• BMB Reports
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• v.57 no.3
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• pp.143-148
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• 2024

Pulmonary fibrosis is a serious lung disease that occurs predominantly in men. Genistein is an important natural soybean-derived phytoestrogen that affects various biological functions, such as cell migration and fibrosis. However, the antifibrotic effects of genistein on pulmonary fibrosis are largely unknown. The antifibrotic effects of genistein were evaluated using in vitro and in vivo models of lung fibrosis. Proteomic data were analyzed using nano-LC-ESI-MS/MS. Genistein significantly reduced transforming growth factor (TGF)-β1-induced expression of collagen type I and α-smooth muscle actin (SMA) in MRC-5 cells and primary fibroblasts from patients with idiopathic pulmonary fibrosis (IPF). Genistein also reduced TGF-β1-induced expression of p-Smad2/3 and p-p38 MAPK in fibroblast models. Comprehensive protein analysis confirmed that genistein exerted an anti-fibrotic effect by regulating various molecular mechanisms, such as unfolded protein response, epithelial mesenchymal transition (EMT), mammalian target of rapamycin complex 1 (mTORC1) signaling, cell death, and several metabolic pathways. Genistein was also found to decrease hydroxyproline levels in the lungs of BLM-treated mice. Genistein exerted an anti-fibrotic effect by preventing fibroblast activation, suggesting that genistein could be developed as a pharmacological agent for the prevention and treatment of pulmonary fibrosis.

• Mass Spectrometry Letters
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• v.15 no.2
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• pp.69 -78
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• 2024

The advancement of high-throughput omics technologies and systems biology is essential for understanding complex biological mechanisms and diseases. The integration of proteomics and metabolomics provides comprehensive insights into cellular functions and disease pathology, driven by developments in mass spectrometry (MS) technologies, including electrospray ionization (ESI). These advancements are crucial for interpreting biological systems effectively. However, integrating these technologies poses challenges. Compared to genomic, proteomics and metabolomics have limitations in throughput, and data integration. This review examines developments in MS equipped electrospray ionization (ESI), and their importance in the effective interpretation of biological mechanisms. The review also discusses developments in sample preparation, such as Simultaneous Metabolite, Protein, Lipid Extraction (SIMPLEX), analytical techniques, and data analysis, highlighting the application of these technologies in the study of cancer or Huntington's disease, underscoring the potential for personalized medicine and diagnostic accuracy. Efforts by the Clinical Proteomic Tumor Analysis Consortium (CPTAC) and integrative data analysis methods such as O2PLS and OnPLS extract statistical similarities between metabolomic and proteomic data. System modeling techniques that mathematically explain and predict system responses are also covered. This practical application also shows significant improvements in cancer research, diagnostic accuracy and therapeutic targeting for diseases like pancreatic ductal adenocarcinoma, non-small cell lung cancer, and Huntington's disease. These approaches enable researchers to develop standardized protocols, and interoperable software and databases, expanding multi-omics research application in clinical practice.

• Journal of Veterinary Science
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• v.25 no.4
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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.

• Journal of Life Science
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• v.16 no.3 s.76
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• pp.447-453
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• 2006

Histidine kinase plays important roles in signal transduction in plant. We characterized the function of Arabidopsis histidine kinase 3 (AHK3) and analyzed the expression patterns of genes and proteins in its mutant ahk3 by trans-zeatin (t-zeatin). The ahk3 exhibited decreased sensitivity to t-zeatin during callus formation, seedling growth, and leaf senescence. From proteomic analysis of ahk3, eukaryotic translation initiation factor 5A-2, auxin binding glutathione S-transferase, and NDPK1 were identified not to be induced by t-zeatin, when compared to the wild-type. In addition, the expression levels of ARR4 and ARR16 among A-type response regulators (ARRs) markedly decreased in ahk3 by t-zeatin treatment. These results suggest that AHK3 plays an important role in cytokinin signaling and the proteins identified from proteomic analysis and specific ARRs, ARR4 and ARR16 may be directly or indirectly associated in AHK3-mediated cytokinin signaling.

