• Bulletin of the Korean Chemical Society
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• 제25권12호
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• pp.1833-1839
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• 2004

Recently mass spectrometry and separation methods such as liquid chromatography have become major tools in the field of proteomics. In this report, we describe in detail our efforts to develop ultra-high pressure capillary reverse-phase liquid chromatography (cRPLC) and its online coupling to a mass spectrometer by a nanoelectrospray (nanoESI) interface. The RPLC system is constructed in house to deliver LC solvents at the pressure up to 20,000 psig, which is four times higher than conventional RPLC systems. The high operation pressure allows the efficient use of packed micro-capillary columns (50, 75 and 150 ${\mu}$m i.d., up to 1.5 m long). We will discuss the effect of column diameter on the sensitivity of cRPLC/MS/MS experiments and the utility of the developed technique for proteome analysis by its application in the analysis of proteome samples having different levels of complexity.

• Journal of Microbiology and Biotechnology
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• 제17권6호
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• pp.879-890
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• 2007

The identification of tumor antigens is essential for the development of anticancer therapeutic vaccines and clinical diagnosis of cancer. SEREX (serological analysis of recombinant cDNA expression libraries) has been used to identify such tumor antigens by screening sera of patients with cDNA expression libraries. SEREX-defined antigens provide markers for the diagnosis of cancers. Potential diagnostic values of these SEREX-defined antigens have been evaluated. SEREX is also a powerful method for the development of anticancer therapeutics. The development of anticancer vaccines requires that tumor antigens can elicit antigen-specific antibodies or T lymphocytes. More than 2,000 antigens have been discovered by SEFEX. Peptides derived from some of these antigens have been evaluated in clinical trials. This review provides information on the application of SEREX for identification of tumor-associated antigens (TAA) for the development of cancer diagnostics and anticancer therapeutics.

• Journal of Plant Biotechnology
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• 제37권2호
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• pp.115-124
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• 2010

As the completion of genome sequencing, large collection of expression data and the great efforts in annotating plant genomes, the next challenge is to systematically assign functions to all predicted genes in the genome. Functional genome analysis of plants has entered the high-throughput stage. The generations and collections of mutants at the genome-wide level form technological platform of functional genomics. However, to identify the exact function of unknown genes it is necessary to understand each gene's role in the complex orchestration of all gene activities in the plant cell. Gene function analysis therefore necessitates the analysis of temporal and spatial gene expression patterns. The most conclusive information about changes in gene expression levels can be gained from analysis of the varying qualitative and quantitative changes of messenger RNAs, proteins and metabolites. New technologies have been developed to allow fast and highly parallel measurements of these constituents of the cell that make up gene activity. We have reviewed currently employed technologies to identify unknown functions of predicted genes including map-based cloning, insertional mutagenesis, reverse genetics, chemical mutagenesis, microarray analysis, FOX-hunting system, gene silencing mutagenesis, proteomics and chemical genomics. Recent improvements in technologies for functional genomics enable whole-genome functional analysis, and thus open new avenues for studies of the regulations and functions of unknown genes in plants.

• 한국균학회소식:학술대회논문집
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• 한국균학회 2015년도 춘계학술대회 및 임시총회
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• pp.14-14
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• 2015

Fungi are of particular interest due to their capacity to produce an extensive array of secondary metabolites. While many secondary metabolites have no known functions to the producing fungal organisms, these metabolites have tremendous importance to humans with beneficial (e.g., antibiotics) or detrimental (e.g., mycotoxins) properties. In this study, two important filamentous fungi, Fusarium verticillioides and Mycosphaerella graminicola were selected as target species and the genes regulatory functions on the biosynthesis of secondary metabolisms were studied. Functional genomics including forward and reverse genetics, and proteomics were utilized to better understand the complex secondary metabolism regulations in both F. verticillioides and M. graminicola. Identified genes in either F. verticillioides or M. graminicola background were CPP1 (a putative protein phosphatase gene), GAC1 (encoding a GTPase activating protein), MCC1(encoding c-type cyclin), and the velvet gene, MVE1. Our data suggest that there are diverse regulatory genes on fungal secondary metabolites with distinct or overlapping functional roles.

• Mass Spectrometry Letters
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• 제5권4호
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• pp.95-103
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• 2014

Characterization and studies of proteome are challenging because biological samples are complex, with a wide dynamic range of abundance. At present the proteins are identified by digestion into peptides, with subsequent identification of the peptides by mass spectrometry (MS). MS is a powerful technique for the purpose, but it cannot identify every peptide in such complex mixtures simultaneously. For accurate analysis and quantification it is important to separate the peptides first by chromatography into fractions of a size that MS can handle. With these less complex fractions, the probability is increased of identifying peptides of low abundance that would otherwise experience ion suppression effects due to the presence of peptides of high abundance. Enrichment for peptides with certain post-translational modifications helps to increase their detection rates as well. Electrostatic repulsion-hydrophilic interaction chromatography (ERLIC) is a mixed-mode chromatographic technique which combines the use of electrostatic repulsion and hydrophilic interaction. This review provides an overview of ERLIC and its various proteomics applications. ERLIC has been demonstrated to have good orthogonality to reverse phase liquid chromatography (RPLC), making it useful as a first dimension in multidimensional liquid chromatography (MDLC) and fractionation of digests in general. Peptides elute in order of their isoelectric points and polarity. ERLIC has also been successfully utilized for the enrichment for phosphopeptides and glycopeptides, facilitating their identification. In addition, it is promising for the study of peptide deamidation. ERLIC performs comparably well or better than established methods for these various applications, and serves as a viable and efficient workflow alternative.

