Predicting disease genes for familial dilated cardiomyopathy based on the codon usage bias

Familial dilated cardiomyopathy （FDC） is a common monogenic disease mostly with autosomal dominant inheritance. Fifteen different loci for autosomal dominant FDC have been mapped; however, only eight FDC genes have been found, and it is still a big challenge to identify additional seven FDC genes in their chromosomal regions. We found that the codon usage frequencies in most of known FDC gene sequences are consistently biased, and significantly different from the average codon usage frequencies of human genes. This unique feature of codon usage was used to develop a novel approach to predicting FDC genes. Leave-oneout cross-validation results demonstrate that this approach can effectively detect FDC genes from numbers of genes in their chromosomal regions. Another advantage of this approach is that it is solely based on DNA sequences and therefore has the ability to identify potential FDC genes whose functions are completely unknown. Further, this approach has been used to analyze the seven FDC loci in which the FDC genes are still unknown. Both the detailed prediction results and the prediction program are available at http：// infosci.hust.edu.cn, which might provide help for relevant experimental researches to find new FDC genes.     

Complete sequence and gene organization of the mitochondrial genome of Batocera lineolata Chevrolat (Coleoptera: Cerambycidae)

Batocera lineolata Chevrolat,1852 is an important forest pest that is found mainly in China,Vietnam,India,and Japan.The complete mitochondrial genome(mitogenome) sequence of B.lineolata was determined by long polymerase chain reaction(PCR) and conserved primer walking approaches.The results showed that the entire mitogenome is 15418 bp long with 74.48% A+T content.The positions and arrangement of the 37 genes encoded by the genome are identical to the mitogenomes of two other longhorn beetles for which the complete gene content and arrangement are publicly available.All protein-coding genes start with the ATN codon that is a typical initiation codon in insects.All transfer RNAs(tRNAs) were predicted to form the standard clover-leaf structure,except for tRNA Ser(AGN),which lacks the dihydrouridine(DHU) arm.The most unusual feature that was found was the use of TCT as the tRNA Ser(AGN) anticodon instead of the GCT that is used in most other arthropods.The lack of tandem repeat motif in the 735 bp long A+T-rich region was another unusual feature of the B.lineolata mitogenome.The short,highly conserved polythymidine stretch that was previously described in the Orthoptera and Diptera orders was also present in the A+T-rich region of the B.lineolata(order Coleoptera) mitogenome.The sequence and annotation of the mitogenome of B.lineolata will provide further insights into the diversity and evolution of the Cerambycidae family of long-horned beetles.The B.lineolata mitogenome sequence has been deposited in GenBank(http://www.ncbi.nlm.nih.gov/Genbank/) under accession number JN986793.     

Bioinformatic prediction of selenoprotein genes in the dolphin genome

Selenium (Se), an essential trace element in vivo, is present mainly as selenocystein (Sec) in various selenoproteins. The Sec residue is translated from an in-frame TGA codon, which traditionally functions as a stop codon. Prediction of selenoprotein genes is difficult due to the lack of an effective method for distinguishing the dual function of the TGA codon in the open reading frame of a selenoprotein gene. In this article a eukaryotic bioinformatic prediction system that we have developed was used to predict selenoprotein genes from the genome of the common bottlenose dolphin, Tursiops truncatus. Sixteen selenoprotein genes were predicted, including selenoprotein P and glutathione peroxidase. In particular, a type II iodothyronine deiodinase was found to have two Sec residues, while the type I iodothyronine deiodinase gene has two alternative splice forms. These results provide important information for the investigation of the relationship between a variety of selenoproteins and the evolution of the marine-living dolphin.     

