• Tuberculosis and Respiratory Diseases
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• v.52 no.5
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• pp.497-505
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• 2002

Background : INF-${\gamma}$ plays an important role in the host response to a mycobacterial infection. A complete IFN-${\gamma}$ receptor 1 deficiency is a life threatening condition because it renders patients highly susceptible to a mycobacterial infection. Several mutations in the IFN-${\gamma}$ receptor and STAT1 gene have been identified in the rare mycobacterial infections. These mutations have partial function of the IFN-${\gamma}$ receptor and similar pathologic features to clinical tuberculosis. Materials and Methods : The function of the IFN-${\gamma}$ receptor was evaluated in the patients with clinical tuberculosis. In addition, the DNA coding sequence of the IFNgR1 and STAT1 gene was also analyzed in disseminated tuberculosis patients who might have a defective IFN-${\gamma}$ receptor. Results : The cell surface expression levels of HLA-DR and CD64 in the PMBC after being stimulation with IFN-${\gamma}$ (100IU/ml, 1000IU/ml) were increased in both controls and patients. However, the rate of increase in both groups was similar. The production of TNF-${\alpha}$ in the response to stimulation with LPS was higher in the both groups ($850.7{\pm}687.8$ vs. $836.7{\pm}564.3$ pg/ml). Pretreatment with IFN-${\gamma}$ prior to LPS stimulation resulted in further increase in TNF-${\alpha}$ production between both groups ($2203.5{\pm}242.5$ vs. $2227.5{\pm}560.4$ pg/ml). However, the rate of the increase in TNF-${\alpha}$ production in the both groups was similar. The known mutations in the IFNgR1 and STAT1 coding sequences were not found in the genomic DNA of patients with disseminated tuberculosis. Conclusion : The functional and genetic defects of the IFN-${\gamma}$ receptor were not identified in clinical tuberculosis. This suggests the defective IFN-${\gamma}$ receptor that predispoe patients to a BCG or NTM infection can not alone account for the cases of clinical tuberculosis.

• Proceedings of the Korean Society of Developmental Biology Conference
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• 2003.10a
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• pp.101-101
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• 2003

Main strategy for a treatment of Parkinson's disease (PD), due to a progressive degeneration of dopaminergic neurons, is a pharmaceutical supplement of dopamine derivatives or ceil replacement therapy. Both of these protocols have pros and cons; former exhibiting a dramatic relief but causing a severe side effects on long-term prescription and latter also having a proven effectiveness but having availability and ethical problems Embryonic stem (ES) cells have several characteristics suitable for this purpose. To investigate a possibility of using ES cells as a carrier of therapeutic gene(s), human ES (hES, MB03) cells were transfected with cDNAs coding for tyrosine hydroxylase (TH) in pcDNA3.1 (+) and the transfectants were selected using neomycin (250 $\mu /ml$). Expression of TH being confirmed, two of the positive clone (MBTH2 & 8) were second transfected with GTP cyclohydrolase 1 (GTPCH 1) in pcDNA3.1 (+)-hyg followed by selection with hygromycin-B (150 $\mu /ml$) and RT-PCR confirmation. By immune-cytochemistry, these genetically modified but undifferentiated dual drug-resistant cells were found to express few of the neuronal markers, such as NF200, $\beta$-tubulin, and MAP2 as well as astroglial marker GFAP. This results suggest that over-production of BH4 by ectopically expressed GTPCH I may be involved in the induction of those markers. Transplantation of the cells into striatum of 6-OHDA- denervated PD animal model relieved symptomatic rotational behaviors of the animals. Immunohistochemical analyses showed the presence of human cells within the striatum of the recipients. These results suggest a possibility of using hES cells as a carrier of therapeutic gene(s).

