• Horticultural Science & Technology
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• v.34 no.1
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• pp.32-45
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• 2016

Fruit bagging has been widely practiced in peach cultivation to produce high quality and unblemished fruit. Moreover, fruit bagging has been utilized to study the effect of shading on the quality of fruit. We conducted a proteomic analysis on peach fruit to elucidate the biochemical and physiological events that characterize the effect of bagging treatment. Comparative analysis of 2D electrophoresis (2-DE) gels showed that relative protein levels differed significantly at 125 DAFB (days after full bloom), as well as at 133 DAFB in fruit that had been bagged until 125 DAFB, followed by exposure to sunlight. Most of the proteins with altered expression were identified by MALDI TOF/TOF. Twenty-one proteins with differential expression among the groups were identified at 125 DAFB, while thirty proteins with differential expression among the groups were identified at 133 DAFB. The analysis revealed that expression of proteins involved in photosynthesis, stress responses, and biochemical processes influencing metabolism were altered during bagging treatment, suggesting that regulation of the synthesis of carbohydrates, amino acids, and proteins influenced fruit size, solid/acid ratio, and peel color. This work provides the first characterization of proteomic changes in peach in response to fruit bagging treatment. Identifying and tracking protein changes may allow us to better understand the mechanisms underlying the effects of bagging treatment.

• Food Science of Animal Resources
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• v.30 no.3
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• pp.385-391
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• 2010

This study was conducted to compare proteins expressed in M. longissimus from Hanwoo and Holstein steers immediately after slaughter. Two-dimensional electrophoresis (2DE)/LC-MS/MS analysis revealed that the total number of detectable protein spots from longissimus muscle tissues was slightly higher in Hanwoo ($575{\pm}65$) than Holstein ($534{\pm}13$) steers, but that these numbers were not statistically significant due to large variation between replicates. A total of twelve protein spots did not match between sample groups, eight of which were expressed in the Hanwoo sample and four that were expressed in the Holstein sample. The protein spots detected in the Hanwoo sample included smooth muscle and non-muscle myosin alkali light chain 6B isomers, ${\alpha}B$ crystallin isomers, hemoglobin ${\beta}$-A chains, slow myosin heavy chains, and slow skeletal muscle troponin T chains. Collectively, these proteins are a class of slow-twitch muscle fiber and mirror that Hanwoo muscle tissue sampled for the current study contained more slow-twitch muscle fibers than Holstein one. Conversely, proteins detected from the Holstein sample included ankyrin repeat domain 2 and creatin kinase isomers. Given that creatin kinase isomers are related to the fast-twitch muscle, these results likely indicate that Holstein muscle tissue sampled for the current study contained more fast-twitch muscle fibers than Hanwoo beef.

• Korean Journal of Agricultural Science
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• v.45 no.4
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• pp.635-643
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• 2018

Bovine milk is widely consumed by humans and is a primary ingredient of dairy foods. Proteomic approaches have the potential to elucidate complex milk proteins and have been used to study milk of various species. Here, we performed a proteomic analysis using 2-dimensional electrophoresis (2-DE) and matrix assisted laser desorption ionization-time of flight mass spectrometer (MALDI-TOF MS) to identify whey proteins in bovine milk obtained soon after parturition (bovine early milk). The major casein proteins were removed, and the whey proteins were analyzed with 2-dimensional polyacrylamide gel electrophoresis (2-D PAGE). The whey proteins (2 mg) were separated by pI and molecular weight across pH ranges of 3.0 - 10.0 and 4.0 - 7.0. The 2-DE gels held about 300 to 700 detectable protein spots. We randomly picked 12 and nine spots that were consistently expressed in the pH 3.0 - 10.0 and pH 4.0 - 7.0 ranges, respectively. Following MALDI-TOF MS analysis, the 21 randomly selected proteins included proteins known to be present in bovine milk, such as albumin, lactoferrin, serum albumin precursor, T cell receptor, polymeric immunoglobulin receptor, pancreatic trypsin inhibitor, aldehyde oxidase and microglobulin. These proteins have major functions in immune responses, metabolism and protein binding. In summary, we herein identified both known and novel whey proteins present in bovine early milk, and our sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis revealed their expression pattern.

