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Pan Y, Zhao Y, Zeng HR, Wu JQ, Song YY, Rao YH, Li GQ, Jin L. Reference Genes for Expression Analyses by qRT-PCR in Enterobacter cancerogenus. Microorganisms 2024; 12:1024. [PMID: 38792853 PMCID: PMC11123693 DOI: 10.3390/microorganisms12051024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
The Enterobacter cancerogenus strain EcHa1 was isolated from the dead larvae of Helicoverpa armigera, and has the potential for biocontrol of some Lepidoptera insects. In order to screen insecticidal-related genes by qRT-PCR, stable endogenous reference genes used for normalizing qRT-PCR data were selected and evaluated from 13 housekeeping genes (HKGs). The expression levels of the HKGs were determined using qRT-PCR under different experimental conditions, including two culture temperatures and three bacterial OD values. Five stability analysis methods (Ct, BestKeeper, NormFinder, geNorm, and RefFinder) were used to comprehensively rank the candidate genes. The results showed that the optimal reference genes varied under different experimental conditions. The combination of gyrA and gyrB was recommended as the best reference gene combination at 28 °C, while gyrA and rpoB was the best combination at 37 °C. When the OD values were 0.5, 1.0 and 2.0, the recommended reference gene combinations were ftsZ and gyrA, rpoB and gyrB, and gyrA and pyk, respectively. The most suitable reference genes were gyrA and gyrB under all experimental conditions. Using gyrA and gyrB as the reference genes for qRT-PCR, EcHa1 was found to invade all tissues of the H. armigera larvae, and expressed a candidate pathogenic factor Hcp at high levels in gut, Malpighian tubules, and epidermis tissues. This study not only establishes an accurate and reliable normalization for qRT-PCR in entomopathogenic bacteria but also lays a solid foundation for further study of functional genes in E. cancerogenus.
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Affiliation(s)
| | | | | | | | | | | | | | - Lin Jin
- Education Ministry Key Laboratory of Integrated Management of Crop Diseases and Pests/State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; (Y.P.); (Y.Z.); (H.-R.Z.); (J.-Q.W.); (Y.-Y.S.); (Y.-H.R.); (G.-Q.L.)
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2
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Yetkin S, Alotaibi H. Selection and validation of novel stable reference genes for qPCR analysis in EMT and MET. Exp Cell Res 2023; 428:113619. [PMID: 37146958 DOI: 10.1016/j.yexcr.2023.113619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 04/18/2023] [Accepted: 04/29/2023] [Indexed: 05/07/2023]
Abstract
Quantitative real-time polymerase chain reaction is a powerful tool for quantifying gene expression. The relative quantification relies on normalizing the data to reference genes or internal controls not modulated by the experimental conditions. The most widely used internal controls occasionally show changed expression patterns in different experimental settings, such as the mesenchymal to epithelial transition. Thus, identifying appropriate internal controls is of utmost importance. We analyzed multiple RNA-Seq datasets using a combination of statistical approaches such as percent relative range and coefficient of variance to define a list of candidate internal control genes, which was then validated experimentally and by using in silico analyses as well. We identified a group of genes as strong internal control candidates with high stability compared to the classical ones. We also presented evidence for the superiority of the percent relative range method for calculating expression stability in data sets with larger sample sizes. We used multiple methods to analyze data collected from several RNA-Seq datasets; we identified Rbm17 and Katna1 as the most stable reference genes in EMT/MET studies. The percent relative range approach surpasses other methods when analyzing datasets of larger sample sizes.
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Affiliation(s)
- Seray Yetkin
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University Health Campus, 35340, Balçova, İzmir, Turkey
| | - Hani Alotaibi
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University Health Campus, 35340, Balçova, İzmir, Turkey; Izmir Biomedicine and Genome Center, Dokuz Eylül University Health Campus, 35340, Balçova, İzmir, Turkey.
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3
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Jureckova K, Raschmanova H, Kolek J, Vasylkivska M, Branska B, Patakova P, Provaznik I, Sedlar K. Identification and Validation of Reference Genes in Clostridium beijerinckii NRRL B-598 for RT-qPCR Using RNA-Seq Data. Front Microbiol 2021; 12:640054. [PMID: 33815328 PMCID: PMC8012504 DOI: 10.3389/fmicb.2021.640054] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/17/2021] [Indexed: 11/23/2022] Open
Abstract
Gene expression analysis through reverse transcription-quantitative real-time polymerase chain reaction (RT-qPCR) depends on correct data normalization by reference genes with stable expression. Although Clostridium beijerinckii NRRL B-598 is a promising Gram-positive bacterium for the industrial production of biobutanol, validated reference genes have not yet been reported. In this study, we selected 160 genes with stable expression based on an RNA sequencing (RNA-Seq) data analysis, and among them, seven genes (zmp, rpoB1, rsmB, greA, rpoB2, topB2, and rimO) were selected for experimental validation by RT-qPCR and gene ontology (GO) enrichment analysis. According to statistical analyses, zmp and greA were the most stable and suitable reference genes for RT-qPCR normalization. Furthermore, our methodology can be useful for selection of the reference genes in other strains of C. beijerinckii and it also suggests that the RNA-Seq data can be used for the initial selection of novel reference genes, however, their validation is required.
