• BMB Reports
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• v.39 no.2
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• pp.216-222
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• 2006

In the present study, we compared six different solubilization buffers and optimized two-dimensional electrophoresis (2-DE) conditions for human lymph node proteins. In addition, we developed a simple protocol for 2-D gel storage. Efficient solubilization was obtained with lysis buffers containing (a) 8M urea, 4% CHAPS (3-[(3-cholamidopropyl) dimethylammonio]-1-propanesulfonate), 40 mM Tris base, 65 mM DTT(dithiothreitol) and 0.2% carrier ampholytes; (b) 5M urea, 2M thiourea, 2% CHAPS, 2% SB 3-10 (N-decyl-N, N-dimethyl-3-ammonio-1-propanesulfonate), 40mM Tris base, 65 mM DTT and 0.2% carrier ampholytes or (c) 7M urea, 2M thiourea, 4% CHAPS, 65 mM DTT and 0.2% carrier ampholytes. The optimal protocol for isoelectric focusing (IEF) was accumulated voltage of 16,500 Vh and 0.6% DTT in the rehydration solution. In the experiments conducted for the sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), best results were obtained with a doubled concentration (50 mM Tris, 384 mM glycine, 0.2% SDS) of the SDS electrophoresis buffer in the cathodic reservoir as compared to the concentration in the anodic reservoir (25 mM Tris, 192 mM glycine, 0.1% SDS). Among the five protocols tested for gel storing, success was attained when the gels were stored in plastic bags with 50% glycerol. This is the first report describing the successful solubilization and 2D-electrophoresis of proteins from human lymph node tissue and a 2-D gel storage protocol for easy gel handling before mass spectrometry (MS) analysis.

• Asian-Australasian Journal of Animal Sciences
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• v.28 no.8
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• pp.1075-1083
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• 2015

Adipose tissue deposited within muscle fibers, known as intramuscular fat (IMF or marbling), is a major determinant of meat quality and thereby affects its economic value. The biological mechanisms that determine IMF content are therefore of interest. In this study, 48 genes involved in the bovine peroxisome proliferator-activated receptor signaling pathway, which is involved in lipid metabolism, were investigated to identify candidate genes associated with IMF in the longissimus dorsi of Hanwoo (Korean cattle). Ten genes, retinoid X receptor alpha, peroxisome proliferator-activated receptor gamma (PPARG), phospholipid transfer protein, stearoyl-CoA desaturase, nuclear receptor subfamily 1 group H member 3, fatty acid binding protein 3 (FABP3), carnitine palmitoyltransferase II, acyl-Coenzyme A dehydrogenase long chain (ACADL), acyl-Coenzyme A oxidase 2 branched chain, and fatty acid binding protein 4, showed significant effects with regard to IMF and were differentially expressed between the low- and high-marbled groups (p<0.05). Analysis of the gene co-expression network based on Pearson's correlation coefficients identified 10 up-regulated genes in the high-marbled group that formed a major cluster. Among these genes, the PPARG-FABP4 gene pair exhibited the strongest correlation in the network. Glycerol kinase was found to play a role in mediating activation of the differentially expressed genes. We categorized the 10 significantly differentially expressed genes into the corresponding downstream pathways and investigated the direct interactive relationships among these genes. We suggest that fatty acid oxidation is the major downstream pathway affecting IMF content. The PPARG/RXRA complex triggers activation of target genes involved in fatty acid oxidation resulting in increased triglyceride formation by ATP production. Our findings highlight candidate genes associated with the IMF content of the loin muscle of Korean cattle and provide insight into the biological mechanisms that determine adipose deposition within muscle.

