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Zhang P, Chen S, Chen S, Zhu Y, Lin Y, Xu X, Liu Z, Zou S. Selection and Validation of qRT-PCR Internal Reference Genes to Study Flower Color Formation in Camellia impressinervis. Int J Mol Sci 2024; 25:3029. [PMID: 38474274 DOI: 10.3390/ijms25053029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
Real-time quantitative PCR (qRT-PCR) is a pivotal technique for gene expression analysis. To ensure reliable and accurate results, the internal reference genes must exhibit stable expression across varied experimental conditions. Currently, no internal reference genes for Camellia impressinervis have been established. This study aimed to identify stable internal reference genes from eight candidates derived from different developmental stages of C. impressinervis flowers. We employed geNorm, NormFinder, and BestKeeper to evaluate the expression stability of these candidates, which was followed by a comprehensive stability analysis. The results indicated that CiTUB, a tubulin gene, exhibited the most stable expression among the eight reference gene candidates in the petals. Subsequently, CiTUB was utilized as an internal reference for the qRT-PCR analysis of six genes implicated in the petal pigment synthesis pathway of C. impressinervis. The qRT-PCR results were corroborated by transcriptome sequencing data, affirming the stability and suitability of CiTUB as a reference gene. This study marks the first identification of stable internal reference genes within the entire genome of C. impressinervis, establishing a foundation for future gene expression and functional studies. Identifying such stable reference genes is crucial for advancing molecular research on C. impressinervis.
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Affiliation(s)
- Peilan Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shuying Chen
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Siyu Chen
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuanming Zhu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuqing Lin
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xinyu Xu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhongjian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shuangquan Zou
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Ai Y, Peng K, Li C, Zhang J, Wang G, Wang B, Huang E. Assessment of Reference Genes Stability in Cortical Bone of Obese and Diabetic Mice. Diabetes Metab Syndr Obes 2024; 17:1081-1091. [PMID: 38455760 PMCID: PMC10917645 DOI: 10.2147/dmso.s453458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 02/15/2024] [Indexed: 03/09/2024] Open
Abstract
Introduction Bone, a pivotal structural organ, is susceptible to disorders with profound health implications. The investigation of gene expression in bone tissue is imperative, particularly within the context of metabolic diseases such as obesity and diabetes that augment the susceptibility to bone fractures. The objective of this study is to identify a set of internal control genes for the analysis of gene expression. Methods This study employs reverse transcription-quantitative real-time polymerase chain reaction (RT-qPCR) to assess gene expression in bone tissue. We selected fourteen housekeeping genes and assessed their stability in the cortical bone of mouse models for obesity and diabetes using four well-established algorithms (GeNorm, BestKeeper, NormFinder, and the comparative Delta Ct method). Results and Conclusion We identified Rpl13a as the mostly stably expressed reference gene in cortical bone tissue from mouse models of obesity and diabetes (db/db), while Gapdh was found to be the most stable reference gene in another diabetes model, KKAy mice. Additionally, Ef1a, Ppia, Rplp0, and Rpl22 were identified as alternative genes suitable for normalizing gene expression in cortical bone from obesity and diabetes mouse models. These findings enhance RT-qPCR accuracy and reliability, offering a strategic guide to select reference gene for studying bone tissue gene expression in metabolic disorders.
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Affiliation(s)
- Yuanli Ai
- Institute of Life Sciences, College of Basic Medicine, Chongqing Medical University, Chongqing, People’s Republic of China
| | - Kun Peng
- Chongqing Medical and Pharmaceutical College, Chongqing, People’s Republic of China
| | - Chunli Li
- Institute of Life Sciences, College of Basic Medicine, Chongqing Medical University, Chongqing, People’s Republic of China
| | - Jun Zhang
- Institute of Life Sciences, College of Basic Medicine, Chongqing Medical University, Chongqing, People’s Republic of China
| | - Gang Wang
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Stomatological Hospital of Chongqing Medical University, Chongqing, People’s Republic of China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education College of Stomatology, College of Stomatology, Chongqing Medical University, Chongqing, People’s Republic of China
| | - Bin Wang
- Institute of Life Sciences, College of Basic Medicine, Chongqing Medical University, Chongqing, People’s Republic of China
| | - Enyi Huang
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Stomatological Hospital of Chongqing Medical University, Chongqing, People’s Republic of China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education College of Stomatology, College of Stomatology, Chongqing Medical University, Chongqing, People’s Republic of China
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Li X, Zhang T, Jiang L, Fan G. Evaluation of Suitable Reference Genes for Quantitative Real-Time PCR in Various Tissues of Apocynum venetum. Genes (Basel) 2024; 15:231. [PMID: 38397220 PMCID: PMC10888412 DOI: 10.3390/genes15020231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/27/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Apocynum venetum L. is an economically valuable plant with tolerance to drought and salinity. Its leaves are utilized in tea production and pharmaceuticals, while the stem bark serves as a high-quality fiber material. To gain insights into the gene expression patterns of A. venetum using quantitative real-time PCR (qRT-PCR), it is crucial to identify appropriate reference genes. This study selected nine candidate genes, including α-tubulin (TUA), β-tubulin (TUB), actin (ACT), cyclophilin (CYP), elongation factor-1α (EF-1α), the B family of regulatory subunits of protein phosphatase (PPP2R2, PPP2R3, and PPP2R5), and phosphoglycerate kinase (PGK), to determine the most appropriate reference genes in the leaf, stem, and root tissues of A. venetum. A comprehensive ranking by geNorm, NormFinder, BestKeeper, and RefFinder software and Venn diagrams was used to screen more stable reference genes in different tissues. The two most stable reference genes were CYP and TUA in leaves, PGK and PPP2R3 in stems, and TUA and EF-1α in roots, respectively. The relative expression values of the four genes involved in proline metabolism under polyethylene glycol treatment were used to validate the screened reference genes, and they exhibited highly stable expression levels. These findings represent the first set of stable reference genes for future gene expression studies in A. venetum. They significantly contribute to enhancing the accuracy and reliability of gene expression analyses in this economically important plant species.
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Affiliation(s)
- Xiaoshuang Li
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin 150040, China (T.Z.)
| | - Tingting Zhang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin 150040, China (T.Z.)
| | - Li Jiang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Guizhi Fan
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin 150040, China (T.Z.)
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Zhang S, Zhu E, Wang Z, Zhong Y, Zha X, Ji H, Meng Q. Evaluation of suitable reference genes for expression profile analyses of target genes in the coffee berry borer, Hypothenemus hampei (Ferrari) (Coleoptera: Curculionidae). Bull Entomol Res 2024; 114:57-66. [PMID: 38180086 DOI: 10.1017/s0007485323000615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
The coffee berry borer, Hypothenemus hampei (Ferrari) (Coleoptera: Curculionidae), is a major destructive insect pest of coffee, which impacts the coffee crops negatively. As a draft genome has been completed for this insect, most molecular studies on gene transcriptional levels under different experimental conditions will be conducted using real-time reverse-transcription quantitative polymerase chain reactions (RT-qPCR). However, the lack of suitable internal reference genes will affect the accuracy of RT-qPCR results. In this study, the expression stability of nine candidate reference genes was evaluated under different developmental stages, temperature stress, and Beauveria bassiana infection. Data analyses were completed by four commonly used programs, BestKeeper, NormFinder, geNorm, and RefFinder. The result showed that RPL3 and EF1α combination were recommended as the most stable reference genes for developmental stages. EF1α and RPS3a combination were the top two stable reference genes for B. bassiana infection. RPS3a and RPL3 combination performed as the optimal reference genes both in temperature stress and all samples. Our results should provide a good foundation for the expression profile analyses of target genes in the future, especially for molecular studies on insect genetic development, temperature adaptability, and immune mechanism to entomogenous fungi in H. hampei.
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Affiliation(s)
- Shaohua Zhang
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, P.R. China
- School of Plant Protection, Hainan University, Haikou 570228, P.R. China
| | - Enhang Zhu
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, P.R. China
- School of Plant Protection, Hainan University, Haikou 570228, P.R. China
| | - Zheng Wang
- Chongqing Municipal Key Laboratory for High Pathogenic Microbes, The First Batch of Key Disciplines On Public Health in Chongqing, Department of Disinfection and Vector Control, Chongqing Center for Disease Control and Prevention, Chongqing 40042, P.R. China
- School of Plant Protection, Hainan University, Haikou 570228, P.R. China
| | - Yaofeng Zhong
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, P.R. China
- School of Plant Protection, Hainan University, Haikou 570228, P.R. China
| | - Xuezong Zha
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning 571533, P.R. China
- School of Plant Protection, Hainan University, Haikou 570228, P.R. China
| | - Hengqing Ji
- Chongqing Municipal Key Laboratory for High Pathogenic Microbes, The First Batch of Key Disciplines On Public Health in Chongqing, Department of Disinfection and Vector Control, Chongqing Center for Disease Control and Prevention, Chongqing 40042, P.R. China
| | - Qianqian Meng
- Institute of Agricultural Resources and Environment, Chongqing Academy of Agricultural Sciences, Chongqing 40042, P.R. China
- School of Plant Protection, Hainan University, Haikou 570228, P.R. China
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de Sousa PRC, da Silva ASM, de Ponte CGG, Nogueira LL, Frota CC, Antas PRZ. Commentary: Identification of optimal reference genes for gene expression normalization in human osteosarcoma cell lines under proliferative conditions. Front Genet 2024; 15:1342447. [PMID: 38333617 PMCID: PMC10850317 DOI: 10.3389/fgene.2024.1342447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 01/02/2024] [Indexed: 02/10/2024] Open
Affiliation(s)
- Paulo R. C. de Sousa
- Programa de Pós-Graduação em Patologia, Universidade Federal do Ceará, Fortaleza, Brazil
| | | | | | - Lucas L. Nogueira
- Programa de Pós-Graduação em Patologia, Universidade Federal do Ceará, Fortaleza, Brazil
| | - Cristiane C. Frota
- Programa de Pós-Graduação em Patologia, Universidade Federal do Ceará, Fortaleza, Brazil
| | - Paulo R. Z. Antas
- Programa de Pós-Graduação em Patologia, Universidade Federal do Ceará, Fortaleza, Brazil
- Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
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Pessoa FMCDP, Viana VBDJ, de Oliveira MB, Nogueira BMD, Ribeiro RM, Oliveira DDS, Lopes GS, Vieira RPG, de Moraes Filho MO, de Moraes MEA, Khayat AS, Moreira FC, Moreira-Nunes CA. Validation of Endogenous Control Genes by Real-Time Quantitative Reverse Transcriptase Polymerase Chain Reaction for Acute Leukemia Gene Expression Studies. Genes (Basel) 2024; 15:151. [PMID: 38397141 PMCID: PMC10887733 DOI: 10.3390/genes15020151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/09/2024] [Accepted: 01/22/2024] [Indexed: 02/25/2024] Open
Abstract
Reference genes are used as internal reaction controls for gene expression analysis, and for this reason, they are considered reliable and must meet several important criteria. In view of the absence of studies regarding the best reference gene for the analysis of acute leukemia patients, a panel of genes commonly used as endogenous controls was selected from the literature for stability analysis: Glyceraldehyde-3-phosphate dehydrogenase (GAPDH), Abelson murine leukemia viral oncogene human homolog 1 (ABL), Hypoxanthine phosphoribosyl-transferase 1 (HPRT1), Ribosomal protein lateral stalk subunit P0 (RPLP0), β-actin (ACTB) and TATA box binding protein (TBP). The stability of candidate reference genes was analyzed according to three statistical methods of assessment, namely, NormFinder, GeNorm and R software (version 4.0.3). From this study's analysis, it was possible to identify that the endogenous set composed of ACTB, ABL, TBP and RPLP0 demonstrated good performances and stable expressions between the analyzed groups. In addition to that, the GAPDH and HPRT genes could not be classified as good reference genes, considering that they presented a high standard deviation and great variability between groups, indicating low stability. Given these findings, this study suggests the main endogenous gene set for use as a control/reference for the gene expression in peripheral blood and bone marrow samples from patients with acute leukemias is composed of the ACTB, ABL, TBP and RPLP0 genes. Researchers may choose two to three of these housekeeping genes to perform data normalization.
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Affiliation(s)
- Flávia Melo Cunha de Pinho Pessoa
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
| | - Vitória Beatriz de Jesus Viana
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (V.B.d.J.V.); (M.B.d.O.); (F.C.M.)
| | - Marcelo Braga de Oliveira
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (V.B.d.J.V.); (M.B.d.O.); (F.C.M.)
| | - Beatriz Maria Dias Nogueira
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
| | | | - Deivide de Sousa Oliveira
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
- Department of Hematology, Fortaleza General Hospital (HGF), Fortaleza 60150-160, CE, Brazil
| | - Germison Silva Lopes
- Department of Hematology, César Cals General Hospital, Fortaleza 60015-152, CE, Brazil;
| | | | - Manoel Odorico de Moraes Filho
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
| | - Maria Elisabete Amaral de Moraes
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
| | - André Salim Khayat
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (V.B.d.J.V.); (M.B.d.O.); (F.C.M.)
| | - Fabiano Cordeiro Moreira
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (V.B.d.J.V.); (M.B.d.O.); (F.C.M.)
| | - Caroline Aquino Moreira-Nunes
- Department of Medicine, Pharmacogenetics Laboratory, Drug Research and Development Center (NPDM), Federal University of Ceará, Fortaleza 60430-275, CE, Brazil; (F.M.C.d.P.P.); (B.M.D.N.); (D.d.S.O.); (M.O.d.M.F.)
- Department of Biological Sciences, Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil; (V.B.d.J.V.); (M.B.d.O.); (F.C.M.)
- Central Unity, Molecular Biology Laboratory, Clementino Fraga Group, Fortaleza 60115-170, CE, Brazil
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Peng S, Ali Sabir I, Hu X, Chen J, Qin Y. Advancements in Reference Gene Selection for Fruit Trees: A Comprehensive Review. Int J Mol Sci 2024; 25:1142. [PMID: 38256212 PMCID: PMC10816256 DOI: 10.3390/ijms25021142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 12/30/2023] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
Real-time quantitative polymerase chain reaction (qRT-PCR) has been widely used in gene expression analyses due to its advantages of sensitivity, accuracy and high throughput. The stability of internal reference genes has progressively emerged as a major factor affecting the precision of qRT-PCR results. However, the stability of the expression of the reference genes needs to be determined further in different cells or organs, physiological and experimental conditions. Methods for evaluating these candidate internal reference genes have also evolved from simple single software evaluation to more reliable and accurate internal reference gene evaluation by combining different software tools in a comprehensive analysis. This study intends to provide a definitive reference for upcoming research that will be conducted on fruit trees. The primary focus of this review is to summarize the research progress in recent years regarding the selection and stability analysis of candidate reference genes for different fruit trees.
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Affiliation(s)
- Shujun Peng
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, College of Horticulture, South China Agricultural University, Guangzhou 510642, China; (S.P.); (X.H.); (J.C.)
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou 510642, China;
| | - Irfan Ali Sabir
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou 510642, China;
| | - Xinglong Hu
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, College of Horticulture, South China Agricultural University, Guangzhou 510642, China; (S.P.); (X.H.); (J.C.)
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou 510642, China;
| | - Jiayi Chen
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, College of Horticulture, South China Agricultural University, Guangzhou 510642, China; (S.P.); (X.H.); (J.C.)
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou 510642, China;
| | - Yonghua Qin
- Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, College of Horticulture, South China Agricultural University, Guangzhou 510642, China; (S.P.); (X.H.); (J.C.)
