• Journal of Microbiology
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• 제44권6호
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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 $K_{C}B$.

• International Journal of Stem Cells
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• 제16권3호
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• pp.342-355
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• 2023

Background and Objectives: Osteoblasts are derived from bone marrow mesenchymal stem cells (BMMSCs) and play important role in bone remodeling. While our previous studies have investigated the cell subtypes and heterogeneity in osteoblasts and BMMSCs separately, cell-to-cell communications between osteoblasts and BMMSCs in vivo in humans have not been characterized. The aim of this study was to investigate the cellular communication between human primary osteoblasts and bone marrow mesenchymal stem cells. Methods and Results: To investigate the cell-to-cell communications between osteoblasts and BMMSCs and identify new cell subtypes, we performed a systematic integration analysis with our single-cell RNA sequencing (scRNA-seq) transcriptomes data from BMMSCs and osteoblasts. We successfully identified a novel preosteoblasts subtype which highly expressed ATF3, CCL2, CXCL2 and IRF1. Biological functional annotations of the transcriptomes suggested that the novel preosteoblasts subtype may inhibit osteoblasts differentiation, maintain cells to a less differentiated status and recruit osteoclasts. Ligand-receptor interaction analysis showed strong interaction between mature osteoblasts and BMMSCs. Meanwhile, we found FZD1 was highly expressed in BMMSCs of osteogenic differentiation direction. WIF1 and SFRP4, which were highly expressed in mature osteoblasts were reported to inhibit osteogenic differentiation. We speculated that WIF1 and sFRP4 expressed in mature osteoblasts inhibited the binding of FZD1 to Wnt ligand in BMMSCs, thereby further inhibiting osteogenic differentiation of BMMSCs. Conclusions: Our study provided a more systematic and comprehensive understanding of the heterogeneity of osteogenic cells. At the single cell level, this study provided insights into the cell-to-cell communications between BMMSCs and osteoblasts and mature osteoblasts may mediate negative feedback regulation of osteogenesis process.

• Asian Pacific Journal of Cancer Prevention
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• 제15권14호
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• pp.5539-5544
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• 2014

Background: To evaluate the location of tumor relapse and imaging modality for detection according to the breast cancer subtype: luminal A, luminal B, HER2 positive luminal B, nonluminal HER2 positive, and triple negative. Materials and Methods: A total of 1244 patients with breast cancer with known estrogen receptor (ER), progesterone receptor (PR), Ki-67 and human epidermal growth factor receptor 2 (HER2), who underwent breast surgery from 2009 to 2012 were analyzed. Patients were classified into the following categories: luminal A (n=458), luminal B (n=241), HER2 positive luminal B (n=227), nonluminal HER2 positive (n=145) and triple negative (n=173). A total of 105 cases of relapse were detected in 102 patients: locoregional recurrence (n=46), recurrence in the contralateral breast (n=28) and distant metastasis (n=31). Comparison of proportions was used to determine the difference between subtypes. Results: Relapse rates by subtypes are as follows: luminal A 23 of 458 (5.02%), luminal B 19 of 241(7.88%), HER2 positive luminal B 15 of 227 (6.61%), nonluminal HER2 postive 19 of 145 (13.10%) and triple negative 29 of 173(16.76%). Luminal A tumors had the lowest rate of recurrence and had significantly lower recurrence rate in comparison with nonluminal HER2 postive (p=0.0017) and triple negative subtypes (p<0.0001). Compared with all other subtypes except nonluminal HER2 positive, triple negative tumors had the highest rate of tumor recurrence (p<0.01). Triple negatives were most likely to develop contralateral recurrence against all subtypes (p<0.05). Detection rate of locoregional and contralateral tumor recurrence were 28.3% on mammography (n=17/60). Conclusions: Luminal A tumors are associated with a low risk of recurrence while triple negative lesions have a high risk. In case of triple negative tumors, the contralateral breast has much more recurrence as compared with all other subtype. In terms of detection rates, breast USG was the best modality for detecting tumor recurrence, compared with other modalities (p<0.05). Subtyping of breast tumors using a molecular gene expression panel can identify patients who have increased risk of recurrence and allow prediction of locations of tumor recurrence for each subtype.

