• Journal of Microbiology and Biotechnology
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• v.29 no.7
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• pp.1155-1164
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• 2019

Lichens contain diverse bioactive secondary metabolites with various chemical and biological properties, which have been widely studied. However, details of the inhibitory mechanisms of their secondary metabolites against influenza A virus (IAV) have not been documented. Here, we investigated the antiviral effect of lichen extracts, obtained from South Korea, against IAV in MDCK cells. Of the lichens tested, Nipponoparmelia laevior (LC24) exhibited the most potent inhibitory effect against IAV infection. LC24 extract significantly increased cell viability, and reduced apoptosis in IAV-infected cells. The LC24 extract also markedly reduced (~ 3.2 log-fold) IAV mRNA expression after 48 h of infection. To understand the antiviral mechanism of LC24 against IAV, proteomic (UPLC-$HDMS^E$) analysis was performed to compare proteome modulation in IAV-infected (V) vs. mock (M) and LC24+IAV (LCV) vs. V cells. Based on Ingenuity Pathway Analysis (IPA), LC24 inhibited IAV infection by modulating several antiviral-related genes and proteins (HSPA4, HSPA5, HSPA8, ANXA1, ANXA2, $HIF-1{\alpha}$, AKT1, MX1, HNRNPH1, HNRNPDL, PDIA3, and VCP) via different signaling pathways, including $HIF-1{\alpha}$ signaling, unfolded protein response, and interferon signaling. These molecules were identified as the specific biomarkers for controlling IAV in vitro and further confirmation of their potential against IAV in vivo is required. Our findings provide a platform for further studies on the application of lichen extracts against IAV.

• Journal of Plant Biotechnology
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• v.49 no.2
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• pp.118-123
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• 2022

To obtain information on the molecular mechanism underlying the low temperature tolerance of sweet potato [Ipomoea batatas (L.) Lam], the proteome expressed in the sweet potato cultivar Xushu 15-1 with high cold storage tolerance and in the cultivar Xushu 15-4 with low cold storage tolerance was analyzed using 2-D and MALDI-TOF/TOF analyses. Compared with the control (without cold treatment), four protein spots were newly expressed in Xushu 15-1. The expression level of one protein spot was higher in Xushu 15-4 than in Xushu 15-1. Spot 2, which was newly expressed in Xushu 15-1, was identified as sporamin. Assessment of the change in protein expression levels over 8 weeks in the storage roots of the two cultivars treated at 4℃ revealed no significant difference in the expression levels in Xushu 15-1 over time. However, in Xushu 15-4, the expression level of one protein spot increased, while those of four spots decreased. Of the proteins with reduced expression levels, spots 7 and 8 were identified as actin and spots 9 and 10 were identified as fructokinase-like proteins. The present results are expected to enhance the understanding of the complex mechanism underlying the low temperature tolerance of sweet potatoes during storage and can be used to identify candidate genes for the development of new varieties of sweet potatoes with improved low temperature tolerance during cold storage in the future.

• Journal of Microbiology
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• v.44 no.6
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• pp.632-640
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• 2006

In this study, the biodegradative activities of monocyclic aromatic compounds were determined from the multi-drug resistant (MDR) Acinetobacter baumannii, which were studied in the form of clinical isolates from a hospital in Korea. These bacteria were capable of biodegrading monocyclic aromatic compounds, such as benzoate and p-hydroxybenzoate. In order to determine which pathways are available for biodegradation in these stains, we conducted proteome analyses of benzoate, and p-hydroxybenzoate-cultured A. baumannii DU202, using 2-DE/MS analysis. As genome DB of A. baumannii was not yet available, MS/MS analysis or de novo sequencing methods were employed in the identification of induced proteins. Benzoate branch enzymes [catechol 1,2-dioxygenase (CatA) and benzoate dioxygenase $\alpha$ subunit (BenA)] of the $\beta$-ketoadipate pathway were identified under benzoate culture condition and p-hydroxybenzoate branch enzymes [protocatechuate 3,4-dioxygenas $\alpha$ subunit (PcaG) and 3-carboxy-cis,cis-muconate cycloisomerase (PcaR)] of the $\beta$-ketoadipate pathway were identified under p-hydroxybenzoate culture condition, respectively, thereby suggesting that strain DU202 utilized the $\beta$-ketoadipate pathway for the biodegradation of monocyclic aromatic compounds. The sequence analysis of two purified dioxygenases (CatA and PcaGH) indicated that CatA is closely associated with the CatA of Acinetobacter radiresistance, but PcaGH is only moderately associated with the PcaGH of Acinetobacter sp. ADPI. Interestingly, the fused form of PcaD and PcaC, carboxymuconolactone decarboxylase (PcaCD), was detected on benzoate-cultured A. baumannii DU202. These results indicate that A. baumannii DU202 exploits a different $\beta$-ketoadipate pathway from other Acinetobacter species.

