1
|
Jiang J, Guo L, Huang X, Zheng K, He S, Shan H. Regulatory role of N6-Methyladenosine on skeletal muscle development in Hu sheep. Front Genet 2024; 15:1449144. [PMID: 39233739 PMCID: PMC11371687 DOI: 10.3389/fgene.2024.1449144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Accepted: 08/05/2024] [Indexed: 09/06/2024] Open
Abstract
N6-Methyladenosine (m6A) RNA modification plays an essential role in many biological processes. To investigate the regulatory role of m6A on the skeletal muscle development in Hu sheep, this study took newborn Hu sheep (b_B Group) and six-month-old Hu sheep (s_B Group) as the objects. MeRIP-seq and RNA-Seq analysis techniques were used to detect differentially methylated genes (DMGs) and differentially expressed genes (DEGs) in the longissimus dorsi muscle of Hu sheep at different months of age. Then, conjoint analysis was further employed to screen for key genes involved in skeletal muscle development that are modified by m6A and expressed by mRNA. According to the results of the MeRIP-seq analysis, there were 285 m6A differentially methylated peaks (DMPs) in total between b_B Group and s_B Group, with 192 significant upregulated peaks and 93 significant downregulated peaks. GO and KEGG analysis revealed that DMGs are mainly enriched in actin-binding, cellular transport, and metabolic pathways. According to the results of the RNA-seq analysis, there were 4,349 DEGs in total between b_B Group and s_B Group, with 2010 upregulated genes and 2,339 downregulated genes. DEGs are found to be mainly enriched in the regulation of actin cytoskeleton tissue, AMPK and FoxO signaling pathways, etc. The conjoint analysis demonstrated that 283 genes were both modified by m6A and expressed by mRNA. Among them, three genes relevant to muscle growth (RGMB, MAPK8IP3, and RSPO3) were selected as candidates for quantitative validation, and the results were in line with the sequencing results. The results mentioned above all suggest that m6A plays a certain role in the skeletal muscle development in Hu sheep.
Collapse
Affiliation(s)
- Junfang Jiang
- Institute of Animal Husbandry and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Liangyong Guo
- Huzhou Agricultural Science and Technology Development Center, Institute of animal Science, Huzhou, China
- Huzhou Key Laboratory of Innovation and Application of Agricultural Germplasm Resources, Huzhou, China
| | - Xin Huang
- Institute of Animal Husbandry and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Kaizhi Zheng
- Institute of Animal Husbandry and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Sangang He
- Institute of Animal Husbandry and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Huili Shan
- Institute of Animal Husbandry and Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| |
Collapse
|
2
|
Vasu M, Ahlawat S, Choudhary V, Kaur R, Arora R, Sharma R, Sharma U, Chhabra P, Mir MA, Kumar Singh M. Identification and validation of stable reference genes for expression profiling of target genes in diverse ovine tissues. Gene 2024; 897:148067. [PMID: 38092161 DOI: 10.1016/j.gene.2023.148067] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 12/05/2023] [Indexed: 12/18/2023]
Abstract
Quantitative PCR (qPCR) is a widely-used technique for quantifying the expression of target genes across various tissues, as well as under different pathological and physiological conditions. One of the challenges associated with this method is the need to identify optimal reference genes (RGs) that maintain consistent expression levels under diverse experimental settings, thereby ensuring accurate biological interpretation. In this study, we conducted a thorough analysis of 18 candidate RGs (ACTB, BACH1, B2M, GAPDH, HMBS, HPRT1, PGK1, PPIA, PPIB, RPLP0, RPL19, RPS9, RPS15, RPS28, SDHA, TBP, UXT, and YWHAZ) across 10 ovine tissues (muscle, skin, kidney, liver, intestine, rumen, lung, testis, heart, and spleen) obtained from five individual sheep. We aimed to identify genes with stable expression across these tissues. A literature-based survey helped us shortlist candidate genes representing various functional classes from multiple livestock species. We employed four algorithms: geNorm, NormFinder, BestKeeper, and Delta Ct (ΔCt), to rank these genes based on their stability. A consistent trend in the rankings was observed across these different algorithms. RefFinder was then used for a comprehensive ranking, integrating the outputs from the various methods. ACTB, PPIB, BACH1, and B2M emerged as the most stable RGs, while RPS9, RPS15, and PGK1 displayed variable expression. We validated our findings through qPCR analysis of four target genes (ACTN2, CRYAB, DLK1, and TRIM54) in the skin samples from two different sheep breeds. Based on these results, we recommend ACTB, PPIB, BACH1, and B2M as reliable internal control genes for qPCR experiments involving diverse ovine tissues.
Collapse
Affiliation(s)
- Mahanthi Vasu
- ICAR-National Bureau of Animal Genetic Resources, Karnal; ICAR-National Dairy Research Institute, Karnal
| | - Sonika Ahlawat
- ICAR-National Bureau of Animal Genetic Resources, Karnal.
| | - Vikas Choudhary
- District Disease Diagnostic Laboratory, Karnal, Department of Animal Husbandry and Dairying, Haryana
| | - Rashmeet Kaur
- ICAR-National Bureau of Animal Genetic Resources, Karnal
| | - Reena Arora
- ICAR-National Bureau of Animal Genetic Resources, Karnal
| | - Rekha Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal
| | - Upasna Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal
| | - Pooja Chhabra
- ICAR-National Bureau of Animal Genetic Resources, Karnal
| | - M A Mir
- Mountain Research Centre for Sheep and Goat, Shuhama (Aulestang), SKUAST-Kashmir
| | | |
Collapse
|
3
|
Chen J, Chen Z, Zhang J, Zhuang W, Zheng X. Screening of reliable reference genes for the normalization of RT-qPCR in chicken gastrointestinal tract. Poult Sci 2023; 102:103169. [PMID: 37918133 PMCID: PMC10641542 DOI: 10.1016/j.psj.2023.103169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/04/2023] [Accepted: 10/06/2023] [Indexed: 11/04/2023] Open
Abstract
The application of reverse transcription quantitative real-time PCR technology for the production of gene tissue expression profiles is a widely employed approach in molecular biology research. It is imperative to ascertain internal reference genes that exhibit stable expression across diverse tissues to ensure the precision of tissue gene expression profiles. While there have been studies documenting the most suitable reference genes for various tissues in chickens, there is a dearth of research on the identification of reference genes in the gastrointestinal (GI) tract of chickens. This study utilized 4 different algorithms (Delta CT, BestKeeper, NormFinder, and Genorm) to assess the stability of 19 internal reference genes in various GI tract tissues, including individual GI tract tissues, the anterior and posterior GI tract, and the entire GI tissue. The RefFinder software was employed to comprehensively rank these genes. The research findings successfully identified the most appropriate internal reference genes for each type of GI tissue. Furthermore, TBP, DNAJC24, Polr2b, RPL13, andAp2m exhibited stable expression in the entire and posterior GI tract, whereas HMBS, TBP, Ap2m, GUSB, DNAJC24, and RPL13 demonstrated stable expression in the anterior GI tract. However, the internal reference genes commonly utilized, namely β-Actin, 18s RNA, and ALB, exhibit poor stability and are not advised for future investigations concerning gene expression in the GI region. Consequently, MUC2 and CDX1, 2 genes that specifically express in the gut, were chosen for examination to ascertain the stability of the aforementioned internal reference genes in this particular study. In summary, this study presents a relatively stable set of internal reference genes that can be employed to enhance the precision of quantifying mRNA expression levels in functional genes within the chicken GI tract.
Collapse
Affiliation(s)
- Jianfei Chen
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Ziwei Chen
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Jilong Zhang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Wuchao Zhuang
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Xiaotong Zheng
- School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China.
| |
Collapse
|
4
|
Christodoulou C, Skourtis A, Kyriakaki P, Satolias FF, Karabinas D, Briche M, Salah N, Zervas G, Mavrommatis A, Tsiplakou E. The Effect of Dietary Supplementation with Probiotic and Postbiotic Yeast Products on Ewes Milk Performance and Immune Oxidative Status. J Fungi (Basel) 2023; 9:1139. [PMID: 38132740 PMCID: PMC10744422 DOI: 10.3390/jof9121139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 12/23/2023] Open
Abstract
The administration of yeast products as feed additives has been proven to beneficially affect animal productivity through energy, oxidative, and immune status improvement. This study evaluated a combination of Saccharomyces cerevisiae live yeast (LY) with yeast postbiotics (rich in mannan-oligosaccharides (MOS) and beta-glucans) and selenium (Se)-enriched yeast on ewes' milk performance and milk quality, energy and oxidative status, and gene expression related to their immune system during the peripartum period. Ewes were fed a basal diet (BD; F:C = 58:42 prepartum and 41:59 postpartum) including inorganic Se (CON; n = 27), the BD supplemented with a LY product, and inorganic Se (AC; n = 29), as well as the combination of the LY, a product of yeast fraction rich in MOS and beta-glucans, and organic-Se-enriched yeast (ACMAN; n = 26) from 6 weeks prepartum to 6 weeks postpartum. The β-hydroxybutyric acid concentration in the blood of AC and ACMAN ewes was lower (compared to the CON) in both pre- and postpartum periods (p < 0.010). Postpartum, milk yield was increased in the AC and ACMAN Lacaune ewes (p = 0.001). In addition, the activity of superoxide dismutase (p = 0.037) and total antioxidant capacity (p = 0.034) measured via the 2,2-Azino-bis (3-ethylbenzthiazoline-6-sulfonic acid) (ABTS) method was increased in the blood plasma of the ACMAN postpartum. Higher ABTS values were also found (p = 0.021), while protein carbonyls were reduced (p = 0.023) in the milk of the treated groups. The relative transcript levels of CCL5 and IL6 were downregulated in the monocytes (p = 0.007 and p = 0.026 respectively), and those of NFKB were downregulated in the neutrophils of the ACMAN-fed ewes postpartum (p = 0.020). The dietary supplementation of ewes with yeast postbiotics rich in MOS and beta-glucans, and organic Se, improved energy status, milk yield and some milk constituents, and oxidative status, with simultaneous suppression of mRNA levels of proinflammatory genes during the peripartum period.
