• The Plant Pathology Journal
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• v.37 no.5
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• pp.476-488
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• 2021

Xanthomonas campestris pv. campestris (Xcc) is the causal agent of black rot for cruciferous vegetables worldwide, especially for the cole crops such as cabbage and cauliflower. Due to the lack of resistant cabbage cultivars, black rot has brought about considerable yield losses in recent years in China. Understanding of the pathogen features is a key step for disease prevention, however, the pathogen diversity, population structure, and virulence are largely unknown. In this study, we studied 50 Xcc strains including 39 Xcc isolates collected from cabbage in 20 regions across China, using multilocus sequence genotyping (MLST), repetitive DNA sequence-based PCR (rep-PCR), and pathogenicity tests. For MLST analysis, a total of 12 allelic profiles (AP) were generated, among which the largest AP was AP1 containing 32 strains. Further cluster analysis of rep-PCR divided all strains into 14 DNA groups, with the largest group DNA I comprising of 34 strains, most of which also belonged to AP1. Inoculation tests showed that the representative Xcc strains collected from diverse regions performed differential virulence against three brassica hosts compared with races 1 and 4. Interestingly, these results indicated that AP1/DNA I was not only the main pathotype in China, but also a novel group that differed from the previously reported type races in both genotype and virulence. To our knowledge, this is the first extensive genetic diversity survey for Xcc strains in China, which provides evidence for cabbage resistance breeding and opens the gate for further cabbage-Xcc interaction studies.

• Journal of Chest Surgery
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• v.53 no.5
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• pp.250-257
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• 2020

Background: Lung adenocarcinoma (LUAD) with ground-glass opacity (GGO) can become aggravated, but the reasons for this aggravation are not fully understood. The goal of this study was to analyze the genetic features and causes of progression of GGO LUAD. Methods: LUAD tumor samples and normal tissues were analyzed using an Illumina HiSeq 4000 system. After the tumor mutational burden (TMB) was calculated, the identified mutations were classified as those found only in GGO LUAD, those present only in nonGGO LUAD, and those common to both tissue types. Ten high-frequency genes were selected from each domain, after which protein interaction network analysis was conducted. Results: Overall, 227 mutations in GGO LUAD, 212 in non-GGO LUAD, and 48 that were common to both tumor types were found. The TMB was 8.8 in GGO and 7.8 in non-GGO samples. In GGO LUAD, mutations of FCGBP and SFTPA1 were identified. FOXQ1, IRF5, and MAGEC1 mutations were common to both types, and CDC27 and NOTCH4 mutations were identified in the non-GGO LUAD. Protein interaction network analysis indicated that IRF5 (common to both tissue types) and CDC27 (found in the non-GGO LUAD) had significant biological functions related to the cell cycle and proliferation. Conclusion: In conclusion, GGO LUAD exhibited a higher TMB than non-GGO LUAD. No clinically meaningful mutations were found to be specific to GGO LUAD, but mutations involved in the epithelial-mesenchymal transition or cell cycle were found in both tumor types and in non-GGO tissue alone. These findings could explain the non-invasiveness of GGO-type LUAD.

• The Journal of Korean Academy of Prosthodontics
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• v.43 no.3
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• pp.393-408
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• 2005

Statement of problem. In the process of bone formation, titanium (Ti) surface roughness is an important factor modulating osteoblastic function. Purpose. This study was carried out to determine the effect of different Ti surface on biologic responses of a human osteoblast-like cell line (MG63). Materials and methods. MG63 cells were cultured on S (smooth), SLA (sandblasted largegrit & acid etching), HA (hydroxyapatite) Ti. The morphology and attachment of the cells were examined by SEM. The cDNAs prepared from total RNAs of MG63 were hybridized to a human cDNA microarray (1,152 elements). Results. The appearances of the surfaces observed with SEM were different in the three types of dental substrates. The surface of SLA and HA were shown to be rougher than S. MG63 cells cultured on SLA and HA were cell-matrix interaction. In the expression of genes involved in osseointegration, upregulated genes were bone morphogenetic protein, Villin, Integrin, Insulin-like growth factors in different surfaces. Downregulated genes were fibroblast growth factor receptor 4, Bcl 2-related protein, collagen, CD4 in different surfaces. Conclusion. The attachment and expression of key osteogenic regulatory genes were enhanced by surface roughness of the dental materials.

