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Development of a 3':5' digital PCR assay to determine horse mRNA integrity. Anal Biochem 2021; 626:114217. [PMID: 33939972 DOI: 10.1016/j.ab.2021.114217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 04/16/2021] [Accepted: 04/18/2021] [Indexed: 10/21/2022]
Abstract
Accurate tools to measure RNA integrity are essential to obtain reliable gene expression data. The reverse transcription quantitative PCR (RT-qPCR) based 3':5' assay permits a direct determination of messenger RNA (mRNA) integrity. However, the use of standard curves and the possible effect of PCR inhibitors make this method cumbersome and prone to variation, especially in small samples. Here we developed a triplex digital PCR (dPCR) 3':5' assay for assessing RNA integrity in equine samples as rapid and simple alternative to RT-qPCR. This dPCR assay not only provides a straight forward analysis of the mRNA integrity, but also of its quantity.
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Hendriks WK, Colleoni S, Galli C, Paris DBBP, Colenbrander B, Stout TAE. Mitochondrial DNA replication is initiated at blastocyst formation in equine embryos. Reprod Fertil Dev 2019; 31:570-578. [PMID: 30423285 DOI: 10.1071/rd17387] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Accepted: 09/13/2018] [Indexed: 11/23/2022] Open
Abstract
Intracytoplasmic sperm injection is the technique of choice for equine IVF and, in a research setting, 18-36% of injected oocytes develop to blastocysts. However, blastocyst development in clinical programs is lower, presumably due to a combination of variable oocyte quality (e.g. from old mares), suboptimal culture conditions and marginal fertility of some stallions. Furthermore, mitochondrial constitution appears to be critical to developmental competence, and both maternal aging and invitro embryo production (IVEP) negatively affect mitochondrial number and function in murine and bovine embryos. The present study examined the onset of mitochondrial (mt) DNA replication in equine embryos and investigated whether IVEP affects the timing of this important event, or the expression of genes required for mtDNA replication (i.e. mitochondrial transcription factor (TFAM), mtDNA polymerase γ subunit B (mtPOLB) and single-stranded DNA binding protein (SSB)). We also investigated whether developmental arrest was associated with low mtDNA copy number. mtDNA copy number increased (P<0.01) between the early and expanded blastocyst stages both invivo and invitro, whereas the mtDNA:total DNA ratio was higher in invitro-produced embryos (P=0.041). Mitochondrial replication was preceded by an increase in TFAM but, unexpectedly, not mtPOLB or SSB expression. There was no association between embryonic arrest and lower mtDNA copy numbers.
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Affiliation(s)
- W Karin Hendriks
- Department of Equine Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 114, 3584CM Utrecht, Netherlands
| | - Silvia Colleoni
- Avantea, Laboratorio di Technologie della Riproduzione, Via Porcellasco 7f, 26100 Cremona, Italy
| | - Cesare Galli
- Avantea, Laboratorio di Technologie della Riproduzione, Via Porcellasco 7f, 26100 Cremona, Italy
| | - Damien B B P Paris
- Discipline of Biomedical Science, College of Public Health, Medical and Veterinary Sciences, James Cook University, Solander Drive, Townsville, Qld 4811, Australia
| | - Ben Colenbrander
- Department of Equine Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 114, 3584CM Utrecht, Netherlands
| | - Tom A E Stout
- Department of Equine Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 114, 3584CM Utrecht, Netherlands
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Ramsauer AS, Kubacki J, Favrot C, Ackermann M, Fraefel C, Tobler K. RNA-seq analysis in equine papillomavirus type 2-positive carcinomas identifies affected pathways and potential cancer markers as well as viral gene expression and splicing events. J Gen Virol 2019; 100:985-998. [PMID: 31084699 DOI: 10.1099/jgv.0.001267] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Equine papillomavirus type 2 (EcPV2) was discovered only recently, but it is found consistently in the context of genital squamous cell carcinomas (SCCs). Since neither cell cultures nor animal models exist, the characterization of this potential disease agent relies on the analysis of patient materials. To analyse the host and viral transcriptome in EcPV2-affected horses, genital tissue samples were collected from horses with EcPV2-positive lesions as well as from healthy EcPV2-negative horses. It was determined by RNA-seq analysis that there were 1957 differentially expressed (DE) host genes between the SCC and control samples. These genes were most abundantly related to DNA replication, cell cycle, extracellular matrix (ECM)-receptor interaction and focal adhesion. By comparison to other cancer studies, MMP1 and IL8 appeared to be potential marker genes for the development of SCCs. Analysis of the viral reads revealed the transcriptional activity of EcPV2 in all SCC samples. While few reads mapped to the structural viral genes, the majority of reads mapped to the non-structural early (E) genes, in particular to E6, E7 and E2/E4. Within these reads a distinct pattern of splicing events, which are essential for the expression of different genes in PV infections, was observed. Additionally, in one sample the integration of EcPV2 DNA into the host genome was detected by DNA-seq and confirmed by PCR. In conclusion, while host MMP1 and IL8 expression and the presence of EcPV2 may be useful markers in genital SCCs, further research on EcPV2-related pathomechanisms may focus on cell cycle-related genes, the viral genes E6, E7 and E2/E4, and integration events.
