Journal of the Korea Academia-Industrial cooperation Society
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v.11
no.2
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pp.720-726
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2010
Haplotype-based research has become increasingly important in the field of personalized medicine since the haplotype reflects a set of SNPs (Single Nucleotide Polymorphisms) that are genetically associated and inherited together. Currently, the most widely used application softwares available for haplotype reconstruction, based on in silico method, include PL-EM, Haplotyper, PHASE and HAP. PL-EM, Haplotyper and PHASE are command-line application running on LINUX or Unix system and HAP is a web-based client-server application. This paper deals with an integrated haplotype reconstruction system that have been developed with PL-EM and Haplotyper selected from the accuracy test with experimentally verified data on public application softwares. This integrated system is a kind of client-sever one with user friendly web interface and can provide end-users with a high quality of haplotype analysis. SNPs genotype data with a length of 5 derived from 5 people and SNPs genotype data with a length of 13 derived from 15 people were used to test the analysis results of Haplotyper and PL-EM respectively. As a result, this system has been confirmed to provide the systematic and easy-to-understand analysis results that consist of two main parts, i.e. individual haplotype information and haplotype pool information. In this respect, the integration system will be utilized as a useful tool for the discovery of disease related genes and the development of personalized drugs through facilitating the reconstruction of haplotype maps.
Khummuang, Saichit;Lee, Hyo Gun;Joo, Sang Seok;Park, Jeong-Woong;Choi, Jae-Young;Oh, Jin Hyeog;Kim, Kyoung Hwan;Youn, Hyun-Hee;Kim, Myunghoo;Cho, Byung-Wook
Asian-Australasian Journal of Animal Sciences
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v.33
no.3
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pp.424-435
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2020
Objective: The study was conducted to investigate variations in the immunophysiological responses to exercise-induced stress in Jeju and Thoroughbred horses. Methods: Blood samples were collected from the jugular veins of adult Jeju (n = 5) and Thoroughbred (n = 5) horses before and after 30 min of exercise. The hematological, biochemical, and immunological profiles of the blood samples were analyzed. Blood smears were stained and observed under a microscope. The concentration of cell-free (cf) DNA in the plasma was determined using real time polymerase chain reaction (PCR). Peripheral blood mononuclear cells (PBMCs) and polymorphonuclear cells were separated using Polymorphprep, and the expression of various stress-related and chemokine receptor genes was measured using reverse transcriptase (RT) and real-time PCR. Results: After exercise, Jeju and Thoroughbred horses displayed stress responses with significantly increased rectal temperatures, cortisol levels, and muscle catabolism-associated metabolites. Red blood cell indices were significantly higher in Thoroughbred horses than in Jeju horses after exercise. In addition, exercise-induced stress triggered the formation of neutrophil extracellular traps (NETs) and reduced platelet counts in Jeju horses but not in Thoroughbred horses. Heat shock protein 72 and heat shock protein family A (Hsp70) member 6 expression is rapidly modulated in response to exercise-induced stress in the PBMCs of Jeju horses. The expression of CXC chemokine receptor 4 in PBMCs was higher in Thoroughbred horses than in Jeju horses after exercise. Conclusion: In summary, the different immunophysiological responses of Jeju and Thoroughbred horses explain the differences in the physiological and anatomical properties of the two breeds. The physiology of Thoroughbred horses makes them suitable for racing as they are less sensitive to exercise-induced stress compared to that of Jeju horses. This study provides a basis for investigating the link between exercise-induced stresses and the physiological alteration of horses. Hence, our findings show that some of assessed parameters could be used to determine the endurance performance of horses.
