• Journal of Gastric Cancer
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• v.13 no.4
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• pp.232-241
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• 2013

Purpose: Gastrokine 1 plays an important role in gastric mucosal defense. Additionally, the Gastrokine 1-miR-185-DNMT1 axis has been shown to suppress gastric carcinogenesis through regulation of epigenetic alteration. Here, we investigated the effects of Gastrokine 1 on DNA methylation and gastritis. Materials and Methods: Expression of Gastrokine 1, DNMT1, EZH2, and c-Myc proteins, and the presence of Helicobacter pylori CagA protein were determined in 55 non-neoplastic gastric mucosal tissue samples by western blot analysis. The CpG island methylation phenotype was also examined using six markers (p16, hMLH1, CDH1, MINT1, MINT2 and MINT31) by methylation-specific polymerase chain reaction. Histological gastritis was assessed according to the updated Sydney classification system. Results: Reduced Gastrokine 1 expression was found in 20 of the 55 (36.4%) gastric mucosal tissue samples and was closely associated with miR-185 expression. The Gastrokine 1 expression level was inversely correlated with that of DNMT1, EZH2, and c-Myc, and closely associated with the degree of gastritis. The H. pylori CagA protein was detected in 26 of the 55 (47.3%) gastric mucosal tissues and was positively associated with the expression of DNMT1, EZH2, and c-Myc. In addition, 30 (54.5%) and 23 (41.9%) of the gastric mucosal tissues could be classified as CpG island methylation phenotype-low and CpG island methylation phenotype-high, respectively. Reduced expression of Gastrokine 1 and miR-185, and increased expression of DNMT1, EZH2, and c-Myc were detected in the CpG island methylation phenotype-high gastric mucosa. Conclusions: Gastrokine 1 has a crucial role in gastric inflammation and DNA methylation in gastric mucosa.

• BMB Reports
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• v.38 no.6
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• pp.739-747
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• 2005

Full-length cDNA sequences of four novel SPATA4 genes in chimpanzee, cow, chicken and ascidian were identified by bioinformatic analysis using mouse or human SPATA4 cDNA fragment as electronic probe. All these genes have 6 exons and have similar protein molecular weight and do not localize in sex chromosome. The mouse SPATA4 sequence is identified as significantly changed in cryptorchidism, which shares no significant homology with any known protein in swissprot databases except for the homologous genes in various vertebrates. Our searching results showed that all SPATA4 proteins have a putative conserved domain DUF1042. The percentages of putative SPATA4 protein sequence identity ranging from 30% to 99%. The high similarity was also found in 1 kb promoter regions of human, mouse and rat SPATA4 gene. The similarities of the sequences upstream of SPATA4 promoter also have a high proportion. The results of searching SymAtlas (http://symatlas.gnf.org/SymAtlas/) showed that human SPATA4 has a high expression in testis, especially in testis interstitial, leydig cell, seminiferous tubule and germ cell. Mouse SPATA4 was observed exclusively in adult mouse testis and almost no signal was detected in other tissues. The pI values of the protein are negative, ranging from 9.44 to 10.15. The subcellular location of the protein is usually in the nucleus. And the signal peptide possibilities for SPATA4 are always zero. Using the SNPs data in NCBI, we found 33 SNPs in human SPATA4 gene genomic DNA region, with the distribution of 29 SNPs in the introns. CpG island searching gives the data about CpG island, which shows that the regions of the CpG island have a high similarity with each other, though the length of the CpG island is different from each other.This research is a fundamental work in the fields of the bioinformational analysis, and also put forward a new way for the bioinformatic analysis of other genes.

