• Asian-Australasian Journal of Animal Sciences
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• v.24 no.1
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• pp.110-124
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• 2011

Anatomically separate fat depots differ in size, function, and contribution to pathological states such as the metabolic syndrome. We isolated pre-adipocytes from different adipose depots, omental, subcutaneous and intramuscular, of beef cattle, and cultured in vitro to determine the basis for the variations and attribute these variations to the inherent properties of adipocyte progenitors. The proliferating cells from all depots before the confluence were harvested and the proteome was analyzed by a functional proteomic approach, involving 2-DE and MALDI-TOF/TOF. More than 252 protein spots were identified, selected and analyzed by Image Master (ver 7.0) and MALDI-TOF/TOF. Further, our analysis showed that there were specific differences in proteome expression patterns among proliferating precursor cells from the three depots. Sixteen proteins were found to be differentially expressed and these were identified as proteins involved in cellular processes, heat shock/chaperones, redox proteins, cytoskeletal proteins and metabolic enzymes. The results also enabled us to understand the basic roles of these proteins in different inherent properties exhibited by adipose tissue depots.

• The Plant Pathology Journal
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• v.24 no.2
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• pp.191-201
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• 2008

Bacillus sp. SB-007 was isolated from pea leaves harvested from the southwestern parts of South Korea through screening on a minimal medium containing 0.2% purified cutin for its ability to induce the cutinase production. However, no cutinase was produced when it was grown in a minimal medium containing 0.2% glucose. A proteomic approach was applied to separate and characterize these differentially secreted proteins. The expression level of 83 extracellular proteins of the cutinase-producing Bacillus sp. strain SB-007 incubated in a cutinase-induced medium increased significantly as compared with that cultured in a non cutinase-induced medium containing glucose. The extracellular proteome of Bacillus sp. SB-007 includes proteins from different functional classes, such as enzymes for the degradation of various macromolecules, proteins involved in energy metabolism, sporulation, transport/binding proteins and lipoproteins, stress inducible proteins, several cellular molecule biosynthetic pathways and catabolism, and some proteins with an as yet unknown function. In addition, the two protein spots showed little similarities with the known lipolytic enzymes in the database. These secreted proteome analysis results are expected to be useful in improving the Bacillus strains for the production of industrial cutinases.

• Journal of Microbiology and Biotechnology
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• v.27 no.1
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• pp.171-178
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• 2017

A series of novel effector molecules secreted by the type three secretion system (T3SS) of Shigella spp. have been reported in recent years. In this study, a proteomic approach was applied to study T3SS effectors systematically. First, proteins secreted by the S. flexneri wild-type strain after Congo Red induction were separated and identified using two-dimensional electrophoresis to display the relative abundance of all kinds of early effectors for the first time. Then, a gene deletion mutant of known virulence repressor (OspD1) and a gene overexpressed mutant of two known virulence activators (MxiE and IpgC) were constructed and analyzed to discover potential late effectors. Furthermore, the supernatant proteins of gene deletion mutants of two known translocators (IpaB and IpaD), which would constantly secrete effectors, were also analyzed. Among all of the secreted proteins identified in our study, IpaH1.4, IpaH_5, and IpaH_7 have not been reported before. These proteomics data of the secreted effectors will be valuable to understand the pathogenesis of S. flexneri.

• Journal of Microbiology and Biotechnology
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• v.27 no.3
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• pp.624-632
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• 2017

Penicillium expansum causes blue mold rot, a prevalent postharvest disease of pome fruit, and is also the main producer of the patulin. However, knowledge on the molecular mechanisms involved in this pathogen-host interaction remains largely unknown. In this work, a two-dimensional gel electrophoresis-based proteomic approach was applied to probe changes in P. expansum 3.3703 cultivated in apple juice medium, which was used to mimic the in planta condition. The results showed that the pH value and reducing sugar content in the apple juice medium decreased whereas the patulin content increased with the growing of P. expansum. A total of 28 protein spots that were up-regulated in P. expansum when grown in apple juice medium were identified. Functional categorization revealed that the identified proteins were mainly related to carbohydrate metabolism, secondary metabolism, protein biosynthesis or degradation, and redox homeostasis. Remarkably, several induced proteins, including glucose dehydrogenase, galactose oxidase, and FAD-binding monooxygenase, which might be responsible for the observed medium acidification and patulin production, were also detected. Overall, the experimental results provide a comprehensive interpretation of the physiological and proteomic responses of P. expansum to the host plant environment, and future functional characterization of the identified proteins will deepen our understanding of fungi-host interactions.