Collapse
Affiliation(s)
- Christos Christodoulou
- Laboratory of Nutritional Physiology and Feeding, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens, Iera Odos 75, GR-11855 Athens, Greece; (C.C.); (A.S.); (P.K.); (F.F.S.); (D.K.); (G.Z.); (A.M.)
| | - Alexis Skourtis
- Laboratory of Nutritional Physiology and Feeding, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens, Iera Odos 75, GR-11855 Athens, Greece; (C.C.); (A.S.); (P.K.); (F.F.S.); (D.K.); (G.Z.); (A.M.)
| | - Panagiota Kyriakaki
- Laboratory of Nutritional Physiology and Feeding, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens, Iera Odos 75, GR-11855 Athens, Greece; (C.C.); (A.S.); (P.K.); (F.F.S.); (D.K.); (G.Z.); (A.M.)
| | - Fotis Fokion Satolias
- Laboratory of Nutritional Physiology and Feeding, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens, Iera Odos 75, GR-11855 Athens, Greece; (C.C.); (A.S.); (P.K.); (F.F.S.); (D.K.); (G.Z.); (A.M.)
| | - Dimitris Karabinas
- Laboratory of Nutritional Physiology and Feeding, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens, Iera Odos 75, GR-11855 Athens, Greece; (C.C.); (A.S.); (P.K.); (F.F.S.); (D.K.); (G.Z.); (A.M.)
| | - Maxime Briche
- Phileo by Lesaffre, 59700 Marcq en Baroeul, Nord, France; (M.B.); (N.S.)
| | - Nizar Salah
- Phileo by Lesaffre, 59700 Marcq en Baroeul, Nord, France; (M.B.); (N.S.)
| | - George Zervas
- Laboratory of Nutritional Physiology and Feeding, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens, Iera Odos 75, GR-11855 Athens, Greece; (C.C.); (A.S.); (P.K.); (F.F.S.); (D.K.); (G.Z.); (A.M.)
| | - Alexandros Mavrommatis
- Laboratory of Nutritional Physiology and Feeding, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens, Iera Odos 75, GR-11855 Athens, Greece; (C.C.); (A.S.); (P.K.); (F.F.S.); (D.K.); (G.Z.); (A.M.)
| | - Eleni Tsiplakou
- Laboratory of Nutritional Physiology and Feeding, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens, Iera Odos 75, GR-11855 Athens, Greece; (C.C.); (A.S.); (P.K.); (F.F.S.); (D.K.); (G.Z.); (A.M.)
| |
Collapse
|
5
|
Kerschner JL, Paranjapye A, Schacht M, Meckler F, Huang F, Bebek G, Van Wettere AJ, Regouski M, Perisse IV, White KL, Polejaeva IA, Leir SH, Harris A. Transcriptomic analysis of lung development in wildtype and CFTR -/- sheep suggests an early inflammatory signature in the CF distal lung. Funct Integr Genomics 2023; 23:135. [PMID: 37085733 PMCID: PMC10121546 DOI: 10.1007/s10142-023-01050-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/22/2023] [Accepted: 04/03/2023] [Indexed: 04/23/2023]
Abstract
The precise molecular events initiating human lung disease are often poorly characterized. Investigating prenatal events that may underlie lung disease in later life is challenging in man, but insights from the well-characterized sheep model of lung development are valuable. Here, we determine the transcriptomic signature of lung development in wild-type sheep (WT) and use a sheep model of cystic fibrosis (CF) to characterize disease associated changes in gene expression through the pseudoglandular, canalicular, saccular, and alveolar stages of lung growth and differentiation. Using gene ontology process enrichment analysis of differentially expressed genes at each developmental time point, we define changes in biological processes (BP) in proximal and distal lung from WT or CF animals. We also compare divergent BP in WT and CF animals at each time point. Next, we establish the developmental profile of key genes encoding components of ion transport and innate immunity that are pivotal in CF lung disease and validate transcriptomic data by RT-qPCR. Consistent with the known pro-inflammatory phenotype of the CF lung after birth, we observe upregulation of inflammatory response processes in the CF sheep distal lung during the saccular stage of prenatal development. These data suggest early commencement of therapeutic regimens may be beneficial.
Collapse
Affiliation(s)
- Jenny L Kerschner
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Alekh Paranjapye
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Department of Genetics, University of Pennsylvania, Philadelphia, PA, USA
| | - Makayla Schacht
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Frederick Meckler
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Felix Huang
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Gurkan Bebek
- Center for Proteomics and Bioinformatics, Cleveland, OH, USA
- Department of Nutrition, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Arnaud J Van Wettere
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UH, USA
| | - Misha Regouski
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UH, USA
| | - Iuri Viotti Perisse
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UH, USA
| | - Kenneth L White
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UH, USA
| | - Irina A Polejaeva
- Department of Animal, Dairy and Veterinary Sciences, Utah State University, Logan, UH, USA
| | - Shih-Hsing Leir
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Ann Harris
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA.
| |
Collapse
|
6
|
Kyriakaki P, Mavrommatis A, Tsiplakou E. Schizochytrium spp. Dietary Supplementation Modulates Immune-Oxidative Transcriptional Signatures in Monocytes and Neutrophils of Dairy Goats. Antioxidants (Basel) 2023; 12:antiox12020497. [PMID: 36830055 PMCID: PMC9952451 DOI: 10.3390/antiox12020497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/07/2023] [Accepted: 02/15/2023] [Indexed: 02/18/2023] Open
Abstract
The high propensity of dietary polyunsaturated fatty acids (PUFA) to oxidation can induce a cascade of cellular immune-oxidative imbalances. On the other hand, PUFA, namely docosapentaenoic acid (ω6-DPA) and docosahexaenoic acid (DHA) can exert immunomodulatory effects by suppressing a pro-inflammatory response. Thus, the objective of this study was to investigate the effect of dietary supplementation with Schizochytrium spp. levels, rich in both ω6-DPA and DHA on the transcriptional profiling of genes involved in oxidative homeostasis and innate immunity of dairy goats' monocytes and neutrophils. Twenty-four dairy goats were divided into four homogeneous sub-groups; the diet of the control group (CON) had no Schizochytrium spp. while those of the treated groups were supplemented daily with 20 (ALG20), 40 (ALG40), and 60 (ALG60) g/goat/day. The mRNA levels of MGST1 in neutrophils were downregulated (p = 0.037), while in monocytes, SOD2 and SOD3 were downregulated (p = 0.010 and p = 0.044, respectively) in ALG60 compared to the CON group. GPX2 mRNA levels were downregulated (p = 0.036) in ALG20 and ALG60 compared to the CON group in neutrophils. NOX1 was upregulated (p = 0.043) in the neutrophiles of ALG60-goats. NOX2 was upregulated (p = 0.042) in the monocytes of ALG40-fed goats, while higher (p = 0.045) levels were also found in the ALG60 group in neutrophils. The mRNA levels of COX2 were downregulated (p = 0.035) in monocytes of the ALG40 and ALG60 groups. The mRNA levels of PTGER2 were also downregulated (p = 0.004) in monocytes of Schizochytrium-fed goats, while in neutrophils, significant downregulation (p = 0.024) was only found for ALG60 compared to the CON group. ALOX5AP mRNA levels were significantly decreased (p = 0.033) in ALG60 compared to the CON group in monocytes. LTA4H mRNA levels were increased (p = 0.015) in ALG60 compared to ALG20 and ALG40 groups in monocytes, while in neutrophils, a significant downregulation (p = 0.028) was observed in ALG20 compared to the CON group. The inclusion of more than 20 g Schizochytrium spp./day in goats' diet induced imbalances in mechanisms that regulate the antioxidant system, while downregulated the expression of pro-inflammatory pathways in monocytes and neutrophils.
Collapse
|
7
|
Selection of species specific panel of reference genes in peripheral blood mononuclear cells of native livestock species adapted to trans-Himalayan region of Leh-Ladakh. Sci Rep 2022; 12:18473. [PMID: 36323741 PMCID: PMC9630269 DOI: 10.1038/s41598-022-22588-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 10/17/2022] [Indexed: 01/06/2023] Open
Abstract
The identification of appropriate references genes is an integral component of any gene expression-based study for getting accuracy and reliability in data interpretation. In this study, we evaluated the expression stability of 10 candidate reference genes (GAPDH, RPL4, EEF1A1, RPS9, HPRT1, UXT, RPS23, B2M, RPS15, ACTB) in peripheral blood mononuclear cells of livestock species that are adapted to high altitude hypoxia conditions of Leh-Ladakh. A total of 37 PBMCs samples from six native livestock species of Leh-Ladakh region such as Ladakhi cattle, Ladakhi yak, Ladakhi donkey, Chanthangi goat, Double hump cattle and Zanskar ponies were included in this study. The commonly used statistical algorithms such as geNorm, Normfinder, BestKeeper and RefFinder were employed to assess the stability of these RGs in all the livestock species. Our study has identified different panel of reference genes in each species; for example, EEF1A1, RPL4 in Ladakhi cattle; GAPDH, RPS9, ACTB in Ladakhi yak; HPRT1, B2M, ACTB in Ladakhi donkey; HPRT1, B2M, ACTB in Double hump camel, RPS9, HPRT1 in Changthangi goat, HPRT1 and ACTB in Zanskar ponies. To the best of our knowledge, this is the first systematic attempt to identify panel of RGs across different livestock species types adapted to high altitude hypoxia conditions. In future, the findings of the present study would be quite helpful in conducting any transcriptional studies to understand the molecular basis of high altitude adaptation of native livestock population of Leh-Ladakh.
