• Title/Summary/Keyword: gene heterogeneity

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Heterogeneity Analysis of the 16S rRNA Gene Sequences of the Genus Vibrio (Vibrio 속 16S rRNA 유전자 염기서열의 이질성 분석)

  • Ki, Jang-Seu
    • Korean Journal of Microbiology
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    • v.45 no.4
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    • pp.430-434
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    • 2009
  • Bacterial 16S rRNA gene sequences have been widely used for the studies on molecular phylogeny, evolutional history, and molecular detections. Bacterial genomes have multiple rRNA operons, of which gene sequences sometimes are variable. In the present study, heterogeneity of the Vibrio 16S rRNA gene sequences were investigated. Vibrio 16S rRNA sequences were obtained from GenBank databases, considering the completion of gene annotation of Vibrio genome sequences. These included V. cholerae, V. harveyi, V. parahaemolyticus, V. splendidus, and V. vulnificus. Chromosome 1 of the studied Vibrio had 7~10 copies of the 16S rRNA gene, and their intragenomic variations were less than 0.9% dissimilarity (more than 99.1% DNA similarity). Chromosome 2 had none or single 16S rRNA gene. Intragenomic 16S rRNA genotypes were detected at least 5 types (V. vulnificus #CMCP6) to 8 types (V. parahaemolyticus #RIMD 2210633, V. harveyi #ATCC BAA-1116). These suggest that Vibrio has high heterogeneity of the 16S rRNA gene sequences.

The AURKA Gene rs2273535 Polymorphism Contributes to Breast Carcinoma Risk - Meta-analysis of Eleven Studies

  • Guo, Xu-Guang;Zheng, Lei;Feng, Wei-Bo;Xia, Yong
    • Asian Pacific Journal of Cancer Prevention
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    • v.15 no.16
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    • pp.6709-6714
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    • 2014
  • The rs2273535 polymorphism in the AURKA gene had proven to be associated with breast carcinoma susceptibility. Nevertheless, the results of different studies remain contradictory. A meta-analysis covering 28, 789 subjects from eleven different studies was here carried out in order to investigate the association in detail. The random effects model was used to analyze the pooled odds ratios (ORs) and their corresponding 95% confidence intervals (95% CIs). A significant relationship between the rs2273535 polymorphism and breast tumors was found in an allelic genetic model (OR: 1.076, 95% CI: 1.004-1.153, p=0.040, $P_{heterogeneity}$=0.002). No significant association was detected in a homozygote model (OR: 1.186, 95% CI: 0.990-1.423, P=0.065, $P_{heterogeneity}$=0.002), a heterozygote model (OR: 1.016, 95% CI: 0.959-1.076, p=0.064, $P_{heterogeneity}$=0.000), a dominant genetic model (OR: 1.147, 95% CI: 0.992-1.325, p=0.217, $P_{heterogeneity}$=0.294) and a recessive genetic model (OR: 1.093, 95% CI: 0.878-1.361, p=0.425, $P_{heterogeneity}$=0.707). A significant relationship between the rs2273535 polymorphism in the AURKA gene and breast tumor in Asian group was found in an allelic genetic model (OR: 1.124, 95% CI: 1.003-1.29, p=0.044, $P_{heterogeneity}$=0.034), a homozygote model (OR: 1.229, 95% CI: 1.038-1.455, p=0.016, $P_{heterogeneity}$=0.266) and a recessive genetic model (OR: 1.227, 95% CI: 1.001-1.504, p=0.049, $P_{heterogeneity}$=0.006). A significant association was thus observed between the rs2273535 polymorphism in the AURKA gene and breast cancer risk. Individuals with the rs2273535 polymorphism in the AURKA gene have a higher risk of breast cancer in Asian populations, but not in Caucasians.

Evaluation and interpretation of transcriptome data underlying heterogeneous chronic obstructive pulmonary disease

  • Ham, Seokjin;Oh, Yeon-Mok;Roh, Tae-Young
    • Genomics & Informatics
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    • v.17 no.1
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    • pp.2.1-2.12
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    • 2019
  • Chronic obstructive pulmonary disease (COPD) is a type of progressive lung disease, featured by airflow obstruction. Recently, a comprehensive analysis of the transcriptome in lung tissue of COPD patients was performed, but the heterogeneity of the sample was not seriously considered in characterizing the mechanistic dysregulation of COPD. Here, we established a new transcriptome analysis pipeline using a deconvolution process to reduce the heterogeneity and clearly identified that these transcriptome data originated from the mild or moderate stage of COPD patients. Differentially expressed or co-expressed genes in the protein interaction subnetworks were linked with mitochondrial dysfunction and the immune response, as expected. Computational protein localization prediction revealed that 19 proteins showing changes in subcellular localization were mostly related to mitochondria, suggesting that mislocalization of mitochondria-targeting proteins plays an important role in COPD pathology. Our extensive evaluation of COPD transcriptome data could provide guidelines for analyzing heterogeneous gene expression profiles and classifying potential candidate genes that are responsible for the pathogenesis of COPD.

