• Mass Spectrometry Letters
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• 제13권4호
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• pp.106-114
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• 2022

A rapid and reliable approach to the identification of microorganisms is a critical requirement for large-scale culturomics analysis. MALDI-TOF MS is a suitable technique that can be a better alternative to conventional biochemical and gene sequencing methods as it is economical both in terms of cost and labor. In this review, the applications of MALDI-TOF MS for the comprehensive identification of microorganisms and bacterial strain typing for culturomics-based approaches for various environmental studies including bioremediation, plant sciences, agriculture and food microbiology have been widely explored. However, the restriction of this technique is attributed to insufficient coverage of the mass spectral database. To improve the applications of this technique for the identification of novel isolates, the spectral database should be updated with the peptide mass fingerprint (PMF) of type strains with not only microbes with clinical relevance but also from various environmental sources. Further, the development of enhanced sample processing methods and new algorithms for automation and de-replication of isolates will increase its application in microbial ecology studies.

• Korean Circulation Journal
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• 제53권1호
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• pp.34-46
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• 2023

Background and Objectives: Diabetes mellitus (DM)-associated heart failure (HF) causes high morbidity and mortality. In this study, we established a zebrafish larvae model for in vivo research on diabetic HF. Methods: DM-like phenotypes were induced by treating zebrafish larvae with a combination of D-glucose (GLU) and streptozotocin (STZ). HF was induced by treatment with terfenadine (TER), a potassium channel blocker. Additionally, myocardial contractility, motility, and viability were evaluated. Results: The zebrafish larvae treated with a combination of GLU and STZ showed significantly higher whole-body glucose concentrations, lower insulin levels, and higher phosphoenolpyruvate carboxykinase levels, which are markers of abnormal glucose homeostasis, than the group treated with only GLU, with no effect on viability. When treated with TER, DM zebrafish showed significantly less myocardial fractional shortening and more irregular contractions than the non-DM zebrafish. Furthermore, in DM-HF with reduced ejection fraction (rEF) zebrafish, a significant increase in the levels of natriuretic peptide B, a HF biomarker, markedly reduced motility, and reduced survival rates were observed. Conclusions: We established a DM-HFrEF zebrafish model by sequentially treating zebrafish larvae with GLU, STZ, and TER. Our findings indicate the potential utility of the developed zebrafish larvae model not only in screening studies of new drug candidates for DM-HFrEF but also in mechanistic studies to understand the pathophysiology of DM-HFrEF.

• 한국응용곤충학회지
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• 제36권4호
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• pp.331-340
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• 1997

곤충 유전자를 이용한 항세균성 펩타이드 생산 및 응용에 관한 기초 연구로서 비병원성 세균(Escherichia coli K12)으로 면역 반응을 유도한 누에로부터 발현량이 증가하는 유전자 중 Hyalophora cecropia의 attacin과 cDNA 상동성을 나타내는 BmInc6 클론을 분리하고 그 특성을 조사하였다. BmInc6 cDNA의 전체염기서열을 분석한 결과 그 크기는 852 bp이고, 35번째 염기에서 변역이 개시되어 679 bp 위치에서 종결되는 open reading frame을 가지며 812번째 위치에 잠정 전사 종결 신호의 존재가 확인되었다(GenBank, AF005384). BmInc6에 의해 coding되는 아미노산은 214개이며, hydropathy 분석 결과 친수성을 나타내는 단백질이었다. 그리고 BmInc6 유전자에 의해 연역되는 펩타이드를 nuecin으로 명명하였다. Nuecin 유전자를 baculovirus 발현 백터계를 이용하여 곤충세포주에서 발현시킨 결과 전사체의 크기는 약 950 bp였고, 세포내 벌현 펩타이드의 분자량은 약 23 kDa이었다. 세포내에서 발현된 nuecin 전구체로 추정되는 23 kDa 펩타이드는 세포외로 분비되는 과정에서 약 3 kDa의 signal 펩타이드가 제거됨으로서 약 20 kDa의 성숙 nuecin으로 된다는 사실을 단백질 전기영동상으로 확인하였다. Nuecin 단백질의 항세균 활성을 수종의 그람 음성 및 양성 세균에 대해 검정한 결과, 특히 E. coli와 Bacillus subtilis에 높은 활성을 나타내었으며, attacin이 한정된 그람 음성 세균에만 항세균 활성을 나타내는데 비해 nuecin은 그람 음성은 물론 그람 양성에도 항세균 활성을 나타내어, 보다 넓은 항세균 스펙트럼을 가지는 것을 알 수 있었다.

