• Molecules and Cells
• /
• v.37 no.9
• /
• pp.691-698
• /
• 2014

SCYL1-BP1 is thought to function in the p53 pathway through Mdm2 and hPirh2, and mutations in SCYL1-BP1 are associated with premature aging syndromes such as Geroderma Osteodysplasticum; however, these mechanisms are unclear. Here, we report significant alterations in miRNA expression levels when SCYL1-BP1 expression was inhibited by RNA interference in HEK293T cells. We functionally characterized the effects of potential kernel miRNA-target genes by miRNA-target network and protein-protein interaction network analysis. Importantly, we showed the diminished SCYL1-BP1 dramatically reduced the expression levels of EEA1, BMPR2 and BRCA2 in HEK293T cells. Thus, we infer that SCYL1-BP1 plays a critical function in HEK293T cell development and directly regulates miRNA-target genes, including, but not limited to, EEA1, BMPR2, and BRCA2, suggesting a new strategy for investigating the molecular mechanism of SCYL1-BP1.

• The Journal of Korean Medicine
• /
• v.33 no.4
• /
• pp.42-49
• /
• 2012

Objectives: The purpose of this study was to investigate effects of Red Ginseng-Ejung-tang Water Extract (ER) on cytokine production in RAW 264.7 mouse macrophages stimulated by lipopolysaccharide (LPS). Methods: Levels of various cytokines such as interleukin (IL)-6, IL-10, IL-2, IL-12p70, vascular endothelial growth factor (VEGF), monocyte chemoattractant protein (MCP)-1, macrophage inflammatory protein (MIP)-2, keratinocyte-derived chemokine (KC), tumor necrosis factor (TNF)-alpha, granulocyte macrophage colony-stimulating factor (GM-CSF) were measured by high-throughput multiplex bead array cytokine assay based on xMAP (multi-analyte profiling beads) technology. Results: ER significantly decreased levels of IL-6, IL-10, IL-2, IL-12p70, VEGF, and MCP-1 for 24 hrs incubation at the concentrations of 25, 50, and $100{\mu}g/mL$ in LPS-induced RAW 264.7 cells (P < 0.05). But ER did not exert significant effects on production of MIP-2, KC, TNF-${\alpha}$, and GM-CSF in LPS-induced RAW 264.7 cells. Conclusions: These results suggest that ER has an anti-inflammatory property related with its inhibition of cytokine production in LPS-induced macrophages.

• Journal of Microbiology and Biotechnology
• /
• v.29 no.6
• /
• pp.887-896
• /
• 2019

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS)-based pathogen identification relies on the ribosomal protein spectra provided in the proprietary database. Although these mass spectra can discern various pathogens at species level, the spectra-based method still has limitations in identifying closely-related microbial species. In this study, to overcome the limits of the current MALDI-TOF MS identification method using ribosomal protein spectra, we applied MALDI-TOF MS of low-mass profiling to the identification of two genetically related Bacillus species, the food-borne pathogen Bacillus cereus, and the insect pathogen Bacillus thuringiensis. The mass spectra of small molecules from 17 type strains of two bacilli were compared to the morphological, biochemical, and genetic identification methods of pathogens. The specific mass peaks in the low-mass range (m/z 500-3,000) successfully identified various closely-related strains belonging to these two reference species. The intensity profiles of the MALDI-TOF mass spectra clearly revealed the differences between the two genetically-related species at strain level. We suggest that small molecules with low molecular weight, 714.2 and 906.5 m/z can be potential mass biomarkers used for reliable identification of B. cereus and B. thuringiensis.

• Journal of Animal Science and Technology
• /
• v.65 no.2
• /
• pp.293-310
• /
• 2023

Protein-translated mRNA analysis has been extensively used to determine the function of various traits in animals. The non-coding RNA (ncRNA), which was known to be non-functional because it was not encoded as a protein, was re-examined as it was studied to actually function. One of the ncRNAs, long non-coding RNA (lncRNA), is known to have a function of regulating mRNA expression, and its importance is emerging. Therefore, lncRNAs are currently being used to understand the traits of various animals as well as human diseases. However, studies on lncRNA annotation and its functions are still lacking in most animals except humans and mice. lncRNAs have unique characteristics of lncRNAs and interact with mRNA through various mechanisms. In order to make lncRNA annotations in animals in the future, it is essential to understand the characteristics of lncRNAs and the mechanisms by which lncRNAs function. In addition, this will allow lncRNAs to be used for a wider variety of traits in a wider range of animals, and it is expected that integrated analysis using other biological information will be possible.

• Asian-Australasian Journal of Animal Sciences
• /
• v.20 no.10
• /
• pp.1612-1617
• /
• 2007

In this study, we have compared the skeletal muscle proteome at various stages of porcine postnatal development. Korean native pigs were divided into five postnatal stages of 30, 70, 130, 170 and 300 d and their loin muscles were analyzed for muscle proteome by using two-dimensional electrophoresis and mass spectrometry. We found 5 proteins showing a consistent pattern during skeletal muscle growth. Four proteins were identified as myosin light chain 1 slow-twitch (MLC1sa) isoform, troponin T, triosephosphate isomerase (TIP) and DJ-1 protein. The remaining protein was not identified. Two muscle fiber proteins of MLC1sa isoform and troponin T showed a high expression level at an early postnatal stage and then their levels were decreased markedly during growth stages. On the other hand, the expression of TIP and DJ-1 protein, which are well known as catalysis enzyme and antioxidant-related protein, respectively, were linearly increased during growth stages. Thus, the stage-related muscle proteins may be useful as parameters for understanding the developmental characteristics of biochemical and physiological properties in Korean native pig skeletal muscle.

