Parallel Cascade Recognition of Exon and Intron DNA Sequences

Many of the current procedures for detecting coding regions on human DNA sequences combine a number of individual techniques such as discriminant analysis and neural net methods. Recent papers have used techniques from nonlinear systems identification, in particular, parallel cascade identification (PCI), as one means for classifying protein sequences into their structure/function groups. In the present paper, PCI is used in a pilot study to distinguish exon (coding) from intron (noncoding; interspersed within genes) human DNA sequences. Only the first exon and first intron sequences with known boundaries in genomic DNA from the T-cell receptor locus were used for training. Then, the parallel cascade classifiers were able to achieve classification rates of about 89% on novel sequences in a test set, and averaged about 82% when results of a blind test were included. In testing over a much wider range of human nucleotide sequences, PCI classifiers averaged 83.6% correct classifications. These results indicate that parallel cascade classifiers may be useful components in future coding region detection programs. © 2002 Biomedical Engineering Society. PAC2002: 8715Cc, 8714Gg, 8715Aa     

Identification and characterization of a second polygalacturonase gene of Aspergillus niger

Summary The filamentous fungus Aspergillus niger produces several endopolygalacturonases that are involved in the degradation of pectin. PGI, the enzyme representing the second most abundant activity in a commmercial enzyme preparation, was further characterized and the corresponding gene was isolated. The nucleotide sequence of the pgaI gene was determined and the protein coding region was found to be interrupted by two short introns, one of which has a unusual donor splice site. The deduced 368 amino acids long protein with a putative prepropeptide of 31 amino acids shows 60% sequence identity to PGII in the mature protein. PGI overproducting A. niger strains were obtained by contransformation with the cloned gene.     

阿尔茨海默病患者早老素-1基因内含子多态性分布的研究

目的 探讨早老素－１（ＰＳ－１）基因第８外显子３’端内含子等位基因多态性在散发性阿尔茨海默病（ＳＡＤ）发病机制中的作用。方法 应用聚合酶链反应－限制性片段长度多态性（ＰＣＲ－ＲＦＬＰ）方法检测７５例ＳＡＤ患者（ＳＡＤ组）和７３例正常老年人（对照组）的ＰＳ－１基因第８外显子３’端内含子等位基因多态性分布。结果 ＳＡＤ组１等位基因频率明显高于对照组（Ｐ〈０．０１,ＲＲ＝１．８３）,２等位基因频率明显低于对照组（Ｐ〈０．０１,ＲＲ＝０．５５）;ＳＡＤ组２／２基因型频率低于对照组（Ｐ〈０．０５,ＲＲ＝０．３２）。结论 ＰＳ－１基因多态性与ＳＡＤ发病有关,ＳＡＤ发病与ＰＳ－１基因２等位基因呈明显负关联,与１等位基因呈明显正关联。ＰＳ－１基因２等位基因对ＳＡＤ发病可能有保护作用,１等位基因可能是ＳＡＤ发病的危险因素之一。     

小儿脑瘤中CD_(44)基因mRNA内含子9的潴留初探

目的　探讨CD4 4基因mRNA中内含子 9在小儿脑瘤中的潴留情况及其肿瘤学意义。方法　采用组织选择性方法提取标本RNA ,应用逆转录 聚合酶链反应 (RT PCR)技术检测 18例小儿恶性脑膜瘤 ,16例脑癌旁组织标本及脑胶质瘤 7例中CD4 4基因mRNA内含子 9的潴留情况。结果　 18例恶性脑膜瘤中有 16例CD4 4内含子 9含量高 ,其中 10例表达明显 (88.9% ) ;16例脑癌旁组织只有 1例内含子潴留 ,15例无潴留现象 (6 .2 5 % ) ;脑胶质瘤 7例有 5例CD4 4基因mRNA内含子 9表达阳性 (71.4% )。恶性脑瘤中含量高于脑癌旁组织 (P <0 .0 1) ,内含子 9的潴留与小儿恶性脑瘤的组织学类型无明显关系。结论　小儿恶性脑瘤组织中存在内含子 9的潴留现象 ,而脑癌旁组织基本无潴留现象。CD4 4基因mRNA中内含子 9的检测在恶性脑瘤中表达阳性可能与肿瘤的发生有关     

Messenger RNA intron in the nuclear 18s ribosomal RNA gene of deuteromycetes

Introns within messenger RNA genes have characteristic border sequences and a conserved region near the 3 end of the intron. All are involved in splicing to produce the mature mRNA. Introns in ribosomal RNA genes have less well-defined borders and contain no internal conservation. We report here mRNA-type introns located near the 3 end of the 18s rRNA genes of the deuteromycetes Phialophora americana and Cenococcum geophilum. Inserted sequences of various sizes have also been located at the same point in several other deuteromycete species.     

