ABSTRACT
A new automatic selection approach of microorganism specific fragment combination is presented in this paper. Genetic algorithm is used to search optimal solution on the basis of classification ability of SNP combination, which is evaluated by the rough set theory. Other related experimental parameters are also been incorporated. Experimental results show that the method can find the best SNP combination pattern efficiently and accurately, which implies that it is a reliable approach to the genechip probe design.
Subject(s)
Algorithms , Microbiological Techniques , Methods , Models, Genetic , Oligonucleotide Array Sequence Analysis , MethodsABSTRACT
Human bocavirus, which was firstly discovered in 2005, is a new human parvovirus associated with lower respiratory tract infection in children. In this study, a human bocavirus, named WLL-1 isolate, was identified in Wenlin County, Zhejiang Province. The genome of bocavirus WLL-1 has been sequenced and analyzed. Phylogenetic analyses showed that WLL-1 shares 99% homology with other bocaviruses recently reported, but also has some special variations.
Subject(s)
Humans , Bocavirus , Classification , Genetics , China , DNA, Viral , Chemistry , Genetics , Genome, Viral , Molecular Sequence Data , Phylogeny , Sequence Analysis, DNAABSTRACT
Microarray imaging is considered as an important tool for large scale analysis of gene expression. The accuracy of the gene expression depends on the experiment itself and further image processing. It's well known that the image analysis introduced during the experiment will greatly affect the accuracy of the gene expression. Microarray image analysis plays a potentially-arge impact on the gene detecting subsequent analysis (image segmentation, spot intensity and spot intensity extraction). In this paper, based on the characters of microarray images, the methods of microarray images' denoising and automatic-identification of the spot are reviewed.
Subject(s)
Gene Expression Profiling , Methods , Image Interpretation, Computer-Assisted , Methods , Oligonucleotide Array Sequence Analysis , Methods , Pattern Recognition, Automated , MethodsABSTRACT
<p><b>OBJECTIVE</b>To screen the antisense oligodeoxynucleotides (asONs) which could hybridize with KDR (kinase insert domain-containing receptor) mRNA in an effective and specific way and to explore their anti-tumor effects on breast cancer MCF-7 cell line in vitro.</p><p><b>METHODS</b>The asONs were firstly selected using oligodeoxynucleotides library hybridization or computer prediction, then their hybridization ability with KDR mRNA was further tested with oligonucleotide microarray. The asONs with strong hybridization intensity were selected. Their inhibitory effects on MCF-7 cells proliferation and KDR expression were assayed by MTT, RT-PCR and Western blotting assay, respectively.</p><p><b>RESULTS</b>In 13 asONs selected with oligodeoxynucleotides library hybridization, 8 (8/13, 61.5%) showed strong hybridization signals, while such was only 1 in 17 asONs designed by computer prediction. 9 asONs with strong hybridization intensity were selected and synthesized with phosphorothioated modification. All these asONs inhibited the MCF-7 cells proliferation in a dose-dependent manner, in which asON4 and asON7 screened by oligodeoxynucleotides library in combination with oligonucleotide microarray were the most effective, with inhibitory rates of 51.6% and 62.2% at 0.8 micromol/L, respectively. The KDR expression at mRNA and protein levels was reduced by both the two asONs, in a dose-dependent manner.</p><p><b>CONCLUSION</b>asONs screened by oligodeoxynucleotides library hybridization are well consistent with that chosen with oligonucleotide microarray. The combination of oligodeoxynucleotides library with oligonucleotide microarray is an effective approach of asONs screening. The asONs targeting KDR mRNA showed prominent anti-tumor activity on breast cancer MCF-7 cells.</p>