• Asian Pacific Journal of Cancer Prevention
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• v.16 no.18
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• pp.8299-8305
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• 2016

Background: In Egypt, breast cancer is estimated to be the most common cancer among females. It is also a leading cause of cancer-related mortality. Use of circulating cell-free DNA (ccf-DNA) as non-invasive biomarkers is a promising tool for diagnosis and follow-up of breast cancer (BC) patients. Objective: To assess the role of circulating cell free DNA (nuclear and mitochondrial) in diagnosing BC. Materials and Methods: Multiplex real time PCR was used to detect the level of ccf nuclear and mitochondrial DNA in the peripheral blood of 50 breast cancer patients together with 30 patients with benign lesions and 20 healthy controls. Laboratory investigations, histopathological staging and receptor studies were carried out for the cancer group. Receiver operating characteristic curves were used to evaluate the performance of ccf-nDNA and mtDNA. Results: The levels of both nDNA and mtDNA in the cancer group were significantly higher in comparison to the benign and the healthy control group. There was a statistically significant association between nDNA and mtDNA levels and well established prognostic parameters; namely, histological grade, tumour stage, lymph node status andhormonal receptor status. Conclusions: Our data suggests that nuclear and mitochondrial ccf-DNA may be used as non-invasive biomarkers in BC.

• Journal of Genetic Medicine
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• v.12 no.2
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• pp.85-91
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• 2015

Purpose: Noninvasive prenatal test (NIPT) by massively parallel sequencing (MPS) of cell-free fetal DNA in maternal plasma marks a significant advancement in prenatal screening, minimizing the need for invasive testing of fetal chromosomal aneuploidies. Here, we report the initial clinical performance of NIPT in Korean pregnant women. Materials and Methods: MPS-based NIPT was performed on 910 cases; 5 mL blood samples were collected and sequenced in the Shenzhen BGI Genomic Laboratory to identify aneuploidies. The risk of fetal aneuploidy was determined by L-score and t-score, and classified as high or low. The NIPT results were validated by karyotyping for the high-risk cases and neonatal follow-up for low-risk cases. Results: NIPT was mainly requested for two clinical indications: abnormal biochemical serum-screening result (54.3%) and advanced maternal age (31.4%). Among 494 cases with abnormal biochemical serum-screening results, NIPT detected only 9 (1.8%) high-risk cases. Sixteen cases (1.8%) of 910 had a high risk for aneuploidy: 8 for trisomy 21, 2 for trisomy 18, 1 for trisomy 13, and 5 for sex chromosome abnormalities. Amniocentesis was performed for 7 of these cases (43.8%). In the karyotyping and neonatal data, no false positive or negative results were observed in our study. Conclusion: MPS-based NIPT detects fetal chromosomal aneuploidies with high accuracy. Introduction of NIPT as into clinical settings could prevent about 98% of unnecessary invasive diagnostic procedures.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.11
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• pp.5563-5568
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• 2012

Based on our previous report on gastric cancer which documented ATP4A and ATP4B mRNA down-regulation in gastric tumors relative to normal gastric tissues, we hypothesized that epigenetic mechanisms could be responsible. ATP4A and ATP4B mRNA expression in gastric cancer cell lines AGS, SNU638 and NUGC-3 was examined using reverse transcriptase PCR (RT-PCR). AGS cells were treated with TSA or 5'-AzaDC and methylation specific PCR (MSP) and bisulfite sequencing PCR (BSP) analysis were performed. MSP analysis was on DNA from paraffin embedded tissues sections and plasma. Expression analysis revealed downregulation of ATP4A and ATP4B genes in gastric cancer cell lines relative to normal gastric tissue, while treatment with 5'-AzaDC re-activated expression of both. Search for CpG islands in their putative promoter regions did not indicate CpG islands (CGI) but only further downstream in the bodies of the genes. Methylation specific PCR (MSP) in the exon1 of the ATP4B gene and exon7 in ATP4A indicated methylation in all the gastric cancer cell lines tested. MSP analysis in tumor tissue samples revealed methylation in the majority of tumor samples, 15/19, for ATP4B and 8/8 for ATP4A. There was concordance between ATP4B and ATP4A down-regulation and methylation status in the tumour samples tested. ATP4B methylation was detectable in cell free DNA from gastric cancer patient's plasma samples. Thus ATP4A and ATP4B down-regulation involves DNA methylation and methylated ATP4B DNA in plasma is a potential biomarker for gastric cancer.