• Asian-Australasian Journal of Animal Sciences
• /
• v.20 no.5
• /
• pp.638-644
• /
• 2007

Differences of meat qualities between Japanese Black and Holstein have been known in Japan, however, the causative proteins and/or the genetic background have been unclear. The aim of this study was to identify candidate proteins causing differences of the meat qualities between the two breeds. Using technique of two-dimensional gel electrophoresis, protein profiling was compared from samples of the longissimus dorsi muscle and subcutaneous adipose tissue. Five protein spots were observed with different expression levels between breeds. By using LC-MS/MS analysis and Mascot program, three of them were identified as ankyrin repeat protein 2, phosphoylated myosin light chain 2 and mimecan protein. Subsequently, we compared the DNA coding sequences of three proteins between breeds to find any nucleotide substitution. However, there was no notable mutation which could affect pI or molecular mass of the proteins. The identified proteins may be responsible for different characteristics of the meat qualities between Japanese Black and Holstein cattle.

• KSBB Journal
• /
• v.21 no.6 s.101
• /
• pp.461-465
• /
• 2006

We investigated the protein productivity of the promoters for genes showing prolonged induction upon cold shock in Escherichia coli. Six low temperature inducible genes (frdA, glpB, hypB, katG, nupG, ompT) were selected based on the previously reported cDNA microarray based global transcription profiling of Escherichia coli Kl2 in response to cold shock. Their promoter regions were isolated from the genomic DNA of E. coli JM109 and expression levels induced by the promoters were examined by using green fluorescence protein (GFP) as a reporter at $15^{\circ}C$ and $37^{\circ}C$. Among the six promoters, the promoter for nupG showed the highest and prolonged expression at both temperatures and the cold inducibility of nupG promoter was not observed.

• Proceedings of the Korean Society for Applied Microbiology Conference
• /
• 2005.06a
• /
• pp.230-232
• /
• 2005

The formation of insoluble aggregation of the recombinant kringle fragment of human apolipoprotein(a), rhLK8, in endoplasmic reticulum was identified as the rate-limiting step in the rhLK8 secretion in Saccharomyces cerevisiae. To analyze the protein secretion pathway, some of yeast genes closely related to protein secretion was rationally selected and their oligomer DNA were arrayed on the chip. The expression profiling of these genes during the induction of rhLK8 in fermentor fed-batch cultures revealed that several foldases including pdi1 gene were up-regulated in the early induction phase, whereas protein transport-related genes were up-regulated in the late induction phase. The coexpression of pdi1 gene increased rhLK8-folding capacity. Hence, the secretion efficiency of rhLK8 in the strain overexpressing pdi1 gene increased by 2-fold comparing in its parental strain. The oligomer DNA chip arrayed with minimum number of the genes selected in this study could be generally applicable to the monitoring system for the heterologous protein secretion and expression in Saccharomyces cerevisiae. With the optimization of fed-batch culture conditions and the alteration of genetic background of host, we obtained extracellular rhLK8 at higher yields than with Pichia pastoris systems, which was a 25-fold increased secretion level of rhLK8 compared to the secretion level at the initiation of this study.

• Molecules and Cells
• /
• v.27 no.2
• /
• pp.257-261
• /
• 2009

Actinobacillus actinomycetemcomitans (A. actinomycetemcomitans) is an important pathogen casuing aggressive periodontitis. The present study was designed to investigate the chemokines expression regulated by A. actinomycetemcomitans lipopolysaccharide (LPS). Chemokines genes expression profiling was performed in Raw 264.7 cells by analyses of microarray and reverse transcription-polymerase chain reaction (RT-PCR). Microarray results showed that the induction of monocyte chemoattractant protein-1 (MCP-1) and macrophage inflammatory protein-$1{\alpha}$ (MIP-$1{\alpha}$), MIP-$1{\beta}$, MIP-$1{\gamma}$, regulated upon activation, normal T-cell expressed and secreted (RANTES), macrophage inflammatory protein-2 (MIP-2), and interferon-${\gamma}$ inducible protein 10 (IP 10) by A. actinomycetemcomitans LPS was increased to 12.5, 1.53, 9.09, 17.3, 2.82, 16.1, and 18.1 folds at 18 h, respectively. To check these chemokines expression by A. actinomycetemcomitans LPS, we examined gene expressions by RT-PCR, and found that the expression of MIP-$1{\beta}$, MIP-$1{\gamma}$, RANTES, MIP-2, and IP 10 was increased 107.1, 93.6, 106.8, 86.5, and 162.0 folds at 18 h, respectively. These results indicate that A. actinomycetemcomitans LPS stimulates the several chemokines expressions (MIP-$1{\alpha}$, MIP-$1{\beta}$, MIP-$1{\gamma}$, RANTES, MIP-2, and IP 10) in Raw 264.7 cells.

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