• Molecular & Cellular Toxicology
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• 제5권3호
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• pp.222-229
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• 2009

Our previous finding that pre-initiation treatment of indole-3-carbinol (I3C) represents a chemopreventive effect in dimethylbenz[a]anthracene (DMBA)-induced mammary carcinogenesis has prompted us to test the global expression of genes at an early stage. Rats were continuously fed 300 ppm I3C in their diet at 6 weeks of age and were injected with DMBA at 7 weeks of age, and were sacrificed at 8 weeks of age. Global gene expression analysis using oligonucleotide microarrays was conducted to detect altered genes in DMBA- or DMBA plus I3C-treated mammary glands. Altered genes were identified by fold changes of 1.2 and by t-test (P<0.05) from the log ratios of the hybridization intensity of samples between control (Group 1) and DMBA (Group 2), and from those of samples between DMBA (Group 2) and DMBA plus I3C (Group 3). From these genes, we chose altered genes that were up- or down-regulated by DMBA treatment and recovered to the control level by I3C treatment. For early stage of carcinogenesis, I3C treatment induced the recovery to normal levels of several genes including cell cycle pathway (cyclin B2, cell division cycle 2 homolog A), MAP signaling pathway (fibroblast growth factor receptor 1, platelet derived growth factor receptor, beta polypeptide), and insulin signaling (protein phosphatase 1, regulatory (inhibitor) subunit 3B and flotillin 2), which were up-regulated by DMBA treatment. In addition, I3C treatment induced the recovery to normal levels of several genes including those of MAPK signaling (transforming growth factor, beta receptor 1 and protein phosphatase 3, catalytic subunit, beta isoform), which were down-regulated by DMBA treatment. These results suggest that the targeting of these genes presents a possible approach for chemoprevention in DMBA-induced mammary carcinogenesis.

• 미생물학회지
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• 제29권6호
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• pp.392-396
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• 1991

Pseudomonas sp. DJ77의 chromosomal DNA로부터 6.9kb XhoI 절편 상에 존재하는 phenanthrene 분해에 관련된 유전자군을 vector pBLUESCRIPT SK(+)에 클로닝하였다. 이렇게 얻은 재조합 plasmid인 pHENX7을 가지고 있는 JM101 균주는 3-methylcarechol을 노란색의 meta-cleavage 화합물로 전환할 수 있었다. 그러나 삽입된 절편의 방향이 반대가 되도록 제조한 pHENX7은 extradiol dioxygenase 활성을 나타내지 않기 때문에 전사방향을 알 수 있었다. pHENX7과 이의 듀도체들을 지니는 JH101균주에서 PhnC(24kDa), PhnD(31KDa), PhnE(34kDa), PhnF(KDa)의 4 polypeptide를 확인 할 수 있었고 개개의 유전자의 위치와 범위를 알 수 있었다. 유전자 순서는 phnC-phnD-phnE-phnF-phnG이었으며, phnC, phnD, phnE, phnF, phnG는 각기 glutathione S-transferase, meta-cleavage compound hydrolase extradiol dioxygenase, meta-cleavage compound dehydrogenase의 유전자이었다.

• Journal of Animal Science and Technology
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• 제54권3호
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• pp.157-163
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• 2012

The male reproduction is precisely controlled by a number of intrinsic and extrinsic factors. These factors usually involve in expressional regulation of various molecules influencing on sperm production in the testis. A number of ways are employed to control the transcription of specific genes, including epigenetic modifications of DNA and histone molecules. DNA methylation of CpG dinucleotides is a commonly used regulatory mechanism for testicular genes associated with the fertility. Previous studies have demonstrated the infertility induced by improper DNA methylation of these genes. In the present research, we attempted to determine transcriptional expression of some of these genes in the rat testis at different postnatal ages using real-time PCR analysis. These genes include neurotrophin 3 (Ntf3), insulin-like growth factor II (Igf2), JmjC-domain-containing histone demethylase 2A 1 (Jhm2da), paired box 8 transcription factor (Pax8), small nuclear ribonucleoprotein polypeptide N (Snrpn), and 5,10-methylenetetrahydrofolate reductase (Mthfr). The expression levels of Ntf3, Igf2, and Snrpn genes were the highest at the neonatal age, followed by transient decreases at the prepubertal age. Expression of Jhm2da and Mthfr genes were continuously increased from the neonate to 1 year of age. The levels of Pax8 mRNA at the early ages were higher than those at the later ages of postnatal development. These findings suggest that expression of some fertility-associated testicular genes in the rat during postnatal period could be differentially regulated by the control of the degree of DNA methylation.

