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Rajkhowa S, Sonowal J, Sengar GS, Pegu SR, Deb R, Das PJ, Doley J, Paul S, Gupta VK. Assessment of reference genes for qRT-PCR normalization to elucidate host response to African swine fever infection. Braz J Microbiol 2024:10.1007/s42770-024-01439-2. [PMID: 38963474 DOI: 10.1007/s42770-024-01439-2] [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: 02/02/2024] [Accepted: 06/24/2024] [Indexed: 07/05/2024] Open
Abstract
Viral infection disrupts the normal regulation of the host gene's expression. In order to normalise the expression of dysregulated host genes upon virus infection, analysis of stable reference housekeeping genes using quantitative real-time-PCR (qRT-PCR) is necessary. In the present study, healthy and African swine fever virus (ASFV) infected porcine tissues were assessed for the expression stability of five widely used housekeeping genes (HPRT1, B2M, 18 S rRNA, PGK1 and H3F3A) as reference genes using standard algorithm. Total RNA from each tissue sample (lymph node, spleen, kidney, heart and liver) from healthy and ASFV-infected pigs was extracted and subsequently cDNA was synthesized, and subjected to qRT-PCR. Stability analysis of reference genes expression was performed using the Comparative delta CT, geNorm, BestKeeper and NormFinder algorithm available at RefFinder for the different groups. Direct Cycle threshold (CT) values of samples were used as an input for the web-based tool RefFinder. HPRT1 in spleen, 18 S rRNA in liver and kidney and H3F3A in heart and lymph nodes were found to be stable in the individual healthy tissue group (group A). The majority of the ASFV-infected organs (liver, kidney, heart, lymph node) exhibited H3F3A as stable reference gene with the exception of the ASFV-infected spleen, where HPRT1 was found to be the stable gene (group B). HPRT1 was found to be stable in all combinations of all CT values of both healthy and ASFV-infected porcine tissues (group C). Of five different reference genes investigated for their stability in qPCR analysis, the present study revealed that the 18 S rRNA, H3F3A and HPRT1 genes were optimal reference genes in healthy and ASFV-infected different porcine tissue samples. The study revealed the stable reference genes found in healthy as well as ASF-infected pigs and these reference genes identified through this study will form the baseline data which will be very useful in future investigations on gene expression in ASFV-infected pigs.
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Affiliation(s)
- Swaraj Rajkhowa
- ICAR-National Research Centre on Pig, Rani, Guwahati, Assam, 781131, India.
| | - Joyshikh Sonowal
- ICAR-National Research Centre on Pig, Rani, Guwahati, Assam, 781131, India
- Krishi Vigyan Kendra Karimganj, Assam Agricultural University, Jorhat, Assam, 788712, India
| | | | - Seema Rani Pegu
- ICAR-National Research Centre on Pig, Rani, Guwahati, Assam, 781131, India
| | - Rajib Deb
- ICAR-National Research Centre on Pig, Rani, Guwahati, Assam, 781131, India
| | - Pranab Jyoti Das
- ICAR-National Research Centre on Pig, Rani, Guwahati, Assam, 781131, India
| | - Juwar Doley
- ICAR-National Research Centre on Pig, Rani, Guwahati, Assam, 781131, India
| | - Souvik Paul
- ICAR-National Research Centre on Pig, Rani, Guwahati, Assam, 781131, India
| | - Vivek Kumar Gupta
- ICAR-National Research Centre on Pig, Rani, Guwahati, Assam, 781131, India
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2
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González F, Cervantes M, Morales A, Valle JA, Camacho R, ngélica Morales-Becerra A, Bernal H, aría Mendoza SM, Htoo JK. Effect of supplementing a Bacillus subtilis-based probiotic on performance, intestinal integrity, and serum antioxidant capacity and metabolites concentrations of heat-stressed growing pigs. J Anim Sci 2024; 102:skae012. [PMID: 38219255 PMCID: PMC10825842 DOI: 10.1093/jas/skae012] [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: 10/13/2023] [Accepted: 01/16/2024] [Indexed: 01/16/2024] Open
Abstract