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Affiliation(s)
- Anna Sophie Ramsauer
- 2 Dermatology Department, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland.,1 Institute of Virology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Jakub Kubacki
- 1 Institute of Virology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Claude Favrot
- 2 Dermatology Department, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Mathias Ackermann
- 1 Institute of Virology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Cornel Fraefel
- 1 Institute of Virology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Kurt Tobler
- 1 Institute of Virology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
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Hendriks WK, Colleoni S, Galli C, Paris DBBP, Colenbrander B, Roelen BAJ, Stout TAE. Maternal age and in vitro culture affect mitochondrial number and function in equine oocytes and embryos. Reprod Fertil Dev 2017; 27:957-68. [PMID: 25881326 DOI: 10.1071/rd14450] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 03/06/2015] [Indexed: 12/12/2022] Open
Abstract
Advanced maternal age and in vitro embryo production (IVP) predispose to pregnancy loss in horses. We investigated whether mare age and IVP were associated with alterations in mitochondrial (mt) DNA copy number or function that could compromise oocyte and embryo development. Effects of mare age (<12 vs ≥12 years) on mtDNA copy number, ATP content and expression of genes involved in mitochondrial replication (mitochondrial transcription factor (TFAM), mtDNA polymerase γ subunit B (mtPOLB) and mitochondrial single-stranded DNA-binding protein (SSB)), energy production (ATP synthase-coupling factor 6, mitochondrial-like (ATP-synth_F6)) and oxygen free radical scavenging (glutathione peroxidase 3 (GPX3)) were investigated in oocytes before and after in vitro maturation (IVM), and in early embryos. Expression of TFAM, mtPOLB and ATP-synth-F6 declined after IVM (P<0.05). However, maternal age did not affect oocyte ATP content or expression of genes involved in mitochondrial replication or function. Day 7 embryos from mares ≥12 years had fewer mtDNA copies (P=0.01) and lower mtDNA:total DNA ratios (P<0.01) than embryos from younger mares, indicating an effect not simply due to lower cell number. Day 8 IVP embryos had similar mtDNA copy numbers to Day 7 in vivo embryos, but higher mtPOLB (P=0.013) and a tendency to reduced GPX3 expression (P=0.09). The lower mtDNA number in embryos from older mares may compromise development, but could be an effect rather than cause of developmental retardation. The general down-regulation of genes involved in mitochondrial replication and function after IVM may compromise resulting embryos.
