• Journal of Microbiology and Biotechnology
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• 제23권11호
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• pp.1560-1568
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• 2013

Salmonella, a main cause of foodborne diseases, encounters a variety of environmental stresses and overcomes the stresses by multiple resistance strategies. One of the general responses to hyperosmotic stress is to import or produce compatible solutes so that cells maintain fluid balance and protect proteins and lipids from denaturation. The ProP and ProU systems are the main transport systems for compatible solutes. The OsmU system, recently identified as a third osmoprotectant transport system, debilitates excessive growth as well by reducing production of trehalose. We studied a fourth putative osmoprotectant transport system, YehZYXW, with high sequence similarity with the OsmU system. A Salmonella strain lacking YehZ, a predicted substrate-binding protein, did not suffer from hyperosmolarity but rather grew more rapidly than the wild type regardless of glycine betaine, an osmoprotectant, suggesting that the YehZYXW system controls bacterial growth irrespective of transporting glycine betaine. However, the growth advantage of ${\Delta}yehZ$ was not attributable to an increase in OtsBA-mediated trehalose production, which is responsible for the outcompetition of the ${\Delta}osmU$ strain. Overexpressed YehZ in trans was capable of deaccelerating bacterial growth vice versa, supporting a role of YehZ in dampening growth. The expression of yehZ was increased in response to nutrient starvation, acidic pH, and the presence of glycine betaine under hyperosmotic stress. Identifying substrates for YehZ will help decipher the role of the YehZYXW system in regulating bacterial growth in response to environmental cues.

• Asian Pacific Journal of Cancer Prevention
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• 제16권18호
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• pp.8467-8471
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• 2016

Background: One of the major mechanisms for drug resistance is associated with altered anticancer drug transport, mediated by the human-adenosine triphosphate binding cassette (ABC) transporter superfamily proteins. The overexpression of adenosine triphosphate binding cassette, sub-family B, member 1 (ABCB1) by multidrug-resistant cancer cells is a serious impediment to chemotherapy. In our study we have studied the possibility that structural single-nucleotide polymorphisms (SNP) are the mechanism of ABCB1 overexpression. Materials and Methods: A total of 101 gastric cancer multidrug resistant cases and 100 controls were genotyped with sequence-specific primed PCR (SSP-PCR). Gene expression was evaluated for 70 multidrug resistant cases and 54 controls by real time PCR. The correlation between the two groups was based on secondary structures of RNA predicted by bioinformatics tool. Results: The results of genotyping showed that among 3 studied SNPs, rs28381943 and rs2032586 had significant differences between patient and control groups but there were no differences in the two groups for C3435T. The results of real time PCR showed over-expression of ABCB1 when we compared our data with each of the genotypes in average mode. Prediction of secondary structures in the existence of 2 related SNPs (rs28381943 and rs2032586) showed that the amount of ${\Delta}G$ for original mRNA is higher than the amount of ${\Delta}G$ for the two mentioned SNPs. Conclusions: We have observed that 2 of our studied SNPs (rs283821943 and rs2032586) may elevate the expression of ABCB1 gene, through increase in mRNA stability, while this was not the case for C3435T.

• BMB Reports
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• 제40권3호
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• pp.373-381
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• 2007

Seed storage proteins (SSPs) are important for seed germination and early seedling growth. We studied the accumulation and degradation profiles of four major Arabidopsis 12S SSPs using a 2-DE scheme combined with mass spectrometric methods. On the 2-DE map of 23 dpa (days post anthesis) siliques, 48 protein spots were identified as putative full-length or partial $\alpha$, $\delta$ subunits. Only 9 of them were found in 12 dpa siliques with none in younger than 8 dpa siliques, indicating that the accumulation of 12S SSPs started after the completion of cell elongation processes both in siliques and in developing seeds. The length and strength of transcription activity for each gene determined the final contents of respective SSP. At the beginning of imbibition, 68 SSP spots were identified while only 2 spots were found at the end of the 4 d germination period, with $\alpha$, subunits degraded more rapidly than the $\alpha$ subunits. The CRC $\delta$ subunit was found to degrade from its C-terminus with conserved sequence motifs. Our data provide an important basis for understanding the nutritional value of developing plant seeds and may serve as a useful platform for other species.

