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Ji Hwan Moon, Sangsoo Lim, Kyuri Jo, Sangseon Lee, Seokjun Seo, Sun Kim
BACKGROUND: Identifying perturbed pathways in a given condition is crucial in understanding biological phenomena. In addition to identifying perturbed pathways individually, pathway analysis should consider interactions among pathways. Currently available pathway interaction prediction methods are based on the existence of overlapping genes between pathways, protein-protein interaction (PPI) or functional similarities. However, these approaches just consider the pathways as a set of genes, thus they do not take account of topological features...
March 14, 2017: BMC Systems Biology
Claudia Barberis, Marisa Almuzara, Olivier Join-Lambert, María Soledad Ramírez, Angela Famiglietti, Carlos Vay
In recent years, MALDI-TOF Mass Spectrometry (MS) method has emerged as a promising and a reliable tool for bacteria identification. In this study we compared Bruker MALDI-TOF MS and conventional phenotypic methods to identify a collection of 333 Gram-positive clinical isolates comprising 22 genera and 60 species. 16S rRNA sequencing was the reference molecular technique, and rpoB gene sequecing was used as a secondary gene target when 16Sr RNA did not allow species identification of Corynebacterium spp. We also investigate if score cut-offs values of ≥ 1,5 and ≥ 1,7 were accurate for genus and species-level identification using the Bruker system...
2014: PloS One
Junjiao Guan, Hong Yu, Yunfeng Xie, Shimei Zuo, Rongfeng Ma, Wenbo Zeng
OBJECTIVE: To establish the EST-SSR marker system for Cordyceps by using ESTs of C. bassiana and C. militaris. METHOD: The ESTs of Cordyceps were downloaded from the public database of NCBI, and the redundant ESTs with low quality were removed. The EST-SSR primers were designed by Sequece Seiner 1. 2. And the primers were screened through PAGE-Electrophoresis. RESULT: The 4 556 non-redundant ESTs which from C. bassiana with total length of 2 953 173 bp were selected...
July 2011: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
Joanna Vermeij, Erik Teugels, Claire Bourgain, Ji Xiangming, Peter in 't Veld, Vanessa Ghislain, Bart Neyns, Jacques De Grève
BACKGROUND: The status of the EGFR and HER2-neu genes has not been fully defined in ovarian cancer. An integrated analysis of both genes could help define the proportion of patients that would potentially benefit from targeted therapies. METHODS: We determined the tumour mutation status of the entire tyrosine kinase (TK) domain of the EGFR and HER2-neu genes in a cohort of 52 patients with invasive epithelial ovarian cancer as well as the gene copy number and protein expression of both genes in 31 of these patients by DGGE and direct sequecing, immunohistochemistry and Fluorescent in Situ Hybridisation (FISH)...
2008: BMC Cancer
Shi-yan Yan, Xiao-yan Zhou, San-jun Cai, Bao-hua Yu, Tai-ming Zhang, Xiao-mei Li, Yong-ming Lu, Heng-hua Zhou, Shan-jing Mo, Xiang Du, Da-ren Shi
OBJECTIVE: To detect the germline mutation of mismatch repair gene (MSH6) in hereditary nonpolyposis colorectal cancer (HNPCC) kindreds fulfilling different clinical criteria. METHODS: The germline mutations of MSH6 gene were detected by PCR based DNA sequencing in 39 unrelated HNPCC probands fulfilling different clinical criteria in which MSH2 and MLH1 mutations were excluded. The exons with missense mutations were analyzed using PCR sequencing in the germline genomic DNA of 137 healthy persons...
December 2007: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
Hong-li Luo, Ying Huang, Li-ming Wang, Zhi-heng Liu, Jian-ping Xie, Chang-hua Hu
156 actinomycetes were isolated from 10 soil samples collected in Tibet by the method of DDC(dispersion and differential centrifugation). The isolates were assigned to 32 different groups on the basis of their morphological characters and colors of substrate mycelium, aerial hyphae and pigment. The result of cell-wall DAP on 65 representative strains selected from these groups was that 9 strains were different from Streptomyces. The analysis of ARDRA and 16S rDNA sequeces showed that the isolates belonged to the genus Streptomyces and five different rare actinomycete genera respectively...
