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Dalai M, Jagota A. Identification of specific reference gene for normalization of RT-qPCR data in rhythmic gene expression studies of the effect of developmental hormone antagonist in postembryonic development in Bombyx mori. FRONTIERS IN INSECT SCIENCE 2024; 4:1362473. [PMID: 39006940 PMCID: PMC11239437 DOI: 10.3389/finsc.2024.1362473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 06/05/2024] [Indexed: 07/16/2024]
Abstract
Bombyx mori is a lepidopteran holometabolous insect with distinct developmental stages: egg, larvae, pupae, and adult. The lepidopteran insect undergoes major modifications in the central nervous system (CNS) so as to adapt to the lifestyle of these distinct stages with specific habitats and functions from voraciously feeding larval stages to flying reproductive adults via dormant pupal stages. Such transitions are linked to transcriptional, epigenetic, and translational complexities. Therefore, studying rhythmic gene expression in CNS of various developmental stages and the effects of antagonists on developmental hormones requires a very stable reference gene (RG). To facilitate rhythmic gene expression studies using reverse transcription quantitative polymerase chain reaction (RT-qPCR) in B. mori and the effect of developmental hormone juvenile hormone (JH) and 20-hydroxy ecdysone hormone (20 HE), antagonists Precocene 1 and testosterone, respectively, were used. Eight candidate RGs, namely, Translational initiation factor 3 subunit 4 (TI3S4), Translational initiation factor 3 subunit 5 (TI3S5), Ribosomal protein subunit 7 (RPs7), TATA-binding protein association factor (TAF13), Translational initiation factor 4 A (TI4A), Ribosomal protein (RPL32), Elongation factor 1 (EF1), and Arginine kinase (AK), were assessed in the CNS of B. mori. The postembryonic developmental (PED) stages used were the fifth late larval instar, early pupa, mid pupa, late pupa, and adult. The assessments were done at four different time points, Zeitgeber time (ZT) 0, 6, 12, and 18, to find stability towards 24-h rhythmic expression. RefFinder, geNorm, and Ct value analysis were performed. RefFinder and geNORM studies suggested stability order as TI3S4 > TI3S5 > RPs7, but Ct value evaluation showed stability order as TI3S5 > TI3S4 > RPs7. We therefore demonstrated that TI3S4, TI3S5, and RPs7 can be used as RG in various PED stages in CNS of B. mori (Strain: CB-hybrid, PM×CSR2) towards studies with effects of JH and 20 HE antagonists.
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Affiliation(s)
- Minurani Dalai
- Neurobiology and Molecular Chronobiology Laboratory, Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Anita Jagota
- Neurobiology and Molecular Chronobiology Laboratory, Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
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Stability of Nuclear and Mitochondrial Reference Genes in Selected Tissues of the Ambrosia Beetle Xylosandrus germanus. INSECTS 2021; 12:insects12121125. [PMID: 34940213 PMCID: PMC8706855 DOI: 10.3390/insects12121125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/13/2021] [Accepted: 12/15/2021] [Indexed: 11/16/2022]
Abstract
The fungus-farming ambrosia beetle Xylosandrus germanus (Blandford) uses a pouch-like structure (i.e., mycangium) to transport spores of its nutritional fungal mutualist. Our current study sought to identify reference genes necessary for future transcriptome analyses aimed at characterizing gene expression within the mycangium. Complementary DNA was synthesized using selected tissue types from laboratory-reared and field-collected X. germanus consisting of the whole body, head + thorax, deflated or inflated mycangium + scutellum, inflated mycangium, and thorax + abdomen. Quantitative reverse-transcription PCR reactions were performed using primers for 28S ribosomal RNA (28S rRNA), arginine kinase (AK), carbamoyl-phosphate synthetase 2-aspartate transcarbamylase-dihydroorotase (CAD), mitochondrial cytochrome oxidase 1 (CO1), and elongation factor-1α (EF1α). Reference gene stability was analyzed using GeNorm, NormFinder, BestKeeper, ΔCt, and a comprehensive final ranking by RefFinder. The gene CO1 was identified as the primary reference gene since it was generally ranked in first or second position among the tissue types containing the mycangium. Reference gene AK was identified as a secondary reference gene. In contrast, EF1α was generally ranked in the last or penultimate place. Identification of two stable reference genes will aid in normalizing the expression of target genes for subsequent gene expression studies of X. germanus' mycangium.