• 한국생물공학회:학술대회논문집
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• 2005.04a
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• pp.47-47
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• 2005

There are many different surface technologies currently applied for preparation of protein chips. However, it requires innovative surface chemistry for capture proteins to be immobilized on chip surface keeping their conformation and activity intact and their orientation right, while they bind tightly and densely in a given array spot. Proteogen has developed 'ProteoChip BP' coated with novel proprietary linker molecules $(ProLinker^{TM})$ for efficient and robust immobilizations of capture proteins by improving surface properties of molecular captures. It was demonstrated that $ProLinker^{TM}$ gave the best surface performance in preparation of protein microarray chip base plates among others currently available on the market. In particular, the $ProLinker^{TM}-based$ surface chemistry has demonstrated to provide excellent performance in preparation of 'Antibody Chip' for analysis of biomarkers as well as proteome expression profiles. The linker molecule has also shown to be well applicable for development of biosensors and micro-beads as well as protein microarray and nano-array. ProteoChip BP can be used either for preparation of high-density array by using a microarrayer or for preparation of 'Well-on-a-Chip' with low density array, which is better applicable for quantitative analysis of biomarkers or protein-protein interactions. The biomarker assay can be performed either by direct or sandwich methods of fluorescence immunoassay. Application of ProteoChip BP has been well demonstrated by the extensive studies of 1) tumor-marker assays, 2) new drug screening by using 'Integrin Chip' and 3) protein expression profile analysis. Some of experimental results will be presented.

• Journal of The Korean Society of Grassland and Forage Science
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• v.34 no.4
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• pp.262-268
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• 2014

In order to reveal the aluminum (Al) stress tolerance mechanisms in alfalfa plant at low pH soil, a proteomic approach has been conducted. Alfalfa plants were exposed to Al stress for 5 days. The plant growth and total chlorophyll content are greatly affected by Al stress. The malondialdehyde (MDA) and $H_2O_2$ contents were increased in a low amount but free proline and soluble sugar contents, and the DPPH-radical scavenging activity were highly increased. These results indicate that antioxidant activity (DPPH activity) and osmoprotectants (proline and sugar) may involve in ROS ($H_2O_2$) homeostasis under Al stress. In proteomic analysis, over 500 protein spots were detected by 2-dimentional gel electrophoresis analysis. Total 17 Al stress-induced proteins were identified, of which 8 protein spots were up-regulated and 9 were down-regulated. The differential expression patterns of protein spots were selected and analyzed by the peptide mass fingerprinting (PMF) using MALDI-TOF MS analysis. Three protein spots corresponding to Rubisco were significantly down-regulated whereas peroxiredoxin and glutamine synthetase were up-regulated in response to Al stress. The different regulation patterns of identified proteins were involved in energy metabolism and antioxidant / ROS detoxification during Al stress in alfalfa. Taken together, these results provide new insight to understand the molecular mechanisms of alfalfa plant in terms of Al stress tolerance.

• Molecules and Cells
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• v.40 no.9
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• pp.685-695
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• 2017

