• Mass Spectrometry Letters
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• v.8 no.4
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• pp.114-118
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• 2017

While saliva can be considered as good biological fluid for monitoring biomarkers due to many advantages including its communication with blood and the non-invasive nature during its sampling, its applications to that purpose is still limited. As a part of efforts to expand the applications of saliva to the protein biomarker research, we carried out global absolute quantitation of proteins in human whole saliva (WS) by bottom-up proteomics techniques mainly based on nLC-Q-IMS-TOF employing $MS^E$. From the analyses of a pooled WS sample collected from 22 healthy Korean volunteers, 93 proteins ranging from $5.89{\times}10^1ng/mL$ (immunoglobulin heavy chain) to $1.59{\times}10^4ng/mL$ (${\alpha}-amylase$ 1) were confirmed. For the validation of the present results, human serum albumin in the same sample was quantitated by ELISA and its result was compared with that from the nLC-Q-IMS-TOF study. As a result, there was no significant difference between two results from individual approaches ($1.18{\times}10^4{\pm}0.03{\times}10^4 ng/mL$ from nLC-Q-IMS-TOF experiments vs. $1.23{\times}10^4{\pm}0.07{\times}10^4ng/mL$ from ELISA experiments, n=3, p=0.309). To our knowledge, this is the first global absolute quantitation of proteins in human whole saliva and information from the present study can be widely used as the first level reference for the discovery of new protein biomarkers from human whole saliva as well as for quantitative applications of human whole saliva proteins.

• Journal of Microbiology and Biotechnology
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• v.22 no.11
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• pp.1575-1579
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• 2012

Paenibacillus polymyxa is known to be a plant-growth-promoting rhizobacterium. The present study describes a quantitative polymerase chain reaction (qPCR) assay for the specific detection and quantitation of P. polymyxa using a primer pair based on the sequence of a membrane-fusion protein for the amplification of a 268 bp DNA fragment. This study reports that the qPCR-based method is applicable for the rapid and sensitive detection of P. polymyxa and can be used as an alternative method for agricultural soil monitoring.

• KSBB Journal
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• v.16 no.2
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• pp.99-106
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• 2001

Proteomics research includes identification and quantitation of single protein and/or protein complex, profiling of protein expression changes in response to biological perturbations, characterization of protein functions and interactions, and elucidation the linkage between proteins and diseases. In this review paper, recent developments in the basic technologies involved in the proteomics research such as 2-dimensional PAGE and mass spectrometry are discussed. Also, the application areas of proteomics technology such as protein expression mapping and cell map proteomics are introduced with the focus on new drug development.

• Korean Journal of Clinical Laboratory Science
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• v.38 no.2
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• pp.111-116
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• 2006

One of the cardinal findings of the renal diseases is proteinuria, which appears in the early phase of kidney diseases and is very important in diagnosis, prognosis and decision making in the treatment process and results of the treatment. The study subjects were 126 patients who visited the nephrology department of Kangbuk Samsung Hospital. Serum was requested for urine protein electrophoresis. Total protein was measured with Bayer Advia 1650 (Biuret). Quantitation of each fraction was done by multiplying the percentage of each fraction by the total protein. Serum creatinine and BUN were also measured with Bayer Advia 1650 (Jaffe and Urease). Serum protein EP was done with REP(rapid electrophoresis) using Helena Kit reagents (REP Ultra SPE Kit, Ponceau S stain, Acetic acid, Methanol, EP Control). Concentrated urine was used for urine protein EP. The SPSS package was used for statistics analysis. Percentage and quantitation of the level of albumin in renal diseases were significantly lower than those in healthy controls. Total protein was correlated with albumin. In terms of proportion, ${\alpha}1$-globulin, ${\alpha}2$-globulin, ${\beta}$-globulin, and ${\gamma}$-globulin fractions were increased in the disease group. But, in the quantified level, ${\alpha}2$-globulin was increased and ${\beta}$-globulin and ${\gamma}$-globulin were decreased. ESRD patients showed an increased secretion of high molecular proteins in urine protein EP. A decreased level in serum total protein correlated with the decreased level of serum albumin and the total amount of urine total protein. This study revealed the variety in the level of serum and urine proteins and their subgroups by EP.

