• Asian Pacific Journal of Cancer Prevention
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• v.15 no.22
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• pp.9791-9795
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• 2014

To study the gene expression change and possible signal pathway during androgen-dependent prostate cancer (ADPC) becoming androgen-independent prostate cancer (AIPC), an LNCaP cell model of AIPC was established using flutamide in combination with androgen-free environment inducement, and differential expression genes were screened by microarray. Then the biological process, molecular function and KEGG pathway of differential expression genes are analyzed by Molecule Annotation System (MAS). By comparison of 12,207 expression genes, 347 expression genes were acquired, of which 156 were up-ragulated and 191 down-regulated. After analyzing the biological process and molecule function of differential expression genes, these genes are found to play crucial roles in cell proliferation, differntiation, cell cycle control, protein metabolism and modification and other biological process, serve as signal molecules, enzymes, peptide hormones, cytokines, cytoskeletal proteins and adhesion molecules. The analysis of KEGG show that the relevant genes of AIPC transformation participate in glutathione metabolism, cell cycle, P53 signal pathway, cytochrome P450 metabolism, Hedgehog signal pathway, MAPK signal pathway, adipocytokines signal pathway, PPAR signal pathway, TGF-${\beta}$ signal pathway and JAK-STAT signal pathway. In conclusion, during the process of ADPC becoming AIPC, it is not only one specific gene or pathway, but multiple genes and pathways that change. The findings above lay the foundation for study of AIPC mechanism and development of AIPC targeting drugs.

• Korean Journal of Head & Neck Oncology
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• v.20 no.2
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• pp.147-155
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• 2004

Objectives: Head and neck squamous cell carcinoma (HNSCC) is the most common head and neck malignant tumor. The molecular genetic changes involving both oncogenes and tumor suppressor genes are known to be involved in head and neck squamous cell carcinogenesis, but the roles of the known tumor suppressor genes in carcinogenesis are not fully elucidated. The objectives of this study are to demonstrate the genetic alterations including the loss of heterozygosity (LOH) , amplification, and microsatellite instability of known tumor suppressor genes in HNSCC and to evaluate the relationship between genetic alterations of tumor suppressor genes and clinicopathologic features. Materials and Methods: Genetic alterations of 10 micro satellite markers of the 6 known tumor suppressor genes (APC, EXT1, DPC4, p16, FHIT, and PTEN) were analysed by DNA-PCR in paraffin-embedded histologically confirmed HNSCC specimens. Results: The genetic alterations of tumor suppressor genes were found frequently. Among the genetic alterations, LOH was most frequently found one. LOH was found frequently in APC (45.4%), EXT1 (36.4%), DPC4 (54.5%), and p16 (50%), but not found in FHIT. Also, the author found that abnormalities of APC gene was related to cervical lymph node metastasis and recurrence and that abnormalities of EXT1 gene were coexisted with those of APC gene or DPC4 gene. But these coexistences had no correlation with clinical features. Conclusion: These results suggested that APC, EXT1, p16, and DPC4 genes might play important roles and multiple tumor suppressor genes may participate dependently or independently in the carcinogenesis of HNSCC. These results also suggested that APC gene might relate to prognosis.

• Journal of Photoscience
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• v.9 no.2
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• pp.373-375
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• 2002

Lhcb genes encoding light-harvesting chlorophyll-a/b binding (LHC) proteins of photosystem (PS) II were comprehensively characterized using the expressed sequence tag (EST) databases in the green alga, Chlamydomonas reinhardtii. The gene family was composed of eight Lhcb genes including four new genes, which were isolated and sequenced. The effects of light intensity on the levels of mRNAs accumulation of multiple Lhcb genes were studied under various conditions. The results indicate that Lhcb genes are coordinately regulated in response to light conditions, and repressed when the input light energy exceeded the requirement for $CO_2$ assimilation. The effects of high light on the expression of the Lhcb genes observed in the presence of an electron transport inhibitor, DCMU, and in mutants deficient in photosynthetic reaction centers suggest the presence of two alternative mechanisms for regulating the genes expression under high-light conditions.

• International journal of advanced smart convergence
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• v.7 no.1
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• pp.48-63
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• 2018

The combination of Simian Virus40 (SV40)'s large T antigen with its replication origin is commonly used in molecular studies to enhance the expression of heterogeneous genes through multiplying the plasmid copy number. There are no reports related to the impact of the SV40 T antigen on plant, multiple fissional, cell-type. This study explores the response of two multiple-fission microalgal cells, Scenedesmus quadricauda and Chlorella vulgaris, to the expression of the T-antigen, with aim of applying SV40 T-antigen to increase the expression efficiency of foreign genes in the two species. Different levels of low-expression have been constructed to control the expression of SV40 T antigen using three heterogenous promoters (NOS, CaMV35S, and CMV). Chlorella cultures showed slowdown in the growth rate for samples harboring the T antigen under the control of CaMV35S and CMV promoters, unlike Scenedesmus cultures which showed no significant difference between samples and could have silenced the expression.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.12
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• pp.7221-7227
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• 2013

