Genomic Organization of the Human DDX13 Gene Located between RD and RP1 in the Class III MHC Complex

Lee, Seong-gene,Song, Kyuyoung Korean Society of Molecular Biology 1997 Molecules and cells Vol.7 No.3

Identification and Characterization of a Bidirectional Promoter from the Intergenic Region between the Human DDX13 and RD Genes

Lee, Seong-Gene,Song, Kyuyoung Korean Society of Molecular Biology 2000 Molecules and cells Vol.10 No.1

Polymorphisms in Epigenetic and Meat Quality Related Genes in Fourteen Cattle Breeds and Association with Beef Quality and Carcass Traits

Liu, Xuan,Usman, Tahir,Wang, Yachun,Wang, Zezhao,Xu, Xianzhou,Wu, Meng,Zhang, Yi,Zhang, Xu,Li, Qiang,Liu, Lin,Shi, Wanhai,Qin, Chunhua,Geng, Fanjun,Wang, Congyong,Tan, Rui,Huang, Xixia,Liu, Airong,Wu, Asian Australasian Association of Animal Productio 2015 Animal Bioscience Vol.28 No.4

Improvement for carcass traits related to beef quality is the key concern in beef production. Recent reports found that epigenetics mediates the interaction of individuals with environment and nutrition. The present study was designed to analyze the genetic effect of single nucleotide polymorphisms (SNPs) in seven epigenetic-related genes (DNMT1, DNMT3a, DNMT3b, DNMT3L, Ago1, Ago2, and HDAC5) and two meat quality candidate genes (CAPN1 and PRKAG3) on fourteen carcass traits related to beef quality in a Snow Dragon beef population, and also to identify SNPs in a total of fourteen cattle populations. Sixteen SNPs were identified and genotyped in 383 individuals sampled from the 14 cattle breeds, which included 147 samples from the Snow Dragon beef population. Data analysis showed significant association of 8 SNPs within 4 genes related to carcass and/or meat quality traits in the beef populations. SNP1 (13154420A>G) in exon 17 of DNMT1 was significantly associated with rib-eye width and lean meat color score (p<0.05). A novel SNP (SNP4, 76198537A>G) of DNMT3a was significantly associated with six beef quality traits. Those individuals with the wild-type genotype AA of DNMT3a showed an increase in carcass weight, chilled carcass weight, flank thicknesses, chuck short rib thickness, chuck short rib score and in chuck flap weight in contrast to the GG genotype. Five out of six SNPs in DNMT3b gene were significantly associated with three beef quality traits. SNP15 (45219258C>T) in CAPN1 was significantly associated with chuck short rib thickness and lean meat color score (p<0.05). The significant effect of SNP15 on lean meat color score individually and in combination with each of other 14 SNPs qualify this SNP to be used as potential marker for improving the trait. In addition, the frequencies of most wild-type alleles were higher than those of the mutant alleles in the native and foreign cattle breeds. Seven SNPs were identified in the epigenetic-related genes. The SNP15 in CAPN1 could be used as a powerful genetic marker in selection programs for beef quality improvement in the Snow Dragon Beef population.

Polymorphisms in Epigenetic and Meat Quality Related Genes in Fourteen Cattle Breeds and Association with Beef Quality and Carcass Traits

Xuan Liu,Tahir Usman,Yachun Wang,Zezhao Wang,Xianzhou Xu,Meng Wu,Yi Zhang,Xu Zhang,Qiang Li,Lin Liu,Wanhai Shi,Chunhua Qin,Fanjun Geng,Congyong Wang,Rui Tan,Xixia Huang,Airong Liu,Hongjun Wu,Shixin Ta 아세아·태평양축산학회 2015 Animal Bioscience Vol.28 No.4