• Applied Biological Chemistry
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• v.17 no.2
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• pp.143-148
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• 1974

The interaction of the carcinogenic mycotoxin, Aflatoxin $B_1$, with the electron-donating molecule, benzene, was studied spectrophotometrically. The formation of charge-transfer complex between Aflatoxin $B_1$ and benzene in the presence of zinc chloride was observed and the apparent equilibrium constant of this charge-transfer complex was found to be 0.198 (liter $mole^{-1}$). It is assumed that, as the result of this study, some charge-transfer complexes could be formed between the weak electron-accepting Aflatoxin $B_1$ and strong electron-donating molecules, and the spectral changes occurred in the binding of Aflatoxin $B_1$ with proteins or DNA is attributed to the existence of charge-transfer type interaction.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.16
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• pp.6505-6510
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• 2014

Objective: This study was conducted to identify whether polymorphic variants of set domain-containing protein 8 (SET8) and tumor protein p53 (TP53) codon 72, either independently or jointly, might be associated with increased risk for cervical cancer. Methods: We genotyped SET8 and TP53 codon 72 polymorphisms of peripheral blood DNA from 114 cervical cancer patients and 200 controls using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and direct DNA sequencing. Results: The frequency of SET8 CC (odds ratios (OR) = 2.717, 95% CI=1.436-5.141) or TP53 GG (OR=2.168, 95% CI=1.149-4.089) genotype was associated with an increased risk of cervical cancer on comparison with the SET8 TT or TP53 CC genotypes, respectively. In additional, interaction between the SET8 and TP53 polymorphisms increased the risk of cervical cancer in a synergistic manner, with the OR being 9.913 (95% CI=2.028-48.459) for subjects carrying both SET8 CC and TP53 GG genotypes. Conclusion: These data suggest that there are significant associations between the miR-502-binding site SNP in the 3'-UTR of SET8 and the TP53 codon 72 polymorphism with cervical cancer in Chinese, and there is a gene-gene interaction.

• Animal cells and systems
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• v.7 no.2
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• pp.139-144
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• 2003

We analyzed seven Y chromosome binary markers (YAP, RPS4Y_711,\;M9,\;M175,\;LINE1,\;SRY_+465$ and 47z) in samples from a total of 254 males from Koreans and tow Mongolian ethnic groups (Buryat and Khalkh) to study the genetic relationship among these populations. We found eight distinct Y haplogroups constructed from the seven binary markers. Haplogroup DE-YAP was present at extremely low frequencies (∼2%) in the Korean and Mongolian populations. This result is consistent with earlier reports that showed the YAP+ chromosomes to be highly polymorphic only in populations from Japan and Tibet in east Asia. The observed high frequency of haplogroup $C-RPS4Y_711$ in the Mongolian populations (∼40%) is concordant with recent findings, showing that the $RPS4Y_711$-T chromosomes were distributed at high frequencies in Siberian and Mongolian populations compared with most other populations from east Asia. Thus, the relatively moderate frequency of haplogroup $C-RPS4Y_711$ in Korean (∼15%) can be seen as genetic evidence for probable interaction with Mongolian and/or Siberian populations. In contrast, the majority (∼75%) of modern Koreans studied here had high frequencies of Y chromosome lineages of haplogroup O-M175 and additional haplogroupts that define sublineage of O-M175, which are most likely related with modern populations in China. In conclusion, our data on the Y chromosome haplogroup distribution may provide evidence for interaction between Korean and Mongolian populations, but Korean tend to be much more related with those from southern-to-northern populations of China than to Mongolians in east Asia.

