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Ma D, Zhang Q, Zhou J, Lu Y, Duan X, He C, Yu J. Identification of Reliable Reference Genes under Different Stresses and in Different Tissues of Toxicodendron succedaneum. Genes (Basel) 2022; 13:genes13122396. [PMID: 36553662 PMCID: PMC9778191 DOI: 10.3390/genes13122396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
Toxicodendron succedaneum (L.) Kuntze (T. succedaneum) is an economic tree species that produces urushiol and urushi wax, and it is of great value in industry and medicine. However, the stability of reference genes (RGs) has not been systematically reported in T. succedaneum to date. In this study, the expression of 10 candidate RGs was analyzed by RT-qPCR in different tissues (roots, stems, leaves), stress treatments (high/low temperature, drought), and hormone stimulation (jasmonic acid, JA). Then, the stability ranking of 10 candidate genes was evaluated by ∆Ct analysis and three software programs: geNorm, NormFinder, and BestKeeper. Finally, RefFinder was used to comprehensively analyze the expression stability of 10 candidate genes. The comprehensive analysis showed that TsRG05/06, TsRG01/06, and TsRG03/ACT were stable under high/low-temperature stress, drought stress, and JA treatment, respectively. TsRG03 and ACT had stable expression in different tissues. While the TsRG03 and ACT were recommended as the suitable RGs for T. succedaneum in all samples. Meanwhile, UBQ was the least suitable as a reference gene for T. succedaneum. In addition, the results of geNorm showed that the combination of two stable RGs could make the results of gene expression more accurate. These results provide alternative RGs for the study of gene function, correction, and normalization of target gene expression and directed molecular breeding in T. succedaneum.
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Affiliation(s)
- Dongxiao Ma
- College of Life Sciences, Southwest Forestry University, Kunming 650224, China
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming 650224, China
| | - Qin Zhang
- College of Life Sciences, Southwest Forestry University, Kunming 650224, China
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming 650224, China
| | - Jintao Zhou
- College of Life Sciences, Southwest Forestry University, Kunming 650224, China
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming 650224, China
| | - Yu Lu
- College of Life Sciences, Southwest Forestry University, Kunming 650224, China
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming 650224, China
| | - Xiaomeng Duan
- College of Life Sciences, Southwest Forestry University, Kunming 650224, China
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming 650224, China
| | - Chengzhong He
- College of Life Sciences, Southwest Forestry University, Kunming 650224, China
- Key Laboratory for Forest Genetic and Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming 650224, China
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming 650224, China
| | - Jinde Yu
- College of Life Sciences, Southwest Forestry University, Kunming 650224, China
- Correspondence:
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Xu J, Huang X, Liu S, Chen D, Xie Y, Zhao Z. The protective effects of lncRNA ZFAS1/miR-421-3p/MEF2C axis on cerebral ischemia-reperfusion injury. Cell Cycle 2022; 21:1915-1931. [PMID: 35880950 PMCID: PMC9415620 DOI: 10.1080/15384101.2022.2060627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
LncRNA ZNFX1 antisense RNA 1 (ZFAS1) could improve neuronal damage and inhibit inflammation and apoptosis. We conducted an in-depth exploration on the protective mechanism of ZFAS1 in cerebral ischemia-reperfusion injury. Overexpressed or silenced plasmids of ZFAS1 were transfected into the cells to analyze the effects of oxygen-glucose deprivation/reperfusion (OGD/R) treatment on the viability, apoptosis and related gene expressions of Neuro-2a cell by performing MTT assay, flow cytometry, qRT-PCR, and Western blot. Bioinformatic analysis, qRT-PCR, dual-luciferase reporter assay and RNA immunoprecipitation were used to screen and verify the miRNA(s) which could competitively bind with ZFAS1 and downstream mRNA(s) targeted by the miRNA(s). The effects of ZFAS1 and the above target miRNA(s) or gene(s) on the apoptosis of OGD/R-injured cells, apoptosis-related proteins, inflammatory factors and p65/IκBα pathway were further verified via the rescue test. The results from the middle cerebral artery occlusion (MCAO) mouse model in vivo were consistent with those from the cellular experiments. The expression of lncRNA ZFAS1 in OGD/R-injured cells was inhibited, and the up-regulation of ZFAS1 protected Neuro-2a cells. MiR-421-3p was predicted to be the target miRNA of ZFAS1 and could offset the protective effect of ZFAS1 overexpression on OGD/R-injured cells following its up-regulation. MEF2C, which was the downstream target gene of miR-421-3p, reversed the OGD/R-induced enhanced cell damage caused by miR-421-3p mimic when MEF2C was overexpressed. In in vivo studies, ZFAS1 overexpression reduced brain tissue infarction, apoptosis and gene regulation caused by MCAO, while miR-421-3p mimic had the opposite effect. Collectively, the regulation of lncRNA ZFAS1/miR-421-3p/MEF2C axis showed protective effects on cerebral ischemia-reperfusion injury.
