基于功率谱分析的基因编码序列单碱基突变研究

针对DNA序列单碱基的不同类型突变,利用数字信号处理方法,研究了单碱基替换突变、删除突变、插入突变对DNA序列三周期功率谱的影响。研究结果表明:对于不同长度的编码序列,替换突变对序列功率谱的影响较小,删除突变和插入突变对序列功率谱的影响较大;随着序列编码区长度的减小,替换、删除、插入突变对序列编码区的功率谱影响会越来越大。对于中等长度外显子,插入突变对序列三周期功率谱影响最大,对于短外显子,删除突变对序列三周期功率谱的影响最大。研究结果可为含突变基因编码区的识别与检测提供参考。     

基于蛋白质基因组学发现的新编码序列在疾病中的研究进展

非编码序列在不同物种全基因组中占了很大的比例,在人类基因组中高达98％以上.近年来,越来越多的研究发现,新编码序列不仅参与调控发育、分化、增殖与凋亡等生命活动,而且在疾病的发生发展等过程中也扮演了重要的角色.现对基于蛋白质基因组学发现的新编码序列在疾病中的鉴定及应用进行综述,有望为疾病预测、分型、诊断、治疗、疗效判断及...     

原核生物全基因组中16S rRNA基因的识别

【目的】识别原核生物全基因组中的16S rRNA基因。【方法】本文依据基因序列的GC碱基含量、碱基3-周期性和马尔可夫链3个方面的特性,构建了识别原核生物全基因组中16S rRNA基因的三层过滤模型。【结果】经检验,模型的特异性、敏感性和马修斯相关系数分别为99.58%、91.60%和91.49%。【结论】结果表明,本文所提出的方法可以高效、准确地识别出16S rRNA基因。     

基于编码序列、基因间序列和氨基酸序列构建的系统发生关系比较

以7种古菌、46种细菌和10种真核生物的基因组为样本,考虑碱基间的短程关联和长程关联作用,得到编码序列的密码对和基因间序列的三联体对中不同位点的二核苷酸频率,据此构建了基于编码序列和基因间序列的系统发生关系。无论是基于编码序列还是基因间序列对信息进行聚类,古菌或真核均被聚在一支上,表明聚类参数的选择是合适的;与基于氨基酸序列构建的系统发生关系进行两两比较,发现大部分硬壁菌的编码序列与基因间序列之间,以及编码序列与氨基酸序列之间的进化都存在较大差异。通过分析认为,只有综合考虑这三类序列的进化信息,才可能得到更自然的系统发生关系。     

黑线仓鼠CRH基因的编码序列及系统进化分析

为探究黑线仓鼠(Cricetulus barabensis)繁殖功能与促肾上腺皮质激素释放激素(CRH)基因结构的关系,参考近缘种的cDNA序列设计引物,采用RT-PCR法克隆得到了黑线仓鼠CRH基因的部分序列,克隆得到长度为1 112bp,为外显子1和外显子2的部分序列,包括全部编码区序列564 bp;编码区共编码187个氨基酸,GenBank登录号为JQ416143.利用编码区序列构建系统进化树,结果显示,黑线仓鼠与大鼠、小鼠亲缘关系最近,与其他哺乳动物亲缘关系较近,而与原鸡亲缘关系最远,此结果与物种的进化关系相一致.同时对其编码的蛋白质进行一级结构分析及二级、三级结构预测,得到了CRH的信号肽序列和41个氨基酸组成.本研究首次报道了黑线仓鼠的CRH基因序列,为进一步探究CRH基因奠定基础,对系统分析CRH的功能具有重要的参考价值,同时该cDNA序列可作为物种亲缘关系或遗传距离研究的理想标记.     