Exposing pigs to heat stress (HS) seems to modify the intestinal microbiota which may compromise the integrity of the small intestine epithelia. Probiotics, live microorganisms, can help pigs to maintain a healthy intestinal environment. Eighty pigs (21.6 ± 3.4 kg body weight) exposed to HS or thermal neutral (TN) conditions were used to evaluate the effect of a Bacillus subtilis-based probiotic on performance, body temperature, and intestinal integrity. Treatments were: TN pigs fed a control diet without (TN-C) or with 1 × 106 CFU probiotic/g of feed (TN-P), and HS pigs fed a control without (HS-C) or with probiotic (HS-P). The control diet was formulated with wheat, soybean meal, and free amino acids (AA). Feed and water were freely available during the 21-d study. At completion, samples from duodenum, jejunum, and ileum were collected to analyze epithelial histology and tight junction protein expression; antioxidant activity, and free AA and metabolites in serum. Relative abundance of Lactobacillus, Bifidobacterium, Escherichia coli, and Bacillus in ileal content was analyzed. Ambient temperature in the TN room ranged from 19 to 25 °C, and in HS room from 30 to 38.5 °C. Intestinal temperature in HS-P pigs was lower than in HS-C pigs. Weight gain and feed intake reduced, but feed:gain and respiration rate increased in HS compared to TN pigs, regardless of diet (P < 0.01). Probiotic increased weight gain and improved feed:gain (P < 0.05) in both TN and HS pigs, but feed intake did not differ. Heat stress decreased villi height in jejunum and villi height:crypt depth in duodenum and jejunum (P < 0.05). Probiotic increased villi height in duodenum and ileum, and villi height:crypt depth in all small intestine segments (P < 0.05). Relative abundance of Lactobacillus and Bifidobacterium tended to reduce, and E. coli tended to increase (P < 0.10) in ileal content of HS-C pigs. Ileal relative abundance of Bacillus was higher (P < 0.01) in HS-P pigs than in HS-C and TN-C pigs. Cystathionine, homocysteine, hydroxylysine, α-amino-adipic acid, citrulline, α-amino-n-butyric acid, P-Ser, and taurine were higher in HS than in TN pigs (P < 0.05). These data confirm the negative effect of HS on performance, body temperature, and intestinal integrity of pigs. These data suggest that supplementing 1 × 106 CFU probiotic/g of feed based on Bacillus subtilis DSM 32540 may help to counteract the negative effects of HS on the performance and intestinal integrity of pigs.
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Affiliation(s)
- Fernanda González
- Instituto de Ciencias Agrícolas, Universidad Autónoma de Baja California, Mexicali, BC, México
| | - Miguel Cervantes
- Instituto de Ciencias Agrícolas, Universidad Autónoma de Baja California, Mexicali, BC, México
| | - Adriana Morales
- Instituto de Ciencias Agrícolas, Universidad Autónoma de Baja California, Mexicali, BC, México
| | - José Alan Valle
- Instituto de Ciencias Agrícolas, Universidad Autónoma de Baja California, Mexicali, BC, México
| | - Reyna Lucero Camacho
- Instituto de Ciencias Agrícolas, Universidad Autónoma de Baja California, Mexicali, BC, México
| | | | - Hugo Bernal
- Facultad de Agronomía, Universidad Autónoma de Nuevo León, Monterrey, NL, México
| | | | - John K Htoo
- Evonik Operations GmbH, Hanau-Wolfgang, Germany
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Lv K, Lou P, Liu S, Wang Y, Yang J, Zhou P, Zhou X, Lu Y, Wang H, Cheng J, Liu J. Injectable Multifunctional Composite Hydrogel as a Combination Therapy for Preventing Postsurgical Adhesion. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2303425. [PMID: 37649233 DOI: 10.1002/smll.202303425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/24/2023] [Indexed: 09/01/2023]
Abstract
Postsurgical adhesion (PA) is a common and serious postoperative complication that affects millions of patients worldwide. However, current commercial barrier materials are insufficient to inhibit diverse pathological factors during PA formation, and thus, highly bioactive materials are needed. Here, this work designs an injectable multifunctional composite hydrogel that can serve as a combination therapy for preventing PA. In brief, this work reveals that multiple pathological events, such as chronic inflammatory and fibrotic processes, contribute to adhesion formation in vivo, and such processes can not be attenuated by barrier material (e.g., hydrogel) alone treatments. To solve this limitation, this work designs a composite hydrogel made of the cationic self-assembling peptide KLD2R and TGF-β receptor inhibitor (TGF-βRi)-loaded mesenchymal stem cell-derived nanovesicles (MSC-NVs). The resulting composite hydrogel displays multiple functions, including physical separation of the injured tissue areas, antibacterial effects, and local delivery and sustained release of anti-inflammatory MSC-NVs and antifibrotic TGF-βRi. As a result, this composite hydrogel effectively inhibited local inflammation, fibrosis and adhesion formation in vivo. Moreover, the hydrogel also exhibits good biocompatibility and biodegradability in vivo. Together, the results highlight that this "all-in-one" composite hydrogel strategy may provide insights into designing advanced therapies for many types of tissue injury.