Collapse
|
8
|
Du J, Garcia JP, Bach FC, Tellegen AR, Grad S, Li Z, Castelein RM, Meij BP, Tryfonidou MA, Creemers LB. Intradiscal injection of human recombinant BMP-4 does not reverse intervertebral disc degeneration induced by nuclectomy in sheep. J Orthop Translat 2022; 37:23-36. [PMID: 36196149 PMCID: PMC9513727 DOI: 10.1016/j.jot.2022.08.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 11/03/2022] Open
Abstract
Background Methods Results Conclusion The Translational Potential of This Article
Collapse
|
9
|
The amino acid profile of Camelina sativa seeds correlates with the strongest immune response in dairy ewes. Animal 2022; 16:100621. [DOI: 10.1016/j.animal.2022.100621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 07/20/2022] [Accepted: 07/22/2022] [Indexed: 11/23/2022] Open
|
10
|
Wen X, Yang G, Dong Y, Luo L, Cao B, Mengesha BA, Zu R, Liao Y, Liu C, Li S, Deng Y, Zhang K, Ma X, Huang J, Wang D, Zhao K, Leng P, Luo H. Selection and Validation of Reference Genes for Pan-Cancer in Platelets Based on RNA-Sequence Data. Front Genet 2022; 13:913886. [PMID: 35770000 PMCID: PMC9234127 DOI: 10.3389/fgene.2022.913886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 04/29/2022] [Indexed: 11/13/2022] Open
Abstract
Many studies in recent years have demonstrated that some messenger RNA (mRNA) in platelets can be used as biomarkers for the diagnosis of pan-cancer. The quantitative real-time polymerase chain reaction (RT-qPCR) molecular technique is most commonly used to determine mRNA expression changes in platelets. Accurate and reliable relative RT-qPCR is highly dependent on reliable reference genes. However, there is no study to validate the reference gene in platelets for pan-cancer. Given that the expression of some commonly used reference genes is altered in certain conditions, selecting and verifying the most suitable reference gene for pan-cancer in platelets is necessary to diagnose early stage cancer. This study performed bioinformatics and functional analysis from the RNA-seq of platelets data set (GSE68086). We generated 95 candidate reference genes after the primary bioinformatics step. Seven reference genes (YWHAZ, GNAS, GAPDH, OAZ1, PTMA, B2M, and ACTB) were screened out among the 95 candidate reference genes from the data set of the platelets’ transcriptome of pan-cancer and 73 commonly known reference genes. These candidate reference genes were verified by another platelets expression data set (GSE89843). Then, we used RT-qPCR to confirm the expression levels of these seven genes in pan-cancer patients and healthy individuals. These RT-qPCR results were analyzed using the internal stability analysis software programs (the comparative Delta CT method, geNorm, NormFinder, and BestKeeper) to rank the candidate genes in the order of decreasing stability. By contrast, the GAPDH gene was stably and constitutively expressed at high levels in all the tested samples. Therefore, GAPDH was recommended as the most suitable reference gene for platelet transcript analysis. In conclusion, our result may play an essential part in establishing a molecular diagnostic platform based on the platelets to diagnose pan-cancer.
Collapse
Affiliation(s)
- Xiaoxia Wen
- Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Guishu Yang
- Department of Clinical Laboratory, Guangyuan Central Hospital, Guangyuan, China
| | | | - Liping Luo
- Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Bangrong Cao
- Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Birga Anteneh Mengesha
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Ruiling Zu
- Department of Clinical Laboratory, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Yulin Liao
- Department of Clinical Laboratory, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Chang Liu
- Department of Clinical Laboratory, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Shi Li
- Department of Clinical Laboratory, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Yao Deng
- Department of Clinical Laboratory, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Kaijiong Zhang
- Department of Clinical Laboratory, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Xin Ma
- GenomCan Inc., Chengdu, China
| | - Jian Huang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Dongsheng Wang
- Department of Clinical Laboratory, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Keyan Zhao
- GenomCan Inc., Chengdu, China
- *Correspondence: Keyan Zhao, ; Ping Leng, ; Huaichao Luo,
| | - Ping Leng
- Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- *Correspondence: Keyan Zhao, ; Ping Leng, ; Huaichao Luo,
| | - Huaichao Luo
- Department of Clinical Laboratory, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
- *Correspondence: Keyan Zhao, ; Ping Leng, ; Huaichao Luo,
| |
Collapse
|
11
|
Molecular and Histological Evaluation of Sheep Ovarian Tissue Subjected to Lyophilization. Animals (Basel) 2021; 11:ani11123407. [PMID: 34944182 PMCID: PMC8697944 DOI: 10.3390/ani11123407] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/19/2021] [Accepted: 11/26/2021] [Indexed: 12/18/2022] Open
Abstract
Simple Summary Freeze-drying (or lyophilization) is a method to preserve cells and tissues in which frozen material is dried by sublimation of ice. One of the main advantages is that nitrogen and dry ice are no longer required for the storage and shipment of biological material, which can be kept at room temperature or 4 °C, resulting in enormous reductions in costs. Although widely used to preserve biomolecules and macromolecular assemblies, freeze-drying of cells and tissues is currently experimental. Here, we lyophilized sheep ovarian tissue with a novel device named Darya and assessed effects on tissue integrity and gene expression. We show that ovarian tissue survives lyophilization procedures, maintaining its general structure and reacting to the different experimental steps by regulation of specific genes. Our results contribute to the optimization of protocols to freeze-dry ovarian tissues and may find application in programs of animal and human reproductive tissue preservation. Abstract Cryopreservation is routinely used to preserve cells and tissues; however, long time storage brings many inconveniences including the use of liquid nitrogen. Freeze-drying could enable higher shelf-life stability at ambient temperatures and facilitate transport and storage. Currently, the possibility to freeze-dry reproductive tissues maintaining vitality and functions is still under optimization. Here, we lyophilized sheep ovarian tissue with a novel device named Darya and a new vitrification and drying protocol and assessed effects on tissue integrity and gene expression. The evaluation was performed immediately after lyophilization (Lio), after rehydration (LR0h) or after two hours of in vitro culture (IVC; LR2h). The tissue survived lyophilization procedures and maintained its general structure, including intact follicles at different stages of development, however morphological and cytoplasmic modifications were noticed. Lyophilization, rehydration and further IVC increasingly affected RNA integrity and caused progressive morphological alterations. Nevertheless, analysis of a panel of eight genes showed tissue survival and reaction to the different procedures by regulation of specific gene expression. Results show that sheep ovarian tissue can tolerate the applied vitrification and drying protocol and constitute a valid basis for further improvements of the procedures, with the ultimate goal of optimizing tissue viability after rehydration.
Collapse
|
12
|
Identification of Reference Genes for Expression Studies in the Whole-Blood from Three Cattle Breeds under Two States of Livestock Weather Safety. Animals (Basel) 2021; 11:ani11113073. [PMID: 34827805 PMCID: PMC8614315 DOI: 10.3390/ani11113073] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/08/2021] [Accepted: 09/14/2021] [Indexed: 01/03/2023] Open
Abstract
Simple Summary Reductions in the fertility, body weight, and growth rate of cattle across the world are associated with the global warming phenomenon. Developing optimal management strategies is an important aspect of breeding programs for different breeds. Blood tissue undergoes dramatic physiological and metabolic changes during heat stress conditions, which involves the expression and regulation of a great number of genes across species. Real-time quantitative PCR (qPCR) is a method for the rapid and reliable quantification of mRNA transcription. Reference genes are used to normalize mRNA levels between different samples. Thus, the selection of high-quality reference genes is necessary for the interpretation of data generated by real-time PCR. Abstract Real-time PCR is widely used to study the relative abundance of mRNA due to its specificity, sensitivity, and repeatability quantification. However, relative quantification requires a reference gene, which should be stable in its expression, showing lower variation by experimental conditions or tissues. The aim of this study was to evaluate the stability of the expression of five commonly used reference genes (actb, ywhaz, b2m, sdha, and 18s rRNA) at different physiological stages (alert and emergency) in three different cattle breeds. In this study, five genes (actb, ywhaz, b2m, sdha, and 18s rRNA) were selected as candidate reference genes for expression studies in the whole blood from three cattle breeds (Romosinuano, Gyr, and Brahman) under heat stress conditions. The transcription stability of the candidate reference genes was evaluated using geNorm and NormFinder. The results showed that actb, 18SrRNA, and b2m expression were the most stable reference genes for whole blood of Gyr and Brahman breeds under two states of livestock weather safety (alert and emergency). Meanwhile, actb, b2m, and ywhaz were the most stable reference genes for the Romosinuano breed.
Collapse
|
13
|
Quirke LD, Maclean PH, Haack NA, Edwards SJ, Heiser A, Juengel JL. Characterization of local and peripheral immune system in pregnant and nonpregnant ewes. J Anim Sci 2021; 99:6317661. [PMID: 34240172 PMCID: PMC8363041 DOI: 10.1093/jas/skab208] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 07/07/2021] [Indexed: 12/16/2022] Open
Abstract
Modulation of the immune system is known to be important for successful pregnancy but how immune function might differ between the lymph nodes draining the reproductive tract and peripheral lymph nodes is not well understood. Additionally, if immune system changes in response to the presence of an embryo during early pregnancy, and if this response differs in local versus peripheral immune tissue, has not been well characterized. To address these questions, we examined expression of genes important for immune function using NanoString technology in the ampulla and isthmus of the oviduct, endometrium, lymph nodes draining the reproductive tract (lumbo-aortic and medial iliac) as well as a peripheral lymph node (axillary), the spleen, and circulating immune cells from ewes on day 5 of the estrous cycle or pregnancy. Concentrations of estradiol and progesterone in plasma were also determined. Principal component analysis revealed separation of the local from the peripheral lymph nodes (MANOVA P = 3.245e-08, R2 = 0.3) as well as separation of tissues from pregnant and nonpregnant animals [lymph nodes (MANOVA P = 2.337e-09, R2 = 0.5), reproductive tissues (MANOVA P = 2.417e-14, R2 = 0.47)]. Nine genes were differentially (FDR < 0.10) expressed between lymph node types, with clear difference in expression of these genes between the lumbo-aortic and axillary lymph nodes. Expression of these genes in the medial iliac lymph node was not consistently different to either the axillary or the lumbo-aortic lymph node. Expression of IL10RB was increased (FDR < 0.05) by 24% in the reproductive tissue of the pregnant animals compared to nonpregnant animals. Analysis of gene categories revealed that expression of genes of the T-cell receptor pathway in reproductive tract tissues was associated (P < 0.05) with pregnancy status. In conclusion, assessment of gene expression of reproductive and immune tissue provides evidence for a specialization of the local immune system around the reproductive tract potentially important for successful establishment of pregnancy. Additionally, differences in gene expression patterns in reproductive tissue from pregnant and nonpregnant animals could be discerned as early as day 5 of pregnancy. This was found to be associated with expression of genes important for T-cell function and thus highlights the important role of these cells in early pregnancy.
