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Hao H, Ren X, Ma Z, Chen Z, Yang K, Wang Q, Liu S. Comprehensive analysis of the differential expression of mRNAs, lncRNAs, and miRNAs in Zi goose testis with high and low sperm mobility. Poult Sci 2024; 103:103895. [PMID: 38917609 DOI: 10.1016/j.psj.2024.103895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 05/20/2024] [Accepted: 05/20/2024] [Indexed: 06/27/2024] Open
Abstract
Sperm mobility (SM) is an objective index for measuring sperm motility; however, the mechanisms underlying its regulation in geese remain unclear. The present study sought to elucidate the genetic mechanism underlying SM traits in Zi geese (Anser cygnoides L.). To this end, three successive experiments were performed. In Experiment I, SM was determined in 40 ganders; the 3 ganders with the highest mobility and three with the lowest mobility were assigned to the high and low sperm mobility rank (SMR) groups, respectively. In Experiment II, the differences in fertility between the two SMR groups were assessed within two breeding flocks comprising the selected six ganders from Experiment I and 30 females (each flock had 3 ganders and 15 females). In Experiment III, the testes of the 6 ganders were harvested for histological observation and whole-transcriptome sequencing. Results revealed better fertility, well-developed seminiferous tubules, and abundant mature sperm in the high-SMR-flock compared to those of the low-SMR-flock (89 vs. 81%) (P < 0.05). Differential expression (DE) analysis identified 76 mRNAs, 344 lncRNAs, and 17 miRNAs between the SMR groups, with LOC106049708, XPNPEP3, GNB3, ADCY8, PRKAG3, oha-miR-182-5p, and ocu-miR-10b-5p identified as key mRNAs and miRNAs contributing to SM. Enrichment analysis implicated these DE RNAs in pathways related to ATP binding, cell metabolism, apelin signaling, Wnt signaling, and Adherens junctions. Additionally, competing endogenous RNA (ceRNA) networks comprising 9 DE mRNAs, 17 DE miRNAs, and 169 DE lncRNAs were constructed. Two ceRNA network pathways (LOC106049708-oha-miR-182-5p-MSTRG.2479.6 and PRKAG3-ocu-miR-10b-5p-MSTRG.9047.14) were identified as key regulators of SM in geese. These findings offer crucial insights into the identification of key genes and ceRNA pathways influencing sperm mobility in geese.
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Affiliation(s)
- Hongrun Hao
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, PR China; Key Laboratory of Exploration and Innovative Utilization of White Goose Germplasm Resources in the Cold Region of Heilongjiang Province, Daqing 163319, PR China
| | - Xiaofang Ren
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, PR China; Key Laboratory of Exploration and Innovative Utilization of White Goose Germplasm Resources in the Cold Region of Heilongjiang Province, Daqing 163319, PR China
| | - Zhigang Ma
- Heilongjiang Academy of Agricultural Sciences, Animal Husbandry Research Institute, Qiqihar 161000, PR China
| | - Zhifeng Chen
- Heilongjiang Academy of Agricultural Sciences, Animal Husbandry Research Institute, Qiqihar 161000, PR China
| | - Kun Yang
- Heilongjiang Academy of Agricultural Sciences, Animal Husbandry Research Institute, Qiqihar 161000, PR China
| | - Qiuju Wang
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, PR China; Key Laboratory of Exploration and Innovative Utilization of White Goose Germplasm Resources in the Cold Region of Heilongjiang Province, Daqing 163319, PR China
| | - Shengjun Liu
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, PR China; Key Laboratory of Exploration and Innovative Utilization of White Goose Germplasm Resources in the Cold Region of Heilongjiang Province, Daqing 163319, PR China.