环氧合酶-3

对环氧合酶(COX)-1和COX-2结构与生物学意义的阐明,促进了非类固醇抗炎药的发展,导致新一代非类固醇抗炎药选择性COX-2抑制剂的产生。最近,第三种环氧合酶同工酶(COX-3)又被发现,它对于非类固醇抗炎药的研究具有重要意义。本文对COX-3的表达、分子结构和药理学性质进行阐述。     

周期性静水压对人软骨细胞IL-1beta和MMP-3 代谢的影响

目的：以正常成人软骨细胞及OA软骨细胞为研究对象,探讨在静水压作用下正常软骨细胞IL-1beta和MMP-3 代谢的变化, 以及与OA软骨细胞之间的差异。同时观察在力学信号刺激下软骨细胞的IL-1beta和MMP-3 代谢有无相关性。方法：将体外培养的 正常成人膝关节软骨第3 代软骨细胞随机分为加压组和对照组。甲苯胺蓝及Ⅱ型胶原免疫细胞化学染色进行细胞鉴定。将加压 组细胞放入高压恒温静水压加压系统,冲入含有95％的空气和5％的CO2混合气体,以10MPa 进行加压2h,共加压5d。分别于 加压前、加压第3 天、加压第5 天后取加压组、对照组和OA 组细胞培养液检测IL-1beta、MMP-3 含量。同时采用MTT 法分析3 组 细胞的增殖情况。对三组细胞中IL-1beta与MMP-3 的水平做双变量相关分析,采用方差分析对三组标本间的IL-1beta、MMP-3 含量进 行比较。结果：各组细胞IL-1beta与MMP-3 两者间存在正相关关系。OA组细胞中IL-1beta与MMP-3含量高于加压组和对照组,加压 组高于对照组。加压组、OA组软骨细胞的生长曲线与对照组相比增殖高峰降低,平台时间缩短。结论：10MPa 间歇性静水压加压 可抑制软骨细胞增殖,增加IL-1beta与MMP-3 分泌。     

周期性静水压对人软骨细胞IL-1β和MMP-3代谢的影响

目的：以正常成人软骨细胞及OA软骨细胞为研究对象,探讨在静水压作用下正常软骨细胞IL-1B和MMP-3代谢的变化,以及与OA软骨细胞之间的差异。同时观察在力学信号刺激下软骨细胞的IL-1β和MMP-3代谢有无相关性。方法：将体外培养的正常成人膝关节软骨第3代软骨细胞随机分为加压组和对照组。甲苯胺蓝及Ⅱ型胶原免疫细胞化学染色进行细胞鉴定。将加压组细胞放入高压恒温静水压加压系统,冲入含有95％的空气和5％的CO2混合气体,以10MPa进行加压2h,共加压5d。分别于加压前、加压第3天、加压第5天后取加压组、对照组和OA组细胞培养液检测IL-1β、MMP-3含量。同时采用MTT法分析3组细胞的增殖情况。对三组细胞中IL-1β与MMP-3的水平做双变量相关分析,采用方差分析对三组标本间的IL-1β、MMP-3含量进行比较。结果：各组细胞IL-1β与MMP-3两者间存在正相关关系。OA组细胞中IL-1β与MMP-3含量高于加压组和对照组,加压组高于对照组。加压组、OA组软骨细胞的生长曲线与对照组相比增殖高峰降低,平台时间缩短。结论：10MPa间歇性静水压加压可抑制软骨细胞增殖,增加IL-1β与MMP-3分泌。     

柞蚕14-3-3基因的鉴定及表达分析

14-3-3蛋白是一种可以改变其结合蛋白构象的酸性蛋白质.柞蚕14-3-3 cDNA序列全长1 220 bp,包括一个126 bp的5'非编码区和一个350 bp的3'非编码区.该基因的开放读码框长度为744 bp,编码247个氨基酸.序列比对结果表明,柞蚕14-3-3蛋白与家蚕的14-3-3蛋白具有高度同源性.此外对柞蚕14-3-3基因进行了原核表达和重组蛋白纯化.SDS-PAGE和免疫印迹结果表明,分子量大小约32 kD的重组蛋白在大肠杆菌中得到了成功表达.     