Exploring Codon Usage Patterns of Alternatively Spliced Genes in Human Chromosome 1

Introduction A large number of species (prokaryotes and eukaryotes) have been used to study the pattern of codon usage bias, and it has also been demonstrated that inter- and intra-genomic variation of the pattern of codon usage is a widespread phenomenon, which may result from various factors. Alternative synonymous codon usage does not modify the amino acid sequence encoded in DNA among species and often among genes from the same genome. It has been suggested that the pattern of codon usag…     

A suppressed gene in integument cells of a fiberless seed mutant in upland cotton

A fiberless seed mutant(fl) was identified in a commercial cotton(Gossypium hirsutum L.) variety Xu-Zhou 142(FL).THis phenotype is associated with lack of fiber cell initiation in the outer integument of the ovule,as was characterized by analysis of genes related to fiber differentiation and development.Two genes,fl-E6 and FL-E6,were cloned from fl-integument cells and FL-fiber or integument cells,respectively.Compared with FL-E6,fl-E6 showed a dramatic change in nucleotide sequence:(1) FL-E6 contained a tandem repetitive sequence in which GGCTCA( Gly-Ser) is repeated five times between the 82nd and the 93rd codon from the first ATG codon,while in fl-E6 the same sequence is repeated four times;(2) The fl-E6 gene encodes a polypeptide of 241 amino acids but lacks two codons between the 90th and 93rd codon and three between the 171st and 174th relative to FL-E6;(3) There are also 12 nucleotide substitutions which would result in 7 amino acid differences between fl-E6 and FL-E6.Analysis of RT-PCR and Northern Blot showed that expression of the fl-E6 gene is suppressed in the fl-integument cells.but highly expressed in FL-fiber cells.The difference between fl-E6 and FL-E6 may be associated with lower expression of fl-E6 in the fli-inbackbones of two arabinogalactan-proteins(AGPs),one from the filtrate of suspension-cultured cells of Pyrus communis (AGPPc2) and the other from Nicotiana alata(AGPNa2),Although the function of the FL-E6 protein in differentation and development of cotton fiber cells is not known,the data indicate that the mutation of fl-E6 gene from FL-E6 gene may inhibit the fiber cell initiation from epidermal cells of the outer integument of the ovule.     

Variation and Characterization Analysis of Partial Fragment of Fibroin Gene From Silkworm, Antheraea pernyi

A 1.4Kb DNA fragment containing 3‘ flanking sequence of fibroin gene of silkworm, Antheraea perny/, was obtained from the silk gland‘s mRNA of 5th larva. Analysis of this sequence with another A. pemyi fibroin protein (accession No. 1383241) revealed that it consists of a completely open reading frame (ORF), which includes 14 polyalanine-containing units (motifs) and 100bp 3‘-UTR. The sequence of the predicted amino acid reveals the highest level of overall iden-tity (90%) with 1383241. It was found that it loses a repeat region at the upstream of TAA codon and some mutations. A putative polyadenylation signal AATAAA tail was found in position 1300, which follows the termination codon.     

Characterization of codon usage bias in the dUTPase gene of duck enteritis virus

A comparative analysis of the codon usage bias in the newly discovered dUTPase gene （Assigned Accession No.： DQ486149） of the duck enteritis virus （DEV） and the dUTPase gene of 32 reference herpesviruses was performed. The results indicated that the DEV dUTPase gene encodes a protein of 477 amino acids, which includes five conserved motifs with a 3-1-2-4-5 arrangement. The codon adaptation index （CAI）, effective number of codons （ENC）, and GC3s values indicated synonymous codon usage bias in the dUTPase gene of herpesviruses, and this synonymous bias was correlated with host evolution. The codon usage patterns of the DEV dUTPase gene were phylogenetically conserved and similar to that of the dUTPase genes of the avian alphaherpesvirus. Although codon usage in each microorganism was different, there were no strain-specific differences among them. Sixty-one codons in the predicted polypeptide, with a strong bias towards A and T at the third codon position, were used. Comparison of the codon usage in the dUTPase gene of different organisms revealed that there were 19 codons showing distinct codon usage differences between the DEV and Escherichia coli dUTPase genes; 16 between the DEV and yeast dUTPase genes; and 15 between the DEV and human dUTPase genes. Analysis of variance （ANOVA） showed significant differences between the DEV and yeast dUTPase genes （r = 0.536, P 〈 0.01）. The extent of codon usage bias in the DEV dUTPase gene was highly correlated with the gene expression level, therefore the results may provide useful information for gene classification and functional studies.     

