• 방사선산업학회지
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• 제10권1호
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• pp.7-12
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• 2016

Ikaros, a transcription factor containing zinc-finger motif, has known as a critical regulator of hematopoiesis in immune system. Ikaros protein modulates the transcription of target genes via binding to the regulatory elements of the genes promoters. However the regulatory function of Ikaros in other organelle except nuclear remains to be determined. This study explored radiation-induced modulatory function of Ikaros in cytoplasm. The results showed that Ikaros protein lost its DNA binding ability after LDIR (low-dose ionizing radiation) exposure. Cell fractionation and Western blot analysis showed that Ikaros protein was translocated into cytoplasm from nuclear by LDIR. This was confirmed by immunofluorescence assay. We identified Autotaxin as a novel protein which potentially interacts with Ikaros through in vitro protein-binding screening. Co-immunoprecipitation assay revealed that Ikaros and Autotaxin are able to bind each other. Autotaxin is a crucial enzyme generating lysophosphatidic acid (LPA), a phospholipid mediator, which has potential regulatory effects on immune cell growth and motility. Our results indicate that LDIR potentially regulates immune system via protein-protein interaction of Ikaros and Autotaxin.

• Mycobiology
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• 제49권3호
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• pp.223-234
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• 2021

Itajahya rosea was found growing in association with Leucaena leucocephala plants at Savitribai Phule Pune University campus in India. The species identity was confirmed by phylogenetic analysis based on ITS and LSU regions of rDNA, wherein, our fugus was placed along with I. rosea in phylogenetic tree. It represents first record of I. rosea from India. Frequent visitation by Drosophila species on I. rosea fruiting body particularly on gleba was observed. The Drosophila got attracted to the detached gleba under the laboratory conditions and even sometimes, they prefer to sit over the gleba as compare to their food banana. It suggested that I. rosea gleba or pseudostipe produces some compounds for attraction and feeding behavior of Drosophila species. Therefore, we characterized the volatile attractants produced by gleba and pseudostipe of I. rosea by GC-MS analysis. Nineteen compounds were identified from gleba while nine compounds were recovered from the pseudostipe. Out of them, blends of three abundant odor producing volatile compounds were reported namely, Hexadecane, Pentadecane and Nonadecane, which are responsible for attraction of Drosophila toward the gleba. Three fatty acids namely 9,12-octadecadienoic acid (Z,Z), hexadecanoic acid and benzoic acid ethyl ester produced are served as an appetitive signal through olfactory response of Drosophila, so the flies were feed on the gleba. Two pheromones' compounds, heneicosane and (+)-(5S,9S)-5,9-dimethylpentadecane, were also reported in pseudostipe and gleba, respectively, which play a role in Drosophila for breeding. Our study highlights an intriguing chemical ecology of fungus-Drosophila interaction.

• The Plant Pathology Journal
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• 제35권3호
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• pp.257-273
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• 2019

Tomato (Solanum lycopersicum) is one of the most widely grown and economically important vegetable crops in the world. Tomato chlorosis virus (ToCV) is one of the recently emerged viruses of tomato distributed worldwide. ToCV-tomato interaction was investigated at the molecular level for determining changes in the expression of tomato genes in response to ToCV infection in this study. A cDNA library enriched with genes induced in response to ToCV infection were constructed and 240 cDNAs were sequenced from this library. The macroarray analysis of 108 cDNAs revealed that the expression of 92 non-redundant tomato genes was induced by 1.5-fold or greater in response to ToCV infection. The majority of ToCV-induced genes identified in this study were associated with a variety of cellular functions including transcription, defense and defense signaling, metabolism, energy, transport facilitation, protein synthesis and fate and cellular biogenesis. Twenty ToCV-induced genes from different functional groups were selected and induction of 19 of these genes in response to ToCV infection was validated by RT-qPCR assay. Finally, the expression of 6 selected genes was analyzed in different stages of ToCV infection from 0 to 45 dpi. While the expression of three of these genes was only induced by ToCV infection, others were induced both by ToCV infection and wounding. The result showed that ToCV induced the basic defense response and activated the defense signaling in tomato plants at different stages of the infection. Functions of these defense related genes and their potential roles in disease development and resistance to ToCV are also discussed.