• Bulletin of the Korean Chemical Society
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• 제31권9호
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• pp.2649-2655
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• 2010

$PKC{\delta}$-catalytic V5 Heptapeptide (FEQFLDI, FP7) interacts with heat shock protein 27 (HSP27) and inhibits HSP27-mediated resistance to cell death against various stimuli including radiation therapy. Here, we prepared radio-iodinated heptapeptide and further investigated its uptake properties in HSP27 expression cells. Peptide sequence of FP7 and a negative control peptide (WSLLEKR, QP7) was modified by substituting their C-terminus residue to tyrosine (FP6Y and QP6Y) to label radio-iodine. Iodinated peptides were confirmed by LC mass analysis with cold iodine reaction mixture. Accumulation of [$^{125}I$]iodo-FP6Y and [$^{125}I$]iodo-QP6Y in NCI-H1299 cell line, with higher level of HSP27, and NCI-H460 cell line, with lower level of HSP27, was measured by NaI(Tl) scintillation counter. The modification of substituting C-terminus residue of FP7 to tyrosine (FP6Y) did not affect its interaction with HSP27. Accumulation of [$^{125}I$]iodo-FP6Y in NCI-H1299 cells was 3 fold higher than in NCI-H460 cells. The novel radio-iodinated FP6Y would be used as a tracer for targeting HSP27 protein.

• The Plant Pathology Journal
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• 제22권2호
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• pp.139-146
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• 2006

The 3' region of Potato virus X (PVX) has the 74 nt 3'-nontranslated region (NTR) that is conserved among all potexviruses and contains several cis-acting elements for minus-strand and plus-strand RNA accumulation. Three stem-loop structures (SL1-SL3), especially formation of SL3 and U-rich sequence of SL2, and near upstream elements in the 3' NTR were previously demonstrated as important cis-acting elements. To Investigate the binding of these cis-acting elements within 3' end with host protein, we used the electrophoretic mobility shift assays (EMSA) and UV-cross linking analysis. The EMSA with cellular extracts from tobacco and RNA transcripts corresponding to the 150 nt of the 3' end of PVX RNA showed that the 3' end of PVX formed complexes with cellular proteins. The specificity of protein binding was confirmed through competition assay by using with 50-fold excess of specific and non-specific probes. We also conducted EMSA with RNAs containing various mutants on those cis-acting elements (${\Delta}10$10, SL3B, SL2A and ${\Delta}21$; J Mol Biol 326, 701-720) required for efficient PVX RNA accumulation. These analyses supported that these cis-acting elements are required for interaction with host protein(s). UV-cross linking analysis revealed that at least three major host proteins of about 28, 32, and 42 kDa in mass bound to these cis-elements. These results indicate that cis-acting elements from 3' end which are important for minus and plus-strand RNA accumulation are also required for host protein binding.

• 한국해양학회지
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• 제30권3호
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• pp.216-226
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• 1995

제주도에 분포하는 플라이스토세 서귀포층에서 산출되는 탄산염 광물로 이루 어진 화석 중에서 속성변질을 받지 않은 복족류, 가리비조개를 포함하는 이매패류, 완족류 및 뿔조개류에 대한 안정동위원소와 미량원소 성분을 분석하였다. 화석들의 각질부분은 고유의 광물성분인 아라고나이트와 방해석으로 보존되어 있으며 미세 구조도 속성변질을 받지 않고 보존되어 있다. 각질내의 높은 산소 및 탄소동위원소 성분과 높은 Na와 Sr성분, 그리고 낮은 Mn과 Fe성분들은 일부 각질들이 퇴적한 후 속성작용에 의해 변질받지 않았음을 지시한다. 산소동위원소성분 분석결과에 의하면 서귀포층 퇴적당시 화석으로 보존된 동물들은 현재보다 약간 낮은 수온 이나 산소동위원소 성분이 약간 부화(enriched)되었던 해수로부터 각질을 형성 하였던 것으로 생각된다. 이러한 결과는 서귀포층의 퇴적동안에 한반도가 빙하기 에 속하였던 것을 암시한다. 서귀포층의 하부로부터 상부에 이르기까지 수직적 온도 변화는 별로 크지 않았다.

• 미생물학회지
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• 제37권2호
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• pp.137-144
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• 2001