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs, College of Horticulture, South China Agricultural University, Guangzhou 510642, China;
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Zhang J, He X, Zhou J, Dong Z, Yu H, Tang Q, Yuan L, Peng S, Zhong X, He Y. Selection and Verification of Standardized Reference Genes of Angelica dahurica under Various Abiotic Stresses by Real-Time Quantitative PCR. Genes (Basel) 2024; 15:79. [PMID: 38254968 PMCID: PMC10815136 DOI: 10.3390/genes15010079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/04/2024] [Accepted: 01/06/2024] [Indexed: 01/24/2024] Open
Abstract
In traditional Chinese medicine, Angelica dahurica is a valuable herb with numerous therapeutic applications for a range of ailments. There have not yet been any articles on the methodical assessment and choice of the best reference genes for A. dahurica gene expression studies. Real-time quantitative PCR (RT-qPCR) is widely employed as the predominant method for investigating gene expression. In order to ensure the precise determination of target gene expression outcomes in RT-qPCR analysis, it is imperative to employ stable reference genes. In this study, a total of 11 candidate reference genes including SAND family protein (SAND), polypyrimidine tract-binding protein (PTBP), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), actin (ACT), TIP41-like protein (TIP41), cyclophilin 2 (CYP2), elongation factor 1 α (EF1α), ubiquitin-protein ligase 9 (UBC9), tubulin β-6 (TUB6), thioredoxin-like protein YLS8 (YLS8), and tubulin-α (TUBA) were selected from the transcriptome of A. dahurica. Subsequently, three statistical algorithms (geNorm, NormFinder, and BestKeeper) were employed to assess the stability of their expression patterns across seven distinct stimulus treatments. The outcomes obtained from these analyses were subsequently amalgamated into a comprehensive ranking using RefFinder. Additionally, one target gene, phenylalanine ammonia-lyase (PAL), was used to confirm the effectiveness of the selected reference genes. According to the findings of this study, the two most stable reference genes for normalizing the expression of genes in A. dahurica are TIP41 and UBC9. Overall, our research has determined the appropriate reference genes for RT-qPCR in A. dahurica and provides a crucial foundation for gene screening and identifying genes associated with the biosynthesis of active ingredients in A. dahurica.
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Affiliation(s)
- Jing Zhang
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (X.H.); (J.Z.); (Z.D.); (H.Y.); (Q.T.); (L.Y.); (S.P.)
| | - Xinyi He
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (X.H.); (J.Z.); (Z.D.); (H.Y.); (Q.T.); (L.Y.); (S.P.)
| | - Jun Zhou
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (X.H.); (J.Z.); (Z.D.); (H.Y.); (Q.T.); (L.Y.); (S.P.)
| | - Zhuang Dong
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (X.H.); (J.Z.); (Z.D.); (H.Y.); (Q.T.); (L.Y.); (S.P.)
| | - Han Yu
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (X.H.); (J.Z.); (Z.D.); (H.Y.); (Q.T.); (L.Y.); (S.P.)
| | - Qi Tang
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (X.H.); (J.Z.); (Z.D.); (H.Y.); (Q.T.); (L.Y.); (S.P.)
| | - Lei Yuan
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (X.H.); (J.Z.); (Z.D.); (H.Y.); (Q.T.); (L.Y.); (S.P.)
| | - Siqing Peng
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (X.H.); (J.Z.); (Z.D.); (H.Y.); (Q.T.); (L.Y.); (S.P.)
| | - Xiaohong Zhong
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (J.Z.); (X.H.); (J.Z.); (Z.D.); (H.Y.); (Q.T.); (L.Y.); (S.P.)
| | - Yuedong He
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
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Xiao J, Li Z, Li X, Lei H, Meng F, Li C. Screening and Identifying Reference Genes for Erythrocyte Production from Cord Blood CD34+ Cells Exposed to Hypoxia. DNA Cell Biol 2024; 43:1-11. [PMID: 38011643 DOI: 10.1089/dna.2023.0201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023] Open
Abstract
Cord blood (CB) CD34+ cells have the potential to be used to achieve artificial hematopoiesis because of their ability to expand and differentiate in multiple directions. However, the mechanism and molecular changes underlying such differentiation are still unclear. The differentiation of CB CD34+ cells is generally driven by subtle changes in gene expression. A crucial method for examining gene expression is quantitative real-time polymerase chain reaction, but the accuracy of the results is dependent on the use of reliable reference genes. Here, the transcription levels of 10 novel candidate reference genes (EIF4G2, DYNC1H1, LUC7L3, CD46, POLR1D, WSB1, GAPVD1, HGS, LGALS8, and RBM5) and 8 traditional reference genes (GAPDH, YWHAZ, ACTB, B2MG, TBP, HMBS, PPIA, HPRT1) in CB CD34+ cells under different oxygen concentrations were screened and evaluated by using the geNorm and NormFinder algorithms. Comprehensive analysis conducted by RefFinder online tool showed that TBP (a traditional reference gene) and EIF4G2 (a novel reference gene) had the most stable expression, whereas GAPDH and HMBS were the least suitable reference genes under these conditions. These results may serve as a basis for selecting reference genes with stable expression for more accurate normalization under different oxygen concentration stimulation during CB CD34+ cells differentiation.
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Affiliation(s)
- Jun Xiao
- Department of Blood Transfusion, Air Force Medical Center, Air Force Medical University, Beijing, China
| | - Zhicai Li
- The Fifth School of Clinical Medicine, Anhui Medical University, Hefei, China
| | - Xiaowei Li
- Department of Blood Transfusion, Air Force Medical Center, Air Force Medical University, Beijing, China
| | - Huifen Lei
- Department of Blood Transfusion, Air Force Medical Center, Air Force Medical University, Beijing, China
| | - Fangyuan Meng
- Department of Blood Transfusion, Air Force Medical Center, Air Force Medical University, Beijing, China
| | - Cuiying Li
- Department of Blood Transfusion, Air Force Medical Center, Air Force Medical University, Beijing, China
- The Fifth School of Clinical Medicine, Anhui Medical University, Hefei, China
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10
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Feng K, Yang ZY, Yan YJ, Sun N, Zhou ZQ, Liu JL, Zhao SP, Wu P, Li LJ. Selection of suitable reference genes for qPCR normalization in different developmental stages of Oenanthe javanica. Front Plant Sci 2023; 14:1287589. [PMID: 38205019 PMCID: PMC10777208 DOI: 10.3389/fpls.2023.1287589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 12/13/2023] [Indexed: 01/12/2024]
Abstract
Gene expression analysis is widely used to unravel molecular regulatory mechanisms and identify key genes in plants. Appropriate reference gene is an important prerequisite to ensure the accuracy and reliability of qPCR analysis results. Water dropwort is a plant of the Oenanthe genus in the Apiaceae family, which has high economic benefits. However, the underlying molecular regulatory mechanisms in the growth and development of water dropwort have not been fully understood and the appropriate reference genes in different developmental stages of water dropwort not yet reported. In this study, 10 candidate reference genes (ACTIN, PP2A, SAND, EF-1α, GAPDH, UBQ, MIP, TBP, RPS-18, eIF-4α) were identified and cloned from Oenanthe javanica. The qPCR primers of candidate reference genes were designed and verified. Four statistical algorithms, geNorm, NormFinder, BestKeeper and RefFinder were used to evaluate the expression stability of 10 candidate reference genes in different developmental stages of water dropwort. The results showed that TBP and UBQ were the most stable genes in different developmental stages of water dropwort, while GAPDH was the most unstable gene. The normalization of EXP1 genes at different developmental stages further confirmed the reliability of internal reference genes. The results of this study provide a theoretical basis for selecting appropriate internal reference genes in different developmental stages of water dropwort. This study also provides technical support and reliable basis for the expression analysis of key genes in different developmental stages of water dropwort.
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Affiliation(s)
- Kai Feng
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
| | - Zhi-Yuan Yang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
| | - Ya-Jie Yan
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
| | - Nan Sun
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
| | - Zi-Qi Zhou
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
| | - Jia-Lu Liu
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
| | - Shu-Ping Zhao
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
| | - Peng Wu
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
| | - Liang-Jun Li
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri−Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
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11
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Wang L, Liu Q, Guo P, Gao Z, Chen D, Zhang T, Ning J. Evaluation of Reference Genes for Quantitative Real-Time PCR Analysis in the Bean Bug, Riptortus pedestris (Hemiptera: Alydidae). Insects 2023; 14:960. [PMID: 38132633 PMCID: PMC10743553 DOI: 10.3390/insects14120960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023]
Abstract
Quantitative real-time PCR (qRT-PCR) is widely accepted as a precise and convenient method for quantitatively analyzing the expression of functional genes. The data normalization strongly depends upon stable reference genes. The bean bug, Riptortus pedestris (Hemiptera: Alydidae), is a significant pest of leguminous crops and broadly distributed across Southeast Asia. In this study, a total of 16 candidate reference genes (RPL32, RPS23, SDHA, UBQ, UCCR, GST, TATA-box, HSP70, GAPDH, RPL7A, SOD, RPS3, Actin, α-tubulin, AK, and EF1) were carefully chosen in R. pedestris, and their expression levels were assessed across various conditions, including different developmental stages, diverse tissues, temperature treatments, adult age, molting time, and mating status. Following this, the stability of these reference genes was evaluated using four algorithms (ΔCt, GeNorm, NormFinder, and BestKeeper). Ultimately, the comprehensive rankings were determined using the online tool RefFinder. Our results demonstrate that the reference gene for qRT-PCR analysis in R. pedestris is contingent upon the specific experimental conditions. RPL7A and EF1 are optimal reference genes for developmental stages. Furthermore, α-tubulin and EF1 exhibit the most stable expression across various adult tissues. RPL32 and RPL7A exhibit the most stable expression for adult age. For nymph age, RPL32 and SOD display the most stable expression. For temperature conditions, RPS23 and RPL7A were identified as the most suitable for monitoring gene expression. Lastly, we verified the practicability of evaluating expression levels of odorant-binding protein 37 (RpedOBP37) and cytochrome P450 6a2 (RpedCYP6) throughout developmental stages, tissues, and temperature conditions. These findings are a significant addition to the qRT-PCR analysis studies on R. pedestris, serving as a fundamental groundwork for future investigations on stable reference genes in R. pedestris as well as other organisms.
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Affiliation(s)
- Liuyang Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (L.W.); (Q.L.)
| | - Qingyu Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (L.W.); (Q.L.)
| | - Pei Guo
- Institute of Plant Protection, Hebei Academy of Agriculture and Forestry Sciences, Integrated Pest Management Center of Hebei Province, Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture, Baoding 071000, China; (P.G.); (Z.G.); (D.C.)
| | - Zhanlin Gao
- Institute of Plant Protection, Hebei Academy of Agriculture and Forestry Sciences, Integrated Pest Management Center of Hebei Province, Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture, Baoding 071000, China; (P.G.); (Z.G.); (D.C.)
| | - Dan Chen
- Institute of Plant Protection, Hebei Academy of Agriculture and Forestry Sciences, Integrated Pest Management Center of Hebei Province, Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture, Baoding 071000, China; (P.G.); (Z.G.); (D.C.)
| | - Tao Zhang
- Institute of Plant Protection, Hebei Academy of Agriculture and Forestry Sciences, Integrated Pest Management Center of Hebei Province, Key Laboratory of IPM on Crops in Northern Region of North China, Ministry of Agriculture, Baoding 071000, China; (P.G.); (Z.G.); (D.C.)
| | - Jun Ning
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (L.W.); (Q.L.)
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Troshev D, Kolacheva A, Pavlova E, Blokhin V, Ugrumov M. Application of OpenArray Technology to Assess Changes in the Expression of Functionally Significant Genes in the Substantia Nigra of Mice in a Model of Parkinson's Disease. Genes (Basel) 2023; 14:2202. [PMID: 38137024 PMCID: PMC10742853 DOI: 10.3390/genes14122202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/07/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
Studying the molecular mechanisms of the pathogenesis of Parkinson's disease (PD) is critical to improve PD treatment. We used OpenArray technology to assess gene expression in the substantia nigra (SN) cells of mice in a 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) model of PD and in controls. Among the 11 housekeeping genes tested, Rps27a was taken as the reference gene due to its most stable expression in normal and experimental conditions. From 101 genes encoding functionally significant proteins of nigrostriatal dopaminergic neurons, 57 highly expressed genes were selected to assess their expressions in the PD model and in the controls. The expressions of Th, Ddc, Maoa, Comt, Slc6a3, Slc18a2, Drd2, and Nr4a2 decreased in the experiment compared to the control, indicating decreases in the synthesis, degradation, and transport of dopamine and the impaired autoregulation of dopaminergic neurons. The expressions of Tubb3, Map2, Syn1, Syt1, Rab7, Sod1, Cib1, Gpx1, Psmd4, Ubb, Usp47, and Ctsb genes were also decreased in the MPTP-treated mice, indicating impairments of axonal and vesicular transport and abnormal functioning of the antioxidant and ubiquitin-proteasome systems in the SN. The detected decreases in the expressions of Snca, Nsf, Dnm1l, and Keap1 may serve to reduce pathological protein aggregation, increase dopamine release in the striatum, prevent mitophagy, and restore the redox status of SN cells.
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Affiliation(s)
| | | | | | | | - Michael Ugrumov
- Laboratory of Neural and Neuroendocrine Regulations, Koltzov Institute of Developmental Biology of the Russian Academy of Sciences, 119334 Moscow, Russia; (D.T.); (A.K.); (E.P.); (V.B.)
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13
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Miao J, Kang L, Lan T, Wang J, Wu S, Jia Y, Xue X, Guo H, Wang P, Li Y. Identification of optimal reference genes in golden Syrian hamster with ethanol- and palmitoleic acid-induced acute pancreatitis using quantitative real-time polymerase chain reaction. Animal Model Exp Med 2023; 6:609-618. [PMID: 37202901 PMCID: PMC10757205 DOI: 10.1002/ame2.12321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 03/28/2023] [Indexed: 05/20/2023] Open
Abstract
BACKGROUND Acute pancreatitis (AP) is a severe disorder that leads to high morbidity and mortality. Appropriate reference genes are important for gene analysis in AP. This study sought to study the expression stability of several reference genes in the golden Syrian hamster, a model of AP. METHODS AP was induced in golden Syrian hamster by intraperitoneal injection of ethanol (1.35 g/kg) and palmitoleic acid (2 mg/kg). The expression of candidate genes, including Actb, Gapdh, Eef2, Ywhaz, Rps18, Hprt1, Tubb, Rpl13a, Nono, and B2m, in hamster pancreas at different time points (1, 3, 6, 9, and 24 h) posttreatment was analyzed using quantitative polymerase chain reaction. The expression stability of these genes was calculated using BestKeeper, Comprehensive Delta CT, NormFinder, and geNorm algorithms and RefFinder software. RESULTS Our results show that the expression of these reference genes fluctuated during AP, of which Ywhaz and Gapdh were the most stable genes, whereas Tubb, Eef2, and Actb were the least stable genes. Furthermore, these genes were used to normalize the expression of TNF-α messenger ribonucleic acid in inflamed pancreas. CONCLUSIONS In conclusion, Ywhaz and Gapdh were suitable reference genes for gene expression analysis in AP induced in Syrian hamster.