• Journal of Ginseng Research
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• v.45 no.1
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• pp.58-65
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• 2021

Background: Panax ginseng, as one of the most widely used herbal medicines worldwide, has been studied comprehensively in terms of the chemical components and pharmacology. The proteins from ginseng are also of great importance for both nutrition value and the mechanism of secondary metabolites. However, the proteomic studies are less reported in the absence of the genome information. With the completion of ginseng genome sequencing, the proteome profiling has become available for the functional study of ginseng protein components. Methods: We optimized the protein extraction process systematically by using SDS-PAGE and one-dimensional liquid chromatography mass spectrometry. The extracted proteins were then analyzed by two-dimensional chromatography separation and cutting-edge mass spectrometry technique. Results: A total of 2,732 and 3,608 proteins were identified from ginseng root and cauline leaf, respectively, which was the largest data set reported so far. Only around 50% protein overlapped between the cauline leaf and root tissue parts because of the function assignment for plant growing. Further gene ontology and KEGG pathway revealed the distinguish difference between ginseng root and leaf, which accounts for the photosynthesis and metabolic process. With in-deep analysis of functional proteins related to ginsenoside synthesis, we interestingly found the cytochrome P450 and UDP-glycosyltransferase expression extensively in cauline leaf but not in the root, indicating that the post glucoside synthesis of ginsenosides might be carried out when growing and then transported to the root at withering. Conclusion: The systematically proteome analysis of Panax ginseng will provide us comprehensive understanding of ginsenoside synthesis and guidance for artificial cultivation.

• 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.

• Animal Bioscience
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• v.34 no.9
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• pp.1439-1450
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• 2021

Objective: With the rapid development of proteomics sequencing and RNA sequencing technology, multi-omics analysis has become a current research hotspot. Our previous study indicated that Xinjiang brown cattle have better meat quality than Kazakh cattle. In this study, Xinjiang brown cattle and Kazakh cattle were used as the research objects. Methods: Proteome sequencing and RNA sequencing technology were used to analyze the proteome and transcriptome of the longissimus dorsi muscle of the two breeds of adult steers (n = 3). Results: In this project, 22,677 transcripts and 1,874 proteins were identified through quantitative analysis of the transcriptome and proteome. By comparing the identified transcriptome and proteome, we found that 1,737 genes were identified at both the transcriptome and proteome levels. The results of the study revealed 12 differentially expressed genes and proteins: troponin I1, crystallin alpha B, cysteine, and glycine rich protein 3, phosphotriesterase-related, myosin-binding protein H, glutathione s-transferase mu 3, myosin light chain 3, nidogen 2, dihydropyrimidinase like 2, glutamate-oxaloacetic transaminase 1, receptor accessory protein 5, and aspartoacylase. We performed functional enrichment of these differentially expressed genes and proteins. The Kyoto encyclopedia of genes and genomes results showed that these differentially expressed genes and proteins are enriched in the fatty acid degradation and histidine metabolism signaling pathways. We performed parallel reaction monitoring (PRM) verification of the differentially expressed proteins, and the PRM results were consistent with the sequencing results. Conclusion: Our study provided and identified the differentially expressed genes and proteins. In addition, identifying functional genes and proteins with important breeding value will provide genetic resources and technical support for the breeding and industrialization of new genetically modified beef cattle breeds.

• BMB Reports
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• v.55 no.11
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• pp.571-576
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• 2022

Advancements in the field of proteomics have provided opportunities to develop diagnostic and therapeutic strategies against various diseases. About half of the world's population remains at risk of malaria. Caused by protozoan parasites of the genus Plasmodium, malaria is one of the oldest and largest risk factors responsible for the global burden of infectious diseases with an estimated 3.2 billion persons at risk of infection. For epidemiological surveillance and appropriate treatment of individuals infected with Plasmodium spp., timely detection is critical. In this study, we used combinations of depletion of abundant plasma proteins, 2-dimensional gel electrophoresis (2-DE), image analysis, LC-MS/MS and western blot analysis on the plasma of healthy donors (100 individuals) and vivax and falciparum malaria patients (100 vivax malaria patients and 8 falciparum malaria patients). These analyses revealed that α1-antichymotrypsin (AACT) protein levels were elevated in vivax malaria patient plasma samples (mean fold-change ± standard error: 2.83 ± 0.11, based on band intensities), but not in plasma from patients with other mosquito-borne infectious diseases. The results of AACT immunoblot analyses showed that AACT protein was significantly elevated in vivax and falciparum malaria patient plasma samples (≥ 2-fold) compared to healthy control donor plasma samples, which has not been previously reported.

