Radiation-induced Hierarchical Topologically Associated Domain Change and Its Role in Cellular Responses to Radiation / 中国生物化学与分子生物学报

The three-dimensional (3D) genome organization plays an important role in gene regulation. As a basic functional unit of the genome, topologically associated domain (TAD) regulates multiplebiological processes such as gene expression and DNA replication and plays a role in radiation-inducedDNA damage repair. Recent studies showed that TAD is not a completely independent domain butcontains hierarchical internal domains, which could be a new mechanism of gene regulation. To explorethe role of hierarchical TAD in cellular responses to radiation, we apply the OnTAD algorithm, anoptimized nested TAD caller from Hi-C data, to identify hierarchical TAD in 26 Hi-C data from Geneexpression omnibus (GEO) database. These data were from irradiated fibroblasts, lymphoblasts andfibroblasts deficient in the ataxia telangiectasia mutated (ATM) gene with 5 Gy X-ray. We observe thatX-ray can regularly affect the hierarchy of TAD in which high-level TAD is prone to change and low-levelTAD is more conservative. We propose that radiation-induced TAD hierarchy change can regulate cellularresponses to radiation by regulating gene expression, and ATM is a necessary factor for radiation-inducedTAD hierarchy change and recovery. This study provides new insights into the role of the 3D genome inradiation-induced cellular responses from the perspective of hierarchical TAD structures.

A genetic optimization designing method for microorganism detection genechip probe based on genetic algorithm / 中国医疗器械杂志

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.

Sequence analysis of the complete genome of bocavirus WLL-1 / 病毒学报

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.

Progress in a research on biochip image analysis / 中国医疗器械杂志

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.

Screening and their anti-tumor activity of antisense oligodeoxynucleotides targeting KDR mRNA in breast cancer MCF-7 cells / 中华肿瘤杂志

<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>