• Journal of Microbiology and Biotechnology
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• v.29 no.11
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• pp.1806-1816
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• 2019

Candida albicans is an opportunistic fungus possessing multiple virulence factors controlling pathogenicity. Cell wall proteins are the most important among these factors, being the first elements contacting the host. Ddr48 is a cell wall protein consisting of 212 amino acids. A DDR48 haploinsufficient mutant strain was previously found necessary for proper oxidative stress response and drug resistance. In this study, we aimed to further elucidate the role of Ddr48 by performing additional phenotypic characterization assays. A combinatory proteomic and bioinformatics approach was also undertaken to determine differentially expressed cell wall proteins. Results showed that the mutant strain exhibited a 10% decrease in adhesion mirrored by a 20% decrease in biofilm formation, and slight sensitivity to menadione, diamide, and SDS. Both strains showed similar hyphae formation, virulence, temperature tolerance, and calcofluor white and Congo red sensitivities. Furthermore, a total of 8 and 10 proteins were identified exclusively in the wild-type strain grown under filamentous and non-filamentous conditions respectively. Results included proteins responsible for superoxide stress resistance (Sod4 and Sod6), adhesion (Als3, Hyr4, Pmt1, and Utr2), biofilm formation (Hsp90, Ece1, Rim9, Ipp1, and Pra1) and cell wall integrity (Utr2 and Pga4). The lack of detection of these proteins in the mutant strain correlates with the observed phenotypes.

• Journal of Plant Biotechnology
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• v.39 no.4
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• pp.261-272
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• 2012

Environmental factors greatly influence the growth, development, and even genetic characteristics of plants. The mechanisms by which sound influences plant growth, however, remain obscure. Previously, our group reported that several genes were differentially regulated by specific frequenciesof sound treatmentusing a sound-treated subtractive library. In this study, we used a proteomic approach to investigate plant responses to sound waves in Arabidopsis. The plants were exposed to 250-Hz or 500-Hz sound waves, and total proteins were extracted from leaves 8 h and 24 h after treatment. Proteins extracted from leaves were subjected to 2-DE analysis. Thirty-eight spots were found to be differentially regulated in response to sound waves and were identified using MALDI-TOF MS and MALDI-TOF/TOF MS. The functions of the identified proteins were classified into photosynthesis, stress and defense, nitrogen metabolism, and carbohydrate metabolism. To the best of our knowledge, this is the first report on the analysis of protein changes in response to sound waves in Arabidopsis leaves. These findings provide a better understanding of the molecular basis of responses to sound waves in Arabidopsis.

• International Journal of Oral Biology
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• v.34 no.1
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• pp.29-36
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• 2009

Cyclosporin A (CsA) has been used clinically as an immunosuppressive drug to prevent organ transplant rejection and in basic research as a mitochondrial permeability blocker. It has been reported that CsA has a protective role in severed neurons and a neurotrophic effect in neuronal cells. However, the molecular mechanisms underlying the stimulation of neuronal cell proliferation by CsA have not yet been elucidated. In our current study, we investigated CsA responsive proteins in PC12 cells using a systematic proteomic approach. The viability of these cells following CsA treatment increased in a dose- and time-dependent manner. Proteins in the CsA-treated PC12 cells were profiled by two-dimensional gel electrophoresis (2-DE) and identified by matrix-assisted laser desorption ionization time-of flight (MALDI-TOF) and electrospray ionization quadupole time-of-flight mass spectrometries (EIQ-TOFMS). This differential expression analysis showed significant changes for 10 proteins (6 up-regulated and 4 down-regulated) upon CsA treatment that were related to cell proliferation, metabolism and the stress response. These proteomics data further our understanding of the proliferation mechanisms of PC12 cells exposed to CsA and demonstrate that our methodology has potential to further elucidate the mechanisms and pathways involved.