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Zhang P, Li Q, Wu Y, Zhang Y, Zhang B, Zhang H. Identification of candidate genes that specifically regulate subcutaneous and intramuscular fat deposition using transcriptomic and proteomic profiles in Dingyuan pigs. Sci Rep 2022; 12:2844. [PMID: 35181733 PMCID: PMC8857214 DOI: 10.1038/s41598-022-06868-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 02/08/2022] [Indexed: 12/13/2022] Open
Abstract
Subcutaneous fat and intramuscular fat (IMF) deposition are closely related to meat production and pork quality. Dingyuan pig, as a native pig breed in China, low selection leads to obvious genetic and phenotypic differences in the population. Individuals with extreme fat content in the population are ideal models for studying the mechanism of fat deposition. In this study, we used RNA-Seq and tandem mass tags-based (TMT) proteomics to analyze the key pathways and genes that specifically regulate subcutaneous fat and IMF deposition in Dingyuan pigs. We identified 191 differentially expressed genes (DEGs) and 61 differentially abundant proteins (DAPs) in the high and low back fat thickness (HBF, LBF) groups, 85 DEGs and 12 DAPs were obtained in the high and low intramuscular fat (HIMF, LIMF) groups. The functional analysis showed that the DEGs and DAPs in the backfat groups were mainly involved in carbohydrates, amino acids, and fatty acids metabolism, whereas the IMF groups were involved in the insulin pathway, longevity, and some disease-related pathways. We found 40 candidate genes that might tissue-specifically lipids deposition for subcutaneous and intramuscular fat. Our research provides theoretical reference materials for the improvement of fat deposition traits of local pig breeds in my country.
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Affiliation(s)
- Pan Zhang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - Qinggang Li
- Institute of Animal Sciences and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, Anhui, China
| | - Yijing Wu
- Institute of Animal Sciences and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, Anhui, China
| | - Yawen Zhang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - Bo Zhang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China.
| | - Hao Zhang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China
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Early differential gene expression in beef Longissimus thoracis muscles from carcasses with normal (<5.8) and high (>5.9) ultimate pH. Meat Sci 2019; 153:117-125. [PMID: 30927683 DOI: 10.1016/j.meatsci.2019.03.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 03/03/2019] [Accepted: 03/18/2019] [Indexed: 01/19/2023]
Abstract
The objective of this study was to investigate early postmortem (0.5 h) gene expression in beef Longissimus thoracis (LT) muscles from carcasses with NORMAL (<5.8) and HIGH (>5.9) ultimate pH (pHu). A total of 53 transcripts were differentially expressed (P-value <.05): 40 showed up-regulation and 13 showed down-regulation in HIGH pHu carcasses. Four up-regulated (PDK4, GADD45B, MAOA, METTL21C) genes were confirmed (P < .05) by q-PCR. HIGH pHu samples resulted with lower values in glycolytic potential and AMP-activated protein kinase activity compared to NORMAL at 0.5 and 24 h postmortem (P < .05). Functional pathway analysis showed that calcium transport and GADD45 signaling pathways are associated with the development of HIGH pH meat. Genes involved in stress-related signaling, such as GADD45B, METTL21C and MAOA were overexpressed. These genes are involved in stress signaling that might be affecting Ca2+ transport and oxidative metabolism pathways in HIGH pH muscles.
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Bongiorni S, Gruber CEM, Bueno S, Chillemi G, Ferrè F, Failla S, Moioli B, Valentini A. Transcriptomic investigation of meat tenderness in two Italian cattle breeds. Anim Genet 2016; 47:273-87. [DOI: 10.1111/age.12418] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/13/2015] [Indexed: 12/23/2022]
Affiliation(s)
- S. Bongiorni
- Department for Innovation in Biological, Agro-food and Forest systems, DIBAF; University of Tuscia; via S. Camillo de Lelliss.n.c. Viterbo 01100 Italy