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Affiliation(s)
- Ke Lv
- Department of General Surgery and NHC Key Laboratory of Transplant Engineering and Immunology, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Peng Lou
- Department of General Surgery and NHC Key Laboratory of Transplant Engineering and Immunology, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Shuyun Liu
- Department of General Surgery and NHC Key Laboratory of Transplant Engineering and Immunology, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Yizhuo Wang
- Department of General Surgery and NHC Key Laboratory of Transplant Engineering and Immunology, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Jinlin Yang
- Department of Gastroenterology and Hepatology, Sichuan University-University of Oxford Huaxi Joint Centre for Gastrointestinal Cancer, West China Hospital, Sichuan University, Chengdu, China
| | - Pingya Zhou
- Department of General Surgery and NHC Key Laboratory of Transplant Engineering and Immunology, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Xiyue Zhou
- Department of General Surgery and NHC Key Laboratory of Transplant Engineering and Immunology, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Yanrong Lu
- Department of General Surgery and NHC Key Laboratory of Transplant Engineering and Immunology, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Hongren Wang
- Department of Pathogenic Biology, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Jingqiu Cheng
- Department of General Surgery and NHC Key Laboratory of Transplant Engineering and Immunology, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Jingping Liu
- Department of General Surgery and NHC Key Laboratory of Transplant Engineering and Immunology, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
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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.
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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.
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Hasuda AL, Person E, Khoshal A, Bruel S, Puel S, Oswald IP, Bracarense APFRL, Pinton P. Emerging mycotoxins induce hepatotoxicity in pigs' precision-cut liver slices and HepG2 cells. Toxicon 2023; 231:107195. [PMID: 37315815 DOI: 10.1016/j.toxicon.2023.107195] [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: 04/20/2023] [Revised: 05/25/2023] [Accepted: 06/09/2023] [Indexed: 06/16/2023]
Abstract
Emerging mycotoxins are currently gaining more attention due to their high frequency of contamination in foods and grains. However, most data available in the literature are in vitro, with few in vivo results that prevent establishing their regulation. Beauvericin (BEA), enniatins (ENNs), emodin (EMO), apicidin (API) and aurofusarin (AFN) are emerging mycotoxins frequently found contaminating food and there is growing interest in studying their impact on the liver, a key organ in the metabolization of these components. We used an ex vivo model of precision-cut liver slices (PCLS) to verify morphological and transcriptional changes after acute exposure (4 h) to these mycotoxins. The human liver cell line HepG2 was used for comparison purposes. Most of the emerging mycotoxins were cytotoxic to the cells, except for AFN. In cells, BEA and ENNs were able to increase the expression of genes related to transcription factors, inflammation, and hepatic metabolism. In the explants, only ENN B1 led to significant changes in the morphology and expression of a few genes. Overall, our results demonstrate that BEA, ENNs, and API have the potential to be hepatotoxic.