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Affiliation(s)
- Katerina Jureckova
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czechia
| | - Hana Raschmanova
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czechia
| | - Jan Kolek
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czechia
| | - Maryna Vasylkivska
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czechia
| | - Barbora Branska
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czechia
| | - Petra Patakova
- Department of Biotechnology, University of Chemistry and Technology Prague, Prague, Czechia
| | - Ivo Provaznik
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czechia
| | - Karel Sedlar
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czechia
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4
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Effect of Nitrogen Sources on Omega-3 Polyunsaturated Fatty Acid Biosynthesis and Gene Expression in Thraustochytriidae sp. Mar Drugs 2020; 18:md18120612. [PMID: 33271856 PMCID: PMC7760700 DOI: 10.3390/md18120612] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 11/26/2020] [Accepted: 11/28/2020] [Indexed: 11/17/2022] Open
Abstract
The molecular mechanism that contributes to nitrogen source dependent omega-3 polyunsaturated fatty acid (n-3 PUFA) synthesis in marine oleaginous protists Thraustochytriidae sp., was explored in this study. The fatty acid (FA) synthesis was significantly influenced by the supplement of various levels of sodium nitrate (SN) (1–50 mM) or urea (1–50 mM). Compared with SN (50 mM) cultivation, cells from urea (50 mM) cultivation accumulated 1.16-fold more n-3 PUFAs (49.49% docosahexaenoic acid (DHA) (w/w, of total FAs) and 5.28% docosapentaenoic acid (DPA) (w/w, of total FAs)). Strikingly higher quantities of short chain FAs (<18 carbons) (52.22-fold of that in urea cultivation) were produced from SN cultivation. Ten candidate reference genes (RGs) were screened by using four statistical methods (geNorm, NormFinder, Bestkeeper and RefFinder). MFT (Mitochondrial folate transporter) and NUC (Nucleolin) were determined as the stable RGs to normalize the RT-qPCR (real-time quantitative polymerase chain reaction) data of essential genes related to n-3 PUFAs-synthesis. Our results elucidated that the gene transcripts of delta(3,5)-delta(2,4)-dienoyl-CoA isomerase, enoyl-CoA hydratase, fatty acid elongase 3, long-chain fatty acid acyl-CoA ligase, and acetyl-CoA carboxylase were up-regulated under urea cultivation, contributing to the extension and unsaturated bond formation. These findings indicated that regulation of the specific genes through nitrogen source could greatly stimulate n-3 PUFA production in Thraustochytriidae sp.
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Abstract
Reverse-transcription quantitative real-time polymerase chain reaction (RT-qPCR) using fluorescent DNA-binding dyes is now a gold-standard methodology to study bacterial gene expression through relative quantitation of target mRNAs under specific experimental conditions, and recent developments in the technology allow for gene expression analysis in single cells. Nevertheless, several critical steps of the RT-qPCR protocol need to be carefully addressed in order to obtain reliable results, particularly regarding RNA sample quality and appropriate choice of reference genes. Besides, accurate reporting of study conditions is essential, as recommended by the MIQE guidelines. Herein, we provide a practical approach to quantitation of the transcript levels of bacterial genes using RT-qPCR, including a general protocol for obtaining good-quality bacterial RNA and a discussion on the selection and validation of candidate bacterial reference genes for data normalization.
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Mahmud R, Shehreen S, Shahriar S, Rahman MS, Akhteruzzaman S, Sajib AA. Non-Caloric Artificial Sweeteners Modulate the Expression of Key Metabolic Genes in the Omnipresent Gut Microbe Escherichia coli. J Mol Microbiol Biotechnol 2019; 29:43-56. [PMID: 31851990 DOI: 10.1159/000504511] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 10/31/2019] [Indexed: 11/19/2022] Open
Abstract
The human gut is inhabited by several hundred different bacterial species. These bacteria are closely associated with our health and well-being. The composition of these diverse commensals is influenced by our dietary intakes. Non-caloric artificial sweeteners (NAS) have gained global popularity, particularly among diabetic patients, due to their perceived health benefits, such as reduction of body weight and maintenance of blood glucose level compared to caloric sugars. Recent studies have reported that these artificial sweeteners can alter the composition of gut microbiota and, thus, affect our normal physiological state. Here, we investigated the effect of aspartame and acesulfame potassium (ace-K), two popular NAS, in a commercial formulation on the growth and metabolic pathways of omnipresent gut commensal Escherichia coliby analyzing the relative expression levels of the key genes, which control over twenty important metabolic pathways. Treatment with NAS preparation (aspartame and ace-K) modulates the growth of E. colias well as inducing the expression of important metabolic genes associated with glucose (pfkA, sucA, aceE, pfkB, lpdA), nucleotide (tmk, adk, tdk, thyA), and fatty acid (fabI) metabolisms, among others. Several of the affected geneswere previously reported to be important for the colonization of the microbes in the gut. These findings may shed light on the mechanism of alteration of gut microbes and their metabolism by NAS.