Collapse
Affiliation(s)
- Laurel D Quirke
- Reproduction, Animal Science, Invermay Agricultural Centre, AgResearch Ltd, Mosgiel, 9092, New Zealand
| | - Paul H Maclean
- Bioinformatics and Statistics, AgResearch Ltd, Grasslands Research Centre, Private Bag 11008, Palmerston North, New Zealand
| | - Neville A Haack
- Infectious Diseases, Hopkirk Research Institute, AgResearch Ltd, Private Bag 11008, Palmerston North, 4442, New Zealand
| | - Sara J Edwards
- Reproduction, Animal Science, Invermay Agricultural Centre, AgResearch Ltd, Mosgiel, 9092, New Zealand
| | - Axel Heiser
- Infectious Diseases, Hopkirk Research Institute, AgResearch Ltd, Private Bag 11008, Palmerston North, 4442, New Zealand
| | - Jennifer L Juengel
- Reproduction, Animal Science, Invermay Agricultural Centre, AgResearch Ltd, Mosgiel, 9092, New Zealand.,Infectious Diseases, Hopkirk Research Institute, AgResearch Ltd, Private Bag 11008, Palmerston North, 4442, New Zealand
| |
Collapse
|
14
|
Mavrommatis A, Theodorou G, Politis I, Tsiplakou E. Schizochytrium sp. Dietary supplementation modify Toll-like receptor 4 (TLR4) transcriptional regulation in monocytes and neutrophils of dairy goats. Cytokine 2021; 148:155588. [PMID: 34403896 DOI: 10.1016/j.cyto.2021.155588] [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: 12/10/2020] [Revised: 04/26/2021] [Accepted: 05/17/2021] [Indexed: 12/29/2022]
Abstract
Animals protect themselves against pathogens or abiotic factors by innate or adaptive mechanisms. Long-chain polyunsaturated fatty acids (ω3) of microalgae modify both human and mice' immune systems resulting in a beneficial balance between pro-inflammatory and anti-inflammatory pathways. However, scarce information exists on their impact on lactating animals' immunity. The objective of this study was to investigate the impact of dietary inclusion of Schizochytrium sp. (rich in docosapentaenoic and docosahexaenoic acid), on the expression of several genes involved in the innate immunity of goats. Twenty-four dairy goats were divided into four homogeneous sub-groups (n = 6). All goats were fed individually with alfalfa hay and concentrate. The concentrate of the control group (CON) had no microalgae while those of the treated groups were supplemented daily with 20 (ALG20), 40 (ALG40), and 60 (ALG60) g Schizochytrium sp. Monocytes and neutrophils were isolated from goats' blood in the 20th, 40th, and 60th days from the beginning of the experimental period. The relative transcript levels of TLR4, MYD88, MAPK, IRF3, IFNG, and pro-inflammatory cytokines (IL1B, IL2, IL8, TNF), and chemokines (CCL5 and CXCL16) were decreased in monocytes of microalgae treated goats compared to the CON. In contrast, MAPK and IL1B relative transcript levels were increased in neutrophils of ALG40 and ALG60 groups. In conclusion, the supplementation of goats' diet with 20 g Schizochytrium sp. resulted in a downregulation of the pro-inflammatory transcriptions, and following further research could be considered as a sustainable alternative strategy to improve immune function.
Collapse
Affiliation(s)
- Alexandros Mavrommatis
- Department of Animal Science, Laboratory of Nutritional Physiology and Feeding, Agricultural University of Athens, Iera Odos 75, Athens GR-11855, Greece
| | - Georgios Theodorou
- Department of Animal Science, Laboratory of Animal Breeding & Husbandry, Agricultural University of Athens, Greece, Iera Odos 75, Athens GR-11855, Greece
| | - Ioannis Politis
- Department of Animal Science, Laboratory of Animal Breeding & Husbandry, Agricultural University of Athens, Greece, Iera Odos 75, Athens GR-11855, Greece
| | - Eleni Tsiplakou
- Department of Animal Science, Laboratory of Nutritional Physiology and Feeding, Agricultural University of Athens, Iera Odos 75, Athens GR-11855, Greece.
| |
Collapse
|
15
|
Szczepkowska A, Harazin A, Barna L, Deli MA, Skipor J. Identification of Reference Genes for Circadian Studies on Brain Microvessels and Choroid Plexus Samples Isolated from Rats. Biomolecules 2021; 11:biom11081227. [PMID: 34439891 PMCID: PMC8394446 DOI: 10.3390/biom11081227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 08/11/2021] [Accepted: 08/13/2021] [Indexed: 12/18/2022] Open
Abstract
Delivery of putative compounds of therapeutic value to the brain is limited by brain barriers: the blood–brain barrier located in the endothelium of the brain microvessels (BrMV) and the blood–cerebrospinal fluid barrier located in the epithelium of the choroid plexus (ChP). Understanding their function and modulation by the circadian clock may enhance the efficacy of brain-targeting therapies. The aim of the present study was to evaluate the stability of 10 reference genes in the BrMV and ChP, isolated from male and female rats at six time points (ZT1, 5, 9, 13, 17, and 21). Gene evaluations were performed by qPCR, analyzed by RefFinder tool, and verified by analyzing the expression of the brain and muscle ARNT-like 1 (Bmal1) using the qPCR and digital PCR methods. We identified as the most stable genes for circadian studies tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta (Ywhaz) and apolipoprotein E (Apoe) for BrMV, and beta actin (Actb) and hypoxanthine-guanine phosphoribosyltransferase (Hprt1) for ChP. After verification, ribosomal protein (Rps18) was also included as a sufficient reference gene. Additionally, the observed gender difference in the Bmal1 oscillations in both BrMV and ChP suggests that separate studies for each gender are recommended.
Collapse
Affiliation(s)
- Aleksandra Szczepkowska
- Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, 10-748 Olsztyn, Poland;
- Correspondence: (A.S.); (M.A.D.); Tel.: +48-89-539-3125 (A.S.); +36-62-599602 (M.A.D.)
| | - András Harazin
- Institute of Biophysics, Biological Research Centre, 6726 Szeged, Hungary; (A.H.); (L.B.)
| | - Lilla Barna
- Institute of Biophysics, Biological Research Centre, 6726 Szeged, Hungary; (A.H.); (L.B.)
| | - Mária A. Deli
- Institute of Biophysics, Biological Research Centre, 6726 Szeged, Hungary; (A.H.); (L.B.)
- Correspondence: (A.S.); (M.A.D.); Tel.: +48-89-539-3125 (A.S.); +36-62-599602 (M.A.D.)
| | - Janina Skipor
- Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, 10-748 Olsztyn, Poland;
| |
Collapse
|
16
|
Puttabyatappa M, Ciarelli JN, Chatoff AG, Padmanabhan V. Developmental programming: Metabolic tissue-specific changes in endoplasmic reticulum stress, mitochondrial oxidative and telomere length status induced by prenatal testosterone excess in the female sheep. Mol Cell Endocrinol 2021; 526:111207. [PMID: 33607270 PMCID: PMC8005473 DOI: 10.1016/j.mce.2021.111207] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 02/02/2021] [Accepted: 02/03/2021] [Indexed: 02/07/2023]
Abstract
Prenatal testosterone (T) excess-induced metabolic dysfunctions involve tissue specific changes in insulin sensitivity with insulin resistant, oxidative and lipotoxic state in liver/muscle and insulin sensitive but inflammatory and oxidative state in visceral adipose tissues (VAT). We hypothesized that mitochondrial dysfunction, endoplasmic reticulum (ER) stress and premature cellular senescence are contributors to the tissue-specific changes in insulin sensitivity. Markers of mitochondrial number, function, and oxidative phosphorylation (OxPhos), ER stress and cellular senescence (telomere length) were assessed in liver, muscle and 4 adipose (VAT, subcutaneous [SAT], epicardiac [ECAT] and perirenal [PRAT]) depots collected from control and prenatal T-treated female sheep at 21 months of age. Prenatal T treatment led to: (a) reduction in mitochondrial number and OxPhos complexes and increase in ER stress markers in muscle; (b) increase in fibrosis with trend towards increase in short telomere fragments in liver (c) depot-specific mitochondrial changes with OxPhos complexes namely increase in SAT and reduction in PRAT and increase in mitochondrial number in ECAT; (d) depot-specific ER stress marker changes with increase in VAT, reduction in SAT, contrasting changes in ECAT and no changes in PRAT; and (d) reduced shorter telomere fragments in SAT, ECAT and PRAT. These changes indicate insulin resistance may be driven by mitochondrial and ER dysfunction in muscle, fibrosis and premature senescence in liver, and depot-specific changes in mitochondrial function and ER stress without involving cellular senescence in adipose tissue. These findings provide mechanistic insights into pathophysiology of metabolic dysfunction among female offspring from hyperandrogenic pregnancies.
Collapse
Affiliation(s)
| | - Joseph N Ciarelli
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
| | - Adam G Chatoff
- Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
| | | |
Collapse
|
17
|
Mitsiopoulou C, Sotirakoglou K, Skliros D, Flemetakis E, Tsiplakou E. The Impact of Whole Sesame Seeds on the Expression of Key-Genes Involved in the Innate Immunity of Dairy Goats. Animals (Basel) 2021; 11:468. [PMID: 33578642 PMCID: PMC7916339 DOI: 10.3390/ani11020468] [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: 01/12/2021] [Revised: 02/02/2021] [Accepted: 02/08/2021] [Indexed: 01/20/2023] Open
Abstract
Whole sesame seeds (WSS) are rich in both linoleic acid (LA) and lignans. However, their impact on the innate immunity of goats is not well studied. Twenty-four goats were divided into three homogeneous sub-groups; comprise one control (CON) and two treated (WWS5 and WWS10). In the treated groups, WSS were incorporated in the concentrates of the CON at 5 (WSS5) and 10% (WSS10) respectively, by partial substitution of both soybean meal and corn grain. The expression levels of MAPK1, IL6, TRIF, IFNG, TRAF3, and JUND genes in the neutrophils of WSS10 fed goats were reduced significantly compared with the CON. The same was found for the expression levels of IFNG and TRAF3 genes in the neutrophils of WSS5 fed goats. Both treated groups primarily affected the MYD88-independent pathway. The dietary supplementation of goats with WSS might be a good nutritional strategy to improve their innate immunity.
