White and brown strains of Flammulina velutipes were inter-crossed. All F1 showed light-brown fruitbody, suggesting that a gene for the brown fruitbody was incompletely dominant against the white one. And backcross experiment showed that more than two genes were involved in color determination. To isolate a molecular marker linked to fruitbody color, a set of primers was designed from a sequence of clones derived by a bulked segregant analysis. These markers showed a specific band which co-segregated with brown fruitbody forming strains.
Clone Cells ; Flammulina* ; Genes, vif

No abstract available.
Genes, vif ; Microsatellite Instability ; Microsatellite Repeats

In microarray technology, many diverse experimental features can cause biases including RNA sources, microarray production or different platforms, diverse sample processing and various experiment protocols. These systematic effects cause a substantial obstacle in the analysis of microarray data. When such data sets derived from different experimental processes were used, the analysis result was almost inconsistent and it is not reliable. Therefore, one of the most pressing challenges in the microarray field is how to combine data that comes from two different groups. As the novel trial to integrate two data sets with batch effect, we simply applied standardization to microarray data before the significant gene selection. In the gene selection step, we used new defined measure that considers the distance between a gene and an ideal gene as well as the between-slide and within-slide variations. Also we discussed the association of biological functions and different expression patterns in selected discriminative gene set. As a result, we could confirm that batch effect was minimized by standardization and the selected genes from the standardized data included various expression pattems and the significant biological functions.
Bias (Epidemiology) ; Computational Biology ; Dataset* ; Genes, vif ; RNA

Recent trends in generating multiple, large-scale datasets provide new challenges to manipulating the relationship of different types of components, such as gene expression and drug response data. Integrative analysis of compound response and gene expression datasets generates an opportunity to capture the possible mechanism of compounds by using signature genes on diverse types of cancer cell lines. Here, we integrated datasets of compound response and gene expression profiles on NCI60 cell lines and constructed a network, revealing the relationship for 801 compounds and 341 gene probes. As examples, obtusol, which shows an exclusive sensitivity on a small number of colon cell lines, is related to a set of gene probes that have unique overexpression in colon cell lines. We also found that the SLC7A11 gene, a direct target of miR-26b, might be a key element in understanding the action of many diverse classes of anticancer compounds. We demonstrated that this network might be useful for studying the mechanisms of varied compound response on diverse cancer cell lines.
Cell Line ; Colon ; Gene Expression ; Genes, vif ; Transcriptome

There have been attempts to use consensus sequences or ancestor sequences for development vaccines against viruses with high diversity and variation. In this study, we generated and compared consensus sequences and ancestor sequences of nef and vif genes of HIV-1 isolated from Koreans. Phylogenetic analyses revealed that majorities of the Korean isolates were clustered to form the Korean clade within subtype B (KcB) where foreign isolates were not included. Consensus sequences inferred from the KcB as well as from all Korean isolates were almost identical but significantly different from subtype B consensus sequence or HIV-1 consensus sequence. The genetic distances from one of the Korean isolates to the other Korean isolates were much longer than to the consensus or ancestor sequences deduced from Korean isolates but similar to those of subtype B or HIV-1. Moreover, the genetic distances from the Korean isolates to the consensus sequences were shorter than to the ancestor sequences both in nef and vif genes. Thus, the consensus sequences may be useful in developing Korean-specific HIV-1 vaccine.
Consensus Sequence* ; Consensus* ; Genes, vif* ; HIV-1* ; Vaccines