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Affiliation(s)
- W Karin Hendriks
- Department of Equine Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 114, 3584 CM Utrecht, The Netherlands
| | - Silvia Colleoni
- Avantea, Laboratorio di Tecnologie della Riproduzione, Via Porcellasco 7f, 26100 Cremona, Italy
| | - Cesare Galli
- Avantea, Laboratorio di Tecnologie della Riproduzione, Via Porcellasco 7f, 26100 Cremona, Italy
| | - Damien B B P Paris
- Department of Equine Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 114, 3584 CM Utrecht, The Netherlands
| | - Ben Colenbrander
- Department of Equine Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 114, 3584 CM Utrecht, The Netherlands
| | - Bernard A J Roelen
- Department of Equine Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 114, 3584 CM Utrecht, The Netherlands
| | - Tom A E Stout
- Department of Equine Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 114, 3584 CM Utrecht, The Netherlands
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Azarpeykan S, Dittmer KE. Evaluation of housekeeping genes for quantitative gene expression analysis in the equine kidney. J Equine Sci 2016; 27:165-168. [PMID: 27974876 PMCID: PMC5155135 DOI: 10.1294/jes.27.165] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 09/01/2016] [Indexed: 02/01/2023] Open
Abstract
Housekeeping genes (HKGs) are used as internal controls for normalising and calculating the relative expression of target genes in RT-qPCR experiments. There
is no unique universal HKG and HKGs vary among organisms and tissues, so this study aimed to determine the most stably expressed HKGs in the equine kidney. The
evaluated HKGs included 18S ribosomal RNA (18S), 28S ribosomal RNA (28S), ribosomal protein L32 (RPL32), β-2-microglobulin (B2M), glyceraldehyde-3-phosphate
dehydrogenase (GAPDH), succinate dehydrogenase complex (SDHA), zeta polypeptide (YWHAZ), and hypoxanthine phosphoribosyltransferase 1 (HPRT1). The HKGs
expression stability data were analysed with two software packages, geNorm and NormFinder. The lowest stability values for geNorm suggests that YWHAZ and HPRT1
would be most optimal (M=0.31 and 0.32, respectively). Further, these two genes had the best pairwise stability value using NormFinder (geNorm V=0.085).
Therefore, these two genes were considered the most useful for RT-qPCR studies in equine kidney.
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Affiliation(s)
- Sara Azarpeykan
- Institute of Veterinary, Animal and Biomedical Science, Massey University, Palmerston North 4442, New Zealand
| | - Keren E Dittmer
- Institute of Veterinary, Animal and Biomedical Science, Massey University, Palmerston North 4442, New Zealand
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Mohammadi-Sangcheshmeh A, Held E, Rings F, Ghanem N, Salilew-Wondim D, Tesfaye D, Sieme H, Schellander K, Hoelker M. Developmental competence of equine oocytes: impacts of zona pellucida birefringence and maternally derived transcript expression. Reprod Fertil Dev 2015; 26:441-52. [PMID: 23622680 DOI: 10.1071/rd12303] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Accepted: 02/22/2013] [Indexed: 12/14/2022] Open
Abstract
In the present study, equine oocytes were classified into groups of presumably high and low developmental competence according to cumulus morphology, as well as oocyte ability to metabolise brilliant cresyl blue (BCB) stain. All oocytes were evaluated individually in terms of morphometry, zona pellucida birefringence (ZPB) and relative abundance of selected candidate genes. Oocytes with an expanded cumulus (Ex), representing those with presumably high developmental competence, had a significantly thicker zona (18.2 vs 17.3µm) and a significantly higher ZPB (64.6 vs 62.1) than oocytes with a compacted cumulus (Cp). Concurrently, oocytes classified as highly developmentally competent (BCB+) had a significantly thicker zona (18.8 vs 16.1µm) and significantly higher ZPB (63.1 vs 61.3) compared with oocytes classified as having low developmental competence. Expression of TFAM, STAT3 and CKS2 was significantly higher in Ex compared with Cp oocytes, whereas expression of COX1, ATPV6E and DNMT1 was lower. Together, the data reveal that developmentally competent equine oocytes are larger in size, have higher ZPB values and exhibit a typical genetic signature of maternally derived transcripts compared with oocytes with lower in vitro developmental competence.
