• BMB Reports
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• 제45권6호
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• pp.365-370
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• 2012

Hepatitis B virus (HBV) DNA is often integrated into hepatocellular carcinoma (HCC). Although the relationship between HBV integration and HCC development has been widely studied, the role of HBV integration in HCC development is still not completely understood. In the present study, we constructed a pooled BAC library of 9 established cell lines derived from HCC patients with HBV infections. By amplifying viral genes and superpooling of BAC clones, we identified 2 clones harboring integrated HBV DNA. Screening of host-virus junctions by repeated sequencing revealed an HBV DNA integration site on chromosome 11q13 in the SNU-886 cell line. The structure and rearrangement of integrated HBV DNA were extensively analyzed. An inverted duplicated structure, with fusion of at least 2 HBV DNA molecules in opposite orientations, was identified in the region. The gene expression of cancer-related genes increased near the viral integration site in HCC cell line SNU-886.

• 대한의생명과학회지
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• 제7권4호
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• pp.167-172
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• 2001

Nebulin is an approximately 700 kDa filamentous protein in vertebrate skeletal muscle. It binds to the Z line and also binds side-by-side to the entire thin actin filament in a sarcomere. The correlation of nebulin size with thin filament length have led to the suggestion that nebulin acts as a molecular ruler for the length of thin filaments. The C-terminal part of human nebulin is anchored in the sarcomeric Z-disk and contains an SH3 domain. SH3 domains have been identified in an ever-increasing number of proteins important for a wide range of cellular processes, from signal transduction to cytoskeleton assembly and membrane localization. However, the exact physiological role of SH3 domains remains, in many cases, unclear. To explore the role of nebulin SH3 in the cytoskeletal rearrangement that accompanies myoblast differentiation, we transfected sense and antisense nebulin SH3 domain fused to enhanced green fluorescent protein in myoblast. Cells expressing nebulin SH3 fragment showed decrease of cell-cell adhesion, and cells transfected with antisense nebulin SH3 gene showed a rounded cell morphology and loss of cell-matrix adhesion. No alteration in cell shape and differentiation were observed in control cells expressing enhanced green fluorescent protein. Perturbation of nebulin altered the cell shape and disrupted cell adhesion in myoblast, demonstrating that nebulin can affect cytoskeleton rearrangement.

• ALGAE
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• 제38권4호
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• pp.253-264
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• 2023

The Ceramiales is the most diverse and species-rich group (2,669 spp.) of red algae, and it is widely distributed from tropical to polar oceans. Mitochondrial genomes (mitogenomes) and other genes have contributed to our knowledge regarding the classification and phylogeny of this diverse red algal group; however, the mitogenome architecture remains understudied. Here, we compared 42 mitogenomes, including 19 newly generated in this study, to expand our knowledge. The number of genes in mitogenome varied from 43 to 68 due to gene duplication. The mitogenome architecture was also variable, categorized into four types (A-D): type A = ancestral type with a basic composition; type B = those with inverse transpositions; type C = those with inverted duplications; and type D = those with both inversion and duplication. The palindromic and inverted repeats were consistently found in flanking regions of the rearrangement, especially near the cob and nad6 genes. The three rearranged mitogenome architectures (types B, C, D) are the first report of these in red algae. Phylogenetic analyses of 23 protein-coding genes supported the current familial classification of the Ceramiales, implying that the diversity of mitogenome architecture preceded the phylogenetic relationships. Our study suggests that palindromic and inverted repeats may drive mitogenome architectural variation.

• ALGAE
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• 제17권1호
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• pp.53-58
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• 2002

