• Asian Pacific Journal of Cancer Prevention
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• 제15권23호
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• pp.10355-10361
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• 2015

Background: MicroRNAs (miRNAs) are small non-coding RNA molecules found in multicellular eukaryotes which are implicated in development of cancer, including cutaneous squamous cell carcinoma (cSCC). Expression is controlled by transcription factors (TFs) that bind to specific DNA sequences, thereby controlling the flow (or transcription) of genetic information from DNA to messenger RNA. Interactions result in biological signal control networks. Materials and Methods: Molecular components involved in cSCC were here assembled at abnormally expressed, related and global levels. Networks at these three levels were constructed with corresponding biological factors in term of interactions between miRNAs and target genes, TFs and miRNAs, and host genes and miRNAs. Up/down regulation or mutation of the factors were considered in the context of the regulation and significant patterns were extracted. Results: Participants of the networks were evaluated based on their expression and regulation of other factors. Sub-networks with two core TFs, TP53 and EIF2C2, as the centers are identified. These share self-adapt feedback regulation in which a mutual restraint exists. Up or down regulation of certain genes and miRNAs are discussed. Some, for example the expression of MMP13, were in line with expectation while others, including FGFR3, need further investigation of their unexpected behavior. Conclusions: The present research suggests that dozens of components, miRNAs, TFs, target genes and host genes included, unite as networks through their regulation to function systematically in human cSCC. Networks built under the currently available sources provide critical signal controlling pathways and frequent patterns. Inappropriate controlling signal flow from abnormal expression of key TFs may push the system into an incontrollable situation and therefore contributes to cSCC development.

• 한국자기공명학회논문지
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• 제20권2호
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• pp.56-60
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• 2016

Adenylate kinase (AK) enzyme which acts as the catalyst of reversible high energy phosphorylation reaction between ATP and AMP which associate with energetic metabolism and nucleic acid synthesis and signal transmission. This enzyme has three distinct domains: Core, AMP binding domain (AMPbd) and Lid domain (LID). The primary role of AMPbd and LID is associated with conformational changes due to flexibility of two domains. Three dimensional structure of human AK1 has not been confirmed and various mutation experiments have been done to determine the active sites. In this study, AK1R138A which is changed arginine[138] of LID domain with alanine[138] was made and conducted with NMR experiments, backbone dynamics analysis and mo-lecular docking dynamic simulation to find the cause of structural change and substrate binding site. Synthetic human muscle type adenylate kinase 1 (hAK1) and its mutant (AK1R138A) were re-combinded with E. coli and expressed in M9 cell. Expressed proteins were purified and finally gained at 0.520 mM hAK1 and 0.252 mM AK1R138A. Multinuclear multidimensional NMR experiments including HNCA, HN(CO)CA, were conducted for amino acid sequence analysis and signal assignments of $^1H-^{15}N$ HSQC spectrum. Our chemical shift perturbation data is shown LID domain residues and around alanine[138] and per-turbation value(0.22ppm) of valine[179] is consid-ered as inter-communication effect with LID domain and the structural change between hAK1 and AK1R138A.

• Journal of Microbiology and Biotechnology
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• 제27권9호
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• pp.1609-1616
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• 2017

The complex roles of cell surface modification in the biofilm formation of Campylobacter jejuni, a major cause of worldwide foodborne diarrheal disease, are poorly understood. In a screen of mutants from random transposon mutagenesis, an insertional mutation in the eptC gene (cj0256) resulted in a significant decrease in C. jejuni NCTC11168 biofilm formation (<20%) on major food contact surfaces, such as polystyrene and borosilicate glass, when compared with wild-type cells (p < 0.05). In C. jejuni strain 81-176, the protein encoded by eptC modified cell surface structures, such as lipid A, the inner core of lipooligosaccharide, and the flagellar rod protein (FlgG), by attaching phosphoethanolamine. To assess the role of eptC in C. jejuni NCTC11168, adherence and motility tests were performed. In adhesion assays with glass surfaces, the eptC mutant exhibited a $0.77log\;CFU/cm^2$ decrease in adherence compared with wild-type cells during the initial 2 h of the assay (p < 0.05). These results support the hypothesis that the modification of cell surface structures by eptC affects the initial adherence in biofilm formation of C. jejuni NCTC11168. In motility tests, the eptC mutant demonstrated reduced motility when compared with wild-type cells, but wild-type cells with the transposon inserted in a gene irrelevant to biofilm formation (cj1111c) also exhibited decreased motility to a similar extent as the eptC mutant. This suggests that although eptC affects motility, it does not significantly affect biofilm formation. This study demonstrates that eptC is essential for initial adherence, and plays a significant role in the biofilm formation of C. jejuni NCTC11168.