BACKGROUND: There are no established reports about the expression of the Piwil gene, a subfamily of the Piwi gene involved in RNA silencing and self-renewal, in colorectal carcinomas. It is known that the degree of PIWIL2 expression is higher in colorectal carcinomas. But its clinicopathologic significance remains undetermined. This study reassessed the relationship between PIWIL2 expression and the clinicopathologic parameters in colorectal carcinomas. METHODS: An immunohistochemistry of PIWIL2 expression was done in 60 cases of colorectal carcinoma. This was followed by an analysis of the correlation between PIWIL2 expression and clinicopathologic features and a survival analysis. RESULTS: There were 44 cases (73.3%) where the degree of PIWIL2 expression was relatively higher. The high degree of PIWIL2 expression was significantly correlated with the lower degree of differentiation (p=0.039), deep invasion (p=0.019) and perineural invasion (p=0.027). The overall survival was longer in patients with the lower degree of PIWIL2 expression than in those with the higher degree of PIWIL2 expression. CONCLUSIONS: Our results showed that the degree of PIWIL2 expression was relatively higher in colorectal carcinomas and it was significantly correlated with variable clinicopathologic indicators for a poor prognosis. This indicates that PIWIL2-positive cells contribute to the progression of colorectal cancer.
Colorectal Neoplasms ; Genes, vif ; Humans ; Immunohistochemistry ; Prognosis ; RNA Interference

PURPOSE: Variable changes occur in the progression from normal gastric epithelium to cancer, including many tumor, tumor suppressor and DNA repair genes, as well as growth factor and its receptors. The mutation and protein expression of the p53 gene may be useful prognostic factors, but their significance is still uncertain. METHODS: Specimens from 296 gastric cancer patients, treated by a curative gastrectomy, between March 1999 and April 2001, at Kyungpook National University Hospital, were used. The p53 gene mutation was assessed using a polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) analysis, and the overexpression of tumor p53 protein using immunohistochemistry. The correlation between the results and clinicopathological parameters were then analyzed. RESULTS: The mutation and protein overexpression of the p53 gene were shown in 61 (20.6%) and 124 (41.9%) tumors, respectively. Of the 61 cases with a p53 mutation, 43 (70.5%) showed overexpression of the p53 protein, and of the 235 without mutation of the p53 gene, 81 (34.5%) had no overexpression of the p53 protein, and also showed statistical significance (P< 0.001). The mutation and protein overexpression of the p53 gene showed no significant differences according to age, gender, stage, location and gross type, but of the 138 intestinal and 128 of the diffuse types, 33 (23.9%) and 18 (14.1%) cases, respectively, showed p53 mutation (P=0.027); whereas, of the 150 well differentiated and 142 poorly differentiated tumors, 75 (50%) and 18 (33.8%), respectively, showed overexpression of the p53 protein. Also, of the 138 intestinal and 128 diffuse types, 71 (51.4%) and 43 (33.6%) showed overexpression of the p53 protein. There were no significant differences in the 5 year survival according to the mutation and protein overexpression of the p53 gene. CONCLUSION: The mutation and protein overexpression of the p53 gene, as assessed by PCR-SSCP and immunohistochemistry, respectively, showed a statistically significant correlation, but had little value as prognostic factors following a curative gastrectomy.
DNA Repair ; Epithelium ; Gastrectomy ; Genes, p53 ; Genes, vif ; Gyeongsangbuk-do ; Humans ; Immunohistochemistry ; Stomach Neoplasms*

OBJECTIVE: To examine the mechanism for the inhibited differentiation of osteoclasts in rheumatoid arthritis synovial CD14+ osteoclast precursors, the different expressions of the osteoclastogenesis-related genes in rheumatoid arthritis (RA) synovial fluid CD14+ osteoclast precursors were compared with those of normal peripheral blood (PB) CD14+ osteoclast precursors. METHODS: The expression of osteoclastogenesis-related genes were examined using a gene expression oligonucleotide microarray. To validate the results of the microarray analysis, the mRNA expressions of osteoclastogenesis-related genes were measured by real-time PCR. RESULTS: Comparative analysis of the mRNA profiles showed significantly different expression of osteoclastogenesis- related genes, such as MafB, Id3 and LILRB4, in the RA synovial CD14+ osteoclast precursors, compared to that of normal PB CD14+ osteoclast precursors. CONCLUSION: The expression of the osteoclastogenesis-related genes in RA synovial CD14+ osteoclast precursors is different from that of the normal PB CD14+ osteoclast precursors. These results suggest that the different expression of osteoclastogenesis-related genes might be involved in the altered osteoclastogenesis in RA synovial osteoclast precursors.
Arthritis, Rheumatoid ; Genes, vif ; Macrophages ; Microarray Analysis ; Oligonucleotide Array Sequence Analysis ; Osteoclasts ; RNA, Messenger ; Synovial Fluid