The Interleukin-18 Promoter -607C>A Polymorphism Contributes to Nasopharyngeal Carcinoma Risk: Evidence from a Meta-analysis Including 1,886 Subjects

  • Guo, Xu-Guang;Xia, Yong
    • Asian Pacific Journal of Cancer Prevention
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    • v.14 no.12
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    • pp.7577-7581
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    • 2013
  • The interleukin-18 promoter -607C>A gene polymorphism may be related to nasopharyngeal carcinoma (NPC) risk but the results of individual studies remain conflicting. A meta-analysis including 1,886 subjects from five individual studies was therefore performed to provide a more accurate estimation. Pooled odds ratios (ORs) and their corresponding 95% confidence intervals (95% CIs) were evaluated by fixed- or random-effects models. A significant relationship between interleukin-18 promoter -607C>A gene polymorphism and NPC was found in a dominant genetic model (OR: 1.351, 95% CI: 1.089-1.676, P=0.006, $P_{heterogeneity}$=0.904), a homozygote model (OR: 1.338, 95% CI: 1.023-1.751, P=0.034, $P_{heterogeneity}$=0.863), and a heterozygote model (OR: 1.357, 95% CI: 1.080-1.704, P=0.009, $P_{heterogeneity}$=0.824). No significant association was detected in either an allelic genetic model (OR: 1.077, 95% CI: 0.960-1.207, 0.207, $P_{heterogeneity}$=0.844) or a recessive genetic model (OR: 1.093, 95% CI: 0.878-1.361, P=0.425, $P_{heterogeneity}$=0.707). In conclusion, a significant association was found between interleukin-18 promoter -607C>A gene polymorphism and NPC risk. Individuals with the C allele of interleukin-18 promoter -607C>A gene polymorphism have a higher risk of NPC development.

Heterogeneity of Chloroplast DNA in Rice (벼 엽록체 DNA의 이질성)

  • 남백희;문은표
    • Proceedings of the Botanical Society of Korea Conference
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    • 1987.07a
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    • pp.391-401
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    • 1987
  • Plant chloroplast DNA exists as an unique circular structure in which large single copy(LSC) region and small single copy (SSC) region are separated by large inverted repeat sequences (IRS). It has been known that the unique existence of inverted repeat sequences in chloroplast DNA has no relation with the stability of the chloroplast DNA, but causes the inversion between inverted repeat its biological significance has not been understood so far. In rice, several gene clusters have been cloned and sequenced which contain ribulose-5-biophosphate car-boxylase large subunit (rbcL). Especially, one rbcL gene is linked with rp12 gene which is located in the IRS region in one of the gene clusters. By comparison of nucleotide sequence, the two genes are found to be linked through 151 bp repeat sequence which is homologous to the rp123 gene in IRS region. The repeat sequence is found to be located 3' downstream of rfcL gene and near psbA gene in LSC region. The existence of these repeat sequences and the presence of gene clusters caused by the gene rearrangement thorough the repeat sequence provide a possible which is found to be dispersed chloroplast DNA provide the model system to explaine the heterogeneity of the chloroplast DNA in rice in term of gene rearrangement.

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Dissecting Cellular Heterogeneity Using Single-Cell RNA Sequencing

  • Choi, Yoon Ha;Kim, Jong Kyoung
    • Molecules and Cells
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    • v.42 no.3
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    • pp.189-199
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    • 2019
  • Cell-to-cell variability in gene expression exists even in a homogeneous population of cells. Dissecting such cellular heterogeneity within a biological system is a prerequisite for understanding how a biological system is developed, homeostatically regulated, and responds to external perturbations. Single-cell RNA sequencing (scRNA-seq) allows the quantitative and unbiased characterization of cellular heterogeneity by providing genome-wide molecular profiles from tens of thousands of individual cells. A major question in analyzing scRNA-seq data is how to account for the observed cell-to-cell variability. In this review, we provide an overview of scRNA-seq protocols, computational approaches for dissecting cellular heterogeneity, and future directions of single-cell transcriptomic analysis.

