• Journal of Microbiology and Biotechnology
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• 제31권4호
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• pp.510-519
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• 2021

The pathological impact of haze upon the phyllosphere microbiota awaits investigation. A moderate degree of haze environment and a clean control were selected in Chengdu, China. Artemisia argyi, a ubiquitously distributed and extensively applied Chinese herb, was also chosen for experiment. Total genome DNA was extracted from leaf samples, and for metagenome sequencing, an Illumina HiSeq 2500 platform was applied. The results showed that the gene numbers of phyllosphere microbiota derived from haze leaves were lower than those of the clean control. The phyllosphere microbiota derived from both haze and clean groups shared the same top ten phyla; the abundances of Proteobacteria, Actinomycetes and Anorthococcuso of the haze group were substantially increased, while Ascomycetes and Basidiomycetes decreased. At the genus level, the abundances of Nocardia, Paracoccus, Marmoricola and Knoelia from haze leaves were markedly increased, while the yeasts were statistically decreased. KEGG retrieval demonstrated that the functional genes were most annotated to metabolism. An interesting find of this work is that the phyllosphere microbiota responsible for the synthesis of primary and secondary metabolites in A. argyi were significantly increased under a haze environment. Relatively enriched genes annotated by eggNOG belong to replication, recombination and repair, and genes classified into the glycoside hydrolase and glycosyltransferase enzymes were significantly increased. In summary, we found that both structure and function of phyllosphere microbiota are globally impacted by haze, while primary and secondary metabolites responsible for haze tolerance were considerably increased. These results suggest an adaptive strategy of plants for tolerating and confronting haze damage.

• Journal of Microbiology and Biotechnology
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• 제25권12호
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• pp.2125-2134
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• 2015

IrrE is a highly conserved global regulator in the Deinococcus genus and contributes to survival from high doses of UV radiation, ionizing radiation, and desiccation. Drad-IrrE and Dgob-IrrE from Deinococcus radiodurans and Deinococcus gobiensis I-0 each share 66% sequence identity. However, Dgob-IrrE showed a stronger protection phenotype against UV radiation than Drad-IrrE in the D. radiodurans irrE-deletion mutant (ΔirrE), which may be due to amino acid residues differences around the DNA-binding HTH domain. Site-directed mutagenesis was used to generate a Drad-IrrE A184S single mutant, which has been characterized and compared with the ΔirrE mutant complemented strain with Drad-irrE, designated ΔirrE-E. The effects of the A184S mutation following UV radiation and mitomycin C (MMC) shock were determined. The A184S mutant displayed significantly increased resistance to UV radiation and MMC shock. The corresponding A184 site in Dgob-IrrE was inversely mutated, generating the S131A mutant, which exhibited a loss of resistance against UV radiation, MMC shock, and desiccation. qPCR analysis revealed that critical genes in the DNA repair system, such as recA, pprA, uvrA, and ddrB, were remarkably induced after UV radiation and MMC shock in the ΔirrE-IE and A184S mutants. These data suggested that A184S improves the ability against UV radiation and MMC shock, providing new insights into the modification of IrrE. We speculated that the serine residue may determine the efficiency of DNA binding, leading to the increased expression of IrrE-dependent genes important for protection against DNA damage.

• Radiation Oncology Journal
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• 제21권1호
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• pp.54-65
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• 2003