The transition of plant life from aquatic algae to land to land plants was one of the major events in the history of life. However, in hypothesizing the exact evolutionary path of the transition, limited shared phenotypic characters in aquatic algae and land plants (embryophytes) have been a major hinderance. Chloroplast genomes contain characters useful in tracing evolutionary histories. Embryophyte chloroplast genomes are distinguished from algal cpDNAs by having over 20 group Ⅱ introns, some of which were gained during the transition from algae to embryophytes (Manhart and Palmer 1990; Lew and Manhart 1993;Lee and Manhart 2002). Here we examine a gene cluster that, in land plants, contains psbB, psbT, psbH, petB and petD with introns found in petB and petD (petB.i and petD.i). In addition the presence/absence of introns in trnA and trnI (trnA.i and trnI.i) were determined in all five major lineages of charophytes. We found that the psbB gene cluster occurs in most surveyed charophytes and embryophytes except Spirogyra (Zygnematales) which lacks it due to intra-genomic rearrangement. All four introns are absent in Chlorokybus but present in some or all of the other four charophyte lineages (Klebsormidiales, Zygnematales, Coleochaetales, and Charales). In addition, Chlorokybus is distinguished from other charophytes and embryophytes by having an unusually long spacer (over 2 kb) between psbH-petB. The results indicate that Chlorokybus diverged before the intron gains but after psbB gene cluster formation, placing the other charophyte lineages closer to embryophytes.

• Molecules and Cells
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• 제23권2호
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• pp.182-191
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• 2007

The complete mitochondrial genome of a troglobite millipede Antrokoreana gracilipes (Verhoeff, 1938) (Dipolopoda, Juliformia, Julida) was sequenced and characterized. The genome (14,747 bp) contains 37 genes (2 ribosomal RNA genes, 22 transfer RNA genes and 13 protein-encoding genes) and two large non-coding regions (225 bp and 31 bp), as previously reported for two diplopods, Narceus annularus (order Spirobolida) and Thyropygus sp. (order Spirostreptida). The A + T content of the genome is 62.1%, and four tRNAs ($tRNA^{Ser(AGN)}$, $tRNA^{Cys}$, $tRNA^{Ile}$ and $tRNA^{Met}$) have unusual and unstable secondary structures. Whereas Narceus and Thyropygus have identical gene arrangements, the $tRNA^{Thr}$ and $tRNA^{Trp}$ of Antrokoreana differ from them in their orientations and/or positions. This suggests that the Spirobolida and Spirostreptida are more closely related to each other than to the Dipolopoda. Three scenarios are proposed to account for the unique gene arrangement of Antrokoreana. The data also imply that the Duplication and Nonrandom Loss (DNL) model is applicable to the order Julida. Bayesian inference (BI) and maximum likelihood (ML) analyses using amino acid sequences deduced from the 12 mitochondrial protein-encoding genes (excluding ATP8) support the view that the three juliformian members are monophyletic (BI 100%; ML 100%), that Thyropygus (Spirostreptida) and Narceus (Spirobolida) are clustered together (BI 100%; ML 83%), and that Antrokoreana (Julida) is a sister of the two. However, due to conflict with previous reports using cladistic approaches based on morphological characteristics, further studies are needed to confirm the close relationship between Spirostreptida and Spirobolida.

• IMMUNE NETWORK
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• 제1권3호
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• pp.236-243
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• 2001

Background: An immunological approach for aging mechanism appears to be important. Lymphocyte subsets analysis in peripheral blood is widely performed to assess the immune status and to diagnose and monitor various diseases. Some lymphocyte subsets are known to change with age, but only few data about age-related reference ragnes for these subsets in healthy individuals have been reported. So we attempted to report reference ranges for these subsets in each age group and review changes of the results with age for the secondary studies about immune cell function as lymphocyte blast transformation and immunoglobulin gene rearrangement (VDJ) including recombination activating genes (RAG-1 and RAG-2). Methods: Lymphocyte subset analysis was performed on 302 subjects, 189 males and 113 females with age group of all decades of life. Two color direct immunofluorescene flow cytometry (FCM) was done using $Simultest^{TM}$ IMK-Lymphocyte kit (Becton Dickinson, USA), $FACScan^{TM}$ (Becton Dickinson, USA) and $FACSCalibur^{TM}$ (Becton Dickinson, USA). Lymphocyte subsets analysed were T ($CD3^+$) and B cells ($CD19^+$), helper/inducer T ($CD4^+$) and suppressor/cytotoxic T cells ($CD8^+$), helper/suppressor ($CD4^+/CD8^+$) ratio and natural killer (NK) cells ($CD3^-CD16^+/CD56^+$). The absolute numbers of each subset were calculated from total lymphocyte counts. Data collected was analysed using SAS 6.12. A P-value of < 0.05 was considered significant. Results: We reported the counts and percentages of lymphocyte and these subsets in each age group. There were no statistically significant differences between male and female subjects. The percentage of $CD4^+$ T cells, and the count of NK cells did not show the significant difference among the various age groups. The age-related changes observed in our study were as following: 1) a decrease in the percentages of T cells, B cells and $CD8^+$ T cells ; 2) a decrease in the counts of B cells and $CD8^+$ T cells ; 3) an increase in the percentage and count of NK cells ; and 4) an increase in the $CD4^+/CD8^+$ ratio. Conclusion: The characteristics of aging process appeared to be showing a marked decrease of lympocyte subsets T and B cells as well as T8 ($CD8^+$). The age-related increase of the percentage of cells bearing NK marker can be interpreted as a compensatory consequence to cope with the decrease of T cells related to the thymic involution. These changes with age appeared to be for the secondary study about immune cell function as lymphocyte blast transformation and immunoglobulin gene rearrangement.