Collapse
Affiliation(s)
- Christina Mitsiopoulou
- Laboratory of Nutritional Physiology and Feeding, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens, Iera Odos 75, 118 55 Athens, Greece;
| | - Kyriaki Sotirakoglou
- Laboratory of Mathematics and Statistics, Department of Natural Resources Management and Agricultural Engineering, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece;
| | - Dimitrios Skliros
- Laboratory of Molecular Biology, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (D.S.); (E.F.)
| | - Emmanouil Flemetakis
- Laboratory of Molecular Biology, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (D.S.); (E.F.)
| | - Eleni Tsiplakou
- Laboratory of Nutritional Physiology and Feeding, Department of Animal Science, School of Animal Biosciences, Agricultural University of Athens, Iera Odos 75, 118 55 Athens, Greece;
| |
Collapse
|
18
|
The impact of rumen-protected amino acids on the expression of key- genes involved in the innate immunity of dairy sheep. PLoS One 2020; 15:e0233192. [PMID: 32407360 PMCID: PMC7224535 DOI: 10.1371/journal.pone.0233192] [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: 01/28/2020] [Accepted: 04/29/2020] [Indexed: 12/28/2022] Open
Abstract
Rumen protected amino acids inclusion in ewes’ diets has been proposed to enhance their innate immunity. The objective of this work was to determine the impact of dietary supplementation with rumen-protected methionine or lysine, as well as with a combination of these amino acids in two different ratios, on the expression of selected key-genes (NLRs, MyD88, TRIF, MAPK-1, IRF-3, JunD, TRAF-3, IRF-5, IL-1α, IL-10, IKK-α, STAT-3 and HO-1). Thus, sixty Chios dairy ewes (Ovis aries) were assigned to one of the following five dietary treatments (12 animals/ treatment): A: basal diet consist of concentrates, wheat straw and alfalfa hay (control group); B: basal diet +6.0 g/head rumen-protected methionine; C: basal diet + 5.0 g/head rumen-protected lysine; D: basal diet +6.0 g/head rumen-protected methionine + 5.0 g/head rumen-protected lysine and E: basal diet +12.0 g/head rumen-protected methionine + 5.0 g/head rumen-protected lysine. The results revealed a significant downregulation of relative transcript level of the IL-1α gene in the neutrophils of C and in monocytes of D ewes compared with the control. Significantly lower mRNA transcript accumulation was also observed for the MyD88 gene in the neutrophils of ewes fed with lysine only (C). The mRNA relative expression levels of JunD gene were highly induced in the monocytes, while those of IL-10 and HO-1 genes were declined in the neutrophils of ewes fed with the C and D diets compared with the control. Lower transcript levels of STAT-3 gene were observed in the neutrophils of ewes fed with either C or with E diets in comparison with the control. In conclusion, our results suggest that the dietary supplementation of ewes with rumen-protected amino acids, down regulate the expression of some genes involved in the pro-inflammatory signalling.
Collapse
|
19
|
Bunma T, Vonnahme KA, Vasquez-Hidalgo MA, Swanson KC, Dorsam ST, Ward AK, Navanukrav C, Grazul-Bilska AT. Nuclear and membrane progesterone receptors expression in placenta from early to late pregnancy in sheep: Effects of restricted nutrition and realimentation. Theriogenology 2020; 148:95-102. [PMID: 32169627 DOI: 10.1016/j.theriogenology.2020.02.041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 02/11/2020] [Accepted: 02/24/2020] [Indexed: 01/01/2023]
Abstract
Nutrient restriction and/or realimentation may affect several placental functions, such as expression of selected regulatory factors, blood flow and other processes in sheep and other species. To determine the effects of the plane of nutrition, nulliparous white face ewes (6-8 months) carrying singletons on day 50 of gestation were randomly assigned to two dietary treatments receiving 100% of National Research Council recommendations (control; C) or 60% of C (restricted; R). Two groups remained on C or R diets from day 50 until day 130. From day 90-130 another group of C fed ewes was switched to the R diet, and another group of R fed ewes was switched to the C diet. This resulted in 7 groups (n = 5-6 ewes/group): C (day 50, 90 and 130), R (day 90 and 130), CR (day 130) and RC (day 130). At these time points, placental tissues were collected for the evaluation of progesterone receptor (PGR) protein expression (whole tissue), and mRNA expression in maternal (caruncular, CAR) and fetal (cotyledon, COT) (separated tissues). Data were statistically analyzed using analysis of variance (SAS 9.4). Protein for PGRAB and PGRB isoforms was detected using immunohistochemistry in all placental tissues, but the pattern of expression differed depending on pregnancy stage and placental compartment (e.g., CAR vs COT). PGRAB protein expression, quantified using image analysis, was greater (P < 0.04) on day 50 than 90 or 130, and was not affected by plane of nutrition. In CAR and COT, PGRAB mRNA expression was greater (P < 0.05) on day 50 than 90 or 130. PGRB mRNA expression was greater (P < 0.03) in CAR on day 50 than 90 and 130, and was greatest (P < 0.02) in COT on day 50, less on day 130, and least on day 90. For the membrane progesterone receptors, PAQR7 (membrane PGR alpha) mRNA expression was greater (P < 0.05) on days 50 and 90 than 130 in CAR, and greater (P < 0.01) on days 50 than 90 and 130 in COT; PAQR8 (membrane PGR beta) was similar throughout pregnancy in CAR and COT, and PAQR5 (membrane PGR gamma) was greatest (P < 0.0001) on day 130 in COT, but similar throughout pregnancy in CAR. Plane of nutrition affected (P < 0.05) mRNA expression for all genes in CAR and COT throughout pregnancy. These data indicate that expression of PGR in ovine placenta is dependent on stage of pregnancy and plane of nutrition in sheep. The mechanisms of how diet and stage of pregnancy influences placental PGR expression and function remains to be elucidated.
Collapse
Affiliation(s)
- Thanya Bunma
- Agricultural Biotechnology Research Center for Sustainable Economy (ANRCE), Department of Animal Sciences, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Kimberly A Vonnahme
- Department of Animal Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | | | - Kendall C Swanson
- Department of Animal Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Sheri T Dorsam
- Department of Animal Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Alison K Ward
- Department of Animal Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Chainarong Navanukrav
- Agricultural Biotechnology Research Center for Sustainable Economy (ANRCE), Department of Animal Sciences, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Anna T Grazul-Bilska
- Department of Animal Sciences, North Dakota State University, Fargo, ND, 58108, USA.
| |
Collapse
|
20
|
Qin N, Shan X, Sun X, Liswaniso S, Chimbaka IM, Xu R. Evaluation and Validation of the Six Housekeeping Genes for Normalizing Mrna Expression in the Ovarian Follicles and Several Tissues in Chicken. BRAZILIAN JOURNAL OF POULTRY SCIENCE 2020. [DOI: 10.1590/1806-9061-2019-1256] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- N Qin
- Jilin Agricultural University, China; Ministry of Education, P. R. China
| | - X Shan
- Jilin Agricultural University, China
| | - X Sun
- Jilin Agricultural University, China; Ministry of Education, P. R. China
| | - S Liswaniso
- Jilin Agricultural University, China; Ministry of Education, P. R. China
| | - IM Chimbaka
- Jilin Agricultural University, China; Ministry of Education, P. R. China
| | - R Xu
- Jilin Agricultural University, China; Ministry of Education, P. R. China
| |
Collapse
|
21
|
Zhang YS, Du YC, Sun LR, Wang XH, Liu SB, Xi JF, Li CC, Ying RW, Jiang S, Wang XZ, Shen H, Jia B. A genetic method for sex determination in Ovis spp. by interruption of the zinc finger protein, Y-linked (ZFY) gene on the Y chromosome. Reprod Fertil Dev 2019; 30:1161-1168. [PMID: 29505743 DOI: 10.1071/rd17339] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 01/02/2018] [Indexed: 01/07/2023] Open
Abstract
The mammalian Y chromosome plays a critical role in spermatogenesis. However, the exact functions of each gene on the Y chromosome have not been completely elucidated, due, in part, to difficulties in gene targeting analysis of the Y chromosome. The zinc finger protein, Y-linked (ZFY) gene was first proposed to be a sex determination factor, although its function in spermatogenesis has recently been elucidated. Nevertheless, ZFY gene targeting analysis has not been performed to date. In the present study, RNA interference (RNAi) was used to generate ZFY-interrupted Hu sheep by injecting short hairpin RNA (shRNA) into round spermatids. The resulting spermatozoa exhibited abnormal sperm morphology, including spermatozoa without tails and others with head and tail abnormalities. Quantitative real-time polymerase chain reaction analysis showed that ZFY mRNA expression was decreased significantly in Hu sheep with interrupted ZFY compared with wild-type Hu sheep. The sex ratio of lambs also exhibited a bias towards females. Together, the experimental strategy and findings of the present study reveal that ZFY also functions in spermatogenesis in Hu sheep and facilitate the use of RNAi in the control of sex in Hu sheep.