목적 : 동시에 대량으로 유전자발현 양상을 검사할 수 있는 cDNA microarray 기법을 이용하여 자궁경부암에서 특징적으로 나타나는 유전자발현 양상을 알아보고, 방사선치료 및 방사선 항암화학요법 병용치료시의 유전자발현 변화양상을 파악하고자 하였다. 대상 및 방법 :자궁경부 편평상피암으로 확진된 후 근치목적 방사선치료를 단독으로 시행한 8명과 항암화학요법을 병행한 8명에서 채취한 종양조직을 대상으로 하고, 정상 자궁경부 3례를 대조군으로 하였다 조직 생검은 치료 전과 외부 방사선치료 16.2$\~$27 Gy에 두 번하였다. 항암화학요법을 병용한 경우, 5-FU 1,000 mg/m$^{2}$을 제 1일부터 5일까지 정주하고, clsplatin 60 mg/m$^{2}$을 제 1일에 정주하였다. cDNA microarray는 종양조직에서 추출한 total RNA를 역전사(reverse transcription)방법을 이용하여 (P-33)을 표지한 cDNAS를 제작, nylon membrane에 hybridization하였다. 이후 membrane을 phosphor-imager screens에 옮겨 1$\~$5일 동안 노출시킨 후 이미지를 스캔하였다. 유전자의 발현정도는 각 스팟(spot)들의 방사능 강도로 나타나는데, 각 스팟의 픽셀(pixel)을 Arrayguage를 사용하여 산출한 후 엑셀파일로 저장하였다. 유전자의 발현정도 비교는 원 자료(original data)를 Z-변환을 통해 보정(normalized)한 후 Z-ratio값을 산출하여 시행하였다. 결과 : 대조군에 비해 자궁경부암에서 Z-ratio 2.0 이상으로 유의한 발현증가를 보인 유전자들은 integrin-linked kinase, CDC28 protein kinase 2, Spry 2, ERK 3 등 15개로 주로 세포성장과 증식, 세포주기, 신호전달 등에 관련된 유전자들이었으며, Z-ratio -2.0 이하의 유의한 발현감소는 G protein-coupled receptor kinase 6외 6개였다. 방사선 단독치료를 시행한 후 Z-ratio 2.0 이상 발현이 증가한 것은 cyclic nucleotlde gated channel외 3개의 Expressed sequence tags (EST)들이었고, Z-ratio -2.0 이하의 발현감소를 보인 것들에는 치료전 종양세포에서 발현이 증가되었던 세포성장과 증식, 세포주기, 신호전달 등에 관련된 유전자들이 포함되었다 방사선치료와 항암화학요법을 병용했을 때는 방사선 단독치료에 비하여 세포성장과 증식 및 신호전달 관련 유전자들이 상대적으로 높게 발현되었으며, 이외에도 혈관형성(angiopoietin-2), 면역반응(formyl peptide receptor-like 1), DNA 손상회복에 관련된 유전자(CAMP phosphodiesterase)의 발현은 증가되고 세포고사(death associated protein kinase)에 관련된 유전자는 발현 감소를 보였다. 결론 : 자궁경부암에서분열과 증식 및 신호전달에 관여하는 여러 종류의 유전자들 발현이 동시다발적으로 증가되어 있다는 것과 방사선치료를 시행하면 이들 유전자의 발현이 감소하여 종양세포의 분열과 증식이 저해된다는 것을 확인하였다. 방사선 단독치료와 항암화학요법 병용치료를 비교하면 그 유전자 발현양상이 다르므로 향후 이번연구에서 나타난 유전자들에 대한 추가 연구가 필요하며, 이는 개별화된 맞춤형 치료법을 개발하는데 기초자료로 사용될 수 있을 것으로 기대된다.

• 대한한방부인과학회지
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• 제20권2호
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• pp.1-24
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• 2007

Purpose : These experiments were undertaken to evaluate the effect of adminis tration of JokyungSan on ovarian functions and differential gene expressions related cell viabilities caspase-3, MAPK and MPG in female mice. Methods : We administered the JokyungSan to 6-week-old female ICR mice for 4, 8, or 12 days. The female mice were injected PMSG and hCG for ovarian hyperstimulation. We chose the caspase-3 for cell apoptosis, MAPK and MPG genes for cell viability and DNA repair. To compare the differences, we set a control group treated with plain water at the same volume by the same way. Results : In case of 4-day administration of JokyungSan, the mean number of total ovulated oocytes and the number of morphologically normal oocytes increased significantly compared to a control group. The administration of JokyungSan, were beneficial effect of embryonic development in preimplantation period and play a role of prevention of cell apoptosis and DNA damages and also increased cell proliferation resulted in ovarian functions. Conclusion : From our results suggested that the medication of JokyungSan has beneficial effect on reproductive functions of female mice via prevention of cell apoptosis and DNA damaging and promotion of cell proliferation.