• Journal of Ginseng Research
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• v.44 no.1
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• pp.50-57
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• 2020

Background: The cellular senescence of primary cultured cells is an irreversible process characterized by growth arrest. Restoration of senescence by ginsenosides has not been explored so far. Rg3(S) treatment markedly decreased senescence-associated β-galactosidase activity and intracellular reactive oxygen species levels in senescent human dermal fibroblasts (HDFs). However, the underlying mechanism of this effect of Rg3(S) on the senescent HDFs remains unknown. Methods: We performed a label-free quantitative proteomics to identify the altered proteins in Rg3(S)-treated senescent HDFs. Upregulated proteins induced by Rg3(S) were validated by real-time polymerase chain reaction and immunoblot analyses. Results: Finally, 157 human proteins were identified, and variable peroxiredoxin (PRDX) isotypes were highly implicated by network analyses. Among them, the mitochondrial PRDX3 was transcriptionally and translationally increased in response to Rg3(S) treatment in senescent HDFs in a time-dependent manner. Conclusion: Our proteomic approach provides insights into the partial reversing effect of Rg3 on senescent HDFs through induction of antioxidant enzymes, particularly PRDX3.

• The Korean Journal of Pain
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• v.21 no.2
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• pp.112-118
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• 2008

Background: This study was conducted to quantitatively analyze proteins associated with the calcitonin gene-related peptide (CGRP) in cerebrospinal fluid (CSF) that was obtained from a rat model of chronic neuropathic pain following administration of intrathecal $CGRP_{8-37}$. Methods: Male Sprague-Dawley rats (100-150 g, 5-6 wks) were divided into two groups, sham controls and neuropathic pain models. At the time of operation for neuropathic pain model, an intrathecal catheter was threaded through the intrathecal space. At 1 or 2 wks after the operation (maximum pain state), a test dose of 1, 5, 10, or 50 nM of $CGRP_{8-37}$ was injected into the intrathecal catheter and the CSF was then aspirated. Conventional proteomics to evaluate the CSF were then performed using high resolution 2-D, gel electrophoresis followed by computational image analysis and protein identification by mass spectrometry. Results: Treatment with $CGRP_{8-37}$ effectively alleviated mechanical allodynia in a dose dependent manner. The most effective response was obtained when a dose of 50 nM was administered, but significant differences were obtained following administration of only 5 nM $CGRP_{8-37}$. Furthermore, the results of the proteomic analysis were consistent with the experimental results. Specially we detected 30 differentially expressed spots in 7 images when 2-D gel electrophoresis was conducted. The intensity of 6 of these spots (spot number: 20 and 26-30) was found decrease the $CGRP_{8-37}$ dose increased; therefore, these spots were evaluated by mass spectrometry. This analysis identified 2 different proteins, CGRP (spot numbers: 26-30) and neurotensin-related peptide (spot number: 20). Conclusions: The results of this study suggest that CGRP plays a role in chronic central neuropathic pain and is a major target of chronic neuropathic pain management.

• Journal of Forest and Environmental Science
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• v.26 no.2
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• pp.83-94
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• 2010

Chinese fir (Latin name: Cunninghaimia lanceolata) is one of the major commercial coniferous trees. Most of Chinese fir forests are managed in successive rotation sites, which lead productivity to decline. Autotoxicity is the important reason for soil degradation of Chinese fir plantation, especially, phenolic acids are considered as the major allelopathic toxins which induce autotoxicity in Chinese fir rotation stands. We performed here proteomic approach to investigate the response of proteins in Chinese fir leaves to salicylic acid. The tube plantlets of Chinese fir clone were treated with 120 mg/L salicylic acid for 1, 3 and 5th day. 2-DE, coupled with MALDI-TOF-TOF/MS, was used to separate and identify the responsive proteins. We found 12, 7, and 12 candidate protein spots that were up- or down-regulated by at least 2.5 fold after 1, 3, and 5th day of the stress, respectively. Of these protein spots, 16 spots were identified successfully. According to the putative physiological functions, these proteins were categorized into five classes (1) the proteins involved in protein stability and folding, including 26S proteome, Grp78, Hsp70, Hsp90 and PPIase; (2) the protein involved in photosynthesis and respiration, including OEC 33 kDa subunit, GAPDH; (3) the protein related to cell endurance to acid, F-ATPase; (4) the protein related to cytoskeleton, tubulin; (5) the protein related to protein translation: prolyl-tRNA synthetase. These results give new insights into autotoxic substance stress response in Chinese fir leaves and provide preliminary footprints for further studies on the molecular signal mechanisms induced by the stress.