순천만 갯벌의 세균 군집의 다양성을 조사하기 위해 16S rDNA의 다양성을 조사하였다. 갯벌로부터 전체 핵산을 분리한 후, 세균에 상보적인 universal primer로 증폭된 16S rDNA로부터 클론 라이브러리를 만들었다. 총 111개의 클론으로부터 HaeIII를 이용하여 amplified rDNA restriction analysis (ARDRA)를 수행하고, Gelcompar II 프로그램을 이용하여 pattern을 clustering하였다. 111개의 클론 중 100가지의 서로 다른 RFLP type이 조사되었고, 이들 중 전체 클론 라이브러리를 대표할 수 있는 20개의 클론을 선별하여 부분적인 염기서열을 분석하여 세균 다양성을 분석하였다. 20개의 클론중에는 RDP와 GenBank에서 제공하는 small subunit RNA database와 동일한 클론은 존재하지 않았으며, 이미 알려진 배양 가능한 세균의 16S rRNA 염기서열과 비교 하였을때 77∼96.8%의 유사도를 보였다. 또한 이들 20개의 클론은 alpha-, delta-, gamma-Proteobacteria, low G+C Gram positive bacteria, high G+C Gram positive bacteria, Sphingobacteria (Cytophaga); Cyanobacteria (Chloroplast)등 주요한 7개 lineage에 속했으며, 클론들 중 Proteobacteria가 우점종을 차지하고 있었다.

• 한국세라믹학회지
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• 제30권12호
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• pp.1045-1053
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• 1993

Alumina hydrates were prepared by the neutralization of AlCl3.6H2O solution with NH3 gas diluted with N2 gas. The values of pH in reaction solution influenced the formation of alumina hydrates minerals. Amorphous alumina hydrates, for example, were formed at ${\gamma}$-Al2O3longrightarrow$\delta$-Al2O3longrightarrow$\theta$-Al2O3longrightarrow$\alpha$-Al2O3. (2) Bayeritelongrightarrowamorphouslongrightarrow${\gamma}$-Al2O3longrightarrow$\delta$-Al2O3longrightarrowη-Al2O3longrightarrow$\theta$-Al2O3longrightarrow$\alpha$-Al2O3. On the other hand, the shape of alumina hydrates whichw ere prepared by the reacton of Al2(SO4)3.16H2O solution and NH3 gas was spherical, the progress of its phase transformation with increasing temperature was amorphouslongrightarrow${\gamma}$-Al2O3longrightarrow$\alpha$Al2O3 in sequence.

• Genomics & Informatics
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• 제17권4호
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• pp.39.1-39.20
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• 2019

Analyzing patterns in data points embedded in linear and non-linear feature spaces is considered as one of the common research problems among different research areas, for example: data mining, machine learning, pattern recognition, and multivariate analysis. In this paper, data points are heterogeneous sets of biosequences (composite data points). A composite data point is a set of ordinary data points (e.g., set of feature vectors). We theoretically extend the derivation of the largest generalized eigenvalue-based distance metric D_ij(γ₁) in any linear and non-linear feature spaces. We prove that D_ij(γ₁) is a metric under any linear and non-linear feature transformation function. We show the sufficiency and efficiency of using the decision rule $\bar{{\delta}}_{{\Xi}i}$(i.e., mean of D_ij(γ₁)) in classification of heterogeneous sets of biosequences compared with the decision rules min_𝚵iand median_𝚵i. We analyze the impact of linear and non-linear transformation functions on classifying/clustering collections of heterogeneous sets of biosequences. The impact of the length of a sequence in a heterogeneous sequence-set generated by simulation on the classification and clustering results in linear and non-linear feature spaces is empirically shown in this paper. We propose a new concept: the limiting dispersion map of the existing clusters in heterogeneous sets of biosequences embedded in linear and nonlinear feature spaces, which is based on the limiting distribution of nucleotide compositions estimated from real data sets. Finally, the empirical conclusions and the scientific evidences are deduced from the experiments to support the theoretical side stated in this paper.

• 생명과학회지
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• 제14권3호
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• pp.429-434
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• 2004

Zymomonas mobilis 유래 levansucrase 유전자(levU)를 GAL1 promoter 하류에 연결시킨 pYES-levU와 GAL10 promoter 하류에 Kluyveromyces marxianus exoinulinase의 분비 신호서열(INU1 ss) 하류에 연결시킨 pYInu-levU를 각각 구축하였다. 이들 plasmid를 invertase 결손 변이주(suc2-$\Delta$9)인 S. cerevisiae SEY2102에 형질전환시켜 고활성 형질전환주를 선발하였다. 효모 형질전환주를 galactose 함유 배지로 배양한 결과, pYES-levU 함유 형질전환주인 경우 levansucrase의 총활성은 7.17U/ml이고, pYInu-levU 함유 형질전환주인 경우 6.61U/ml에 도달하였다. 발현된 levansucrase 약 50% 정도가 배지와 periplasmic space에 존재하였고, INU1 ss에 의한 분비효율 증가는 관찰할 수 없었다. 또한, 효모에서 발현된 재조합 levansucrase는 과당쇄화된 형으로 생산되는 것으로 보여진다.