A simplified genomic DNA extraction protocol for pre-germination genotyping in rice.

Genotyping is a critical step for molecular marker-assisted selection in rice. Rice genomic DNA samples for genotyping are typically isolated from living tissues such as seedlings. This requires the germination of all candidate seeds and extraction of DNA from the seedlings. Currently, an ideal individual is selected from a very large number of plants, which is time- and labor-consuming, requiring several transplantations of materials and sampling processes. In this study, we developed a simplified genomic DNA extraction protocol in rice by using amylase to treat half-seeds. The yields of genomic DNA from a half-seed of Indica and Japonica rice were greater than 203.8 ± 32.5 and 143.2 ± 25.5 ng, respectively, and the 260/280 nm absorbance ratio was 1.75-2.10. The DNA was confirmed to be sufficient for polymerase chain reaction amplification and can be used in a marker-assisted selection program.

Construction of a gene-gene interaction network with a combined score across multiple approaches.

Recent progress in computational methods for inves-tigating physical and functional gene interactions has provided new insights into the complexity of biological processes. An essential part of these methods is presented visually in the form of gene interaction networks that can be valuable in exploring the mechanisms of disease. Here, a combined network based on gene pairs with an extra layer of re-liability was constructed after converting and combining the gene pair scores using a novel algorithm across multiple approaches. Four groups of kidney cancer data sets from ArrayExpress were downloaded and analyzed to identify differentially expressed genes using a rank prod-ucts analysis tool. Gene co-expression network, protein-protein interac-tion, co-occurrence network and a combined network were constructed using empirical Bayesian meta-analysis approach, Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) database, an odds ratio formula of the cBioPortal for Cancer Genomics and a novel rank algorithm with combined score, respectively. The topological features of these networks were then compared to evaluate their performances. The results indicated that the gene pairs and their relationship rank-ings were not uniform. The values of topological parameters, such as clustering coefficient and the fitting coefficient R(2) of interaction net-work constructed using our ranked based combination score, were much greater than the other networks. The combined network had a classic small world property which transferred information quickly and displayed great resilience to the dysfunction of low-degree hubs with high-clustering and short average path length. It also followed distinct-ly a scale-free network with a higher reliability.

Application value of multislice spiral computed tomography angiography in the evaluation of renal artery variation in living donor kidney transplantation.

This study aims to investigate the accuracy and value of multislice spiral computed tomography (MSCT) angiography in the evaluation of renal artery variation in living donor kidney transplantation. Two hundred seventy-three kidney transplantation donors underwent preoperative MSCT scanning. Two doctors determined the running direction and variation of the renal artery through joint analysis of the preoperative original MSCT image and the recombination image using the blind reading method, compared the imaging results with the intraoperative results, and evaluated the accuracy and application value of MSCT angiography in the evaluation of renal artery variation in living donor kidney transplantation. CT angiography (CTA) can better show the renal artery and its variation. A total of 52 accessory renal arteries were found in the 273 kidney transplant operations, whereas 55 accessory renal arteries were found in preoperative MSCT. Four accessory renal arteries indicated in the MSCT were not found during the operation, and one accessory renal artery found during the operation was not indicated in the preoperative MSCT. The sensitivity, specificity, positive predictive value, negative predictive value, and accuracy of MSCT in the diagnosis of accessory renal arteries were 98.1, 98.2, 92.7, 99.5, and 98.2%, respectively. MSCT angiography can sensitively and accurately show the renal artery and its variation in living donor kidney transplantation, and has important clinical value for the formulation of the operative scheme before the transplantation.