• 대한한방부인과학회지
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• 제20권3호
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• pp.91-110
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• 2007

Purpose : These experiments were undertaken to evaluate the effect of administration of Palmultang on ovarian functions and differential gene expressions related cell viabilities caspase-3, MAPK and MPG in female mice. Materials and Methods : We administered the Palmultang to 6-week-old female ICR mice for 4, 8, or 12 days. The female mice were injected PMSG and hCG for ovarian hyperstimulation. And then recovered ovaries were minced and extracted mRNA and analyzed cell viability related gene expression. We chose the caspase-3 for cell apoptosis, MAPK and MPG genes for cell viability and DNA repair. To compare the differences, we set a control group treated with plain water at the same volume by the same way. Results : In case of administration of Palmultang, the mean number of total ovulated oocytes and the number of morphologically normal oocytes increased significantly compared to a control group. We were also examined the embryonic developmental competence in vitro. The administration of Palmultang in a concentration with 10 and 100 mg/ml were beneficial effect of embryonic development in preimplantation period. The administration of Palmultang play a role of prevention of cell apoptosis and DNA damages and also increased cell proliferation resulted in ovarian functions. Conclusion : From our results suggested that the medication of Palmultang has beneficial effect on reproductive functions of female mice via prevention of cell apoptosis and DNA damaging and promotion of cell proliferation.

• Journal of Radiation Protection and Research
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• 제43권2호
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• pp.66-74
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• 2018

Background: Tumor response to anticancer therapies can much be influenced by microenvironmental factors. In this study, we determined the effect of these microenvironmental factors on DNA methylation using A549 human lung adenocarcinoma cell line. Materials and Methods: We subjected A549 cells to various conditions mimicking tumor microenvironment including hypoxia, acidosis (sodium lactate), oxidative stress ($H_2O_2$), bystander effect (supernatant from doxorubicin (Dox)-treated or irradiated cells), and immune cell infiltration (supernatant from THP-1 or Jurkat T cells). Genomic DNA was isolated from these cells and analyzed for DNA methylation. Clonogenic cell survival, gene expression, and metabolism were analyzed in cells treated with some of these conditions. Results and Discussion: We found that DNA methylation level was significantly decreased in A549 cells treated with conditioned media from Dox-treated cells or Jurkat T cells, or sodium lactate, indicating an active transcription. To determine whether the decreased DNA methylation affects radiation sensitivity, we exposed cells to these conditions followed by 6 Gy irradiation and found that cell survival was significantly increased by sodium lactate while it was decreased by conditioned media from Dox-treated cells. We further observed that cells treated with conditioned media from Dox-treated cells exhibited significant changes in expression of genes including BAX and FAS (involved in apoptosis), NADPH dehydrogenase (mitochondria), EGFR (cellular survival) and RAD51 (DNA damage repair) while sodium lactate increased cellular metabolism rather than changing the gene expression. Conclusion: Our results suggest that various tumor microenvironmental factors can differentially influence DNA methylation and hence radiosensitivity and gene expression in A549 cancer cells.

• Animal Bioscience
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• 제37권5호
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• pp.929-943
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• 2024

Objective: The present study was executed to explore the molecular mechanism of fibroblast growth factor 10 (FGF10) gene in bovine adipogenesis. Methods: The bovine FGF10 gene was overexpressed through Ad-FGF10 or inhibited through siFGF10 and their negative control (NC) in bovine adipocytes, and the multiplicity of infection, transfection efficiency, interference efficiency were evaluated through quantitative real-time polymerase chain reaction, western blotting and fluorescence microscopy. The lipid droplets, triglycerides (TG) content and the expression levels of adipogenic marker genes were measured during preadipocytes differentiation. The differentially expressed genes were explored through deep RNA sequencing. Results: The highest mRNA level was found in omasum, subcutaneous fat, and intramuscular fat. Moreover, the highest mRNA level was found in adipocytes at day 4 of differentiation. The results of red-oil o staining showed that overexpression (Ad-FGF10) of the FGF10 gene significantly (p<0.05) reduced the lipid droplets and TG content, and their down-regulation (siFGF10) increased the measurement of lipid droplets and TG in differentiated bovine adipocytes. Furthermore, the overexpression of the FGF10 gene down regulated the mRNA levels of adipogenic marker genes such as CCAAT enhancer binding protein alpha (C/EBPα), fatty acid binding protein (FABP4), peroxisome proliferator-activated receptor-γ (PPARγ), lipoprotein lipase (LPL), and Fas cell surface death receptor (FAS), similarly, down-regulation of the FGF10 gene enriched the mRNA levels of C/EBPα, PPARγ, FABP4, and LPL genes (p<0.01). Additionally, the protein levels of PPARγ and FABP4 were reduced (p<0.05) in adipocytes infected with Ad-FGF10 gene and enriched in adipocytes transfected with siFGF10. Moreover, a total of 1,774 differentially expressed genes (DEGs) including 157 up regulated and 1,617 down regulated genes were explored in adipocytes infected with Ad-FGF10 or Ad-NC through deep RNA-sequencing. The top Kyoto encyclopedia of genes and genomes pathways regulated through DEGs were the PPAR signaling pathway, cell cycle, base excision repair, DNA replication, apoptosis, and regulation of lipolysis in adipocytes. Conclusion: Therefore, we can conclude that the FGF10 gene is a negative regulator of bovine adipogenesis and could be used as a candidate gene in marker-assisted selection.