朊蛋白与信号蛋白14-3-3β的相互作用研究

为进一步确定PrP蛋白与14-3-3蛋白是否发生分子间的相互作用并确定PrP蛋白与14-3-3蛋白相互作用的区域,利用免疫共沉淀、pull down和能量共振转移(FRET)实验检测PrP蛋白与人14-3-3蛋白是否发生分子间的相互作用及相互作用的部位。结果证明,PrP蛋白与人14-3-3蛋白在体外、组织水平及细胞水平均可以发生相互作用,且证实作用的部位在PrP蛋白的106-126位氨基酸。该结果为进一步研究14-3-3蛋白在Prion疾病中的影响及Prion疾病的发病机制奠定了一定基础。     

Theoretical justification of computing the 3-base periodicity using nucleotide distribution variance

In a previous paper (Yin and Yau, 2005), a novel method was proposed to measure the power spectrum of a DNA sequence at frequency N/3 in order to distinguish protein-coding and non-coding regions in DNA sequences. This was accomplished by computing the distribution of the four nucleotides in the three reading frames (codon positions) and identifying variance as an indicator of 3-base periodicity. That work included an empirical justification for the claim that there exists a linear, 3:2 correlation between the variance and the power spectrum. In this note, we provide a theoretical justification for that observation in the form of a mathematical proof of this correlation. This work thus provides a more rigorous justification for the use of the variance instead of the more computationally expensive power spectrum, allowing users of this technique to apply it with absolute confidence that no compromise in accuracy is incurred.     

Prediction of protein coding regions by the 3-base periodicity analysis of a DNA sequence

With the exponential growth of genomic sequences, there is an increasing demand to accurately identify protein coding regions (exons) from genomic sequences. Despite many progresses being made in the identification of protein coding regions by computational methods during the last two decades, the performances and efficiencies of the prediction methods still need to be improved. In addition, it is indispensable to develop different prediction methods since combining different methods may greatly improve the prediction accuracy. A new method to predict protein coding regions is developed in this paper based on the fact that most of exon sequences have a 3-base periodicity, while intron sequences do not have this unique feature. The method computes the 3-base periodicity and the background noise of the stepwise DNA segments of the target DNA sequences using nucleotide distributions in the three codon positions of the DNA sequences. Exon and intron sequences can be identified from trends of the ratio of the 3-base periodicity to the background noise in the DNA sequences. Case studies on genes from different organisms show that this method is an effective approach for exon prediction.     

HIV—1融膜肽的编码DNA序列比较

通过分析GenBank中的全部95个HIV－1完整基因组序列,设计融膜肽“探针序列”,对所获得的95段融膜肽的编码DNA序列进行了翻译、对准和分析。得到融膜肽及其编码序称的“优势序列”及突变分布。     

Profile-Statistical Periodicity of DNA Coding Regions

Novel methods for identifying a new type of DNA latent periodicity, called latent profile periodicity or latent profility, are used to search for periodic structures in genes. These methods reveal two distinct levels of organization of genetic information encoding. It is shown that latent profility in genes may correlate with specific structural features of their encoded proteins.     

Sequence Structure of Hidden 10.4-base Repeat in the Nucleosomes of C. elegans

Abstract

By measuring prevailing distances between YY, YR, RR, and RY dinucleotides in the large database of the nucleosome DNA fragments from C. elegans, the consensus sequence structure of the nucleosome DNA repeat of C. elegans was reconstructed: (YYYYYRRRRR)_n. An actual period was estimated to be 10.4 bases. The pattern is fully consistent with the nucleosome DNA patterns of other eukaryotes, as established earlier, and, thus, the YYYYYRRRRR repeat can be considered as consensus nucleosome DNA sequence repeat across eukaryotic species. Similar distance analysis for [A, T] dinucleotides suggested the related pattern (TTTYTARAAA)_n where the TT and AA dinucleotides display rather out of phase behavior, contrary to the “AA or TT” in-phase periodicity, considered in some publications. A weak 5-base periodicity in the distribution of TA dinucleotides was detected.     