Obesity and the metabolic disorders that constitute metabolic syndrome are a primary cause of morbidity and mortality in the world. Nonetheless, the changes in the proteins and the underlying molecular pathways involved in the relevant pathogenesis are poorly understood. In this study a proteomic analysis of the visceral adipose tissue isolated from metabolically healthy and unhealthy obese patients was used to identify presence of altered pathway(s) leading to metabolic dysfunction. Samples were obtained from 18 obese patients undergoing bariatric surgery and were subdivided into two groups based on the presence or absence of comorbidities as defined by the International Diabetes Federation. Two dimensional difference in-gel electrophoresis coupled with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry was carried out. A total of 28 proteins were identified with a statistically significant difference in abundance and a 1.5-fold change (ANOVA, $p{\leq}0.05$) between the groups. 11 proteins showed increased abundance while 17 proteins were decreased in the metabolically unhealthy obese compared to the healthy obese. The differentially expressed proteins belonged broadly to three functional categories: (i) protein and lipid metabolism (ii) cytoskeleton and (iii) regulation of other metabolic processes. Network analysis by Ingenuity pathway analysis identified the $NF{\kappa}B$, IRK/MAPK and PKC as the nodes with the highest connections within the connectivity map. The top network pathway identified in our protein data set related to cellular movement, hematological system development and function, and immune cell trafficking. The VAT proteome between the two groups differed substantially between the groups which could potentially be the reason for metabolic dysfunction.

• Korean Journal of Veterinary Research
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• v.45 no.2
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• pp.155-161
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• 2005

Proteomics is a useful approach to know protein expression, post-translational modification and protein function. We investigated the protein expression pattern and identity in chickens fed with the tissue culture medium waste after harvest of Korean wild ginseng (TCM-KWG) (Panax ginseng). Two groups (n=60/group) of day old broiler chickens were administered with 0 (control) and 0.8% (treatment) TCM-KWG through drinking water. After 5 weeks, we examined the protein expression pattern of fibularis longus and superficial pectoral muscle by Two-dimensional electrophoresis analysis. Interestingly, TCM-KWG treatment significantly increased five spot's density, and markedly reduced five spot's density in the muscles. We identified 10 proteins (desmin, myosin light chain 1, heat shock 25 kDa protein, collapsin response mediator protein-2A, alpha enolase, vimentin, actin alpha 1, my023 protein, pyruvate kinase and troponin T) by the matrix-assisted laser desorption ionization time of flight (MALDI-TOF).

• BMB Reports
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• v.41 no.8
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• pp.597-603
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• 2008

Atopic dermatitis (AD) is a chronic inflammatory skin disease that induces changes in various inflammatory skin cells. The prevalence of AD is as high as 18% in some regions of the world, and is steadily rising. However, the pathophysiology of AD is poorly understood. To identify the proteins involved in AD pathogenesis, a comparative proteomic analysis of protein expression in peripheral blood mononuclear cells isolated from AD patients and healthy donors was conducted. Significant changes were observed in the expressions of fourteen proteins, including the vinculin, PITPNB, and Filamin A proteins. Among the proteins, $\alpha$-SNAP and FLNA decreased significantly, and PITPNB increased significantly in AD patients compared with control subjects; these findings were further confirmed by real-time PCR and Western blot analysis. The comparative proteome data may provide a valuable clue to further understand AD pathogenesis, and several differentially regulated proteins may be used as biomarkers for diagnosis and as target proteins for the development of novel drugs.

• KSBB Journal
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• v.22 no.6
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• pp.393-400
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• 2007

Analysis of protein interactions/functions in a microarray format has been of great potential in drug discovery, diagnostics, and cell biology, because it is amenable to large-scale and high-throughput biological assays in a rapid and economical way. In recent years, the protein microarray have broaden their utility towards the global analysis of protein interactions on a proteome scale, the functional activity analysis based on protein interactions and post-translational modifications (PTMs), and the discovery of biomarkers through profiling of protein expression between sample and reference pool. As a promising tool for proteomics, the protein microarray technology has advanced outstandingly over the past decade in terms of surface chemistry, acquisition of relevant proteins on a proteomic level, and detection methods. In this article, we briefly describe various techniques for development of protein microarray, and introduce developmental state of protein microarray and its applications.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.51 no.1
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• pp.66-72
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• 2006

Spikelet proteins expressed at the young microspore stage in rice were separated and analysed by two-dimensional polyacrylamide gel electrophoresis (2DE). The separated proteins were electro blotted onto a polyvinylidene difluoride (PVDF) membrane, and 50 proteins were analyzed by a gas-phase protein sequencer. The N-terminal amino acid sequences of 20 out of 50 proteins were determined. N-terminal regions of the remaining proteins could not be sequenced because of blocking. The internal amino acid sequences of proteins were determined by sequence analysis of peptides obtained by the Cleveland peptide mapping method. Results revealed the presence of the photosynthetic apparatus at rice young microspore stage. Major proteins identified in this study could be used as a marker for various studies on physiological stresses.