• Korean Journal of Veterinary Research
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• v.48 no.4
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• pp.441-449
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• 2008

The genus Lactobacillus is the largest of the genera included in lactic acid bacteria and is associated with mucosal membranes of human and animal. Only a few Lactobacillus plasmid-encoded functions have been discovered and used. In this study, a novel plasmid (pILR091) was isolated from a wild L. reuteri isolated from pig and described the characteristics of its replicons, genetic organization, and relationship with other plasmids. After digestion of the plasmid, pILR091, with SalI, plasmid DNA was cloned into the pQE-30Xa vector and sequenced. The complete sequence was confirmed by the sequencing of PCR products and analyzed with the Genbank database. The isolate copy number and stability were determined by quantitative-PCR. The complete sequence of L. reuteri contained 7,185 nucleotides with 39% G-C content and one cut site by two enzymes, SalI and HindIII. The similar ori sequence of the pC194- rolling circle replication family (TTTATATTGAT) was located 63 bp upstream of the protein replication sequence, ORF 1. Total of five ORFs was identified and the coding sequence represented 4,966 nucleotides (70.4%). ORF1 of pILR091 had a low similarity with the sequence of pTE44. Other ORFs also showed low homology and E-values. The average G-C content of pILR091 was 39%, similar with that of genomic DNA. The copy number of pILR091 was determined at approximately 24 to 25 molecules per genomic DNA. These results suggested that pILR091 might be a good candidate to construct a new vector, which could be used for cloning and expression of foreign genes in lactobacilli.

• Proceedings of the Korea Contents Association Conference
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• 2007.11a
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• pp.522-526
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• 2007

Since newly emerged disease, the Severe Acute Respiratory Syndrome (SARS), spread from Asia to North America and Europe rapidly in 2003, many researchers have tried to determine where the virus came from. In the phylogenetic point of view, SARS virus has been known to be one of the genus Coronavirus, but, the overall conservation of SARS virus sequence was not highly similar to that of known coronaviruses. The natural reservoirs of SARS-CoV are not clearly determined, yet. In the present study, the genomic sequences of SARS-CoV were analyzed by bioinformatics techniques such as multiple sequence alignment and phylogenetic analysis methods as well multivariate statistical analysis. All the calculating processes, including calculations of the relative synonymous codon usage (RSCU) and other genomic parameters using 30,305 coding sequences from the two genera, Coronavirus, and Lentivirus, and one family, Orthomyxoviridae, were performed on SMP cluster in KISTI, Supercomputing Center. As a result, SARS_CoV showed very similar RSCU patterns with feline coronavirus on the both axes of the correspondence analysis, and this result showed more agreeable results with serological results for SARS_CoV than that of phylogenetic result itself. In addition, SARS_CoV, human immunodeficiency virus, and influenza A virus commonly showed the very low RSCU differences among each synonymous codon group, and this low RSCU bias might provide some advantages for them to be transmitted from other species into human beings more successfully. Large-scale genomic analysis using bioinformatics techniques may be useful in genetic epidemiology field effectively.

• Journal of fish pathology
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• v.19 no.2
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• pp.127-139
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• 2006

From 2002 to 2004, various vibrios were isolated from the olive flounder, Paralichthys olivaceus of culturing size with disease signs. During this survey, it was known that the high proportion of Vibrio ichthyoenteri was occupied among the isolated vibrios. Generally, V. ichthyoenteri is well known as the pathogen of bacterial enteritis of olive flounder larvae. The aim of the present study was the compare the characteristics of two groups of V. ichthyoenteri, culturing sized olive flounder, and larvae of olive flounder showing the intestinal necrosis. The research was focused on the physiology, biochemistry, genetics in the two bacterial groups. The physiological and biochemical characteristics of the tested strains were very similar. The intergenic spacer (IGS) region between the 16S and 23S rRNA genes of 21 isolated strains and 3 reference strains, V. ichthyoenteri, were investigated by PCR fragment length typing and DNA sequencing. After the isolated strains were identified as V. ichthyoenteri, not only phenotypic characteristics of the isolated and reference strains but also homology of 16S-23S IGS of all isolated strains and reference strains as 99.1~100%. The V. ichthyoenteri showed 4 specific 16S-23S patterns and contained no-tRNA, tRNAGlu(TTC) , tRNAIle(GAT) tRNAAla(TGC) type .