Periodicity in prokaryotic and eukaryotic genomes identified by power spectrum analysis

We used a power spectrum method to identify periodic patterns in nucleotide sequence, and characterized nucleotide sequences that confer periodicities to prokaryotic and eukaryotic genomes and genomes. A 10-bp periodicity was prevalent in hyperthermophilic bacteria and archaebacteria, and an 11-bp periodicity was prevalent in eubacteria. The 10-bp periodicity was also prevalent in the eukaryotes such as the worm Caenorhabditis elegans. Additionally, in the worm genome, a 68-bp periodicity in chromosome I, a 59-bp periodicity in chromosome II, and a 94-bp periodicity in chromosome III were found. In human chromosomes 21 and 22, approximately 167- or 84-bp periodicity was detected along the entire length of these chromosomes. Because the 167-bp is identical to the length of DNA that forms two complete helical turns in nucleosome organization, we speculated that the respective sequences may correspond to arrays of a special compact form of nucleosomes clustered in specific regions of the human chromosomes. This periodic element contained a high frequency of TGG. TGG-rich sequences are known to form a specific subset of folded DNA structures, and therefore, the sequences might have potential to form specific higher order structures related to the clustered occurrence of a specific form of the speculated nucleosomes.     

Using Triplet Periodicity of Nucleotide Sequences for Finding Potential Reading Frame Shifts in Genes

We introduce a novel approach for the detection of possible mutations leading to a reading frame (RF) shift in a gene. Deletions and insertions of DNA coding regions are considerable events for genes because an RF shift results in modifications of the extensive region of amino acid sequence coded by a gene. The suggested method is based on the phenomenon of triplet periodicity (TP) in coding regions of genes and its relative resistance to substitutions in DNA sequence. We attempted to extend 326 933 regions of continuous TP found in genes from the KEGG databank by considering possible insertions and deletions. We revealed totally 824 genes where such extension was possible and statistically significant. Then we generated amino acid sequences according to active (KEGG''s) and hypothetically ancient RFs in order to find confirmation of a shift at a protein level. Consequently, 64 sequences have protein similarities only for ancient RF, 176 only for active RF, 3 for both and 581 have no protein similarity at all. We aimed to have revealed lower bound for the number of genes in which a shift between RF and TP is possible. Further ways to increase the number of revealed RF shifts are discussed.     

The Informational Concept of Searching for Periodicity in Symbol Sequences

A method of informational decomposition has been developed, allowing one to reveal hidden periodicity in any symbol sequence. The informational decomposition is calculated without conversion of a symbol sequence into a numerical one, which facilitates finding periodicities in a symbol sequence. The method permits introducing an analog of the autocorrelation function of a symbol sequence. The method developed by us has been applied to reveal hidden periodicities in nucleotide and amino acid sequences, as well as in different poetical texts. Hidden periodicity has been detected in various genes, testifying to their quantum structure. The functional and structural role of hidden periodicity is discussed.     

Stretch Coding and Block Coding: Two New Strategies to Represent Questionably Aligned DNA Sequences

Most coding strategies that address the problem of questionable alignment (elision, case sensitive, missing, polymorphic, gaps as presence/absence matrix) conflict with phylogenetic principles, particularly those relating to the concept of homology (shared similiarity explained by common ancestry). In some cases, the test of conjunction is failed. In other cases, characters that are coded ambiguously can lead to character-state optimization in the terminal taxa that conflicts with the original observations. Only data exclusion and contraction avoid these pitfalls. In highly dissimilar sequences additional character states can represent the available information. Two new methods that accomplish this—block and stretch coding—are introduced here. These two new coding strategies are not in conflict with the test of conjunction and do not contradict the original observations. They are comparable to coding practices with morphological data once the intrinsic differences due to character-state identity and topographical identity have been taken into account. It is suggested that, of the three recoding methods, the one is selected that preserves the maximum potential phylogenetic information as measured with the minimum number of steps required for the particular part of the data matrix. Received: 1 August 2000 / Accepted: 10 July 2001     

Identification of protein-coding regions in DNA sequences using a time-frequency filtering approach

Accurate identification of protein-coding regions (exons) in DNA sequences has been a challenging task in bioinformatics. Particularly the coding regions have a 3-base periodicity, which forms the basis of all exon identification methods. Many signal processing tools and techniques have been applied successfully for the identification task but still improvement in this direction is needed. In this paper, we have introduced a new promising model-independent time-frequency filtering technique based on S-transform for accurate identification of the coding regions. The S-transform is a powerful linear time-frequency representation useful for filtering in time-frequency domain. The potential of the proposed technique has been assessed through simulation study and the results obtained have been compared with the existing methods using standard datasets. The comparative study demonstrates that the proposed method outperforms its counterparts in identifying the coding regions.