This study was to undertaken to investigate the impacts of AhR, CYP1A1, GSTM1 genetic polymorphisms on the R273G mutation in exon 8 of the tumor suppressor p53 gene (TP53) among polycyclic aromatic hydrocarbons (PAHs) exposed to coke-oven workers. One hundred thirteen workers exposed to PAH and 82 control workers were recruited. We genotyped for polymorphisms in the AhR, CYP1A1, GSTM1, and TP53 R273G mutation in blood by PCR methods, and determined the levels of 1-hydroxypyrene as PAH exposure marker in urine using the high pressure liquid chromatography assay. We found that the distribution of alcohol users and the urinary excretion of 1-OHP in the exposed workers were significantly higher than that of the control workers (p=0.004, p<0.001, respectively). Significant differences were observed in the p53 genotype distributions of smoking subjects (p=0.01, 95%CI: 1.23-6.01) and PAH exposure (p=0.008, 95%CI: 1.24-4.48), respectively. Further, significant differences were observed in the p53 exon 8 mutations for the genetic polymorphisms of Lys/Arg for AhR (p=0.02, 95%CI: 0.70-15.86), Val/Val for CYP1A1 (p=0.04, 95%CI: 0.98-19.09) and null for GSTM1 (p=0.02, 95%CI: 1.19-6.26), respectively. Our findings indicated that polymorphisms of PAH metabolic genes, such as AhR, CYP1A1, GSTM1 polymorphisms may interact with p53 genetic variants and may contribute to PAH related cancers.
Purpose: The objective of the present study was to determine whether fermentation can increase the protective effects of blueberry liquid in a high-fat diet-induced obese mice model. Methods: Male C57BL/6J mice were fed a high-fat diet (HD, 60% fat, w/w,), HD supplemented with 10 ml/kg BW/day of blueberry liquid (BHD, blueberry high-fat diet), or HD supplemented with 10 ml/kg BW/day of fermented blueberry liquid (FBHD, fermented blueberry high-fat diet) for 10 weeks. Results: There were significant decreases in the body, epididymal adipose tissue, and liver weights of blueberry-fed groups compared to HD, whereas there were no significant differences in food intake among the groups. Furthermore, blueberry liquid groups, especially fermented blueberry liquid, significantly attenuated the contents of hepatic triglycerides and total cholesterol induced by HD. Serum LDL-cholesterol was significantly lower in the BHD and FBHD-fed groups, whereas FBHD significantly increased the serum HDL-cholesterol level compared to the control. Concentrations of aspartate transaminase, alanine transaminase, and leptins in serum were also reduced by blueberry liquid supplementation. The mRNA expression of hepatic acetyl CoA carboxylase was significantly reduced in both the BHD and FBHD groups compared to HD. Furthermore, FBHD altered the mRNA expression level of hepatic lipolysis genes. Conclusion: In conclusion, these results suggest that blueberry, especially fermented blueberry liquid, may improve obesity-related abnormalities.
The Sporosarcina psychrophilia pyrB gene, which encodes aspartate transcarbamylase (ATcase), was cloned on Sau3AI restriction endonuclease fragment inserted into pUC19 plasmid vector, S. psychrophilia pyrB gene was expressed in Escherichia coli pyrB mutant for the complementation test. The sequence of 2,606 nucleotides including putative pyrB gene was determined. The region contained one full open reading frame (ORf) and two partial ORFs. The deduced amino acid sequence of the second ORF showed 59% identity with that of Bacillus caldolyticus ATCase. The first and third partial ORFs were closely related to the uracil permease (pyrP) and dihydroorotase (pyrC), respectively. Besides, potential terminator, antiterminator, and anti-antiterminator structures were found in the intergenic region between pyrP and pyrB. These results suggested that S. psychrophilia pyrimidine nucleotide biosynthesis genes are clustered as well as other Bacillus sp. Over-expressed product of pyrB encoding ATCase was purified and analyzed by the SDS-PAGE. The purified PyrB protein turned out to be molecular mass of 27 kDa and showed ATCase activity.