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Azemi NFH, Misnan R, Keong PB, Yadzir ZHM. Reference gene and tropomyosin expression in mud crab Scylla olivacea, Scylla paramamosain and Scylla tranquebarica. Mol Biol Rep 2020; 47:9765-9777. [PMID: 33170423 DOI: 10.1007/s11033-020-05966-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 10/30/2020] [Indexed: 12/25/2022]
Abstract
Tropomyosin, a muscle tissue protein is a major allergen in most of shellfish including mud crab. Quantitative real time-PCR (qRT-PCR) using a stable reference gene is the most sensitive approach to produce accurate relative gene expression that has yet to be demonstrated for allergenic tropomyosin in mud crab species. This study was conducted to identify the suitable reference gene and tropomyosin expression in different body parts of local mud crabs, Scylla olivacea, Scylla paramamosain and Scylla tranquebarica. Myosin, 18S rRNA, GADPH and EF1α were selected as candidate reference genes and their expression was measured in the abdomen, walking leg and cheliped tissues of local Scylla spp. The expression stability was analyzed using the comparative delta-Ct method, BestKeeper, NormFinder and geNorm then comprehensively ranked by RefFinder algorithm. Findings showed that EF1α was the most suitable reference gene across three mud crab species. Meanwhile, the abdomen, walking leg and cheliped selected their own suitable reference gene either Myosin, 18S rRNA, EF1α or GADPH. Overall, tropomyosin was the highest in S. tranquebarica, whereas the least was in S. paramamosain. Interestingly, tropomyosin was the highest in the abdomen of all mud crab species. This is the first analysis on reference genes selection for qRT-PCR data normalization of tropomyosin expression in mud crab. These results will provide more accurate findings for further gene expression and allergen analysis in Scylla spp.
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Affiliation(s)
- Nur Farah Hani Azemi
- Department of Biology, Faculty of Science and Mathematics, Universiti Pendidikan Sultan Idris, 35900 Tanjong Malim, Perak, Malaysia
| | - Rosmilah Misnan
- Department of Biology, Faculty of Science and Mathematics, Universiti Pendidikan Sultan Idris, 35900 Tanjong Malim, Perak, Malaysia.
| | - Poh Bun Keong
- Department of Biology, Faculty of Science and Mathematics, Universiti Pendidikan Sultan Idris, 35900 Tanjong Malim, Perak, Malaysia
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Bento FM, Marques RN, Campana FB, Demétrio CG, Leandro RA, Parra JRP, Figueira A. Gene silencing by RNAi via oral delivery of dsRNA by bacteria in the South American tomato pinworm, Tuta absoluta. PEST MANAGEMENT SCIENCE 2020; 76:287-295. [PMID: 31207074 DOI: 10.1002/ps.5513] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 05/24/2019] [Accepted: 06/06/2019] [Indexed: 05/10/2023]
Abstract
BACKGROUND RNA interference (RNAi) has been evaluated in several insect pests as a novel strategy to be included in integrated pest management. Lepidopterans are recognized to be recalcitrant to gene silencing by RNAi. As such, double-stranded RNA (dsRNA) delivery needs to be adjusted to assure its stability until it reaches the target gene transcript for silencing. Gene silencing by RNAi offers the potential to be used in the control of Tuta absoluta (Meyrick), one of the main insect pests of tomato (Solanum lycopersicum) worldwide. Here, we tested the delivery of dsRNA expressed in Escherichia coli HT115(DE3) and supplied to larvae in an artificial diet by screening target genes for silencing. We tested six target genes: juvenile hormone inducible protein (JHP); juvenile hormone epoxide hydrolase protein (JHEH); ecdysteroid 25-hydroxylase (PHM); chitin synthase A (CHI); carboxylesterase (COE); and arginine kinase (AK). RESULTS Based on larval mortality, the duration of the larval stage in days, pupal weight, and the accumulation of the target gene transcript, we demonstrated the efficacy of bacterial dsRNA delivery for the functional effects on larval development. Providing dsRNA targeted to JHP, CHI, COE and AK by bacteria led to a significant decrease in transcript accumulation and an increase in larval mortality. CONCLUSION Bacteria expressing dsRNA targeting essential T. absoluta genes supplied in artificial diet are efficient to screen RNAi target-genes. The oral delivery of dsRNA by bacteria is a novel potential alternative for the control of T. absoluta based on RNAi. © 2019 Society of Chemical Industry.
