• Membrane and Water Treatment
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• v.3 no.1
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• pp.35-49
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• 2012

In membrane processes, various agents are used to enhance, protect, and recover membrane performance. Applying these agents in membrane modification could potentially be considered as a simple method to improve membrane performance without additional process. Citric acid (CI) and sodium bisulfite (SB) are two chemicals that are widely used in membrane feed water pretreatment and cleaning processes. In this work, preadsorptions of CI and SB were developed as simple methods for polysulfone ultrafiltration membrane modification. It was found that hydrogen bonding and Van Der Waals attraction could be responsible for the adsorptions of CI and SB onto membranes, respectively. After modification with CI or SB, the membrane surfaces became more hydrophilic. Membrane permeability improved when modified by SB while decreased a little when modified by CI. The modified membranes had an increase in PEG and BSA rejections and better antifouling properties with higher flux recovery ratios during filtration of a complex pharmaceutical wastewater. Moreover, membrane chlorine tolerance was elevated after modification with either agent, as shown by the mechanical property measurements.

• Genomics & Informatics
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• v.9 no.3
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• pp.136-137
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• 2011

Methylation of cytosine is a post-synthesis modification that does not affect the primary DNA sequence but greatly influences gene expression level and phenotypes of an organism. As high-throughput sequencing of bisulfite-treated DNA is the most efficient method to identify methylated sites, several tools to map sequencing reads on a reference are available. But tools to visualize and to interpret the methylation level of methylation sites are currently insufficient. Herein, we present a novel tool to visualize the methylation level of CpG sites.

• Journal of Microbiology and Biotechnology
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• v.11 no.5
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• pp.819-824
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• 2001

The principal DNA modification systems of the amino-acid-producing bacteria Corynebacterium glutamicum AS019, Brevibacterium flavum BF4, and B. lactofermentum BL1 was investigated using two approaches; digestion of plasmid DNA isolated from these species TseI and Fnu4HI, and sequence analysis of the putative methyltransferase target sites following the derivatization of DNA using metabisulfite treatment. The C. glutamicum and B. flavum strains showed similar digestion patterns to the two enzymes, indicating that the target for cytidine methyltransferase recognizes 5'-GCSGC-3'(where S is either G or C). Mapping the methylated cytidine sites by bisulfite derivatization, followed by PCR amplification and sequencing, was only possible when the protocol included an additional step eliminating any underivatized DNA after PCR amplification, thereby indicating that the derivatization was not $100\%$ efficient. This may have been due to the high G0C content of this genus. It was confirmed that C. glutamicum AS019 and B. flavum BF4 methylated the cytidine in the $Gm^5CCGC$ sequences, yet there were no similar patterns of methylation in B. lactofermentum, which was consistent with the distinctive degradation pattern seen for the above enzymes. These findings demonstrate the successful application of a modified bisulfite derivatization method with the Corynebacterium species for determining methylation patterns, and showed that different species in the geneus contain distinctive restriction and modification systems.

• Proceedings of the KSAR Conference
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• 2001.03a
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• pp.49-49
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• 2001

To elucidate overall changes in DNA methylation that occurs by inappropriate epigenetic control during ageing, we compared fetal bovine fibroblasts and their aged neomycin-resistant versions using bisulfite-PCR technology. Reduction in DNA methylation was observed in euchromatic repeats (18S-rRNA/art2) and promoter regions of sing1e-copy genes (the cytokeratin/-lactoglobulin/interleukin-13 genes). Contrastingly, a stable maintenance of DNA methylation was revealed in various heterochromatic sequences (satellite I/IIalphoid and Bov-B). The differential inheritance modes of DNA methylation was confirmed through the analysis of individual neomycin-resistant clones. These global, multi-loci analyses provide evidence on the tendency of differential epigenetic modification between genomic DNA regions during ageing.

• Genomics & Informatics
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• v.11 no.1
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• pp.7-14
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• 2013

As the International Human Epigenome Consortium (IHEC) launched officially at the 2010 Washington meeting, a giant step toward the conquest of unexplored regions of the human genome has begun. IHEC aims at the production of 1,000 reference epigenomes to the international scientific community for next 7-10 years. Seven member institutions, including South Korea, Korea National Institute of Health (KNIH), will produce 25-200 reference epigenomes individually, and the produced data will be publically available by using a data center. Epigenome data will cover from whole genome bisulfite sequencing, histone modification, and chromatin access information to miRNA-seq. The final goal of IHEC is the production of reference maps of human epigenomes for key cellular status relevant to health and disease.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.22
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• pp.9607-9610
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• 2014

Breast cancer, a leading cause of death among women in most countries worldwide, is rapidly increasing in incidence in Vietnam. One of biomarkers is the disruption of the genetic material including epigenetic changes like DNA methylation. With the aim of finding hypermethylation at CpG islands of promoter of BRCA1 gene, belonged to the tumor suppressor gene family, as the biomarker for breast cancer in Vietnamese population, sensitive methyl specific PCR (MSP) was carried out on 115 samples including 95 breast cancer specimens and 20 normal breast tissues with other diseases which were obtained from Ho Chi Minh City Medical Hospital, Vietnam. The result indicated that the frequency of BRCA1 hypermethylation reached 82.1% in the cases (p<0.001). In addition, the DNA hypermethylation of this candidate gene increased the possibility to be breast cancer with high incidence via calculated odd ratios (p<0.05). In conclusion, hypermethylation of this candidate gene could be used as the promising biomarker application with Vietnamese breast cancer patients.

