In silico cloning, expression and bioinformatics analysis of NtODB from common tobacco / 生物工程学报

It has been reported that ODB genes play an important role in homologous recombination-directed DNA repair, suggesting their potential applications in plant breeding. To analyze the expression characteristics of tobacco NtODB gene, the cDNA sequence of NtODB was obtained using in silico cloning technique. The physicochemical properties, signal peptide, and advanced structures of the predicted protein were analyzed using bioinformatics tools. The results showed that the NtODB gene has a 579-bp open reading frame which encodes a protein with 192 amino acid residues. The protein NtODB is predicted to be alkaline and hydrophilic. Real-time quantitative PCR showed that NtODB was constitutively expressed in different tissues. Subcellular localization showed that NtODB was mainly expressed in cell membrane and chloroplast. These results may help us to better understand and elucidate the roles of ODB genes in the homologous recombination-directed DNA repair.

In silico cloning and bioinformatics analysis of HSP21 in Manihot esculenta / 生物工程学报

HSP21 gene is a key gene to respond high temperature stress in plant and plays an important role in preventing protein denaturation, protecting cell structure and maintaining normal growth and development. Therefore, cloning HSP21 gene is the basis for revealing the molecular mechanism of resistance to high temperature stress in cassava. To obtain cassava HSP21 homologous gene and analyze the properties of predicted protein, electronic cloning technology was used to assemble and derivate new gene in this study, and bioinformatics analysis method was used to analyze the primary to highest structure, hydrophilicity/hydrophobicity, signal peptide, protein homology and phylogenetic evolution of expressed protein. HSP21 gene was 969 bp, its open reading frame was 705 bp, and the predicted protein contains 234 amino acids. The predicted protein is a non-transmembrane protein that is alkaline and hydrophilic, and is mainly localized in the chloroplast. Through multiple sequence alignment and phylogenetic analysis, it was found that the cassava HSP21 protein has high homology with other plants such as Hevea brasiliensis, Ricinus communis, and Jatropha curcas. The results could provide reference for the study of cloning and transformation of this gene.

In silico cloning and comparative analysis of NAD1 gene in three common human parasites / 中国血吸虫病防治杂志

Objective To in silico clone the NAD1 gene of three common parasites and analyze their bioinformatics,so as to lay the foundation for further research on the NAD gene. Methods By using the in silico cloning method,the full length cDNA (s)of NAD 1 genes of Clonorchis sinensis,Ascaris lumbricoides and Schistosoma japonicum were got,then their physical and chemical properties,compositions of amino acids,subcellular localizations,binary and ternary structures were contrastively an-alyzed.Results The three kinds of NAD1 proteins were similar in the relative molecular weight,subcellular localization,and physical and chemical properties.The NAD1 proteins were highly similar in binary and ternary structures of A.lumbricoides and S.japonicum.The phylogenetic analysis showed that C.sinensis,A.lumbricoides and S.japonicum belonged to the different evolu-tionary branches with a certain of genetic distance. Conclusion The three NAD1 genes got from C.sinensis,A.lumbricoides and S.japonicum by in silico cloning belong to the same gene of different species,which can be widely used in the researches of heritable variation of parasites.

In Silico Cloning and Bioinformatics Analysis of AP2/ERF Family Gene from Brassica Oleracea / 中国药师

Objective:To obtain AP2/ERF genes from Brassica oleracea by using in silico cloning. Methods: AP2/ERF genes were cloned by retnieving the EST database and using the bioinformatics software with the Arabidopsis thaliana AP2/ERF as a querying probe. Results:Two AP2/ERF family transcriptional regulators (BoAP2/ERF1 and BoAP2/ERF2) were isolated from Brassica olera-cea by the in silico cloning method. Some characters of AP2/ERF protein were analyzed and predicted by the tools of bioinformatics in the following aspects including the composition of amino acid sequence, hydrophilicity and hydrophobicity, subcellular localization, secondary and tertiary structure of protein and function. Conclusion:Bioinformatical analysis shows BoAP2/ERF1 and BoAP2/ERF2 gene encode 40. 85kDa and 39. 44kDa protein with 371 and 352 amino acids. The domain is predicted to locate on nucleus. Sequence analysis indicates the protein may be involved in signaling transducer and stressing response roles in plantbiotic stresses.

In Silico Cloning and Bioinformatics Analysis of Chalcone Synthase Gene from Ribes Americanum / 中国药师

Objective:To study the in silico cloning and bioinformatics of chalcone synthase gene from Ribes americanum. Meth-ods:Ribes nigrum chalcone synthase sequence and Ribes americanum were cloned by retrieving the EST database as the querying probe, which were assembled by CAP3 sequence assembly program, and the bioinformatics database and related software were used to predict the structure and perform the function analysis. Results:Bioinformatical analysis showed chalcone synthase gene encoded 1423 bp and contained a 1173bp ORF, the protein was with 390 amino acid, which was a hydrophilic protein located in cytoplasm including three transmembrane regions with the secondary structure composed of alpha helix. Conclusion:The study is helpful to the further ex-planation for the molecular function mechanism of chalcone synthase gene from Ribes americanum.

In silico cloning and bioinformatics analysis of cyclophilin from Lotus corniculatus / 中草药

Objective: Using electronic cloning technology to predict cyclophilin gene of Lotus corniculatus. Methods: Using glycine max cyclophilin sequence as probe sequence, based on EST sequence from NCBI and assembled by CAP3 sequence assembly programme, using bioinformatic database and related software, the structure prediction and function analysis were performed. Results: The full length of cyclophilin gene was 1 346 bp, it contained a 771 bp ORF, encoding 256 amino acids, and the protein was a hydrophilic protein. Conclusion: The study is intended to further explain the molecular genetic function theory and experimental basis.

Technique of silico cloning and its application in medicine / 国际生物医学工程杂志

The strategy of silico cloning based on the express sequence tags sequence (ESTs)and genome database is a new technique developed in recent years,and the core of the technique is to use bioinformatics technique to assemble and extend ESTs to get part of cDNA and even all sequence.It has the virtue of low investment,high speed,low and well-targeted technical requirements,etc.The relationship between human disease and genes has been widely confirmed,therefore,silico cloning technology will become the important means of disease research.This paper aims at elaborating the progress of silico cloning in medicine.