• Proceedings of the Microbiological Society of Korea Conference
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• 2007.05a
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• pp.120-122
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• 2007

All living organisms use numerous signal-transduction pathways to sense and respond to their environments and thereby survive and proliferate in a range of biological niches. Molecular dissection of these signalling networks has increased our understanding of these communication processes and provides a platform for therapeutic intervention when these pathways malfunction in disease states, including infection. Owing to the expanding availability of sequenced genomes, a wealth of genetic and molecular tools and the conservation of signalling networks, members of the fungal kingdom serve as excellent model systems for more complex, multicellular organisms. Here, we employed Cryptococcus neoformans as a model system to understand how fungal-signalling circuits operate at the molecular level to sense and respond to a plethora of environmental stresses, including osmoticshock, UV, high temperature, oxidative stress and toxic drugs/metabolites. The stress-activated p38/Hog1 MAPK pathway is structurally conserved in many organisms as diverse as yeast and mammals, but its regulation is uniquely specialized in a majority of clinical Cryptococcus neoformans serotype A and D strains to control differentiation and virulence factor regulation. C. neoformans Hog1 MAPK is controlled by Pbs2 MAPK kinase (MAPKK). The Pbs2-Hog1 MAPK cascade is controlled by the fungal "two-component" system that is composed of a response regulator, Ssk1, and multiple sensor kinases, including two-component.like (Tco) 1 and Tco2. Tco1 and Tco2 play shared and distinct roles in stress responses and drug sensitivity through the Hog1 MAPK system. Furthermore, each sensor kinase mediates unique cellular functions for virulence and morphological differentiation. We also identified and characterized the Ssk2 MAPKKK upstream of the MAPKK Pbs2 and the MAPK Hog1 in C. neoformans. The SSK2 gene was identified as a potential component responsible for differential Hog1 regulation between the serotype D sibling f1 strains B3501 and B3502 through comparative analysis of their meiotic map with the meiotic segregation of Hog1-dependent sensitivity to the fungicide fludioxonil. Ssk2 is the only polymorphic component in the Hog1 MAPK module, including two coding sequence changes between the SSK2 alleles in B3501 and B3502 strains. To further support this finding, the SSK2 allele exchange completely swapped Hog1-related phenotypes between B3501 and B3502 strains. In the serotype A strain H99, disruption of the SSK2 gene dramatically enhanced capsule biosynthesis and mating efficiency, similar to pbs2 and hog1 mutations. Furthermore, ssk2, pbs2, and hog1 mutants are all hypersensitive to a variety of stresses and completely resistant to fludioxonil. Taken together, these findings indicate that Ssk2 is the critical interface protein connecting the two-component system and the Pbs2-Hog1 pathway in C. neoformans.

• Analytical Science and Technology
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• v.18 no.4
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• pp.362-367
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• 2005

The human mitochondrial genome (mtDNA) has been an important tool in the field of forensic investigations. Within the entire mtDNA molecule, the non-coding control region which is approximately 1,100 bp including hypervariable region I and II (HV1 and HV2) is widely studied because it is highly polymorphic and useful for human identification purposes. In this study, 360 unrelated Koreans were analyzed in HV1. The number of polymorphic sites and genetic lineage were 124 and 210, respectively. The most prevalent substitution was C-T and 75.8% of DNA showed C-T substitution at 16223. There were 20 kinds of polymorphism between 16180 and 16193 including insertion and deletion. The most frequent haplotype was [16223T, 16362C] representing 5%. Approximately 25.9% of DNA showed the same haplotype in at least two samples. The gene diversity was calculated to 0.996 and the probability of two unrelated perosons having the same haplotype was determined to 0.7%.

• Asian-Australasian Journal of Animal Sciences
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• v.30 no.7
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• pp.912-919
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• 2017

Objective: Identification of the candidate genes that play key roles in phenotypic variations can provide new information about evolution and positive selection. Interleukin (IL)-32 is involved in many biological processes, however, its role for the immune response against various diseases in mammals is poorly understood. Therefore, the current investigation was performed for the better understanding of the molecular evolution and the positive selection of single nucleotide polymorphisms in IL-32 gene. Methods: By using fixation index ($F_{ST}$) based method, IL-32 (9375) gene was found to be outlier and under significant positive selection with the provisional combined allocation of mean heterozygosity and $F_{ST}$. Using nucleotide sequences of 11 mammalian species from National Center for Biotechnology Information database, the evolutionary selection of IL-32 gene was determined using Maximum likelihood model method, through four models (M1a, M2a, M7, and M8) in Codeml program of phylogenetic analysis by maximum liklihood. Results: IL-32 is detected under positive selection using the $F_{ST}$ simulations method. The phylogenetic tree revealed that goat IL-32 was in close resemblance with sheep IL-32. The coding nucleotide sequences were compared among 11 species and it was found that the goat IL-32 gene shared identity with sheep (96.54%), bison (91.97%), camel (58.39%), cat (56.59%), buffalo (56.50%), human (56.13%), dog (50.97%), horse (54.04%), and rabbit (53.41%) respectively. Conclusion: This study provides evidence for IL-32 gene as under significant positive selection in goat.