• KSBB Journal
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• 제26권6호
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• pp.517-522
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• 2011

In our previous study, we isolated and characterized a 1-deoxynojirimycin (DNJ)-producing bacterium, Bacillus subtilis MORI, from chungkookjang, a Korean traditional food. B. subtilis MORI was subjected to ${\gamma}$-irradiation and the resulting bacteria were screened for increased DNJ production. A mutant was identified that produced 7.6 times more DNJ and named B. subtilis MORI 3K-85. In this study, the protein profiles of both strains were compared by one-dimensional and two-dimensional gel electrophoresis (1-DE and 2-DE, respectively) under both native and denaturing conditions. The 1-DE native-PAGE and 1-DE SDS-PAGE analyses identified 5 and 7 bands, respectively, that were found at higher concentrations in B. subtilis MORI 3K-85 than in B. subtilis MORI. Similarly, 2-DE analyses identified 20 protein spots which were found at higher concentrations in B. subtilis MORI 3K-85. The peptide mass profiles of these 20 proteins were analyzed by MALDI-TOF and compared with peptide sequences of B. subtilis and B. amyloliquefaciens in the MASCOT database. This screening suggested that three dehydrogenases, an aldolase, a synthetase, an isomerase, a reductase, and a peroxidase are elevated in B. subtilis MORI 3K-85. Based on this data, one or more of the elevated 8 enzymes might be related to the DNJ biosynthetic pathway.

• Journal of Microbiology and Biotechnology
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• 제18권3호
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• pp.410-416
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• 2008

The gene SfXyn10, which encodes a protease-resistant xylanase, was isolated using colony PCR screening from a genomic library of a feather-degrading bacterial strain Streptomyces fradiae var. k11. The full-length gene consists of 1,437bp and encodes 479 amino acids, which includes 41 residues of a putative signal peptide at its N terminus. The amino acid sequence shares the highest similarity (80%) to the endo-1,4-${\beta}$-xylanase from Streptomyces coelicolor A3, which belongs to the glycoside hydrolase family 10. The gene fragment encoding the mature xylanase was expressed in Escherichia coli BL21 (DE3). The recombinant protein was purified to homogeneity by acetone precipitation and anion-exchange chromatography, and subsequently characterized. The optimal pH and temperature for the purified recombinant enzyme were 7.8 and $60^{\circ}C$, respectively. The enzyme showed stability over a pH range of 4.0-10.0. The kinetic values on oat spelt xylan and birchwood xylan substrates were also determined. The enzyme activity was enhanced by $Fe^{2+}$ and strongly inhibited by $Hg^{2+}$ and SDS. The enzyme also showed resistance to neutral and alkaline proteases. Therefore, these characteristics suggest that SfXyn10 could be an important candidate for protease-resistant mechanistic research and has potential applications in the food industry, cotton scouring, and improving animal nutrition.

• The Korean Journal of Physiology and Pharmacology
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• 제19권2호
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• pp.105-109
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• 2015

NgR1, a Nogo receptor, is involved in inhibition of neurite outgrowth and axonal regeneration and regulation of synaptic plasticity. P19 embryonal carcinoma cells were induced to differentiate into neuron-like cells using all trans-retinoic acid and the presence and/or function of cellular molecules, such as NgR1, NMDA receptors and STAT3, were examined. Neuronally differentiated P19 cells expressed the mRNA and protein of NgR1, which could stimulate the phosphorylation of STAT3 when activated by Nogo-P4 peptide, an active segment of Nogo-66. During the whole period of differentiation, mRNAs of all of the NMDA receptor subtypes tested (NR1, NR2A-2D) were consistently expressed, which meant that neuronally differentiated P19 cells maintained some characteristics of neurons, especially central nervous system neurons. Our results suggests that neuronally differentiated P19 cells expressing NgR1 may be an efficient and convenient in vitro model for studying the molecular mechanism of cellular events that involve NgR1 and its binding partners, and for screening compounds that activate or inhibit NgR1.