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Affiliation(s)
- Amanda Lopes Hasuda
- Laboratory of Animal Pathology, Universidade Estadual de Londrina, P.O. Box 10.011, Londrina, PR, 86057-970, Brazil; TOXALIM (UMR 1331), Institute National de Recherche pour L'Agriculture L'Alimentation et L'Environnement Centre Occitanie-Toulouse, UPS, 31027, Toulouse, France.
| | - Elodie Person
- TOXALIM (UMR 1331), Institute National de Recherche pour L'Agriculture L'Alimentation et L'Environnement Centre Occitanie-Toulouse, UPS, 31027, Toulouse, France.
| | - Abdullah Khoshal
- TOXALIM (UMR 1331), Institute National de Recherche pour L'Agriculture L'Alimentation et L'Environnement Centre Occitanie-Toulouse, UPS, 31027, Toulouse, France.
| | - Sandrine Bruel
- TOXALIM (UMR 1331), Institute National de Recherche pour L'Agriculture L'Alimentation et L'Environnement Centre Occitanie-Toulouse, UPS, 31027, Toulouse, France
| | - Sylvie Puel
- TOXALIM (UMR 1331), Institute National de Recherche pour L'Agriculture L'Alimentation et L'Environnement Centre Occitanie-Toulouse, UPS, 31027, Toulouse, France.
| | - Isabelle P Oswald
- TOXALIM (UMR 1331), Institute National de Recherche pour L'Agriculture L'Alimentation et L'Environnement Centre Occitanie-Toulouse, UPS, 31027, Toulouse, France.
| | - Ana Paula F R L Bracarense
- Laboratory of Animal Pathology, Universidade Estadual de Londrina, P.O. Box 10.011, Londrina, PR, 86057-970, Brazil.
| | - Philippe Pinton
- TOXALIM (UMR 1331), Institute National de Recherche pour L'Agriculture L'Alimentation et L'Environnement Centre Occitanie-Toulouse, UPS, 31027, Toulouse, France.
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Eugenio FA, van Milgen J, Duperray J, Sergheraert R, Le Floc’h N. Apparent jejunal amino acid digestibility, gut morphology, and the expression of intestinal amino acid transporters in pigs fed protein or free amino acids. J Anim Sci 2023; 101:skac417. [PMID: 36583730 PMCID: PMC9904176 DOI: 10.1093/jas/skac417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/30/2022] [Indexed: 12/31/2022] Open
Abstract
Dietary amino acids (AA) supplied as protein or in free form are not only digested and absorbed at different rates but can also induce differences in the intestinal physiology of pigs. We compared the apparent jejunal AA digestibility, intestinal morphology, and gene expression of AA transporters of pigs fed diets providing different forms of AA. Thirty growing pigs (33.7 ± 4.1 kg) were fed one of three experimental diets that provided AA either as protein from feather meal (INT), as free AA and small peptides obtained by extensive acid hydrolysis of feathers (HYD), or as a mix of individual purified AA with the same AA profile as HYD (FAA). Pigs were fed the same quantity of feed, energy, and AA. After 14 d, pigs were slaughtered 3 h after feeding a meal with indigestible markers. Digesta and tissue were collected from different sections of the small intestine. Jejunal digesta was used to measure apparent jejunal digestibility of AA. Samples of the duodenum, jejunum, and ileum were used to measure intestinal morphology and the gene expression of intestinal AA transporters. The measured apparent jejunal digestibility of AA of INT was lower compared to HYD and FAA (P < 0.05). The apparent jejunal digestibility of Cys, Gly, His, Met, and Pro was lower for FAA compared to HYD (P < 0.05). This may be due to the small peptides in HYD, which are absorbed faster than individual AA. The villi area in the ileum of HYD fed pigs was the highest (P < 0.05) among the treatments, which may be associated with the reabsorption of endogenous proteins, which occurs mostly in the ileum. In the duodenum, HYD and FAA had lower expression of PepT1 (P < 0.01) probably due to the rapid transit time of digesta compared to INT fed pigs. Pigs fed HYD expressed more ASCT2 (P = 0.02) and CAT-1 (P = 0.04) in the jejunum compared to the pigs fed the other diets. The expression of these transporters along the intestine depended on the relative abundance of readily absorbable dietary AA. Results showed that dietary AA form can have an influence on the morphology and on the expression of different AA transporters along the different sections of the small intestine.