Paraoxonase 1 (PON1) Q192R Gene Polymorphism and Cancer Risk: A Meta-Analysis Based on 30 Publications

  • Zhang, Meng;Xiong, Hu;Fang, Lu;Lu, Wei;Wu, Xun;Huang, Zhan-Sen;Wang, Yong-Qiang;Cai, Zhi-Ming;Wu, Song
    • Asian Pacific Journal of Cancer Prevention
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    • v.16 no.10
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    • pp.4457-4463
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    • 2015
  • Common genetic variation Q192R in the paraoxonase 1 (PON1) gene has been considered to be implicated in the development of many cancers. Nevertheless, results from the related studies were inconsistent. To elucidate the association, we performed a meta-analysis for 8,112 cases and 10,037 controls from 32 published case-control studies. Odds ratios (ORs) with 95% confidence intervals (CIs) were used to assess the strength of the association by STATA 12.0 software. Overall, we revealed that the PON1-192R allele was associated with a reduced risk of the overall cancers. Moreover, in the stratified analysis by cancer types (breast cancer, prostate cancer, brain cancer etc.), the results showed that PON1-192R allele was associated with a decreased risk in breast cancer (R vs Q: OR=0.605, 95% CI=0.378-0.967, $P_{heterogeneity}=0.000$; RR vs QQ: OR=0.494, 95% CI=0.275-0.888, $P_{heterogeneity}=0.002$; RQ vs QQ: OR=0.465, 95% CI=0.259-0.835, $P_{heterogeneity}=0.000$; and RR+RQ vs QQ: OR=0.485, 95% CI=0.274-0.857, $P_{heterogeneity}=0.000$), and associated with prostate cancer in homozygote (RR vs QQ: OR=0.475, 95% CI=0.251-0.897, $P_{heterogeneity}=0.001$) and recessive models (RR vs RQ+QQ: OR=0.379, 95% CI=0.169-0.853, $P_{heterogeneity}=0.000$), while an increased risk was identified in lymphoma (R vs Q: OR=1.537, 95% CI=1.246-1.896, $P_{heterogeneity}=0.944$; RR vs QQ: OR=2.987, 95% CI=1.861-4.795, $P_{heterogeneity}=0.350$; RR+RQ vs QQ: OR=1.354, 95% CI=1.021-1.796, $P_{heterogeneity}=0.824$; and RR vs RQ+QQ: OR=2.934, 95% CI=1.869-4.605, $P_{heterogeneity}=0.433$), and an increased risk in prostate cancer under heterozygote comparison (RQ vs QQ: OR=1.782, 95% CI=1.077-2.950, $P_{heterogeneity}=0.000$) and dominant models (RR+RQ vs QQ: OR=1.281, 95% CI=1.044-1.573, $P_{heterogeneity}=0.056$). When subgroup analysis that performed by the control source (hospital based or population based), a decreased risk of the overall cancers was revealed by homozygote (RR vs QQ: OR=0.601, 95% CI=0.366-0.987, $P_{heterogeneity}=0.000$) and dominant models (RR vs RQ+QQ: OR= 0.611, 95% CI=0.384-0.973, $P_{heterogeneity}=0.000$) in hospital based group. Stratifying by ethnicity, a significantly reduced risk of the overall cancers under allele contrast model (R vs Q: OR=0.788, 95% CI=0.626-0.993, $P_{heterogeneity}=0.000$) was uncovered in Caucasian. In summary, these findings suggested that PON1 Q192R polymorphism was associated with a reduced risk of the overall cancers, nevertheless, it might increase cancer susceptibility of prostate and lymphoma risk. Large well-designed epidemiological studies will be continued on this issue of interest.

No Association Between MTHFR A1298C Gene Polymorphism and Head and Neck Cancer Risk: A Meta-analysis Based on 9,952 Subjects