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Affiliation(s)
- Jinxin Miao
- Academy of Chinese Medicine ScienceHenan University of Chinese MedicineZhengzhouChina
| | - Le Kang
- Academy of Chinese Medicine ScienceHenan University of Chinese MedicineZhengzhouChina
| | - Tianfeng Lan
- Sino‐British Research Centre for Molecular Oncology, National Center for International Research in Cell and Gene Therapy, School of Basic Medical Sciences, Academy of Medical SciencesZhengzhou UniversityZhengzhouChina
| | - Jianyao Wang
- Sino‐British Research Centre for Molecular Oncology, National Center for International Research in Cell and Gene Therapy, School of Basic Medical Sciences, Academy of Medical SciencesZhengzhou UniversityZhengzhouChina
| | - Siqing Wu
- Academy of Chinese Medicine ScienceHenan University of Chinese MedicineZhengzhouChina
| | - Yifan Jia
- Academy of Chinese Medicine ScienceHenan University of Chinese MedicineZhengzhouChina
| | - Xia Xue
- Henan Key Laboratory of Helicobacter pylori and Microbiota and Gastrointestinal Cancer, Marshall Medical Research CenterThe Fifth Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Haoran Guo
- Sino‐British Research Centre for Molecular Oncology, National Center for International Research in Cell and Gene Therapy, School of Basic Medical Sciences, Academy of Medical SciencesZhengzhou UniversityZhengzhouChina
| | - Pengju Wang
- Sino‐British Research Centre for Molecular Oncology, National Center for International Research in Cell and Gene Therapy, School of Basic Medical Sciences, Academy of Medical SciencesZhengzhou UniversityZhengzhouChina
| | - Yan Li
- Academy of Chinese Medicine ScienceHenan University of Chinese MedicineZhengzhouChina
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14
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Tscherner AK, McClatchie T, Macaulay AD, Baltz JM. Relationship of quantitative reverse transcription polymerase chain reaction (RT-PCR) to RNA Sequencing (RNAseq) transcriptome identifies mouse preimplantation embryo reference genes†. Biol Reprod 2023; 109:601-617. [PMID: 37669129 PMCID: PMC10651071 DOI: 10.1093/biolre/ioad107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/04/2023] [Accepted: 08/25/2023] [Indexed: 09/07/2023] Open
Abstract
Numerous reference genes for use with quantitative reverse transcription polymerase chain reaction (RT-qPCR) have been used for oocytes, eggs, and preimplantation embryos. However, none are actually suitable because of their large variations in expression between developmental stages. To address this, we produced a standardized and merged RNA sequencing (RNAseq) data set by combining multiple publicly available RNAseq data sets that spanned mouse GV oocytes, MII eggs, and 1-cell, 2-cell, 4-cell, 8-cell, morula, and blastocyst stage embryos to identify transcripts with essentially constant expression across all stages. Their expression was then measured using RT-qPCR, with which they did not exhibit constant expression but instead revealed a fixed quantitative relationship between measurements by the two techniques. From this, the relative amounts of total messenger RNA at each stage from the GV oocyte through blastocyst stages were calculated. The quantitative relationship between measurements by RNAseq and RT-qPCR was then used to find genes predicted to have constant expression across stages in RT-qPCR. Candidates were assessed by RT-qPCR to confirm constant expression, identifying Hmgb3 and Rb1cc1 or the geometric mean of those plus either Taf1d or Cd320 as suitable reference genes. This work not only identified transcripts with constant expression from mouse GV oocytes to blastocysts, but also determined a general quantitative relationship between expression measured by RNAseq and RT-qPCR across stages that revealed the relative levels of total mRNA at each stage. The standardized and merged RNA data set should also prove useful in determining transcript expression in mouse oocytes, eggs, and embryos.
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Affiliation(s)
- Allison K Tscherner
- Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Department of Obstetrics and Gynecology, University of Ottawa Faculty of Medicine, Ottawa, ON, Canada
| | - Taylor McClatchie
- Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Department of Obstetrics and Gynecology, University of Ottawa Faculty of Medicine, Ottawa, ON, Canada
| | | | - Jay M Baltz
- Ottawa Hospital Research Institute, Ottawa, ON, Canada
- Department of Obstetrics and Gynecology, University of Ottawa Faculty of Medicine, Ottawa, ON, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa Faculty of Medicine, Ottawa, ON, Canada
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15
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Liu Y, Zhong W, Feng S, Tang Z, Zhang Y, Ai L, Xiong Z. Identification of new reference genes for colony counting by reverse-transcription quantitative PCR in Bifidobacterium animalis. J Dairy Sci 2023; 106:7477-7485. [PMID: 37641239 DOI: 10.3168/jds.2022-23000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 05/12/2023] [Indexed: 08/31/2023]
Abstract
Bifidobacterium animalis, one of the predominant bacteria in the intestines of humans and other mammals, is widely added to dairy products. We employed RNA sequencing to analyze gene expression variance on a genome-wide scale and found stable reference genes (RG) in B. animalis. A total of 1,665 genes were identified by analyzing the data from the transcriptome under 4 different conditions, and 13 probable candidate RG with variation coefficient values <0.1 were validated using reverse-transcription quantitative PCR (RT-qPCR). The amplification efficiency of candidate RG were ranging from 94.16% to 126.25%. We integrated the analysis results of BestKeeper, geNorm, NormFinder, and RefFinder algorithms and revealed that rplD and atpA comprehensive ranked 1.68 and 2.82, respectively, which were more stable than traditional RG. Compared with plate count (1.58 × 106 cfu/mL), the concentrations of B. animalis AR668 by RT-qPCR using rplD, atpA, and 16S rRNA as RG were 2.27 × 106, 2.24 × 106, and 6.66 × 106 cfu/mL, respectively, after 10 h of fermentation in fermented skim milk. It suggested that rplD and atpA as RG can be accurate for colony counting of B. animalis. Our study provides the foundation for more accurate analysis of colony counting by RT-qPCR of B. animalis in dairy foods.
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Affiliation(s)
- Yaping Liu
- Shanghai Engineering Research Center of Food Microbiology, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Wanting Zhong
- Shanghai Engineering Research Center of Food Microbiology, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Shuo Feng
- Shanghai Engineering Research Center of Food Microbiology, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Ziteng Tang
- Shanghai Engineering Research Center of Food Microbiology, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Yingzhi Zhang
- Shanghai Engineering Research Center of Food Microbiology, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Lianzhong Ai
- Shanghai Engineering Research Center of Food Microbiology, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Zhiqiang Xiong
- Shanghai Engineering Research Center of Food Microbiology, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China.
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16
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Pérez-Gómez JM, Porcel-Pastrana F, De La Luz-Borrero M, Montero-Hidalgo AJ, Gómez-Gómez E, Herrera-Martínez AD, Guzmán-Ruiz R, Malagón MM, Gahete MD, Luque RM. LRP10, PGK1 and RPLP0: Best Reference Genes in Periprostatic Adipose Tissue under Obesity and Prostate Cancer Conditions. Int J Mol Sci 2023; 24:15140. [PMID: 37894825 PMCID: PMC10606769 DOI: 10.3390/ijms242015140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/02/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Obesity (OB) is a metabolic disorder characterized by adipose tissue dysfunction that has emerged as a health problem of epidemic proportions in recent decades. OB is associated with multiple comorbidities, including some types of cancers. Specifically, prostate cancer (PCa) has been postulated as one of the tumors that could have a causal relationship with OB. Particularly, a specialized adipose tissue (AT) depot known as periprostatic adipose tissue (PPAT) has gained increasing attention over the last few years as it could be a key player in the pathophysiological interaction between PCa and OB. However, to date, no studies have defined the most appropriate internal reference genes (IRGs) to be used in gene expression studies in this AT depot. In this work, two independent cohorts of PPAT samples (n = 20/n = 48) were used to assess the validity of a battery of 15 literature-selected IRGs using two widely used techniques (reverse transcription quantitative PCR [RT-qPCR] and microfluidic-based qPCR array). For this purpose, ΔCt method, GeNorm (v3.5), BestKeeper (v1.0), NormFinder (v.20.0), and RefFinder software were employed to assess the overall trends of our analyses. LRP10, PGK1, and RPLP0 were identified as the best IRGs to be used for gene expression studies in human PPATs, specifically when considering PCa and OB conditions.
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Grants
- PID2022-1381850B-I00 Spanish Ministry of Science, Innovation, and Universities
- PID2019-105564RB-I00 Spanish Ministry of Science, Innovation, and Universities
- FPU18-06009 Spanish Ministry of Science, Innovation, and Universities
- PRE2020-094225 Spanish Ministry of Science, Innovation, and Universities
- FPU18-02485 Spanish Ministry of Science, Innovation, and Universities
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Affiliation(s)
- Jesús M. Pérez-Gómez
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004 Cordoba, Spain; (J.M.P.-G.); (F.P.-P.); (M.D.L.L.-B.); (A.J.M.-H.); (E.G.-G.); (A.D.H.-M.); (R.G.-R.); (M.M.M.); (M.D.G.)
- Department of Cell Biology, Physiology, and Immunology, University of Cordoba, 14004 Cordoba, Spain
- Reina Sofia University Hospital (HURS), 14004 Cordoba, Spain
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), 14004 Cordoba, Spain
| | - Francisco Porcel-Pastrana
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004 Cordoba, Spain; (J.M.P.-G.); (F.P.-P.); (M.D.L.L.-B.); (A.J.M.-H.); (E.G.-G.); (A.D.H.-M.); (R.G.-R.); (M.M.M.); (M.D.G.)
- Department of Cell Biology, Physiology, and Immunology, University of Cordoba, 14004 Cordoba, Spain
- Reina Sofia University Hospital (HURS), 14004 Cordoba, Spain
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), 14004 Cordoba, Spain
| | - Marina De La Luz-Borrero
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004 Cordoba, Spain; (J.M.P.-G.); (F.P.-P.); (M.D.L.L.-B.); (A.J.M.-H.); (E.G.-G.); (A.D.H.-M.); (R.G.-R.); (M.M.M.); (M.D.G.)
- Department of Cell Biology, Physiology, and Immunology, University of Cordoba, 14004 Cordoba, Spain
- Reina Sofia University Hospital (HURS), 14004 Cordoba, Spain
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), 14004 Cordoba, Spain
| | - Antonio J. Montero-Hidalgo
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004 Cordoba, Spain; (J.M.P.-G.); (F.P.-P.); (M.D.L.L.-B.); (A.J.M.-H.); (E.G.-G.); (A.D.H.-M.); (R.G.-R.); (M.M.M.); (M.D.G.)
- Department of Cell Biology, Physiology, and Immunology, University of Cordoba, 14004 Cordoba, Spain
- Reina Sofia University Hospital (HURS), 14004 Cordoba, Spain
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), 14004 Cordoba, Spain
| | - Enrique Gómez-Gómez
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004 Cordoba, Spain; (J.M.P.-G.); (F.P.-P.); (M.D.L.L.-B.); (A.J.M.-H.); (E.G.-G.); (A.D.H.-M.); (R.G.-R.); (M.M.M.); (M.D.G.)
- Reina Sofia University Hospital (HURS), 14004 Cordoba, Spain
- Urology Service, Reina Sofia University Hospital, 14004 Cordoba, Spain
| | - Aura D. Herrera-Martínez
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004 Cordoba, Spain; (J.M.P.-G.); (F.P.-P.); (M.D.L.L.-B.); (A.J.M.-H.); (E.G.-G.); (A.D.H.-M.); (R.G.-R.); (M.M.M.); (M.D.G.)
- Reina Sofia University Hospital (HURS), 14004 Cordoba, Spain
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), 14004 Cordoba, Spain
- Endocrinology and Nutrition Service, Reina Sofia University Hospital, 14004 Cordoba, Spain
| | - Rocío Guzmán-Ruiz
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004 Cordoba, Spain; (J.M.P.-G.); (F.P.-P.); (M.D.L.L.-B.); (A.J.M.-H.); (E.G.-G.); (A.D.H.-M.); (R.G.-R.); (M.M.M.); (M.D.G.)
- Department of Cell Biology, Physiology, and Immunology, University of Cordoba, 14004 Cordoba, Spain
- Reina Sofia University Hospital (HURS), 14004 Cordoba, Spain
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), 14004 Cordoba, Spain
| | - María M. Malagón
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004 Cordoba, Spain; (J.M.P.-G.); (F.P.-P.); (M.D.L.L.-B.); (A.J.M.-H.); (E.G.-G.); (A.D.H.-M.); (R.G.-R.); (M.M.M.); (M.D.G.)
- Department of Cell Biology, Physiology, and Immunology, University of Cordoba, 14004 Cordoba, Spain
- Reina Sofia University Hospital (HURS), 14004 Cordoba, Spain
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), 14004 Cordoba, Spain
| | - Manuel D. Gahete
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004 Cordoba, Spain; (J.M.P.-G.); (F.P.-P.); (M.D.L.L.-B.); (A.J.M.-H.); (E.G.-G.); (A.D.H.-M.); (R.G.-R.); (M.M.M.); (M.D.G.)
- Department of Cell Biology, Physiology, and Immunology, University of Cordoba, 14004 Cordoba, Spain
- Reina Sofia University Hospital (HURS), 14004 Cordoba, Spain
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), 14004 Cordoba, Spain
| | - Raúl M. Luque
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), 14004 Cordoba, Spain; (J.M.P.-G.); (F.P.-P.); (M.D.L.L.-B.); (A.J.M.-H.); (E.G.-G.); (A.D.H.-M.); (R.G.-R.); (M.M.M.); (M.D.G.)
- Department of Cell Biology, Physiology, and Immunology, University of Cordoba, 14004 Cordoba, Spain
- Reina Sofia University Hospital (HURS), 14004 Cordoba, Spain
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), 14004 Cordoba, Spain
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17
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Wong L, Tsang YS, Kenny R, Lyburn M, McMahon LP. MiR-423-5p as Optimal Endogenous Control for Quantification of Circulating MicroRNAs in Patients With CKD. Kidney Int Rep 2023; 8:2150-2152. [PMID: 37849998 PMCID: PMC10577311 DOI: 10.1016/j.ekir.2023.07.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/20/2023] [Accepted: 07/24/2023] [Indexed: 10/19/2023] Open
Affiliation(s)
- Limy Wong
- Department of Renal Medicine, Monash University Eastern Health Clinical School, Victoria, Australia
- Department of Renal Medicine, Eastern Health, Victoria, Australia
| | - Yung Shing Tsang
- Department of Renal Medicine, Monash University Eastern Health Clinical School, Victoria, Australia
| | - Rachel Kenny
- Department of Renal Medicine, Monash University Eastern Health Clinical School, Victoria, Australia
| | - Matthew Lyburn
- Department of Renal Medicine, Eastern Health, Victoria, Australia
| | - Lawrence P. McMahon
- Department of Renal Medicine, Monash University Eastern Health Clinical School, Victoria, Australia
- Department of Renal Medicine, Eastern Health, Victoria, Australia
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18
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Wang X, Shu X, Su X, Xiong Y, Xiong Y, Chen M, Tong Q, Ma X, Zhang J, Zhao J. Selection of Suitable Reference Genes for RT-qPCR Gene Expression Analysis in Centipedegrass under Different Abiotic Stress. Genes (Basel) 2023; 14:1874. [PMID: 37895223 PMCID: PMC10606319 DOI: 10.3390/genes14101874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023] Open
Abstract
As a C4 warm-season turfgrass, centipedegrass (Eremochloa ophiuroides (Munro) Hack.) is known for its exceptional resilience to intensive maintenance practices. In this research, the most stably expressed reference genes in the leaves of centipedegrass under different stress treatments, including salt, cold, drought, aluminum (Al), and herbicide, were screened by the quantitative real-time PCR (RT-qPCR) technique. The stability of 13 candidate reference genes was evaluated by software GeNorm V3.4, NormFinder V20, BestKeeper V1.0, and ReFinder V1.0. The results of this experiment demonstrated that the expression of the UBC (ubiquitin-conjugating enzyme) remained the most stable under cold and Al stress conditions. On the other hand, the MD (malate dehydrogenase) gene exhibited the best performance in leaf tissues subjected to salt and drought stresses. Under herbicide stress, the expression level of the RIP (60S ribosomal protein L2) gene ranked the highest. The expression levels of abiotic stress-associated genes such as PIP1, PAL, COR413, ALMT9, and BAR were assessed to validate the reliability of the selected reference genes. This study provides valuable information and reference points for gene expression under abiotic stress conditions in centipedegrass.