• 대한의생명과학회지
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• 제26권3호
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• pp.244-248
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• 2020

Skin and soft tissue infections caused by methicillin-resistant Staphylococcus aureus (MRSA) can occur especially in community populations such as military training camps. We investigated antimicrobial resistance patterns and molecular epidemiological characteristics of MRSA isolated from nasal swabs in healthy army trainees. From January 2018 to March 2018, one MRSA strain was isolated from nasal swab and hand of healthy army trainees. mecA gene detection, SCCmec and mec complex typing were performed to analyze the antimicrobial resistance patterns and molecular epidemiological characteristics of MRSA isolates. As a result, SCCmec and mec complex type of MRSA isolate from military trainees was not-typeable (n=1). In conclusion, not-typeable subtype of MRSA isolate from military trainees need to be confirmed by continuous follow-up study to determine whether there is a different genotype or a new subtype of genotype present in the Republic of Korea.

• 대한바이러스학회지
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• 제29권2호
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• pp.107-118
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• 1999

To characterize the molecular nature of human immunodeficiency virus (HIV)-1, we determined the full-length HIV-1 sequences from cultured peripheral blood mononuclear cells (PBMC) of a Korean long-term nonprogressor (LTNP). Without antiretroviral therapy, the individual has maintained CD4+ T counts over $500/{\mu}l$ from 1989 to 1999. Plasma viral RNA copy was 992 U/ml in 1998. Culture supernatant showed positive from culture days 9. A series of 9 overlapping PCR products were amplified from cultured PBMC and cloned About 9.2 kb from R of 5' LTR to R of 3' LTR was determined by automated sequencing. The G-to-A hypermutations were shown throughout the entire region. As a result of G to A hypermutations, premature stop codon was found in integrase coding region. Though there was no recombination between subtypes over all genomes, TATA box in both LTRs was TAAAA which is detected in subtype E instead of TATAA in subtype B. And, there were nucleotide GC insertion between $NF-{\kappa}B$ I and Sp1 III, and duplication of $TCF-1{\alpha}$ in LTR. We could not find any deletion of amino acid in Nef, Gag, Pol and Env gene. This study is the first report on molecular nature of full genomes of HIV-1 isolated in Korea.

• Journal of Veterinary Science
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• 제23권1호
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• pp.14.1-14.11
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• 2022

Background: Carnivore protoparvovirus 1, also known as canine parvovirus type 2 (CPV-2), is the main pathogen in hemorrhagic gastroenteritis in dogs, with a high mortality rate. Three subtypes (a, b, c) have been described based on VP2 residue 426, where 2a, 2b, and 2c have asparagine, aspartic acid, and glutamic acid, respectively. Objectives: This study examined the presence of CPV-2 variants in the fecal samples of dogs diagnosed with canine parvovirus in Bogotá. Methods: Fecal samples were collected from 54 puppies and young dogs (< 1 year) that tested positive for the CPV through rapid antigen test detection between 2014-2018. Molecular screening was developed for VP1 because primers 555 for VP2 do not amplify, it was necessary to design a primer set for VP2 amplification of 982 nt. All samples that were amplified were sequenced by Sanger. Phylogenetics and structural analysis was carried out, focusing on residue 426. Results: As a result 47 out of 54 samples tested positive for VP1 screening, and 34/47 samples tested positive for VP2 980 primers as subtype 2a (n = 30) or 2b (n = 4); subtype 2c was not detected. All VP2 sequences had the amino acid, T, at 440, and most Colombian sequences showed an S514A substitution, which in the structural modeling is located in an antigenic region, together with the 426 residue. Conclusions: The 2c variant was not detected, and these findings suggest that Colombian strains of CPV-2 might be under an antigenic drift.

• Genomics & Informatics
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• 제17권1호
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• pp.3.1-3.4
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• 2019

Intratumor heterogeneity within a single tumor mass is one of the hallmarks of malignancy and has been reported in various tumor types. The molecular characterization of intratumor heterogeneity in breast cancer is a significant challenge for effective treatment. Using single-cell RNA sequencing (RNA-seq) data from a public resource, an ERBB pathway activated triple-negative cell population was identified. The differential expression of three subtyping marker genes (ERBB2, ESR1, and PGR) was not changed in the bulk RNA-seq data, but the single-cell transcriptomes showed intratumor heterogeneity. This result shows that ERBB signaling is activated using an indirect route and that the molecular subtype is changed on a single-cell level. Our data propose a different view on breast cancer subtypes, clarifying much confusion in this field and contributing to precision medicine.