| | - C. E. M. Gruber
- Molecular Digital Diagnostics (MDD); s.r.l., via San Camillo de Lellis Viterbo 01100 Italy
| | - S. Bueno
- Cineca Supercomputing Center; via dei Tizii 6 Rome 00185 Italy
| | - G. Chillemi
- Cineca Supercomputing Center; via dei Tizii 6 Rome 00185 Italy
| | - F. Ferrè
- Cineca Supercomputing Center; via dei Tizii 6 Rome 00185 Italy
- Centre for Molecular Bioinformatics; Biology Department; University of Rome Tor Vergata; Rome Italy
| | - S. Failla
- Consiglio per la Ricerca e la sperimentazione in Agricoltura; Monterotondo Italy
| | - B. Moioli
- Consiglio per la Ricerca e la sperimentazione in Agricoltura; Monterotondo Italy
| | - A. Valentini
- Department for Innovation in Biological, Agro-food and Forest systems, DIBAF; University of Tuscia; via S. Camillo de Lelliss.n.c. Viterbo 01100 Italy
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Yang G, Zhou H, Wang R, Hickford J. Variation in the ovine PRKAG3 gene. Gene 2015; 567:251-4. [PMID: 25967386 DOI: 10.1016/j.gene.2015.05.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 04/08/2015] [Accepted: 05/02/2015] [Indexed: 10/23/2022]
Abstract
The 5'AMP-activated protein kinase (AMPK) is a heterotrimeric enzyme that controls cellular energy homeostasis in response to environmental or nutritional stress. The PRKAG3 gene (PRKAG3) encodes the γ3 subunit of the AMPK. Variation in this gene has been found to be associated with meat quality traits in pigs. In this study, we used polymerase chain reaction-single stranded conformational polymorphism (PCR-SSCP) to investigate variation in exon 3 and exons 4-6 of ovine PRKAG3. In 160 New Zealand Suffolk sheep, two variant sequences (named a and b) were identified in the exon 3 region of the gene and three variant sequences (named A, B and C) were identified in the exon 4-6 region of the gene, respectively. A total of three nucleotide substitutions were revealed and these were located in intron 4, exon 4 and intron 5, respectively. The nucleotide substitution identified in the exon 4 (g.2656 C>T) could nominally lead to an amino acid substitution of tryptophan to arginine at position 230 (R230W) in ovine PRKAG3. In comparison with the PRKAG3 amino acid sequences in other species, this R230W substitution appeared to occur only in sheep. This is the first report of genetic variation in ovine PRKAG3, and the variation found in this study could be functionally important for AMPK activity, which in turn may affect meat quality traits in sheep.
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Affiliation(s)
- Guo Yang
- Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou 730000, China; Gene-Marker Laboratory, Faculty of Agriculture and Life Sciences, P.O. Box 84, Lincoln University, Lincoln 7647, New Zealand
| | - Huitong Zhou
- Gene-Marker Laboratory, Faculty of Agriculture and Life Sciences, P.O. Box 84, Lincoln University, Lincoln 7647, New Zealand
| | - Ruoyu Wang
- Cold and Arid Regions Environmental and Engineering Research Institute, Chinese Academy of Sciences, Lanzhou 730000, China.
| | - Jon Hickford
- Gene-Marker Laboratory, Faculty of Agriculture and Life Sciences, P.O. Box 84, Lincoln University, Lincoln 7647, New Zealand.
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Abstract
AMP-activated kinase (AMPK) is a heterotrimeric complex composed of three subunits and is the core energy sensor of the cell. The AMPK activity is important for survival during periods of stress and starvation and also has implications in type II diabetes, obesity, metabolic syndrome, longevity and cancer, etc. The activation of AMPK is triggered through binding of Adenosine Monophosphate Activated Proteins (AMP) to the Bateman domains of the gamma subunit, leading to increased phosphorylation of the threonine 172 on the alpha subunit by inducing allosteric activation and inhibiting dephosphorylation. AMPK and its subunits have been the focuses of many researchers dealing with genetic and metabolic issues. The study makes a comprehensive review on the structure, function, distribution, enzyme activity, the genetic mutation and other aspects of AMPK and its subunit genes, with the aim to outline main aspects of present researches on AMPK and its subunits in animal genetics.
