• BMB Reports
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• v.38 no.6
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• pp.725-738
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• 2005

Resistance to imatinib mesylate (also known as Gleevec, Glivec, and STI571) often becomes a barrier to the treatment of chronic myelogenous leukemia (CML). In order to identify markers of the action of imatinib mesylate, we used a mass spectrometry approach to compare protein expression profiles in human leukemia cells (K562) and in imatinib mesylate-resistant human leukemia cells (K562-R) in the presence and absence of imatinib mesylate. We identified 118 differentially regulated proteins in these two leukemia cell-lines, with and without a $1\;{\mu}M$ imatinib mesylate challenge. Nine proteins of unknown function were discovered. This is the first comprehensive report regarding differential protein expression in imatinib mesylate-treated CML cells.

• Journal of Veterinary Clinics
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• v.32 no.1
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• pp.62-68
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• 2015

There is no reliable indicator available for the diagnosis of horse laminitis, although the disease is common and costly. This study was performed to develop a specific diagnostic biomarker for laminitis. We have identified 33 differentially expressed proteins in plasma of a horse suffering laminitis that is experimentally induced by an overdose of oligofructose, in comparison with normal horse plasma. Among the proteins, myosin-9 mRNA was found in RNA sequencing analysis to be expressed specifically in laminitis tissues compared to other horse tissues. It is thus suggested that expression of plasma myosin-9 may be used for the diagnosis of equine laminitis.

• Genomics & Informatics
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• v.17 no.1
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• pp.2.1-2.12
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• 2019

Chronic obstructive pulmonary disease (COPD) is a type of progressive lung disease, featured by airflow obstruction. Recently, a comprehensive analysis of the transcriptome in lung tissue of COPD patients was performed, but the heterogeneity of the sample was not seriously considered in characterizing the mechanistic dysregulation of COPD. Here, we established a new transcriptome analysis pipeline using a deconvolution process to reduce the heterogeneity and clearly identified that these transcriptome data originated from the mild or moderate stage of COPD patients. Differentially expressed or co-expressed genes in the protein interaction subnetworks were linked with mitochondrial dysfunction and the immune response, as expected. Computational protein localization prediction revealed that 19 proteins showing changes in subcellular localization were mostly related to mitochondria, suggesting that mislocalization of mitochondria-targeting proteins plays an important role in COPD pathology. Our extensive evaluation of COPD transcriptome data could provide guidelines for analyzing heterogeneous gene expression profiles and classifying potential candidate genes that are responsible for the pathogenesis of COPD.

• Molecules and Cells
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• v.23 no.1
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• pp.100-107
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• 2007

The moss Physcomitrella patens has two life cycles, filamentous protonema and leafy gametophore. A modified from of suppression subtractive hybridization (SSH), mirror orientation selection (MOS), was applied to screen genes differentially expressed in the P. patens protonema. Using reverse Northern blot analysis, differentially expressed clones were identified. The identified genes were involved mainly in metal binding and detoxification. One of these genes was an AP2 (APETALA2) domain-containing protein (PpACP1), which was highly up-regulated in the protonema. Alignment with other AP2/EREBPs (Ethylene Responsive Element Binding Proteins) revealed significant sequence homology of the deduced amino acid sequence in the AP2/EREBP DNA binding domain. Northern analysis under various stress conditions showed that PpACP1 was induced by ethephon, cadmium, copper, ABA, IAA, and cold. In addition, it was highly expressed in suspension-cultured protonema. We suggest that PpACP1 is involved in responses to metals, and that suspension culture enhance the expression of genes responding to metals.

• Proceedings of the Korea Society of Poultry Science Conference
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• 2004.11a
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• pp.37-38
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• 2004

Salmonella gallinarum is a pathogen that is capable of causing disease in Korean native chicken. Although Salmonella gallinarum is important world-wide pathogens of poultry, little is understood of the mechanisms of pathogenesis of Salmonella gallinarum in the chicken. This study was to investigate chicken liver proteins affected by infection of Salmonella gallinarum in Korean native chicken. The differentially expressed proteins of chicken livers were identified by using 2-dimensional electro- phoresis (2D-E) and mass spectrometry (MS). We detected more than 300 protein spots on silver stained 2D gels using pH 3∼10 gradients. Three differentially expressed protein spots were analyzed by MALDI-TOF MS and MS/MS. The obtained MS and MS/MS data were searched against a protein database using the Mascot search engine. Further researches on the identified proteins can give valuable information of mechanism of pathogenesis in chicken.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.130-130
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• 2017

Sorghum bicolor is considered as copper-tolerant species. The present study was conducted to understand the copper tolerance mechanism in Sorghum seedling roots. Morphological and effects of Cu on other interacting ions were observed prominently in the roots when the plants were subjected to different concentrations (0, 50, and $100{\mu}M$) of $CuSO_4$. However, the morphological characteristics were reduced by Cu stress, and the most significant growth inhibition was observed in plants treated with the highest concentration of $Cu^{2+}$ ions ($100{\mu}M$). In the proteome analysis, high-throughput two-dimensional polyacrylamide gel electrophoresis coupled with MALDI-TOF-TOF mass spectrometry was performed to explore the molecular responses of Cu-induced sorghum seedling roots. In two-dimensional silver-stained gels, a total of 422 differentially expressed proteins (${\geq}1.5-fold$) were identified using Progenesis SameSpot software. A total of 21 protein spots (${\geq}1.5-fold$) from Cu-induced sorghum roots were analyzed by mass spectrometry. Of the 21 differentially expressed protein spots from Cu-induced sorghum roots, a total of 10 proteins were up-regulated, and 11 proteins were down-regulated. The abundance of the most identified protein species from the roots that function in stress response and metabolism was significantly enhanced, while protein species involved in transcription and regulation were severely reduced. The results obtained from the present study may provide insights into the tolerance mechanism of seedling roots in Sorghum.

