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넙치와 조기의 원산지 판별을 위한 random amplified polymorphic DNA 패턴 연구
강덕진,이석근,진덕희,최석정,Kang Duk-Jin,Lee Suk-Keun,Jin Deuk-Hee,Choi Suk-Jung 한국생명과학회 2006 생명과학회지 Vol.16 No.1
본 연구에서 넙치와 조기의 원산지를 판별하기 위한 도구로 RAPD PCR 방법의 가능성을 확인하였다. 넙치는 한국의 주문진 자연산, 통영 양식산, 거제 양식산 그리고 북한 자연산을 실험에 사용하였다. 조기는 한국산과 중국산을 사용하였다. 넙치의 RAPD 패턴에서는 뚜렷하고 일관성이 있는 진단용 띠들을 쉽게 찾을 수 있었다. 조기의 경우에는 유전적인 이질성으로 인하여 각 개체의 RAPD 패턴에서는 일관성이 있는 진단용 띠를 찾기 어려웠지만 각 원산지별로 얻은 RAPD 패턴에서는 가능성이 있는 진단용 띠들을 찾을 수 있었다. The random amplified polymorphic DNA (RAPD) technique was investigated as a potential tool for the origin identification of olive flounder (Paralichthys olivaceus) and redlip croaker (Pseudosciaena polyactis). Olive flounder specimens were collected from North Korea and several locations of South Korea (Jumunjin, Tongyoung and Geoje). Fishes obtained from Tongyeong and Geoje were cultured products. Redlip croaker specimens were collected from South Korea and China. Consistent and distinct diagnostic bands were easily identified in the RAPD patterns of the olive flounder specimens. Although consistent diagnostic bands rarely appeared in the RAPD pattern of redlip croaker specimens because of their genetic heterogeneity, we were able to find potential diagnostic bands in the average RAPD pattern of each origin.
Enrichment Strategies for Identification and Characterization of Phosphoproteome
홍종기,강덕진,이선영 사단법인 한국질량분석학회 2015 Mass spectrometry letters Vol.6 No.2
Phosphorylation upon protein is well known to a key regulator that implicates in modulating many cellular processes like growth, migration, and differentiation. Up to date, grafting of multidimensional separation techniques onto advanced mass spectrometry (MS) has emerged as a promising tool for figuring out the biological functions of phosphorylation in a cell. However, advanced MS-based phosphoproteomics is still challenging, due to its intrinsic issues, i.e., low stoichiometry, less susceptibility in positive ion mode, and low abundance in biological sample. To overcome these bottlenecks, diverse techniques (e.g., SCX, HILIC, ERLIC, IMAC, TiO2, etc.) are continuously developed for on-/off-line enrichment of phosphorylated protein (or peptide) from biological samples, thereby helping qualitative/quantitative determination of phosphorylated protein and its phosphorylated sites. In this review, we introduce to the overall views of enrichment tools that are universally used to selectively isolate targeted phosphorylated protein (or peptide) from ordinary ones before MS-based phospoproteomic analysis.
김한수,김형직,강덕진,문명희 연세대학교의과대학 2014 Yonsei medical journal Vol.55 No.4
Purpose: Vaccine strategies utilizing dendritic cells (DCs) to elicit anti-tumor immunityare the subject of intense research. Although we have shown that DCs pulsed with heat-treated tumor lysate (HTL) induced more potent anti-tumor immunitythan DCs pulsed with conventional tumor lysate (TL), the underlying molecularmechanism is unclear. In order to explore the molecular basis of this approachand to identify potential antigenic peptides from pancreatic cancer, we analyzed and compared the major histocompatibility complex (MHC) ligands derivedfrom TL- and HTL-pulsed dendritic cells by mass spectrophotometry. Materialsand Methods: Human monocyte-derived dendritic cells were pulsed with TL or HTL prior to maturation induction. To delineate differences of MHC-bound peptide repertoire eluted from DCs pulsed with TL or HTL, nanoflow liquid chromatography-electrospray ionization-tandem mass spectrometry (nLC-ESI-MS-MS) was employed. Results: HTL, but not TL, significantly induced DC function, assessed by phenotypic maturation, allostimulation capacity and IFN-γ secretion by stimulated allogeneic T cells. DCs pulsed with TL or HTL displayed pancreas or pancreatic cancer-related peptides in context of MHC class I and II molecules. Some of the identified peptides had not been previously reported as expressed in pancreatic cancer or cancer of other tissue types. Conclusion: Our partial lists of MHC-associated peptides revealed the differences between peptide profiles eluted from HTL-and TL-loaded DCs, implying that induced heat shock proteins in HTL chaperone tumor-derived peptides enhanced their delivery to DCs and promoted cross-presentation by DC. These findings may aid in identifying novel tumor antigensor biomarkers and in designing future vaccination strategies.