• Journal of Microbiology and Biotechnology
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• 제20권1호
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• pp.138-145
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• 2010

A bacterial strain isolated from soil for its potential to control the anthracnose disease caused by Colletotrichum gloeosporioides was identified as a Bacillus subtilis. Bacillus subtilis CMB32 produced antifungal agents on M9 broth at $30^{\circ}C$. Biosurfactant lipopeptides produced by Bacillus subtilis CMB32 were precipitated by adjusting to pH 2 and extracting using chloroform/methanol, and then were purified using column chromatography and reverse-phase HPLC. The molecular masses of the lipopeptides were estimated by MALDI-TOF mass spectrometry as (a) 1,080, (b) 1,486, and (c) 1,044 Da, respectively. They had cyclic structures and amino acid compositions of (a) Pro, Asx, Ser, Tyr, Glx, (b) Glx, Tyr, Thr, Ala, Pro, lie, and (c) Glx, Leu, Val, Asx, respectively. Further analysis revealed that Bacillus subtilis CMB32 produced three antifungal lipopeptides: (a) iturin A, (b) fengycin, and (c) surfactin A.

• Journal of Veterinary Science
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• 제25권4호
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• pp.54.1-54.16
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• 2024

Importance: As one of the main etiologic agents of infectious diseases in pigs, pseudorabies virus (PRV) infections have caused enormous economic losses worldwide. EP0, one of the PRV early proteins (EP) plays a vital role in PRV infections, but the mechanisms are unclear. Objective: This study examined the function of EP0 to provide a direction for its in-depth analysis. Methods: In this study, the EP0-deleted PRV mutant was obtained, and Tandem Mass Tag-based proteomic analysis was used to screen the differentially expressed proteins (DEPs) quantitatively in EP0-deleted PRV- or wild-type PRV-infected porcine kidney 15 cells. Results: This study identified 7,391 DEPs, including 120 and 21 up-regulated and down-regulated DEPs, respectively. Western blot analysis confirmed the changes in the expression of the selected proteins, such as speckled protein 100. Comprehensive analysis revealed 141 DEPs involved in various biological processes and molecular functions, such as transcription regulator activity, biological regulation, and localization. Conclusions and Relevance: These results holistically outlined the functions of EP0 during a PRV infection and might provide a direction for more detailed function studies of EP0 and the stimulation of lytic PRV infections.

• 농업생명과학연구
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• 제50권3호
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• pp.129-139
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• 2016

Curcumin은 항산화제로서 신경세포의 보호작용에 관여하며, peroxiredoxin-5는 활성산소의 형성을 저해하여 산화적 스트레스로부터 신경세포를 보호한다고 알려져 있다. 본 연구는 허혈성 대뇌손상모델에서 curcumin에 의해 조절되는 peroxiredoxin-5 발현의 변화에 관하여 조사하였다. 실험동물은 흰쥐(Sprague-Dawley, 수컷)를 사용했으며, 허혈성 대뇌손상을 유도하기 위하여 중간대뇌동맥폐쇄술(MCAO)을 실시하였다. MCAO를 시행한 1시간 후에 curcumin(50mg/kg B.W.) 또는 vehicle을 복강으로 주사하였고, MCAO을 실시한 24시간 후 대뇌피질의 조직을 적출하였다. Hematoxylin과 eosin 조직염색 결과 MCAO를 시행한 대뇌피질에서는 신경세포의 괴사 소견을 보였지만, curcumin 투여군에서 이들 신경세포의 손상이 완화되어 있어 MCAO로 유도된 대뇌 손상시 curcumin의 보호효과를 확인하였다. 또한 MCAO를 실시한 vehicle+MCAO 실험군에서 peroxiredoxin-5 단백질의 발현은 감소하였으나, curcumin을 처리한 curcumin+MCAO 실험군에서는 vehicle+MCAO 실험군의 감소에 비해 감소의 폭이 현저히 줄어들어 MCAO를 시행하지 않은 sham군의 발현 수준으로 유지되었다. Reverse-transcription PCR과 Western blot 분석을 통해 중간대뇌동맥폐쇄술로 유도된 허혈성 대뇌손상 모델에서 peroxiredoxin-5 발현의 감소와 curcumin의 투여에 의한 peroxiredoxin-5 발현 감소의 완화를 확인하였다. 본 연구의 결과는 curcumin의 처리는 MCAO로 인한 peroxiredoxin-5 발현의 감소를 억제시킨다는 것을 보여주었다. 따라서, 대뇌손상 모델동물에서 curcumin은 MCAO로 유도된 peroxiredoxin-5 발현의 감소 정도를 완화시킴으로서 curcumin이 신경세포 보호작용에 기여하는 것으로 사료된다.