• Korean Journal of Environmental Agriculture
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• v.25 no.4
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• pp.371-381
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• 2006

New proteomic techniques have been pioneered extensively in recent years, enabling the high-throughput and systematic analyses of cellular proteins in combination with bioinformatic tools. Furthermore, the development of such novel proteomic techniques facilitates the elucidation of the functions of proteins under stress or disease conditions, resulting in the discovery of biomarkers for responses to environmental stimuli. The ultimate objective of proteomics is targeted toward the entire proteome of life, subcellular localization biochemical activities, and the regulation thereof. Comprehensive analysis strategies of proteomics can be classified into three categories: (i) protein separation via 2-dimensional gel electrophoresis (2-DE) or liquid chromatography (LC), (ii) protein identification via either Edman sequencing or mass spectrometry (MS), and (iii) proteome quantitation. Currently, MS-based proteomics techniques have shifted from qualitative proteome analysis via 2-DE or 2D-LC coupled with off-line matrix assisted laser desorption ionization (MALDI) and on-line electrospray ionization (ESI) MS, respectively, toward quantitative proteome analysis. In vitro quantitative proteomic techniques include differential gel electrophoresis with fluorescence dyes. protein-labeling tagging with isotope-coded affinity tags, and peptide-labeling tagging with isobaric tags for relative and absolute quantitation. In addition, stable isotope-labeled amino acids can be in vivo labeled into live culture cells via metabolic incorporation. MS-based proteomics techniques extend to the detection of the phosphopeptide mapping of biologically crucial proteins, which ale associated with post-translational modification. These complementary proteomic techniques contribute to our current understanding of the manner in which life responds to differing environment.

• Asian-Australasian Journal of Animal Sciences
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• v.21 no.8
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• pp.1116-1126
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• 2008

The objective of this study was to investigate the expression and localization of heat shock protein 70 (Hsp70) and its mRNA in the heart, liver, and kidney of acutely heat-stressed broilers at various stressing times. Male AA broilers (n = 100) were randomly divided into 5 groups of 20 birds per group. After 30 d of adaptive feeding at ambient temperature, 80 experimental broilers were suddenly heat stressed by increasing the environmental temperature from $22{\pm}1^{\circ}C$ to $37{\pm}1^{\circ}C$. The 4 groups were heat stressed for 2, 3, 5, and 10 h, respectively. The localizations of Hsp70 protein and mRNA, determined by immunohistochemical staining and in situ hybridization, respectively, were demonstrated to be tissue dependent, implying that different tissues have differential sensibilities to heat stress. Intense Hsp70 staining was identified in the vascular endothelial cell of heart, liver and kidney, suggesting an association between expression of Hsp70 in vascular endothelial cell and functional recovery of blood vessels after heat shock treatment. Ante-mortem heat stress had a significant effect on the expression of Hsp70 protein and mRNA. The quantitation of Hsp70 protein and mRNA were both time and tissue dependent. During the exposure to heat stress, the heart, liver and kidney of broiler chickens exhibited increased amounts of Hsp70 protein and mRNA. The expression of hsp70 mRNA in the heart, liver and kidney of heat-stressed broilers increased significantly and attained the highest level after a 2-h exposure to elevated temperatures. However, significant elevations in Hsp70 protein occurred after 2, 5, and 3 h of heat stressing, respectively, indicating that the stress-induced responses vary among different tissues.

• Tuberculosis and Respiratory Diseases
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• v.39 no.3
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• pp.242-247
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• 1992

Background: The ability to precisely measure specific mRNA levels by hybridization to complementary DNA probes is an important tool for analyzing the regulation of gene expression. Surfactant proteins have important roles in regulating surfactant metabolism as well as in determing its physical properties. Method: The complete coding regions for rat surfactant protein complementary DNA of surfactant protein B were subcloned into pGem 3Z or 4Z such that either antisense or sense transcripts were obtained by using SP 6 RNA polymerase. Surfactant protein B mRNA was measured by filter hybridization. Results: Equation of standard curve between counts per minute (Y) and surfactant protein B mRNA transcript input (X) was Y=2034.9 X+159.1. Correlation coefficient was 1.0. Couclusions: Filter hybridization assay is suited to situation when rapid, accurate quantitation of multiple samples is required.

