• Journal of Microbiology
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• v.41 no.3
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• pp.232-238
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• 2003

Previous phylogenetic studies on human immunodeficiency virus type 1 (HIV-1) isolated from Korean patients suggest that the major subtype of Korean isolate is subtype B. In this subtype, some of the Korean isolates seem to be clustered exclusively of foreign isolates. Presence of this so-called “Korean clade” among Korean isolates is unique but needs verification since the number of Korean isolates used in previous studies was limited. This study aimed to identify the presence of the “Korean clade” by molecular phylogenetic analysis using all the Korean nef gene sequences registered in the NCBI GenBank (N=243) together with 32 reference strains and 77 foreign isolates. Extensive analysis of the nef gene nucleotide sequences by neighbor-joining method revealed the following. Most (83.1 ％) of the Korean isolates belonged to subtype B, and 81.2％ of subtype B were clustered together and excluded foreign isolates (bootstrap value=91.9％ ). Within Korean subtype B cluster, no characteristic subcluster formation was evident since the bootstrap values for the subcluster were very low. Due to limited information, the phylogenetic analysis failed to identify the epidemiological linkage among specific groups such as homosexuals and hemophiliacs within the Korean subtype B cluster. Detailed analysis and epidemiological information are needed to clarify the origin and significance of the Korean subtype B cluster.

• Journal of Ginseng Research
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• v.43 no.2
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• pp.312-318
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• 2019

Background: To date, no study has described disease progression in Asian patients infected with HIV-1 subtype D. Methods: To determine whether the disease progression differs in patients infected with subtypes D and B prior to starting combination antiretroviral therapy, the annual decline (AD) in $CD^{4+}$ T cell counts over $96{\pm}59months$ was retrospectively analyzed in 163 patients and compared in subtypes D and B based on the nef gene. Results: $CD^{4+}$ T cell AD was significantly higher in the six subtype D-infected patients than in the 157 subtype B-infected patients irrespective of Korean Red Ginseng (KRG) treatment (p < 0.001). Of these, two subtype D-infected patients and 116 subtype B-infected patients had taken KRG. AD was significantly lower in patient in the KRG-treated group than in those in the $KRG-na{\ddot{i}}ve$ group irrespective of subtype (p < 0.05). To control for the effect of KRG, patients not treated with KRG were analyzed, with AD found to be significantly greater in subtype D-infected patients than in subtype B-infected patients (p < 0.01). KRG treatment had a greater effect on AD in subtype D-infected patients than in subtype B-infected patients (4.5-fold vs. 1.6-fold). Mortality rates were significantly higher in both the 45 $KRG-na{\ddot{i}}ve$ (p < 0.001) and all 163 (p < 0.01) patients infected with subtype D than subtype B. Conclusion: Subtype D infection is associated with a >2-fold higher risk of death and a 2.9-fold greater rate of progression than subtype B, regardless of KRG treatment.

• Journal of Ginseng Research
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• v.46 no.6
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• pp.731-737
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• 2022

Background: The number of primary human immunodeficiency virus (HIV)-1 non-B subtype infections (non-B) and that of reports regarding the differences in the pathogenesis of subtype B and non-B infections are increasing. However, to the best of our knowledge, there have been no reports on gross deletion in the nef gene (g∆nef) in non-B infections. Methods: To determine whether there is a difference in the change in CD4⁺ T cells after treatment with Korean Red Ginseng (KRG) between patients with subtype B and non-B infections, we retrospectively analyzed and compared the annual decrease in CD4⁺ T cells (AD) and the proportion of g∆nef in 77 patients who were followed for more than 10 years in the absence of combination antiretroviral therapy. Results: Overall, AD was significantly faster in patients with non-B infections than in those with subtype B infections. Survival analysis showed that the survival probability was significantly higher in subtype B than in non B-infected patients. These differences mainly resulted from significant differences in the amount of KRG and age. In the patients treated with KRG, there was a significant correlation between the amount of KRG and the AD in both subtypes. Interestingly, there was a significant correlation between the amount of KRG and the proportion of g∆nef in patients infected with subtype B, but not in those infected with non-B. The same phenomenon was observed when the KRG dose was adjusted. Conclusion: Our results suggest that non-B may be biologically more stable than subtype B.