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Affiliation(s)
- Jiangqi Xu
- Geriatrics Department, Jiu Jiang No. 1 People's Hospital Jiujiang, China
| | - Xiaohong Huang
- Geriatrics Department, Jiu Jiang No. 1 People's Hospital Jiujiang, China
| | - Shixiang Liu
- Geriatrics Department, Jiu Jiang No. 1 People's Hospital Jiujiang, China
| | - Dongdong Chen
- Geriatrics Department, Jiu Jiang No. 1 People's Hospital Jiujiang, China
| | - Yufang Xie
- Geriatrics Department, Jiu Jiang No. 1 People's Hospital Jiujiang, China
| | - Zhenwu Zhao
- Emergency Department, Beijing University of Chinese Medicine Third Affiliated Hospital, Beijing, China
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Sinha R, Bala M, Prabha P, Ranjan A, Chahota RK, Sharma TR, Singh AK. Identification and validation of reference genes for qRT-PCR based studies in horse gram ( Macrotyloma uniflorum). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2859-2873. [PMID: 35035141 PMCID: PMC8720121 DOI: 10.1007/s12298-021-01104-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 11/10/2021] [Accepted: 11/17/2021] [Indexed: 06/14/2023]
Abstract
UNLABELLED The quantitative real-time polymerase chain reaction (qRT-PCR) is the most sensitive and commonly used technique for gene expression studies in biological systems. However, the reliability of qRT-PCR results depends on the selection of reference gene(s) for data normalization. Horse gram (Macrotyloma uniflorum) is an important legume crop on which several molecular studies have been reported. However, the stability of reference genes has not been evaluated. In the present study, nine candidate reference genes were identified from horse gram RNA-seq data and evaluated in two horse gram genotypes, HPK4 and HPKM317 under six abiotic stresses viz. cold, drought, salinity, heat, abscisic acid and methyl viologen-induced oxidative stress. The results were evaluated using geNorm, Bestkeeper, Normfinder and delta-delta Ct methods and comprehensive ranking was assigned using RefFinder and RankAggreg software. The overall result showed that TCTP was one of the most stable genes in all samples and in genotype HPK4, while in HPKM317 profilin was most stably expressed. However, PSMA5 was identified as least stable in all the experimental conditions. Expression of target genes dehydrin and early response to dehydration 6 under drought stress was also validated using TCTP and profilin for data normalization, either alone or in combination, which confirmed their suitability for qRT-PCR data normalization. Thus, TCTP and profilin genes may be used for qRT-PCR data normalization for molecular and genomic studies in horse gram. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01104-0.