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Affiliation(s)
- W Y Liu
- Faculty of Scientific and Research, Fuyang Normal College, China
| | - R S Jiang
- Department of Animal Sciences, Anhui Agricultural University, China
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Djari A, Esquerré D, Weiss B, Martins F, Meersseman C, Boussaha M, Klopp C, Rocha D. Gene-based single nucleotide polymorphism discovery in bovine muscle using next-generation transcriptomic sequencing. BMC Genomics 2013; 14:307. [PMID: 23651547 PMCID: PMC3751807 DOI: 10.1186/1471-2164-14-307] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Accepted: 05/01/2013] [Indexed: 01/28/2023] Open
Abstract
Background Genetic information based on molecular markers has increasingly being used in cattle breeding improvement programmes, as a mean to improve conventionally phenotypic selection. Advances in molecular genetics have led to the identification of several genetic markers associated with genes affecting economic traits. Until recently, the identification of the causative genetic variants involved in the phenotypes of interest has remained a difficult task. The advent of novel sequencing technologies now offers a new opportunity for the identification of such variants. Despite sequencing costs plummeting, sequencing whole-genomes or large targeted regions is still too expensive for most laboratories. A transcriptomic-based sequencing approach offers a cheaper alternative to identify a large number of polymorphisms and possibly to discover causative variants. In the present study, we performed a gene-based single nucleotide polymorphism (SNP) discovery analysis in bovine Longissimus thoraci, using RNA-Seq. To our knowledge, this represents the first study done in bovine muscle. Results Messenger RNAs from Longissimus thoraci from three Limousin bull calves were subjected to high-throughput sequencing. Approximately 36–46 million paired-end reads were obtained per library. A total of 19,752 transcripts were identified and 34,376 different SNPs were detected. Fifty-five percent of the SNPs were found in coding regions and ~22% resulted in an amino acid change. Applying a very stringent SNP quality threshold, we detected 8,407 different high-confidence SNPs, 18% of which are non synonymous coding SNPs. To analyse the accuracy of RNA-Seq technology for SNP detection, 48 SNPs were selected for validation by genotyping. No discrepancies were observed when using the highest SNP probability threshold. To test the usefulness of the identified SNPs, the 48 selected SNPs were assessed by genotyping 93 bovine samples, representing mostly the nine major breeds used in France. Principal component analysis indicates a clear separation between the nine populations. Conclusions The RNA-Seq data and the collection of newly discovered coding SNPs improve the genomic resources available for cattle, especially for beef breeds. The large amount of variation present in genes expressed in Limousin Longissimus thoracis, especially the large number of non synonymous coding SNPs, may prove useful to study the mechanisms underlying the genetic variability of meat quality traits.
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Affiliation(s)
- Anis Djari
- INRA, UMR 1313 GABI, Unité Génétique Animale et Biologie Intégrative, Domaine de Vilvert, 78352 Jouy-en-Josas, France
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Jin H, Chen HQ, Qin J, Zhu YJ, Chen H, Chen GW, Xie YN, Pan ZT, Jiao MH, Huang SQ, Chu MX. The Polymorphism in 5 'Regulatory Region and Exon 13 of PRKAG3 Gene and its Distribution Pattern in Different Goat Breeds. ACTA ACUST UNITED AC 2012. [DOI: 10.3923/ajava.2012.568.577] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Kowalewska-Luczak I, Kulig H. Association between polymorphism in bovine PRKAG3 gene and milk production traits. RUSS J GENET+ 2011. [DOI: 10.1134/s1022795411060123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Reardon W, Mullen AM, Sweeney T, Hamill RM. Association of polymorphisms in candidate genes with colour, water-holding capacity, and composition traits in bovine M. longissimus and M. semimembranosus. Meat Sci 2010; 86:270-5. [PMID: 20510534 DOI: 10.1016/j.meatsci.2010.04.013] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2009] [Revised: 03/11/2010] [Accepted: 04/11/2010] [Indexed: 01/08/2023]
Abstract
The objective of this study was to determine the association of single nucleotide polymorphisms (SNP) in selected candidate genes with sensory and technological meat quality traits in commercial cattle. SNP in seven candidate genes were genotyped in 130 crossbred Bos taurus cattle using PCR-RFLP. Reported associations between calpastatin (CAST) and Warner-Bratzler shear force and carboxypeptidase E (CPE) and intra-muscular fat were not confirmed. However, SNP in CAST, amp-activated protein kinase, gamma-3 subunit (PRKAG3), growth hormone receptor (GHR) and stearoyl coA desaturase (SCD) genes were significantly associated with colour traits (p<0.05). The PRKAG3 SNP was additionally associated with cook loss in M. longissimus thoracis et lumborum (p<0.05) and tended towards association in M. semimembranosus (p<0.1). An association with pH was identified for the SCD SNP (p<0.001). The GHR polymorphism was influential on moisture and intra-muscular fat in M. semimembranosus and protein content in both muscles (p<0.05). Only CPE was associated with sensory traits (flavour in M. longissimus, p<0.01).