The actin gene of the glaucocystophyte Cyanophora paradoxa: analysis of the coding region and introns, and an actin phylogeny of eukaryotes

We isolated the actin gene of the glaucocystophyte alga Cyanophora paradoxa and analyzed the coding region and its introns. Phylogenetic analyses of the actin coding region and the inferred protein sequence in data sets containing 47 other actin sequences show Cyanophora to be a member of the eukaryotic crown-group radiation in agreement with ribosomal DNA sequence analyses. Four of the five Cyanophora actin introns are relatively short (55–59 nt) and occupy novel positions in a catalogue of actin introns containing 56 distinct sites. The fifth intron has a length of 171 nt and occurs also in actin genes from green algae and the crustacean Artemia. Received: 4 December 1996 / Accepted: 5 February 1997     

支气管肺发育不良患儿肺表面活性蛋白-B内含子4基因多态性

目的 了解支气管肺发育不良( bronchopulmonary dysplasia,BPD)患儿肺表面活性蛋白-B(surfactant protein-B,SP-B)内含子4基因多态性的改变. 方法 对2008年7月至2011年7月在华中科技大学同济医学院附属同济医院新生儿重症监护病房收治的45例BPD患儿(BPD组)采用聚合酶链反应技术、琼脂糖凝胶电泳分离以及克隆测序法行SP-B内含子4片段长度多态性检测,并以无肺部疾病的99例患儿为对照(对照组),分析其等位基因[野生等位基因、变异等位基因(插入等位基因和缺失等位基因)]频率和基因型[野生型、变异型(插入型和缺失型)]频率在2组间的差异.研究结果采用两样本均数t检验或x2检验进行统计学分析. 结果 BPD组与对照组野生等位基因频率分别为83.3％(75/90)和91.9％ (182/198),变异等位基因频率分别为16.7％(15/90,其中插入等位基因8例,缺失等位基因7例)和8.1％(16/198,其中插入等位基因8例,缺失等位基因8例),2组比较差异有统计学意义(x2 =4.75,P=0.029).BPD组基因型频率野生型为71.1％(32例),变异型为28.9％(13例,其中插入型7例,缺失型6例),对照组野生型为85.8％(85例),变异型为14.1％(共14例,插入型6例,缺失型8例),2组比较,差异有统计学意义(x2=4.42,P=0.036). 结论 BPD患儿SP-B内含子4基因变异发生率高,提示SP-B内含子4变异可能与BPD遗传易感性相关.     

基因组序列分析HLA新等位基因B*3818内含子和外显子同时突变

目的 分析HLA新等位基因B*3818的基因组序列.方法 克隆测序方法 对PCRSBT中发现的1个未知HLA-B等位基因的基因组序列进行双向全长测序,并采用微量淋巴细胞毒方法 鉴定该等位基因编码分子的抗原特异性,通过群体调查和家系分析了解该等位基因的群体分布频率和单倍型组成情况.结果 新等位基因HLA-B*3818(序列注册号为FJ561482)与B*380201在第4外显子和第5内含子同时存在1个核苷酸的差异.第4外显子的第660位碱基由C变为A,导致第196个密码子由GAC变为GAA,相应氨基酸由天门冬氨酸变为谷氨酸,与IMGT/HLA中的HLA-B等位基因的序列进行对比,该突变为新的单核苷酸多态性位点.第5内含子的第2133位碱基由A变为C,除此之外,B*3818的内含子序列与B*380101、B*380201和B*3814相同.该新HLA等位基因的血清学特异性为B38,其在中国汉族人群中的分布频率小于0.000 5,家系调查结果 表明携带该新等位基因的单倍型为A*030101-CW*010201-B*3818-DRB1-1312-DQB1*060101.结论 新等位基因HLA-B*3818的内含子和外显子同时存在变异,研究新等位基因的基因组序列可为HLA基因相关研究和应用提供更多的序列信息.     

The complete DNA sequence of the mitochondrial genome of Podospora anserina

Summary The complete 94,192 bp sequence of the mitochondrial genome from race s of Podospora anserina is presented (1 kb=10³ base pairs). Three regions unique to race A are also presented bringing the size of this genome to 100,314 bp. Race s contains 31 group I introns (33 in race A) and 2 group II introns (3 in race A). Analysis shows that the group I introns can be categorized according to families both with regard to secondary structure and their open reading frames. All identified genes are transcribed from the same strand. Except for the lack of ATPase 9, the Podospora genome contains the same genes as its fungal counterprts, N. crassa and A. nidulans. About 20% of the genome has not yet been identified. DNA sequence studies of several excision-amplification plasmids demonstrate a common feature to be the presence of short repeated sequences at both termini with a prevalence of GGCGCAAGCTC.