Collapse
Affiliation(s)
- Yong Sheng Zhang
- College of Animal Science and Technology, Shihezi University, The Xinjiang Uygur Autonomous Region, China
| | - Ying Chun Du
- The Aquatic Wildlife Rescue and Conservation Center, Beijing, China
| | - Li Rong Sun
- Tongliao City Quality and Safety Centre of Agricultural and Livestock, Tongliao, China
| | - Xu Hai Wang
- College of Animal Science and Technology, Shihezi University, The Xinjiang Uygur Autonomous Region, China
| | - Shuai Bing Liu
- Nanhu District of Jiaxing City Animal Husbandry and Veterinary Bureau, Jiaxing, China
| | - Ji Feng Xi
- College of Animal Science and Technology, Shihezi University, The Xinjiang Uygur Autonomous Region, China
| | - Chao Cheng Li
- College of Animal Science and Technology, Shihezi University, The Xinjiang Uygur Autonomous Region, China
| | - Rui Wen Ying
- College of Animal Science and Technology, Shihezi University, The Xinjiang Uygur Autonomous Region, China
| | - Song Jiang
- College of Animal Science and Technology, Shihezi University, The Xinjiang Uygur Autonomous Region, China
| | - Xiang Zu Wang
- College of Animal Science and Technology, Shihezi University, The Xinjiang Uygur Autonomous Region, China
| | - Hong Shen
- College of Animal Science and Technology, Shihezi University, The Xinjiang Uygur Autonomous Region, China
| | - Bin Jia
- College of Animal Science and Technology, Shihezi University, The Xinjiang Uygur Autonomous Region, China
| |
Collapse
|
22
|
Toscano JHB, Lopes LG, Giraldelo LA, da Silva MH, Okino CH, de Souza Chagas AC. Identification of appropriate reference genes for local immune-related studies in Morada Nova sheep infected with Haemonchus contortus. Mol Biol Rep 2018; 45:1253-1262. [DOI: 10.1007/s11033-018-4281-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 07/24/2018] [Indexed: 01/23/2023]
|
23
|
Armstrong E, Iriarte A, Nicolini P, De Los Santos J, Ithurralde J, Bielli A, Bianchi G, Peñagaricano F. Comparison of transcriptomic landscapes of different lamb muscles using RNA-Seq. PLoS One 2018; 13:e0200732. [PMID: 30040835 PMCID: PMC6057623 DOI: 10.1371/journal.pone.0200732] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 07/02/2018] [Indexed: 11/18/2022] Open
Abstract
Transcriptome deep sequencing is a powerful tool for exploring the genetic architecture of complex traits. Gene expression patterns may explain a high degree of the observed phenotypic differences in histochemical and metabolic parameters related to meat quality among different muscles. In this study, we sequenced by RNA-Seq the whole transcriptome of nine lamb muscles: Semimembranosus (SM), Semitendinosus (ST), Cranial gluteobiceps, Gluteus medius (GM), Rectus femoris, Supraspinatus (SS), Longissimus lumborum (LL), Adductor and Psoas major. Significant gene expression differences were detected between almost all pairwise comparisons, being more pronounced between SS and ST, SM and LL, and ST and GM. These differences can be explained in terms of ATPase and glycolytic activities, muscle fiber typing and oxidative score, clustering muscles as fast glycolytic, intermediate or slow oxidative. ST showed up-regulation of gene pathways related to carbohydrate metabolism, energy generation and protein turnover as expected from a fast white muscle. SS showed myosin isoforms typical of slow muscles and high expression of genes related to calcium homeostasis and vascularization. SM, LL and GM showed in general intermediate gene expression patterns. Several novel transcripts were detected, mostly related to muscle contraction and structure, oxidative metabolism, lipid metabolism and protein phosphorylation. Expression profiles were consistent with previous histochemical and metabolic characterization of these muscles. Up-regulation of ion transport genes may account for significant differences in water holding capacity. High expression of genes related to cell adhesion, cytoskeleton organization, extracellular matrix components and protein phosphorylation may be related to meat yellowness and lower tenderness scores. Differential expression of genes related to glycolytic activity and lactic acid generation among fast, intermediate and slow muscles may explain the detected final meat pH differences. These results reveal new candidate genes associated with lamb meat quality, and give a deeper insight into the genetic architecture of these complex traits.
Collapse
Affiliation(s)
- Eileen Armstrong
- Departamento de Genética y Mejora Animal, Facultad de Veterinaria, Universidad de la República, Montevideo, Uruguay
- * E-mail:
| | - Andres Iriarte
- Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Paula Nicolini
- Polo de Desarrollo Universitario Instituto Superior de la Carne, Centro Universitario de Tacuarembó, Universidad de la República, Tacuarembó, Uruguay
| | - Jorge De Los Santos
- Department of Animal Sciences, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Javier Ithurralde
- Departamento de Morfología y Desarrollo, Facultad de Veterinaria, Universidad de la República, Montevideo, Uruguay
| | - Alejandro Bielli
- Departamento de Morfología y Desarrollo, Facultad de Veterinaria, Universidad de la República, Montevideo, Uruguay
| | | | - Francisco Peñagaricano
- Department of Animal Sciences, University of Florida, Gainesville, Florida, United States of America
- University of Florida Genetics Institute, University of Florida, Gainesville, Florida, United States of America
| |
Collapse
|
24
|
Tsiplakou E, Mavrommatis A, Skliros D, Sotirakoglou K, Flemetakis E, Zervas G. The effects of dietary supplementation with rumen-protected amino acids on the expression of several genes involved in the immune system of dairy sheep. J Anim Physiol Anim Nutr (Berl) 2018; 102:1437-1449. [PMID: 30043476 DOI: 10.1111/jpn.12968] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 07/04/2018] [Accepted: 07/04/2018] [Indexed: 12/14/2022]
Abstract
Amino acids might be a tool to transform animals from a pro- to an anti-inflammatory phenotype through the downregulation of several genes (TLR-4, NF-κB, TNFa, IL-1β, IL-2, IL-6, IL-8, CCL-5 and CXCL-16) whose expression increases during inflammation. To examine this possibility, each of sixty Chios dairy sheep was assigned to one of the following five dietary treatments: A: basal diet (control group); B: basal diet +6.0 g/head rumen-protected methionine (MetaSmart™ ); C: basal diet +5.0 g/head rumen-protected lysine (LysiGEM™ ); D: basal diet +6.0 g/head MetaSmart™ + 5.0 g/head LysiGEM™ ; and E: basal diet +12.0 g/head MetaSmart™ + 5.0 g/head LysiGEM. The results showed a significant downregulation in the expression of the TLR-4 gene in both the macrophages and the neutrophils of ewes fed rumen-protected amino acids. Significantly lower mRNA transcript accumulation was also observed for the TNFa, IL-1β and CXCL-16 genes in the macrophages and for the IL-1β gene in the neutrophils of ewes supplemented with amino acids. The ewes that received dietary supplementation with rumen-protected lysine alone (C) had significantly lower CCL-5 transcript levels in their macrophages than the ewes fed the other supplemented diets. Diet D enhanced the mRNA expression of the IL-2 gene in ewe neutrophils. Negative correlations were found between: a. TLR-4, TNFa, IL-1β and CXCL-16 gene expression in macrophages and the milk fat and total solids content; b. CCL-5 gene expression in neutrophils and the milk yield and FCM(6%) ; and c. CXCL-16 gene expression and the milk protein content. Moreover, positive correlations were found between the BHBA concentration and the expression of the TLR-4 and CXCL-16 genes in macrophages. In conclusion, the rumen-protected amino acids improved sheep metabolism (as indicated by reduced blood BHBA and urea concentrations), milk chemical composition and immune system function.
Collapse
Affiliation(s)
- Eleni Tsiplakou
- Department of Nutritional Physiology and Feeding, Agricultural University of Athens, Athens, Greece
| | - Alexandros Mavrommatis
- Department of Nutritional Physiology and Feeding, Agricultural University of Athens, Athens, Greece
| | - Dimitrios Skliros
- Laboratory of Molecular Biology, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, Athens, Greece
| | - Kyriaki Sotirakoglou
- Department of Plant Breeding and Biometry, Agricultural University of Athens, Athens, Greece
| | - Emmanouil Flemetakis
- Laboratory of Molecular Biology, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, Athens, Greece
| | - George Zervas
- Department of Nutritional Physiology and Feeding, Agricultural University of Athens, Athens, Greece
| |
Collapse
|
25
|
Kaur R, Sodhi M, Sharma A, Sharma VL, Verma P, Swami SK, Kumari P, Mukesh M. Selection of suitable reference genes for normalization of quantitative RT-PCR (RT-qPCR) expression data across twelve tissues of riverine buffaloes (Bubalus bubalis). PLoS One 2018; 13:e0191558. [PMID: 29509770 PMCID: PMC5839537 DOI: 10.1371/journal.pone.0191558] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 01/08/2018] [Indexed: 12/14/2022] Open
Abstract
Selection of reference genes has become an integral step in any real time quantitative PCR (RT-qPCR) based expression studies. The importance of this study stems from the fact that riverine buffaloes are major dairy species of Indian sub-continent and the information generated here will be of great interest to the investigators engaged in functional genomic studies of this important livestock species. In this study, an effort was made to evaluate a panel of 10 candidate reference genes (glyceraldehyde 3-phosphate dehydrogenase (GAPDH), beta- actin (ACTB), ubiquitously expressed transcript (UXT), ribosomal protein S15 (RPS15), ribosomal protein L-4 (RPL4), ribosomal protein S9 (RPS9), ribosomal protein S23 (RPS23), hydroxymethylbilane synthase (HMBS), β2 Microglobulin (β2M) and eukaryotic translation elongation factor 1 alpha 1 (EEF1A1) across 12 tissues (mammary gland, kidney, spleen, liver, heart, intestine, ovary, lung, muscle, brain, subcutaneous fat and testis) of riverine buffaloes. In addition to overall analysis, tissue wise evaluation of expression stability of individual RG was also performed. Three different algorithms provided in geNorm, NormFinder and BestKeeper softwares were used to evaluate the stability of 10 potential reference genes from different functional classes. The M-value given by geNorm ranged from 0.9797 (RPS9 and UXT) to 1.7362 (RPS15). From the most stable to the least stable, genes were ranked as: UXT/RPS9> RPL4> RPS23> EEF1A1> ACTB> HMBS> GAPDH> B2M> RPS15. While NormFinder analysis ranked the genes as: UXT> RPS23> RPL4> RPS9> EEF1A1> HMBS> ACTB> β2M> GAPDH> RPS15. Based on the crossing point SD value and range of fold change expression, BestKeeper analysis ranked the genes as: RPS9> RPS23/UXT> RPL4> GAPDH> EEF1A1> ACTB> HMBS> β2M> RPS15. Overall the study has identified RPS23, RPS9, RPL4 and UXT genes to be the most stable and appropriate RGs that could be utilized for normalization of transcriptional data in various tissues of buffaloes. This manuscript thus provide useful information on panel of reference genes that could be helpful for researchers conducting functional genomic studies in riverine buffaloes.