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Affiliation(s)
- Flavia Mm Bento
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, Brazil
- Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ), Universidade de São Paulo, Piracicaba, Brazil
| | - Rodrigo N Marques
- Centro de Ciências Agrárias, Universidade Federal de São Carlos, Araras, Brazil
| | - Felippe B Campana
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, Brazil
| | - Clarice Gb Demétrio
- Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ), Universidade de São Paulo, Piracicaba, Brazil
| | - Roseli A Leandro
- Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ), Universidade de São Paulo, Piracicaba, Brazil
| | - José Roberto P Parra
- Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ), Universidade de São Paulo, Piracicaba, Brazil
| | - Antonio Figueira
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Piracicaba, Brazil
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Lü J, Yang C, Zhang Y, Pan H. Selection of Reference Genes for the Normalization of RT-qPCR Data in Gene Expression Studies in Insects: A Systematic Review. Front Physiol 2018; 9:1560. [PMID: 30459641 PMCID: PMC6232608 DOI: 10.3389/fphys.2018.01560] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 10/18/2018] [Indexed: 02/03/2023] Open
Abstract
Reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) is a reliable technique for quantifying expression levels of targeted genes during various biological processes in numerous areas of clinical and biological research. Selection of appropriate reference genes for RT-qPCR normalization is an elementary prerequisite for reliable measurements of gene expression levels. Here, by analyzing datasets published between 2008 and 2017, we summarized the current trends in reference gene selection for insect gene expression studies that employed the most widely used SYBR Green method for RT-qPCR normalization. We curated 90 representative papers, mainly published in 2013–2017, in which a total of 78 insect species were investigated in 100 experiments. Furthermore, top five journals, top 10 frequently used reference genes, and top 10 experimental factors have been determined. The relationships between the numbers of the reference genes, experimental factors, analysis tools on the one hand and publication date (year) on the other hand was investigated by linear regression. We found that the more recently the paper was published, the more experimental factors it tended to explore, and more analysis tools it used. However, linear regression analysis did not reveal a significant correlation between the number of reference genes and the study publication date. Taken together, this meta-analysis will be of great help to researchers that plan gene expression studies in insects, especially the non-model ones, as it provides a summary of appropriate reference genes for expression studies, considers the optimal number of reference genes, and reviews the average number of experimental factors and analysis tools per study.
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Affiliation(s)
- Jing Lü
- Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, Department of Entomology, South China Agricultural University, Guangzhou, China
| | - Chunxiao Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, China
| | - Youjun Zhang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huipeng Pan
- Key Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, Department of Entomology, South China Agricultural University, Guangzhou, China
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Ossa-López PA, Castaño-Villa GJ, Rivera-Páez FA. Genotoxic effects and gene expression in Danio rerio (Hamilton 1822) (Cypriniformes: Cyprinidae) exposed to mining-impacted tributaries in Manizales, Colombia. ENVIRONMENTAL MONITORING AND ASSESSMENT 2017; 189:520. [PMID: 28948416 DOI: 10.1007/s10661-017-6231-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Accepted: 09/12/2017] [Indexed: 06/07/2023]
Abstract
The zebrafish (Danio rerio) is one of the most studied aquatic organisms for water biomonitoring, due to its sensitivity to environmental degradation and resistance to toxic substances. This study determined the presence of micronuclei and nuclear abnormalities in peripheral blood erythrocytes, and assessed the gene expression of caspase-3 (CASP-3) and metallothionein 1 (MT-1) in the gills and liver of D. rerio. The study fish (n = 45) were exposed to water collected from two stations with mining impact (E2 and E3) and a reference station without evident mining contamination (E1), all located in La Elvira stream (Manizales-Colombia). In addition, a positive control (PC) with HgCl2 (50 μg/L) and negative control (NC) with tap water were included. The fish from the PC and E2 and E3 treatments displayed genotoxic effects and changes in gene expression, with significant differences in micronuclei formation and the presence of blebbed nuclei. The cytochrome oxidase subunit I (COI) gene was used as reference and proved to be stable compared to the β-actin and 28S ribosomal RNA (28S) genes. In gills, CASP-3 expression was higher in the PC, and MT-1 expression was higher in the PC and E3 treatment. In liver, CASP-3 was expressed in the E2 treatment, and MT-1 expression was low. These results show that the genotoxic effects and differential gene expression observed in fish exposed to water from La Elvira stream could also be affecting the organisms present in this habitat.
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Affiliation(s)
- Paula A Ossa-López
- Grupo de Investigación GEBIOME, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas y Naturales, Universidad de Caldas, Calle 65 No. 26-10 Apartado Aéreo 275, Manizales, Caldas, Colombia
| | - Gabriel J Castaño-Villa
- Grupo de Investigación GEBIOME, Departamento de Desarrollo Rural y Recursos Naturales, Facultad de Ciencias Agropecuarias, Universidad de Caldas, Calle 65 No. 26-10 Apartado Aéreo 275, Manizales, Caldas, Colombia
| | - Fredy A Rivera-Páez
- Grupo de Investigación GEBIOME, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas y Naturales, Universidad de Caldas, Calle 65 No. 26-10 Apartado Aéreo 275, Manizales, Caldas, Colombia.
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