• Journal of Gastric Cancer
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• v.21 no.4
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• pp.335-351
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• 2021

Purpose: An underlying factor for the failure of several clinical trials of anti-epidermal growth factor receptor (EGFR) therapies is the lack of an effective method to identify patients who overexpress EGFR protein. The quantitative dot blot method (QDB) was used to measure EGFR protein levels objectively, absolutely, and quantitatively. Its feasibility was evaluated for the prognosis of overall survival (OS) of patients with gastric cancer. Materials and Methods: Slices of 2×5 ㎛ from formalin-fixed paraffin-embedded gastric cancer specimens were used to extract total tissue lysates for QDB measurement. Absolutely quantitated EGFR protein levels were used for the Kaplan-Meier OS analysis. Results: EGFR protein levels ranged from 0 to 772.6 pmol/g (n=246) for all gastric cancer patients. A poor correlation was observed between quantitated EGFR levels and immunohistochemistry scores with ρ=0.024 and P=0.717 in Spearman's correlation analysis. EGFR was identified as an independent negative prognostic biomarker for gastric cancer patients only through absolute quantitation, with a hazard ratio of 1.92 (95% confidence interval, 1.05-3.53; P=0.034) in multivariate Cox regression OS analysis. A cutoff of 208 pmol/g was proposed to stratify patients with a 3-year survival probability of 44% for patients with EGFR levels above the cutoff versus 68% for those below the cutoff based on Kaplan-Meier OS analysis (log rank test, P=0.002). Conclusions: A QDB-based assay was developed for gastric cancer specimens to measure EGFR protein levels absolutely, quantitatively, and objectively. This assay should facilitate clinical trials aimed at evaluation of anti-EGFR therapies retrospectively and prospectively for gastric cancer.

• Journal of Ginseng Research
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• v.22 no.4
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• pp.316-323
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• 1998

To study e(feces of Korean Binseng (Parfax ginseff C. A. hfeyer) total saponin fraction on spermidine and spermine metabolism in rat reproductive systems, we administrated the saponin fractation to rats for 2 years. Then, we determined the activities of S-adenosylmethionine decarboxylase (SAMDC), the quantitation of the enzyme protein and the amounts of spermidine and spermine contents In prostate and testis. In young sexually immature stage, administration of Korean ginseng saponin fraction showed no effect on SAMDC activities. The stimulatory effect on the activities of SAMDC gradually increased and reached maximal activities in test groups of prostate and testis at sexually mature stage. The amounts of SAMDC protein in test groups were paralleled by the changes of SAMDC activities in test groups, indicating that all of the increased activity occurring in administration of ginseng saponin fraction was not due to the activation of SAMDC activity but to the Increase in enzyme protein. However, the spermidine and spermine contents of test groups showed small increase in compared to that of control groups. From these results, we suggest that administration of ginseng saponin fraction alter the spermidine and spermine metabolism in sexually mature and aged reproductive systems in rats.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2006.02a
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• pp.38-44
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• 2006

프로테오믹스는 생물체 안에 포함되어 있는 단백질을 통합적으로 연구하는 학문이다. 단백질을 동정(Protein identification)하고, 단백질의 상태를 분석(Protein characterization)하며, 단백질의 양적 변화를 관찰(Protein quantitation)한다. 유전자로부터 mRNA 로 복제되고 codon 의 규칙에 따라 합성되는 단백질이 세포 내에 얼만큼 존재하는가라는 단백질의 양적인 변화는 세포 내의 환경에 따라 시시각각 변화할 수 있으며, 이러한 변화의 추적은 단백질의 기능을 밝히는 기초자료로서 중요성을 가진다. 특히 질병의 조기 진단을 위한 바이오마커를 발굴하기 위한 스크리닝 역할로서, 단백질의 발현 양상을 비교하는 프로테오믹스는 기대를 모으고 있다. 단백질에 대한 분석, 특히 질량분석기에 의해 초고속으로 대량의 단백질 데이터를 생산하는 프로테오믹스의 연구는 정량적인 단백질 발현양상 분석의 정확도를 높이기 위해 다양한 실험기법과 데이터 분석기법을 동원하고 있다. 이번 발표에서는 프로테오믹스에서 단백질의 양을 측정하기 위한 실험 방법들과 그에 따른 데이터 분석 방법들을 소개하고자 한다. 프로테오믹스 연구의 초창기부터 사용되어온 2차원 전기영동법에 의해 생성되는 2D-gel image 에서의 spot 분석법으로부터, 탄뎀 질량분석기를 사용하는 ICAT, iTRAQ 등의 labeling 방법에 의한 정량분석, 그리고 질량분석기의 정확도를 최대한으로 활용하는 label-free 방법에 대한 기본 개념을 살펴보고 데이터 분석 기술의 적용 방법을 알아본다.