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Affiliation(s)
- Ragini Sinha
- School of Genetic Engineering, ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, 834010 India
| | - Meenu Bala
- School of Genetic Engineering, ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, 834010 India
| | - Pragya Prabha
- School of Genetic Engineering, ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, 834010 India
| | - Alok Ranjan
- School of Genetic Engineering, ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, 834010 India
| | - Rakesh K. Chahota
- Department of Agricultural Biotechnology, Choudhary Sarwan Kumar Himachal Pradesh Agricultural University, Palampur, 176061 India
| | - Tilak Raj Sharma
- School of Genetic Engineering, ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, 834010 India
| | - Anil Kumar Singh
- School of Genetic Engineering, ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, 834010 India
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
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4
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Gnat S, Łagowski D, Nowakiewicz A, Trościańczyk A, Dyląg M. New Reference Genes for qRT-PCR Analysis as a Potential Target for Identification of Trichophyton verrucosum in Different Culture Conditions. Pathogens 2021; 10:pathogens10111361. [PMID: 34832515 PMCID: PMC8618703 DOI: 10.3390/pathogens10111361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/09/2021] [Accepted: 10/18/2021] [Indexed: 11/17/2022] Open
Abstract
Dermatophytes are a group of filamentous fungi infecting skin, hair, and nails that raise great diagnostic difficulties. qRT-PCR is a reliable technique for quantifying gene expression with increasingly frequent use in mycological diagnostics. Knowledge of genes and molecular markers with potential to be used in the identification of dermatophytes is of great importance for the development of this branch of diagnostics. In this article, the suitability of six candidate reference genes (TUBB, ACTB, ADPRF, RPL2, SDHA, and EEF1A1) was investigated for gene expression analysis in the dermatophyte Trichophyton verrucosum, which was cultured in various mycological media that are commonly used in a diagnostic laboratory, i.e., Sabouraud, potato dextrose, and keratin-supplemented MM-Cove. The different culture conditions are extremely important factors for the growth and physiology of dermatophytes. Gene expression stability was evaluated using geNorm, NormFinder, BestKeeper, and RefFinder algorithms. Regarding the stability of expression, SDHA was the most stable housekeeping gene; hence, this gene is recommended for future qRT-PCR studies on T. verrucosum strains. These results allow us to conclude that the SDHA gene can be an additional good candidate as an identification target in the qRT-PCR technique.
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Affiliation(s)
- Sebastian Gnat
- Department of Veterinary Microbiology, Faculty of Veterinary Medicine, University of Life Sciences, Akademicka 12, 20-033 Lublin, Poland; (A.N.); (A.T.)
- Correspondence: (S.G.); (D.Ł.); Tel.: +48-81-445-60-93 (S.G.); +48-81-445-66-96 (D.Ł.)
| | - Dominik Łagowski
- Department of Veterinary Microbiology, Faculty of Veterinary Medicine, University of Life Sciences, Akademicka 12, 20-033 Lublin, Poland; (A.N.); (A.T.)
- Correspondence: (S.G.); (D.Ł.); Tel.: +48-81-445-60-93 (S.G.); +48-81-445-66-96 (D.Ł.)
| | - Aneta Nowakiewicz
- Department of Veterinary Microbiology, Faculty of Veterinary Medicine, University of Life Sciences, Akademicka 12, 20-033 Lublin, Poland; (A.N.); (A.T.)
| | - Aleksandra Trościańczyk
- Department of Veterinary Microbiology, Faculty of Veterinary Medicine, University of Life Sciences, Akademicka 12, 20-033 Lublin, Poland; (A.N.); (A.T.)