• Molecules and Cells
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• 제45권6호
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• pp.413-424
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• 2022

Suppressor of mothers against decapentaplegic homolog (SMAD) 4 is a pluripotent signaling mediator that regulates myriad cellular functions, including cell growth, cell division, angiogenesis, apoptosis, cell invasion, and metastasis, through transforming growth factor β (TGF-β)-dependent and -independent pathways. SMAD4 is a critical modulator in signal transduction and functions primarily as a transcription factor or cofactor. Apart from being a DNA-binding factor, the additional SMAD4 mechanisms in tumor suppression remain elusive. We previously identified methyl malonyl aciduria cobalamin deficiency B type (MMAB) as a critical SMAD4 binding protein using a proto array analysis. This study confirmed the interaction between SMAD4 and MMAB using bimolecular fluorescence complementation (BiFC) assay, proximity ligation assay (PLA), and conventional immunoprecipitation. We found that transient SMAD4 overexpression down-regulates MMAB expression via a proteasome-dependent pathway. SMAD4-MMAB interaction was independent of TGF-β signaling. Finally, we determined the effect of MMAB downregulation on cancer cells. siRNA-mediated knockdown of MMAB affected cancer cell metabolism in HeLa cells by decreasing ATP production and glucose consumption as well as inducing apoptosis. These findings suggest that SMAD4 controls cancer cell metabolism by regulating MMAB.

• Biomolecules & Therapeutics
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• 제30권6호
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• pp.593-602
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• 2022

The human papillomavirus (HPV)-18 E7 (E7) oncoprotein is a major transforming protein that is thought to be involved in the development of cervical cancer. It is well-known that E7 stimulates tumour development by inactivating pRb. However, this alone cannot explain the various characteristics acquired by HPV infection. Therefore, we examined other molecules that could help explain the acquired cancer properties during E7-induced cancer development. Using the yeast two-hybrid (Y2H) method, we found that the Elk-1 factor, which is crucial for cell proliferation, invasion, cell survival, anti-apoptotic activity, and cancer development, binds to the E7. By determining which part of E7 binds to which domain of Elk-1 using the Y2H method, it was found that CR2 and CR3 of the E7 and parts 1-206, including the ETS-DNA domain of Elk-1, interact with each other. As a result of their interaction, the transcriptional activity of Elk-1 was increased, thereby increasing the expression of target genes EGR-1, c-fos, and E2F. Additionally, the colony forming assay revealed that overexpression of Elk-1 and E7 promotes C33A cell proliferation. We expect that the discovery of a novel E7 function as an Elk-1 activator could help explain whether the E7 has novel oncogenic activities in addition to p53 inactivation. We also expect that it will offer new methods for developing improved strategies for cervical cancer treatment.

• 환경생물
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• 제21권2호
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• pp.194-202
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• 2003

남조류의 대발생이 자주 발생하는 석촌호수와 팔당호로부터 시료를 채취하여 남조류 분해세균의 분리를 시도하였다. MDM배지 상에서 Anabaena cylindrica를 숙주로 하는 over-layer method를 이용하여 Anabaena cylindrica lawn에서 남조류 분해 세균을 분리하여 HY0210-AK1으로 명명하였다. HY0210-AK1의 형태적, 생화학적 특성은 Rhizobium속과 유사하였으며, 16S rDNA 염기서열을 분석한 결과 Sphingobium herbicido vorans IFO 16415$^{T}$ 와 99.1%의 높은 유연관계를 보여 Sphingobium herbicidovorans HY0210-AK1로 동정하였다. 잠복기, 대수성장기, 정체기에 있는 Sphingobium herbicidovorans HY0210-AK1를 Anabaena cylindrica NIES-19와 혼합 배양하였을 때, 접종 초기에는 정체기의 Sphingobium herbicidovorans HY0210-AK1를 접종한 처리구에서 가장 좋은 살조 효과를 나타냈으나, 접종 7일 이후에는 커다란 차이를 보이지 않았다 또한,Sphingobium herbicidovorans HY0210-AK1는 $1\times 10^{8}$ CFU $ml^{-1}$ 이상의 농도로 처리하였을 때, Anabaena cylindrica NIES-19가 완전히 분해되었다. Sphingo bium herbicidovorans HY0210-AK1와 Anabaena cylin dricaNIES-19를 혼합 배양한 상등액을 여과하여 접종 하였을때는 납조류 성장 저해 효과가 나타나지 않았다. 따라서 Sphingobium herbicidovorans HY0210-AK1는 Anabaena cylindrica NIES-19를 직접 공격하여 분해하는 것으로 사료된다. Sphingobium herbicidovorans HY0210-AK1는 Microcystis aeruginosa 분해하였다..