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Affiliation(s)
- Xiaoyun Wang
- College of Grassland Science and Technology, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Xin Shu
- College of Grassland Science and Technology, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Xiaoli Su
- College of Grassland Science and Technology, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Yanli Xiong
- College of Grassland Science and Technology, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Yi Xiong
- College of Grassland Science and Technology, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Minli Chen
- Sichuan Academy of Grassland Sciences, Pidu, Chengdu 611731, China
| | - Qi Tong
- Sichuan Academy of Grassland Sciences, Pidu, Chengdu 611731, China
| | - Xiao Ma
- College of Grassland Science and Technology, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
| | - Jianbo Zhang
- Sichuan Academy of Grassland Sciences, Pidu, Chengdu 611731, China
| | - Junming Zhao
- College of Grassland Science and Technology, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China
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19
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Buttstedt A, Pirk CWW, Yusuf AA. Differences in the suitability of published honey bee (Apis mellifera) reference genes between the African subspecies Apis mellifera scutellata and European derived Apis mellifera. Mol Ecol 2023. [PMID: 37740659 DOI: 10.1111/mec.17139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 07/28/2023] [Accepted: 09/04/2023] [Indexed: 09/24/2023]
Abstract
Quantitative real-time polymerase chain reaction (qPCR) is a method widely used to determine changes and differences in gene expression. As target gene expression is most often quantified relative to the expression of reference genes, the validation of suitable reference genes is of critical importance. In practice, however, such validation might not be thoroughly conducted if the same species and the same tissue or body parts are used for qPCR experiments. Here we show, that qPCR reference genes published for workers of European honey bee (Apis mellifera) subspecies fail to be stably expressed in workers of the African subspecies Apis mellifera scutellata. This is the case even when the sampled workers are in the same life stage, the same organ was dissected and the same reagents were used. Thus, reference genes need to be thoroughly re-tested before they can be used as suitable references even when the only thing that changes is the subspecies used.
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Affiliation(s)
- Anja Buttstedt
- Social Insects Research Group, Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
| | - Christian W W Pirk
- Social Insects Research Group, Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
| | - Abdullahi A Yusuf
- Social Insects Research Group, Department of Zoology and Entomology, University of Pretoria, Pretoria, South Africa
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20
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Jia X, Xiong Y, Xiong Y, Li D, Yu Q, Lei X, You M, Bai S, Zhang J, Ma X. Identification and Validation of Reference Genes for RT-qPCR Analysis in Reed Canary Grass during Abiotic Stress. Genes (Basel) 2023; 14:1790. [PMID: 37761930 PMCID: PMC10530813 DOI: 10.3390/genes14091790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/07/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Reed canary grass (Phalaris arundinacea L.) is known for its tolerance to drought, heavy metals, and waterlogging, making it a popular choice for forage production and wetland restoration in the Qinghai-Tibet Plateau (QTP). To accurately assess gene expression in reed canary grass under different abiotic stresses, suitable reference genes need to be identified and validated. Thirteen candidate reference gene sequences were selected and screened using RT-qPCR to detect their expression levels in reed canary grass leaves under drought, salt, cadmium, and waterlogging stresses. Four algorithms were used to assess the stability of the expression levels of the candidate reference genes. The most stably expressed genes were UBC and H3 under drought Cd, ETF and CYT under salt stress, and ETF and TUB under waterlogging stress. GAPDH was found to be less stable under abiotic stresses. PIP-1, PAL, NAC 90, and WRKY 72A were selected as response genes for quantitative expression assessment under drought, salt, Cd, and waterlogging stresses to confirm the accuracy of the selected stable reference genes. These results provide a theoretical reference for assessing gene expression in reed canary grass under abiotic stresses.
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Affiliation(s)
- Xuejie Jia
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.J.)
- Sichuan Academy of Grassland Science, Chengdu 610097, China; (D.L.)
| | - Yi Xiong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.J.)
| | - Yanli Xiong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.J.)
| | - Daxu Li
- Sichuan Academy of Grassland Science, Chengdu 610097, China; (D.L.)
| | - Qinqin Yu
- Sichuan Academy of Grassland Science, Chengdu 610097, China; (D.L.)
| | - Xiong Lei
- Sichuan Academy of Grassland Science, Chengdu 610097, China; (D.L.)
| | - Minghong You
- Sichuan Academy of Grassland Science, Chengdu 610097, China; (D.L.)
| | - Shiqie Bai
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621002, China
| | - Jianbo Zhang
- Sichuan Academy of Grassland Science, Chengdu 610097, China; (D.L.)
| | - Xiao Ma
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.J.)
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Zhou Y, Zhang Y, Mu D, Lu Y, Chen W, Zhang Y, Zhang R, Qin Y, Yuan J, Pan L, Tang Q. Selection of Reference Genes in Evodia rutaecarpa var. officinalis and Expression Patterns of Genes Involved in Its Limonin Biosynthesis. Plants (Basel) 2023; 12:3197. [PMID: 37765365 PMCID: PMC10534417 DOI: 10.3390/plants12183197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/02/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023]
Abstract
E. rutaecarpa var. officinalis is a traditional Chinese medicinal plant known for its therapeutic effects, which encompass the promotion of digestion, the dispelling of cold, the alleviation of pain, and the exhibition of anti-inflammatory and antibacterial properties. The principal active component of this plant, limonin, is a potent triterpene compound with notable pharmacological activities. Despite its significance, the complete biosynthesis pathway of limonin in E. rutaecarpa var. officinalis remains incompletely understood, and the underlying molecular mechanisms remain unexplored. The main purpose of this study was to screen the reference genes suitable for expression analysis in E. rutaecarpa var. officinalis, calculate the expression patterns of the genes in the limonin biosynthesis pathway, and identify the relevant enzyme genes related to limonin biosynthesis. The reference genes play a pivotal role in establishing reliable reference standards for normalizing the gene expression data, thereby ensuring precision and credibility in the biological research outcomes. In order to identify the optimal reference genes and gene expression patterns across the diverse tissues (e.g., roots, stems, leaves, and flower buds) and developmental stages (i.e., 17 July, 24 August, 1 September, and 24 October) of E. rutaecarpa var. officinalis, LC-MS was used to analyze the limonin contents in distinct tissue samples and developmental stages, and qRT-PCR technology was employed to investigate the expression patterns of the ten reference genes and eighteen genes involved in limonin biosynthesis. Utilizing a comprehensive analysis that integrated three software tools (GeNorm ver. 3.5, NormFinder ver. 0.953 and BestKeeper ver. 1.0) and Delta Ct method alongside the RefFinder website, the best reference genes were selected. Through the research, we determined that Act1 and UBQ served as the preferred reference genes for normalizing gene expression during various fruit developmental stages, while Act1 and His3 were optimal for different tissues. Using Act1 and UBQ as the reference genes, and based on the different fruit developmental stages, qRT-PCR analysis was performed on the pathway genes selected from the "full-length transcriptome + expression profile + metabolome" data in the limonin biosynthesis pathway of E. rutaecarpa var. officinalis. The findings indicated that there were consistent expression patterns of HMGCR, SQE, and CYP450 with fluctuations in the limonin contents, suggesting their potential involvement in the limonin biosynthesis of E. rutaecarpa var. officinalis. This study lays the foundation for further research on the metabolic pathway of limonin in E. rutaecarpa var. officinalis and provides reliable reference genes for other researchers to use for conducting expression analyses.
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Affiliation(s)
- Yu Zhou
- National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (Y.Z.); (Y.Z.); (D.M.); (Y.L.); (W.C.); (Y.Z.); (R.Z.)
| | - Yuxiang Zhang
- National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (Y.Z.); (Y.Z.); (D.M.); (Y.L.); (W.C.); (Y.Z.); (R.Z.)
| | - Detian Mu
- National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (Y.Z.); (Y.Z.); (D.M.); (Y.L.); (W.C.); (Y.Z.); (R.Z.)
| | - Ying Lu
- National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (Y.Z.); (Y.Z.); (D.M.); (Y.L.); (W.C.); (Y.Z.); (R.Z.)
| | - Wenqiang Chen
- National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (Y.Z.); (Y.Z.); (D.M.); (Y.L.); (W.C.); (Y.Z.); (R.Z.)
| | - Yao Zhang
- National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (Y.Z.); (Y.Z.); (D.M.); (Y.L.); (W.C.); (Y.Z.); (R.Z.)
| | - Ruiying Zhang
- National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (Y.Z.); (Y.Z.); (D.M.); (Y.L.); (W.C.); (Y.Z.); (R.Z.)
| | - Ya Qin
- Guangxi Botanical Garden of Medicinal Plants, Nanning 530023, China;
| | - Jianhua Yuan
- Changsha Hemao Agricultural Development Co., Ltd., Ningxiang County, Changsha 410609, China;
| | - Limei Pan
- Guangxi Botanical Garden of Medicinal Plants, Nanning 530023, China;
| | - Qi Tang
- National Research Center of Engineering Technology for Utilization of Botanical Functional Ingredients, College of Horticulture, Hunan Agricultural University, Changsha 410128, China; (Y.Z.); (Y.Z.); (D.M.); (Y.L.); (W.C.); (Y.Z.); (R.Z.)
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22
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Zhou Y, Liu H, Wu T, Zheng Y, Wang R, Xue D, Yan Q, Yuan X, Chen X. Screening of Reference Genes under Biotic Stress and Hormone Treatment of Mung Bean ( Vigna radiata) by Quantitative Real-Time PCR. Genes (Basel) 2023; 14:1739. [PMID: 37761879 PMCID: PMC10530681 DOI: 10.3390/genes14091739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 08/26/2023] [Accepted: 08/29/2023] [Indexed: 09/29/2023] Open
Abstract
Mung bean (Vigna radiata) production has been greatly threatened by numerous diseases. Infection with these pathogens causes extensive changes in gene expression and the activation of hormone signal transduction. Quantitative real-time PCR (qRT-PCR) is the most common technique used for gene expression validation. Screening proper reference genes for mung bean under pathogen infection and hormone treatment is a prerequisite for ensuring the accuracy of qRT-PCR data in mung bean disease-resistance research. In this study, six candidate reference genes (Cons4, ACT, TUA, TUB, GAPDH, and EF1α) were selected to evaluate the expression stability under four soil-borne disease pathogens (Pythium myriotylum, Pythium aphanidermatum, Fusarium oxysporum, and Rhizoctonia solani) and five hormone treatments (SA, MeJA, ETH, ABA, and GA3). In the samples from different treatments, the Ct value distribution of the six candidate reference genes was different. Under the condition of hormone treatment, the Ct value ranged from a minimum of 17.87 for EF1α to a maximum of 29.63 for GAPDH. Under the condition of pathogen infection, the Ct value ranged from a minimum of 19.43 for EF1α to a maximum of 31.82 for GAPDH. After primer specificity analysis, it was found that GAPDH was not specific, so the five reference genes Cons4, ACT, TUA, TUB, and EF1α were used in subsequent experiments. The software products GeNorm, NormFinder, BestKeeper and RefFinder were used for qRT-PCR data analysis. In general, the best candidates reference genes were: TUA for SA, ABA, GA3, and Pythium myriotylum treatment; TUB for ETH treatment; ACT for MeJA and Fusarium oxysporum treatment; and EF1α for Pythium aphanidermatum and Rhizoctonia solani treatment. The most stably expressed genes in all samples were TUA, while Cons4 was the least stable reference gene. Finally, the reliability of the reference gene was further validated by analysis of the expression profiles of four mung bean genes (Vradi0146s00260, Vradi0158s00480, Vradi07g23860, and Vradi11g03350) selected from transcriptome data. Our results provide more accurate information for the normalization of qRT-PCR data in mung bean response to pathogen interaction.
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Affiliation(s)
- Yanyan Zhou
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China (H.L.)
| | - Huan Liu
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China (H.L.)
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Ting Wu
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China (H.L.)
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Yu Zheng
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China
| | - Ruimin Wang
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Dong Xue
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Qiang Yan
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Xingxing Yuan
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China (H.L.)
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Xin Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China (H.L.)
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences/Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China
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23
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Liu Y, Zhang C, Harijati N, Diao Y, Liu E, Hu Z. Selection and Evaluation of Reference Genes for RT-qPCR Analysis in Amorphophallus Konjac Based on Transcriptome Data. Genes (Basel) 2023; 14:1513. [PMID: 37628565 PMCID: PMC10454643 DOI: 10.3390/genes14081513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 07/18/2023] [Accepted: 07/21/2023] [Indexed: 08/27/2023] Open
Abstract
Combined with the Konjac transcriptome database of our laboratory and internal reference genes commonly used in plants, the eight candidate internal reference genes were screened and detected. They are the 25S ribosomal RNA gene (25S rRNA), 18S ribosomal RNA gene (18S rRNA), actin gene (ACT), glyceraldehyde-3-phosphate dehydrogenase gene (GAPDH), ubiquitin gene (UBQ), β-tubulin gene (β-TUB), eukaryotic elongation factor 1-αgene(eEF-1α), and eukaryotic translation initiation factor 4α-1 gene (eIF-4α). The results of GeNorm, Normfinder, and BestKeeper were analyzed comprehensively. The data showed that the expression levels of 25S rRNA, 18S rRNA, and ACT at the reproductive periods, eEF-1α and eIF-4α at the nutritional periods, and eEF-1α, UBQ, and ACT at different leaf developmental periods were stable. These identified and stable internal reference genes will provide the basis for the subsequent molecular biology-related studies of Konjac.
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Affiliation(s)
- Yanli Liu
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, China; (Y.L.); (Y.D.)
| | - Chengcheng Zhang
- Lotus Engineering Research Center of Hubei Province, College of Life Science, Wuhan University, Wuhan 430072, China;
| | - Nunung Harijati
- Department of Biology, Faculty of Mathematics and Natural Sciences, Brawijaya University, Jl. Veteran, Malang 65145, Indonesia;
| | - Ying Diao
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, China; (Y.L.); (Y.D.)
| | - Erxi Liu
- Institute of Konjac, Enshi Academy of Agricultural Sciences, Enshi 445000, China;
| | - Zhongli Hu
- College of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, China; (Y.L.); (Y.D.)
- Lotus Engineering Research Center of Hubei Province, College of Life Science, Wuhan University, Wuhan 430072, China;
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Li G, Sun X, Zhu X, Wu B, Hong H, Xin Z, Xin X, Peng J, Jiang S. Selection and Validation of Reference Genes in Virus-Infected Sweet Potato Plants. Genes (Basel) 2023; 14:1477. [PMID: 37510381 PMCID: PMC10379385 DOI: 10.3390/genes14071477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/13/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Quantitative real-time PCR (qRT-PCR) in sweet potatoes requires accurate data normalization; however, there are insufficient studies on appropriate reference genes for gene expression analysis. We examined variations in the expression of eight candidate reference genes in the leaf and root tissues of sweet potatoes (eight nonvirus-infected or eight virus-infected samples). Parallel analyses with geNorm, NormFinder, and Best-Keeper show that different viral infections and origin tissues affect the expression levels of these genes. Based on the results of the evaluation of the three software, the adenosine diphosphate-ribosylation factor is suitable for nonvirus or virus-infected sweet potato leaves. Cyclophilin and ubiquitin extension proteins are suitable for nonvirus-infected sweet potato leaves. Phospholipase D1 alpha is suitable for virus-infected sweet potato leaves. Actin is suitable for roots of nonvirus-infected sweet potatoes. Glyceraldehyde-3-phosphate dehydrogenase is suitable for virus-infected sweet potato roots. The research provides appropriate reference genes for further analysis in leaf and root samples of viruses in sweet potatoes.