• Journal of Microbiology and Biotechnology
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• v.24 no.6
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• pp.748-755
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• 2014

In the genome annotation of Escherichia coli MG1655, the orf382 (1,149 bp) is designated as a gene encoding an alcohol dehydrogenase that may be Fe-dependent. In this study, the gene was amplified from the genome by PCR and overexpressed in Escherichia coli BL21(DE3). The recombinant $6{\times}$His-tag protein was then purified and characterized. In an enzymatic assay using different hydroxyl-containing substrates (n-butanol, $\small{L}$-threonine, ethanol, isopropanol, glucose, glycerol, $\small{L}$-serine, lactic acid, citric acid, methanol, or $\small{D}$-threonine), the enzyme showed the highest activity on $\small{L}$-threonine. Characterization of the mutant constructed using gene knockout of the orf382 also implied the function of the enzyme in the metabolism of $\small{L}$-threonine into glycine. Considering the presence of tested substrates in living E. coli cel ls and previous literature, we believed that the suitable nomenclature for the enzyme should be an $\small{L}$-threonine dehydrogenase (LTDH). When using $\small{L}$-threonine as the substrate, the enzyme exhibited the best catalytic performance at $39^{\circ}C$ and pH 9.8 with $NAD^+$ as the cofactor. The determination of the Km values towards $\small{L}$-threonine (Km = $11.29{\mu}M$), ethanol ($222.5{\mu}M$), and n-butanol ($8.02{\mu}M$) also confirmed the enzyme as an LTDH. Furthermore, the LTDH was shown to be an ion-containing protein based on inductively coupled plasma-atomic emission spectrometry with an isoelectronic point of pH 5.4. Moreover, a circular dichroism analysis revealed that the metal ion was structurally and enzymatically essential, as its deprivation remarkably changed the ${\alpha}$-helix percentage (from 12.6% to 6.3%).

• Journal of Microbiology and Biotechnology
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• v.30 no.4
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• pp.526-532
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• 2020

A bacterial strain, designated B301^T and isolated from raw chicken meat obtained from a local market in Korea, was characterized and identified using a polyphasic taxonomic approach. Cells were gram-negative, non-motile, obligate-aerobic coccobacilli that were catalase-positive and oxidase-negative. The optimum growth conditions were 30℃, pH 7.0, and 0% NaCl in tryptic soy broth. Colonies were round, convex, smooth, and cream-colored on tryptic soy agar. Strain B301^T has a genome size of 3,102,684 bp, with 2,840 protein-coding genes and 102 RNA genes. The 16S rRNA gene analysis revealed that strain B301^T belongs to the genus Acinetobacter and shares highest sequence similarity (97.12%) with A. celticus ANC 4603^T and A. sichuanensis WCHAc060041^T. The average nucleotide identity and digital DNA-DNA hybridization values for closely related species were below the cutoff values for species delineation (95-96% and 70%, respectively). The DNA G+C content of strain B301^T was 37.0%. The major respiratory quinone was Q-9, and the cellular fatty acids were primarily summed feature 3 (C_16:1 ω6c/C_16:1 ω7c), C_16:0, and C_18:1 ω9c. The major polar lipids were phosphatidylethanolamine, diphosphatidyl-glycerol, phosphatidylglycerol, and phosphatidyl-serine. The antimicrobial resistance profile of strain B301^T revealed the absence of antibiotic-resistance genes. Susceptibility to a wide range of antimicrobials, including imipenem, minocycline, ampicillin, and tetracycline, was also observed. The results of the phenotypic, chemotaxonomic, and phylogenetic analyses indicate that strain B301^T represents a novel species of the genus Acinetobacter, for which the name Acinetobacter pullorum sp. nov. is proposed. The type strain is B301^T (=KACC 21653^T = JCM 33942^T).