• KSBB Journal
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• 제28권1호
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• pp.54-59
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• 2013

Three isolates, E. faecium P1, P2 and P3, from intestinal drugs of three phamaceutical companies, four clinical vancomycin resistant isolates, E. faecium V1, V2, V3 and E. faecalis V4, and three isolates, E. faecalis DW01, DW07 and DW14, from infant feces were tested for the presence of virulence genes, ace, agg, esp, efaA, gelE, sprE, vanA and vanB as well as fsrABC, regulatory genes of gelE and sprE, cylMBA, cytolysin activation genes and cpd, cob and ccf, pheromone genes by PCR and for their phenotype activities such as protease, biofilm formation, cell clumping and hemolysis. The genes encoding cell surface adherence proteins, ace, agg, esp and efaA, were predominantly amplified from the vancomycin resistant strain V4 and the fecal isolates DW01, DW07 and DW14. Both protease and biofilm formation activity were detected only from E. faecalis V4 from which the PCR products of gelE and spreE as well as fsrABC were amplified. The pheromone genes were amplified from the V4, DW01, DW07 and DW14 strains and these strains showed clumping activity. Biofilm formation was observed from the strains DW01, DW07 and DW14, all of which produced PCR products of pheromone, and V4 as well. Whole cytolysin regulator genes were amplified from DW01, DW07 and DW14 and ${\beta}$-hemolysis activity was detected from these strains. Any virulence genes or activities except the pheomone gene ccf were not detected from the pharmaceutical isolates, E. faecium P1, P2 and P3.

• Journal of Microbiology and Biotechnology
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• 제31권11호
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• pp.1533-1544
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• 2021

n-Caproic acid (CA) is gaining increased attention due to its high value as a chemical feedstock. Ruminococcaceae bacterium strain CPB6 is an anaerobic mesophilic bacterium that is highly prolific in its ability to perform chain elongation of lactate to CA. However, little is known about the genome-wide transcriptional analysis of strain CPB6 for CA production triggered by the supplementation of exogenous lactate. In this study, cultivation of strain CPB6 was carried out in the absence and presence of lactate. Transcriptional profiles were analyzed using RNA-seq, and differentially expressed genes (DEGs) between the lactate-supplemented cells and control cells without lactate were analyzed. The results showed that lactate supplementation led to earlier CA p,roduction, and higher final CA titer and productivity. 295 genes were substrate and/or growth dependent, and these genes cover crucial functional categories. Specifically, 5 genes responsible for the reverse β-oxidation pathway, 11 genes encoding ATP-binding cassette (ABC) transporters, 6 genes encoding substrate-binding protein (SBP), and 4 genes encoding phosphotransferase system (PTS) transporters were strikingly upregulated in response to the addition of lactate. These genes would be candidates for future studies aiming at understanding the regulatory mechanism of lactate conversion into CA, as well as for the improvement of CA production in strain CPB6. The findings presented herein reveal unique insights into the biomolecular effect of lactate on CA production at the transcriptional level.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2001년도 제2회 생물정보 워크샵 (DNA Chip Bioinformatics)
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• pp.45-60
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• 2001

. Mediator of transcriptional regulation is the evolutionary conserved coactivator complex that plays He central role in the integration and recruitment of diverse regulatory signals and transcription machinery to certain promoters. In yeast, each Mediator subunit is required for transcriptional regulation of a distinct group of genes. In order to decipher the mechanistic roles of Mediator proteins in regulating developmental specific gene expression, we isolated, and analyzed a multiprotein complex containing Drosophila Mediate. homologs (dMediato.). dMediato. interacts with several sequence-sperific transcription factors and basal transcription machinery, and is critical for activated transcription in response to diverse transcriptional activators. In order to elucidate the function of Mediator in metazoan development, we isolated mutants of a conserved Mediate. subunit, Drosophila Med6 (dMed6). dMed6 null homozygotes failed to pupate and died in the third larval instar. Larval mitotic cells and most imaginal discs showed severe defects in proliferation, but no apparent morphological defect was observed in other larval tissues. Clonal analysis of dMed6 mutant cells revealed that dMed6 is essential for cell viability and proliferation of most adult cell types. Drosophila cDNA microarray, quantitative RT-PCR, and in situ expression analyses of developmentally regulated genes in dMed6 mutants showed that transcriptional activation of a subset of genes involved in neuroblast proliferation in the larval brain were most affected. Our results suggest that dMed6 is required in most for transcriptional regulation of a subset of genes important for cell proliferation and metabolism.