• 한국균학회소식:학술대회논문집
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• 2016.05a
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• pp.27-27
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• 2016

The ascomycete fungus Fusarium graminearum is the most common pathogen of Fusarium head blight (FHB), a devastating disease for major cereal crops worldwide. FHB causes significant crop losses by reducing grain yield and quality as well as contaminating cereals with trichothecenes and zearalenone (ZEA) that pose a serious threat to animal health and food safety. ZEA is a causative agent of hyperestrogenic syndrome in mammals and can result in reproductive disorders in farm animals. In F. graminearum, the ZEA biosynthetic cluster is composed of four genes, PKS4, PKS13, ZEB1, and ZEB2, which encode a reducing polyketide synthase, a nonreducing polyketide synthase, an isoamyl alcohol oxidase, and a transcription factor, respectively. Although it is known that ZEB2 primarily acts as a regulator of ZEA biosynthetic cluster genes, the mechanism underlying this regulation remains undetermined. In this study, two isoforms (ZEB2L and ZEB2S) from the ZEB2 gene in F. graminearum were characterized. It was revealed that ZEB2L contains a basic leucine zipper (bZIP) DNA-binding domain at the N-terminus, whereas ZEB2S is an N-terminally truncated form of ZEB2L that lacks the bZIP domain. Interestingly, ZEA triggered the induction of both ZEB2L and ZEB2S transcription. In ZEA producing condition, the expression of ZEB2S transcripts via alternative promoter usage was directly or indirectly initiated by ZEA. Physical interaction between ZEB2L and ZEB2L as well as between ZEB2L and ZEB2S was observed in the nucleus. The ZEB2S-ZEB2S interaction was detected in both the cytosol and the nucleus. ZEB2L-ZEB2L oligomers activated ZEA biosynthetic cluster genes, including ZEB2L. ZEB2S inhibited ZEB2L transcription by forming ZEB2L-ZEB2S heterodimers, which reduced the DNA-binding activity of ZEB2L. This study provides insight into the autoregulation of ZEB2 expression by alternative promoter usage and a feedback loop during ZEA production.

• Korean Journal of Veterinary Research
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• v.15 no.1
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• pp.57-67
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• 1975

The poxvirus group is considered to be a typical cytoplasmic inclusion forming virus. Every poxvirus has been reported to produce only one kind of inclusion in the infected tissues. A vague concept that inclusions of poxviruses are eosinophilic or acidophilic has prevailed. Although many papers and theories about the nature of the inclusion have been presented, most of them are not quite convincing on the point of the relations with virus multiplication, and an analysis of papers published showed that there seem to be many discrepancies in the descriptions of the nature of the poxvirus inclusions. Comparative studies on host-virus interaction with cowpox, orf, swinepox and fowlpox viruses which selected from each Group (I-IV) of poxviruses were performed from the morphological and virological standpoints. At first, in cowpox virus-FL cell system, as a comparative model, cytoplasmic inclusion, nucleic acid metabolism by autoradiography and detection of viral antigen by immunofluorescence were studied and obtained the results as follows: 1. The focus-like cytopathic effect (CPE) at early stage developed to entire culture at terminal stage of infection, and also the developing status of CPE was correlated to viral doses for inoculation. Two kinds of cytoplasmic inclusions which named A and B type were easily observed by Giemsa, hematoxylin-eosin (H & E) and May-Greenwald Giemsa (MGG) stainings in the infected cells. The B type inclusions were formed at early stage of infection and the A type inclusions were produced subsequently the B type formation. The B type which common type inclusion in poxviruses was a small compact or aggregate at early stage and developed to a large diffuse body at terminal stage of infection. On the other hand, the A type inclusion which depend upon the kind of virus was appeared as round and discrete shape, and its size and number was increased gradually during the culture period. It was characteristic to form distinct halos around the both types of inclusions in acid fixed, H & E stained preparations of infected cultures. The B type inclusion was always positive in Feulgen reaction and showed as DNA containing body but the A type inclusion was not. 2. In the relationship between inclusion and DNA metabolism of infected cells by the qualitative autoradiography using 3H-thymidine, the appearance of silver grains was coincided with B type inclusion but not with A type inclusion. This showed that the DNA synthesis was proceeded in all B type inclusions except those in the terminal stage with a diffuse form. This suggested that the B type inclusions are only sites of DNA synthesis and this was proceeded after the cell infection independently. The activity of DNA synthesis of the inclusions was nearly the same as that of the nucleic of normal cells and non-inclusion bearing cells. and non-inclusion bearing cells. Regardless of the size of the degree of DNA synthesis of the B type inclusion, inclusion bearing cells all showed remarkable suppression of nuclear DNA synthesis. 3. By the direct fluorescent antibody technique viral antigen in infected cells was detected. The B type inclusions have been proved to contain a great deal of viral antigen, whereas the basic substance of A type inclusion did not show antigenicity except the round edge. It was suggested that the round edge fluorescence might be caused by the glare of cytoplasmic viral antigen which pushed out and concentrated by the A type inclusion development. 4. Hemorrhagic red pock formations on chorioallantoic membrane of embryonated chicken egg had proved the characteristic of used viral strain. 5. By the above studies on the nature of two types of inclusions and the role they play in virus multiplication, it was concluded that the B type inclusion must be the site of the synthesis of viral DNA and protein as well as the site of the virus.