• Korean Journal of Microbiology
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• v.47 no.1
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• pp.30-37
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• 2011

This ultra real-time PCR (UPCR) based diagnosis system for avian influenza A virus (AIV) subtype was designed. The target primer in this study was derived from H5N1 subtype-specific 133 bp partial gene of hemagglutinin (HA), and was synthesized by using PCR-based gene synthesis on the ground of safety. UPCR was operated by Mini-Opticon Q-PCR Quantitative Thermal Cycler using aptamer-based molecular beacon, total 10 ${\mu}l$ of reaction mixture with extraordinarily short time in each steps in PCR. The detection including UPCR and analysis of melting temperature was totally operated within 15 min. The AIV-specific 133 bp PCR product was correctly amplified until 5 molecules of HA gene as minimum of templates. This kind of PCR was drafted as UPCR in this study and it could be used to detect not only AIV subtype, but also other pathogens using UPCR-based diagnosis.

• The Korean Journal of Physiology and Pharmacology
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• v.2 no.6
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• pp.771-778
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• 1998

To investigate interaction of angiotensin converting enzyme (ACE) inhibitor with local tissue renin- angiotensin system (RAS), changes in gene expression of the RAS components in various tissues in response to chronic administration of an ACE inhibitor, enalapril, were examined in Sprague-Dawley male rats. Enalapril was administered in their drinking water $(3{\sim}4\;mg/day)$ over 8 wk. Plasma and renal ACE activity increased significantly after 4 and 8 wk of enalapril treatment. Renin levels of the plasma and kidney of the enalapril-treated rats markedly increased after 4 wk and decreased thereafter, but still remained significantly higher than those of control rats. Kidney mRNA levels of renin markedly increased after 4 and 8 wk of enalapril treatment, but those of angiotensinogen and ANG II-receptor subtypes, $AT_{1A}$ and $AT_{1B}$, did not change significantly. The liver expressed genes for renin, angiotensinogen and $AT_{1A}$ receptor subtype, but $AT_{1B}$ receptor subtype mRNA was not detectable by RT-PCR. None of mRNA for these RAS components in the liver changed significantly by enalapril treatment. The hypothalamus showed mRNA expressions of renin, angiotensinogen, $AT_{1A}$ and $AT_{1B}$ receptor subtypes. $AT_{1A}$ receptor subtype mRNA was more abundant than $AT_{1B}$ receptor subtype in the hypothalamus as shown in the kidney. However, gene expression of the RAS components remained unchanged during 8-wk treatment of enalapril. In the present study, chronic ACE inhibition increased plasma and renal levels of ACE and renin, but did not affect mRNA levels of other RAS components such as angiotensinogen, ANG II receptor subtypes in the kidney. Gene levels of the RAS components in the liver and hypothalamus were not altered by chronic treatment of enalapril. These results suggest the differential expression of the RAS components in response to enalapril, and localized action and some degree of tissue specificity of enalapril.

• Journal of Institute of Control, Robotics and Systems
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• v.10 no.12
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• pp.1172-1180
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• 2004

Recently, the gene expression data, product of high-throughput technology, appeared in earnest and the studies related with it (so-called bioinformatics) occupied an important position in the field of biological and medical research. The microarray is a revolutionary technology which enables us to monitor several thousands of genes simultaneously and thus to gain an insight into the phenomena in the human body (e.g. the mechanism of cancer progression) at the molecular level. To obtain useful information from such gene expression measurements, it is essential to analyze the data with appropriate techniques. However the high-dimensionality of the data can bring about some problems such as curse of dimensionality and singularity problem of matrix computation, and hence makes it difficult to apply conventional data analysis methods. Therefore, the development of method which can effectively treat the data becomes a challenging issue in the field of computational biology. This research focuses on the gene selection and classification for cancer subtype discrimination based on gene expression (microarray) data.

• Biomedical Science Letters
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• v.29 no.4
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• pp.330-335
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• 2023

The corazonin (Crz) gene showed two subtypes of different length at laval and pupal stage. The long subtype fade out in adult central nerve system (CNS) but the short one survive through all the life cycle from larva to adult. The short subtype has the same base sequences with mature Crz mRNA and detected in both brain and ventral nerve cord (VNC). The long one, on the contrary, was detected only in the brain tissue. As observed in above results, Crz neurons develop in different pattern in the CNS of scuttle fly and the Crz gene expresses two different subtypes. These results suggest that this neurotransmitter may perform differential neurophysiological functions in the scuttle fly. Variation in the amino acid composition of the final active undecapeptide supports in strong those possibilities. We expect further studies on the relationship between neurophysiological functions of Crz and behavioral characteristics of the scuttle fly.