• International Journal of Computer Science & Network Security
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• 제22권10호
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• pp.73-82
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• 2022

Early detection continues to be the mainstay of breast cancer control as well as the improvement of its treatment. Even so, the absence of cancer symptoms at the onset has early detection quite challenging. Therefore, various researchers continue to focus on cancer as a topic of health to try and make improvements from the perspectives of diagnosis, prevention, and treatment. This research's chief goal is development of a system with deep learning for classification of the breast cancer as non-malignant and malignant using mammogram images. The following two distinct approaches: the first one with the utilization of patches of the Region of Interest (ROI), and the second one with the utilization of the overall images is used. The proposed system is composed of the following two distinct stages: the pre-processing stage and the Convolution Neural Network (CNN) building stage. Of late, the use of meta-heuristic optimization algorithms has accomplished a lot of progress in resolving these problems. Teaching-Learning Based Optimization algorithm (TIBO) meta-heuristic was originally employed for resolving problems of continuous optimization. This work has offered the proposals of novel methods for training the Residual Network (ResNet) as well as the CNN based on the TLBO and the Genetic Algorithm (GA). The classification of breast cancer can be enhanced with direct application of the hybrid TLBO- GA. For this hybrid algorithm, the TLBO, i.e., a core component, will combine the following three distinct operators of the GA: coding, crossover, and mutation. In the TLBO, there is a representation of the optimization solutions as students. On the other hand, the hybrid TLBO-GA will have further division of the students as follows: the top students, the ordinary students, and the poor students. The experiments demonstrated that the proposed hybrid TLBO-GA is more effective than TLBO and GA.

• 생명과학회지
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• 제15권4호
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• pp.513-521
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• 2005

흑두로 제조한 청국으로부터 혈전용해력이 우수한 균을 선발하여 동정하였으며, 그를 Bacillus subtilis BB-1로 명명하였다. 이 균은 혈전용해효소 isozyme을 적어도 5개이상 생성하는 균주로 확인되었다. 이 균으로부터 크로모좀을 분리하여 shot gun법으로 혈전용해효소 유전자를 크로닝하였으며, 이 유전자를 BSF-1이라 명명하였다. 이 유전자는 714개의 아미노산을 암호화하고 있으며 기존에 밝혀진 혈전용해효소 유전자와 상동성은 검출되지 않은 새로운 혈전용해효소 유전자였다. 혈전용해효소활성 최적 pH 및 온도는 5.0과 $35^{\circ}C$였다. 기질특이성은 적혈구 배지 또는 skim milk, gelatin등에 전혀 분해활성이 없었다. 이는 혈전만을 특이적으로 분해하는 기질특이성을 보였으며, 혈전분해효소로서의 이용가능성이 충분한 것으로 판단된다.