• BMB Reports
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• v.55 no.5
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• pp.226-231
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• 2022

It is well-known that some species of lizard have an exceptional ability known as caudal autotomy (voluntary self-amputation of the tail) as an anti-predation mechanism. After amputation occurs, they can regenerate their new tails in a few days. The new tail section is generally shorter than the original one and is composed of cartilage rather than vertebrae bone. In addition, the skin of the regenerated tail distinctly differs from its original appearance. We performed a proteomics analysis for extracts derived from regenerating lizard tail tissues after amputation and found that endoplasmin (ENPL) was the main factor among proteins up-regulated in expression during regeneration. Thus, we performed further experiments to determine whether ENPL could induce chondrogenesis of tonsil-derived mesenchymal stem cells (T-MSCs). In this study, we found that chondrogenic differentiation was associated with an increase of ENPL expression by ER stress. We also found that ENPL was involved in chondrogenic differentiation of T-MSCs by suppressing extracellular signal-regulated kinase (ERK) phosphorylation.

• Mass Spectrometry Letters
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• v.13 no.3
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• pp.84-94
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• 2022

Neoadjuvant chemoradiotherapy (nCRT) is a standard therapy used for locally advanced rectal cancer prior to surgery, which can more effectively reduce the locoregional recurrence rate and radiation toxicity compared to postoperative chemoradiotherapy. The response of patients to nCRT varies, and thus, robust biomarkers for predicting a pathological complete response are necessary. This study aimed to identify possible biomarkers involved in the complete response/non-response of rectal cancer patients to nCRT. Comparative proteomic analysis was performed on rectal tissue samples before and after nCRT. Proteins were extracted for label-free proteomic analysis. Western blot and real-time PCR were performed using rectal cancer cell line SNU-503 and radiation-resistant rectal cancer cell line SNU-503R80Gy. A total of 135 up- and 93 down-regulated proteins were identified in the complete response group. Six possible biomarkers were selected to evaluate the expression of proteins and mRNA in SNU-503 and SNU-503R80Gy cell lines. Lyso-phosphatidylcholine acyltransferase 2, annexin A13, aldo-ketose reductase family 1 member B1, and cathelicidin antimicrobial peptide appeared to be potential biomarkers for predicting a pathological complete response to nCRT. This study identified differentially expressed proteins and some potential biomarkers in the complete response group, which would be further validated in future studies.

• Fisheries and Aquatic Sciences
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• v.25 no.7
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• pp.390-402
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• 2022

In this study we investigate physical and chemical characteristics of immature and mature skipjack tuna (Katsuwonus pelamis) roes in fresh and dried forms. Fresh roes were studied for histological structure and also dried by three methods: hot air drying (HD), vacuum drying (VD) and freeze drying (FD). The obtained roe powders were analysed for proximate composition, color value, fatty acid composition, amino acid profile, equivalent umami concentration (EUC) and protein pattern. Unyolked oocytes were more common in immature roes, while fully yolked oocytes were more common in mature roes. All dried tuna roes contained high content of protein and lipid (69.31%-70.55% and 11.14%-16.02%, respectively). The powders obtained by FD provided the highest lightness value (L^*). The main fatty acid found in all roe powders was docosahexaenoic acid (DHA) (23.49%-27.02%). Glutamic acid, leucine, and aspartic acid were the three most abundant amino acids found in the powders (13.58-14.61, 8.06-8.42, and 7.81-8.39 g/100 g of protein, respectively). The mature roe powder obtained from HD provided the highest EUC value (73.09 g monosodium glutamate/100 g of samples). The protein band at molecular weight of 97 kDa (vitelline) represented the major protein. Therefore, dried tuna roe could be a functional ingredient source of protein and lipid rich in DHA and it also has potential to be used as taste enhancer with umami compound.