BACKGROUND: LOH11A is a region with frequent allele loss (>75%) in lung cancer that is located on the centromeric part of chromosome 11p15.5. Clinical and cell biological studies suggest that this region contains a gene associated with metastatic tumor spread. RRM1 encoding the M1 subunit of ribonucleotide reductase, which is an enzyme that catalyses the rate-limiting step in deoxyribonucleotide synthesis, is located in the LOH11A region. METHODS: Polymorphisms were found at nucleotide position (-)37 (C/A) and (-)524 (C/T) from the beginning of exon 1 of the RRM1 gene that might regulate the expression of RRM1. We studied the polymorphisms in 127 Korean individuals (66 lung cancer and 61 normal controls) and compared with those of 140 American patients with lung cancer. RESULTS: CC, AC and AA were found at the (-)37 position in 64(50.4%), 55(43.3%), and 8(6.3%) out of 127 Korean individuals (66 cancer, 61 non-cancer patients), respectively. There was a similar frequency of allele A at (-)37 in the American(27.9%) and Korean population(28.0%). CC, CT and TT was found at the (-)524 position in 24(18.9%), 44(34.6%), and 59(46.5%) out of the 127 Korean individuals, respectively. There was a similar frequency of allele C at (-)524 in the American(34.6%) and Korean population(36.2%).There was no difference in the frequency of the (-)37 and (-)524 genotypes between the cancer and non-cancer group. However there was a significant correlation of the genotypes between (-)37 and (-)524 (p<0.001), which suggests the possible coordination of these polymorphisms in the regulation of the promoter activity of the RRM1 gene. CONCLUSION: RRM1 promoter polymorphisms were not found to be significant risk factors for lung cancer. However, a further study of the promoter activity and expression of the RRM1 gene according to the pattern of the polymorphism will be needed.
Alleles ; Catalysis ; Exons ; Genes, vif ; Genotype ; Humans ; Lung Neoplasms* ; Lung* ; Ribonucleotide Reductases ; Risk Factors

PURPOSE: The determination of HER-2/neu gene amplification has become necessary for the selection of breast cancer patients to undergo anti-HER-2/neu therapy, using a humanized monoclonal antibody. Chromogenic in situ hybridization (CISH) detection of the HER-2/neu gene, a newly developed method, utilizes a robust and unique-sequence DNA probe labeled with digoxygenin, which is sequentially incubated with antidigoxygenin fluorescein, antifluorescein peroxidase and diaminobenzidine. The aim of this study was to establish a CISH assay for the detection of HER-2/neu amplification. The results were compared with those of the immunohistochemistry (IHC) methods, most frequently used for detecting HER-2/neu alteration. METHODS: CISH was performed in 4 groups of infiltrating breast carcinomas. Each group was comprised of 20 cases in which the HER-2/neu stati had previously been scored on a four value scale: 0, 1+, 2+ and 3+ by IHC. The results of CISH and IHC were compared for each tumor group. The HER-2/neu gene amplification detected by CISH was thpically visualized as large DAB-stained clusters or by many dots in the nucleus. RESULTS: The concordance between the CISH and IHC was 95% (kappa=0.901). Three IHC-positive cases (score 2+) showed no gene amplification and one IHC-negative case (score 1+) showed gene amplification by CISH. CONCLUSION: The current study showed excellent agreement between the CISH and IHC methods. CISH is an accurate, practical and economical approach for determining the HER-2/neu stati in breast carcinomas. It is also a useful methodology for confirming the IHC results in paraffin- embedded tumor samples, so offers a promising alternative to IHC in a routine diagnostic setting.
Breast Neoplasms* ; Breast* ; DNA ; Fluorescein ; Gene Amplification ; Genes, vif ; Humans ; Immunohistochemistry ; In Situ Hybridization* ; Peroxidase