• Journal of Genetic Medicine
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• v.12 no.2
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• pp.72-78
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• 2015

Recently, noninvasive prenatal test (NIPT) has been adopted as a primary screening tool for fetal chromosomal aneuploidy. The principle of NIPT lies in isolating the fetal fraction of cell-free DNA in maternal plasma and analyzing it with bioinformatic tools to measure the amount of gene from the target chromosome, such as chromosomes 21, 18, and 13. NIPT will contribute to decreasing the need for unnecessary invasive procedures, including amniocentesis and chorionic villi sampling, for confirming fetal aneuploidy because of its higher positive predictive value than that of the conventional prenatal screening method. However, its greater cost than that of the current antenatal screening protocol may be an obstacle to the adoption of this innovative technique in clinical practice. Digital polymerase chain reaction (dPCR) is a novel approach for detecting and quantifying nucleic acid. dPCR provides real-time diagnostic advantages with higher sensitivity, accuracy, and absolute quantification than conventional quantitative PCR. Since the groundbreaking discovery that fetal cell-free nucleic acid exists in maternal plasma was reported, dPCR has been used for the quantification of fetal DNA and for screening for fetal aneuploidy. It has been suggested that dPCR will decrease the cost by targeting specific sequences in the target chromosome, and dPCR-based noninvasive testing will facilitate progress toward the implementation of a noninvasive approach for screening for trisomy 21, 18, and 13. In this review, we highlight the principle of dPCR and discuss its future implications in clinical practice.

• Archives of Pharmacal Research
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• v.28 no.1
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• pp.93-99
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• 2005

Intracellular trafficking of transferrin-conjugated dimethyldioctadecyl-ammonium bromide liposome $(T_f-liposome)/DNA$ complexes in HeLa cells was studied using the double-labeled fluorescence technique and confocal microscopy. The size of the $T_f-liposome/DNA$ complex was about 367 nm in diameter and the zeta-potential of it at a 5:1 (w/w) ratio was almost neutral. The intracellular pathway of the $T_f-liposome/DNA$ complex, noted as green (FITC), red (rhodamine) or yellow (FITC + rhodamine) fluorescence, was elucidated from the plasma membrane to the endosome (or lysosome), and finally to the nucleus. The results of this study indicate that plasmid DNA enters into the nucleus not only as a free form but as an associated form complexed with $T_f-liposome$. More interestingly, the $T_f-liposome$ undergoes a nuclear location in the form of ordered structures. This could be a very useful piece of information in designing a safe and advanced gene delivery system.

• Journal of the East Asian Society of Dietary Life
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• v.16 no.4
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• pp.414-420
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• 2006

The present study evaluated the effects of pomegranate peel (Granati pericarpium) extract on the lipid profiles and antioxidant biomarkers in mice fed a high fat and cholesterol diet: the measured biomarkers included the TBARS value, GPx, GR, SOD and GST activities. Body fat depositions were significantly decreased in the group that received pomegranate peel. In addition, the activities of GPx, GST and SOD were significantly higher in the liver and plasma of the pomegranate peel group than in the control group. Also, the pomegranate peel diet decreased lipid peroxidation of the liver and kidney. Alkaline single-cell gel electrophoresis (comet assay) showed that the DNA damage in the plasma of the pomegranate peel group was decreased compared to that of control. The present results show that a diet with added pomegranate peel exerts protective effects against oxidative DNA damage and lipid peroxidation possibly via effects on the free radical levels in mice fed a high fat and cholesterol diet.

• Microbiology and Biotechnology Letters
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• v.14 no.6
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• pp.455-460
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• 1986

Dane particle was prepared from the plasma of chronic HBsAg carrier with high levels of HBsAg activity. DNA extracted front Dane particle core after a DNA polymerase reaction with $\alpha$-($^{32}$P) dNTP, was identified as HBV DNA by liquid scintillation counter and agarose gel electrophoresis-G.M. counting. To produce Hepatitis B surface antigen for use as a vaccine against Hepatitis B virus infection, yeast strains harboring recombinant plasmid with Apase promoter was used. Recombinant plasmid was construced from pHBV 130 and pAN 82, transformed into E coli, and then transferred into yeast strains. HBsAg was produced by derepression in Burkholder minimal medium with controlled inorganic phosphate concentration. The kinetics of HBsAg production was also investigated. Total HBsAg activity increased rapidly between 3 and 6 hours after transfer to phosphate-free medium and reached a maximum at around 9th hour. The transfer into phosphate-free medium after 6 hours in high phosphate cell growth medium gave maximum activity.