Collapse
Affiliation(s)
- Ramneek Kaur
- Department of Animal Biotechnology, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
- Department of Zoology, Panjab University, Chandigarh, India
| | - Monika Sodhi
- Department of Animal Biotechnology, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Ankita Sharma
- Department of Animal Biotechnology, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | | | - Preeti Verma
- Department of Animal Biotechnology, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Shelesh Kumar Swami
- Department of Animal Biotechnology, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Parvesh Kumari
- Department of Animal Biotechnology, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Manishi Mukesh
- Department of Animal Biotechnology, ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
- * E-mail: ,
| |
Collapse
|
26
|
Schulze F, Malhan D, El Khassawna T, Heiss C, Seckinger A, Hose D, Rösen-Wolff A. A tissue-based approach to selection of reference genes for quantitative real-time PCR in a sheep osteoporosis model. BMC Genomics 2017; 18:975. [PMID: 29258442 PMCID: PMC5735898 DOI: 10.1186/s12864-017-4356-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 11/29/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In order to better understand the multifactorial nature of osteoporosis, animal models are utilized and compared to healthy controls. Female sheep are well established as a model for osteoporosis induced by ovariectomy, calcium and vitamin D low diet, application of steroids, or a combination of these treatments. Transcriptional studies can be performed by applying quantitative real time PCR (RT-qPCR). RT-qPCR estimates mRNA-levels of target genes in relation to reference genes. A chosen set of reference genes should not show variation under experimental conditions. Currently, no standard reference genes are accepted for all tissue types and experimental conditions. Studies examining reference genes for sheep are rare and only one study described stable reference in mandibular bone. However, this type of bone differs from trabecular bone where most osteoporotic fractures occur. The present study aimed at identifying a set of reference genes for relative quantification of transcriptional activity of ovine spine bone and ovine in vitro differentiated mesenchymal stromal cells (MSC) for reliable comparability. METHODS Twelve candidate reference genes belonging to different functional classes were selected and their expression was measured from cultured ovMSCs (n = 18) and ovine bone samples (n = 16), respectively. RefFinder was used to rank the candidate genes. RESULTS We identified B2M, GAPDH, RPL19 and YWHAZ as the best combination of reference genes for normalization of RT-qPCR results for transcriptional analyses of these ovine samples. CONCLUSION This study demonstrates the importance of applying a set of reference genes for RT-qPCR analysis in sheep. Based on our data we recommend using four identified reference genes for relative quantification of gene expression studies in ovine bone or for in vitro experiments with osteogenically differentiated ovine MSCs.
Collapse
Affiliation(s)
- Felix Schulze
- Department of Pediatrics, University Hospital Carl Gustav Carus, TU Dresden, Fetscherstraße 74, 01307, Dresden, Germany
| | - Deeksha Malhan
- Experimental Trauma Surgery, Justus-Liebig University, Aulweg 128, 35392, Giessen, Germany
| | - Thaqif El Khassawna
- Experimental Trauma Surgery, Justus-Liebig University, Aulweg 128, 35392, Giessen, Germany
| | - Christian Heiss
- Experimental Trauma Surgery, Justus-Liebig University, Aulweg 128, 35392, Giessen, Germany.,Department of Trauma, Hand and Reconstructive Surgery, University Hospital of Giessen-Marburg, Rudolf-Buchheim-Strasse 7, 35385, Giessen, Germany
| | - Anja Seckinger
- Labor für Myelomforschung, Medizinische Klinik V, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
| | - Dirk Hose
- Labor für Myelomforschung, Medizinische Klinik V, Universitätsklinikum Heidelberg, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
| | - Angela Rösen-Wolff
- Department of Pediatrics, University Hospital Carl Gustav Carus, TU Dresden, Fetscherstraße 74, 01307, Dresden, Germany.
| |
Collapse
|
27
|
Crookenden M, Walker C, Kuhn-Sherlock B, Murray A, Dukkipati V, Heiser A, Roche J. Technical note: Evaluation of endogenous control gene expression in bovine neutrophils by reverse-transcription quantitative PCR using microfluidics gene expression arrays. J Dairy Sci 2017. [DOI: 10.3168/jds.2016-12460] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
28
|
Elgendy R, Giantin M, Castellani F, Grotta L, Palazzo F, Dacasto M, Martino G. Transcriptomic signature of high dietary organic selenium supplementation in sheep: A nutrigenomic insight using a custom microarray platform and gene set enrichment analysis. J Anim Sci 2017; 94:3169-3184. [PMID: 27695782 DOI: 10.2527/jas.2016-0363] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The objective of this study was to investigate the effect of a high dietary Se supplementation on the whole transcriptome of sheep. A custom sheep whole-transcriptome microarray, with more than 23,000 unique transcripts, was designed and then used to profile the global gene expression of sheep after feeding a high dietary supplementation of organic Se. Lactating crossbred ewes ( = 10; 3 to 4 yr of age and 55 to 65 kg BW) at late lactation (100 ± 8 d in milk) were acclimated to indoor individual pen feeding of a basal control diet (0.40 mg Se/d, sodium selenite) for 4 wk. Sheep were then kept on a diet with an extra (high) supplementation of organic Se (1.45 mg Se/d as Sel-Plex; Alltech Biotechnology Pty Ltd, Dandenong, Victoria, Australia) for 40 d. Whole blood was collected at 2 time points (last day of the acclimatization period [T0] and after 40 d of the organic Se supplementation [T40]), and then total RNA was isolated and labeled for the subsequent microarray analysis. Significance Analysis of Microarrays, using the -statistic, of the microarray data (T40 versus T0) evidenced the up- and downregulation of 942 and 244 transcripts (false discovery rate < 0.05), respectively. Seven genes showed the same trend of expression (up- or downregulation) when tested by quantitative real-time PCR (qPCR) in a cross-validation step. The microarray showed significant upregulation of the following selenoproteins at T40: selenium binding protein 1 (SELENBP1), selenoprotein W1 (SEPW1), glutathione peroxidase 3 (GPX3), and septin 8 (SEPT8). And the expression trends for SEPW1 and SEPT8 were validated using qPCR. Functional annotation of the differentially expressed genes showed the enrichment of several immune system-related biological processes (lymphocyte activation, cytokine binding, leukocyte activation, T cell differentiation, and B cell activation) and pathways (cytokine and interleukin signaling). Moreover, Gene Set Enrichment Analysis evidenced the enrichment of B and T cell receptors signaling pathways, with an enrichment score of 0.63 and 0.59, respectively. Overall, from a global gene expression (whole-transcriptome) point of view, short-term supplementation of a high dietary organic Se to Se-nondeficient sheep results in a transcriptomic signature that mainly reflects an induced immune system and a modulation of transcription effect. Also, the present study provides a custom whole-transcriptome microarray platform that can be used in further global gene expression studies in the ovine species.
Collapse
|
29
|
Quantitative Evaluation and Selection of Reference Genes for Quantitative RT-PCR in Mouse Acute Pancreatitis. BIOMED RESEARCH INTERNATIONAL 2016; 2016:8367063. [PMID: 27069927 PMCID: PMC4812220 DOI: 10.1155/2016/8367063] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 01/19/2016] [Accepted: 02/07/2016] [Indexed: 02/05/2023]
Abstract
The analysis of differences in gene expression is dependent on normalization using reference genes. However, the expression of many of these reference genes, as evaluated by quantitative RT-PCR, is upregulated in acute pancreatitis, so they cannot be used as the standard for gene expression in this condition. For this reason, we sought to identify a stable reference gene, or a suitable combination, for expression analysis in acute pancreatitis. The expression stability of 10 reference genes (ACTB, GAPDH, 18sRNA, TUBB, B2M, HPRT1, UBC, YWHAZ, EF-1α, and RPL-13A) was analyzed using geNorm, NormFinder, and BestKeeper software and evaluated according to variations in the raw Ct values. These reference genes were evaluated using a comprehensive method, which ranked the expression stability of these genes as follows (from most stable to least stable): RPL-13A, YWHAZ > HPRT1 > GAPDH > UBC > EF-1α > 18sRNA > B2M > TUBB > ACTB. RPL-13A was the most suitable reference gene, and the combination of RPL-13A and YWHAZ was the most stable group of reference genes in our experiments. The expression levels of ACTB, TUBB, and B2M were found to be significantly upregulated during acute pancreatitis, whereas the expression level of 18sRNA was downregulated. Thus, we recommend the use of RPL-13A or a combination of RPL-13A and YWHAZ for normalization in qRT-PCR analyses of gene expression in mouse models of acute pancreatitis.
Collapse
|
30
|
Chen IH, Wang JH, Chou SJ, Wu YH, Li TH, Leu MY, Chang WB, Yang WC. Selection of reference genes for RT-qPCR studies in blood of beluga whales (Delphinapterus leucas). PeerJ 2016; 4:e1810. [PMID: 26998411 PMCID: PMC4797766 DOI: 10.7717/peerj.1810] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 02/23/2016] [Indexed: 12/04/2022] Open
Abstract
Reverse transcription quantitative PCR (RT-qPCR) is used for research in gene expression, and it is vital to choose appropriate housekeeping genes (HKGs) as reference genes to obtain correct results. The purpose of this study is to determine stably expressed HKGs in blood of beluga whales (Delphinapterus leucas) that can be the appropriate reference genes in relative quantification in gene expression research. Sixty blood samples were taken from four beluga whales. Thirteen candidate HKGs (ACTB, B2M, GAPDH, HPRT1, LDHB, PGK1, RPL4, RPL8, RPL18, RPS9, RPS18, TFRC, YWHAZ) were tested using RT-qPCR. The stability values of the HKGs were determined by four different algorithms. Comprehensive analysis of the results revealed that RPL4, PGK1 and ACTB are strongly recommended for use in future RT-qPCR studies in beluga blood samples. This research provides recommendation of reference gene selection, which may contribute to further mRNA relative quantification research in the peripheral blood leukocytes in captive cetaceans. The gene expression assessment of the immune components in blood have the potential to serve as an important approach to evaluating cetacean health influenced by environmental insults.