• Tuberculosis and Respiratory Diseases
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• 제50권1호
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• pp.29-41
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• 2001

결핵환자에 있어 rpoB 유전자 염기서열 돌연변이로 인해 생겨나는 rifampin(RIF)내성은 화학요법치료에서 나타나는 다제내성의 표지자로서 많은 연구가 되어 있으며 rifabutin(RIB)은 이러한 RIF의 내성을 보이는 일부 점돌연변이에 대하여 감성 또는 내성을 보이는 것으로 보고되고 있다. 그러므로 본 연구에서는 mycobacteria rpoB 유전자의 특정 DNA 서열(17 bp)을 고정한 올리고뉴클레오티드 칩을 개발하여 rpoB 유전자의 점돌연변이으로 인한 RIF과 RIB의 감수성을 조사하고자 하였다. 방법 : 사용된 올리고뉴클레오티드 칩은 RIF 내성 프로브 및 RIB 감성 프로브를 포함하도록 고안되었으며, 각각의 돌연변이에 상응하는 야생형 프로브를 동일한 염기서열에서 선정하여 형광 시그날 세기의 직접비교에 의해 보다 정확한 탐지를 가능하게 하였다. 결과 : 15개의 임상 분리체를 검사한 결과 RIF 내성으로 밝혀진 돌연변이중 13개의 임상 분리체에서 RIB 감수성 돌연변이 종류를 판별할 수 있었다. 결론 : 올리고뉴레오티드 칩으로 rpoB 유전자에 대한 점돌연변이 연구는 결핵환자에 대한 RIF과 RIB 약제내성 유무를 판단케 함으로써 효과적인 화학요법치료를 가능케 할 것이며 기존 방법과 비교시 효율 및 재현성이 매우 높다고 판단되었다.

• Asian Pacific Journal of Cancer Prevention
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• 제15권11호
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• pp.4513-4518
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• 2014

The prevalence of BRCA1 gene mutations in breast cancer differs between diverse ethnic groups. Relatively little information is known about patterns of BRCA1 mutations in early-onset breast cancer in women of Uighur or Han descent, the major ethnic populations of the Xinjiang region in China. The aim of this study was to identify BRCA1 mutations in Uighur and Han patients with early-onset (age <35 years), and sporadic breast cancer for genetic predisposition to breast cancer. For detection of BRCA1 mutations, we used a polymerase chain reaction single-stranded conformation polymorphism approach, followed by direct DNA sequencing in 22 Uighur and 13 Han women with early-onset sporadic breast cancer, and 32 women with benign breast diseases. The prevalence of BRCA1 mutations in this population was 22.9% (8/35) among early-onset sporadic breast cancer cases. Of these, 31.8% (7/22) of Uighur patients and 7.69% (1/13) of Han patients were found to have BRCA1 mutations. In 7 Uighur patients with BRCA1 mutations, there were 11 unique sequence alterations in the BRCA1 gene, including 4 clearly disease-associated mutations on exon 11 and 3 variants of uncertain clinical significance on exon 11, meanwhile 4 neutral variants on intron 20 or 2. None of the 11 BRCA1 mutations identified have been previously reported in the Breast Cancer Information Core database. These findings reflect the prevalence of BRCA1 mutations in Uighur women with early-onset and sporadic breast cancer, which will allow for provision of appropriate genetic counseling and treatment for Uighur patients in the Xinjiang region.

• Asian-Australasian Journal of Animal Sciences
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• 제33권3호
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• pp.398-407
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• 2020

Objective: The Yip1 domain family (YIPF) proteins were proposed to function in endoplasmic reticulum (ER) to Golgi transport and maintenance of the morphology of the Golgi, which were homologues of yeast Yip1p and Yif1p. YIPF3, the member 3 of YIPF family was a homolog of Yif1p. The aim of present study was to investigate the expression and regulation mechanism of porcine YIPF3. Methods: Quantitative realtime polymerase chain reaction (qPCR) was used to analyze porcine YIPF3 mRNA expression pattern in different tissues and pig kidney epithelial (PK15) cells stimulated by polyinosine-polycytidylic acid (poly [I:C]). Site-directed mutations combined with dual luciferase reporter assays and electrophoretic mobility shift assay (EMSA) were employed to reveal transcription regulation mechanism of porcine YIPF3. Results: Results showed that the mRNA of porcine YIPF3 (pYIPF3) was widely expressed with the highest levels in lymph and lung followed by spleen and liver, while weak in heart and skeletal muscle. Subcellular localization results indicated that it expressed in Golgi apparatus and plasma membranes. Upon stimulation with poly (I:C), the level of this gene was dramatically up-regulated in a time- and concentration-dependent manner. pYIPF3 core promoter region harbored three cis-acting elements which were bound by ETS proto-oncogene 2 (ETS2), zinc finger and BTB domain containing 4 (ZBTB4), and zinc finger and BTB domain containing 14 (ZBTB14), respectively. In which, ETS2 and ZBTB4 both promoted pYIPF3 transcription activity while ZBTB14 inhibited it, and these three transcription factors all played important regulation roles in tumorigenesis and apoptosis. Conclusion: The pYIPF3 mRNA expression was regulated by ETS2, ZBTB4, and ZBTB14, and its higher expression in immune organs might contribute to enhancing ER to Golgi transport of proteins, thus adapting to the immune response.