October 2005: Wei Sheng Wu Xue Bao, Acta Microbiologica Sinica
Hui-Ying Luo, Bin Yao, Tie-Zheng Yuan, Ya-Rul Wang, Xiu-Yun Shi, Ning-Feng Wu, Yun-Liu Fan
High-level expression of phytase with high specific activity is an effective way to improve phytase fermentation potency and reduce its production cost. The gene appA encoding Escherchia coli phytase AppA with high specific activity was modified and artificially synthesized according to the bias in codon choice of the high expression gene in Pichia pastoris without changing the amino acid sequence of the AppA. The modified gene, appA-m, was inserted in the Pichia pastoris expression vector pPIC9, then introduced into the host Pichia pastoris by electroporation...
January 2004: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
Julio Antonio Barrios Olivera, Luis Sarmiento Pérez, Odalys Valdés, Pedro Mas Lago, Rosa Puentes Palomera
The introduction of a mollecular method to identify the Entoviruses based on the amplification sequecing and phylogenetic analysis of protein VPI was described. It was proved that this method reduces significantly the time required for the identification of the isolated Entoviruses and that it is very useful in the characterization of isolates which are difficult to typify by the routine immunoloigical reagents. As it is a very fast technqiue, its use is very important during epidemics to determine the causal agent rapidly...
September 2003: Revista Cubana de Medicina Tropical
Zhong Xia Qi, Hui Zeng, Xiu Lan Li, Cheng Bin Chen, Wen Qin Song, Rui Yang Chen
The origin and evolution of B chromosomes could be explained by the specific DNA sequence on them. But the specific sequences known were quite limited. To investigate maize B chromosome sqicific DNA sequeces, maize genomes with and without B chromosomes were analyzed by AFLP. Only 5 markers were found specific to genomes with B chromosomes among about 2000 AFLP markers. Southern hybridization and sequence analysis revealed that only the sequence of M8-2D was a B chromosome specific sequence. This sequence contained the telomeric repeat unit AGG...
March 2002: Cell Research
Christian Beuret, Dorothe Kohler, Andreas Baumgartner, Thomas M Lüthi
In a recent study, RNA with nucleotide sequeces specific for "Norwalk-like viruses" (NLV) was detected in 11 different brands of European mineral waters. To clarify this finding, a 1-year monitoring study was conducted. Samples of three European brands of mineral water without gas were monitored weekly by reverse transcriptase PCR using generic and genogroup-specific oligonucleotides. Additional analyses were performed to investigate a possible correlation between NLV sequence contamination and mineral water lot numbers, the long-term stability (persistence) of NLV sequences in mineral water, and the level of contamination...
April 2002: Applied and Environmental Microbiology
J Wang, F Dong, P Yong
OBJECTIVE: To detect p53 exon 6 mutation pattern in pleomorphic adenoma of salivary gland. METHODS: Single-strand conformational polymorphism (SSCP) and DNA sequecing were used. RESULTS: SSCP analysis showed that 6 of 11 cases with SSCP positive were exon 6 abnormal. Comparison of the SSCP results with DNA sequecing, 4 cases with p53 exon 6 mutations were SSCP positive. Mutation pattern included base substitution (point mutation, G-->T, T-->G) and frame-shift mutation (base insertion and base loss)...
September 1999: Zhonghua Kou Qiang Yi Xue za Zhi, Zhonghua Kouqiang Yixue Zazhi, Chinese Journal of Stomatology
D R Holmes, W F McKeever
The present experiment was concerned with an assessment of possible serial, as opposed to general, memory deficit in dyslexia. Previous studies had consistently confounded general and serial memory assessments. Fifteen specifically dyslexic adolescents and 15 normal-reading controls were administered four separate memory tasks. In the general memory for verbal material task they were shown 20 words, each for three seconds, and were then given a deck of 40 word cards and required to pick out the 20 words just seen...
March 1979: Cortex; a Journal Devoted to the Study of the Nervous System and Behavior
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