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Affiliation(s)
- W Reardon
- Teagasc, Ashtown Food Research Centre, Ashtown, Dublin 15, Ireland
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Proszkowiec-Weglarz M, Richards MP, McMurtry JP. Molecular cloning, genomic organization, and expression of three chicken 5'-AMP-activated protein kinase gamma subunit genes. Poult Sci 2006; 85:2031-41. [PMID: 17032841 DOI: 10.1093/ps/85.11.2031] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The 5'-AMP-activated protein kinase (AMPK) plays a key role in regulating cellular energy homeostasis. The AMPK is a heterotrimeric enzyme complex that consists of 1 catalytic (alpha) and 2 regulatory (beta and gamma) subunits. Mutations of the gamma subunit genes are known to affect AMPK functioning. In this study, we characterized the genomic organization and expression of 3 chicken AMPK gamma subunit genes (cPRKAG). Alternative splicing of the second exon of the cPRKAG1 gene resulted in 2 transcript variants that code for predicted proteins of 298 and 276 amino acids. Use of an alternate promoter and alternative splicing of the cPRKAG2 gene resulted in 4 transcript variants that code for predicted proteins of 567, 452, 328, and 158 amino acids. Alternative splicing of exon 3 of the cPRKAG3 gene resulted in the production of "long" and "short" transcript variants that code for predicted proteins of 382 and 378 amino acids, respectively. We found evidence for differential expression of individual gamma subunit gene transcript variants and, in some cases, tissue-specific expression was observed. The cPRKAG subunit genes displayed similar structural features and high sequence homology compared with corresponding mammalian gamma subunit gene homologues.
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Affiliation(s)
- M Proszkowiec-Weglarz
- Growth Biology Laboratory, Animal and Natural Resources Institute, USDA-ARS, Beltsville, MD 20705, USA.
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Tosca L, Chabrolle C, Uzbekova S, Dupont J. Effects of metformin on bovine granulosa cells steroidogenesis: possible involvement of adenosine 5' monophosphate-activated protein kinase (AMPK). Biol Reprod 2006; 76:368-78. [PMID: 17123942 DOI: 10.1095/biolreprod.106.055749] [Citation(s) in RCA: 131] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
In mammals, IGFs are important for the proliferation and steroidogenesis of ovarian cells. Metformin is an insulin sensitizer molecule used for the treatment of the infertility of women with polycystic ovary syndrome. It is, however, unclear whether metformin acts on ovarian cells. Adenosine 5' monophosphate-activated protein kinase (AMPK) is involved in metformin action in various cell types. We investigated the effects of metformin on bovine granulosa cell steroidogenesis in response to IGF1 and FSH, and studied AMPK in bovine ovaries. In granulosa cells from small follicles, metformin (10 mM) reduced production of both progesterone and estradiol and decreased the abundance of HSD3B, CYP11A1, and STAR proteins in presence or absence of FSH (10(-8) M) and IGF1 (10(-8) M). In cows, the different subunits of AMPK are expressed in various ovarian cells including granulosa and theca cells, corpus luteum, and oocytes. In bovine granulosa cells from small follicles, metformin, like AICAR (1 mM) a pharmaceutical activator of AMPK, increased phosphorylation of both Thr172 of AMPK alpha and Ser 79 of ACACA (Acetyl-CoA Carboxylase). Both metformin and AICAR treatment reduced progesterone and estradiol secretion in presence or absence of FSH and IGF1. Metformin decreased phosphorylation levels of MAPK3/MAPK1 and MAPK14 in a dose- and time-dependent manner. The adenovirus-mediated production of dominant negative AMPK abolished the effects of metformin on secretion of progesterone and estradiol and on MAPK3/MAPK1 phosphorylation but not on MAPK14 phosphorylation. Thus, in bovine granulosa cells, metformin decreases steroidogenesis and MAPK3/MAPK1 phosphorylation through AMPK activation.
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Affiliation(s)
- Lucie Tosca
- Unité de Physiologie de la Reproduction et des Comportements, Institut National de la Recherche Agronomique, 37380 Nouzilly, France
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Revisiting the conversion of muscle into meat and the underlying mechanisms. Meat Sci 2006; 74:44-58. [DOI: 10.1016/j.meatsci.2006.05.010] [Citation(s) in RCA: 240] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2006] [Revised: 04/27/2006] [Accepted: 05/08/2006] [Indexed: 01/25/2023]
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