• Asian-Australasian Journal of Animal Sciences
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• v.24 no.2
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• pp.272-278
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• 2011

Bovine whey protein expression patterns of colostrum are much different from that of milk. Moreover, bovine colostrum is an important source of protective, nutritional and developmental factors for the newborn. However, to our knowledge, no research has been performed to date using a comparative proteomic method on the changes in the bovine whey proteome during the transition from colostrum to milk. This study therefore separated whey protein of days 1, 3, 7 and 21 after calving using two dimension electrophoresis. Differentially expressed proteins at different collection times were identified using high-performance liquid chromatography in tandem with mass spectrometry (LC/MS) and validated by enzyme-linked immunosorbent assay (ELISA) in order to understand the developmental changes in the bovine whey proteome during the transition from colostrum to milk. The expression patterns of whey protein of days 1 and 3 post-partum were similar except that immunoglobulin G was down-regulated on day 3, and four proteins were found to be down-regulated on days 7 and 21 compared with day 1 after delivering, including immunoglobulin G, immunoglobulin M, albumin, and lactotransferrin, which are involved in immunity and molecule transport. The results of this study confirm the comparative proteomic method has the advantage over other methods such as ELISA and immunoassays in that it can simultaneously detect more differentially expressed proteins. In addition, the difference in composition of milk indicates a need for adjustment of the colostrum feeding regimen to ensure a protective immunological status for newborn calves.

• Animal Bioscience
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• v.34 no.5
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• pp.922-930
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• 2021

Objective: Tibetan pigs, predominantly originating from the Tibetan Plateau, have been subjected to long-term natural selection in an extreme environment. To characterize the metabolic adaptations to hypoxic conditions, transcriptomic and proteomic expression patterns in the livers of Tibetan and Yorkshire pigs were compared. Methods: RNA and protein were extracted from liver tissue of Tibetan and Yorkshire pigs (n = 3, each). Differentially expressed genes and proteins were subjected to gene ontology and Kyoto encyclopedia of genes and genomes functional enrichment analyses. Results: In the RNA-Seq and isobaric tags for relative and absolute quantitation analyses, a total of 18,791 genes and 3,390 proteins were detected and compared. Of these, 273 and 257 differentially expressed genes and proteins were identified. Evidence from functional enrichment analysis showed that many genes were involved in metabolic processes. The combined transcriptomic and proteomic analyses revealed that small molecular biosynthesis, metabolic processes, and organic hydroxyl compound metabolic processes were the major processes operating differently in the two breeds. The important genes include retinol dehydrogenase 16, adenine phosphoribosyltransferase, prenylcysteine oxidase 1, sorbin and SH3 domain containing 2, ENSSSCG00000036224, perilipin 2, ladinin 1, kynurenine aminotransferase 1, and dimethylarginine dimethylaminohydrolase 1. Conclusion: The findings of this study provide novel insight into the high-altitude metabolic adaptation of Tibetan pigs.

• Molecules and Cells
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• v.37 no.6
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• pp.457-466
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• 2014

Proteomic analysis is helpful in identifying cancerassociated proteins that are differentially expressed and fragmented that can be annotated as dysregulated networks and pathways during metastasis. To examine metastatic process in lung cancer, we performed a proteomics study by label-free quantitative analysis and N-terminal analysis in 2 human non-small-cell lung cancer cell lines with disparate metastatic potentials - NCI-H1703 (primary cell, stage I) and NCI-H1755 (metastatic cell, stage IV). We identified 2130 proteins, 1355 of which were common to both cell lines. In the label-free quantitative analysis, we used the NSAF normalization method, resulting in 242 differential expressed proteins. For the N-terminal proteome analysis, 325 N-terminal peptides, including 45 novel fragments, were identified in the 2 cell lines. Based on two proteomic analysis, 11 quantitatively expressed proteins and 8 N-terminal peptides were enriched for the focal adhesion pathway. Most proteins from the quantitative analysis were upregulated in metastatic cancer cells, whereas novel fragment of CRKL was detected only in primary cancer cells. This study increases our understanding of the NSCLC metastasis proteome.

• Reproductive and Developmental Biology
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• v.32 no.4
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• pp.255-261
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• 2008

The early diagnosis of bovine pregnancy is an essential component of successful reproductive planning on farms, because lack of bovine pregnancy over the long term results in reproductive failure and low milk yield-the latter of which is a special concern on dairy farms. This study was designed to identify early pregnancy-specific whey proteins in bovine, by comparing milk samples collected from cattle during pregnancy (Days 30 and 50) and from non-pregnant cattle. In this study, differentially expressed proteins in five pregnant and five non-pregnant Holstein dairy cattle were investigated and compared, using proteomics analysis. The first dimension was applied to a pH $3.0{\sim}10.0$ strip, by loading a 2-mg milk protein sample. After the second-dimension separation was performed, the gels were stained with colloidal Coomassie brilliant blue. The stained gels were scanned and the images were analyzed, to detect variations in protein spots between non-pregnant and pregnant cattle milk protein spots, using ImageMaster, this was followed by analysis with MALDI TOF-MS. Analysis of the 2-DE gel image resulted in a total of approximately $500{\sim}600$ protein spots, of which 12 spots were differentially expressed, six spots were up-regulated, and four spots were down-regulated; two spots were identified as pregnancy-specific proteins. These proteins were identified as lactoferrin, NA-DH dehydrogenase subunit 2, albumin, serum albumin precursor and transferrin. Our results via 2-D PAGE analysis revealed composite profiles of several milk proteins related to early bovine pregnancy, implying the possible use of these milk proteins in the early detection of bovine pregnancy.