• Tuberculosis and Respiratory Diseases
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• v.56 no.4
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• pp.393-404
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• 2004

Background : Nucleic acid hybridization has become an essential technique in the development of our understanding of gene structure and function. The quantitative analysis of hybridization has been used in the measurement of genome complexity and gene copy number. The filter hybridization assay is rapid, sensitive and can be used to measure RNAs complementary to any cloned DNA sequence. Methods : The authors assessed the accuracy, linearity, correlation coefficient and specificity of the hybridization depending on the added dose(0, 1, 5, and $10{\mu}g$) of non-specific rat spleen RNA to hybridization of surfactant protein A mRNA. Filter hybridization assays were used to obtain the equation of standard curve and thereby to quantitate the mRNA quantitation. Results : 1. Standard curve equation of filter hybridization assay between counts per minute (X) and spleen RNA input (Y) was Y=0.13X-19.35. Correlation coefficient was 0.98. 2. Standard curve equation of filter hybridization assay between counts per minute (X) and surfactant protein A mRNA transcript input (Y) was Y=0.00066X-0.046. Correlation coefficient was 0.99. 3. Standard curve equation of filter hybridization assay between counts per minute (X) and surfactant protein A mRNA transcript input (Y) after the addition of $1{\mu}g$ spleen RNA was Y=0.00056X-0.051. Correlation coefficient was 0.99. 4. Standard curve equation of filter hybridization assay between counts per minute (X) and surfactant protein A mRNA transcript input (Y) after the addition of $5{\mu}g$ spleen RNA was Y=0.00065X-0.088. Correlation coefficient was 0.99. 5. Standard curve equation of filter hybridization assay between counts per minute (X) and surfactant protein A mRNA transcript input (Y) after the addition of $10{\mu}g$ spleen RNA was Y=0.00051X-0.10. Correlation coefficient was 0.99. Conclusions : Comparison of cpm/filter in a linear range allowed accurate and reproducible estimation of surfactant protein A mRNA copy number irrespective of the addition dosage of non-specific rat spleen RNA over the range $0-10{\mu}g$.

• BMB Reports
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• v.28 no.6
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• pp.509-514
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• 1995

A putative secondary structure of the mRNA for the human hepatitis B virus (HBV) X gene is proposed based on not only chemical and enzymatic determination of its single- and double-stranded regions but also selection by the computer program MFOLD for energy minimum conformation under the constraints that the experimentally determined nucleotides were forced or prohibited to base pair. An RNA of 536 nucleotides including the 461-nucleotide HBV X mRNA sequence was synthesized in vitro by the phage T7 RNA polymerase transcription. The thermally renatured transcripts were subjected to chemical modifications with dimethylsulfate and kethoxal and enzymatic hydrolysis with single strand-specific RNase T1 and double strand-specific RNase V1, separately. The sites of modification and cleavage were detected by reverse transcriptase extension of 4 different primers. Many nucleotides could be assigned with high confidence, twenty in double-stranded and thirty-seven in Single-stranded regions. These nucleotides were forced and prohibited, respectively, to base pair in running the recursive RNA folding program MFOLD. The results suggest that 6 different regions (5 within X mRNA) of 14~23 nucleotides are Single-stranded. This putative structure provides a good working model and suggests potential target sites for antisense and ribozyme inhibitors and hybridization probes for the HBV X mRNA.

• Tuberculosis and Respiratory Diseases
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• v.39 no.3
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• pp.242-247
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• 1992

Background: The ability to precisely measure specific mRNA levels by hybridization to complementary DNA probes is an important tool for analyzing the regulation of gene expression. Surfactant proteins have important roles in regulating surfactant metabolism as well as in determing its physical properties. Method: The complete coding regions for rat surfactant protein complementary DNA of surfactant protein B were subcloned into pGem 3Z or 4Z such that either antisense or sense transcripts were obtained by using SP 6 RNA polymerase. Surfactant protein B mRNA was measured by filter hybridization. Results: Equation of standard curve between counts per minute (Y) and surfactant protein B mRNA transcript input (X) was Y=2034.9 X+159.1. Correlation coefficient was 1.0. Couclusions: Filter hybridization assay is suited to situation when rapid, accurate quantitation of multiple samples is required.