• 한국균학회소식:학술대회논문집
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• 한국균학회 2015년도 추계학술대회 및 정기총회
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• pp.37-37
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• 2015

dsRNA was found in malformed cultures of Lentinula edodes strain FMRI0339, one of the three most popular sawdust cultivated commercial strains of shiitake, and was also found in healthy-looking fruiting bodies and actively growing mycelia. Cloning of the partial genome of the dsRNA revealed the presence of the RdRp sequence of a novel L. edodes mycovirus (LeV), and sequence comparison of the cloned amplicon showed an identical sequence to known RdRp genes of LeV found in strain HKA. The meiotic stability of dsRNA was examined by measuring the ratio of the presence of dsRNA among sexual monokaryotic progeny. More than 40% of the monokaryotic progeny still contained the dsRNA, indicating the persistence of dsRNA during sexual reproduction. Comparing the mycelia growth of monokaryotic progeny suggested that, although variations in the growth rate existed among progeny and virus infection was observed in highly actively growing progeny, there appeared to be a tendency toward a lower frequency of virus incidence in actively growing progeny. This study attempted to cure the edible mushroom L. edodes strain FMRI0339 of the L. edodes mycovirus (LeV) in order to obtain an isogenic virus-free fungal strain as well as a virus-infected strain for comparison. Mycelial fragmentation, followed by being spread on a plate with serial dilutions resulted in a virus-free colony. Viral absence was confirmed with gel electrophoresis after dsRNA-specific virus purification, Northern blot analysis, and PCR using reverse transcriptase (RT-PCR). Once cured, all of fungal cultures remained virus-free over the next two years. Interestingly, the viral titer of LeV varied depending on the culture condition. The titer from the plate culture showed at least a 20-fold higher concentration than that grown in the liquid culture. However, the reduced virus titer in the liquid culture was recovered by transferring the mycelia to a plate containing the same medium. In addition, oxygen-depleted culture conditions resulted in a significant decrease of viral concentration, but not to the extent seen in the submerged liquid culture. Although no $discernable phenotypic changes in colony morphology were observed, virus-cured strains showed significantly higher growth rates and mycelial mass than virus-infected strains. We were also explored effects of LeV on fruiting body formation and mushroom yield. The fruiting body formation yield of virus-free L. edodes was larger than virus-infected L. edodes. These results indicate that LeV infection has a deleterious effect on mycelial growth and fruiting body formation. In addition, we have been investigated host-parasite interaction between L. edodes and its mycovirus interaction to study viral mechanism by establishment of proteomics.

• 생명과학회지
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• 제33권2호
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• pp.208-215
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• 2023

최근 수십년간 노화연구의 영역은 유전자 수준에서부터 세포 수준을 거쳐 혈액을 교환하는 in vivo 모델까지 진보를 거듭하면서 발전하고 있다. 예쁜꼬마선충에서 수명을 연장시킬 수 있는 유전자의 존재가 알려지면서, 유전체학, 단백질체학, 대사체학, 전사체학과 같은 다양한 분석방법이 사용되면서 보다 다양한 노화 연관 표적분자들이 발견되었다. 따라서, 표적분자들 간의 상호관계에 대한 연구결과도 증가하고 있다. 또한, 두 실험동물을 외과적으로 결합시킨 개체병렬결합 방법을 사용한 노화연구로 노화 현상을 역행시킬 수도 있는 인자가 보고되었고, 젊은 개체의 혈액 내에 존재할 수 있는 노화 역행 인자를 찾기 위한 더 정확하고, 효과적인 연구로 확장되면서, 노화연구의 방법에 새로운 패러다임이 확립되었다. 2022년 실험동물에 정교하게 혈액을 교환할 수 있는 장치에 대한 논문이 발표되었고, 이 장치를 사용한 연구가 노화 역행에 영향을 줄 수 있는 새로운 결과를 제시하였다. 새롭게 고안된 장치와 그로 인한 결과뿐만 아니라 젊은 혈액 또는 조건화된 혈액을 주입하여 얻은 최신 연구결과로 처음 발표되었던 GDF11 외에도 혈액 내에 존재하는 노화 역행 후보물질로서 β2m, TIMP2, VCAM1, Gpld1, clusterin과 같은 혈액 내 용해성 인자뿐만 아니라 mcicroglia 세포와 neuroinflammation과 같은 생화학적 현상이 직접적으로 노화요인으로 증명되고 있다. 이 총설에서는 이 같은 노화연구에 대한 최신 결과에 대해 논의하고자 한다.