• Clinical and Experimental Pediatrics
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• v.48 no.6
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• pp.634-639
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• 2005

Purpose : An understanding of the immunological process is required if primary prevention of atopic diseases is to be developed in early childhood. But, it is too hard to distinguish atopy from nonatopy under the age of two clinically, because the expression of phenotype and cytokines is vague in early childhood. We evaluated DNA methylation changes at Th2 interleukin-4 gene in peripheral blood from atopic children. Methods : We selected 15 allergic children(mild : eight, moderate to severe : seven) and seven normal controls by using family allergy scores and clinical histories. We measured Total IgE and Der f II specific IgE levels and cultured peripheral blood mononuclear cells with Der f II stimulation and extracted DNA from Der f II specific T cells. We examined the change of CpG methylation in DNA from atopic and nonatopic children. Results : In T cells from normal children, IL-4 DNA were predominantly methylated; otherwise, CpG demethylation occurred in Der f II specific T cells from allergic children. Conclusion : IL-4 DNA methylation changes occurred in T genes from allergic children and DNA methylation assay in early childhood.

• Asian-Australasian Journal of Animal Sciences
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• v.26 no.4
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• pp.529-536
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• 2013

The objective of this study was to investigate the effect of levels of cottonseed meal with various carbohydrate sources in concentrate on feed intake, nutrient digestibility, rumen fermentation and microbial protein synthesis in dairy bulls. Four, 6 months old dairy bulls were randomly assigned to receive four dietary treatments according to a $2{\times}2$ factorial arrangement in a $4{\times}4$ Latin square design. Factor A was carbohydrate source; cassava chip (CC) and cassava chip+rice bran in the ratio of 3:1 (CR3:1), and factor B was cotton seed meal levels in the concentrate; 109 g CP/kg (LCM) and 328 g CP/kg (HCM) at similar overall CP levels (490 g CP/kg). Bulls received urea-lime treated rice straw ad libitum and were supplemented with 10 g of concentrate/kg BW. It was found that carbohydrate source and level of cotton seed meal did not have significant effects on ruminal pH, ammonia nitrogen concentration, microbial protein synthesis or feed intake. Animals which received CC showed significantly higher BUN concentration, ruminal propionic acid and butyric acid proportions, while dry matter, organic matter digestibility, populations of total viable bacteria and proteolytic bacteria were lower than those in the CR3:1 treatment. The concentration of total volatile fatty acids was higher in HCM than LCM treatments, while the concentration of butyric acid was higher in LCM than HCM treatments. The population of proteolytic bacteria with the LCM treatments was higher than the HCM treatments; however other bacteria groups were similar among the different levels of cotton seed meal. Bulls which received LCM had higher protein digestibility than those receiving HCM. Therefore, using high levels of cassava chip and cotton seed meal might positively impact on energy and nitrogen balance for the microbial population in the rumen of the young dairy bull.

• Korean Journal of Food Science and Technology
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• v.29 no.6
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• pp.1151-1157
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• 1997

The chemical identities of purified polysaccharide, methylan, were analyzed by various chemical methods. The polysaccharide contained 79%(w/w) sugar, 6% protein, and 16% organic acids such as uronic acid, pyruvic acid, and acetic acid. With proceeding fermentation, the acids content in methylan increased from 10% at 34 hr to 17% at 72 hr, and the viscosity of methylan in the same concentration also increased. The correlation between viscosity and acid content in methylan was studied using chemically or biologically modified methylan. Methylan with a high content of pyruvic acid exhibited a high apparent and an intrinsic ·viscosity. When the pyruvic acid content of methylan with the same content of uronic acid was increased 1%, apparent viscosity and intrinsic viscosity increased 290 cp and 6 dL/g, respectively. Methylan with a high content of uronic acid exhibited a high apparent and an intrinsic viscosity. When the uronic acid content of methylan with the same content of pyruvic acid was increased 1%, apparent viscosity and intrinsic viscosity increased 85 cp and 1.5 dL/g, respectively. It was found that the increased viscosity of methylan resulted from the increased content of organic acids in methylan, and pyruvic acid was more an important factor contributed to the increase of methylan viscosity than uronic acid.