| | - Mariusz Dyląg
- Department of Mycology and Genetics, Faculty of Biological Sciences, University of Wroclaw, 51-148 Wroclaw, Poland;
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Han W, Kong D, Lu Q, Zhang W, Fan Z. Aloperine Inhibits Proliferation and Promotes Apoptosis in Colorectal Cancer Cells by Regulating the circNSUN2/miR-296-5p/STAT3 Pathway. DRUG DESIGN DEVELOPMENT AND THERAPY 2021; 15:857-870. [PMID: 33664565 PMCID: PMC7924259 DOI: 10.2147/dddt.s288473] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/16/2021] [Indexed: 12/14/2022]
Abstract
Background Aloperine can regulate miR-296-5p/Signal Transducer and Activator of Transcription 3 (STAT3) pathway to inhibit the malignant development of colorectal cancer (CRC), but the regulatory mechanism is unclear. This study explored the upstream mechanism of Aloperine in reducing CRC damage from the perspective of the circRNA-miRNA-mRNA regulatory network. Methods After treatment with gradient concentrations of Aloperine (0.1 mmol/L, 0.2 mmol/L, 0.4 mmol/L, 0.8 mmol/L and 1 mmol/L) for 24 hours, changes in CRC cell proliferation and apoptosis were detected by functional experiments. Data of the differential expression of miR-296-5p in CRC patients and healthy people were obtained from Starbase. The effects of Aloperine on 12 differentially expressed circRNAs were detected. The binding of miR-296-5p with NOP2/Sun RNA methyltransferase 2 (circNSUN2) and STAT3 was predicted by TargetScan and confirmed through dual-luciferase experiments. The expressions of circNSUN2, miR-296-5p and STAT3 as well as apoptosis-related genes in CRC cells were detected by qRT-PCR and Western blot as needed. Rescue experiments were conducted to test the regulatory effects of circNSUN2, miR-296-5p and STAT3 on CRC cells. Results Aloperine at a concentration gradient inhibited proliferation and promoted apoptosis in CRC cells. The abnormally low expression of miR-296-5p in CRC could be upregulated by Aloperine. Among the differentially expressed circRNAs in CRC, only circNSUN2 not only targets miR-296-5p, but also can be regulated by Aloperine. The up-regulation of circNSUN2 offset the inhibitory effect of Aloperine on cancer cells. The rescue experiments finally confirmed the regulation of circNSUN2/miR-296-5p/STAT3 axis in CRC cells. Conclusion By regulating the circNSUN2/miR-296-5p/STAT3 pathway, Aloperine prevents the malignant development of CRC cells.
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Affiliation(s)
- Wei Han
- Nanjing University of Chinese Medicine, Nanjing, People's Republic of China.,Chinese Medicine Modernization and Big Data Research Center, Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing, People's Republic of China.,General Surgery Department, Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing, People's Republic of China
| | - Desong Kong
- Chinese Medicine Modernization and Big Data Research Center, Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing, People's Republic of China
| | - Qin Lu
- Proctology Department, Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing, People's Republic of China
| | - Wei Zhang
- Anesthesiology Department, Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing, People's Republic of China
| | - Zhimin Fan
- Proctology Department, Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing, People's Republic of China
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6
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Ciesielska A, Kawa A, Kanarek K, Soboń A, Szewczyk R. Metabolomic analysis of Trichophyton rubrum and Microsporum canis during keratin degradation. Sci Rep 2021; 11:3959. [PMID: 33597693 PMCID: PMC7889620 DOI: 10.1038/s41598-021-83632-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 02/04/2021] [Indexed: 11/12/2022] Open
Abstract
Keratin is important and needed for the growth of dermatophytes in the host tissue. In turn, the ability to invade keratinised tissues is defined as a pivotal virulence attribute of this group of medically important fungi. The host–dermatophyte interaction is accompanied by an adaptation of fungal metabolism that allows them to adhere to the host tissue as well as utilize the available nutrients necessary for their survival and growth. Dermatophyte infections pose a significant epidemiological and clinical problem. Trichophyton rubrum is the most common anthropophilic dermatophyte worldwide and its typical infection areas include skin of hands or feet and nail plate. In turn, Microsporum canis is a zoophilic pathogen, and mostly well known for ringworm in pets, it is also known to infect humans. The aim of the study was to compare the intracellular metabolite content in the T. rubrum and M. canis during keratin degradation using liquid chromatography system coupled with tandem mass spectrometer (LC-MS/MS). The metabolite “fingerprints” revealed compounds associated with amino acids metabolism, carbohydrate metabolism related to the glycolysis and the tricarboxylic acid cycle (TCA), as well as nucleotide and energy metabolism. The metabolites such as kynurenic acid, l-alanine and cysteine in case of T. rubrum as well as cysteine and riboflavin in case of M. canis were detected only during keratin degradation what may suggest that these compounds may play a key role in the interactions of T. rubrum and M. canis with the host tissue. The metabolomic results were completed by qPCR gene expression assay. Our findings suggest that metabolomic analysis of T. rubrum and M. canis growing in culture media that mimic the dermatophyte infection could allow the understanding of processes involved in the pathogenesis of dermatophytes.