• Journal of Veterinary Clinics
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• v.30 no.6
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• pp.442-448
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• 2013

The aim of the present study was to develop glycerol-free TRIS extender using glucose for dog sperm cryopreservation. We determined the appropriate concentration of glucose in glycerol-free TRIS and the exposure time in glycerol-free TRIS containing 0.3 M glucose at $4^{\circ}C$. Ejaculates of six dog sperm were cooled in glycerol-free TRIS through $4^{\circ}C$ for 100 min, cooled at $4^{\circ}C$ in TRIS with different glucose concentrations 0 M, 0.04 M, 0.1 M, 0.2 M and 0.3 M, respectively for 30 min followed by cryopreservation. After thawing at $37^{\circ}C$ for 25 sec, membrane and acrosome integrities of dog sperm were evaluated. In addition, the effect of exposure time (10, 30, 50 and 70 min) of sperm to glycerol-free TRIS containing 0.3 M glucose at $4^{\circ}C$ on progressive motility, viability, and DNA integrity following sperm cryopreservation was studied. Membrane integrity and acrosome integrity were assessed by 6-carboxyfluoresceindiacetate (6-CFDA)/propidium iodide (PI) fluorescent staining and Pisum sativum agglutinin conjugated to fluorescein isothiocyanate, respectively. DNA integrity was assessed by terminal deoxynucleotidyl transferase dUTP nick end labeling, using flow cytometry. Sperm frozen in glycerol-free TRIS supplemented with 0.2 M or 0.3 M glucose have an intact plasma membrane (CFDA+/PI-) after cryopreservation than sperm frozen in the extenders with lower glucose concentrations (p<0.05). Acrosome integrity was significantly higher in the 0.3 M group than less than 0.1 M groups (p<0.05). The sperm DNA fragmentation index did not differ according to exposure time, although progressive motility was significantly higher in the 50 min exposure group than the other groups (p<0.05). These results indicate that cryopreservation of dog sperm is feasible and yields more motile sperm following freezing and thawing in glycerol-free TRIS containing 0.3 M glucose with the exposure time for 50 min at $4^{\circ}C$.

• Journal of Nutrition and Health
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• v.40 no.2
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• pp.138-146
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• 2007

Food irradiation has been steadily increased in many countries concomitantly with increasing international trades. Harmful contaminants naturally occurred from foods which contain high levels of unsaturated fatty acids that are easily oxidized can affect the human anti-oxidation system through the generation of free radicals. Moreover, previous studies proved that ${\gamma}$-irradiation may cause production of free radicals in food. We investigated the effect of ${\gamma}$-irradiated soybeans in relation to oxidative stress in mice. Oxidative index of mice was evaluated by TBARS, DNA fragmentation in various organs such as blood lymphocytes, liver and kidney. Forty male ICR mice were equally divided into 4 groups and fed control diet or ${\gamma}$-irradiated diet containing 50% soybeans (5, 10, and 20 kGy, respectively) for 8 weeks. Peroxide values of the irradiated diets were higher than that of the non-irradiated one and increased according to the storage period. There was no significant difference in weight gain as well as in TBARS value in plasma and kidney of all groups. Liver TBARS value of the group fed with irradiated diet at 20 kGy increased significantly compared with the control group (p < 0.05). DNA oxidative damage as measured by alkaline comet assay showed that % tail DNA in the blood lymphocytes of 5 kGy and 10 kGy groups increased significantly over the control group (p < 0.05). Also, tail moments of 5 kGy and 10 kGy groups were higher than that of the control group. Ultrastructural examination shows myeline figures and swollen mitochondria in parietal and intestinal epithelial cells of the group fed with irradiated diet. Therefore, considering unsaturated fatty acid content, consumption of soybeans ${\gamma}$-irradiated with over 20 kGy or repeatedly may decrease the body's antioxidant mechanism.

• Journal of Microbiology and Biotechnology
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• v.31 no.11
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• pp.1481-1489
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• 2021

Early and accurate detection of pathogens is important to improve clinical outcomes of bloodstream infections (BSI), especially in the case of drug-resistant pathogens. In this study, we aimed to develop a culture-independent digital PCR (dPCR) system for multiplex detection of major sepsis-causing gram-negative pathogens and antimicrobial resistance genes using plasma DNA from BSI patients. Our duplex dPCR system successfully detected nine targets (five bacteria-specific targets and four antimicrobial resistance genes) through five reactions within 3 hours. The minimum detection limit was 50 ag of bacterial DNA, suggesting that 1 CFU/ml of bacteria in the blood can be detected. To validate the clinical applicability, cell-free DNA samples from febrile patients were tested with our system and confirmed high consistency with conventional blood culture. This system can support early identification of some drug-resistant gram-negative pathogens, which can help improving treatment outcomes of BSI.