• 한국미생물생명공학회:학술대회논문집
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• 한국미생물생명공학회 2001년도 Proceedings of 2001 International Symposium
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• pp.83-89
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• 2001

Recent advances in the structural and molecular biology uncovered that a set of translation factors resembles a tRNA shape and, in one case, even mimics a tRNA function for deciphering the genetic ：ode. Nature must have evolved this 'art' of molecular mimicry between protein and ribonucleic acid using different protein architectures to fulfill the requirement of a ribosome 'machine'. Termination of protein synthesis takes place on the ribosomes as a response to a stop, rather than a sense, codon in the 'decoding' site (A site). Translation termination requires two classes of polypeptide release factors (RFs)： a class-I factor, codon-specific RFs (RFI and RF2 in prokaryotes; eRFI in eukaryotes), and a class-IT factor, non-specific RFs (RF3 in prokaryotes; eRF3 in eukaryotes) that bind guanine nucleotides and stimulate class-I RF activity. The underlying mechanism for translation termination represents a long-standing coding problem of considerable interest since it entails protein-RNA recognition instead of the well-understood codon-anticodon pairing during the mRNA-tRNA interaction. Molecular mimicry between protein and nucleic acid is a novel concept in biology, proposed in 1995 from three crystallographic discoveries, one, on protein-RNA mimicry, and the other two, on protein-DNA mimicry. Nyborg, Clark and colleagues have first described this concept when they solved the crystal structure of elongation factor EF- Tu：GTP：aminoacyl-tRNA ternary complex and found its overall structural similarity with another elongation factor EF-G including the resemblance of part of EF-G to the anticodon stem of tRNA (Nissen et al. 1995). Protein mimicry of DNA has been shown in the crystal structure of the uracil-DNA glycosylase-uracil glycosylase inhibitor protein complex (Mol et al. 1995; Savva and Pear 1995) as well as in the NMR structure of transcription factor TBP-TA $F_{II}$ 230 complex (Liu et al. 1998). Consistent with this discovery, functional mimicry of a major autoantigenic epitope of the human insulin receptor by RNA has been suggested (Doudna et al. 1995) but its nature of mimic is. still largely unknown. The milestone of functional mimicry between protein and nucleic acid has been achieved by the discovery of 'peptide anticodon' that deciphers stop codons in mRNA (Ito et al. 2000). It is surprising that it took 4 decades since the discovery of the genetic code to figure out the basic mechanisms behind the deciphering of its 64 codons.

• 한국동물학회지
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• 제31권1호
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• pp.49-55
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• 1988

SV80와 같은 SV40로 형질전환된 사람세포는 종양을 일으킬 수 있는 능력을 가지고 있으나 면역기구인 흉선이 없는 누드마우스에서는 거부반응을 일으켜 종양을 일으키지 않는다. 그러나, 예외적으로 WI18/VA-2세포는 누드마우스에서 종양을 일으키며 이에서 얻는 두클론중 NW18C11은 종양을 일으키나 NW18C12는 종양을 일으키지 않는다. 본 실험에서는 이들 두 클론의 차이점들을 조사하였다. 실험결과, NW18C11은 NW18C12보다 더 많은수의 SV40 sequence를 포함하고 있음을 southern blot방법을 통해 확인하였으며 또한 immunofluoresce와 immunoprecipitation방법을 사용하여 두 클론 모두 정상크기의 SV40유전자산물인 large T와 small t 단백질을 생성함을 확인하였다. 한편 두 클론내에 포함되어 있는 바이러스유전자가 비형질전환새포로 하여금 생체내에서 악성종양 형성능력을 획득하도록 형질전환시킬수 있는지 확인하기 위해 두 클론의 DNA를 추출하여 마우스 NIH3T3세포에 주입시켜 형질전환된 세포를 선별하였다. 이 세포들은 모두 large T단백질을 생성하였으며 누드마우스에서 종양을 일으켰다. 이들 결과로써 NW18C12세포의 형질전환능은 완전하며, 이 세포가 누드마우스에서 거부반응에 기인하는 것으로 생각된다.