Kim, Ji Hyung;Affan, Abu;Jang, Jiyi;Kang, Mee-Hye;Ko, Ah-Ra;Jeon, Seon-Mi;Oh, Chulhong;Heo, Soo-Jin;Lee, Youn-Ho;Ju, Se-Jong;Kang, Do-Hyung
Journal of Microbiology and Biotechnology
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v.25
no.2
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pp.238-246
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2015
A unicellular red microalga was isolated from environmental freshwater in Korea, and its morphological, molecular, and biochemical properties were characterized. Morphological analysis revealed that the isolate was a unicellular biflagellated green microalga that formed a non-motile, thick-walled palmelloid or red aplanospore. To determine the taxonomical position of the isolate, its 18S rRNA and rbcL genes were sequenced and phylogenetic analysis was performed. We found that the isolate was clustered together with other related Haematococcus strains showing differences in the rbcL gene. Therefore, the isolated microalga was classified into the genus Haematococcus, and finally designated Haematococcus sp. KORDI03. The microalga could be cultivated in various culture media under a broad range of pH and temperature conditions. Compositions of the microalgal cellular components were analyzed, and its protein, carbohydrate, and lipid compositions were estimated to be 21.1 ± 0.2%, 48.8 ± 1.8%, and 22.2 ± 0.9%, respectively. In addition, D-glucose and D-mannose were the dominant monosaccharides in the isolate, and its amino acids were composed mainly of aspartic acid, glutamic acid, alanine, and leucine. Moreover, several polyunsaturated fatty acids accounted for about 80% of the total fatty acids in Haematococcus sp. KORDI03, and the astaxanthin content in the red aplanospores was estimated to be 1.8% of the dry cell weight. To the best of our knowledge, this is the first report of an Haematococcus sp. isolated from Korea, which may be used for bioresource production in the microalgal industry.
Kim, Yong-Sang;Jeong, Jin-Oh;Cho, Sung-Ho;Jeong, Do-Yeon;Uhm, Tai-Boong
Korean Journal of Microbiology
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v.48
no.2
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pp.163-170
/
2012
In order to inhibit the growth of pathogens and degrade biogenic amines during the fermentation of soybean products, an isolate with antimicrobial activity against pathogens and biogenic amine-degrading property was obtained from 83 traditionally fermented soybean products. The morphological and biochemical tests and the phylogenetic relationship among 16S rRNA gene sequences indicated that the isolate named as the strain SCK B11 was most closely related to Bacillus licheniformis. The cell-free supernatant of two day cultures was active against several pathogens including Enterococcus faecalis, Listeria monocytosis, Micrococcus luteus, Pseudomonas aeruginosa, Bacillus cereus, and Staphylococcus aureus. PCR analysis was conducted to determine relatedness to antimicrobial lantibiotics and biosurfactants produced by Bacillus spp., but showed negative for the genes encoding surfactin, lichenysin, and lichenicidine. Electron microscopic observation indicated that the antimicrobial agent seemed to attack the membrane of the pathogens, leaving the ghost or shrunken cells. The strain was found to degrade histamine by 72% and tyramine by 66% in the cooked soybean containing 5.3% of biogenic amine over 10 days of fermentation time. The use of selected strain would be a potential control measure in manufacturing traditionally fermented soybean products that are difficult to control pathogens and biogenic amine levels.
Kim, MinYeong;Shin, YuOck;Lee, JooYoung;Lee, AhReum;Shin, SungHo;Kwon, OJun;Seo, BuIl;Roh, Seong-Soo
The Korea Journal of Herbology
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v.30
no.4
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pp.37-44
/
2015
Objectives : The present study was designed to evaluate the anti-inflammatory and anti-oxidative stress activities through regulation of Nrf2-mediated genes by Rhei rhizoma and Glycyrrhiza rhizoma combined extract (RGE) in reflux esophagitis.Methods : The antioxidant activity of RGE in vitro was measured in terms of radical scavenging capacity such as DPPH and ABTS. RGE was administered at 350 mg/kg body weight prior to induction of reflux esophagitis. Reflux esophagitis was induced that tied the pylorus and the transitional junction between the forestomach and the corpus in Sprague-Dawley rats.Results : RGE scavenged DPPH and ABTS effectively and IC50of RGE each were 4.9 μg/ml and 45.6 μg/ml. Our results show that RGE administration markedly ameliorated mucosal damage upon histological evaluation. In serum and esophagus tissue, RGE significantly suppressed the oxidative stress biomarkers. Reflux esophagitis induced rats exhibited down-regulation of antioxidant-related proteins in the esophagus; however, the levels with treatment of RGE were significantly higher than those of vehicle reflux esophagitis rats. RGE treatment caused significant reductions in activation of NF-κB transcription factor. Thus, RGE significantly exhibited potent anti-inflammatory activities by suppressing the protein expression levels of pro-inflammatory proteins such as COX-2 and iNOS and inflammatory cytokines such as TNF-αin the esophagus tissue.Conclusions : Reflux esophagitis caused considerable levels of oxidative stress in the esophageal mucosa and the administration of RGE reduced the esophageal mucosa damage through the regulation of Nrf2 and NF-κB pathways. Our findings can considered as supplementary therapy in the prevention or treatment of reflux esophagitis.