• Journal of Microbiology and Biotechnology
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• 제14권3호
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• pp.620-627
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• 2004

On the foundation of a database of genome sequences and protein analyses, the ability to clone a gene based on a peptide analysis is becoming more feasible and effective for identifying a specific gene and its protein product of interest. As such, the current study conducted a protein analysis using 2-D PAGE followed by MALDI- TOF and ESI-MS to identify a highly expressed gene product of C. parasitica. A distinctive and highly expressed protein spot with a molecular size of 47.2 kDa was randomly selected and MALDI-TOF MS analysis was conducted. A homology search indicated that the protein appeared to be a fungal enolase (enol). Meanwhile, multiple alignments of fungal enolases revealed a conserved amino acid sequence, from which degenerated primers were designed. A screening of the genomic $\lambda$ library of C. parasitica, using the PCR amplicon as a probe, was conducted to obtain the full-length gene, while RT-PCR was performed for the cDNA. The E. coli-expressed eno 1 exhibited enolase enzymatic activity, indicating that the cloned gene encoded the C. parasitica enolase. Moreover, ESI-MS of two of the separated peptides resolved from the protein spot on 2-D PAGE revealed sequences identical to the deduced sequences, suggesting that the cloned gene indeed encoded the resolved protein spot. Northern blot analysis indicated a consistent accumulation of an eno1 transcript during the cultivation.

• Parasites, Hosts and Diseases
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• 제53권6호
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• pp.789-793
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• 2015

In order to explore tick proteins as potential targets for further developing vaccine against ticks, the total proteins of unfed female Dermacentor silvarum were screened with anti-D. silvarum serum produced from rabbits. The results of western blot showed that 3 antigenic proteins of about 100, 68, and 52 kDa were detected by polyclonal antibodies, which means that they probably have immunogenicity. Then, unfed female tick proteins were separated by 12% SDS-PAGE, and target proteins (100, 68, and 52 kDa) were cut and analyzed by LC-MS/MS, respectively. The comparative results of peptide sequences showed that they might be vitellogenin (Vg), heat shock protein 60 (Hsp60), and fructose-1, 6-bisphosphate aldolase (FBA), respectively. These data will lay the foundation for the further validation of antigenic proteins to prevent infestation and diseases transmitted by D. silvarum.

• 한국축산식품학회지
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• 제26권4호
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• pp.511-516
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• 2006

발효 소시지의 제조에 starter로 사용한 균주를 선발하기 위해 각 유산균 균주들의 ACE 저해 활성, 콜레스테롤 흡착능력, 발효 육제품 저장 중 S. aureus에 대한 저해 황성을 평가하였다. ACE 저해 활성은 L. plantarum L167이 가장 우수하였고(58.75%), 콜레스테롤 흡착 능력이 우수한 균주로는 L. plantarum L155를 선발하였다. 박테리오신을 생산하는 P. damnosus를 starter로 이용하여 제조한 발효 소시지에 S. aureus를 접종하여 상온 저장 중 생균수를 측정한 결과 저장 35일째에 대조구에 비하여 1 log의 균수 감소 효과가 나타났다.

• BMB Reports
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• 제44권11호
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• pp.758-763
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• 2011

Immunostimulatory CpG-DNA targeting TLR9 is one of the most extensively evaluated vaccine adjuvants. Previously, we found that a particular form of natural phosphodiester bond CpG-DNA (PO-ODN) encapsulated in a phosphatidyl-${\beta}$-oleoyl-${\gamma}$-palmitoyl ethanolamine (DOPE) : cholesterol hemisuccinate (CHEMS) (1 : 1 ratio) complex (Lipoplex(O)) is a potent adjuvant. Complexes containing peptide and Lipoplex(O) are extremely useful for B cell epitope screening and antibody production without carriers. Here, we showed that IL-12 production was increased in bone marrow derived dendritic cells in a CpG sequence-dependent manner when PO-ODN was encapsulated in Lipoplex(O), DOTAP or lipofectamine. However, the effects of Lipoplex(O) surpassed those of PO-ODN encapsulated in DOTAP or lipofectamine and also other various forms of liposome-encapsulated CpG-DNA in terms of potency for protein antigen-specific IgG production and Th1- associated IgG2a production. Therefore, Lipoplex(O) may have a unique potent immunoadjuvant activity which can be useful for various applications involving protein antigens as well as peptides.