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Affiliation(s)
- Anita Ciesielska
- Department of Molecular Microbiology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland.
| | - Anna Kawa
- Department of Molecular Microbiology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Katarzyna Kanarek
- Department of Molecular Microbiology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Adrian Soboń
- Department of Molecular Microbiology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
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Gene expression profiling of protease and non-protease genes in Trichophyton mentagrophytes isolates from dermatophytosis patients by qRT-PCR analysis. Sci Rep 2021; 11:403. [PMID: 33432046 PMCID: PMC7801629 DOI: 10.1038/s41598-020-79839-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 10/06/2020] [Indexed: 11/19/2022] Open
Abstract
Trichophyton mentagrophytes secretes Metallocarboxypeptidase A and B of the M14 family as endoproteases and exoprotease. T. mentagrophytes produce Metalloprotease 3 and 4 which degrades the protein into the short peptides and amino acids. To understand the host fungal relationship and identification of such genes expressed during infection is utmost important. T. mentagrophytes encodes some proteins which are associated with the glyoxylate cycle. The glyoxylate cycle enzymes have been involving in virulence of dermatophytes and their up-regulation during dermatophytes growth on keratin. On comparing the expression level of virulence protease and non-protease genes, we observed, among exoprotease protease genes, Metallocarboxypeptidase B was strongly up regulated (134.6 fold high) followed by Metallocarboxypeptidase A (115.6 fold high) and Di-peptidyl-peptidases V (10.1 fold high), in dermatophytic patients as compared to ATCC strain. Furthermore, among endoprotease, Metalloprotease 4 was strongly up regulated (131.6 fold high) followed by Metalloprotease 3 (16.7 fold high), in clinical strains as compared to T. mentagrophytes ATCC strain. While among non-protease genes, Citrate Synthase was highly expressed (118 fold high), followed by Isocitrate Lyase (101.6 fold high) and Malate Synthase (52.9 fold high). All the studied virulence genes were considered the best suitable ones by geNorm, Best keeper, Norm Finder and Ref finder.
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8
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Liu W, Yuan X, Yuan S, Dai L, Dong S, Liu J, Peng L, Wang M, Tang Y, Xiao Y. Optimal reference genes for gene expression analysis in polyploid of Cyprinus carpio and Carassius auratus. BMC Genet 2020; 21:107. [PMID: 32943013 PMCID: PMC7499967 DOI: 10.1186/s12863-020-00915-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 08/31/2020] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Reference genes are usually stably expressed in various cells and tissues. However, it was reported that the expression of some reference genes may be distinct in different species. In this study, we intend to answer whether the expression of reported traditional reference genes changes or not in the polyploid fish RESULTS: By retrieving the mRNA sequencing data of three different ploidy fish from the NCBI SRA database, we selected 12 candidate reference genes, and examined their expression levels in the 10 tissues and in the four cell lines of three different ploidy fish by real-time PCR. Then, the expression profiles of these 12 candidate reference genes were systematically evaluated by using the software platforms: BestKeeper, NormFinder and geNorm. CONCLUSION The 28S ribosomal protein S5 gene (RPS5) and the ribosomal protein S18 gene (RPS18) are the most suitable reference genes for the polyploid of Cyprinus carpio and Carassius auratus, demonstrated by both of the tissues and the cultured cells.
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Affiliation(s)
- Wenbin Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, P.R. China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, P.R. China
| | - Xiudan Yuan
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, P.R. China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, P.R. China
| | - Shuli Yuan
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, P.R. China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, P.R. China
| | - Liuye Dai
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, P.R. China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, P.R. China
| | - Shenghua Dong
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, P.R. China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, P.R. China
| | - Jinhui Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, P.R. China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, P.R. China
| | - Liangyue Peng
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, P.R. China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, P.R. China
| | - Minmeng Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, P.R. China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, P.R. China
| | - Yi Tang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, P.R. China.,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, P.R. China
| | - Yamei Xiao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, P.R. China. .,College of Life Sciences, Hunan Normal University, Changsha, 410081, Hunan, P.R. China.