• Journal of Chest Surgery
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• v.36 no.4
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• pp.219-228
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• 2003

Background:Liquid nitrogen freezing techniques have already met with widespread success in biology and medicine as a means of long-term storage for cells and tissues. The use of cryoprotectants such as glycerol and dimethylsulphoxide to prevent ice crystal formation, with carefully controlled rates of freezing and thawing, allows both structure and viability to be retained almost indefinitely. Cryopreservation of various tissues has various con-trolled rates of freezing. Material and Method: To find the optimal freezing curve and the chamber temperature, we approached the thermodynamic calculation of tissues in two ways. One is the direct calculation method. We should know the thermophysical characteristics of all components, latent heat of fusion, area, density and volume, etc. This kind of calculation is so sophisticated and some variables may not be determined. The other is the indirect calculation method. We performed the tissue freezing with already used freezing curve and we observed the actual freezing curve of that tissue. And we modified the freezing curve with several steps of calculation, polynomial regression analysis, time constant calculation, thermal response calculation and inverse calculation of chamber temperature. Result: We applied that freezing program on mesenchymal stem cell, chondrocyte, and osteoblast. The tissue temperature decreased according to the ideal freezing curve without temperature rising. We did not find any differences in survival. The reason is postulated to be that freezing material is too small and contains cellular components. We expect the significant difference in cellular viability if the freezing curve is applied on a large scale of tissues. Conclusion: This program would be helpful in finding the chamber temperature for the ideal freezing curie easily.

• Journal of the Korean Chemical Society
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• v.53 no.2
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• pp.175-188
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• 2009

In this study, we developed an experimental method of the Charles' law applicable to school. Science textbooks and literatures on this principle were analyzed to extract factors utilized in organizing the experimental setup and method. A combined structure such as with a vial and a glass tube, the former of which is for deciding the total volume and the latter of which is for easy measurement of volume, was better in measurement of volume with temperature rather than a simple structure such as syringe. Use of graduated cylinder as a water bath to control the temperature showed advantage in cooling time than using other bath of larger volume such as a beaker. A liquid drop was used as a plug in the glass tube. This plug has little resistance with the glass wall when the gas volume changes. Water as a liquid drop in the glass tube had a significant effect in volume change of gas due to evaporation, especially in the beginning of the measurement. Glycerol showing negligible effect in volume change was used. This method took about one hour and produced a good linear relationship between the temperature and volume of gas with $R^2$ = 0.999 and absolute zero temperature = $-216.7\;{^{\circ}C}$. The Charles' law experiment developed in this study can be performed with appropriate adjustment of procedure considering the purpose of the curriculum of science and chemistry subject at each school level.

• KSBB Journal
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• v.9 no.3
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• pp.246-252
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• 1994

Enzyme-catalyzed polycondensatlon reaction of aliphatic polyesters with several repeating units was studied using the biocatalytic activities of lipases from different sources. Porcine pancreatic lipase (PPL) was found to be best in utilizing bls(2,2,2-trichloroethyl) glutarate and 1,4-butanediol as substrafes. The reaction was also catalyzed to some extent by the lipases from Humicola lanuginos and Psudomonas sp. In the series of short-chain diols(C2-C4), bis(2,2,2-trichloroethyl) glutarate was iransesterified fastest with 1,4-butanediol and for the long-chain diols (PEG-300-PEG-1000), the reaction was fastest with PEG-400. With PEGs, only monoesterification product was obtained. PPL functioned well in relatively hydrophilic organic solvents such as tetrahydrofuran(THF), ether and acetonitrile. The reaction rate was accelerated as the reaction temperature was raised from $20^{\circ}C$ to $60^{\circ}C$ while Mn values of the reaction products were not affected by the reaction temperature. End group analysis by NMR showed that Mn values of the polymer were in the range of 1500-4000 daltons.