• 대한약학회:학술대회논문집
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• 대한약학회 2003년도 Proceedings of the Convention of the Pharmaceutical Society of Korea Vol.2-2
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• pp.178.3-178.3
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• 2003

P2X receptors are ligand gated cation channels activated by the binding of extracellular adenosine 5'-triphosphate (ATP) and classified into 7 subtype families. $P2X_1$ receptors are abundantly expressed in smooth muscle mediates blood vessel and mediate constriction upon binding of neuronal ATP. The activation of $P2X_3$ receptor by ATP has been known to initiate the pain signaling in the peripheral nervous system, which is involved in chronic inflammatory nociception and neuropathic pain by nerve injury. (omitted)

• 대한의생명과학회지
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• 제2권1호
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• pp.31-40
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• 1996

비뇨기계 병원성 대장균의 중요한 병원성 인자 중의 하나로 인정되고 있는p-fimbriae의 subtype의 분포를 확인하기 위하여 요로감염증으로 확진된 환자의 혈청을 이용하여 immunoblotting 을 실시하였고, 이와 동시에 효소면역 측정법을 실시하여 p-fimbriae특이 항체 보유를 확인하였다. Immunoblotting 결과 우리나라 요로감염증환자에서 높은 빈도로 확인되는 p-fimbriae subtype의 분포는 $F7_1$34(56.7%), $F7_2$28(46.7%), F13 30(50%)등이 높게 나타났으며, 이와 같은 결과는 효소면역측정법에서도 동일하게 나타났다. 그러나 P-pili를 순수분리하지 않고 whole cell을 이용한 효소면역 측정법은 교차반응 때문에 비뇨기 감염증의 혈청학적인 진단에 적합하지 않는 것으로 나타났다. 또 우리 나라의 요로감염 환자에서 항체 양성율이 높은 $F7_1$, $F7_2$, F13만을 혼합하여 항원으로 이용한 효소면역측정법의 특이도와 민감도가 각각 92.6%, 90%로 나타나, 이와 같은 방법을 임상진단에 응용할 수 있을 것으로 판단되었다.

• 대한바이러스학회지
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• 제27권1호
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• pp.19-27
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• 1997

본 연구에서는 영장류에서 감염성 면역결핍 증상을 일으키는 type D simian retrovirus (SRV)를 검출하기 위해 SRV env 유전자의 특정 지역을 선정하여 증폭, 검색하는 중합효소 연쇄반응 (PCR)법을 개발하였다. 증폭반응의 대상부위인 SRV env 유전자의 3' 후반부는 서로 다른 3 종류의 SRV subtype 1, 2, 그리고 subtype 3에 걸쳐 높은 보존율을 보이고 있다. 반응 결과, 1차 PCR 만으로 3 종류의 SRV subtypes를 동시에 검출, 증폭하였으며 SRV와 더불어 영장류에서 감염성 면역결핍을 유도하는 주요 바이러스 simian immunodeficiency virus 또는 simian T-Iymphotropic virus type 1에 감염된 영장류의 peripheral blood mononuclear cells (PBMCs)을 비교, 완전한 증폭 특이성이 확인되었고 교차반응으로 인한 위양성반응은 발견되지 않았다. 한편, 위 증폭반응의 검출 민감도 측정을 위해 준정량적 적정 PCR을 수행하였으며 SRV 게놈과 증폭 대상 부위의 분자량을 기준으로 한 본 PCR법의 검출 한계는 단 한번의 증폭과 간단한 ethidium bromide 염색만으로 적어도 $5-7{\times}10^4$ 개의 PBMCs 중 한 개의 감염세포를 검출할 수 있는 것으로 확인되었다. 본 연구에서 확인된 신속성과 반응 특이성, 그리고 높은 민감도의 본 PCR 법은 현재 유일한 AIDS 연구모델인 영장류의 SIV 감염 연구 전후에 반드시 필요한 효과적인 SRV 감염검색에서 ELISA법의 위양성에 의한 약점을 보완하고 보다 높은 검출 민감도를 확보함으로써 연구모델 실험의 오류를 최소화하는 데 중요한 역할을 하게 될 것이다.