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Affiliation(s)
- Rizwan Mahmud
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, Bangladesh.,Department of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh
| | - Saadlee Shehreen
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Shayan Shahriar
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Md Siddiqur Rahman
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Sharif Akhteruzzaman
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Abu Ashfaqur Sajib
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, Bangladesh,
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7
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Jiang N, Lyu Q, Han S, Xu X, Walcott RR, Li J, Luo L. Evaluation of suitable reference genes for normalization of quantitative reverse transcription PCR analyses in Clavibacter michiganensis. Microbiologyopen 2019; 8:e928. [PMID: 31578822 PMCID: PMC6925165 DOI: 10.1002/mbo3.928] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 08/08/2019] [Accepted: 08/09/2019] [Indexed: 01/10/2023] Open
Abstract
Clavibacter michiganensis, the causal agent of bacterial canker of tomato, is a Gram-positive bacterium and a model for studying plant diseases. The real-time quantitative reverse transcription PCR (real-time qRT-PCR) assay is widely used to quantify gene expression in plant pathogenic bacteria. However, accurate quantification of gene expression requires stably expressed reference genes that are consistently expressed during the experimental conditions of interest. The use of inappropriate reference genes leads to a misinterpretation of gene expression data and false conclusions. In current study, we empirically assessed the expression stability of six housekeeping genes (gyrB, rpoB, tufA, bipA, gapA, and pbpA) of C. michiganensis under five experimental conditions using two algorithms, geNorm and NormFinder. C. michiganensis expressed gyrB, bipA, and gapA stably when growing in nutrient-rich broth (TBY broth and modified M9 broth). We concluded that pbpA, tufA, and gyrB were suitable reference genes in C. michiganensis-tomato interaction studies. We also recommended bipA and rpoB to be used to study bacterial gene expression under nutrient-poor conditions. Finally, gyrB, pbpA, and rpoB can be used to normalize the quantification of C. michiganensis gene expression while the bacterium is in the viable but nonculturable (VBNC) state. This study identified the most suitable reference genes depending on the experimental conditions for calibrating real-time qRT-PCR analyses of C. michiganensis and will be useful in studies that seek to understand the molecular interactions between C. michiganensis and tomato.
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Affiliation(s)
- Na Jiang
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Qingyang Lyu
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Sining Han
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Xin Xu
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Ronald R Walcott
- Department of Plant Pathology, 4315 Miller Plant Sciences, the University of Georgia, Athens, GA, USA
| | - Jianqiang Li
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Laixin Luo
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
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Screening the Reference Genes for Quantitative Gene Expression by RT-qPCR During SE Initial Dedifferentiation in Four Gossypium hirsutum Cultivars that Have Different SE Capability. Genes (Basel) 2019; 10:genes10070497. [PMID: 31261792 PMCID: PMC6678594 DOI: 10.3390/genes10070497] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 06/24/2019] [Accepted: 06/25/2019] [Indexed: 12/29/2022] Open
Abstract
RNA sequencing (RNA-Seq)-based gene expression analysis is applicable to a wide range of biological purposes in various species. Reverse transcription quantitative PCR (RT-qPCR) is also used to assess target gene expression utilizing stably expressed reference genes as internal control under a given set of conditions. However, investigations of the reference genes for RT-qPCR normalization in the process of somatic embryogenesis (SE) initial dedifferentiation in Gossypium hirsutum are rarely reported. In this study, on the basis of our previous transcriptome data of three different induction stages during SE initial dedifferentiation process in four G. hirsutum cultivars that have different SE capability, 15 candidate genes were selected during SE initial dedifferentiation process, and their expression stability was evaluated by geNorm, NormFinder, and BestKeeper. The results indicated that the two genes of endonuclease 4 (ENDO4) and 18S ribosomal RNA (18S rRNA) showed stable expression in the four different G. hirsutum cultivars, endowing them to be appropriate reference genes during three induction stages in the four cotton cultivars. In addition, the stability and reliability of the two reference genes of ENDO4 and 18S rRNA were further verified by comparing the expressions of auxin-responsive protein 22 (AUX22) and ethylene-responsive transcription factor 17 (ERF17) between RT-qPCR results and the RNA-seq data, which showed strong positive correlation coefficient (R2 = 0.8396–0.9984), validating again the steady expression of ENDO4 and 18S rRNA as the reliable reference genes. Our results provide effective reference genes for RT-qPCR normalization during SE process in different G. hirsutum cultivars.
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Zhou Z, Yang H, Li H, Li X, Li X, Wu B, Tian S, Wu J, Wang Z, Hu S. Sodium butyrate ameliorates Corynebacterium pseudotuberculosis infection in RAW264.7 macrophages and C57BL/6 mice. Microb Pathog 2019; 131:144-149. [PMID: 30965088 DOI: 10.1016/j.micpath.2019.04.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 03/23/2019] [Accepted: 04/05/2019] [Indexed: 12/22/2022]
Abstract
Corynebacterium pseudotuberculosis (CP) infection in livestock has become highly difficult to control. To decrease the incidence of CP infection, the supplementation of feed with non-antibiotic antibacterial substances is a potential approach. The aim of this study was to assess the effects of sodium butyrate (NaB), a potential alternative to antibiotics, on CP infection in RAW264.7 macrophages and C57BL/6 mice. Our data showed that NaB (2 mM) significantly ameliorated CPinfection in RAW264.7 macrophages and decreased the bacterial load in the spleens of infected mice. By real-time PCR, we found that NaB induced significant decreases in zinc-dependent superoxide dismutase (sodC) and tip protein C (spaC) expression in CP from infected-RAW264.7 cells and in phospholipase D (pld) and spaC expression in CP from the spleens of infected mice. NaB treatment significantly up-regulated cathelicidin-related antimicrobial peptide (cramp) expression in spleens of mice infected with CP. Furthermore, NaB alleviated histopathological changes in spleens of CP-infected mice. In conclusion, NaB ameliorated CP infection in RAW264.7 macrophages and C57BL/6 mice, and these effects may be related to the modulation of sodC, spaC, pld, and cramp expression.