이선영,김권성,오한빈,홍종기,강덕진 사단법인 한국질량분석학회 2017 Mass spectrometry letters Vol.8 No.3
In clinical diagnosis, it’s well known that the abnormal level of uric acid (UA) in human body is implicated in diverse human diseases, for instance, chronic heart failure, gouty arthritis, diabetes, and so on. As a primary method, an isotope dilution mass spectrometry (IDMS) has been used to obtain the accurate quantity of UA in blood or serum and also develop the certifi-cated reference material (CRM) so as to provide a SI-traceability to clinical laboratories. Due to the low solubility of UA in water, an ammonium hydroxide (NH 4 OH) has been considered as a promising solvent to increase the solubility of UA that enables the preparation of both UA and its isotope standard solution for next IDMS-based absolute quantification. But, because of using this NH 4 OH solvent, it gives rise to the unwanted degradation of UA. In this study, we sought to optimize condition for the stability of UA in NH 4 OH solution by varying the mole ratios of UA to NH 4 OH, followed by ID-LC-MRM analysis. In addi-tion, we also inspected minutely the effect of the storage temperatures. Additionally, we also performed the quantitative analysis of UA in the KRISS serum certificated reference material (CRM, 111-01-02A) with diverse mixing ratios of UA to NH 4 OH and then compared those values to its certification value. Based on our experiments, adjusting the mole ratio of 1/2 (UA/NH 4 OH) with the storage temperature of -20 o C is an effective way to secure both the solubility and stability of UA in NH 4 OH solution for next IDMS-based quantification of UA in serum.
A Simple Carbamidomethylation-Based Isotope Labeling Method for Quantitative Shotgun Proteomics
오동근,이선영,권미향,김숙경,문명희,강덕진 사단법인 한국질량분석학회 2014 Mass spectrometry letters Vol.5 No.3
In this study, we present a new isotope-coded carbamidomethylation (iCCM)-based quantitative proteomics, as acomplementary strategy for conventional isotope labeling strategies, with providing the simplicity, ease of use, and robustness. In iCCM-based quantification, two proteome samples can be separately isotope-labeled by means of covalently reaction of allcysteinyl residues in proteins with iodoacetamide (IAA) and its isotope (IAA-13C2, D2), denoted as CM and iCCM, respectively,leading to a mass shift of all cysteinyl residues to be + 4 Da. To evaluate iCCM-based isotope labeling in proteomic quantification,6 protein standards (i.e., bovine serum albumin, serotransferrin, lysozyme, beta-lactoglobulin, beta-galactosidase, andalpha-lactalbumin) isotopically labeled with IAA and its isotope, mixed equally, and followed by proteolytic digestion. Theresulting CM-/iCCM-labeled peptide mixtures were analyzed using a nLC-ESI-FT orbitrap-MS/MS. From our experimentalresults, we found that the efficiency of iCCM-based quantification is more superior to that of mTRAQ, as a conventional nonisobariclabeling method, in which both of a number of identified peptides from 6 protein standards and the less quantitative variationsin the relative abundance ratios of heavy-/light-labeled corresponding peptide pairs. Finally, we applied the developediCCM-based quantitative method to lung cancer serum proteome in order to evaluate the potential in biomarker discovery study
이선영,김권성,권현수,김영은,김기영,정지선,오한빈,김태영,홍종기,강덕진 대한화학회 2019 Bulletin of the Korean Chemical Society Vol.40 No.5
Certified reference materials (CRMs), KRISS CRM 111-01-010 and 111-01-011, were first developed in Korea to provide SI-traceability in the measurement of triglycerides (TGs) in human frozen serum. For absolute TG quantification in KRISS CRMs, isotope dilution-liquid chromatography?tandem mass spectrometry (ID-LC?MS/MS) was used. Both certification and short-term stability assessment of TG in KRISS CRMs were performed for each of 10 and eight selected units. The TG certified values and expanded uncertainties in KRISS CRMs were as follows: 0.608?± 0.025?mmol/kg for CRM 111-01-010 and 1.825?± 0.072?mmol/kg for CRM 111-01-011. The short-term TG stability results were not significantly changed relative to the certified values, and therefore both KRISS CRMs were stable during the monitoring period at each temperature. Based on our experiments, the developed KRISS CRMs can provide accurate, precise, and reproducible TG measurements in human frozen serum for clinical laboratories with SI-traceability.