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Affiliation(s)
- Guangyan Li
- Shandong Key Laboratory of Plant Virology, Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Xiaohui Sun
- Shandong Key Laboratory of Plant Virology, Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Xiaoping Zhu
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian 271018, China
| | - Bin Wu
- Shandong Key Laboratory of Plant Virology, Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Hao Hong
- Shandong Key Laboratory of Plant Virology, Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Zhimei Xin
- Shandong Key Laboratory of Plant Virology, Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Xiangqi Xin
- Shandong Key Laboratory of Plant Virology, Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Jiejun Peng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Shanshan Jiang
- Shandong Key Laboratory of Plant Virology, Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan 250100, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
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25
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Barreiro K, Dwivedi OP, Rannikko A, Holthöfer H, Tuomi T, Groop PH, Puhka M. Capturing the Kidney Transcriptome by Urinary Extracellular Vesicles-From Pre-Analytical Obstacles to Biomarker Research. Genes (Basel) 2023; 14:1415. [PMID: 37510317 PMCID: PMC10379145 DOI: 10.3390/genes14071415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/30/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
Urinary extracellular vesicles (uEV) hold non-invasive RNA biomarkers for genitourinary tract diseases. However, missing knowledge about reference genes and effects of preanalytical choices hinder biomarker studies. We aimed to assess how preanalytical variables (urine storage temperature, isolation workflow) affect diabetic kidney disease (DKD)-linked miRNAs or kidney-linked miRNAs and mRNAs (kidney-RNAs) in uEV isolates and to discover stable reference mRNAs across diverse uEV datasets. We studied nine raw and normalized sequencing datasets including healthy controls and individuals with prostate cancer or type 1 diabetes with or without albuminuria. We focused on kidney-RNAs reviewing literature for DKD-linked miRNAs from kidney tissue, cell culture and uEV/urine experiments. RNAs were analyzed by expression heatmaps, hierarchical clustering and selecting stable mRNAs with normalized counts (>200) and minimal coefficient of variation. Kidney-RNAs were decreased after urine storage at -20 °C vs. -80 °C. Isolation workflows captured kidney-RNAs with different efficiencies. Ultracentrifugation captured DKD -linked miRNAs that separated healthy and diabetic macroalbuminuria groups. Eleven mRNAs were stably expressed across the datasets. Hence, pre-analytical choices had variable effects on kidney-RNAs-analyzing kidney-RNAs complemented global correlation, which could fade differences in some relevant RNAs. Replicating prior DKD-marker results and discovery of candidate reference mRNAs encourages further uEV biomarker studies.
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Affiliation(s)
- Karina Barreiro
- Institute for Molecular Medicine Finland FIMM, HiLIFE, University of Helsinki, 00290 Helsinki, Finland
- Institute for Molecular Medicine Finland FIMM, EV and HiPREP Core, University of Helsinki, 00290 Helsinki, Finland
| | - Om Prakash Dwivedi
- Institute for Molecular Medicine Finland FIMM, HiLIFE, University of Helsinki, 00290 Helsinki, Finland
| | - Antti Rannikko
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
- Department of Urology, University of Helsinki, Helsinki University Hospital, 00290 Helsinki, Finland
| | - Harry Holthöfer
- Institute for Molecular Medicine Finland FIMM, HiLIFE, University of Helsinki, 00290 Helsinki, Finland
- III Department of Medicine, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Tiinamaija Tuomi
- Institute for Molecular Medicine Finland FIMM, HiLIFE, University of Helsinki, 00290 Helsinki, Finland
- Lund University Diabetes Centre, Department of Clinical Sciences, Lund University, 214 28 Malmö, Sweden
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, 00290 Helsinki, Finland
- Endocrinology, Abdominal Centre, Helsinki University Hospital, 00029 Helsinki, Finland
| | - Per-Henrik Groop
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, 00290 Helsinki, Finland
- Department of Nephrology, University of Helsinki, Helsinki University Hospital, 00290 Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC 3800, Australia
| | - Maija Puhka
- Institute for Molecular Medicine Finland FIMM, HiLIFE, University of Helsinki, 00290 Helsinki, Finland
- Institute for Molecular Medicine Finland FIMM, EV and HiPREP Core, University of Helsinki, 00290 Helsinki, Finland
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Sandal S, Singh S, Bansal G, Kaur R, Mogilicherla K, Pandher S, Roy A, Kaur G, Rathore P, Kalia A. Nanoparticle-Shielded dsRNA Delivery for Enhancing RNAi Efficiency in Cotton Spotted Bollworm Earias vittella (Lepidoptera: Nolidae). Int J Mol Sci 2023; 24:ijms24119161. [PMID: 37298113 DOI: 10.3390/ijms24119161] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 05/15/2023] [Accepted: 05/18/2023] [Indexed: 06/12/2023] Open
Abstract
The spotted bollworm Earias vittella (Lepidoptera: Nolidae) is a polyphagous pest with enormous economic significance, primarily affecting cotton and okra. However, the lack of gene sequence information on this pest has a significant constraint on molecular investigations and the formulation of superior pest management strategies. An RNA-seq-based transcriptome study was conducted to alleviate such limitations, and de novo assembly was performed to obtain transcript sequences of this pest. Reference gene identification across E. vittella developmental stages and RNAi treatments were conducted using its sequence information, which resulted in identifying transcription elongation factor (TEF), V-type proton ATPase (V-ATPase), and Glyceraldehyde -3-phosphate dehydrogenase (GAPDH) as the most suitable reference genes for normalization in RT-qPCR-based gene expression studies. The present study also identified important developmental, RNAi pathway, and RNAi target genes and performed life-stage developmental expression analysis using RT-qPCR to select the optimal targets for RNAi. We found that naked dsRNA degradation in the E. vittella hemolymph is the primary reason for poor RNAi. A total of six genes including Juvenile hormone methyl transferase (JHAMT), Chitin synthase (CHS), Aminopeptidase (AMN), Cadherin (CAD), Alpha-amylase (AMY), and V-type proton ATPase (V-ATPase) were selected and knocked down significantly with three different nanoparticles encapsulated dsRNA conjugates, i.e., Chitosan-dsRNA, carbon quantum dots-dsRNA (CQD-dsRNA), and Lipofectamine-dsRNA conjugate. These results demonstrate that feeding nanoparticle-shielded dsRNA silences target genes and suggests that nanoparticle-based RNAi can efficiently manage this pest.
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Affiliation(s)
- Shelja Sandal
- Regional Research Station, Punjab Agricultural University, Faridkot 151203, Punjab, India
- Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala 140072, Punjab, India
| | - Satnam Singh
- Regional Research Station, Punjab Agricultural University, Faridkot 151203, Punjab, India
| | - Gulshan Bansal
- Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala 140072, Punjab, India
| | - Ramandeep Kaur
- Regional Research Station, Punjab Agricultural University, Faridkot 151203, Punjab, India
| | - Kanakachari Mogilicherla
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamýcká 129, 165 21 Praha, Czech Republic
| | - Suneet Pandher
- Regional Research Station, Punjab Agricultural University, Faridkot 151203, Punjab, India
| | - Amit Roy
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamýcká 129, 165 21 Praha, Czech Republic
| | - Gurmeet Kaur
- Regional Research Station, Punjab Agricultural University, Faridkot 151203, Punjab, India
| | - Pankaj Rathore
- Regional Research Station, Punjab Agricultural University, Faridkot 151203, Punjab, India
| | - Anu Kalia
- Electron Microscopy and Nanoscience Laboratory, Punjab Agricultural University, Ludhiana 141004, Punjab, India
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Imperadore P, Cagnin S, Allegretti V, Millino C, Raffini F, Fiorito G, Ponte G. Transcriptome-wide selection and validation of a solid set of reference genes for gene expression studies in the cephalopod mollusk Octopus vulgaris. Front Mol Neurosci 2023; 16:1091305. [PMID: 37266373 PMCID: PMC10230085 DOI: 10.3389/fnmol.2023.1091305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 02/20/2023] [Indexed: 06/03/2023] Open
Abstract
Octopus vulgaris is a cephalopod mollusk and an active marine predator that has been at the center of a number of studies focused on the understanding of neural and biological plasticity. Studies on the machinery involved in e.g., learning and memory, regeneration, and neuromodulation are required to shed light on the conserved and/or unique mechanisms that these animals have evolved. Analysis of gene expression is one of the most essential means to expand our understanding of biological machinery, and the selection of an appropriate set of reference genes is the prerequisite for the quantitative real-time polymerase chain reaction (qRT-PCR). Here we selected 77 candidate reference genes (RGs) from a pool of stable and relatively high-expressed transcripts identified from the full-length transcriptome of O. vulgaris, and we evaluated their expression stabilities in different tissues through geNorm, NormFinder, Bestkeeper, Delta-CT method, and RefFinder. Although various algorithms provided different assemblages of the most stable reference genes for the different kinds of tissues tested here, a comprehensive ranking revealed RGs specific to the nervous system (Ov-RNF7 and Ov-RIOK2) and Ov-EIF2A and Ov-CUL1 across all considered tissues. Furthermore, we validated RGs by assessing the expression profiles of nine target genes (Ov-Naa15, Ov-Ltv1, Ov-CG9286, Ov-EIF3M, Ov-NOB1, Ov-CSDE1, Ov-Abi2, Ov-Homer2, and Ov-Snx20) in different areas of the octopus nervous system (gastric ganglion, as control). Our study allowed us to identify the most extensive set of stable reference genes currently available for the nervous system and appendages of adult O. vulgaris.
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Affiliation(s)
- Pamela Imperadore
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Stefano Cagnin
- Department of Biology, University of Padova, Padova, Italy
- CIR-Myo Myology Center, University of Padova, Padova, Italy
| | - Vittoria Allegretti
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | | | - Francesca Raffini
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Graziano Fiorito
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
| | - Giovanna Ponte
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Napoli, Italy
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Liu Y, Zhou J, Qiu Z, Hu P, Chen X, Yang Z. Identification and Validation of Reference Genes for Expression Analysis Using RT-qPCR in Leptocybe invasa Fisher and La Salle (Hymenoptera: Eulophidae). Insects 2023; 14:insects14050456. [PMID: 37233084 DOI: 10.3390/insects14050456] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 05/27/2023]
Abstract
Leptocybe invasa (Hymenoptera: Eulophidae) is a globally intrusive pest. Despite extensive research into the physiological responses of this pest, our understanding of the molecular mechanisms still needs to be improved. We want to accurately investigate the expression of L. invasa's target genes, so it is imperative to select fitting reference genes. In this study, eight housekeeping genes' stability (RPS30, ACTR, 18S rRNA, ACT, RPL18, GAPDH, 28S rRNA, and TUB) was tested under five different experimental conditions, including male or female adults, somites (head, thorax, and abdomen), temperatures (0 °C, 25 °C, and 40 °C), diets (starvation, clear water, 10% honey water, Eucalyptus sap), and pesticides (acetone was used as a control, imidacloprid, monosultap). Gene stability was calculated using RefFinder, which integrates four algorithms (the ∆Ct method, geNorm, NormFinder, and BestKeeper). The findings implied that ACT and ACTR were the most accurate when comparing sexes. For analyzing different somites, 28S rRNA and RPL18 were ideal; the 28S rRNA and RRS30 were perfect for analyzing at different temperatures. The combination of ACT and GAPDH helped to analyze gene expression in different diets, and GAPDH and 28S rRNA were suitable for various pesticide conditions. Overall, this research offers a complete list of reference genes from L. invasa for precise analysis of target gene expression, which can improve the trustworthiness of RT-qPCR and lay the foundation for further investigations into the gene function of this pest.
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Affiliation(s)
- Ya Liu
- College of Forestry, Guangxi University, Nanning 530004, China
| | - Jing Zhou
- College of Forestry, Guangxi University, Nanning 530004, China
| | - Zhisong Qiu
- College of Forestry, Guangxi University, Nanning 530004, China
| | - Ping Hu
- College of Forestry, Guangxi University, Nanning 530004, China
- Guangxi Key Laboratory of Forest Ecology and Conservation, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning 530004, China
| | - Xiao Chen
- College of Forestry, Guangxi University, Nanning 530004, China
| | - Zhende Yang
- College of Forestry, Guangxi University, Nanning 530004, China
- Guangxi Key Laboratory of Forest Ecology and Conservation, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry, Guangxi University, Nanning 530004, China
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Dash PK, Rai R, Pradhan SK, Shivaraj SM, Deshmukh R, Sreevathsa R, Singh NK. Drought and Oxidative Stress in Flax ( Linum usitatissimum L.) Entails Harnessing Non-Canonical Reference Gene for Precise Quantification of qRT-PCR Gene Expression. Antioxidants (Basel) 2023; 12:antiox12040950. [PMID: 37107326 PMCID: PMC10136167 DOI: 10.3390/antiox12040950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/04/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023] Open
Abstract
Flax (Linum usitatissimum L.) is a self-pollinating, annual, diploid crop grown for multi-utility purposes for its quality oil, shining bast fiber, and industrial solvent. Being a cool (Rabi) season crop, it is affected by unprecedented climatic changes such as high temperature, drought, and associated oxidative stress that, globally, impede its growth, production, and productivity. To precisely assess the imperative changes that are inflicted by drought and associated oxidative stress, gene expression profiling of predominant drought-responsive genes (AREB, DREB/CBF, and ARR) was carried out by qRT-PCR. Nevertheless, for normalization/quantification of data obtained from qRT-PCR results, a stable reference gene is mandatory. Here, we evaluated a panel of four reference genes (Actin, EF1a, ETIF5A, and UBQ) and assessed their suitability as stable reference genes for the normalization of gene expression data obtained during drought-induced oxidative stress in flax. Taking together, from the canonical expression of the proposed reference genes in three different genotypes, we report that EF1a as a stand-alone and EF1a and ETIF5A in tandem are suitable reference genes to be used for the real-time visualization of cellular impact of drought and oxidative stress on flax.
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Affiliation(s)
- Prasanta K Dash
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | - Rhitu Rai
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | - Sharat Kumar Pradhan
- ICAR-National Rice Research Institute, Cuttack 753006, India
- Indian Council of Agricultural Research, Krishi Bhawan, New Delhi 110012, India
| | | | - Rupesh Deshmukh
- Department of Biotechnology, Central University of Haryana, Mahendragarh 123031, India
| | - Rohini Sreevathsa
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | - Nagendra K Singh
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
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Duncan S, Johansson HE, Ding Y. Reference genes for quantitative Arabidopsis single molecule RNA fluorescence in situ hybridization. J Exp Bot 2023; 74:2405-2415. [PMID: 36579724 PMCID: PMC10082928 DOI: 10.1093/jxb/erac521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/28/2022] [Indexed: 06/06/2023]
Abstract
Subcellular mRNA quantities and spatial distributions are fundamental for driving gene regulatory programmes. Single molecule RNA fluorescence in situ hybridization (smFISH) uses fluorescent probes to label individual mRNA molecules, thereby facilitating both localization and quantitative studies. Validated reference mRNAs function as positive controls and are required for calibration. Here we present selection criteria for the first set of Arabidopsis smFISH reference genes. Following sequence and transcript data assessments, four mRNA probe sets were selected for imaging. Transcript counts per cell, correlations with cell size, and corrected fluorescence intensities were all calculated for comparison. In addition to validating reference probe sets, we present sample preparation steps that can retain green fluorescent protein fluorescence, thereby providing a method for simultaneous RNA and protein detection. In summary, our reference gene analyses, modified protocol, and simplified quantification method together provide a firm foundation for future quantitative single molecule RNA studies in Arabidopsis root apical meristem cells.