• Experimental and Molecular Medicine
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• 제50권12호
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• pp.1.1-1.14
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• 2018

DNA methylation is a regulatory mechanism in epigenetics that is frequently altered during human carcinogenesis. To detect critical methylation events associated with gastric cancer (GC), we compared three DNA methylomes from gastric mucosa (GM), intestinal metaplasia (IM), and gastric tumor (GT) cells that were microscopically dissected from an intestinal-type early gastric cancer (EGC) using methylated DNA binding domain sequencing (MBD-seq) and reduced representation bisulfite sequencing (RRBS) analysis. In this study, we focused on differentially methylated promoters (DMPs) that could be directly associated with gene expression. We detected 2,761 and 677 DMPs between the GT and GM by MBD-seq and RRBS, respectively, and for a total of 3,035 DMPs. Then, 514 (17%) of all DMPs were detected in the IM genome, which is a precancer of GC, supporting that some DMPs might represent an early event in gastric carcinogenesis. A pathway analysis of all DMPs demonstrated that 59 G protein-coupled receptor (GPCR) genes linked to the hypermethylated DMPs were significantly enriched in a neuroactive ligand-receptor interaction pathway. Furthermore, among the 59 GPCRs, six GI hormone receptor genes (NPY1R, PPYR1, PTGDR, PTGER2, PTGER3, and SSTR2) that play an inhibitory role in the secretion of gastrin or gastric acid were selected and validated as potential biomarkers for the diagnosis or prognosis of GC patients in two cohorts. These data suggest that the loss of function of gastrointestinal (GI) hormone receptors by promoter methylation may lead to gastric carcinogenesis because gastrin and gastric acid have been known to play a role in cell differentiation and carcinogenesis in the GI tract.

• Animal Bioscience
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• 제34권5호
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• pp.867-879
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• 2021

Objective: Fibronectin 3 (FN3) and immunoglobulin like modules (Ig) are usually collocated beside modular cellulase catalytic domains. However, very few researches have investigated the role of these modules. In a previous study, we have sequenced and analyzed bacterial metagenomic DNA in Vietnamese goats' rumen and found that cellulase-producing bacteria and cellulase families were dominant. In this study, the properties of modular cellulases and the role of a FN3 in unique endoglucanase belonging to glycosyl hydorlase (GH) family 5 were determined. Methods: Based on Pfam analysis, the cellulases sequences containing FN3, Ig modules were extracted from 297 complete open reading frames (ORFs). The alkaline, thermostability, tertiary structure of deduced enzymes were predicted by AcalPred, TBI software, Phyre2 and Swiss models. Then, whole and truncated forms of a selected gene were expressed in Escherichia coli and purified by His-tag affinity column for assessment of FN3 ability to enhance enzyme activity, solubility and conformation. Results: From 297 complete ORFs coding for cellulases, 148 sequences containing FN3, Ig were identified. Mostly FN3 appeared in 90.9% beta-glucosidases belonging to glycosyl hydrolase family 3 (GH3) and situated downstream of catalytic domains. The Ig was found upstream of 100% endoglucanase GH9. Rarely FN3 was seen to be situated downstream of X domain and upstream of catalytic domain endoglucanase GH5. Whole enzyme (called XFN3GH5 based on modular structure) and truncate forms FN3, XFN3, FN3GH5, GH5 were cloned in pET22b (+) and pET22SUMO to be expressed in single and fusion forms with a small ubiquitin-related modifier partner (S). The FN3, SFN3 increased GH5 solubility in FN3GH5, SFN3GH5. The SFN3 partly served for GH5 conformation in SFN3GH5, increased modules interaction and enzyme-soluble substrate affinity to enhance SXFN3GH5, SFN3GH5 activities in mixtures. Both SFN3 and SXFN3 did not anchor enzyme on filter paper but exfoliate and separate cellulose chains on filter paper for enzyme hydrolysis. Conclusion: Based on these findings, the presence of FN3 module in certain cellulases was confirmed and it assisted for enzyme conformation and activity in both soluble and insoluble substrate.