  • Niu, Yu-Ming;Shen, Ming;Li, Hui;Ni, Xiao-Bing;Zhou, Juan;Zeng, Xian-Tao;Leng, Wei-Dong;Wu, Ming-Yue
    • Asian Pacific Journal of Cancer Prevention
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    • v.13 no.8
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    • pp.3943-3947
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    • 2012
  • Objective: Findings for associations between the methylenetetrahydrofolate reductase (MTHFR) A1298C gene polymorphism and head and neck cancer risk have been conflicting. We therefore performed a meta-analysis to derive a more precise relationship. Methods: Ten published case-control studies were collected and odds ratios (ORs) with 95% confidence intervals (CIs) were used to assess the association between MTHFR A1298C polymorphism and head and neck cancer risk. Sensitivity analysis and publication bias assessment also were performed to guarantee the statistical power. Results: Overall, no significant association between MTHFR A1298C polymorphism and head and neck cancer risk was found in this meta-analysis (C vs. A: OR=1.04, 95%CI=0.87-1.25, P=0.668, Pheterogeneity<0.001; CC vs. AA: OR=1.07, 95%CI=0.70-1.65, P=0.748, $P_{heterogeneity}<0.001$; AC vs. AA: OR=1.06, 95%CI=0.88-1.27, P=0.565, $P_{heterogeneity}<0.001$; CC+AC vs. AA: OR=1.06, 95%CI=0.86-1.30, P=0.571, $P_{heterogeneity}<0.001$; CC vs. AA+AC: OR=1.02, 95%CI=0.69-1.52, P=0.910, $P_{heterogeneity}<0.001$). Similar results were also been found in succeeding analysis of HWE and stratified analysis of ethnicity. Conclusion: In conclusion, our meta-analysis demonstrates that MTHFR A1298C polymorphism may not be a risk factor for developing head and neck cancer.

Phosphorylation of rpS3 by Lyn increases translation of Multi-Drug Resistance (MDR1) gene

  • Woo Sung Ahn;Hag Dong Kim;Tae Sung Kim;Myoung Jin Kwak;Yong Jun Park;Joon Kim
    • BMB Reports
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    • v.56 no.5
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    • pp.302-307
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    • 2023
  • Lyn, a tyrosine kinase that is activated by double-stranded DNA-damaging agents, is involved in various signaling pathways, such as proliferation, apoptosis, and DNA repair. Ribosomal protein S3 (RpS3) is involved in protein biosynthesis as a component of the ribosome complex and possesses endonuclease activity to repair damaged DNA. Herein, we demonstrated that rpS3 and Lyn interact with each other, and the phosphorylation of rpS3 by Lyn, causing ribosome heterogeneity, upregulates the translation of p-glycoprotein, which is a gene product of multidrug resistance gene 1. In addition, we found that two different regions of the rpS3 protein are associated with the SH1 and SH3 domains of Lyn. An in vitro immunocomplex kinase assay indicated that the rpS3 protein acts as a substrate for Lyn, which phosphorylates the Y167 residue of rpS3. Furthermore, by adding various kinase inhibitors, we confirmed that the phosphorylation status of rpS3 was regulated by both Lyn and doxorubicin, and the phosphorylation of rpS3 by Lyn increased drug resistance in cells by upregulating p-glycoprotein translation.

Current Evidence on the Relationship Between Two Polymorphisms in the NBS1 Gene and Breast Cancer Risk: a Meta-analysis

  • Zhang, Zhi-Hua;Yang, Lin-Sheng;Huang, Fen;Hao, Jia-Hu;Su, Pu-Yu;Sun, Ye-Huan
    • Asian Pacific Journal of Cancer Prevention
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    • v.13 no.11
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    • pp.5375-5379
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    • 2012
  • Introduction: Published studies on the association between Nijmegen breakage syndrome 1(NBS1) gene polymorphisms and breast cancer risk have been inconclusive, and a meta-analysis was therefore performed for clarification. Methods: Eligible articles were identified by a search of MEDLINE and EMBASE bibliographic databases for the period up to March 2012. The presence of between-study heterogeneity was investigated using the chi-square-based Cochran's Q statistic test. When there was statistical heterogeneity, the random effects model was chosen; otherwise, fixed effects estimates were reported as an alternative approach. Results: A total of 11 eligible articles (14 case-control studies) were identified, nine case-control studies were for the 657del5 mutation (7,534 breast cancer cases, 14,034 controls) and five case-control studies were for the I171V mutation (3,273 breast cancer cases, 4,004 controls). Our analysis results indicated that the 657del5 mutation was associated with breast cancer risk (carriers vs. non-carriers: pooled OR =2.63, 95% CI: 1.76-3.93), whereas the I171V mutation was not (carriers vs. non-carriers: pooled OR =1.52, 95% CI: 0.70-3.28). Conclusion: The present meta-analysis suggests that the 657del5 gene mutation in the NBS1 gene plays a role in breast cancer risk, while the I171V mutation does not exert a significant influence.