Characteristic Innovation Project of Colleges and Universities in Guangdong Province of China,No.2018KTSCX075(to HFW)+3 种基金the Key Project of Social Development of Dongguan of China,No.20185071521640(to HFW)College Students’ Science and Technology Innovation Training Project,China,Nos.201810571058,GDMU2018024,GDMU2018056,GDMU2018061(to HFW)College Students’ Innovative Experimental Project in Guangdong Medical University,China,No.ZZDS001(to HFW)College Students’ Science and Technology Innovation Cultivation Project in Guangdong of China,No.pdjh2019b0217(to HFW)
文摘Long non-coding RNAs(lncRNAs)are abundantly expressed in the central nervous system and exert a critical role in gene regulation via multiple biological processes.To uncover the functional significance and molecular mechanisms of lncRNAs in spinal cord injury(SCI),the expression signatures of lncRNAs were profiled using RNA sequencing(RNA-seq)technology in a Sprague-Dawley rat model of the 10th thoracic vertebra complete transection SCI.Results showed that 116 of 14,802 detected lncRNAs were differentially expressed,among which 16—including eight up-regulated(H19,Vof16,Hmox2-ps1,LOC100910973,Ybx1-ps3,Nnat,Gcgr,LOC680254)and eight down-regulated(Rmrp,Terc,Ngrn,Ppp2r2b,Cox6a2,Rpl37a-ps1,LOC360231,Rpph1)—demonstrated fold changes>2 in response to transection SCI.A subset of these RNA-seq results was validated by quantitative real-time PCR.The levels of 821 mRNAs were also significantly altered post-SCI;592 mRNAs were up-regulated and 229 mRNAs were down-regulated by more than 2-fold.Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)analyses showed that differentially expressed mRNAs were related to GO biological processes and molecular functions such as injury and inflammation response,wound repair,and apoptosis,and were significantly enriched in 15 KEGG pathways,including cell phagocytosis,tumor necrosis factor alpha pathway,and leukocyte migration.Our results reveal the expression profiles of lncRNAs and mRNAs in the rat spinal cord of a complete transection model,and these differentially expressed lncRNAs and mRNAs represent potential novel targets for SCI treatment.We suggest that lncRNAs may play an important role in the early immuno-inflammatory response after spinal cord injury.This study was approved by the Administration Committee of Experimental Animals,Guangdong Province,China.
文摘Small non-coding RNAs with important regulatory roles are not confined to eukaryotes. Recent work has uncovered a growing number of bacterial small RNAs （sRNAs）, some of which have been shown to regulate critical cellular processes. Computational approaches, in combination with molecular experiments, have played an important role in the identification of these sRNAs. At present, there is no information on the presence of small non-coding RNAs and their genes in the Agrobacterium tumefaciens genome. To identify potential sRNAs in this important bacterium, deep sequencing of the short RNA populations isolated from Agrobacterium tumefaciens C58 was carried out. From a data set of more than 10,000 short sequences, 16 candidate sRNAs have been tentatively identified based on computational analysis. All of these candidates can form stem-loop structures by RNA folding predictions and the majority of the secondary structures are rich in GC base-pairs：：Some are followed by a short stretch of U residues, indicative of a rho-independent transcription terminator, whereas some of the short RNAs are found in the stem region of the hairpin, indicative of eukaryotic-like sRNAs. Experimental strategies will need to be used to verify these candidates. The study of an expanded list of candidate sRNAs in Agrobacterium will allow a more complete understanding of the range of roles played by regulatory RNAs in prokaryotes.
文摘目的通过对不明原因复发性流产(URSA)孕妇绒毛组织的lncRNA比对参考基因组进行注释,探究URSA中潜在的lncRNA生物学靶点。方法收集4例URSA(实验组)和4例选择性终止妊娠(ETP)孕妇(对照组)的绒毛组织样本,使用StringTie处理并预测各转录本,DESeq2获得差异表达lncRNA,Kyoto Encyclopedia of Genes and Genomes(KEGG)富集分析对lncRNA反式调控及lncRNA顺式调控潜在通路进行探索。结果使用4种编码潜能分析方法对候选lncRNA进行进一步的筛选,共有474个共表达转录本,接着DESeq2获得差异表达lncRNA,有705个显著上调lncRNA数目和107个显著下调表达lncRNA数目,对差异表达的lncRNA和所有差异表达的基因进行共表达分析,其中lncRNA反式调控分子功能主要作用在蛋白结合,生物过程发生在细胞外基质组织,存在于细胞表面。KEGG结果显示其主要是作用于lncRNA HLA-DQA2进而富集在金黄色葡萄球菌感染通路。lncRNA顺式调控分子功能主要作用在蛋白结合,生物过程发生在RNA聚合酶对转录的调节,存在于核染色质。KEGG富集结果显示其主要是作用于lncRNA HLA-DQA2以及BIRCT进而富集在弓形体病感染通路。结论lncRNA HLA-DQA2可能通过调控炎症感染信号通路导致不明原因复发性流产,其可能成为潜在的治疗靶点。
文摘针对非周期长码直接序列扩频(Non-Periodic Long Code Direct Sequence Spread Spectrum,NPLC-DSSS)信号扩频码盲估计的问题,在已知扩频周期,信息码码元宽度以及码速率的条件下,本文提出了一种基于相似度的伪码序列盲估计方法.该方法通过构造信息码库,利用平均相似度对信息码进行同步,再利用特征值分解对扩频码序列进行估计.仿真实验表明,该算法较现有算法不仅抗噪声性能提高了1 dB,而且能够对信息码同步位置及伪码序列进行联合盲估计.