Improvement for carcass traits related to beef quality is the key concern in beef production. Recent reports found that epigenetics mediates the interaction of individuals with environment and nutrition. The present study was designed to analyze the genetic effect of single nucleotide polymorphisms (SNPs) in seven epigenetic-related genes (DNMT1, DNMT3a, DNMT3b, DNMT3L, Ago1, Ago2, and HDAC5) and two meat quality candidate genes (CAPN1 and PRKAG3) on fourteen carcass traits related to beef quality in a Snow Dragon beef population, and also to identify SNPs in a total of fourteen cattle populations. Sixteen SNPs were identified and genotyped in 383 individuals sampled from the 14 cattle breeds, which included 147 samples from the Snow Dragon beef population. Data analysis showed significant association of 8 SNPs within 4 genes related to carcass and/or meat quality traits in the beef populations. SNP1 (13154420A>G) in exon 17 of DNMT1 was significantly associated with rib-eye width and lean meat color score (p<0.05). A novel SNP (SNP4, 76198537A>G) of DNMT3a was significantly associated with six beef quality traits. Those individuals with the wild-type genotype AA of DNMT3a showed an increase in carcass weight, chilled carcass weight, flank thicknesses, chuck short rib thickness, chuck short rib score and in chuck flap weight in contrast to the GG genotype. Five out of six SNPs in DNMT3b gene were significantly associated with three beef quality traits. SNP15 (45219258C>T) in CAPN1 was significantly associated with chuck short rib thickness and lean meat color score (p<0.05). The significant effect of SNP15 on lean meat color score individually and in combination with each of other 14 SNPs qualify this SNP to be used as potential marker for improving the trait. In addition, the frequencies of most wild-type alleles were higher than those of the mutant alleles in the native and foreign cattle breeds. Seven SNPs were identified in the epigenetic-related genes. The SNP15 in CAPN1 could be used as a powerful genetic marker in selection programs for beef quality improvement in the Snow Dragon Beef population.

Human Immunodeficiency Virus-1 Tat 단백에 의한 인간 CD99유전자의 조절기전에 대한 연구

이유진,김예리,이미경,이임순,Lee, Eu-Gene,Kim, Ye-Ri,Lee, Mi-Kyung,Lee, Im-Soon 한국미생물학회 2008 미생물학회지 Vol.44 No.4

HIV에 감염된 환자의 경우 다양한 종류의 암이 발생하는 것으로 알려져 있다. 이러한 암종의 높은 발생률의 원인으로, 감염에 의한 면역세포의 감소 및 결핍과 같은 간접적인 이유 뿐 아니라, HIV 바이러스 단백질의 발현이 직접적으로 병의 발생에 관여한다는 보고가 있다. 본 연구에서는 HIV 환자에서 높게 나타나는 암의 발생에 대한 기전을 이해하기 위하여 HIV-1 Tat 유전자와, 다수의 암 발생과 관련이 있는 세포막단백 CD99와의 관계를 규명하였다. 먼저 CD99의 발현에 미치는 Tat의 영향을 알아보기 위하여 HIV-1 Tat 발현 안정화 세포주를 확립하고 Tat 단백에 의한 CD99 유전자의 발현 양상 변화를 분석하였다. 실험결과 Tat의 발현에 의하여 CD99 유전자의 발현이 활성화되는 것이 관찰되었으며 이와 반대로 STAT3의 발현은 낮아졌다. CD99 프로모터는 CpG 함량이 높기 때문에 Tat 단백이 DNA 메칠화를 통해서 CD99 유전자의 발현을 조절하는지 확인하기 위하여 methylation specific PCR을 수행하였고 Tat의 발현이 높은 곳에서 특이적으로 CD99 프로모터 부위가 탈메칠화되는 것을 발견하였다. Tat 발현 세포에서만 특이적인 발현 차이를 보이는 유전자 분석을 위한 Differentially Expressed Gene keratin 17과 collagen, type IV 증가됨이 확인되었다. 위의 결과는 HIV Tat 단백이 직접 세포 단백들을 조절하여 암을 발생시킬 수 있다는 보고를 뒷받침한다. HIV affects many organ systems. Patients with HIV infection have substantially increased risk of developing various cancers, primarily by opportunistic infection with oncogenic viruses due to their immunocompromised status. However, extensive evidence also indicates that the viral protein, Tat itself, may playas a major factor in the development of AIDS-related neoplasms. The molecular mechanism underlying Tat's oncogenic activity may include deregulation of cellular genes. Therefore, in this study, we examined the effect of HIV-l Tat on CD99 as one of the target cellular genes, which is a well-known tumor marker in several cancers. By using established HeLa clones that are stably expressing Tat, we found that CD99 is upregulated by endogenous Tat, whereas STAT3 is down regulated. Upon the screening of genes differentially expressed between Tat-stable cells and the control cells by using the gene fishing technique, DEG, we detected 3 genes which expression is affected by the presence of Tat. Furthermore, the methylation specific PCR analysis of the stably Tat expressing cell lines revealed that the CD99 promoter is de methylated in the presence of Tat. Taken together, these results open a potential role of CD99 in AIDS-related oncogenesis via epigenetic regulation by HIV-1 Tat.