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Affiliation(s)
- Zuoyong Zhou
- College of Animal Science, Rongchang Campus of Southwest University, No. 160 Xueyuan Road, Rongchang District, Chongqing, 402460, China; Veterinary Science Engineering Research Center of Chongqing, No. 160 Xueyuan Road, Rongchang District, Chongqing, 402460, China.
| | - Haoyue Yang
- College of Animal Science, Rongchang Campus of Southwest University, No. 160 Xueyuan Road, Rongchang District, Chongqing, 402460, China.
| | - Hexian Li
- College of Animal Science, Rongchang Campus of Southwest University, No. 160 Xueyuan Road, Rongchang District, Chongqing, 402460, China.
| | - Xiaoxia Li
- College of Animal Science, Rongchang Campus of Southwest University, No. 160 Xueyuan Road, Rongchang District, Chongqing, 402460, China.
| | - Xiao Li
- College of Animal Science, Rongchang Campus of Southwest University, No. 160 Xueyuan Road, Rongchang District, Chongqing, 402460, China.
| | - Bi Wu
- College of Animal Science, Rongchang Campus of Southwest University, No. 160 Xueyuan Road, Rongchang District, Chongqing, 402460, China.
| | - Shangquan Tian
- College of Animal Science, Rongchang Campus of Southwest University, No. 160 Xueyuan Road, Rongchang District, Chongqing, 402460, China.
| | - Junjun Wu
- College of Animal Science, Rongchang Campus of Southwest University, No. 160 Xueyuan Road, Rongchang District, Chongqing, 402460, China.
| | - Zhiying Wang
- College of Animal Science, Rongchang Campus of Southwest University, No. 160 Xueyuan Road, Rongchang District, Chongqing, 402460, China; Veterinary Science Engineering Research Center of Chongqing, No. 160 Xueyuan Road, Rongchang District, Chongqing, 402460, China.
| | - Shijun Hu
- College of Animal Science, Rongchang Campus of Southwest University, No. 160 Xueyuan Road, Rongchang District, Chongqing, 402460, China; Veterinary Science Engineering Research Center of Chongqing, No. 160 Xueyuan Road, Rongchang District, Chongqing, 402460, China.
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Ciesielska A, Oleksak B, Stączek P. Reference genes for accurate evaluation of expression levels in Trichophyton interdigitale grown under different carbon sources, pH levels and phosphate levels. Sci Rep 2019; 9:5566. [PMID: 30944363 PMCID: PMC6447595 DOI: 10.1038/s41598-019-42065-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 03/25/2019] [Indexed: 11/11/2022] Open
Abstract
Tinea pedis is a type of dermatophytosis caused by anthropophilic keratinolytic fungi such as Trichophyton interdigitale. Quantitative reverse transcription PCR (RT-qPCR) is a reliable and reproducible technique for measuring changes in target gene expression across various biological conditions. A crucial aspect of accurate normalization is the choice of appropriate internal controls. To identify reference genes for accurate evaluation of expression levels in T. interdigitale, the transcription levels of eight candidate reference genes (adp-rf, β-act, ef1-α, gapdh, psm1, sdha, rpl2 and ubc) and one target gene (Tri m4) were analysed by RT-qPCR after growing the dermatophyte under different environmental conditions. The results obtained from expression stability evaluations with NormFinder, geNorm, BestKeeper, and RefFinder software demonstrated that adp-rf and psm1 were the most stable internal control genes across all experimental conditions. The present study constitutes the first report of the identification and validation of reference genes for RT-qPCR normalization for T. interdigitale grown under different environmental conditions resembling the conditions encountered by fungi during invasion of skin.
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Affiliation(s)
- Anita Ciesielska
- Department of Microbial Genetics, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland.
