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

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

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

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: A relevant part of the social and personal burden caused by Bipolar Disorder (BD) is related to depressive phases. Authors investigated the genetic impact of a set of variations located in CRY1, a gene involved in the control of the circadian rhythms, towards depressive episodes in a sample of bipolar patients from the STEP-BD sample. As a secondary analysis, CYR1 variations were analyzed as predictors of sleep disruption. METHODS: 654 bipolar patients were included in the analysis. Data were available genome-wide. The part of the genome coding for the CRY1 was imputed and pruned according to standards in the field. 7 SNPs were available for the analysis. A correction for multitesting was applied and we had sufficient power (0.80) to detect a small-medium effect size (0.22) between two allelic frequencies each one represented by at least 300 subjects. RESULTS: Intronic rs10861688 was associated with the number of depressive events corrected for the times patients were assessed during the period of observation. In particular, AA subjects (n=21) had 4.46+/-3.15 events, AG (n=141) had 3.08+/-3.17 and GG (n=342) 2.65+/-2.97 (p=0.0048, beta=-0.22). No other significant associations were reported. CONCLUSION: We bring further evidence that genes involved in the regulation of circadian rhythms may be relevant to depressive bipolar phases. Independent confirmation analyses are mandatory.
Bipolar Disorder ; Circadian Rhythm ; Clinical Coding ; Genes, vif ; Genome ; Humans ; Introns ; Polymorphism, Single Nucleotide ; Recurrence*

This summary of literature during the past year reviews published studies relating to risk factors for depressive disorders in children and adolescents. Risk factors include environmental toxins, socio-environmental, and genetic factors. As depression has a complex, multifactorial causal mechanism, it is likely that the accumulation and/ or interaction among multiple risk factors lead to depression. Findings related to the result of toxin exposure have been difficult to interpret given that risk factors tend to interact and that higher mental functions are not easily measurable. However, some findings have been consistent. Clinical research data has also shown that the risk for negative outcomes may be modified both by genetic and environmental factors through a gene environment interplay mechanism.
Adolescent ; Child ; Depression ; Depressive Disorder ; Genes, vif ; Humans ; Risk Factors ; Stress, Psychological

BACKGROUND: About 60~70% of hospital isolates of staphylococci are resistant to methicillin. The level of resistance varies from low to high depending upon the genetic background of the strains. The purpose of this study was twofold : (i) to understand the relationship between beta-lactamase and methicillin-resistance genes(mecA, mecI, mecR1, femA) and the level of resistance and (ii) to survey the distribution of mec regulator genes(mec I, mecR1) among methicillin-resistant staphylococci. METHODS: Eighty-three isolates of Staphylococus aureus and 29 of coagulase-negative staphylococci(CNS) at Catholic University Hospital were examined. The level of methicillin resistance was studied using disk diffusion test and agar dilution test. MecA, mecI, mecR1, and femA genes detected by polymerase chain reaction. RESULTS: beta-lactamase production was significantly high in S. aureus and CNS isolates with low-level resistance. MecA and mecR1 genes amplification correlated with the level of resistance in S. aureus and CNS isolates. There was no correlation between the level of resistance and mecI and fem A genes amplification in S. aureus and CNS isolates. Methicillin- resistant S. aureus isolates showed more variety in mec regulator region than methicillin-resistant CNS isolates. CONCLUSION: From this study, we conclude that mecR1 gene could be considered as one of the important factors influencing the level of methicillin resistance in staphylococcal strains.
Agar ; beta-Lactamases ; Diffusion ; Genes, vif ; Methicillin Resistance* ; Methicillin* ; Polymerase Chain Reaction