Linkage Disequilibrium (LD) Mapping and Tagging SNP Selection of C-Fos Induced Growth Factor (Figf) Gene in Korean Population

Kim, Sook,Yoo, Yeon-Kyung,Jang, Hye-Yoon,Shin, Eun-Soon,Cho, Eun-Young,Kim, Eu-Gene,NamKung, Jung-Hyun,Yang, Jun-Mo,Lee, Jong-Eun The Korean Society of Toxicogenomics and Toxicopro 2006 Molecular & cellular toxicology Vol.2 No.1

We performed comprehensive SNP validation and linkage disequilibrium (LD) analysis of the c-fos induced growth factor (Figf) gene in Korean population. Out of 32 SNPs, only 9 SNPs were polymorphic in Korean population. Validated SNPs formed a single extended haplotype block with strong LD through the entire length of the gene. Tagging SNP analysis picked only 2 SNPs to represent most of the genetic variation information of the Figf gene. Our results demonstrate the utility of LD block and tagging SNP analysis for an efficient way of performing a candidate gene based association study.

Quantitative PCR for Etiologic Diagnosis of Methicillin-Resistant Staphylococcus aureus Pneumonia in Intensive Care Unit

Kwon, Sun-Jung,Jeon, Tae-Hyeon,Seo, Dong-Wook,Na, Moon-Joon,Choi, Eu-Gene,Son, Ji-Woong,Yoo, Eun-Hyung,Park, Chang-Gyo,Lee, Hoi-Young,Kim, Ju-Ock,Kim, Sun-Young,Kang, Jae-Ku The Korean Academy of Tuberculosis and Respiratory 2012 Tuberculosis and Respiratory Diseases Vol.72 No.3

Background: Ventilator-associated pneumonia (VAP) requires prompt and appropriate treatment. Since methicillin-resistant Staphylococcus aureus (MRSA) is a frequent pathogen in VAP, rapid identification of it, is pivotal. Our aim was to evaluate the utility of quantitative polymerase chain reaction (qPCR) as a useful method for etiologic diagnoses of MRSA pneumonia. Methods: We performed qPCR for mecA, S. aureus-specific femA-SA, and S. epidermidis-specific femA-SE genes from bronchoalveolar lavage or bronchial washing samples obtained from clinically-suspected VAP. Molecular identification of MRSA was based on the presence of the mecA and femA-SA gene, with the absence of the femA-SE gene. To compensate for the experimental and clinical conditions, we spiked an internal control in the course of DNA extraction. We estimated number of colony-forming units per mL (CFU/mL) of MRSA samples through a standard curve of a serially-diluted reference MRSA strain. We compared the threshold cycle (Ct) value with the microbiologic results of MRSA. Results: We obtained the mecA gene standard curve, which showed the detection limit of the mecA gene to be 100 fg, which corresponds to a copy number of 30. We chose cut-off Ct values of 27.94 (equivalent to $1{\times}10^4$ CFU/mL) and 21.78 (equivalent to $1{\times}10^5$ CFU/mL). The sensitivity and specificity of our assay were 88.9% and 88.9% respectively, when compared with quantitative cultures. Conclusion: Our results were valuable for diagnosing and identifying pathogens involved in VAP. We believe our modified qPCR is an appropriate tool for the rapid diagnosis of clinical pathogens regarding patients in the intensive care unit.

Quantitative PCR for Etiologic Diagnosis of Methicillin-Resistant Staphylococcus aureus Pneumonia in Intensive Care Unit

( Sun Jung Kwon ),( Taeh Yeon Jeon ),( Dong Wook Seo ),( Moon Joon Na ),( Eu Gene Choi,),( Ji Woong Son ),( Eun Hyung Yoo ),( Chang Gyo Park ),( Hoi Young Lee ),( Ju Ock Kim ),( Sun Young Kim ),( Jae 대한결핵 및 호흡기학회 2012 Tuberculosis and Respiratory Diseases Vol.72 No.3