| | - Beata Oleksak
- Department of Microbial Genetics, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
| | - Paweł Stączek
- Department of Microbial Genetics, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
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Dror B, Savidor A, Salam BB, Sela N, Lampert Y, Teper-Bamnolker P, Daus A, Carmeli S, Sela Saldinger S, Eshel D. High Levels of CO 2 Induce Spoilage by Leuconostoc mesenteroides by Upregulating Dextran Synthesis Genes. Appl Environ Microbiol 2019; 85:e00473-18. [PMID: 30367004 PMCID: PMC6293096 DOI: 10.1128/aem.00473-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 10/10/2018] [Indexed: 11/20/2022] Open
Abstract
During nonventilated storage of carrots, CO2 gradually accumulates to high levels and causes modifications in the carrot's microbiome toward dominance of Lactobacillales and Enterobacteriales The lactic acid bacterium Leuconostoc mesenteroides secretes a slimy exudate over the surface of the carrots. The objective of this study was to characterize the slime components and the potential cause for its secretion under high CO2 levels. A proteomic analysis of the exudate revealed bacterial glucosyltransferases as the main proteins, specifically, dextransucrase. A chemical analysis of the exudate revealed high levels of dextran and several simple sugars. The exudate volume and dextran amount were significantly higher when L. mesenteroides was incubated under high CO2 levels than when incubated in an aerated environment. The treatment of carrot medium plates with commercial dextransucrase or exudate protein extract resulted in similar sugar profiles and dextran production. Transcriptome analysis demonstrated that dextran production is related to the upregulation of the L. mesenteroides dextransucrase-encoding genes dsrD and dsrT during the first 4 to 8 h of exposure to high CO2 levels compared to aerated conditions. A phylogenetic analysis of L. mesenteroides YL48 dsrD revealed a high similarity to other dsr genes harbored by different Leuconostoc species. The ecological benefit of dextran production under elevated CO2 requires further investigation. However, this study implies an overlooked role of CO2 in the physiology and fitness of L. mesenteroides in stored carrots, and perhaps in other food items, during storage under nonventilated conditions.IMPORTANCE The bacterium Leuconostoc mesenteroides is known to cause spoilage of different types of foods by secreting a slimy fluid that damages the quality and appearance of the produce. Here, we identified a potential mechanism by which high levels of CO2 affect the spoilage caused by this bacterium by upregulating dextran synthesis genes. These results have broader implications for the study of the physiology, degradation ability, and potential biotechnological applications of Leuconostoc.
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Affiliation(s)
- Barak Dror
- Department of Postharvest and Food Sciences, Agricultural Research Organization (ARO), The Volcani Center, Rishon LeZion, Israel
- Department of Food Quality and Safety, ARO, The Volcani Center, Rishon LeZion, Israel
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Alon Savidor
- De Button Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Bolaji Babajide Salam
- Department of Postharvest and Food Sciences, Agricultural Research Organization (ARO), The Volcani Center, Rishon LeZion, Israel
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Noa Sela
- Department of Plant Pathology and Weed Science, ARO, The Volcani Center, Rishon LeZion, Israel
| | - Yael Lampert
- Department of Postharvest and Food Sciences, Agricultural Research Organization (ARO), The Volcani Center, Rishon LeZion, Israel
- Department of Food Quality and Safety, ARO, The Volcani Center, Rishon LeZion, Israel
| | - Paula Teper-Bamnolker
- Department of Postharvest and Food Sciences, Agricultural Research Organization (ARO), The Volcani Center, Rishon LeZion, Israel
| | - Avinoam Daus
- Department of Postharvest and Food Sciences, Agricultural Research Organization (ARO), The Volcani Center, Rishon LeZion, Israel
| | - Shmuel Carmeli
- Raymond and Beverly Sackler School of Chemistry and Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Shlomo Sela Saldinger
- Department of Food Quality and Safety, ARO, The Volcani Center, Rishon LeZion, Israel
| | - Dani Eshel
- Department of Postharvest and Food Sciences, Agricultural Research Organization (ARO), The Volcani Center, Rishon LeZion, Israel
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12
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Gomide ACP, Ibraim IC, Alves JTC, de Sá PG, de Oliveira Silva YR, Santana MP, Silva WM, Folador EL, Mariano DCB, de Paula Castro TL, Barbosa S, Dorella FA, Carvalho AF, Pereira FL, Leal CAG, Figueiredo HCP, Azevedo V, Silva A, Folador ARC. Transcriptome analysis of Corynebacterium pseudotuberculosis biovar Equi in two conditions of the environmental stress. Gene 2018; 677:349-360. [PMID: 30098432 DOI: 10.1016/j.gene.2018.08.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 07/10/2018] [Accepted: 08/06/2018] [Indexed: 11/30/2022]
Abstract
Corynebacterium pseudotuberculosis has been widely studied in an effort to understand its biological evolution. Transcriptomics has revealed possible candidates for virulence and pathogenicity factors of strain 1002 (biovar Ovis). Because C. pseudotuberculosis is classified into two biovars, Ovis and Equi, it was interesting to assess the transcriptional profile of biovar Equi strain 258, the causative agent of ulcerative lymphangitis. The genome of this strain was re-sequenced; the reassembly was completed using optical mapping technology, and the sequence was subsequently re-annotated. Two growth conditions that occur during the host infection process were simulated for the transcriptome: the osmotic and acid medium. Genes that may be associated with the microorganism's resilience under unfavorable conditions were identified through RNAseq, including genes present in pathogenicity islands. The RT-qPCR was performed to confirm the results in biological triplicate for each condition for some genes. The results extend our knowledge of the factors associated with the spread and persistence of C. pseudotuberculosis during the infection process and suggest possible avenues for studies related to the development of vaccines, diagnosis, and therapies that might help minimize damage to agribusinesses.