• Tuberculosis and Respiratory Diseases
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• v.51 no.6
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• pp.517-529
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• 2001

Background : Surfactant protein C(SP-C) is a hydrophobic 5,000 dalton molecule. SP-C has the primary roles in accelerating surface spreading of a surfactant phospholipid. The filter hybridization and solution hybridization assays are both rapid and sensitive and can be used to measure the RNAs complementary to any cloned DNA sequence. Methods : The authors measured the SP-C mRNA levels quantitatively using solution hybridization and filter hybridization assays to obtain a standard curve equation to quantify the mRNA of unknown samples comparatively. Results : 1. The minimum level of the specimens by solution hybridization was 3 pg for SP-C mRNA. 2. The standard curve equation of the solution hybridization assay between the counts per minute(Y) and the SP-C mRNA transcript input(X) was Y=6.46 X+244. The correlation coefficient was 0.99. 3. The minimum detection level of specimens by filter hybridization was 0.1 ng for SP-C mRNA. 4. The standard curve equation of the filter hybridization assay between the counts per minute(Y) and SP-C mRNA transcript input(X) is Y=2541.6 X+252.7. The correlation coefficient was 0.99. Conclusions : A comparison of CPM/filter in the linear range allowed an accurate and reproducible estimation of the SP-C mRNA copy number. Filter hybridization and solution hybridization assays are both rapid and sensitive and can be used to measure the RNAs complementary to any cloned DNA sequence. It is ideally suited to situations where accurate quantitation of multiple samples is required.

• BMB Reports
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• v.54 no.3
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• pp.176-181
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• 2021

Bcl-x, a member of the Bcl-2 family, plays a key role in apoptosis. Alternative splicing of Bcl-x pre-mRNA through alternative 5' splice-site selection produces an anti-apoptotic mRNA isoform that includes exon 2b and a pro-apoptotic Bcl-x mRNA isoform that excludes exon 2b. Here we used Bcl-x minigene and identified SRSF2 and SRSF6 as two regulatory factors of 5' splice-site selection of Bcl-x pre-mRNA. We selected binding clusters closer to 5' splice-sites from multiple potential binding sites of SRSF2 and SRSF6 to perform loss of functions analysis through site-directed mutagenesis. Our results demonstrated that these mutations did not abolish regulatory functions of SRSF2 or SRSF6, indicating that a single binding motif or a cluster was not a functional target of these proteins in Bcl-x pre-mRNA splicing. Random deletion mutagenesis did not disrupt the role of SRSF2 and SRSF6. Importantly, mutagenesis of 5' splice-site to a conserved or a weaker score demonstrated that the weaker strength of the target 5' splice-site or higher strength of the other 5' splice-site strength limited the role of SRSF2 and SRSF6 in 5' splice-site activation.

• Journal of the Korean Child Neurology Society
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• v.23 no.2
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• pp.45-50
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• 2015

Purpose: X-linked adrenoleukodystrophy (X-ALD) is a fatal, axonal demyelinating, neurodegenerative disease, and is caused by mutations the in ABCD1 (ATP-binding cassette transporter subfamily D member 1). Oxidative damage of proteins caused by very long chain fatty acid accumulating in X-ALD, is an early event in the neurodegenerative cascade. We evaluated valproic acid (VPA) as a possible option for oxidative damage in X-ALD. Method: We generated fibroblast of the childhood cerebral ALD from patient. We evaluated mRNA (ribonucleic acid) level of ABCD2 by real-time polymerase chain reaction, and reactive oxygen species (ROS) levels by flow cytometry. Results: VPA increased expression of ABCD2 in both control and ALD fibroblast. ABCD2 gene mRNA expression was increased 1.76 fold in normal fibroblasts, and 2.22 fold in the X-ALD fibroblasts. ROS levels were decreased in VPA treated X-ALD fibroblast, especially in treated with 1 mM of VPA. ROS levels revealed 13.7 in control fibroblast, on the other hand, 5.83 in X-ALD fibroblast treated with 1 mM of VPA. Conclusion: We propose VPA as a promising novel therapeutic approach in oxidant damage that warrants further clinical investigation in X-ALD.