• Asian Pacific Journal of Cancer Prevention
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• 제17권4호
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• pp.1917-1923
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• 2016

Background: Lynch Syndrome (LS) is a familial cancer condition caused by germline mutations in DNA mismatch repair genes. Individuals with LS have a greatly increased risk of developing colorectal cancer (CRC) and it is therefore important to identify mutation carriers so they can undergo regular surveillance. Tumor DNA from LS patients characteristically shows microsatellite instability (MSI). Our aim here was to screen young CRC patients for MSI as a first step in the identification of unrecognized cases of LS in the Saudi population. Materials and Methods: Archival tumor tissue was obtained from 284 CRC patients treated at 4 institutes in Dammam and Riyadh between 2006 and 2015 and aged less than 60 years at diagnosis. MSI screening was performed using the BAT-26 microsatellite marker and positive cases confirmed using the pentaplex MSI analysis system. Positive cases were screened for BRAF mutations to exclude sporadic CRC and were evaluated for loss of expression of 4 DNA mismatch repair proteins using immunohistochemistry. Results: MSI was found in 33/284 (11.6%) cases, of which only one showed a BRAF mutation. Saudi MSI cases showed similar instability in the BAT-26 and BAT-25 markers to Australian MSI cases, but significantly lower frequencies of instability in 3 other microsatellite markers. Conclusions: MSI screening of young Saudi CRC patients reveals that approximately 1 in 9 are candidates for LS. Patients with MSI are strongly recommended to undergo genetic counselling and germline mutation testing for LS. Other affected family members can then be identified and offered regular surveillance for early detection of LS-associated cancers.

• Asian Pacific Journal of Cancer Prevention
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• 제13권6호
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• pp.2541-2545
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• 2012

Objective: To investigate any association between XRCC1 and XRCC3 polymorphisms and outcome of platinum-based chemotherapy in ovarian cancer patients. Methods: With a prospective study design was cases were consecutively collected from January 2005 to January 2007. All 310 included patients were followed-up until the end of January 2010. Genotyping of XRCC1 and XRCC3 polymorphisms was conducted by TaqMan Gene Expression assays. Results: A total of 191 patients died during follow-up. Our study showed a lower survival rate in XRCC1 399 Arg/Arg genotype than Gln/Gln, with a significant increased risk of death (HR=1.69, 95%CI=1.07-2.78). Similarly, those carrying XRCC3 Thr/Thr genotype had a increased risk as compare to the Met/Met genotype, with a HR (95% CI) of 1.90 (1.12-3.41). There was no significant association between XRCC1 Arg194Trp and XRCC1Arg280His gene polymorphisms and ovarian cancer death. Conclusion: Our study demonstrates that polymorphisms in DNA repair genes have roles in the susceptibility and survival of ovarian cancer patients.

• Environmental Analysis Health and Toxicology
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• 제19권3호
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• pp.321-326
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• 2004

The study of p53 tumor suppressor protein is one of most important subjects in an environmental toxicology as well as in cancer biology. Generally, p53 has been known to involve the cell cycle regulation and apoptosis by the activation of its target genes such as p21 and bax in a number of cellular stress responses. In addition, associations of p53 with cellular proteins presumably reflect the involvement of p53 in critical cellular processes such as DNA repair. The complex formation of p53 and exogenous proteins such as viral or cellular proteins has been shown in many cases to play important roles in carcinogenic processes against environmental mutagen. Recently, the disruption of p53 protein by oxidative stress has been also reported to have relevance to carcinogenesis. These findings suggested that the maintaining of stability and functional activity of p53 protein was also important aspect to play as a tumor suppressor protein. Therefore, the detection of functional status of p53 proteins might be an effective biomarker for the cancer and human diseases under the environmental toxicologic carcinogen.