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Affiliation(s)
- Abdollah Mohammadi-Sangcheshmeh
- Institute of Animal Science, Animal Breeding and Husbandry Group, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany
| | - Eva Held
- Institute of Animal Science, Animal Breeding and Husbandry Group, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany
| | - Franca Rings
- Institute of Animal Science, Animal Breeding and Husbandry Group, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany
| | - Nasser Ghanem
- Animal Production Department, Faculty of Agriculture, Cairo University, 12613 Giza, Egypt
| | - Dessie Salilew-Wondim
- Institute of Animal Science, Animal Breeding and Husbandry Group, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany
| | - Dawit Tesfaye
- Institute of Animal Science, Animal Breeding and Husbandry Group, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany
| | - Harald Sieme
- Clinic for Horses, Unit of Reproductive Medicine of Clinics, University of Veterinary Medicine Hannover Foundation, 30559 Hannover, Germany
| | - Karl Schellander
- Institute of Animal Science, Animal Breeding and Husbandry Group, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany
| | - Michael Hoelker
- Institute of Animal Science, Animal Breeding and Husbandry Group, University of Bonn, Endenicher Allee 15, 53115 Bonn, Germany
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Jeong JK, Kang MH, Gurunathan S, Cho SG, Park C, Seo HG, Kim JH. Evaluation of reference genes in mouse preimplantation embryos for gene expression studies using real-time quantitative RT-PCR (RT-qPCR). BMC Res Notes 2014; 7:675. [PMID: 25256308 PMCID: PMC4181407 DOI: 10.1186/1756-0500-7-675] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Accepted: 09/05/2014] [Indexed: 01/26/2023] Open
Abstract
Background Real-time quantitative reverse-transcriptase polymerase chain reaction (RT-qPCR) is the most sensitive, and valuable technique for rare mRNA detection. However, the expression profiles of reference genes under different experimental conditions, such as different mouse strains, developmental stage, and culture conditions have been poorly studied. Results mRNA stability of the actb, gapdh, sdha, ablim, ywhaz, sptbn, h2afz, tgfb1, 18 s and wrnip genes was analyzed. Using the NormFinder program, the most stable genes are as follows: h2afz for the B6D2F-1 and C57BL/6 strains; sptbn for ICR; h2afz for KOSOM and CZB cultures of B6D2F-1 and C57BL/6 strain-derived embryos; wrnip for M16 culture of B6D2F-1 and C57BL/6 strain-derived embryos; ywhaz, tgfb1, 18 s, 18 s, ywhaz, and h2afz for zygote, 2-cell, 4-cell, 8-cell, molular, and blastocyst embryonic stages cultured in KSOM medium, respectively; h2afz, wrnip, wrnip, h2afz, ywhaz, and ablim for zygote, 2-cell, 4-cell, 8-cell, molular, and blastocyst stage embryos cultured in CZB medium, respectively; 18 s, h2afz, h2afz, actb, h2afz, and wrnip for zygote, 2-cell, 4-cell, 8-cell, molular, and blastocyst stage embryos cultured in M16 medium, respectively. Conclusions These results demonstrated that candidate reference genes for normalization of target gene expression using RT-qPCR should be selected according to mouse strains, developmental stage, and culture conditions. Electronic supplementary material The online version of this article (doi:10.1186/1756-0500-7-675) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | - Jin-Hoi Kim
- Department of Animal Biotechnology, KonKuk University, Seoul 143-701, Republic of Korea.
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Gu Y, Shen X, Zhou D, Wang Z, Zhang N, Shan Z, Jin L, Lei L. Selection and expression profiles of reference genes in mouse preimplantation embryos of different ploidies at various developmental stages. PLoS One 2014; 9:e98956. [PMID: 24927500 PMCID: PMC4057156 DOI: 10.1371/journal.pone.0098956] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 05/09/2014] [Indexed: 12/21/2022] Open
Abstract
Real-time reverse transcription quantitative polymerase chain reaction (qPCR) has become the most frequently used system for studies of gene expression. Manystudies have provided reliable evidence that the transcription levels of reference genes are not constant at different developmental stages and in different experimental conditions. However, suitable reference genes which are stably expressed in polyploid preimplantation embryos of different developmental stages have not yet been identified. Therefore, it is critical to verify candidate reference genes to analyze gene expression accurately in both diploid and polyploid embryos. We examined the expression levels of 12 candidate reference genes in preimplantation embryos of four different ploidies at six developmental stages. Stability analysis of the reference genes was performed by four independent software programs, and the stability of three genes was evaluated by comparison with the Oct4 expression level during preimplantation development in diploid embryos. The expression levels of most genes in the polyploid embryos were higher than that in the diploid embryos, but the increasing degree were disproportionate with the ploidies. There were no significant difference in reference gene expressions among embryos of different ploidies when they reached the morula stage, and the expression level remained flat until the blastocyst stage. Ubc, Ppia, and Pgk1 were the three most stable reference genes in diploid and polyploid embryos.