• Journal of the Korean Association of Oral and Maxillofacial Surgeons
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• 제26권4호
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• pp.355-362
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• 2000

Neoplastic growth is characterized by alterations of oncogenes and antioncogenes. The interaction between activated oncogenes and functional deletion of antioncogene appears to be the driving force directing normal cells to uncontrolled growth resulting in tumor. In addition to those genes mentioned, other genes controlling the entry of cells into the cell cycle have recently been implicated in cancer development. The overexpression of the cyclin D1 gene, which has been mapped to 11q13, either by gene rearrangement or amplification has been noted in various malignant tumors. The product of the cyclin D1 gene forms a complex with cyclin-dependent protein kinases(CDK4) that governs a key transition in the cell cycle. The relationships between the overexpression of cyclin D1 assessed by immunihistochemistry and the amplification of the cyclin D1 gene by differential polymerase chain reaction(DPCR) using primers for dopamin D2 receptor gene in 13 cases of squamous cell carcinomas of the oral cavity have been studied. The semiquantitative assay of cyclin D1 amplification has been made by cyclin D1/dopamin D2 receptor(CD/DR) ratio. The results were as follows; 1. In the normal tissue and the tumor, the CD/DR ratios were 0.82 and 1.36 respectively. This implicates 1.65-fold amplification of cyclin D1 gene in tumor compared to that in normal tissue. 2. The tumor tissue which showed overexpression of cyclin D1 by immunohistochemistry revealed 2-fold amplification of cyclin D1 compared to the normal tissue. 3. The tumor tissue which showed mild expression of cyclin D1 by immunihistochemistry revealed 1.7-fold amplification of cyclin D compared to the normal tissue. 4. The cyclin D1 was overexpressed in the tumor tissue at the rate of 38%. Above results suggest that cyclin D1 has close correlation with the development of carcinoma in the oral cavity. But further studies were needed to elucidate the carcinogeneic mechanisms by comparative studies among cyclin D1, pRb and p53.

• 대한임상검사과학회지
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• 제48권4호
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• pp.371-377
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• 2016

탈회방법은 골수조직의 병리학적 진단을 위해서 항상 시행되는 과정이다. HCl 탈회용액과 같이 주로 사용하고 있는 산성용액은 탈회과정 동안에 조직내의 항원성에 손상을 입힌다. 특히, 골수조직 내의 RNA나 DNA에 심하게 손상을 준다. 따라서 조직의 항원성을 보존하기 위한 표준화된 탈회방법이 필요하다. 본 연구는 일반적으로 가장 많이 사용되는 HCl 기반의 상품화된 탈회용액과 직접 제조한 EDTA 탈회용액이 골수조직의 탈회과정에 어떤 영향을 미치는지 분석하였다. 환자로부터 채취된 73예의 골수생검조직을 HCl 탈회와 EDTA 탈회의 두 그룹으로 나누어 탈회과정을 진행하였다. 골수생검조직의 탈회과정 후 결과의 차이는 hematoxylin & eosin 염색과 reticulum 염색, Ki-67, CD20, CD138의 항체를 이용한 면역조직화학염색, DNA 추출 및 분석, in situ hybridization, IGH gene rearrangement 와 같은 분자병리검사를 시행하여 분석하였다. 일반적인 염색과 특수염색에서는 두 탈회용액간의 차이는 없었다. 또한 세포증식 표지자와 같은 세포막 혹은 세포질에서 발현되는 항체는 탈회용액간의 차이 없이 잘 염색되었다. 반면 HCl 탈회 용액에 처리한 후 핵 내 단백질인 Ki-67의 염색상은 현저히 불량한 것으로 관찰되었다. HCl 탈회용액과 비교하여 EDTA 탈회용액에서의 골수생검조직 내의 DNA와 RNA가 잘 보존되었음을 다양한 분자병리검사를 통해 확인할 수 있었다. 특히 HCl 탈회용액에 처리한 28예와 EDTA 탈회용액에 처리한 12예의 DNA의 순도와 농도을 비교한 결과 통계학적으로 유의한 수준으로 차이가 있음을 확인하였다. 이로써 EDTA 탈회용액이 조직 내의 항원성을 잘 유지시키며, 면역조직화학염색과 분자병리검사에 적합한 방법임을 확인 할 수 있었다.

