• Title/Summary/Keyword: Real-Time polymerase chain reaction (PCR)

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Molecular Characterization and Tissue Distribution of Estrogen Receptor Genes in Domestic Yak

  • Fu, Mei;Xiong, Xian-Rong;Lan, Dao-Liang;Li, Jian
    • Asian-Australasian Journal of Animal Sciences
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    • v.27 no.12
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    • pp.1684-1690
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    • 2014
  • Estrogen and its receptors are essential hormones for normal reproductive function in males and females during developmental stage. To better understand the effect of estrogen receptor (ER) gene in yak (Bos grunniens), reverse transcription-polymerase chain reaction (PCR) was carried out to clone $ER{\alpha}$ and $ER{\beta}$ genes. Bioinformatics methods were used to analyze the evolutionary relationship between yaks and other species, and real-time PCR was performed to identify the mRNA expression of $ER{\alpha}$ and $ER{\beta}$. Sequence analysis showed that the ER open reading frames (ORFs) encoded 596 and 527 amino acid proteins. The yak $ER{\alpha}$ and $ER{\beta}$ shared 45.3% to 99.5% and 53.9% to 99.1% protein sequence identities with other species homologs, respectively. Real-time PCR analysis revealed that $ER{\alpha}$ and $ER{\beta}$ were expressed in a variety of tissues, but the expression level of $ER{\alpha}$ was higher than that of $ER{\beta}$ in all tissues, except testis. The mRNA expression of $ER{\alpha}$ was highest in the mammary gland, followed by uterus, oviduct, and ovary, and lowest in the liver, kidney, lung, testis, spleen, and heart. The $ER{\beta}$ mRNA level was highest in the ovary; intermediary in the uterus and oviduct; and lowest in the heart, liver, spleen, lung, kidney, mammary gland, and testis. The identification and tissue distribution of ER genes in yaks provides a foundation for the further study on their biological functions.

Cloning and expression of lin-28 homolog B gene in the onset of puberty in Duolang sheep

  • Xing, Feng;Zhang, Chaoyang;Kong, Zhengquan
    • Asian-Australasian Journal of Animal Sciences
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    • v.32 no.1
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    • pp.23-30
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    • 2019
  • Objective: Recent studies have demonstrated that lin-28 homolog B (LIN28B)/miRNA let-7 (let-7) plays a role in the regulation of pubertal onset in mammals. However, the role of LIN28B/let-7 in the onset of ovine puberty remains unknown. We cloned the Duolang sheep Lin28B cDNA sequence, detected the expression change of LIN28B, let-7a and let-7g in hypothalamus, pituitary and ovary tissues at three different pubertal stages. Methods: The reverse transcriptase polymerase chain reaction (RT-PCR) was used to clone the cDNA sequence of LIN28B gene from Duolang sheep and the bioinformatics methods were applied to analyze the amino acid sequence of LIN28B protein. The mRNA expression levels of the LIN28B gene at different pubertal stages were examined by real time RT-PCR. Results: LIN28B cDNA of Duolang sheep was cloned, and two transcripts were obtained. The amino acid sequence of transcript 1 shares 99.60%, 98.78%, and 94.80% identity with those of goat, wild yak and pig, respectively. Strong LIN28B mRNA expression was detected in the hypothalamus, pituitary, ovary, oviduct and uterus, while moderate expression was found in the liver, kidney, spleen and heart, weak expression was observed in the heart. No expression was found in the lungs. Quantitative real-time PCR (QPCR) and western-blot analysis revealed that the LIN28B was highly expressed in the hypothalamus and ovary at prepuberty stages, and this expression significantly decreased from the prepuberty to puberty stages (p<0.05). Markedly increased levels of mRNA expression were detected in the pituitary from prepuberty to puberty (p<0.05) and then significantly decreased from puberty to post-puberty (p<0.05). The expression levels of let-7a and let-7g showed no significant changes among different pubertal stages (p>0.05). Conclusion: These results provided a foundation for determining the functions of LIN28B/let-7 and their role in the onset of sheep puberty.