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Affiliation(s)
| | - Hans E Johansson
- LGC Biosearch Technologies, 2199 S. McDowell Blvd, Petaluma, CA 94954, USA
| | - Yiliang Ding
- John Innes Centre, Norwich Research Park, Norwich, UK
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31
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Lewczuk A, Boratyńska-Jasińska A, Zabłocka B. Validation of the Reference Genes for Expression Analysis in the Hippocampus after Transient Ischemia/Reperfusion Injury in Gerbil Brain. Int J Mol Sci 2023; 24:ijms24032756. [PMID: 36769080 PMCID: PMC9917415 DOI: 10.3390/ijms24032756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/19/2023] [Accepted: 01/30/2023] [Indexed: 02/04/2023] Open
Abstract
Transient brain ischemia in gerbils is a common model to study the mechanisms of neuronal changes in the hippocampus. In cornu ammonnis 2-3, dentate gyrus (CA2-3,DG) regions of the hippocampus, neurons are resistant to 5-min ischemia/reperfusion (I/R) insult, while cornu ammonnis 1 (CA1) is found to be I/R-vulnerable. The quantitative polymerase chain reaction (qRT-PCR) is widely used to study the expression of genes involved in these phenomena. It requires stable and reliable genes for normalization, which is crucial for comparable and reproducible analyses of expression changes of the genes of interest. The aim of this study was to determine the best housekeeping gene for the I/R gerbil model in two parts of the hippocampus in controls and at 3, 48, and 72 h after recanalization. We selected and tested six reference genes frequently used in central nervous system studies: Gapdh, Actb, 18S rRNA, Hprt1, Hmbs, Ywhaz, and additionally Bud23, using RefFinder, a comprehensive tool based on four commonly used algorithms: delta cycle threshold (Ct), BestKeeper, NormFinder, and geNorm, while Hprt1 and Hmbs were the most stable ones in CA2-3,DG. Hmbs was the most stable in the whole hippocampal formation. This indicates that the general use of Hmbs, especially in combination with Gapdh, a highly expressed reference gene, seems to be suitable for qRT-PCR normalization in all hippocampal regions in this model.
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Bharati R, Sen MK, Kumar R, Gupta A, Žiarovská J, Fernández-Cusimamani E, Leuner O. Systematic Identification of Suitable Reference Genes for Quantitative Real-Time PCR Analysis in Melissa officinalis L. Plants (Basel) 2023; 12:470. [PMID: 36771553 PMCID: PMC9919226 DOI: 10.3390/plants12030470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/04/2023] [Accepted: 01/09/2023] [Indexed: 06/18/2023]
Abstract
Melissa officinalis L. is well known for its lemon-scented aroma and various pharmacological properties. Despite these valuable properties, the genes involved in the biosynthetic pathways in M. officinalis are not yet well-explored when compared to other members of the mint family. For that, gene expression studies using quantitative real-time PCR (qRT-PCR) are an excellent tool. Although qRT-PCR can provide accurate results, its accuracy is highly reliant on the expression and stability of the reference gene used for normalization. Hence, selecting a suitable experiment-specific reference gene is very crucial to obtain accurate results. However, to date, there are no reports for experiment-specific reference genes in M. officinalis. Therefore, in the current study, ten commonly used reference genes were assessed for their suitability as optimal reference genes in M. officinalis under various abiotic stress conditions and different plant organs. The candidate genes were ranked based on BestKeeper, comparative ΔCt, geNorm, NormFinder, and RefFinder. Based on the results, we recommend the combination of EF-1α and GAPDH as the best reference genes to normalize gene expression studies in M. officinalis. On the contrary, HLH71 was identified as the least-performing gene. Thereafter, the reliability of the optimal gene combination was assessed by evaluating the relative gene expression of the phenylalanine ammonia lyase (PAL) gene under two elicitor treatments (gibberellic acid and jasmonic acid). PAL is a crucial gene involved directly or indirectly in the production of various economically important secondary metabolites in plants. Suitable reference genes for each experimental condition are also discussed. The findings of the current study form a basis for current and future gene expression studies in M. officinalis and other related species.
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Affiliation(s)
- Rohit Bharati
- Department of Crop Sciences and Agroforestry, The Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague, Czech Republic
| | - Madhab Kumar Sen
- Department of Agroecology and Crop Production, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague, Czech Republic
| | - Ram Kumar
- Department of Plant Protection, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague, Czech Republic
| | - Aayushi Gupta
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague, Czech Republic
| | - Jana Žiarovská
- Research Centre AgroBioTech, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 94976 Nitra, Slovakia
| | - Eloy Fernández-Cusimamani
- Department of Crop Sciences and Agroforestry, The Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague, Czech Republic
| | - Olga Leuner
- Department of Crop Sciences and Agroforestry, The Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague, Czech Republic
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Hou Q, Yuan L, Jin H, Yan H, Li F, Wu S. Identification and validation of reference genes for normalization of gene expression analysis using qRT-PCR in Megalurothrips usitatus (thysanoptera: thripidae). Front Physiol 2023; 14:1161680. [PMID: 37143927 PMCID: PMC10151585 DOI: 10.3389/fphys.2023.1161680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 04/04/2023] [Indexed: 05/06/2023] Open
Abstract
Introduction: Gene expression analysis by reverse transcription quantitative polymerase chain reaction (qRT-PCR) has been widely used in research including insects. The selection of appropriate reference genes is the key to obtaining accurate and reliable results from qRT-PCR. However, studies on the expression stability of reference genes in Megalurothrips usitatus remain lacking. Methods: In this study, qRT-PCR was used to analyze the expression stability of candidate reference genes in M. usitatus. The expression levels of six candidate reference gene transcription of M. usitatus were analyzed. GeNorm, NormFinder, BestKeeper, and ΔCt were used to analyze the expression stability of M. usitatus treated with biological factors (developmental period treatment) and abiotic factors (light, temperature, insecticide treatment, respectively). Comprehensive stability ranking of candidate reference genes was recommended by RefFinder. Results and Discussion: Results showed that ribosomal protein S (RPS) was the most suitable expression in insecticide treatment. Ribosomal protein L (RPL) was the most suitable expression at developmental stage and light treatment, whereas elongation factor was the most suitable expression in temperature treatment. RefFinder was used to comprehensively analyze the above four treatments, and the results showed that RPL and actin (ACT) showed high stability in each treatment. Therefore, this study identified these two genes as reference genes in the qRT-PCR analysis of different treatment conditions of M. usitatus. Ourfindings will be beneficial for improving the accuracy of qRT-PCR analysis for future functional analysis of the target gene expression in M. usitatus.
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Affiliation(s)
- Qingfang Hou
- Sanya Nanfan Research Institute, Hainan University, Sanya, China
- School of Plant Protection, Hainan University, Haikou, China
| | - Linlin Yuan
- Sanya Nanfan Research Institute, Hainan University, Sanya, China
- School of Plant Protection, Hainan University, Haikou, China
| | - Haifeng Jin
- Sanya Nanfan Research Institute, Hainan University, Sanya, China
- School of Plant Protection, Hainan University, Haikou, China
| | - Han Yan
- Sanya Nanfan Research Institute, Hainan University, Sanya, China
- School of Plant Protection, Hainan University, Haikou, China
| | - Fen Li
- Sanya Nanfan Research Institute, Hainan University, Sanya, China
- School of Plant Protection, Hainan University, Haikou, China
- *Correspondence: Fen Li, ; Shaoying Wu,
| | - Shaoying Wu
- Sanya Nanfan Research Institute, Hainan University, Sanya, China
- School of Plant Protection, Hainan University, Haikou, China
- *Correspondence: Fen Li, ; Shaoying Wu,
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Wei H, Qiao H, Liu S, Yuan X, Xu C. Transcriptome-Based Selection and Validation of Reference Genes for Gene Expression in Goji Fruit Fly ( Neoceratitis asiatica Becker) under Developmental Stages and Five Abiotic Stresses. Int J Mol Sci 2022; 24:ijms24010451. [PMID: 36613890 PMCID: PMC9820723 DOI: 10.3390/ijms24010451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/17/2022] [Accepted: 12/24/2022] [Indexed: 12/29/2022] Open
Abstract
Goji fruit fly, Neoceratitis asiatica, is a major pest on the well-known medicinal plant Lycium barbarum. Dissecting molecular mechanisms of infestation and host selection of N. asiatica will contribute to the determination of best management practices for pest fly control. Gene expression normalization by Real-time quantitative PCR (qPCR) requires the selection and validation of appropriate reference genes (RGs). Hence, 15 candidate RGs were selected from transcriptome data of N. asiatica. Their expression stability was evaluated with five algorithms (∆Ct, Normfinder, GeNorm, BestKeeper, and RefFinder) for sample types differing in the developmental stage, sex, tissue type, and in response to five different abiotic stresses. Our results indicated that the RGs β-Actin + GST for sex, RPL32 + EF1α for tissue type, RPS13+ EF1α for developmental stages along with odor stimulation, color induction, and starvation-refeeding stresses, EF1α + GAPDH under insecticide stress, RPS13 + RPS18 under temperature stress, respectively, were selected as the most suitable RGs for qPCR normalization. Overall, RPS18 and EF1α were the two most stable RGs in all conditions, while RPS15 and EF1β were the least stable RGs. The corresponding suitable RGs and one unstable RG were used to normalize a target odorant-binding protein OBP56a gene in male and female antennae, different tissues, and under odor stimulation. The results of OBP56a expression were consistent with transcriptome data. Our study is the first research on the most stable RGs selection in N. asiatica, which will facilitate further studies on the mechanisms of host selection and insecticide resistance in N. asiatica.
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Zhao X, Guo J, Lu Y, Sun T, Tian J, Huang J, Xu H, Wang Z, Lu Z. Reference Genes for Expression Analysis Using RT-qPCR in Cnaphalocrocis medinalis (Lepidoptera: Pyralidae). Insects 2022; 13:insects13111046. [PMID: 36421949 PMCID: PMC9697642 DOI: 10.3390/insects13111046] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 05/31/2023]
Abstract
Cnaphalocrocis medinalis is a destructive migratory rice pest. Although many studies have investigated its behavioral and physiological responses to environmental changes and migration-inducing factors, little is known about its molecular mechanisms. This study was conducted to select suitable RT-qPCR reference genes to facilitate future gene expression studies. Here, thirteen candidate housekeeping genes (EF1α, AK, EF1β, GAPDH, PGK, RPL13, RPL18, RPS3, 18S rRNA, TBP1, TBP2, ACT, and UCCR) were selected to evaluate their stabilities under different conditions using the ∆CT method; the geNorm, NormFinder, BestKeeper algorithms; and the online tool RefFinder. The results showed that the most stable reference genes were EF1β, PGK, and RPL18, related to developmental stages; RPS3 and RPL18 in larval tissues; EF1β and PGK in larvae feeding on different rice varieties; EF1α, EF1β, and PGK in larvae temperature treatments; PGK and RPL13, related to different adult ages; PGK, EF1α, and ACT, related to adult nutritional conditions; RPL18 and PGK, related to adult mating status; and, RPS3 and PGK, related to different adult take-off characteristics. Our results reveal reference genes that apply to various experimental conditions and will greatly improve the reliability of RT-qPCR analysis for the further study of gene function in this pest.
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Affiliation(s)
- Xiaoyu Zhao
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jiawen Guo
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Yanhui Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Tianyi Sun
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Junce Tian
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jianlei Huang
- College of Agriculture and Forestry, Hebei North University, Zhangjiakou 075000, China
| | - Hongxing Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Zhengliang Wang
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Zhongxian Lu
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
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Liu H, He L, Cheng Q, Luo W, Zhao T, Yang D. Validation of superior reference genes in mouse submandibular glands under developmental and functional regeneration states. Int J Mol Med 2022; 50:132. [PMID: 36069228 PMCID: PMC9559174 DOI: 10.3892/ijmm.2022.5188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 08/10/2022] [Indexed: 11/06/2022] Open
Abstract
Saliva is crucial for lubricating the mouth and aiding in food digestion. However, the occurrence of oral dysfunction, such as xerostomia, dysphagia or oral infection can markedly reduce the quality of life of affected individuals. The major salivary glands include the submandibular gland (SMG), and sublingual and parotid glands; they are the larger glands in mammals that produce the majority of the saliva. The SMG serves as an effective model for the study of branching morphogenesis and functional regeneration. In order to better understand the key dynamic gene expression patterns during salivary gland development and functional regeneration, it is crucial to search for a panel of reliable reference genes. The present study thus aimed to identify superior reference genes to normalize gene expression data in the SMG under states of development and functional regeneration. First, the developmental SMG samples were harvested from mice in the embryonic and post-natal periods. Functional regeneration samples from a ductal ligation/de-ligation model were obtained at several stages. A total of 12 reference genes (Actb, Actg1, Ubc, Uba1, Uba52, Ube2c, Tuba1a, Tuba1b, Tubb5, H2afy, H2afx and Gapdh) from 430 candidates involving tubulin, histone, actin, ubiquitin and GAPDH family members were screened via transcriptome sequencing (RNA-seq) analysis. RT-qPCR (SYBR-Green) and western blot analysis were then used to semi-quantitatively assess gene and protein expression. The stability of expression was evaluated using the ΔCq, geNorm, BestKeeper, NormFinder and RefFinder methods and software. Actg1 exhibited the highest stability in the SMG developmental stage, while Tubb5 was recommended as the most stable reference gene for the SMG regenerative stage. In summary, the present study provides evidence-based selections for superior reference genes in the SMG during the stages of development and functional regeneration.
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Affiliation(s)
- Huikai Liu
- Department of Endodontics, Stomatological Hospital of Chongqing Medical University, Chongqing 401147, P.R. China
| | - Liwen He
- Department of Endodontics, Stomatological Hospital of Chongqing Medical University, Chongqing 401147, P.R. China
| | - Qianyu Cheng
- Department of Endodontics, Stomatological Hospital of Chongqing Medical University, Chongqing 401147, P.R. China
| | - Wenping Luo
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing 401147, P.R. China
| | - Tianyu Zhao
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing 401147, P.R. China
| | - Deqin Yang
- Department of Endodontics, Stomatological Hospital of Chongqing Medical University, Chongqing 401147, P.R. China
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Bharati R, Sen MK, Kumar R, Gupta A, Sur VP, Melnikovová I, Fernández-Cusimamani E. Selection and Validation of the Most Suitable Reference Genes for Quantitative Real-Time PCR Normalization in Salvia rosmarinus under In Vitro Conditions. Plants (Basel) 2022; 11:2878. [PMID: 36365331 PMCID: PMC9655146 DOI: 10.3390/plants11212878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/12/2022] [Accepted: 10/25/2022] [Indexed: 06/16/2023]
Abstract
Salvia rosmarinus L. (rosemary) is known to have a wide range of pharmacological effects including antidiabetic, anticarcinogenic, and antitumorigenic properties owing to its secondary metabolites. Studies aiming to elevate these metabolites have utilized various elicitors and stresses under in vitro conditions, although underlying molecular mechanisms remain unexplored. Gene expression studies using RT-qPCR might provide valuable information regarding how plant and plant cells interact and perceive various treatments and elicitors. However, despite being able to calculate accurate fold changes, the accuracy of the RT-qPCR data highly depends on the expression of reference genes. To the best of our knowledge, there is no information available on the stable reference genes in rosemary under in vitro conditions. Thus, in this paper, we assessed the stability of seven commonly used reference genes under different elicitor and stress conditions using RT-qPCR. Thereafter, the five most commonly used software and algorithms (comparative ΔCt, BestKeeper, NormFinder, geNorm, and RefFinder) were used to rank the candidates based on their expression stabilities. In conclusion, we recommend using a combination of F1-ATPase, ATP synthase and ACCase to normalize the gene expression experiments in rosemary under in vitro conditions. The selected reference genes were verified using 4-coumarate-CoA ligase, a pharmacologically important gene, whose expression might alter under nanoparticle treatment. Additionally, reference genes for several plant tissues, elicitors, and stresses are also proposed. The conclusions obtained from this current study will accelerate the future molecular work in S. rosmarinus and other related species.