• Journal of Microbiology
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• v.44 no.6
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• pp.655-659
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• 2006

Phylogenetic studies of nef, pol, and env gene sequences of HIV-1 isolated from Koreans suggested the presence of a Korean clade in which Korean sequences are clustered to the exclusion of foreign sequences. We attempted to identify and characterize the Korean clade using all vif gene sequences isolated from Koreans registered in the NCBI GenBank database (n = 233). Most (77 %) of the Korean isolates belonged to the Korean clade as a large subcluster in subtype B, designated the Korean clade subtype B ($K_{C}B$). $K_{C}B$ sequences were relatively homogenous compared to Korean subtype B sequences that did not belong to the $K_{C}B$ (non-Korean clade subtype B; $NK_{C}B$). Comparison of amino acid frequencies of $K_{C}B$ and $NK_{C}B$ sequences revealed several positions where the amino acid frequencies were significantly different. These amino acid residues were critical in separating $K_{C}B$ from $NK_{C}B$ or from foreign sequences, since substitution of these amino acids in $K_{C}B$ with the $NK_{C}B$ amino acids relocated the $K_{C}B$ sequences to $NK_{C}B$, and vice versa. Further analyses of $K_{C}B$ will help us to understand the origin and evolutionary history of $K_{C}B$.

• The Journal of Korean Society of Virology
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• v.29 no.2
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• pp.119-127
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• 1999

Phylogenetic analysis was conducted to monitor transmission of HIV and to investigate the genetic structure of primary isolates from 12 HIV-1 subtype A infected Koreans. The individuals infected with subtype A viruses had been diagnosed as HIV-1 seropositives during the period 1987 to 1995 and blood samples have been collected from 1991 to 1997. DNA of each individual was isolated from uncultured or cultured peripheral blood mononuclear cells. V3-V5 (0.7 kb) fragment of HIV-1 env gene was amplified by nested polymerase chain reaction and the PCR products were sequenced. The mean value of the divergence of nucleotide of HIV-1 env V3-V5 fragment was $17.0{\pm}4.06%$ ($8.6{\sim}25.8%$) within HIV-1 subtype A isolates from Koreans. This diversity was higher than those of African isolates ($13.7{\pm}2.66%$). In the phylogenetic tree, Korean subtype A isolates were not grouped together, but intermingled into African isolates. The results of this study suggested that HIV-1 subtype A variants be introduced from multiple sites of Africa into Korea and the big genetic diversity of Korea HIV-1 subtype A isolates may be further influenced by the range of geographic locations in which the infection occurred rather than the elapsed time between infection and collection of samples and the disease progression.

• The Korean Journal of Zoology
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• v.26 no.3
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• pp.211-217
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• 1983

Genetic polymorphism of transferrin $(T_f)$ subtypes in Jeju population was studied by isoelectric focusing of human sera on polyacrylamide gels under high voltage, and haptolobin (Hp) polymorphism in Seoul and Jeju population was studied by polyacrylamide gel electrophoresis. Among 946 normal samples, three common types of transferrin, $T_{f}C_{1}, T_{f}C_{1}-C_{2} and T_{f}C_{2}$ were observed with some variants migrating slower than $T_{f}C$ subtypes, while among 139 patient (hepatitis) samples, only three common types were found. The gene frequencies were calculated as follows; in normal population, $T_{f}C^{1}$ was 0.7220; $T_{f}C^{2}, 0.2743; T_{f}D^{Jeju}, 0.0037$, and in patient population, $T_{f}C^{1} was 0.7194; T_{f}C^{2}, 0.2806$ respectively. Among 460 samples in Seoul and 502 in Jeju population, three types of haptoglobin, Hp 1-1, Hp 2-1 and Hp 2-2 were observed. The gene frequency of $Hp^1$ was 0.304, $Hp^2$, 0.696 in Seoul and in Jeju, $Hp^1$ was 0.269 and $Hp^2$, 0.731, respectively. The frequencies of the genes and the polymorphic phenotypes were discussed comparatively with the other populations.