• BMB Reports
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• 제37권2호
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• pp.139-143
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• 2004

The antioxidant responsive element (ARE) is a cis-acting regulatory element of genes encoding phase II detoxification enzymes and antioxidant proteins, such as NAD(P)H: quinone oxidoreductase 1, glutathione S-transferases, and glutamate-cysteine ligase. Interestingly, it has been reported that Nrf2 (NF-E2-related factor 2) regulates a wide array of ARE-driven genes in various cell types. Nrf2 is a basic leucine zipper transcription factor, which was originally identified as a binding protein of locus control region of ss-globin gene. The DNA binding sequence of Nrf2 and ARE sequence are very similar, and many studies demonstrated that Nrf2 binds to the ARE sites leading to up-regulation of downstream genes. The function of Nrf2 and its downstream target genes suggests that the Nrf2-ARE pathway is important in the cellular antioxidant defense system. In support of this, many studies showed a critical role of Nrf2 in cellular protection and anti-carcinogenicity, implying that the Nrf2-ARE pathway may serve as a therapeutic target for neurodegenerative diseases and cancers, in which oxidative stress is closely implicated.

• The Plant Pathology Journal
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• 제35권1호
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• pp.84-89
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• 2019

Two-component systems (TCSs) are critical to the pathogenesis of Xanthomonas oryzae pv. oryzae (Xoo). We mutated 55 of 62 genes annotated as responsive regulators (RRs) of TCSs in the genome of Xoo strain PXO99A and identified 9 genes involved in Xoo virulence. Four (rpfG, hrpG, stoS, and detR) of the 9 genes were previously reported as key regulators of Xoo virulence and the other 5 have not been characterized. Lesion lengths on rice leaves inoculated with the mutants were shorter than those of the wild type and were significantly restored with gene complementation. The population density of the 5 mutants in planta was smaller than that of PXO99A at 14 days after inoculation, but the growth curves of the mutants in rich medium were similar to those of the wild type. These newly reported RR genes will facilitate studies on the function of TCSs and of the integrated regulation of TCSs for Xoo pathogenesis.

• Genomics & Informatics
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• 제20권1호
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• pp.5.1-5.10
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• 2022

Non-syndromic hearing loss (NSHL) is a common hereditary disorder. Both clinical and genetic heterogeneity has created many obstacles to understanding the causes of NSHL. The present study has attempted to ravel the genetic aetiology in NSHL progression and to screen out potential target genes using computational approaches. The reported NSHL target genes (2009-2020) have been studied by analyzing different biochemical and signaling pathways, interpretation of their functional association network, and discovery of important regulatory interactions with three previously established miRNAs in the human inner ear as well as in NSHL such as miR-183, miR-182, and miR-96. This study has identified SMAD4 and SNAI2 as the most putative target genes of NSHL. But pathogenic and deleterious non-synonymous single nucleotide polymorphisms discovered within SMAD4 is anticipated to have an impact on NSHL progression. Additionally, the identified deleterious variants in the functional domains of SMAD4 added a supportive clue for further study. Thus, the identified deleterious variant i.e., rs377767367 (G491V) in SMAD4 needs further clinical validation. The present outcomes would provide insights into the genetics of NSHL progression.

• Genomics & Informatics
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• 제20권4호
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• pp.40.1-40.8
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• 2022

The concepts of phylogeny and floral genetics play a crucial role in understanding the origin and diversification of flowers in angiosperms. Angiosperms evolved a great diversity of ways to display their flowers for reproductive success with variations in floral color, size, shape, scent, arrangements, and flowering time. The various innovations in floral forms and the aggregation of flowers into different kinds of inflorescences have driven new ecological adaptations, speciation, and angiosperm diversification. Evolutionary developmental biology seeks to uncover the developmental and genetic basis underlying morphological diversification. Advances in the developmental genetics of floral display have provided a foundation for insights into the genetic basis of floral and inflorescence evolution. A number of regulatory genes controlling floral and inflorescence development have been identified in model plants such as Arabidopsis thaliana and Antirrhinum majus using forward genetics, and conserved functions of many of these genes across diverse non-model species have been revealed by reverse genetics. Transcription factors are vital elements in systems that play crucial roles in linked gene expression in the evolution and development of flowers. Therefore, we review the sex-linked genes, mostly transcription factors, associated with the complex and dynamic event of floral development and briefly discuss the sex-linked genes that have been characterized through next-generation sequencing.