Selection and evaluation of reference genes for gene expression using quantitative real-time PCR in Mythimna separata walker (Lepidoptera: Noctuidae)

  • ZHANG, Bai-Zhong;LIU, Jun-Jie;CHEN, Xi-Ling;YUAN, Guo-Hui
    • Entomological Research
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    • v.48 no.5
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    • pp.390-399
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    • 2018
  • In order to precisely assess gene expression levels, the suitable internal reference genes must be served to quantify real-time reverse transcription polymerase chain reaction (RT-qPCR) data. For armyworm, Mythimna separata, which reference genes are suitable for assessing the level of transcriptional expression of target genes have yet to be explored. In this study, eight common reference genes, including ${\beta}$-actin (${\beta}$-ACT), 18 s ribosomal (18S), 28S ribosomal (28S), glyceraldehyde-3-phosphate (GAPDH), elongation fator-alpha ($EF1{\alpha}$), TATA box binding protein (TBP), ribosomal protein L7 (RPL7), and alpha-tubulin (${\alpha}$-TUB) that in different developmental stages, tissues and insecticide treatments of M. separata were evaluated. To further explore whether these genes were suitable to serve as endogenous controls, three software-based approaches (geNorm, BestKeeper, and NormFinder), the delta Ct method, and one web-based comprehensive tool (RefFinder) were employed to analyze and rank the tested genes. The optimal number of reference genes was determined using the geNorm program, and the suitability of particular reference genes was empirically validated according to normalized HSP70, and MsepCYP321A10 gene expression data. We found that the most suitable reference genes for the different experimental conditions. For developmental stages, 28S/RPL7 were the optimal reference genes, both $RPL7/EF1{\alpha}$ were suitable for experiments of different tissues, whereas for insecticide treatments, $28S/{\alpha}-TUB$ were suitable for normalizations of expression data. In addition, $28S/{\alpha}-TUB$ were the suitable reference genes because they have the most stable expression among different developmental stages, tissues and insecticide treatments. Our work is the first report on reference gene selection in M. separata, and might serve as a precedent for future gene expression studies.

Quantitative PCR for Etiologic Diagnosis of Methicillin-Resistant Staphylococcus aureus Pneumonia in Intensive Care Unit

  • Kwon, Sun-Jung;Jeon, Tae-Hyeon;Seo, Dong-Wook;Na, Moon-Joon;Choi, Eu-Gene;Son, Ji-Woong;Yoo, Eun-Hyung;Park, Chang-Gyo;Lee, Hoi-Young;Kim, Ju-Ock;Kim, Sun-Young;Kang, Jae-Ku
    • Tuberculosis and Respiratory Diseases
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    • v.72 no.3
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    • pp.293-301
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    • 2012
  • Background: Ventilator-associated pneumonia (VAP) requires prompt and appropriate treatment. Since methicillin-resistant Staphylococcus aureus (MRSA) is a frequent pathogen in VAP, rapid identification of it, is pivotal. Our aim was to evaluate the utility of quantitative polymerase chain reaction (qPCR) as a useful method for etiologic diagnoses of MRSA pneumonia. Methods: We performed qPCR for mecA, S. aureus-specific femA-SA, and S. epidermidis-specific femA-SE genes from bronchoalveolar lavage or bronchial washing samples obtained from clinically-suspected VAP. Molecular identification of MRSA was based on the presence of the mecA and femA-SA gene, with the absence of the femA-SE gene. To compensate for the experimental and clinical conditions, we spiked an internal control in the course of DNA extraction. We estimated number of colony-forming units per mL (CFU/mL) of MRSA samples through a standard curve of a serially-diluted reference MRSA strain. We compared the threshold cycle (Ct) value with the microbiologic results of MRSA. Results: We obtained the mecA gene standard curve, which showed the detection limit of the mecA gene to be 100 fg, which corresponds to a copy number of 30. We chose cut-off Ct values of 27.94 (equivalent to $1{\times}10^4$ CFU/mL) and 21.78 (equivalent to $1{\times}10^5$ CFU/mL). The sensitivity and specificity of our assay were 88.9% and 88.9% respectively, when compared with quantitative cultures. Conclusion: Our results were valuable for diagnosing and identifying pathogens involved in VAP. We believe our modified qPCR is an appropriate tool for the rapid diagnosis of clinical pathogens regarding patients in the intensive care unit.

Cloning and Expression Analysis of a Grape asr gene, VlASR Containing a Promoter Region. (포도 VIASR 유전자 프로모터의 분리 및 발현 분석)

  • Kihl, Joon-Yeong;Pyee, Jae-Ho
    • Journal of Life Science
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    • v.17 no.8 s.88
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    • pp.1157-1165
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    • 2007
  • VvMSA, a grapevine ASR which is highly inducible by sugar and abscisic acid signals was previously shown to be a transcription factor for a hexose transporter gene VvHT1. We isolated a cDNA clone, VlASR which is regulated temporally during the grape berry development by ACP RT-PCR (annealing control primer reverse transcriptase-polymerase chain reaction) and it proved identical to VvMSA. RT-PCR and real-time PCR analyses revealed that the VlASR gene was expressed in berries at fruit set and that its expression increased as berries aged but decreased at the late ripening stage. In order to understand the regulatory mechanism of the asr gene, a genomic fragment was cloned from grapevine. The genomic DNA was 1375 bp long and a sugar box (sucrose box 3 and sucrose responsive element 1) was identified in the 611 bp upstream region of the open reading frame. Analysis of the VlASR promoter::reporter gene fusion demonstrated that this promoter was expressed in transgenic Arabidopsis even without sucrose treatment. This result suggests that the ASR/VvHT1-mediated sugar/ABA signaling, previously reported in grapevine, may not function in Arabidopsis which has no ASR homologue.