铅污染对条斑紫菜的毒害影响

研究分析了不同浓度Pb2+对条斑紫菜植物体叶绿素a含量,POD、SOD活性,MDA含量,总抗氧化能力以及可溶性蛋白质含量的影响.结果表明,随着Pb2+浓度的增加,叶绿素a含量,POD、SOD活性,MDA的含量,总抗氧化能力,可溶性蛋白质及均呈先升后降趋势.条斑紫菜对Pb2+具有较高的耐性.     

条斑紫菜ACEI肽结构鉴定与性能试验

对条斑紫菜蛋白酶解获得的血管紧张素转换酶抑制肽(ACEI)进行纯化和结构鉴定,并研究了条斑紫菜ACEI肽体外贮存稳定性和对原发性高血压大鼠的降血压作用.结果表明:通过2步反相高效液相制备色谱纯化得到2种单一组分ACEI肽,经液质联用质谱分析肽序列分别为Cys-Ser-Asn-Arg和Pro-Cys-His-Trp,二者对血管紧张素转换酶半数抑制浓度分别为24.71和5.38 μmol·L-1;条斑紫菜ACEI肽不耐高温,在中性或酸性条件下较稳定;用分子质量小于3 ku条斑紫菜ACEI肽组分对原发性高血压大鼠灌胃后有显著降血压效果,且降血压幅度随灌胃剂量增大而提高.     

Cd~(2+)对条斑紫菜的胁迫作用

以条斑紫菜中叶绿素a含量、光合作用强度、SOD活性、POD活性、总抗氧化能力及可溶性蛋白含量等6项指标参数,研究分析了不同浓度Cd2+对条斑紫菜的胁迫作用.结果表明,用较低浓度Cd2+处理时,条斑紫菜的6项指标参数值均较对照组有一定的提高;随着Cd2+处理浓度的增加,6项指标参数值均开始下降,其中,处理浓度为5~100 mg/L时,光合作用强度、POD活性逐渐下降;处理浓度为10~100 mg/L时,叶绿素a含量、SOD活性、总抗氧化能力下降;处理浓度为20~100 mg/L时,可溶性蛋白含量下降.条斑紫菜对Cd2+具有较高的耐受性,但高浓度的Cd2+对条斑紫菜具有明显的胁迫作用.     

13种哺乳动物OTR密码子使用偏性及其聚类分析

目的研究13种哺乳动物催产素受体基因(OTR)密码子使用偏性,并探讨其影响因素;通过对偏性情况进行聚类分析,研究其与系统发育的关系.方法计算RSCU,CBI,ENC等密码子偏性指标,与可能的几种影响因素做相关性分析,采用SPASS 15.0软件,以相对同义密码子使用度为变量对偏性情况进行聚类分析.结果与结论 1)CUG,GUG,GCC,UUC,AUC,CGC为哺乳动物OTR使用频率较高的密码子;2)密码子第3位碱基的GC含量是影响哺乳动物OTR密码子偏性的主要因素,基因的GC含量次之,而芳香族氨基酸的含量和蛋白疏水水平对其密码子使用偏性的影响不大;3)对于功能相同的基因,亲缘关系相近的物种密码子使用偏性指标较接近,但某些物种仍有一定差异.     

不同海藻凝集素对鲤免疫活性物的诱导作用

以条斑紫菜（Porphyra yezaensis）和裙带菜（Undaria pinnatifida）的凝集素作为免疫增强剂，来研究它对鲤免疫活性的诱导作用．实验结果表明，投喂和灌喂凝集素后，鲤血清中凝集素、超氧化物歧化酶（SOD）、过氧化氢酶（CAT）、溶菌酶活性与对照组相比都有提高，其中投喂条斑紫菜凝集素组比投喂对照组依次提高3．0倍、0．8倍、3．9倍、1.0倍；投喂裙带菜凝集素组比投喂对照组依次提高1.0倍、0．4倍、3．0倍、0．7倍，灌喂裙带菜凝集素组比灌喂对照组依次提高3．0倍、0．3倍、1．8倍；灌喂条斑紫菜凝集素组比灌喂对照组依次提高3.0倍、0．7倍．由此可看出：两种凝集素都可以作为一种免疫添加剂激活鲤的免疫系统，对鲤的非特异性免疫功能具有明显的增强作用．其中投喂条斑紫菜的效果更好．     