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Affiliation(s)
- Anne Cybelle Pinto Gomide
- Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Av. Antônio Carlos, Belo Horizonte 31.270-901, Brazil.
| | - Izabela Coimbra Ibraim
- Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Av. Antônio Carlos, Belo Horizonte 31.270-901, Brazil
| | - Jorianne T C Alves
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil, Rua Augusto Corrêa, Belém 66.075-110, Brazil
| | - Pablo Gomes de Sá
- Federal Rural University of Amazonia, Rodovia PA 140, 2428 Tomé-Açu, PA, Brazil
| | - Yuri Rafael de Oliveira Silva
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil, Rua Augusto Corrêa, Belém 66.075-110, Brazil
| | - Mariana Passos Santana
- Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Av. Antônio Carlos, Belo Horizonte 31.270-901, Brazil
| | - Wanderson Marques Silva
- National Institute of Agricultural Technology, Los Reseros y Nicolás Repetto, Hurlingham 1686, Argentina
| | - Edson Luiz Folador
- Biotechnology Center, Federal University of Paraíba, João Pessoa, Brazil.
| | - Diego C B Mariano
- Department of Computer Sciences, Institute of Exact Sciences, Federal University of Minas Gerais, Av. Antônio Carlos, Belo Horizonte 31.270-901, Brazil.
| | - Thiago Luiz de Paula Castro
- Department of Biointeraction, Institute of Health Sciences, Federal University of Bahia, Av. Reitor Miguel Calmon, s/n, Vale do Canela, Bahia, Brazil
| | - Silvanira Barbosa
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil, Rua Augusto Corrêa, Belém 66.075-110, Brazil
| | - Fernanda Alves Dorella
- AQUACEN - National Reference Laboratory of Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Alex F Carvalho
- AQUACEN - National Reference Laboratory of Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Felipe L Pereira
- AQUACEN - National Reference Laboratory of Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Brazil.
| | - Carlos A G Leal
- AQUACEN - National Reference Laboratory of Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Brazil.
| | - Henrique C P Figueiredo
- AQUACEN - National Reference Laboratory of Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Vasco Azevedo
- Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Av. Antônio Carlos, Belo Horizonte 31.270-901, Brazil.
| | - Artur Silva
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil, Rua Augusto Corrêa, Belém 66.075-110, Brazil.
| | - Adriana Ribeiro Carneiro Folador
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil, Rua Augusto Corrêa, Belém 66.075-110, Brazil.
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Corrêa JI, Stocker A, Trindade SC, Vale V, Brito T, Bastos B, Raynal JT, de Miranda PM, de Alcantara AC, Freire SM, Costa LM, Meyer R. In vivo and in vitro expression of five genes involved in Corynebacterium pseudotuberculosis virulence. AMB Express 2018; 8:89. [PMID: 29846821 PMCID: PMC5976562 DOI: 10.1186/s13568-018-0598-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 04/18/2018] [Indexed: 11/18/2022] Open
Abstract
Caseous lymphadenitis (LC) is a chronic contagious disease caused by Corynebacterium pseudotuberculosis, which mainly affects goats and sheep. Vaccination is an effective but not yet well-established method, partly due to a lack of knowledge surrounding the most effective immunoprotective components. The present study aimed to quantify and compare the in vivo expression of genes pld (phospholipase D), cpp (CP40), nanH (neuraminidase H), sodC (superoxide dismutase C) and spaC (adhesin) using qRT-PCR, with the respective expression in vitro. Caseous material of abscesses removed from five animals was cultured, with colonies suggestive of C. pseudotuberculosis identified. RNA extraction was performed on these samples, as well as on the respective pellets derived from liquid cultures brain heart infusion. After evaluating RNA integrity, complementary DNA was synthesized, followed by the relative quantification each of the genes of interest. Mean mRNA expression of the five genes found in abscesses and in cultures differed significantly, with respective values of: nanH 811.50 ± 198.27 and 359.35 ± 75.45 (p = 0.009); cpp 856.31 ± 385.11 and 154.54 ± 94.34 (p = 0.0039); plD 922.70 ± 450.73 and 212.41 ± 153.10 (p = 0.016); sodC 1,293.53 ± 564.75 and 223.63 ± 145.58 (p = 0.016); spaC 1,157.10 ± 525.13 and 214.26 ± 125.70 (p = 0,016). Expression was observed to be 6–8 times higher in abscesses than in cultures, Indicative that is a genetic expression of the in vitro bacterium exists, yet in vivo has a greater magnitude corroborating to one of these virulence factors in the pathogenesis of LC.
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Polese V, de Paula Soares C, da Silva PRA, Simões-Araújo JL, Baldani JI, Vidal MS. Selection and validation of reference genes for RT-qPCR indicates that juice of sugarcane varieties modulate the expression of C metabolism genes in the endophytic diazotrophic Herbaspirillum rubrisubalbicans strain HCC103. Antonie Van Leeuwenhoek 2017; 110:1555-1568. [DOI: 10.1007/s10482-017-0906-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 06/28/2017] [Indexed: 12/24/2022]
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Chlamydia psittaci reference genes for normalisation of expression data differ depending on the culture conditions and selected time points during the chlamydial replication cycle. J Vet Res 2016. [DOI: 10.1515/jvetres-2016-0060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
Introduction: Chlamydia psittaci is a gram-negative obligate intracellular pathogen of birds. Poultry infections lead to economic losses and can be transmitted to humans. No vaccine is available and the bacterium-host cell interaction is not completely understood. Replicating bacteria cause pneumonia, but C. psittaci can also be non-replicating and persistent inside the cytoplasm of avian cells. RT-qPCR provides insight into the molecular pathogenesis of both active replicating and persistent Chlamydia psittaci in birds, but requires identification of stably expressed reference genes to avoid biases. Material and Methods: We investigated the expression stability of 10 C. psittaci candidate reference genes for gene expression analysis during normal growth and penicillin-induced persistence. C. psittaci Cal10 was cultured in HeLa229 and RNA was extracted. The expression level of each candidate was examined by RT-qPCR and Cq values were analysed using geNorm. Results: The genes tyrS, gidA, radA, and 16S rRNA ranked among the most stably expressed. The final selected reference genes differed according to the bacterial growth status (normal growth versus persistent status), and the time points selected during the duration of the normal chlamydial developmental cycle. Conclusion: The study data show the importance of systematic validation of reference genes to confirm their stability within the strains and under the conditions selected.