Optimization of Reference Genes for Normalization of the Quantitative Polymerase Chain Reaction in Tissue Samples of Gastric Cancer

  • Zhao, Lian-Mei;Zheng, Zhao-Xu;Zhao, Xiwa;Shi, Juan;Bi, Jian-Jun;Pei, Wei;Feng, Qiang
    • Asian Pacific Journal of Cancer Prevention
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    • v.15 no.14
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    • pp.5815-5818
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    • 2014
  • For an exact comparison of mRNA transcription in different samples or tissues with real time quantitative reverse transcription-polymerase chain reaction (qRT-PCR), it is crucial to select a suitable internal reference gene. Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and beta-actin (ACTB) have been frequently considered as house-keeping genes to normalize for changes in specific gene expression. However, it has been reported that these genes are unsuitable references in some cases, because their transcription is significantly variable under particular experimental conditions and among tissues. The present study was aimed to investigate which reference genes are most suitable for the study of gastric cancer tissues using qRT-PCR. 50 pairs of gastric cancer and corresponding peritumoral tissues were obtained from patients with gastric cancer. Absolute qRT-PCR was employed to detect the expression of GAPDH, ACTB, RPII and 18sRNA in the gastric cancer samples. Comparing gastric cancer with corresponding peritumoral tissues, GAPDH, ACTB and RPII were obviously upregulated 6.49, 5.0 and 3.68 fold, respectively. Yet 18sRNA had no obvious expression change in gastric cancer tissues and the corresponding peritumoral tissues. The expression of GAPDH, ${\beta}$-actin, RPII and 18sRNA showed no obvious changes in normal gastric epithelial cells compared with gastric cancer cell lines. The carcinoembryonic antigen (CEA), a widely used clinical tumor marker, was used as a validation gene. Only when 18sRNA was used as the normalizing gene was CEA obviously elevated in gastric cancer tissues compared with peritumoral tissues. Our data show that 18sRNA is stably expressed in gastric cancer samples and corresponding peritumoral tissues. These observations confirm that there is no universal reference gene and underline the importance of specific optimization of potential reference genes for any experimental condition.

The Efficacy of Rapid Antigen Tests for Detection of Seasonal Influenza Virus (계절 인플루엔자 진단에서 신속항원검사의 유용성)

  • Lee, Jun Yeol;Lee, Sol;Kim, Han Sung;Kim, Kwang Nam
    • Pediatric Infection and Vaccine
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    • v.24 no.1
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    • pp.31-36
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    • 2017
  • Purpose: This study aimed to examine the accuracy of rapid influenza diagnostic tests (RIDT) in children with an influenza-like illness and to evaluate factors associated with greater accuracy. Methods: Pediatric patients, who visited Hallym University Sacred Heart Hospital with an influenza-like illness between June 2011 and May 2016, were enrolled in this study. We tested 798 samples using a real-time polymerase chain reaction (PCR) for respiratory viruses and compared the results with rapid influenza tests. Results: In comparison with the results of the multiplex PCR, the positive agreement rates of RIDT for influenza A and B virus were 75.7% and 60.0%, respectively. The performance of RIDT varied according to days after fever onset. The positive agreement rates of RIDT for influenza A and B tests, performed within 4 days of fever onset, were 77.6% and 73.2%, but the rates for tests performed more than 5 days after fever onset were 66.7% and 21.4%, respectively. Conclusions: The RIDT is a quick and simple aid to diagnosis, but is less sensitive than the labeled sensitivity. Moreover, test performance varied according to days after fever onset. Test specimens for RIDT should be collected as soon as possible after the onset of symptoms (less than 4 days).