Collapse
Affiliation(s)
- I-Hua Chen
- Department of Veterinary Medicine, National Chiayi University , Chiayi , Taiwan, ROC
| | - Jiann-Hsiung Wang
- Department of Veterinary Medicine, National Chiayi University , Chiayi , Taiwan, ROC
| | - Shih-Jen Chou
- Department of Veterinary Medicine, National Chiayi University , Chiayi , Taiwan, ROC
| | - Yeong-Huey Wu
- Department of Veterinary Medicine, National Pingtung University of Science and Technology , Pingtung , Taiwan, ROC
| | - Tsung-Hsien Li
- Department of Biology, National Museum of Marine Biology and Aquarium , Pingtung , Taiwan, ROC
| | - Ming-Yih Leu
- Department of Biology, National Museum of Marine Biology and Aquarium, Pingtung, Taiwan, ROC; Graduate Institute of Marine Biology, National Dong Hwa University, Pingtung, Taiwan, ROC
| | - Wen-Been Chang
- Department of Biology, National Museum of Marine Biology and Aquarium , Pingtung , Taiwan, ROC
| | - Wei Cheng Yang
- Department of Veterinary Medicine, National Chiayi University , Chiayi , Taiwan, ROC
| |
Collapse
|
31
|
Mahakapuge TAN, Scheerlinck JPY, Rojas CAA, Every AL, Hagen J. Assessment of reference genes for reliable analysis of gene transcription by RT-qPCR in ovine leukocytes. Vet Immunol Immunopathol 2016; 171:1-6. [PMID: 26964711 DOI: 10.1016/j.vetimm.2015.10.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 10/21/2015] [Accepted: 10/28/2015] [Indexed: 12/11/2022]
Abstract
With the availability of genetic sequencing data, quantitative reverse transcription PCR (RT-qPCR) is increasingly being used for the quantification of gene transcription across species. Too often there is little regard to the selection of reference genes and the impact that a poor choice has on data interpretation. Indeed, RT-qPCR provides a snapshot of relative gene transcription at a given time-point, and hence is highly dependent on the stability of the transcription of the reference gene(s). Using ovine efferent lymph cells and peripheral blood mono-nuclear cells (PBMCs), the two most frequently used leukocytes in immunological studies, we have compared the stability of transcription of the most commonly used ovine reference genes: YWHAZ, RPL-13A, PGK1, B2M, GAPDH, HPRT, SDHA and ACTB. Using established algorithms for reference gene normalization "geNorm" and "Norm Finder", PGK1, GAPDH and YWHAZ were deemed the most stably transcribed genes for efferent leukocytes and PGK1, YWHAZ and SDHA were optimal in PBMCs. These genes should therefore be considered for accurate and reproducible RT-qPCR data analysis of gene transcription in sheep.
Collapse
Affiliation(s)
- T A N Mahakapuge
- Centre for Animal Biotechnology, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria 3010, Australia.
| | - J-P Y Scheerlinck
- Centre for Animal Biotechnology, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria 3010, Australia
| | - C A Alvarez Rojas
- Centre for Animal Biotechnology, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria 3010, Australia
| | - A L Every
- Centre for Animal Biotechnology, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria 3010, Australia
| | - J Hagen
- Centre for Animal Biotechnology, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria 3010, Australia; Department of Life Sciences, Imperial College London, SW7 2AZ London, UK
| |
Collapse
|
32
|
Selection of suitable reference genes for normalization of quantitative RT-PCR in peripheral blood samples of bottlenose dolphins (Tursiops truncatus). Sci Rep 2015; 5:15425. [PMID: 26486099 PMCID: PMC4614023 DOI: 10.1038/srep15425] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 09/17/2015] [Indexed: 12/25/2022] Open
Abstract
Quantitative RT-PCR is often used as a research tool directed at gene transcription. Selection of optimal housekeeping genes (HKGs) as reference genes is critical to establishing sensitive and reproducible qRT-PCR-based assays. The current study was designed to identify the appropriate reference genes in blood leukocytes of bottlenose dolphins (Tursiops truncatus) for gene transcription research. Seventy-five blood samples collected from 7 bottlenose dolphins were used to analyze 15 candidate HKGs (ACTB, B2M, GAPDH, HPRT1, LDHB, PGK1, RPL4, RPL8, RPL18, RPS9, RPS18, TFRC, YWHAZ, LDHA, SDHA). HKG stability in qRT-PCR was determined using geNorm, NormFinder, BestKeeper and comparative delta Ct algorithms. Utilization of RefFinder, which combined all 4 algorithms, suggested that PGK1, HPRT1 and RPL4 were the most stable HKGs in bottlenose dolphin blood. Gene transcription perturbations in blood can serve as an indication of health status in cetaceans as it occurs prior to alterations in hematology and chemistry. This study identified HKGs that could be used in gene transcript studies, which may contribute to further mRNA relative quantification research in the peripheral blood leukocytes in captive cetaceans.
Collapse
|
33
|
Hayes CJ, Dalton TM. Microfluidic droplet-based PCR instrumentation for high-throughput gene expression profiling and biomarker discovery. BIOMOLECULAR DETECTION AND QUANTIFICATION 2015; 4:22-32. [PMID: 27077035 PMCID: PMC4822205 DOI: 10.1016/j.bdq.2015.04.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 04/23/2015] [Accepted: 04/24/2015] [Indexed: 01/02/2023]
Abstract
PCR is a common and often indispensable technique used in medical and biological research labs for a variety of applications. Real-time quantitative PCR (RT-qPCR) has become a definitive technique for quantitating differences in gene expression levels between samples. Yet, in spite of this importance, reliable methods to quantitate nucleic acid amounts in a higher throughput remain elusive. In the following paper, a unique design to quantify gene expression levels at the nanoscale in a continuous flow system is presented. Fully automated, high-throughput, low volume amplification of deoxynucleotides (DNA) in a droplet based microfluidic system is described. Unlike some conventional qPCR instrumentation that use integrated fluidic circuits or plate arrays, the instrument performs qPCR in a continuous, micro-droplet flowing process with droplet generation, distinctive reagent mixing, thermal cycling and optical detection platforms all combined on one complete instrument. Detailed experimental profiling of reactions of less than 300 nl total volume is achieved using the platform demonstrating the dynamic range to be 4 order logs and consistent instrument sensitivity. Furthermore, reduced pipetting steps by as much as 90% and a unique degree of hands-free automation makes the analytical possibilities for this instrumentation far reaching. In conclusion, a discussion of the first demonstrations of this approach to perform novel, continuous high-throughput biological screens is presented. The results generated from the instrument, when compared with commercial instrumentation, demonstrate the instrument reliability and robustness to carry out further studies of clinical significance with added throughput and economic benefits.
Collapse
Affiliation(s)
- Christopher J Hayes
- Stokes Institute, Department of Mechanical, Aeronautical and Biomedical Engineering, University of Limerick, Limerick, Ireland; Department of Life Sciences, University of Limerick, Limerick, Ireland
| | - Tara M Dalton
- Stokes Institute, Department of Mechanical, Aeronautical and Biomedical Engineering, University of Limerick, Limerick, Ireland
| |
Collapse
|
34
|
Puech C, Dedieu L, Chantal I, Rodrigues V. Design and evaluation of a unique SYBR Green real-time RT-PCR assay for quantification of five major cytokines in cattle, sheep and goats. BMC Vet Res 2015; 11:65. [PMID: 25889787 PMCID: PMC4369058 DOI: 10.1186/s12917-015-0382-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 02/27/2015] [Indexed: 11/24/2022] Open
Abstract
Background Today, when more than 60% of animal diseases are zoonotic, understanding their origin and development and identifying protective immune responses in ruminants are major challenges. Robust, efficient and cost-effective tools are preconditions to solve these challenges. Cytokines play a key role in the main mechanisms by which the immune system is balanced in response to infectious pathogens. The cytokine balance has thus become the focus of research to characterize immune response in ruminants. Currently, SYBR Green reverse transcriptase quantitative PCR (RT-qPCR) is the most widely method used to investigate cytokine gene expression in ruminants, but the conditions in which the many assays are carried out vary considerably and need to be properly evaluated. Accordingly, the quantification of gene expression by RT-qPCR requires normalization by multiple reference genes. The objective of the present study was thus to develop an RT-qPCR assay to simultaneously quantify the expression of several cytokines and reference genes in three ruminant species. In this paper, we detail each stage of the experimental protocol, check validation parameters and report assay performances, following MIQE guidelines. Results Ten novel primer sets were designed to quantify five cytokine genes (IL-4, IL-10, IL-12B, IFN-γ and TNF-α) and five reference genes (ACTB, GAPDH, H3F3A, PPIA and YWHAZ) in cattle, sheep, and goats. All the primer sets were designed to span exon-exon boundaries and use the same hybridization temperature. Each stage of the RT-qPCR method was detailed; their specificity and efficiency checked, proved and are reported here, demonstrating the reproducibility of our method, which is capable of detecting low levels of cytokine mRNA up to one copy whatever the species. Finally, we checked the stability of candidate reference gene expression, performed absolute quantification of cytokine and reference gene mRNA in whole blood samples and relative expression of cytokine mRNA in stimulated PBMC samples. Conclusions We have developed a novel RT-qPCR assay for the simultaneous relative quantification of five major cytokines in cattle, sheep and goats, and their accurate normalization by five reference genes. This accurate and easily reproducible tool can be used to investigate ruminant immune responses and is widely accessible to the veterinary research community. Electronic supplementary material The online version of this article (doi:10.1186/s12917-015-0382-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Carinne Puech
- INRA, UMR1309 CMAEE, Montpellier, F-34398, France. .,CIRAD, UMR CMAEE, Montpellier, F-34398, France.
| | | | | | - Valérie Rodrigues
- INRA, UMR1309 CMAEE, Montpellier, F-34398, France. .,CIRAD, UMR CMAEE, Montpellier, F-34398, France.
| |
Collapse
|
35
|
Vorachek WR, Bobe G, Hall JA. Reference gene selection for quantitative PCR studies in bovine neutrophils. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/abb.2013.410a3002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|