紫菜腐霉侵染条斑紫菜叶状体过程研究

对我国北方沿海条斑紫菜栽培海区发生的条斑紫菜赤腐病进行了研究.揭示了病原菌紫菜腐霉(Pythium porphyrae)侵袭条斑紫菜叶状体的过程.紫菜腐霉的丝状菌丝侵袭并穿透紫菜细胞,导致细胞色素溶出,细胞萎缩,最后死亡.紫菜腐霉发育到一定阶段,在菌丝末端形成孢子囊,孢子囊成熟后,形成排放管,放出游孢子,游孢子可以再次侵袭紫菜细胞.在一定条件下,紫菜腐霉可以进行有性生殖,通过藏精器与藏卵器结合,形成卵孢子,卵孢子沉入海底,在条件适宜时可再次萌发.冷藏网上细胞同样可以被病原菌所感染,然而使用冷藏网可以阻止病害的蔓延,并能提高紫菜品质.     

浙江海区条斑紫菜养成的研究

１９９１－１９９８年在浙江海区进行了要斑紫菜引种和栽培试验,在不同海区、分期分批进行多种茁源的养成试验,结果认为浙江海区全苗网养成的适宜时期在１２月至翌年４月。浙南海区（平阳、苍南、洞头）成菜栽培的成功较低。浙中以北海区适于条斑紫菜的养成,可与当地坛紫菜轮栽。应用冷藏网能清除杂藻、避开不良环境,提高质量、产量。单孢子菌网对条斑紫菜的栽培有重要作用。条斑紫菜与坛紫菜可以轮栽,既能提高单位面积的产量、     

杨树部分基因起始密码子AUG侧翼序列特征分析

对297条杨树基因序列的起始密码子AUG侧翼区序列(-20位点- 6位点)的碱基分布特性进行了统计学分析,并对高表达基因和低表达基因翻译起始位点侧翼序列碱基的保守性和关联性进行了对比分析。结果表明:紧邻起始密码子5′端的-1、-2、-3、-4、-5和-6位点均强烈偏好A, 4位点强烈偏好G,同时高表达和低表达基因的-20位到 4位中某些位点的保守性存在较大差异,其中高表达基因的-6,-3和 4位可能与其高表达的特性有关;通过关联性分析可以看出,在起始密码子侧翼序列的某些特定区域碱基之间的关联性可能也与翻译起始效率有关系;相关性分析表明低表达基因的AUGCAI主要受到"AUG"侧翼区序列的GC含量的影响,低表达基因在"AUG"侧翼区富集GC对翻译有一定影响。     

藻胆蛋白提取分离及抗氧化活性的测定

藻胆蛋白是一种多功能细胞色素蛋白。从条斑紫菜藻中提取藻胆蛋白,用饱和硫酸铵沉淀法、DEAE-纤维素离子交换层析对提取的藻胆蛋白进行纯化,并首次采用邻苯三酚自氧化法来测定藻胆蛋白的抗氧化活性。从而得出:从红藻中提取分离出具有一定纯度、较高抗氧化活力的藻胆蛋白提取品。     

两种超嗜热菌基因组中同义密码子使用的分析

对两种超嗜热菌敏捷气热菌(Aeropyrum pernix)和风产液菌(Aqui fex aeolicus)的密码子使用进行分析．相对密码子使用值(RSCU)的计算表明,它们在密码子使用上具有一定的相似性,但也有不同的使用模式,导致这一现象的机制可能存在差异．密码子RSCU值对应分析表明,两种菌中高表达基因均具有相对较高的GC含量,但基因表达水平对密码子使用偏好的影响程度却不一样．在A．pernix中,它是造成整个基因组密码子使用偏好的最主要因素,而在A．aeolicus中却不是．