• Molecules and Cells
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• 제22권3호
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• pp.314-322
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• 2006

The whole mitochondrial genome (14,915 nt) of Pollicipes mitella (Crustacea, Maxillopoda, Cirripedia, Thoracica) was sequenced and characterized. It is the shortest of the 31 completely sequenced crustacean mitochondrial genomes, with the exception of a copepod Tigriopus japonicus (14,628 nt). It consists of the usual 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 relatively short non-coding region (294 nt). The thoracican cirripeds apart from Megabalanus volcano have the same arrangement of protein-coding genes as Limulus polypemus, but there are frequent tRNA gene translocations (at least 8). Some interesting translocation features that may be specific to the thoracican cirriped lineage are as follows: 1) trnK-trnQ lies between the control region and trnI, 2) trnA-trnE lies between trnN and trnS1, 3) trnP lies between ND4L and trnT, and 4) trnY-trnC lies between trnS2 and ND1. In P. mitella there are two trnL genes (L1 and L2) in the typical crustacean positions (ND1-L1-LrRNA and CO1-L2-CO2). The present result is compared and discussed with the other three cirriped mitochondrial genomes from one pedunculate (Pollicipes polymerus) and two sessiles (Tetraclita japonica and M. volcano) published so far. Mitochondrial protein phylogenies reconstructed by the BI and ML algorithms show that the thoracican Cirripedia is monophyletic (BPP 100/BP 100) and associated with Remipedia (BPP 98/BP 35). In addition, Oligostraca, including Ostracoda, Branchiura, and Pentastomida, is a monophyletic group (BPP 99/BP 68), and is basal to all the other examined arthropods. Remipedia + Cirripedia appears as an independent lineage within Arthropoda, apart from Thoracopoda (Malacostraca, Branchiopda, and Cephalocarida). The Thoracopoda is paraphyletic to Hexapoda. The present result suggests that the monophylies of Crustacea and Maxillopoda should be reconsidered.

• 한국임상수의학회지
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• 제29권1호
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• pp.98-102
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• 2012

A 1.5-year-old male Golden Retriever was presented with worsening lameness of two month duration. Abnomral findings of blood works and serum chemistry included anemia, thrombocytopenia, hypercalcemia and hyperglobulinemia. Radiography revealed osteolysis of polyostotic regions including right femur and tibia, bilateral ilium, and spinous processes from the 13th thoracic vertebra to 5th lumbar vertebra. Enlarged multiple lymph nodes and mixed echo pattern of muscular region ventral to vertebra were observed with ultrasonography. Because concentrations of both parathyroid hormone and parathyroid hormone related peptide were all within reference ranges, humoral hypercalcemia by tumor was ruled out and extensive osteolysis was considered as the cause of hypercalcemia. Based on radiographic and ultrasonographic study, lymphoma, multiple myeloma and osteomyelitis were included in differential diagnosis. Fungal serologic test was negative. Monoclonal gammopathy was not found on serum protein electrophoresis. Cytological and histopathological examinations of the lytic lesions revealed neoplastic lymphoid proliferation, and B cell type clonal expansion was detected by polymerase chain reaction for the antigen receptor gene rearrangement. The case was diagnosed as B cell lymphoma involving polyostotic regions.