• Journal of Microbiology and Biotechnology
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• 제28권11호
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• pp.1916-1927
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• 2018

Corynebacterium glutamicum is an excellent platform for the production of amino acids, and is widely used in the fermentation industry. Most industrial strains are traditionally obtained by repeated processes of random mutation and selection, but the genotype of these strains is often unclear owing to the absence of genomic information. As such, it is difficult to improve the growth and amino acid production of these strains via metabolic engineering. In this study, we generated a complete genome map of an industrial L-valine-producing strain, C. glutamicum XV. In order to establish the relationship between genotypes and physiological characteristics, a comparative genomic analysis was performed to explore the core genome, structural variations, and gene mutations referring to an industrial L-leucine-producing strain, C. glutamicum CP, and the widely used C. glutamicum ATCC 13032. The results indicate that a 36,349 bp repeat sequence in the CP genome contained an additional copy each of lrp and brnFE genes, which benefited the export of L-leucine. However, in XV, the kgd and panB genes were disrupted by nucleotide insertion, which increase the availability of precursors to synthesize L-valine. Moreover, the specific amino acid substitutions in key enzymes increased their activities. Additionally, a novel strategy is proposed to remodel central carbon metabolism and reduce pyruvate consumption without having a negative impact on cell growth by introducing the CP-derived mutant $H^+$/citrate symporter. These results further our understanding regarding the metabolic networks in these strains and help to elucidate the influence of different genotypes on these processes.

• Journal of Plant Biotechnology
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• 제45권1호
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• pp.17-29
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• 2018

본 연구에서는 국내외에서 수집한 벼 294개 유전자원 핵심집단을 대상으로 벼의 지엽각 특성에 대한 조사를 수행하였고, GWAS를 이용하여 지엽각 연관 유전자를 추출 및 분석하였다. 표현형 데이터를 이용한 GWAS의 Manhattan plot 결과 분석을 통해, 각 집단에서 염색체를 대상으로 표현형과 통계적 유의성을 나타내 연관성을 보이는 SNP를 발굴하였다. 지엽각 관련 특성에 대하여 선행 연구된 QTL region과의 비교를 통하여 본 연구에서 발굴된 SNP간의 유의성을 조사한 결과, 지엽각과 유의성이 있는 SNP (S8-19815442)가 이미 확인된 QTL region에 위치하는 것으로 나타났으며, 후보유전자 Os08g31950 대해 연관 유전자 변이를 관찰하기 위해서 형질 특이적 품종군 간의 염기서열을 비교한 결과 1개의 지역에서 단일염기변이가 검출되었다. Os08g31950의 조직별 RNA의 상대적 발현량 수준을 비교한 결과, Os08g31950 유전자는 모든 조직에서 높은 발현량을 확인할 수 있었으며 조직별로 다양한 발현 양상을 관찰할 수 있었다. 또한, 모두 직립형 품종군에서 상대적으로 발현량이 높게 나타났으며 뿌리보다 잎에서의 발현율이 높게 나타났다. 본 연구를 통해 동정된 지엽각 연관 후보유전자 Os08g31950는 벼 생육 및 수량 증대에 이용할 수 있는 마커제작 및 육종의 기초자료가 될 것으로 기대된다.