• KSBB Journal
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• v.27 no.1
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• pp.67-74
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• 2012

In this study, the optimum conditions of fermentation were determined by isolating the microorganisms with the ability to bioconvert the Citrus peel flavonoid, and the effect of the fermented Citrus peel extract which was bioconverted on the oxidative damage of HIT-T15 cell was investigated. The Aureobasidium pullulans Y-12 was isolated and identified with the strains having bioconversion activity. The fermentation conditions for bioconversion activity were confirmed to be optimal when culturing for three days at $25^{\circ}C$, 150 rpm in a culture medium containing 5% Citrus peel power and 0.8% casitone. As a result of bioconversion, 32.8 mg/g and 21.5 mg/g of naringenin and hesperetin, which were aglycone flavones, were produced respectively. Also in the flavonoid content, it was confirmed that FCP produced 154.8 mg/g while CP produced 33.7 mg/g, thus producing more by approximately 4.6 times. As a result of treating FCP and CP after inducing the oxidative damage for HIT-T15 cell by treating the deoxy-D-ribose with $IC_{50}$ (38 mM) concentration, the surviving rate was recovered to 90% for FCP treatments in the 0.01 mg/mL concentration and for CP treatments in the 0.025 mg/mL concentration. Also in the insulin secretion rate, FCP treatments increased by 206% and CP treatments by 132% when treated in the 0.1 mg/mL concentration. As the bioconverted FCP can inhibit the oxidative damage of HIT-T15 cell in the low concentration, it was considered its usability as the functional material for prevention of the type 2 diabetes.

• BMB Reports
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• v.56 no.10
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• pp.569-574
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• 2023

Aberrant DNA methylation plays a pivotal role in the onset and progression of colorectal cancer (CRC), a disease with high incidence and mortality rates in Korea. Several CRC-associated diagnostic and prognostic methylation markers have been identified; however, due to a lack of comprehensive clinical and methylome data, these markers have not been validated in the Korean population. Therefore, in this study, we aimed to obtain the CRC methylation profile using 172 tumors and 128 adjacent normal colon tissues of Korean patients with CRC. Based on the comparative methylome analysis, we found that hypermethylated positions in the tumor were predominantly concentrated in CpG islands and promoter regions, whereas hypomethylated positions were largely found in the open-sea region, notably distant from the CpG islands. In addition, we stratified patients by applying the CpG island methylator phenotype (CIMP) to the tumor methylome data. This stratification validated previous clinicopathological implications, as tumors with high CIMP signatures were significantly correlated with the proximal colon, higher prevalence of microsatellite instability status, and MLH1 promoter methylation. In conclusion, our extensive methylome analysis and the accompanying dataset offers valuable insights into the utilization of CRC-associated methylation markers in Korean patients, potentially improving CRC diagnosis and prognosis. Furthermore, this study serves as a solid foundation for further investigations into personalized and ethnicity-specific CRC treatments.

• BMB Reports
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• v.57 no.3
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• pp.161-166
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• 2024

Aberrant DNA methylation plays a critical role in the development and progression of colorectal cancer (CRC), which has high incidence and mortality rates in Korea. Various CRC-associated methylation markers for cancer diagnosis and prognosis have been developed; however, they have not been validated for Korean patients owing to the lack of comprehensive clinical and methylome data. Here, we obtained reliable methylation profiles for 228 tumor, 103 adjacent normal, and two unmatched normal colon tissues from Korean patients with CRC using an Illumina Infinium EPIC array; the data were corrected for biological and experiment biases. A comparative methylome analysis confirmed the previous findings that hypermethylated positions in the tumor were highly enriched in CpG island and promoter, 5' untranslated, and first exon regions. However, hypomethylated positions were enriched in the open-sea regions considerably distant from CpG islands. After applying a CpG island methylator phenotype (CIMP) to the methylome data of tumor samples to stratify the CRC patients, we consolidated the previously established clinicopathological findings that the tumors with high CIMP signatures were significantly enriched in the right colon. The results showed a higher prevalence of microsatellite instability status and MLH1 methylation in tumors with high CMP signatures than in those with low or non-CIMP signatures. Therefore, our methylome analysis and dataset provide insights into applying CRC-associated methylation markers for Korean patients regarding cancer diagnosis and prognosis.