• Journal of Embryo Transfer
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• v.27 no.2
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• pp.113-119
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• 2012

Epigenetic modification including genome-wide DNA demethylation is essential for normal embryonic development. Insufficient demethylation of somatic cell genome may cause various anomalies and prenatal loss in the development of nuclear transfer embryos. Hence, the source of nuclear donor often affects later development of nuclear transfer (NT) embryos. In this study, appropriateness of porcine embryonic germ (EG) cells as karyoplasts for NT with respect to epigenetic modification was investigated. These cells follow methylation status of primordial germ cells from which they originated, so that they may contain less methylated genome than somatic cells. This may be advantageous to the development of NT embryos commonly known to be highly methylated. The rates of blastocyst development were similar among embryos from EG cell nuclear transfer (EGCNT), somatic cell nuclear transfer (SCNT), and intracytoplasmic sperm injection (ICSI) (16/62, 25.8% vs. 56/274, 20.4% vs. 16/74, 21.6%). Genomic DNA samples from EG cells (n=3), fetal fibroblasts (n=4) and blastocysts from EGCNT (n=8), SCNT (n=14) and ICSI (n=6) were isolated and treated with sodium bisulfite. The satellite region (GenBank Z75640) that involves nine selected CpG sites was amplified by PCR, and the rates of DNA methylation in each site were measured by pyrosequencing technique. The average methylation degrees of CpG sites in EG cells, fetal fibroblasts and blastocysts from EGCNT, SCNT and ICSI were 17.9, 37.7, 4.1, 9.8 and 8.9%, respectively. The genome of porcine EG cells were less methylated than that of somatic cells (p<0.05), and DNA demethylation occurred in embryos from both EGCNT (p<0.05) and SCNT (p<0.01). Interestingly, the degree of DNA methylation in EGCNT embryos was approximately one half of SCNT (p<0.01) and ICSI (p<0.05) embryos, while SCNT and ICSI embryos contained demethylated genome with similar degrees. The present study demonstrates that porcine EG cell nuclear transfer resulted in hypomethylation of DNA in cloned embryos yet leading normal preimplantation development. Further studies are needed to investigate whether such modification affects long-term survival of cloned embryos.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.22
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• pp.9797-9800
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• 2014

Background: Nasopharyngeal carcinoma (NPC) is a common cancer in Southern China and Southeast Asia. Alu elements are among the most prevalent repetitive sequences and constitute 11% of the human genome. Although Alu methylation has been evaluated in many types of cancer, few studies have examined the levels of this modification in serum from NPC patients. Objective: To compare the Alu methylation levels and patterns between serum from NPC patients and normal controls. Materials and Methods: Sera from 50 NPC patients and 140 controls were examined. Quantitative combined bisulfite restriction analysis-Alu (qCOBRA-Alu) was applied to measure Alu methylation levels and characterize Alu methylation patterns. Amplified products were classified into four patterns according to the methylation status of 2 CpG sites: hypermethylated (methylation at both loci), partially methylated (methylation of either of the two loci), and hypomethylated (unmethylated at both loci). Results: A comparison of normal control sera with NPC sera revealed that the latter presented a significantly lower methylation level (p=0.0002) and a significantly higher percentage of hypomethylated loci (p=0.0002). The sensitivity of the higher percentage of Alu hypomethyted loci for distinguishing NPC patients from normal controls was 96%. Conclusions: Alu elements in the circulating DNA of NPC patients are hypomethylated. Moreover, Alu hypomethylated loci may represent a potential biomarker for NPC screening.

• Asian Pacific Journal of Cancer Prevention
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• v.17 no.9
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• pp.4487-4490
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• 2016

Background: Methylation at cg 16941656 of FRY is exclusively found in normal pancreatic tissue and has been proven to be specific for pancreatic-in-origin among several adenocarcinomas. Here, we investigated methylated DNA in the bile as a biomarker to differentiate the cause of obstruction between pancreatic cancer and benign causes. Materials and Methods: Bile samples of 45 patients with obstructive jaundice who underwent ERCP were collected and classified into pancreatic cancer (group 1) and benign causes (group 2) in 24 and 21 patients, respectively. DNA was extracted from bile and bisulfite modification was performed. After, methylation in cg 16941656 of FRY was identified by real-time PCR, with beta-actin used as a positive control. Results: Methylated DNA was identified in 10/24 (41.67%) and 1/21 (4.8%) of cases in groups 1 and 2, respectively (P= 0.012). The sensitivity, specificity, positive predictive value and negative predictive value to differentiate pancreatic cancer from benign causes were 42%, 95%, 91%, and 59%, respectively. Conclusions: Detecting a methylation at cg 16941656 of FRY in bile has high specificity, with an acceptable positive likelihood rate, and may therefore be helpful in distinguish pancreatic cancer from benign strictures.

• Asian-Australasian Journal of Animal Sciences
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• v.29 no.7
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• pp.1037-1043
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• 2016

Epigenetic processes in the development of skeletal muscle have been appreciated for over a decade. DNA methylation is a major epigenetic modification important for regulating gene expression and suppressing spurious transcription. Up to now, the importance of epigenetic marks in the regulation of Pax7 and myogenic regulatory factors (MRFs) expression is far less explored. In the present study, semi-quantitative the real-time polymerase chain reaction (RT-PCR) analyses showed MyoD and Myf5 were expressed in activated and quiescent C2C12 cells. MyoG was expressed in a later stage of myogenesis. Pax7 was weakly expressed in differentiated C2C12 cells. To further understand the regulation of expression of these genes, the DNA methylation status of Pax7, MyoD, and Myf5 was determined by bisulfite sequencing PCR. During the C2C12 myoblasts fusion process, the changes of promoter and exon 1 methylation of Pax7, MyoD, and Myf5 genes were observed. In addition, an inverse relationship of low methylation and high expression was found. These results suggest that DNA methylation may be an important mechanism regulating Pax7 and MRFs transcription in cell myogenic differentiation.