• Journal of Mushroom
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• v.9 no.3
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• pp.123-131
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• 2011

Winter mushroom was monitored to investigate the influence of storage temperature on its quality during the storage and distribution phase. In measuring its quality, the contents of saccharides were quantified with its fruiting bodies using HPLC. Although it has been known to be difficult to separate saccharide isomers, our results indicated that Grace Prevail carbohydrate ES $5{\mu}column$ was the best in the separation to analyze the saccharide out of six columns used in this study. In our results, xylose was the main component of saccharide in the fruiting body of winter mushroom(White line mushroom:47.68mg/g, brown line mushroom: 63.28mg/g). In long-term storage, the total amount of saccharide tended to increase, but trehalose content of the disaccharide decreased. In comparison with the paramount amount of lactose and myo-inositol contents in long-term storage at $4^{\circ}C$, lactose wasn't detected when stored at $-1^{\circ}C$.

• The Korean Journal of Mycology
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• v.49 no.2
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• pp.199-209
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• 2021

The present study was performed to improve the technique used for fermenting the mushroom growth medium. Taxonomic analysis of 16S rDNA sequence from the predominant Bacillus strain CY-24 isolated during the fermentation phase of the rice straw medium identified it as Bacillus licheniformis. In addition, the growth environment of B. licheniformis was also examined in this study, which revealed the optimal growth temperature and pH to be 30 ℃ and 6.0, respectively. This study also revealed that carboxymethyl cellulase (CMCase) and polygalacturonase (PGase) enzymes isolated from B. licheniformis achieved their maximal activities at 50 ℃ and 60 ℃ respectively. Furthermore, the study confirmed that the two enzymes, i.e., CMCase and PGase in B. licheniformis are stable at temperatures above 60 ℃. The present study thus demonstrates that B. licheniformis CY-24 possesses excellent enzymatic properties. It also reveals that the action of enzymes during the production of growth mediums used for the cultivation of mushrooms is closely associated with the promotion of fermentation and softening of the rice straw. Overall, this study provides elementary information regarding the role of B. licheniformis enzymes during growth medium fermentation for Agaricus bisporus cultivation.

• Korean Journal of Medicinal Crop Science
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• v.28 no.6
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• pp.395-411
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• 2020

Background: This study investigated the anti-obesity effect of the flavonoid rich fraction (FRF) and its constituent, rutin obtained from the leaf of Morus alba L., on the lipid accumulation mechanism in 3T3-L1 adipocyte and C57BL/6 mouse models. Methods and Results: In Oil Red O staining, FRF (1,000 ㎍/㎖) treatments showed inhibition rate of 35.39% in lipid accumulation compared to that in the control. AdipoRedTM assay indicated that the triglyceride content in 3T3-L1 adipocytes treated with FRF (1,000 ㎍/㎖) was reduced to 23.22%, and free glycerol content was increased to 106.04% that of the control. FRF and its major constituent, rutin affected mRNA gene expression. Rutin contributed to the inhibition of Sterol regulatory element binding protein-1c (SREBP-1c) gene expression, and inhibited the transcription factors SREBP-1c, peroxisome proliferator-activated receptor gamma (PPAR-γ), CCAAT/enhancer binding protein α (C/EBPα), fatty acid synthase (FAS) and acetyl-CoA carboxylase (ACC). In addition, the effect of FRF administration on obesity development in C57BL/6 mice fed high-fat diet (HFD) was investigated. FRF suppressed weight gain, and reduced liver triglyceride and leptin secretion. FRF exerted potential anti-inflammatory effects by improving insulin resistance and adiponectin levels, and could thus be used to help counteract obesity. The mRNA expressions of PPAR-γ, FAS, ACC, and CPT-1 were determined in liver tissue. Quantitative real-time PCR analysis was also performed to evaluate the expression of IL-1β, IL-6, and TNF-α in epididymal adipose tissue. Compared to the control group, mice fed the HFD showed the up-regulation in PPAR-γ, FAS, IL-6, and TNF-α genes, and down-regulation in CPT1 gene expression. FRF treatement markedly reduced the expression of PPAR-γ, FAS, IL-6, and TNF-α compared to those in HFD control, whereas increased the expression level of CPT1. Conclusions: These results suggest that the FRF and its major active constituent, rutin, can be used as effective anti-obesity agents.