• Journal of Veterinary Clinics
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• v.27 no.6
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• pp.679-685
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• 2010

Many animal models of osteoarthritis (OA) have been developed, aimed at understanding the long-term progression of OA and difficulty of identifying patients in the initial stage of the disease. In canines, coxofemoral luxation and hip dysplasia are common orthopedic ailments related to OA in the hip joint. Transecting the ligament of the head of the femur (LHF) aids in diagnosis of coxofemoral joint OA. Presently, mobility of this joint was increased by transected LHF in 10 mature, 2-3-year-old (average $2.57{\pm}0.20$ years), healthy male beagles. The animals were normally gaited 1-week post-operatively. During the experimental period, examinations including X-ray, complete blood count and serum chemistry were unremarkable. Proteomic examination revealed protein alterations in synovial fluid, with significant increases in Vitamin D-binding protein precursor (ANOVA, p < 0.004) and Kinogen-1 (ANOVA, p < 0.039). Both proteins correlated with arthritis.

• Development and Reproduction
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• v.8 no.1
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• pp.1-9
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• 2004

The potential importance of proteomic approaches has been clearly demonstrated in other fields of human medical research, including liver and heart disease and certain forms of cancer. However, reproductive researches have been applied to proteomics poorly. Proteomics can be defined as the systematic analysis of proteins for their identity, quantity, and function. It could increase the predictability of early drug development and identify non-invasive biomarkers of toxicity or efficacy. Proteome analysis is most commonly accomplished by the combination of two-dimensional gel electrophoresis(2DE) and MALDI-TOF(matrix-assisted laser desorption ionization-time of flight) MS(mass spectrometry) or protein chip array and SELDI-TOF(surface-enhanced laser desorption ionization-time of flight) MS. In addition understanding the possessing knowledge of the developing biomarkers used to assess reproductive biology will also be essential components relevant to the topic of reproduction. The continued integration of proteomic and genomic data will have a fundamental impact on our understanding of the normal functioning of cells and organisms and will give insights into complex cellular processes and disease and provides new opportunities for the development of diagnostics and therapeutics. The challenge to researchers in the field of reproduction is to harness this new technology as well as others that are available to a greater extent than at present as they have considerable potential to greatly improve our understanding of the molecular aspects of reproduction both in health and disease.

• Analytical Science and Technology
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• v.30 no.6
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• pp.348-354
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• 2017

In this study, patterns of proteome expression were monitored and specifically expressed proteins in human milk were detected in collected human milk after 1 week, 3 weeks, and 6 weeks from delivery. A quantitative shotgun proteomic approach was used to identify human milk proteins and reveal their relative expression amounts. For each sample, two independent human milk samples from two mothers were pooled, and then three replicated shotgun proteomic analyses were carried out. Casein, which is a highly abundant protein in human milk, was removed, and then trypsin was treated to produce a digested peptide mixture. The peptides were loaded in the home-made reversed-phase C18 fused-silica capillary column, and then the eluted peptides were analyzed by using a linear ion-trap mass spectrometer. The relative quantitation of proteins was performed by the normalized spectral count method. For each sample, 81-109 non-redundant proteins were identified. The identified proteins consisted of glycoproteins, metabolic enzyme, and chaperon enzymes such as lactoferrin, carboxylic ester hydrolase, and clusterin. The comparative analysis for the 63 proteins, which were reproducibly identified in all three replications, revealed that 25 proteins were statically significant differentially expressed. Among the differentially expressed proteins, Ig lambda-7 chain C region and tenascin drastically decreased with the delivery time.