Background: Ventilator-associated pneumonia (VAP) requires prompt and appropriate treatment. Since methicillin- resistant Staphylococcus aureus (MRSA) is a frequent pathogen in VAP, rapid identification of it, is pivotal. Our aim was to evaluate the utility of quantitative polymerase chain reaction (qPCR) as a useful method for etiologic diagnoses of MRSA pneumonia. Methods: We performed qPCR for mecA, S. aureus-specific femA-SA, and S. epidermidis-specific femA-SE genes from bronchoalveolar lavage or bronchial washing samples obtained from clinically-suspected VAP. Molecular identification of MRSA was based on the presence of the mecA and femA-SA gene, with the absence of the femA-SE gene. To compensate for the experimental and clinical conditions, we spiked an internal control in the course of DNA extraction. We estimated number of colony-forming units per mL (CFU/mL) of MRSA samples through a standard curve of a serially-diluted reference MRSA strain. We compared the threshold cycle (Ct) value with the microbiologic results of MRSA. Results: We obtained the mecA gene standard curve, which showed the detection limit of the mecA gene to be 100 fg, which corresponds to a copy number of 30. We chose cut-off Ct values of 27.94 (equivalent to 1×104 CFU/mL) and 21.78 (equivalent to 1×105 CFU/mL). The sensitivity and specificity of our assay were 88.9% and 88.9% respectively, when compared with quantitative cultures. Conclusion: Our results were valuable for diagnosing and identifying pathogens involved in VAP. We believe our modified qPCR is an appropriate tool for the rapid diagnosis of clinical pathogens regarding patients in the intensive care unit.

Mesenchymal-to-epithelial transition of osteoblasts induced by Fam20c knockout

Geng Ya-Wei,Zhang Zhen,Jin Han,Da Jun-Long,Zhang Kai,Wang Jian-Qun,Guo Yu-Yao,Zhang Bin,Li Ying 한국유전학회 2022 Genes & Genomics Vol.44 No.2

Background: Fam20c is intimately related to tissue development and diseases. At present, it has been reported that Fam20c regulates the mineralization of osteoblasts, but there are few reports on other effects. Objective: To study the effect of Fam20c on osteoblasts by knocking out the Fam20c gene. Methods: Fam20c knockout osteoblasts were constructed by transfecting mouse osteoblasts with lentivirus. The proliferation, migration and mineralization of Fam20c knockout cells were detected by CCK-8, scratch test and alizarin red staining assays. The subcellular structure was observed by transmission electron microscopy. RT-PCR was used to detect the differential expression of mesenchymal-to-epithelial transition (MET)-related marker genes and core transcription factors. The differential expression of MET-related proteins was detected by immunofluorescence or Western blot. Transcriptome analysis of Fam20c knockout osteoblasts was performed, and real-time PCR was used to verify transcriptome analysis related to MET. Results: The proliferation ability of osteoblasts was not significantly changed after Fam20c deletion, but the migration ability and mineralization ability were significantly weakened. There were tight junctions between Fam20c knockout cells. The expression of mesenchymal cell marker genes and core transcription factors was significantly decreased, and the expression of epithelial cell marker genes was significantly increased. The expression of mesenchymal cell marker proteins was significantly decreased, and the expression of epithelial cell marker proteins was significantly increased. Multiple signalling molecules and pathways involved in MET have changed. Conclusions: Knockdown of Fam20c resulted in MET. Fam20c affects the transcription of key factors in osteoblast MET.

Aik Sang Busik System내의 종속영양세균의 분포 및 특성에 관한 연구

정팔진,김성진,김민정 全北大學校 附設 都市및環境硏究所 1997 都市 및 環境硏究 Vol.12 No.1

Aik Sang Busik System(ASBS) was developmented in Japan. In currently, this system is operating at many night soil treatment plants in our country. The purpose of this study is to exame the effects of heterotrophic bacteria on the aeration basin of this system to remove organic compounds. As a result of tests, isolated heterotrophic bacteria are about 115 genes. The predominant gene is Acaligenus spp which about 32 percent of isolated genes. Because the floc foming bacteria of isolated heterotrophic bacteria are about 54 percent, a major removal mechanism for organic compounds in this system depends on the floc foming bacteria. The total amount of hetrotrophic bacteria is 2.32×10 exp (7) c.f.u/㎖, which is a little lower than that in the activated sludge system. As liquid degradable heterotrophic bacteria are 1.57×10 exp (7) c.f.u/㎖, carbohydrate degradable heterotrophic bacteria are 1.22×10 exp (7) c.f.u/㎖10^7, protein degradable heterotrophic bactera are 1.48×10 exp (7) c.f.u/㎖, The distribution of liquid, protein, carbohydrate degradable heterotrophic bacteria are similar to that of the sludge system.