Background: Psoriasis is a multifactorial autoimmune skin disease with a pathogenesis that has remained obscure. Recently, T cells bearing natural killer receptors (NKRs) were precisely and strongly targeted as new putative pathogenic immunocytes in psoriasis. Among NKRs, killer cell immunoglobulin-like receptor (KIR) is the major molecule recognizing HLA class I allotypes and might be closely related to psoriasis. Methods: To investigate the association of KIR genotype and patients with psoriasis in Korean, we defined the 14 KIR genotypes in 96 patients with psoriasis and 86 healthy controls using PCR-SSP methods. Results: The frequencies of KIR2DS4 and KIR3DL1 were significantly decreased in psoriasis compared with controls (RR=0.21, p<0.02). When patients were divided into two subgroups at the age of onset, type I (<30 years) and type II ((≥30 years) respectively, these phenomena were similarly observed independent of groups divided (type I: RR=0.26, p<0.005; type II: RR=0.14, p<0.0006). When the patients were divided into subgroups according to the age of onset and family history, the frequencies of KIR2DS4, KIR3DL1, and KIR2DS3 were significantly decreased in type I compared with type II psoriasis (3DL1, 2DS4: p<0.004; 2DS3: p<0.04) and were significantly decreased in psoriasis without family history compared to with family history (3DL1, 2DS4: p<0.007; 2DS3: p<0.05). The frequency of haplotype combination BB was significantly increased in psoriasis compared with controls (RR=2.74, p<0.009). Conclusion: These results suggest that KIR genotype is a factor for the occurrence and development of psoriasis and in future how combinations of HLA and KIR genes influence psoriasis needs to be defined.
Kim, Kyusoon;Jung, Chung Ryul;Yang, Chang Yeol;Kwon, Gimyeon;Kim, Yonggyun
Korean journal of applied entomology
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v.56
no.1
/
pp.61-67
/
2017
Two major sex pheromone components (Z-8-dodecenyl acetate and E-8-dodecenyl acetate) are known in the peach fruit moth, Grapholita molesta. From a putative biosynthetic pathway of these sex pheromone components, delta 10 desaturase (10Δ DES) has been proposed to play a crucial role in synthesizing a species-specific stereoisomer of the double bond. However, its molecular identity was not known. This study determined a putative desaturase (Gm-comp1575) as a 10Δ DES candidate from G. molesta transcriptome constructed from the sex pheromone gland. Its open reading frame encodes 370 amino acid sequence with a predicted molecular weight at 43.2 kDa and isoelectric point at 8.77. It was predicted to have four transmembrane domains and six glycosylation sites at N-terminal or cytosolic domains. A phylogenetic analysis with its predicted amino acid sequence indicated that Gm-comp1575 is closely related with known 10Δ DES genes of other insects. Gm-comp1575 transcript was detected in female adults at sex pheromone gland and other abdominal tissues. RNA interference of Gm-comp1575 significantly reduced attractiveness of virgin females in apple orchard compared to control females. These results suggest that Gm-comp1575 is associated with sex pheromone biosynthesis of G. molesta.
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