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Paryuni AD, Indarjulianto S, Widyarini S. Dermatophytosis in companion animals: A review. Vet World 2020; 13:1174-1181. [PMID: 32801570 PMCID: PMC7396343 DOI: 10.14202/vetworld.2020.1174-1181] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 04/29/2020] [Indexed: 11/17/2022] Open
Abstract
Dermatophytosis, a zoonotic disease, is caused by fungi of three main genera, namely, Micropsorum, Trichophyton, and Epidermophyton. Specific lesions of dermatophyte infections are localized in the face, legs, and/or tail. Skin lesions in infected animals demonstrate localized alopecia, erythema, and crust, which are more commonly known as ringworm. Factors that affect dermatophytosis include the dermatophyte species; virulence factors of the agent; and the immune status, age, and sex of the host. High levels of cortisol and pro-inflammatory cytokines have also been reported to play an important role in dermatophyte infection. This review aims to explore and understand factors that affect dermatophyte infection with an emphasis on the prevalence, clinical signs, pathogenesis, immune response, and the roles of cortisol and cytokines in companion animals infected by a dermatophyte.
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Affiliation(s)
- Alsi Dara Paryuni
- Department of Pathology, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - Soedarmanto Indarjulianto
- Department of Internal Medicine, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - Sitarina Widyarini
- Department of Pathology, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
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Paul S, Singh S, Chakrabarti A, Rudramurthy SM, Ghosh AK. Selection and evaluation of appropriate reference genes for RT-qPCR based expression analysis in Candida tropicalis following azole treatment. Sci Rep 2020; 10:1972. [PMID: 32029802 PMCID: PMC7004996 DOI: 10.1038/s41598-020-58744-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 12/12/2019] [Indexed: 11/09/2022] Open
Abstract
Candida tropicalis arises as one of the predominant non-Candida albicans Candida (NCAC) species causing invasive candidiasis in Asian countries. A rise in reports of C. tropicalis with a parallel increase in fluconazole resistance has also been observed. The genes and underlying pathways associated with azole antifungal resistance in C. tropicalis is still not properly understood. The RT-qPCR is the most promising approach for expression analysis of target genes to understand the mechanisms of resistance. The reliability and reproducibility of this technique depend on the selection of suitable reference genes for the normalization in expression study. The present study investigated the expression stability levels of ten genes including ACT1, EF1, GAPDH, PGK1, RDN5.8, RDN18, RDN28, SDHA, TUB1, and UBC13 for their suitability in fluconazole treated/untreated C. tropicalis. The stability levels of these genes were examined by the ∆∆CT, ΔCT, Pfaffl methods and five independent software including hkgFinder, geNorm, NormFinder, BestKeeper, and RefFinder software. We report, the EF1 and ACT1 were the most stable reference genes for normalization and can be used for the gene expression analysis in C. tropicalis. To the best of our knowledge, our study is the first to select and validate the reference genes in C. tropicalis for RT-qPCR based expression analysis.
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Affiliation(s)
- Saikat Paul
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, 160012, India
| | - Shreya Singh
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, 160012, India
| | - Arunaloke Chakrabarti
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, 160012, India
| | - Shivaprakash M Rudramurthy
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, 160012, India
| | - Anup K Ghosh
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, 160012, India.
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Ciesielska A, Oleksak B, Stączek P. Reference genes for accurate evaluation of expression levels in Trichophyton interdigitale grown under different carbon sources, pH levels and phosphate levels. Sci Rep 2019; 9:5566. [PMID: 30944363 PMCID: PMC6447595 DOI: 10.1038/s41598-019-42065-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 03/25/2019] [Indexed: 11/11/2022] Open
Abstract
Tinea pedis is a type of dermatophytosis caused by anthropophilic keratinolytic fungi such as Trichophyton interdigitale. Quantitative reverse transcription PCR (RT-qPCR) is a reliable and reproducible technique for measuring changes in target gene expression across various biological conditions. A crucial aspect of accurate normalization is the choice of appropriate internal controls. To identify reference genes for accurate evaluation of expression levels in T. interdigitale, the transcription levels of eight candidate reference genes (adp-rf, β-act, ef1-α, gapdh, psm1, sdha, rpl2 and ubc) and one target gene (Tri m4) were analysed by RT-qPCR after growing the dermatophyte under different environmental conditions. The results obtained from expression stability evaluations with NormFinder, geNorm, BestKeeper, and RefFinder software demonstrated that adp-rf and psm1 were the most stable internal control genes across all experimental conditions. The present study constitutes the first report of the identification and validation of reference genes for RT-qPCR normalization for T. interdigitale grown under different environmental conditions resembling the conditions encountered by fungi during invasion of skin.