Background: Fascin, an actin-bundling protein forming actin bundles including filopodia and stress fibers, is overexpressed in multiple human epithelial cancers including esophageal squamous cell carcinoma (ESCC). Previously we conducted a microarray experiment to analyze fascin knockdown by RNAi in ESCC. Method: In this study, the differentially expressed genes from mRNA expression profilomg of fascin knockdown were analyzed by multiple bioinformatics methods for a comprehensive understanding of the role of fascin. Results: Gene Ontology enrichment found terms associated with cytoskeleton organization, including cell adhesion, actin filament binding and actin cytoskeleton, which might be related to fascin function. Except GO categories, the differentially expressed genes were annotated by 45 functional categories from the Functional Annotation Chart of DAVID. Subpathway analysis showed thirty-nine pathways were disturbed by the differentially expressed genes, providing more detailed information than traditional pathway enrichment analysis. Two subpathways derivated from regulation of the actin cytoskeleton were shown. Promoter analysis results indicated distinguishing sequence patterns and transcription factors in response to the co-expression of downregulated or upregulated differentially expressed genes. MNB1A, c-ETS, GATA2 and Prrx2 potentially regulate the transcription of the downregulated gene set, while Arnt-Ahr, ZNF42, Ubx and TCF11-MafG might co-regulate the upregulated genes. Conclusions: This multiple bioinformatic analysis helps provide a comprehensive understanding of the roles of fascin after its knockdown in ESCC.

• Journal of Microbiology and Biotechnology
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• v.28 no.5
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• pp.826-830
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• 2018

A Cre/loxP-${\delta}$-integration system was developed to allow sequential and simultaneous integration of a multiple gene expression cassette in Saccharomyces cerevisiae. To allow repeated integrations, the reusable Candida glabrata MARKER (CgMARKER) carrying loxP sequences was used, and the integrated CgMARKER was efficiently removed by inducing Cre recombinase. The XYLP and XYLB genes encoding endoxylanase and ${\beta}$-xylosidase, respectively, were used as model genes for xylan metabolism in this system, and the copy number of these genes was increased to 15.8 and 16.9 copies/cell, respectively, by repeated integration. This integration system is a promising approach for the easy construction of yeast strains with enhanced metabolic pathways through multicopy gene expression.

• BMB Reports
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• v.49 no.5
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• pp.255-262
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• 2016

The disease known as cerebral cavernous malformations mostly occurs in the central nervous system, and their typical histological presentations are multiple lumen formation and vascular leakage at the brain capillary level, resulting in disruption of the blood-brain barrier. These abnormalities result in severe neurological symptoms such as seizures, focal neurological deficits and hemorrhagic strokes. CCM research has identified 'loss of function' mutations of three ccm genes responsible for the disease and also complex regulation of multiple signaling pathways including the WNT/β-catenin pathway, TGF-β and Notch signaling by the ccm genes. Although CCM research is a relatively new and small scientific field, as CCM research has the potential to regulate systemic blood vessel permeability and angiogenesis including that of the blood-brain barrier, this field is growing rapidly. In this review, I will provide a brief overview of CCM pathogenesis and function of ccm genes based on recent progress in CCM research.

• BMB Reports
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• v.46 no.7
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• pp.338-345
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• 2013

microRNAs (miRNAs) are small non-coding RNAs that regulate gene expression by targeting the 3'-untranslated region of multiple target genes. Pathogenesis results from defects in several gene sets; therefore, disease progression could be prevented using miRNAs targeting multiple genes. Moreover, recent studies suggest that miRNAs reflect the stage of the specific disease, such as carcinogenesis. Cystic diseases, including polycystic kidney disease, polycystic liver disease, pancreatic cystic disease, and ovarian cystic disease, have common processes of cyst formation in the specific organ. Specifically, epithelial cells initiate abnormal cell proliferation and apoptosis as a result of alterations to key genes. Cysts are caused by fluid accumulation in the lumen. However, the molecular mechanisms underlying cyst formation and progression remain unclear. This review aims to introduce the key miRNAs related to cyst formation, and we suggest that miRNAs could be useful biomarkers and potential therapeutic targets in several cystic diseases.

• Quantitative Bio-Science
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• v.36 no.1
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• pp.23-31
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• 2017

Datasets from DNA microarray experiments, which are in the form of large matrices of expression levels of genes, often have missing values. However, the existing statistical methods including the principle components analysis (PCA) and Hotelling's t-test are not directly applicable for the datasets having missing values due to the fact that they assume the observed dataset is complete in general. Many methods have been proposed in previous literature to impute the missing in the observed data. Troyanskaya et al. [1] study the k-nearest neighbor (kNN) imputation, Kim et al. [2] propose the local least squares (LLS) method and Rubin [3] propose the multiple imputation (MI) for missing values. To identify differentially expressed genes, we propose a new testing procedure when the missing exists in the observed data. The proposed procedure uses the Stouffer's z-scores and combines the test results of individual imputed samples, which are dependent to each other. We numerically show that the proposed test procedure based on MI performs better than the existing test procedures based on single imputation (SI) by comparing their ROC curves. We apply the proposed method to analyzing a public microarray data.

• Korean Journal of Clinical Laboratory Science
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• v.39 no.3
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• pp.161-166
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• 2007

To develop a rapid and reliable single-tube-based PCR technique for detection simultaneously the quinolone resistance qnrA, qnrB and qnrS genes. After multiple alignment, primers were designed to detect known qnr variants. I was used for A total of 43 extented-spectrum ${\beta}$-lactamases (ESBLs) producing Escherichia coli and Klebsiella pneumoniae isolated from university hospital were tested for screening, as with qnr genes. In optimized conditions, all positive controls confirmed the specificity of the PCR primers. Out of 43 isolates, qnrA genes were detected 19 (44.2%), qnrB genes 5 (11.7%), qnrS genes 15 (34.9%) and 8 (18.6%) isolates were not detected. I report here a fast and reliable technique for rapid screening of qnr positive strains to be used for epidemiological surveys.