• Journal of Animal Science and Technology
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• v.66 no.1
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• pp.145-155
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• 2024

This study was conducted to determine the effects of amino acid (AA) supplementation in low-protein (LP) diets on growth performance and nitrogen (N) excretion. A total of 175 7-day-old Ross 308 male broilers, with a mean body weight (BW) of 165 g (standard deviation = 11.2 g), were grouped into five blocks by BW and allocated to seven treatments according to a randomized complete block design with five replicate cages at five birds per cage. Dietary treatments comprised a control diet containing 20.0% crude protein (CP) and six LP diets containing either 18.5% or 17.0% CP. These LP diets were supplemented with either no AA supplementation, indispensable AA, or both indispensable and dispensable AA (glutamic acid and glycine). Birds were fed experimental grower diets from day 7 to 21 and then commercial finisher diets until day 28. During the grower period (day 7 to 21), birds fed LP diets supplemented with indispensable AA exhibited greater (p < 0.05) BW, body weight gain (BWG), feed intake (FI), and gain-to-feed ratio (G:F) than birds fed LP diets without crystalline AA and were comparable to birds fed the control diet. During the finisher period (day 21 to 28), birds fed LP diets supplemented with indispensable AA showed greater (p < 0.05) BW than birds fed LP diets without crystalline AA, and their growth performance was comparable to birds fed the control diet. Throughout the overall period, supplementing indispensable AA in LP diets resulted in elevated (p < 0.05) BWG, FI, and G:F more than those of LP diets without crystalline AA and were comparable to those of the control diet. Supplementing indispensable AA in LP diets decreased amount and coefficient of N excretion as much as the control diet. Dispensable AA supplementation in LP diets did not influence growth performance and N excretion. In conclusion, supplementing indispensable AA in LP diets maintains growth performance and N excretion until the dietary CP lowers from 20.0% to 17.0% during the grower period. As long as dietary CP is above 17.0%, dispensable AA may not be deficient in LP diets during the grower period.

• Asian-Australasian Journal of Animal Sciences
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• v.21 no.6
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• pp.873-882
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• 2008

Eight ileally cannulated pigs (BW $35.9{\pm}0.9kg$) were randomly allotted according to a $4{\times}3$ Latin square design to determine the effects of cellulose, pectin and starch on standardized ileal digestibility (SID) and apparent total tract digestibility (ATTD) of crude protein (CP) and amino acids (AA) as well as on the bacterial AA contribution in feces. The pigs were fed the control diet (20.2% CP, % dry matter (DM)) or one of the three experimental diets in which 25% of the control diet was substituted by cellulose, starch or pectin. Due to this substitution, dietary CP levels were lower in the cellulose (15.5% CP, % DM), pectin (15.4% CP, % DM) and starch diet (15.2% CP, % DM). Following a 15-d adaptation period, feces were collected for 5 d and ileal digesta for a total of 24 h. Starch increased SID of CP, while cellulose and pectin had no significant effect on the digestibility of CP. Overall, starch supplementation resulted in higher (p<0.05) SID values of histidine, isoleucine, threonine, alanine, aspartic acid, cysteine, glycine and serine compared with cellulose, while pectin decreased (p<0.05) SID of valine and proline compared with the starch and control diet. Both cellulose and pectin reduced (p<0.05) the ATTD of CP and AA, while starch decreased (p<0.05) ATTD of phenylalanine, alanine, proline and serine compared with the control. With regard to bacterial AA composition of the fecal mixed bacterial mass (MBM), cellulose supplementation increased (p<0.05) its content of N and almost all AA, except for valine, while pectin caused higher contents of arginine, histidine and proline compared with the control (p<0.05). The bacterial contribution of arginine in feces was higher (p<0.05) in the cellulose treatment, while pectin reduced (p<0.05) the bacterial contribution of leucine, alanine, glutamic acid and proline in feces compared with the control. In conclusion, the effects of cellulose, starch and pectin on SID were rather small. Bacterial activity in the large intestine can only explain the reduced ATTD values for arginine in the cellulose treatment, but not for the other AA in the cellulose and pectin treatments, suggesting higher endogenous losses of these AA in the large intestine.