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Affiliation(s)
- Anita Ciesielska
- Department of Microbial Genetics, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland.
| | - Beata Oleksak
- Department of Microbial Genetics, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
| | - Paweł Stączek
- Department of Microbial Genetics, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
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Yang Z, Shi Y, Zhang Y, Cheng Q, Li X, Zhao C, Zhang D. Different pathways for 4-n-nonylphenol biodegradation by two Aspergillus strains derived from estuary sediment: Evidence from metabolites determination and key-gene identification. JOURNAL OF HAZARDOUS MATERIALS 2018; 359:203-212. [PMID: 30036750 DOI: 10.1016/j.jhazmat.2018.07.058] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 07/11/2018] [Accepted: 07/12/2018] [Indexed: 06/08/2023]
Abstract
Nonylphenols (NPs) are known as Endocrine Disputing Chemicals (ECDs) and Persistent Organic Pollutants (POPs) and have attracted continuous attention. Biodegradation is one of the effective ways for pollutant removal in aquatic, sedimentary and soil environments. In this study, two estuarine derived fungi strains, NPF2 and NPF3, were screened from Moshui river estuarine sediment and identified as genus Aspergillus. The growth curves of the two strains as well as the removal and degradation rates for 4-n-NP in Potato Dextrose(PD)medium were used to evaluate their degradation ability. Both strains showed high efficiency for 4-n-NP degradation with 86.03% and 98.76% removal rates in 3 days for NPF2 and NPF3, respectively. Determination of degradation intermediates by LC-MS suggested that the mechanisms for 4-n-NP biodegradation by NPF2 and NPF3 are quite different. Some key functional genes for the two strains also provided supplementary evidences for the different biodegradation mechanism. On strain NPF2, with participation of Cox1, 2 and 3, 4-n-NP degradation starts from reaction at the terminal of the long alkyl chain. The chain reduces one carbon atom once within a cycle of hydroxylation, subsequent oxidation at α-C position and decarboxylation. However, on NPF3, with involvement of sMO, Cel7A, Cel7B and ATEG-00639, 4-n-NP degradation starts from benzene ring, converting into fatty acids. The latter bio-pathway was the first time reported for NPs degradation on fungi.
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Affiliation(s)
- Zonglin Yang
- Key Laboratory of Marine Chemistry Theory and Technology (Ocean University of China), Ministry of Education, Qingdao, 266100, Shandong, PR China
| | - Yaqi Shi
- Key Laboratory of Marine Chemistry Theory and Technology (Ocean University of China), Ministry of Education, Qingdao, 266100, Shandong, PR China
| | - Yan Zhang
- Key Laboratory of Marine Chemistry Theory and Technology (Ocean University of China), Ministry of Education, Qingdao, 266100, Shandong, PR China
| | - Qingzheng Cheng
- Forest Products Development Center, Forest Products Lab, School of Forestry and Wildlife Sciences, Auburn University, United States
| | - Xianguo Li
- Key Laboratory of Marine Chemistry Theory and Technology (Ocean University of China), Ministry of Education, Qingdao, 266100, Shandong, PR China.
| | - Chunhong Zhao
- Gaomi Environmental Monitoring Station, Shandong, PR China
| | - Dahai Zhang
- Key Laboratory of Marine Chemistry Theory and Technology (Ocean University of China), Ministry of Education, Qingdao, 266100, Shandong, PR China.
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