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Affiliation(s)
- Rohit Bharati
- Department of Crop Sciences and Agroforestry, The Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague 6, Czech Republic
| | - Madhab Kumar Sen
- Department of Agroecology and Crop Production, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague 6, Czech Republic
| | - Ram Kumar
- Department of Plant Protection, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague 6, Czech Republic
| | - Aayushi Gupta
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague 6, Czech Republic
| | - Vishma Pratap Sur
- Laboratory of Reproductive Biology, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Prumyslova 595, 252 50 Vestec, Czech Republic
| | - Ingrid Melnikovová
- Department of Crop Sciences and Agroforestry, The Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague 6, Czech Republic
| | - Eloy Fernández-Cusimamani
- Department of Crop Sciences and Agroforestry, The Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Prague 6, Czech Republic
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Gu Z, Yin H, Zhang H, Zhang H, Liu X, Zeng X, Zheng X. Optimization of a method for the clinical detection of serum exosomal miR-940 as a potential biomarker of breast cancer. Front Oncol 2022; 12:956167. [PMID: 36338741 PMCID: PMC9634127 DOI: 10.3389/fonc.2022.956167] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 10/05/2022] [Indexed: 10/20/2023] Open
Abstract
Serum exosomal microRNAs (miRNAs) are potential biomarkers for tumor diagnosis. Clinically, reverse transcription-quantitative polymerase chain reaction (RT-qPCR) can be used to determine the expression of exosomal miRNAs in the serum of breast cancer patients. The prerequisites for obtaining meaningful serum exosomal miRNA data of breast cancer patients include a suitable extraction method for exosomes and RT-qPCR data standardized by internal reference genes. However, the appropriate methods for the extraction of exosomes and the applicability of reference genes for analyzing exosomal miRNAs in breast cancer patients remain to be studied. This study compared the effects of three exosome extraction methods as well as the expression of exosomal miRNA in different initial serum amounts and at different serum states to identify the selection of the best method for serum exosome extraction. Five candidate reference genes including miR-16, miR-484, miR-1228, miR-191 and miR-423 for standardizing serum exosomal miRNAs were screened using five algorithms and were used for the quantification of serum exosomal miR-940. Significant downregulation of serum exosomal miR-940 expression in breast cancer was detected using miR-191 and miR-1228, whereas no significant down or up regulation was observed with miR-484, miR-423 and miR-16. Previous studies have shown that the expression level of miR-940 is downregulated in breast cancer tissues. The absolute quantitative results showed that miR-940 was significantly downregulated in breast cancer serum exosomes, which was consistent with the results from the analysis using miR-191 or miR-1228 as reference genes. Therefore, miR-191 and miR-1228 could serve as reference genes for the relative quantification of serum exosomal miRNAs. This finding indicated the importance of rigorously evaluating the stability of reference genes and standardization for serum exosomal miRNA expression. Moreover, the level of serum exosomal miR-940 in breast cancer could reflect the presence of lymph node metastasis and the status of HER2/neu, which indicates its potential as a biomarker for breast cancer metastasis. In summary, an optimized protocol for the detection of serum exosomal miR-940 as a breast cancer marker was preliminarily established.
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Affiliation(s)
- Zhiyun Gu
- Department of Oncology Laboratory, Chongqing University Cancer Hospital, Chongqing, China
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, China
| | - Haojie Yin
- Bioengineering College, Chongqing University, Chongqing, China
| | - Haiwei Zhang
- Department of Oncology Laboratory, Chongqing University Cancer Hospital, Chongqing, China
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, China
| | - Hui Zhang
- Department of Oncology Laboratory, Chongqing University Cancer Hospital, Chongqing, China
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, China
| | - Xiaoyu Liu
- Department of Oncology Laboratory, Chongqing University Cancer Hospital, Chongqing, China
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, China
| | - Xiaohua Zeng
- Department of Oncology Laboratory, Chongqing University Cancer Hospital, Chongqing, China
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, China
| | - Xiaodong Zheng
- Department of Oncology Laboratory, Chongqing University Cancer Hospital, Chongqing, China
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, China
- Medical College of Chongqing University, Chongqing University, Chongqing, China
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Valenzuela F, D’Afonseca V, Hernández R, Gómez A, Arencibia AD. Validation of Reference Genes in a Population of Blueberry (Vaccinium corymbosum) Plants Regenerated in Colchicine. Plants (Basel) 2022; 11:2645. [PMID: 36235509 PMCID: PMC9573746 DOI: 10.3390/plants11192645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 09/20/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
For the first time we report the validation of reference genes in plants from a population of blueberry (Vaccinium corymbosum) clones cultured in vitro on a colchicine-supplemented medium. Nodal segment explants of the cultivar Duke were regenerated by organogenesis under different periods of colchicine 1 mg/L exposure (1, 2, 3, 5, 30 days). The clones selected for the study showed variability for phenotypic traits after 2 years of adaptation to field conditions, compared to plants of the donor genotype that were regenerated on a medium without colchicine. Vaccinium myrtillus (GAPDH) and Vaccinium macrocarpon (ATP1, NADH, RPOB and COX2) were used as reference genomes for primer design. The results show that colchicine treatments can cause genomic changes in blueberry plants. At the molecular level, exposure of plants to colchicine in early periods could promote an increase in gene expression of specific genes such as ATP1, COX2, GAPDH, MATK, NADH and RPOB. However, prolonged exposure (30 days) could decrease gene expression of the genes studied. For qPCR assays, the primers designed for ATP1, COX2, GAPDH and MATK genes showed high efficiency. In addition, the GAPDH, ATP1, NADH and COX2 genes showed high stability and could be recommended as potential reference genes for gene expression assays in Vaccinium.
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Affiliation(s)
- Francisca Valenzuela
- Centro de Biotecnología en Recursos Naturales, Facultad de Ciencias Agrarias y Forestales, Universidad Católica del Maule, Ave San Miguel 3605, Talca 3466706, Chile
| | - Vivían D’Afonseca
- Departamento de Ciencias Preclínicas, Facultad de Medicina, Universidad Católica del Maule, Ave San Miguel 3605, Talca 3466706, Chile
| | - Ricardo Hernández
- Centro de Biotecnología en Recursos Naturales, Facultad de Ciencias Agrarias y Forestales, Universidad Católica del Maule, Ave San Miguel 3605, Talca 3466706, Chile
- Doctorado en Biotecnología Traslacional. Facultad de Ciencias Agrarias y Forestales, Universidad Católica del Maule, Ave San Miguel 3605, Talca 3466706, Chile
| | - Aleydis Gómez
- Centro de Biotecnología en Recursos Naturales, Facultad de Ciencias Agrarias y Forestales, Universidad Católica del Maule, Ave San Miguel 3605, Talca 3466706, Chile
| | - Ariel D. Arencibia
- Centro de Biotecnología en Recursos Naturales, Facultad de Ciencias Agrarias y Forestales, Universidad Católica del Maule, Ave San Miguel 3605, Talca 3466706, Chile
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Tian Y, Chu Z, Wang L, Wang H, Yuan X, Wu S, Yang Y. Evaluation and validation of reference genes in Cymbidium faberi for real-time quantitative PCR. Biotechniques 2022. [PMID: 36178123 DOI: 10.2144/btn-2022-0025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
For all organs at all Cymbidium faberi stages, ACT, UBQ3 and GAPDH can be selected as reference genes. For organs of the vegetative stage, UBQ2 and UBQ3 can be chosen for analysis of normalized gene expression. For the bud stage, ACT and UBQ3 can be used for analysis of gene expression. For the full blossom stage, ACT, UBQ3 and UBQ2 can be introduced into relative gene expression analysis. For vegetative organs, UBQ2 and ACT can be used as reference genes. For reproductive organs, ACT, UBQ3 and UBQ2 can be used as a reference for data processing. CfAG1 gene expression is more consistent when UBQ3, GAPDH and ACT are used as reference genes.
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Hildyard JC, Wells DJ, Piercy RJ. Identification of qPCR reference genes suitable for normalising gene expression in the developing mouse embryo. Wellcome Open Res 2022; 6:197. [PMID: 35509373 PMCID: PMC9024131 DOI: 10.12688/wellcomeopenres.16972.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2022] [Indexed: 07/30/2023] Open
Abstract
Background: Progression through mammalian embryogenesis involves many interacting cell types and multiple differentiating cell lineages. Quantitative polymerase chain reaction (qPCR) analysis of gene expression in the developing embryo is a valuable tool for deciphering these processes, but normalisation to stably-expressed reference genes is essential for such analyses. Gene expression patterns change globally and dramatically as embryonic development proceeds, rendering identification of consistently appropriate reference genes challenging. Methods: We have investigated expression stability in mouse embryos from mid to late gestation (E11.5-E18.5), both at the whole-embryo level, and within the head and forelimb specifically, using 15 candidate reference genes ( ACTB, 18S, SDHA, GAPDH, HTATSF1, CDC40, RPL13A, CSNK2A2, AP3D1, HPRT1, CYC1, EIF4A, UBC, B2M and PAK1IP1), and four complementary algorithms (geNorm, Normfinder, Bestkeeper and deltaCt). Results: Unexpectedly, all methods suggest that many genes within our candidate panel are acceptable references, though AP3D1, RPL13A and PAK1IP1 are the strongest performing genes overall (scoring highly in whole embryos, heads or forelimbs alone, and in all samples collectively). HPRT1 and B2M are conversely poor choices, and show strong developmental regulation. We further show that normalisation using our three highest-scoring references can reveal subtle patterns of developmental expression even in genes ostensibly ranked as acceptably stable ( CDC40, HTATSF1). Conclusion: AP3D1, RPL13A and PAK1IP1 represent universally suitable reference genes for expression studies in the E11.5-E18.5 mouse embryo.
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Affiliation(s)
- John C.W. Hildyard
- Comparative Neuromuscular Diseases Laboratory, Clinical Science and Services, Royal Veterinary College, London, NW1 0TU, UK
| | - Dominic J. Wells
- Comparative Biomedical Sciences, Royal Veterinary College, London, London, NW1 0TU, UK
| | - Richard J. Piercy
- Comparative Neuromuscular Diseases Laboratory, Clinical Science and Services, Royal Veterinary College, London, NW1 0TU, UK
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Zhao J, Yang J, Wang X, Xiong Y, Xiong Y, Dong Z, Lei X, Yan L, Ma X. Selection and Validation of Reference Genes for qRT-PCR Gene Expression Analysis in Kengyilia melanthera. Genes (Basel) 2022; 13:genes13081445. [PMID: 36011356 PMCID: PMC9408421 DOI: 10.3390/genes13081445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 08/11/2022] [Accepted: 08/12/2022] [Indexed: 11/16/2022] Open
Abstract
Kengyilia is a newly established genus. Most species in this genus survive in hash environment, which might be an indicator of an acquirement of stress resistance genes and the potential for molecular breeding in Triticeae species. Quantitative real-time PCR (qRT-PCR) is a widely used technique with varied sensitivity heavily dependent on the optimal level of the reference genes. K. melanthera is a typical psammophyte species which has high drought resistance. The reference genes of K. melanthera are not yet reported. This study aims to evaluate the expression stability of 14 candidate reference genes (EF1A, GAPDH, ACT1, UBI, TUBB3, TIPRL, CACS, PPP2R1B, TUBA1A, EIF4A1, CYPA3, TCTP, ABCG11L, and FBXO6L) under five treatments (drought, heat, cold, salt, and ABA) and find the most stable and suitable one even upon stressed conditions. The software NormFinder, GeNorm, BestKeeper, and RefFinder were used for data analysis. In general, the genes CACS and PPP2R1B are concluded to have the best overall performance under the various treatments. With the ABA treatment, TCTP and TIPRL show the best stability. CACS and TCTP, as well as TIPRL and CYPA3, were most stable under the treatments of cold and salt, respectively. CACS and FBXO6L were ranked the highest with the heat treatment and drought treatment, respectively. Finally, the Catalase-1 (CAT1) gene was used to verify the reliability of the above reference genes. Accordingly, CAT1’s expression pattern remained unchanged after normalization with stable reference genes. This study provides beneficial information about the stability and reliability of potential reference genes for qRT-PCR in K. melanthera.
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Affiliation(s)
- Junming Zhao
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jian Yang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaoyun Wang
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yanli Xiong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yi Xiong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhixiao Dong
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiong Lei
- Sichuan Academy of Grassland Science, Chengdu 611731, China
| | - Lijun Yan
- Sichuan Academy of Grassland Science, Chengdu 611731, China
- Correspondence: (L.Y.); (X.M.)
| | - Xiao Ma
- College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
- Correspondence: (L.Y.); (X.M.)
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Kummerfeld DM, Skryabin BV, Brosius J, Vakhrushev SY, Rozhdestvensky TS. Reference Genes across Nine Brain Areas of Wild Type and Prader-Willi Syndrome Mice: Assessing Differences in Igfbp7, Pcsk1, Nhlh2 and Nlgn3 Expression. Int J Mol Sci 2022; 23. [PMID: 35955861 DOI: 10.3390/ijms23158729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/01/2022] [Accepted: 08/02/2022] [Indexed: 11/18/2022] Open
Abstract
Prader−Willi syndrome (PWS) is a complex neurodevelopmental disorder caused by the deletion or inactivation of paternally expressed imprinted genes at the chromosomal region 15q11−q13. The PWS-critical region (PWScr) harbors tandemly repeated non-protein coding IPW-A exons hosting the intronic SNORD116 snoRNA gene array that is predominantly expressed in brain. Paternal deletion of PWScr is associated with key PWS symptoms in humans and growth retardation in mice (PWScr model). Dysregulation of the hypothalamic−pituitary axis (HPA) is thought to be causally involved in the PWS phenotype. Here we performed a comprehensive reverse transcription quantitative PCR (RT-qPCR) analysis across nine different brain regions of wild-type (WT) and PWScr mice to identify stably expressed reference genes. Four methods (Delta Ct, BestKeeper, Normfinder and Genorm) were applied to rank 11 selected reference gene candidates according to their expression stability. The resulting panel consists of the top three most stably expressed genes suitable for gene-expression profiling and comparative transcriptome analysis of WT and/or PWScr mouse brain regions. Using these reference genes, we revealed significant differences in the expression patterns of Igfbp7, Nlgn3 and three HPA associated genes: Pcsk1, Pcsk2 and Nhlh2 across investigated brain regions of wild-type and PWScr mice. Our results raise a reasonable doubt on the involvement of the Snord116 in posttranscriptional regulation of Nlgn3 and Nhlh2 genes. We provide a valuable tool for expression analysis of specific genes across different areas of the mouse brain and for comparative investigation of PWScr mouse models to discover and verify different regulatory pathways affecting this complex disorder.
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Zhao ZQ, Zheng KY, Ou Q, Xu PZ, Qin S, Sun X, Li MW, Wu YC, Wang XY. Identification of optimal reference genes in Bombyx mori (Lepidoptera) for normalization of stress-responsive genes after challenge with pesticides. Arch Insect Biochem Physiol 2022; 110:e21896. [PMID: 35355317 DOI: 10.1002/arch.21896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
Pesticides are frequently used to control pests in agriculture due to their ease of use and effectiveness, but their use causes serious economic losses to sericulture when their production overlaps with agriculture. However, no suitable internal reference genes (RGs) have been reported in the study of silkworms in response to pesticides. In this study, a standard curve was established to detect the expression levels of seven RGs in different tissues of different silkworm strains after feeding with pesticides using reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR), including BmGAPDH, BmActin3, BmTBP, BmRPL3, Bm28sRNA, Bmα-tubulin, and BmUBC, and the stability of them was evaluated by using NormFinder, geNorm, Delta CT, BestKeeper, and RefFinder. The results showed that BmGAPDH and Bmα-tubulin were relatively stable in the midgut after feeding with fenvalerate, BmGAPDH and Bmactin3 were relatively stable in the fat body, and Bmα-tubulin and Bmactin3 were relatively stable in the hemolymph, indicating that Bmactin3 was the most suitable RG when evaluating fenvalerate, followed by BmGAPDH and Bmα-tubulin. Besides, BmGAPDH and Bmactin3 were relatively stable in the midgut after treatment with DDVP, BmGAPDH and Bmα-tubulin were relatively stable in the fat body, and BmGAPDH and Bmα-tubulin were relatively stable in the hemolymph, indicating that Bmα-tubulin was the most stable RG when evaluating DDVP, followed by BmGAPDH and Bmactin3. Of note, BmGAPDH was shared by the two pesticides. The results will be valuable for RG selection in studying the pesticide response mechanism of silkworms and other lepidopteran insects.