• Biomedical Science Letters
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• v.23 no.4
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• pp.416-420
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• 2017

Endoplasmic reticulum (ER) stress induces unfolded protein response (UPR) via inositol-requiring enzyme 1 (IRE1) activation, which sends a molecular signal for X box-binding protein 1 (XBP1) mRNA splicing in the cytosol. IRE1 endoribonuclease activity induces cleavage of XBP1 mRNA. The XBP1 mRNA is then ligated by an uncharacterized RNA ligase and translated to produce spliced XBP1 by 23 nt removed in which contains the PstI restriction enzyme site. The splicing of XBP1 mRNA can be detected by semiquantitative RT-PCR, and then splicing of XBP1 is a useful tool to measure the genetic variability in ER stress. In this study, we have estimated IRE1-dependent splicing of XBP1 mRNA under conditions of various hypothermia. The results indicated that hypothermia regulated ER stress. This study demonstrated that hypothermia is closely related to ER stress and may be useful for early diagnosis of ER-associated disease.

• Asian-Australasian Journal of Animal Sciences
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• v.20 no.10
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• pp.1587-1593
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• 2007

A single factorial experiment was conducted to test the effects of three dietary levels of energy on mRNA expression of fatty acid synthase (FAS-mRNA) and hormone-sensitive lipase (HSL-mRNA) and their association with intramuscular fat in finishing pigs. 72 crossbred (Large $White{\times}Rongchang$) barrows with an average initial body weight of 20.71 (s.e. 0.1) kg, were randomly allotted to three dietary treatments (11.75, 13.05 and 14.36 MJ DE/kg) and fed until slaughtered at 100 or 101 kg. The diets were iso-nitrogenous and iso-essential amino acids. The growth performances including the duration of finishing were changed linearly (p<0.05) or quadratically (p<0.05) with increased dietary energy levels. The effects of dietary energy content on the percentage of external fat, intramuscular backfat and the fat thickness were linear (p<0.05). The content of dietary energy increased FAS-mRNA linearly or quadratically, while HSL-mRNA decreased linearly or quadratically in backfat and Longissmus dorsi muscle. Meanwhile, significant positive correlations (p<0.05) were found between energy level and intramuscular fat, FAS-mRNA or the ratio of FAS-mRNA to HSL-mRNA, between the ratio of FAS-mRNA to HSL-mRNA and intramuscular fat. However, the correlations between HSL mRNA and dietary energy or intramuscular fat were negative (p<0.05). The results indicated that dietary energy level regulates lipid accumulation, especially intramuscular fat, possibly by modulating the mRNA of FAS and HSL together rather than individually.

• Journal of the Korea Convergence Society
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• v.10 no.2
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• pp.331-337
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• 2019

Objective: We studied the effects of 4x, 30x, 30c, and 200c homeopathic dilutions of A. montana on inflammation in primary cultured mouse chondrocytes. Methods: Examined expression of Coll-2 and COX-2, and secretion of PGE2. Results: Treatment with 4x, 30x, and 30c A. montana decreased mRNA expression of Coll-2 and 30x A. montana increased mRNA expression of COX-2, while treatment with 30x and 30c A. montana increased protein expression of COX-2. Treatment with the 30c A. montana increased release of PGE2. Conclusion: Treatment with A. montana induces dedifferentiation and inflammatory responses, including increased COX-2 expression and PGE2 secretion.

• Korean Journal of Plant Tissue Culture
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• v.21 no.2
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• pp.111-115
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• 1994

Two different gravity specific cDNA, namely, GSC 13 and GSC 124 with length of 1.34 and 0.67 kilobase pairs, and transcripts of 2.0 and 1.9 kilobase pairs, respectively. were isolated by differential screening and northern hybridization of the total RNA isolated from treated and untreated cultured cells showed that maximum levels of trannscripts were achieved after 4 h of gravity stress at 450, 000 x g for both, GSC 13 and GSC 124, suggesting that these mRNA could be expressed and translated into polyeptites related to the cell to extream gravity stress.