• Molecules and Cells
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• v.40 no.7
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• pp.466-475
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• 2017

Dietary supplements have exhibited myriads of positive health effects on human health conditions and with the advent of new technological advances, including in the fields of proteomics, genomics, and metabolomics, biological and pharmacological activities of dietary supplements are being evaluated for their ameliorative effects in human ailments. Recent interests in understanding and discovering the molecular targets of phytochemical-gene-protein-metabolite dynamics resulted in discovery of a few protein signature candidates that could potentially be used to assess the effects of dietary supplements on human health. Persimmon (Diospyros kaki) is a folk medicine, commonly used as dietary supplement in China, Japan, and South Korea, owing to its different beneficial health effects including anti-diabetic implications. However, neither mechanism of action nor molecular biomarkers have been discovered that could either validate or be used to evaluate effects of persimmon on human health. In present study, Mass Spectrometry (MS)-based proteomic studies were accomplished to discover proteomic molecular signatures that could be used to understand therapeutic potentials of persimmon leaf extract (PLE) in diabetes amelioration. Saliva, serum, and urine samples were analyzed and we propose that salivary proteins can be used for evaluating treatment effectiveness and in improving patient compliance. The present discovery proteomics study demonstrates that salivary proteomic profile changes were found as a result of PLE treatment in prediabetic subjects that could specifically be used as potential protein signature candidates.

• Journal of Life Science
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• v.17 no.12
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• pp.1649-1653
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• 2007

High temperature stresses have caused growth inhibition and delayed heading in highland cultivation Chinese cabbage during summer in Korea. We have studied high temperature stress responses in the terms of changes of inorganic components and proteins by proteomic analyses. Insufficiencies of nitrogen and phosphorus have affected growth rate and calcium deficiency has caused blunted heading. Proteins extracted from Brassica seedling grown at the altitude of 600m and 900m in the Mount Jilun were extracted and analysed by 2-dimentional polyacrylamide gel electrophoresis. Profiles of protein expression was then analyzed by 2-dimentional gel analyses. Protein spots showing different expression level were picked using the spot handling workstation and subjected to MALDI-TOF MS. Total 48 protein spots were analyzed by MALDI-TOF MS and 30 proteins spots out of 48 were identified by peptide mass fingerprinting analyses. Fourteen proteins were up-regulated in extracts from the altitude of 900m and they were identified as oxygen-evolving proteins, rubisco activase and ATPase etc. Sixteen proteins were up-regulated in extracts from the altitude of 600m and they were identified as glutathione S-transferase(1, 28kD cold induced- and 24 kD auxin-binding proteins) and salt-stress induced protein etc. These stress-induced proteins were related to the mediated protective mechanism against oxidative damage during various stresses. The results indicated that physiological phenomenon in response to high temperature stresses might be resulted by complex and multiple array of responses with drought, heat, oxidative, salt, and cold by high temperature.

• Journal of Plant Biotechnology
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• v.48 no.3
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• pp.165-172
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• 2021

The solubilization of isolated proteins into the adequate buffer containing of surfactants is primary step for proteomic analysis. Particularly, sodium dodecyl sulfate (SDS) is the most widely used surfactant, however, it is not compatible with mass spectrometry (MS). Therefore, it must be removed prior to MS analysis through rigorous washing, which eventually results in inevitable protein loss. Recently, photocleavable surfactant, 4-hexylphenylazosulfonate (Azo), was reported which can be easily degraded by UV irradiation and is compatible with MS during proteomic approach using animal tissues. In this study, we employed comparative label-free proteomic analysis for evaluating the solubilization efficacies of the Azo and SDS surfactants using rice leave proteins. This approach led to identification of 3,365 proteins of which 682 proteins were determined as significantly modulated. Further, according to the subcellular localization prediction in SDS and Azo, proteins localized in the chloroplast were the major organelle accounting for 64% of the total organelle in the SDS sample, while only 37.5% of organelle proteins solubilized in the Azo were predicted to be localized in chloroplast. Taken together, this study validates the efficient solubilization of total protein isolated from plant material for bottom-up proteomics. Azo surfactant is suitable as substitute of SDS and promising for bottom-up proteomics as it facilitates robust protein extraction, rapid washing step during enzymatic digestion, and MS analysis.