• Journal of Life Science
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• v.15 no.4 s.71
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• pp.542-547
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• 2005

Hypersensitivity of cells lacking Brcal to DNA interstrand .ross-link (ICL) agents such as cisplatin and mitomycin C(MMC) implicates the important role of Brcal in cellular response following ICL treatment. Brca1 plays an essential role in DNA double-strand break (DSB) repair through homologous recombination (HR)-dependent and -independent process. Recently, our group has been reported that Brca1 involves in cellular ICL response through HR-dependent repair process (Yun J. et at., Oncogene 2005). In this report, the involvement of Brca1 protein in HR-independent repair process is examined using isogenic $p53^{-/-}\;and\;p53^{-/-}\;Brcal^{-/-}$ mouse embryonic fibroblast (MEF) and psoralen cross-linked reporter reactivation assay. Brcal-deficient MEFs showed significantly low HR-independent repair activity compare to Brca1-proficient MEFs. Hypersensitivity to MMC and ICL reporter repair activity were restored by the reconstitution of Brca1 expression. Interestingly, MEFs expressing exon 11-deleted isoform of Brca1 $(Brca1^{\Delta11/\Delta11})$ showed high resistance to MMC and ICL reporter repair activity comparable to Brca1-reconstituted MEFs. Taken together, these results suggest that Brca1 involves in ICL repair through not only HR-dependent process but also HR-independent process using N-terminal RINC finger domain or C-terminal BRCT domain rather than exon 11 region which mediate interaction with Rad50.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.13
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• pp.5311-5317
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• 2015

Cigarette smoke derivatives like NNK (4-(Methylnitrosamino)-1-(3-pyridyl)-1-butanone) and NNAL (4-(methylnitrosamino)-1-(3-pyridyl)-1-butan-1-ol) are well-known carcinogens. We analyzed the interaction of enzymes involved in the NER (nucleotide excision repair) pathway with ligands (NNK and NNAL). Binding was characterized for the enzymes sharing equivalent or better interaction as compared to +Ve control. The highest obtained docking energy between NNK and enzymes RAD23A, CCNH, CDK7, and CETN2 were -7.13 kcal/mol, -7.27 kcal/mol, -8.05 kcal/mol and -7.58 kcal/mol respectively. Similarly the highest obtained docking energy between NNAL and enzymes RAD23A, CCNH, CDK7, and CETN2 were -7.46 kcal/mol, -7.94 kcal/mol, -7.83 kcal/mol and -7.67 kcal/mol respectively. In order to find out the effect of NNK and NNAL on enzymes involved in the NER pathway applying protein-protein interaction and protein-complex (i.e. enzymes docked with NNK/NNAL) interaction analysis. It was found that carcinogens are well capable to reduce the normal functioning of genes like RAD23A (HR23A), CCNH, CDK7 and CETN2. In silico analysis indicated loss of functions of these genes and their corresponding enzymes, which possibly might be a cause for alteration of DNA repair pathways leading to damage buildup and finally contributing to cancer formation.