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Affiliation(s)
- Yanli Gu
- Department of Histology and Embryology, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Xinghui Shen
- Department of Histology and Embryology, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Dongjie Zhou
- Department of Histology and Embryology, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Zhendong Wang
- Department of Histology and Embryology, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Na Zhang
- Department of Histology and Embryology, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Zhiyan Shan
- Department of Histology and Embryology, Harbin Medical University, Harbin, Heilongjiang Province, China
| | - Lianhong Jin
- Department of Histology and Embryology, Harbin Medical University, Harbin, Heilongjiang Province, China
- * E-mail: (LL); (LJ)
| | - Lei Lei
- Department of Histology and Embryology, Harbin Medical University, Harbin, Heilongjiang Province, China
- * E-mail: (LL); (LJ)
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O'Connor T, Wilmut I, Taylor J. Quantitative Evaluation of Reference Genes for Real-Time PCR DuringIn VitroMaturation of Ovine Oocytes. Reprod Domest Anim 2012; 48:477-83. [DOI: 10.1111/rda.12112] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2012] [Accepted: 09/17/2012] [Indexed: 12/18/2022]
Affiliation(s)
- T O'Connor
- MRC Centre for Regenerative Medicine; The University of Edinburgh; Edinburgh; UK
| | - I Wilmut
- MRC Centre for Regenerative Medicine; The University of Edinburgh; Edinburgh; UK
| | - J Taylor
- MRC Centre for Regenerative Medicine; The University of Edinburgh; Edinburgh; UK
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Mohammadi-Sangcheshmeh A, Held E, Ghanem N, Rings F, Salilew-Wondim D, Tesfaye D, Sieme H, Schellander K, Hoelker M. G6PDH-activity in equine oocytes correlates with morphology, expression of candidate genes for viability, and preimplantative in vitro development. Theriogenology 2011; 76:1215-26. [PMID: 21820165 DOI: 10.1016/j.theriogenology.2011.05.025] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2011] [Revised: 05/17/2011] [Accepted: 05/19/2011] [Indexed: 11/28/2022]
Abstract
Efficiencies for in vitro production of equine embryos are still low due to highly variable developmental competences of equine immature oocytes. In contrast to the equine, in vitro developmental competence of immature oocytes has been predicted successfully by the activity of glucose-6-phosphate dehydrogenase (G6PDH) indicated by brilliant cresyl blue (BCB) dye in a range of different species. Therefore, the aim of the present study was to test the association between G6PDH activity in equine oocytes with: (1) cumulus morphology and oocyte properties in terms of diameter and volume; (2) maturational competence; (3) gene expression of certain molecular markers; and (4) in vitro embryo development after intracytoplasmic sperm injection. Equine oocytes were exposed to BCB stain and were classified as BCB+ or BCB- according to their ability to convert the dye from blue to colorless. Additionally, BCB+ and BCB- oocytes were subclassified as having a compact (Cp) or expanded (Ex) cumulus complex. As a result, BCB+ oocytes had a greater proportion of expanded cumulus oocyte complexes compared with BCB- oocytes (71.2% vs. 49.5%). Moreover, we observed a significant difference in oocyte diameter and volume between BCB+ and BCB- oocytes irrespective of cumulus morphology. BCB+ oocytes reached a higher maturation rate compared with BCB- oocytes (59.0% vs. 28.7%). Regarding the analyzed candidate genes, relative transcript abundance was significantly different for nine genes. The expression of eight genes was significantly higher (P < 0.05) for BCB+ oocytes, including ATPV6E, IF-3, TFAM, DNMT1, STAT3, Aurora-A, ODC1, and CKS2 whereas BCB- oocytes showed higher in expression of COX1. These results are in line with the observed developmental competence. Cleavage rate (45.9% vs. 29.0%) and percentage of embryos that reached the blastocyst stage (9.2% vs. 1.4%) were significantly higher for embryos derived from BCB+ oocytes compared with BCB- oocytes. In conclusion, the present study provides evidence that G6PDH-activity in immature equine oocytes is a useful predictor for subsequent in vitro developmental competence.
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Affiliation(s)
- A Mohammadi-Sangcheshmeh
- Institute of Animal Science, Animal Breeding and Husbandry Group, University of Bonn, Bonn, Germany
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