• Asian-Australasian Journal of Animal Sciences
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• v.30 no.7
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• pp.957-966
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• 2017

Objective: To understand the dynamic structure, function, and influence on nutrient metabolism in hosts, it was crucial to assess the genetic potential of gut microbial community in yaks of different ages. Methods: The denaturing gradient gel electrophoresis (DGGE) profiles and Illumina-based metagenomic sequencing on colon contents of 15 semi-domestic yaks were investigated. Unweighted pairwise grouping method with mathematical averages (UPGMA) clustering and principal component analysis (PCA) were used to analyze the DGGE fingerprint. The Illumina sequences were assembled, predicted to genes and functionally annotated, and then classified by querying protein sequences of the genes against the Kyoto encyclopedia of genes and genomes (KEGG) database. Results: Metagenomic sequencing showed that more than 85% of ribosomal RNA (rRNA) gene sequences belonged to the phylum Firmicutes and Bacteroidetes, indicating that the family Ruminococcaceae (46.5%), Rikenellaceae (11.3%), Lachnospiraceae (10.0%), and Bacteroidaceae (6.3%) were dominant gut microbes. Over 50% of non-rRNA gene sequences represented the metabolic pathways of amino acids (14.4%), proteins (12.3%), sugars (11.9%), nucleotides (6.8%), lipids (1.7%), xenobiotics (1.4%), coenzymes, and vitamins (3.6%). Gene functional classification showed that most of enzyme-coding genes were related to cellulose digestion and amino acids metabolic pathways. Conclusion: Yaks' age had a substantial effect on gut microbial composition. Comparative metagenomics of gut microbiota in 0.5-, 1.5-, and 2.5-year-old yaks revealed that the abundance of the class Clostridia, Bacteroidia, and Lentisphaeria, as well as the phylum Firmicutes, Bacteroidetes, Lentisphaerae, Tenericutes, and Cyanobacteria, varied more greatly during yaks' growth, especially in young animals (0.5 and 1.5 years old). Gut microbes, including Bacteroides, Clostridium, and Lentisphaeria, make a contribution to the energy metabolism and synthesis of amino acid, which are essential to the normal growth of yaks.

• Journal of Genetic Medicine
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• v.8 no.1
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• pp.53-57
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• 2011

Purpose: Wilson disease is an autosomal recessive disorder which causes excessive copper accumulation in the hepatic region. So far, ATP7B gene is the only disease-causing gene of Wilson disease known to date. However, ATP7B mutations have not been found in ~15% of the patients. This study was performed to identify any causative gene in Wilson disease patients without an ATP7B mutation in either allele. Materials and Methods: The sequence of the coding regions and exon-intron boundaries of the five ATP7B-interacting genes, ATOX1, COMMD1, GLRX, DCTN4, and ZBTB16, were analyzed in the 12 patients with Wilson disease. Results: Three nonsynonymous variants including c.1084A>G (p.Thr362Ala) in the exon 12 of the DCTN4 gene were identified in the patients examined. Among these, only p.Thr362Ala was predicted as possibly damaging protein function by in silico analysis. Examination of allele frequency of c.1084A>G (p.Thr362Ala) variant in the 176 patients with Wilson disease and in the 414 normal subjects revealed that the variant was more prevalent in the Wilson disease patients (odds ratio [OR]=3.14, 95% confidence interval=1.36-7.22, P=0.0094). Conclusion: Our result suggests that c.1084A>G (p.Thr362Ala) in the ATP7B-interacting DCTN4 gene may be associated with the pathogenesis of Wilson disease.