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Affiliation(s)
- Zi-Qin Zhao
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - Kai-Yi Zheng
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - Qi Ou
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - Ping-Zhen Xu
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang, Jiangsu, China
| | - Sheng Qin
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang, Jiangsu, China
| | - Xia Sun
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang, Jiangsu, China
| | - Mu-Wang Li
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang, Jiangsu, China
| | - Yang-Chun Wu
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang, Jiangsu, China
| | - Xue-Yang Wang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang, Jiangsu, China
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Yang J, Han F, Yang L, Wang J, Jin F, Luo A, Zhao F. Identification of Reference Genes for RT-qPCR Analysis in Gleditsia microphylla under Abiotic Stress and Hormone Treatment. Genes (Basel) 2022; 13:genes13071227. [PMID: 35886010 PMCID: PMC9315665 DOI: 10.3390/genes13071227] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 07/05/2022] [Accepted: 07/06/2022] [Indexed: 11/25/2022] Open
Abstract
Gleditsia microphylla is an important galactomannan gums source plant with characteristics of drought resistance, barren tolerance, and good adaptability. However, the underlying molecular mechanisms of the biological process are not yet fully understood. Real-time quantitative PCR (RT-qPCR) is an accurate and convenient method to quantify the gene expression level and transcription abundance of suitable reference genes. This study aimed to screen the best internal reference genes in G. microphylla under abiotic stresses, hormone treatments, and different tissues. Based on the transcriptome data, twelve candidate reference genes were selected, and ultimately, nine of them were further evaluated by the geNorm, NormFinder, BestKeeper, and RefFinder algorithms. These results show that TATA-binding protein 1 (TBP1)and Eukaryotic translation initiation factor 4A1 (EIF4A1)were the two most stable reference genes, and glyceraldehyde-3-phosphate dehydrogenase A subunit, chloroplastic (GAPA)and glyceraldehyde-3-phosphate dehydrogenase B subunit, chloroplastic (GAPB)were the two most unstable reference genes across all samples under the given experimental conditions. Meanwhile, the most stable reference genes varied among the different groups and tissues. Therefore, this study suggests that it is better to use a specific reference gene for a particular case rather than using a common reference gene.
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Dong Z, Zhan B, Li S. Selection and Validation of Reference Genes for Gene Expression Studies Using Quantitative Real-Time PCR in Prunus Necrotic Ringspot Virus-Infected Cucumis sativus. Viruses 2022; 14:v14061269. [PMID: 35746740 PMCID: PMC9227502 DOI: 10.3390/v14061269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 06/04/2022] [Accepted: 06/06/2022] [Indexed: 12/10/2022] Open
Abstract
Several members of the genus Ilarvirus infect fruit trees and are distributed worldwide. Prunus necrotic ringspot virus (PNRSV) is one of the most prevalent viruses, causing significant losses. Cucumissativus can be infected by several ilarviruses, leading to obvious symptoms, including PNRSV, which suggests that cucumbers could be good hosts for the study of the pathogenesis of ilarviruses. Real-time quantitative PCR is an optimal choice for studying gene expression because of its simplicity and its fast and high sensitivity, while its accuracy is highly dependent on the stability of the reference genes. In this study, we assessed the stability of eleven reference genes with geNorm, NormFinder, ΔCt method, BestKeeper, and the ranking software, RefFinder. The results indicated that the combined use of EF1α and F-BOX was the most accurate normalization method. In addition, the host genes AGO1, AGO4, and RDR6 were selected to test the reliability of the reference genes. This study provides useful information for gene expression analysis during PNRSV infection and will facilitate gene expression studies associated with ilarvirus infection.
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Affiliation(s)
- Zhenfei Dong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
- Department of Fruit Science, College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Binhui Zhan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
- Correspondence: (B.Z.); (S.L.)
| | - Shifang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
- Correspondence: (B.Z.); (S.L.)
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Li J, Fu N, Ren L, Luo Y. Identification and Validation of Reference Genes for Gene Expression Analysis in Monochamus saltuarius Under Bursaphelenchus xylophilus Treatment. Front Physiol 2022; 13:882792. [PMID: 35547586 PMCID: PMC9082747 DOI: 10.3389/fphys.2022.882792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/21/2022] [Indexed: 11/13/2022] Open
Abstract
A special mutual relationship exists between the pine wood nematode (PWN) Bursaphelenchus xylophilus and its vector beetles of genus Monochamus, which enables PWN to spread, at the same time provides longhorned beetles with more weak hosts. PWN are attracted to the pupal chambers and then carried inside the trachea of beetle adults, which is a necessary part to complete the B. xylophilus infection cycle. The growth and immune responses of the vector beetle will affect this carrying process, however, they were rarely studied in Monochamus saltuarius. Real-time quantitative polymerase chain reaction (RT-qPCR), one of the most common methods for quantitative gene expression analysis, was performed to explore the key genes and pathways involved in the growth, development and immune responses of M. saltuarius at different developmental stages associated with infection of PWN and PWN treatment conditions. To enhance the accuracy of RT-qPCR data, the expression of target genes needs to be normalized with reference genes, which are stably expressed under varied experimental conditions. In our study, the stability of 14 candidate reference genes in M. saltuarius samples at different developmental stages associated with infection of PWN or PWN treatment conditions was evaluated using delta Ct, geNorm, NormFinder, BestKeeper and RefFinder algorithms. Moreover, KLF gene was used to validate the stability of the selected reference genes. Under experimental conditions of this study, RPL7 and TER were suitable reference genes at different developmental stages associated with infection of PWN. RPL7 and RPS5 were considered the most stable reference genes in the pupae treated with PWN. RPS5 and SNX6 could be used as reference genes in the adults treated with PWN. RPL7, EF1-γ, and RPS5 could be used as stable reference genes in all the samples. This work is the first to evaluate reference genes in M. saltuarius, laying a foundation for further gene expression experimental procedures and understanding the phoretic relationship between M. saltuarius and B. xylophilus.
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Affiliation(s)
- Jiaxing Li
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China
| | - Ningning Fu
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China
| | - Lili Ren
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China
| | - Youqing Luo
- Beijing Key Laboratory for Forest Pest Control, Beijing Forestry University, Beijing, China
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Pomierny B, Krzyzanowska W, Jurczyk J, Strach B, Skorkowska A, Leonovich I, Budziszewska B, Pera J. Identification of optimal reference genes for gene expression studies in a focal cerebral ischaemia model-Spatiotemporal effects. J Cell Mol Med 2022; 26:3060-3067. [PMID: 35451185 PMCID: PMC9097850 DOI: 10.1111/jcmm.17284] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 02/17/2022] [Accepted: 02/21/2022] [Indexed: 11/28/2022] Open
Abstract
A proper reference gene (RG) is required to reliably measure mRNA levels in biological samples via quantitative reverse transcription PCR (RT‐qPCR). Various experimental paradigms require specific and stable RGs. In studies using rodent models of brain ischaemia, a variety of genes, such as β‐actin (Actb), hypoxanthine phosphoribosyltransferase 1 (Hprt1), peptidyl‐propyl isomerase A (Ppia) and glyceraldehyde‐3‐phosphate dehydrogenase (Gapdh), are used as RGs. However, most of these genes have not been validated in specific experimental settings. The aim of this study was to evaluate the time‐ and brain region‐dependent expression of RG candidates in a rat model of transient middle cerebral artery occlusion (tMCAO). The following genes were selected: Actb, Hprt1, Ppia, Gapdh, tyrosine 3‐monooxygenase/tryptophan 5‐monooxygenase activation protein, zeta (Ywhaz) and beta‐2 microglobulin (B2m). Focal cerebral ischaemia was induced by 90 min of tMCAO in male Sprague‐Dawley rats. Expression was investigated at four time points (12 and 24 h; 3 and 7 days) and in three brain areas (the frontal cortex, hippocampus and dorsal striatum) within the ischaemic brain hemisphere. The RT‐qPCR results were analysed using variance analysis and the ΔCt, GeNorm, NormFinder and BestKeeper methods. Data from these algorithms were ranked using the geometric mean of ranks of each analysis. Ppia, Hprt1 and Ywhaz were the most stable genes across the analysed brain areas and time points. B2m and Actb exhibited the greatest fluctuations, and the results for Gapdh were ambiguous.
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Affiliation(s)
- Bartosz Pomierny
- Department of Toxicological Biochemistry, Faculty of Pharmacy, Jagiellonian University Medical College, Kraków, Poland
| | - Weronika Krzyzanowska
- Department of Toxicological Biochemistry, Faculty of Pharmacy, Jagiellonian University Medical College, Kraków, Poland
| | - Jakub Jurczyk
- Department of Toxicological Biochemistry, Faculty of Pharmacy, Jagiellonian University Medical College, Kraków, Poland
| | - Beata Strach
- Department of Neurology, Faculty of Medicine, Jagiellonian University Medical College, Kraków, Poland
| | - Alicja Skorkowska
- Department of Toxicological Biochemistry, Faculty of Pharmacy, Jagiellonian University Medical College, Kraków, Poland
| | - Innesa Leonovich
- Department of Toxicological Biochemistry, Faculty of Pharmacy, Jagiellonian University Medical College, Kraków, Poland
| | - Bogusława Budziszewska
- Department of Toxicological Biochemistry, Faculty of Pharmacy, Jagiellonian University Medical College, Kraków, Poland
| | - Joanna Pera
- Department of Neurology, Faculty of Medicine, Jagiellonian University Medical College, Kraków, Poland
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Bantulà M, Arismendi E, Picado C, Mullol J, Roca-Ferrer J, Tubita V. Reference Gene Validation for RT-qPCR in PBMCs from Asthmatic Patients with or without Obesity. Methods Protoc 2022; 5:35. [PMID: 35645343 PMCID: PMC9149987 DOI: 10.3390/mps5030035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/10/2022] [Accepted: 04/19/2022] [Indexed: 01/26/2023] Open
Abstract
Obesity is known to impair the efficacy of glucocorticoid medications for asthma control. Glucocorticoid-induced gene expression studies may be useful to discriminate those obese asthmatic patients who present a poor response to glucocorticoids. The expression of genes of interest is normalized with respect to reference genes (RGs). Ideally, RGs have a stable expression in different samples and are not affected by experimental conditions. The objective of this work was to analyze suitable RGs to study the role of glucocorticoid-induced genes in obese asthmatic patients in further research. The gene expression of eight potential RGs (GUSB, B2M, POLR2A, PPIA, ACTB, GAPDH, HPRT1, and TBP) was assessed with reverse transcription-quantitative polymerase chain reaction in peripheral blood mononuclear cells (PBMCs) from asthmatic, obese asthmatic, and healthy individuals. Their stability was analyzed using four different algorithms-BestKeeper, ΔCt, geNorm, and NormFinder. geNorm analysis recommended the use of a minimum of three genes for normalization. Moreover, intergroup variation due to the treatment was calculated by NormFinder, which found that B2M was the gene that was least affected by different treatments. Comprehensive rankings indicated GUSB and HPRT1 as the best RGs for qPCR in PBMCs from healthy and asthmatic subjects, while B2M and PPIA were the best for obese asthmatic subjects. Finally, our results demonstrated that B2M and HPRT1 were the most stable RGs among all groups, whereas ACTB, TBP, and GAPDH were the worst shared ones.
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Affiliation(s)
- Marina Bantulà
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Hospital Clinic, Universitat de Barcelona, 08036 Barcelona, Spain; (E.A.); (C.P.); (J.M.); (J.R.-F.); (V.T.)
| | - Ebymar Arismendi
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Hospital Clinic, Universitat de Barcelona, 08036 Barcelona, Spain; (E.A.); (C.P.); (J.M.); (J.R.-F.); (V.T.)
- Department of Pneumology, Hospital Clinic, 08036 Barcelona, Spain
- Centre for Biomedical Investigation in Respiratory Diseases (CIBERES), 08036 Barcelona, Spain
| | - César Picado
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Hospital Clinic, Universitat de Barcelona, 08036 Barcelona, Spain; (E.A.); (C.P.); (J.M.); (J.R.-F.); (V.T.)
- Department of Pneumology, Hospital Clinic, 08036 Barcelona, Spain
- Centre for Biomedical Investigation in Respiratory Diseases (CIBERES), 08036 Barcelona, Spain
| | - Joaquim Mullol
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Hospital Clinic, Universitat de Barcelona, 08036 Barcelona, Spain; (E.A.); (C.P.); (J.M.); (J.R.-F.); (V.T.)
- Centre for Biomedical Investigation in Respiratory Diseases (CIBERES), 08036 Barcelona, Spain
- Rhinology Unit and Smell Clinic, ENT Department, Hospital Clinic, 08036 Barcelona, Spain
| | - Jordi Roca-Ferrer
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Hospital Clinic, Universitat de Barcelona, 08036 Barcelona, Spain; (E.A.); (C.P.); (J.M.); (J.R.-F.); (V.T.)
- Centre for Biomedical Investigation in Respiratory Diseases (CIBERES), 08036 Barcelona, Spain
| | - Valeria Tubita
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Hospital Clinic, Universitat de Barcelona, 08036 Barcelona, Spain; (E.A.); (C.P.); (J.M.); (J.R.-F.); (V.T.)
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Meng Q, Shu B, Sun S, Wang Y, Yang M, Zhu E, Liu A, Gao S, Gou Y, Wang Z. Selection of reference genes for quantitative real-time PCR normalization in the coffee white stem borer, Xylotrechus quadripes Chevrolat (Coleoptera: Cerambycidae). Bull Entomol Res 2022; 112:151-161. [PMID: 35301961 DOI: 10.1017/s0007485321000596] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The coffee white stem borer, Xylotrechus quadripes Chevrolat (Coleoptera: Cerambycidae), is a major destructive pest of Coffea arabica L. (Gentianales: Rubiaceae), widely planted in many Asian countries, including China. Quantitative real-time polymerase chain reaction (qRT-PCR) is a common method for quantitative analysis of gene transcription levels. To obtain accurate and reliable qRT-PCR results, it is necessary to select suitable reference genes to different experimental conditions for normalizing the target gene expression. However, the stability of the expression of reference genes in X. quadripes has rarely been studied. In this study, the expression stability of nine candidate reference genes were investigated under biotic and abiotic conditions for use in qRT-PCR's normalization. By integrating the results of four algorithms of NormFinder, BestKeeper, geNorm, and RefFinder, the optimal reference gene combinations in different experimental conditions were performed as follows: RPL10a and EIF3D were the optimal reference genes for developmental stage samples, EIF4E, RPL10a, and RPS27a for tissue samples, V-ATP and EF1α for the sex samples, EIF3D and V-ATP for temperature treatment, RPS27a and RPL10a for insecticide stress, and RPL10a, RPS27a, and EF1α for all the samples. This study will help to obtain the stable internal reference genes under biotic and abiotic conditions and lay the foundation for in-depth functional research of target genes or genomics on olfactory molecular mechanisms, temperature adaptability, and insecticide resistance in X. quadripes.
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Affiliation(s)
- Qianqian Meng
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning571533, P.R. China
| | - Benshui Shu
- Guangzhou City Key Laboratory of Subtropical Fruit Trees Outbreak Control, Zhongkai University of Agriculture and Engineering, Guangzhou510000, P.R. China
| | - Shiwei Sun
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning571533, P.R. China
| | - Ying Wang
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning571533, P.R. China
- College of Tropical Crops, Yunnan Agricultural University, Puer665000, P.R. China
| | - Mei Yang
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning571533, P.R. China
- College of Tropical Crops, Yunnan Agricultural University, Puer665000, P.R. China
| | - Enhang Zhu
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning571533, P.R. China
- College of Tropical Crops, Yunnan Agricultural University, Puer665000, P.R. China
| | - Aiqin Liu
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning571533, P.R. China
| | - Shengfeng Gao
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning571533, P.R. China
| | - Yafeng Gou
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning571533, P.R. China
| | - Zheng Wang
- Hainan Provincial Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops, Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning571533, P.R. China
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