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Pessoa DDV, Vidal MS, Baldani JI, Simoes-Araujo JL. Validation of reference genes for RT-qPCR analysis in Herbaspirillum seropedicae. J Microbiol Methods 2016; 127:193-196. [PMID: 27302038 DOI: 10.1016/j.mimet.2016.06.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 06/09/2016] [Accepted: 06/10/2016] [Indexed: 11/17/2022]
Abstract
The RT-qPCR technique needs a validated set of reference genes for ensuring the consistency of the results from the gene expression. Expression stabilities for 9 genes from Herbaspirillum seropedicae, strain HRC54, grown with different carbon sources were calculated using geNorm and NormFinder, and the gene rpoA showed the best stability values.
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Affiliation(s)
- Daniella Duarte Villarinho Pessoa
- Universidade Federal do Rio de Janeiro - UFRJ, Programa de Pós-Graduação em Biotecnologia Vegetal, Centro de Ciências da Saúde - CCS, Campus Ilha do Fundão, Av. Carlos Chagas Filho, 373 - Cidade Universitária, CEP: 21941-590 Rio de Janeiro, RJ, Brazil; Centro Nacional de Pesquisa de Agrobiologia, CNPAB, Embrapa, Laboratório de Genética e Bioquímica, Embrapa Agrobiologia, BR 465, Km 7, s/n, Pavilhão Johanna Döbereiner, Bairro Ecologia, CEP: 23890-000 Seropédica, RJ, Brazil.
| | - Marcia Soares Vidal
- Centro Nacional de Pesquisa de Agrobiologia, CNPAB, Embrapa, Laboratório de Genética e Bioquímica, Embrapa Agrobiologia, BR 465, Km 7, s/n, Pavilhão Johanna Döbereiner, Bairro Ecologia, CEP: 23890-000 Seropédica, RJ, Brazil
| | - José Ivo Baldani
- Centro Nacional de Pesquisa de Agrobiologia, CNPAB, Embrapa, Laboratório de Genética e Bioquímica, Embrapa Agrobiologia, BR 465, Km 7, s/n, Pavilhão Johanna Döbereiner, Bairro Ecologia, CEP: 23890-000 Seropédica, RJ, Brazil
| | - Jean Luiz Simoes-Araujo
- Centro Nacional de Pesquisa de Agrobiologia, CNPAB, Embrapa, Laboratório de Genética e Bioquímica, Embrapa Agrobiologia, BR 465, Km 7, s/n, Pavilhão Johanna Döbereiner, Bairro Ecologia, CEP: 23890-000 Seropédica, RJ, Brazil.
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Almeida S, Tiwari S, Mariano D, Souza F, Jamal SB, Coimbra N, Raittz RT, Dorella FA, Carvalho AFD, Pereira FL, Soares SDC, Leal CAG, Barh D, Ghosh P, Figueiredo H, Moura-Costa LF, Portela RW, Meyer R, Silva A, Azevedo V. The genome anatomy of Corynebacterium pseudotuberculosis VD57 a highly virulent strain causing Caseous lymphadenitis. Stand Genomic Sci 2016; 11:29. [PMID: 27066196 PMCID: PMC4826502 DOI: 10.1186/s40793-016-0149-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 03/30/2016] [Indexed: 11/29/2022] Open
Abstract
Corynebacterium pseudotuberculosis strain VD57 (Cp_VD57), a highly virulent, nonmotile, non-sporulating, and a mesophilic bacterium, was isolated from a goat’s granulomatous lesion in the municipality of Juazeiro, Bahia State, Brazil. Here, we describe a set of features of the strain, together with the details of its complete genome sequence and annotation. The genome comprises of a 2.5 Mbp long, single circular genome with 2,101 protein-coding genes, 12 rRNA, 49 tRNA and 47 pseudogenes and a G + C content of 52.85 %. Genetic variation was detected in Cp_VD57 using C. pseudotuberculosis strain 1002 as reference, wherein small genomic insertions and deletions were identified. The comparative analysis of the genome sequence provides means to better understand the host pathogen interactions of this strain and can also help us to understand the molecular and genetic basis of virulence of this bacterium.