Rapid Molecular Diagnosis using Real-time Nucleic Acid Sequence Based Amplification (NASBA) for Detection of Influenza A Virus Subtypes

  • Lim, Jae-Won;Lee, In-Soo;Cho, Yoon-Jung;Jin, Hyun-Woo;Choi, Yeon-Im;Lee, Hye-Young;Kim, Tae-Ue
    • Biomedical Science Letters
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    • v.17 no.4
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    • pp.297-304
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    • 2011
  • Influenza A virus of the Orthomyxoviridae family is a contagious respiratory pathogen that continues to evolve and burden in the human public health. It is able to spread efficiently from human to human and have the potential to cause pandemics with significant morbidity and mortality. It has been estimated that every year about 500 million people are infected with this virus, causing about approximately 0.25 to 0.5 million people deaths worldwide. Influenza A viruses are classified into different subtypes by antigenicity based on their hemagglutinin (HA) and neuraminidase (NA) proteins. The sudden emergence of influenza A virus subtypes and access for epidemiological analysis of this subtypes demanded a rapid development of specific diagnostic tools. Also, rapid identification of the subtypes can help to determine the antiviral treatment, because the different subtypes have a different antiviral drug resistance patterns. In this study, our aim is to detect influenza A virus subtypes by using real-time nucleic acid sequence based amplification (NASBA) which has high sensitivity and specificity through molecular beacon. Real-time NASBA is a method that able to shorten the time compare to other molecular diagnostic tools and is performed by isothermal condition. We selected major pandemic influenza A virus subtypes, H3N2 and H5N1. Three influenza A virus gene fragments such as HA, NA and matrix protein (M) gene were targeted. M gene is distinguished influenza A virus from other influenza virus. We designed specific primers and molecular beacons for HA, NA and M gene, respectively. In brief, the results showed that the specificity of the real-time NASBA was higher than reverse transcription polymerase chain reaction (RT-PCR). In addition, time to positivity (TTP) of this method was shorter than real-time PCR. This study suggests that the rapid detection of neo-appearance pandemic influenza A virus using real-time NASBA has the potential to determine the subtypes.

Expression of c-Type Lysozyme from the Fleshy Shrimp Fenneropenaeus chinensis Is Upregulated Following Vibrio anguillarum and Lipopolysaccharide Injection

  • Qiao, Guo;Kim, Su-Kyoung;Cho, Yeong-Rok;Kim, Sukyoung;Jang, In-Kwon
    • Fisheries and Aquatic Sciences
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    • v.16 no.4
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    • pp.267-272
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    • 2013
  • Chicken-type lysozyme (c-lysozyme) is present in shrimp and is active against some bacteria. To further understand the regulation of c-lysozyme in the fleshy shrimp Fenneropenaeus chinensis, we determined the tissue-specific gene expression of c-lysozyme and the time-course of mRNA expression in response to Vibrio anguillarum and lipopolysaccharide (LPS) injection by quantitative reverse real-time polymerase chain reaction. The results showed that c-lysozyme was expressed in all tissues tested, including gill, eyestalk, eye, hemocytes, hepatopancreas, intestine, heart, and pleopod. It was most highly expressed in the intestine followed by the eyestalk, gill, hemocytes and hepatopancreas. The mRNA expression level began to decline in a short time after V. anguillarum challenge and was then upregulated by two fold or more at 24 h post injection (hpi) compared to that at 0 h. Expression was suppressed shortly after LPS injection and began to increase with higher levels of 5.8-, 5.2- and 8.4-fold at 24, 48, and 72 hpi, respectively. Higher expression was sustained and showed a gradual increasing trend until the end of the experiment (72 hpi). These results increase our understanding of the regulation of defense mechanisms and facilitate an evaluation of the effects of probiotics or immunostimulants in shrimp culture.

Comprehensive Evaluation of the Anti-Helicobacter pylori Activity of Scutellariae Radix

  • Lee, Ba Wool;Park, Il-Ho;Yim, Dongsool;Choi, Sung Sook
    • Natural Product Sciences
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    • v.23 no.1
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    • pp.46-52
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    • 2017
  • The aim of this study was to evaluate the anti-Helicobacter pylori activity of fractions and major aglycon compounds (baicalein, chrysin, oroxylin A, wogonin) of Scutellariae Radix. Minimum inhibitory concentration (MIC) measurement, DPPH radical-scavenging assay, DNA protection assay, and urease inhibition analysis were performed. The ethyl acetate (EtOAc) fraction showed the potent anti-Helicobacter activity, and therefore, compounds in the EtOAc fraction were subjected to further assay. The MICs of chrysin, oroxylin A, and wogonin against Helicobacter pylori 26695 were 6.25, 12.5 and $25{\mu}g/mL$, respectively. Baicalein exhibited the most effective DPPH radical-scavenging activity. DNA protection using Fenton reaction, chrysin, oroxylin A, and wogonin showed effective DNA protective effect. This result was also confirmed by quantitative real-time polymerase chain reaction (qRT-PCR). Regarding Jack bean urease (0.5 mg/mL, 50 unit/mg) inhibition, 20 mM ofbaicalein and chrysin inhibited urease activity by 88.2% and 72.5%, respectively.