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Affiliation(s)
- Sintia Almeida
- Institute of Biologic Sciences, Federal University of Minas Gerais, Belo Horizonte, MG Brazil
| | - Sandeep Tiwari
- Institute of Biologic Sciences, Federal University of Minas Gerais, Belo Horizonte, MG Brazil
| | - Diego Mariano
- Institute of Biologic Sciences, Federal University of Minas Gerais, Belo Horizonte, MG Brazil
| | - Flávia Souza
- Institute of Biologic Sciences, Federal University of Minas Gerais, Belo Horizonte, MG Brazil
| | - Syed Babar Jamal
- Institute of Biologic Sciences, Federal University of Minas Gerais, Belo Horizonte, MG Brazil
| | - Nilson Coimbra
- Laboratory of Bioinformatics, Professional and Technological Education Sector, Federal University of Paraná, Curitiba, PR Brazil
| | - Roberto Tadeu Raittz
- Laboratory of Bioinformatics, Professional and Technological Education Sector, Federal University of Paraná, Curitiba, PR Brazil
| | - Fernanda Alves Dorella
- Aquacen - National Reference Laboratory for Aquatic Animal Diseases, Federal University of Minas Gerais, Belo Horizonte, MG Brazil
| | - Alex Fiorine de Carvalho
- Aquacen - National Reference Laboratory for Aquatic Animal Diseases, Federal University of Minas Gerais, Belo Horizonte, MG Brazil
| | - Felipe Luiz Pereira
- Aquacen - National Reference Laboratory for Aquatic Animal Diseases, Federal University of Minas Gerais, Belo Horizonte, MG Brazil
| | - Siomar de Castro Soares
- Aquacen - National Reference Laboratory for Aquatic Animal Diseases, Federal University of Minas Gerais, Belo Horizonte, MG Brazil
| | - Carlos Augusto Gomes Leal
- Aquacen - National Reference Laboratory for Aquatic Animal Diseases, Federal University of Minas Gerais, Belo Horizonte, MG Brazil
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, West Bengal India
| | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA USA
| | - Henrique Figueiredo
- Aquacen - National Reference Laboratory for Aquatic Animal Diseases, Federal University of Minas Gerais, Belo Horizonte, MG Brazil
| | | | | | - Roberto Meyer
- Institute of Health Sciences, Federal University of Bahia, Salvador, BA Brazil
| | - Artur Silva
- Institute of Biologic Sciences, Federal University of Para, Belem, PA Brazil
| | - Vasco Azevedo
- Institute of Biologic Sciences, Federal University of Minas Gerais, Belo Horizonte, MG Brazil
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Hu Y, Xie S, Yao J. Identification of Novel Reference Genes Suitable for qRT-PCR Normalization with Respect to the Zebrafish Developmental Stage. PLoS One 2016; 11:e0149277. [PMID: 26891128 PMCID: PMC4758726 DOI: 10.1371/journal.pone.0149277] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 01/29/2016] [Indexed: 12/20/2022] Open
Abstract
Reference genes used in normalizing qRT-PCR data are critical for the accuracy of gene expression analysis. However, many traditional reference genes used in zebrafish early development are not appropriate because of their variable expression levels during embryogenesis. In the present study, we used our previous RNA-Seq dataset to identify novel reference genes suitable for gene expression analysis during zebrafish early developmental stages. We first selected 197 most stably expressed genes from an RNA-Seq dataset (29,291 genes in total), according to the ratio of their maximum to minimum RPKM values. Among the 197 genes, 4 genes with moderate expression levels and the least variation throughout 9 developmental stages were identified as candidate reference genes. Using four independent statistical algorithms (delta-CT, geNorm, BestKeeper and NormFinder), the stability of qRT-PCR expression of these candidates was then evaluated and compared to that of actb1 and actb2, two commonly used zebrafish reference genes. Stability rankings showed that two genes, namely mobk13 (mob4) and lsm12b, were more stable than actb1 and actb2 in most cases. To further test the suitability of mobk13 and lsm12b as novel reference genes, they were used to normalize three well-studied target genes. The results showed that mobk13 and lsm12b were more suitable than actb1 and actb2 with respect to zebrafish early development. We recommend mobk13 and lsm12b as new optimal reference genes for zebrafish qRT-PCR analysis during embryogenesis and early larval stages.
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Affiliation(s)
- Yu Hu
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Shuying Xie
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Jihua Yao
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, China
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Bacterial reference genes for gene expression studies by RT-qPCR: survey and analysis. Antonie van Leeuwenhoek 2015; 108:685-93. [PMID: 26149127 DOI: 10.1007/s10482-015-0524-1] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2015] [Accepted: 06/29/2015] [Indexed: 10/23/2022]
Abstract
The appropriate choice of reference genes is essential for accurate normalization of gene expression data obtained by the method of reverse transcription quantitative real-time PCR (RT-qPCR). In 2009, a guideline called the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) highlighted the importance of the selection and validation of more than one suitable reference gene for obtaining reliable RT-qPCR results. Herein, we searched the recent literature in order to identify the bacterial reference genes that have been most commonly validated in gene expression studies by RT-qPCR (in the first 5 years following publication of the MIQE guidelines). Through a combination of different search parameters with the text mining tool MedlineRanker, we identified 145 unique bacterial genes that were recently tested as candidate reference genes. Of these, 45 genes were experimentally validated and, in most of the cases, their expression stabilities were verified using the software tools geNorm and NormFinder. It is noteworthy that only 10 of these reference genes had been validated in two or more of the studies evaluated. An enrichment analysis using Gene Ontology classifications demonstrated that genes belonging to the functional categories of DNA Replication (GO: 0006260) and Transcription (GO: 0006351) rendered a proportionally higher number of validated reference genes. Three genes in the former functional class were also among the top five most stable genes identified through an analysis of gene expression data obtained from the Pathosystems Resource Integration Center. These results may provide a guideline for the initial selection of candidate reference genes for RT-qPCR studies in several different bacterial species.
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