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Affiliation(s)
- Francis Amann Eugenio
- PEGASE, INRAE, Institut Agro, 35590, Saint-Gilles, France
- BCF Life Sciences, Boisel, 56140 Pleucadeuc, France
| | | | | | | | - Nathalie Le Floc’h
- PEGASE, INRAE, Institut Agro, 35590, Saint-Gilles, France
- BCF Life Sciences, Boisel, 56140 Pleucadeuc, France
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Morales A, Sánchez V, Pérez B, Camacho RL, Arce N, Avelar E, González-Vega JC, Htoo JK, Cervantes M. Effect of dl-methionine supplementation above requirement on performance; intestinal morphology, antioxidant activity, and gene expression; and serum concentration of amino acids in heat stressed pigs. J Anim Sci 2023; 101:skac379. [PMID: 36383458 PMCID: PMC9833035 DOI: 10.1093/jas/skac379] [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: 08/09/2022] [Accepted: 11/11/2022] [Indexed: 11/17/2022] Open
Abstract
The intestinal morphology and function can be compromised in pigs exposed to heat stress (HS), partly due to increased production of reactive-oxygen species. Because methionine (Met) functions as intracellular antioxidant, the requirement of Met may be increased in HS-pigs. The effect of dietary supplementation with dl-Met above requirement on performance, small intestine morphology, antioxidant enzymes activity, amino acid transporters expression, and serum concentration (SC) of free AA in HS-pigs was evaluated. A basal wheat-soybean meal diet was formulated to meet 100% Met requirement with the other indispensable AA exceeding at least 20% their requirement. Sixty individually housed pigs (23.0 ± 2.4 kg BW, 12 pigs per treatment) were randomly assigned to five treatments: TN100, thermal-neutral (22.7 °C) housed pigs fed the basal diet; HS100, HS120, HS140, HS160; HS-pigs (29.6 °C to 39.4 °C) fed the basal diet supplemented with dl-Met to contain 0%, 20%, 40%, and 60% dl-Met above the requirement, respectively. Pigs had free access to feed and water during the 21-d trial. Blood samples were collected on day 18 to analyze the absorptive AA-SC. The effect of ambient temperature (HS100 vs. TN100), as well as the linear and quadratic effects of increasing Met levels in the diets for HS-pigs were analyzed. The HS100 pigs gained less weight than TN100 and HS120 pigs (P < 0.01); gain:feed was also higher in HS120 pigs than in HS100 pigs (P ≤ 0.05). Feed intake of TN100 pigs was higher than that of HS-pigs fed the dl-Met supplemented diets (P < 0.05). Villi height reduced in pigs HS, but Met supplementation quadratically increased it (P < 0.05). Superoxide dismutase and catalase activities, reduced glutathione concentration, and relative expression of B0AT2 in ileum decreased (P < 0.05), but glutathione peroxidase activity increased in HS-pigs. dl-Met supplementation linearly affected catalase and glutathione peroxidase activities, as well as the relative expression of b0,+AT in jejunum (P < 0.05) of HS-pigs. The SC of Ile, Leu, Lys, Phe, and Val were higher in HS100 pigs than in TN100 pigs (P < 0.05). Graded levels of supplemental dl-Met in diets for HS-pigs linearly decreased SC of Ile, Leu, and Val (P < 0.05), tended to decrease His, Lys, and Thr (P < 0.10), and increased Met (P < 0.01). In conclusion, HS had negative effect on weight gain and intestinal morpho-physiology; however, it was ameliorated by adding 20% Met above the requirement in diets for growing pigs.
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Affiliation(s)
- Adriana Morales
- ICA-Universidad Autónoma de Baja California, 21100 Mexicali, B.C., México
| | - Verónica Sánchez
- ICA-Universidad Autónoma de Baja California, 21100 Mexicali, B.C., México
| | - Bayron Pérez
- ICA-Universidad Autónoma de Baja California, 21100 Mexicali, B.C., México
| | - Reyna L Camacho
- ICA-Universidad Autónoma de Baja California, 21100 Mexicali, B.C., México
| | - Néstor Arce
- ICA-Universidad Autónoma de Baja California, 21100 Mexicali, B.C., México
| | - Ernesto Avelar
- ICA-Universidad Autónoma de Baja California, 21100 Mexicali, B.C., México
| | | | | | - Miguel Cervantes
- ICA-Universidad Autónoma de Baja California, 21100 Mexicali, B.C., México
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Xu J, Yang M, Shao AZ, Pan HW, Fan YX, Chen KP. Identification and Validation of Common Reference Genes for Normalization of Esophageal Squamous Cell Carcinoma Gene Expression Profiles. BIOMED RESEARCH INTERNATIONAL 2022; 2022:9125242. [PMID: 36467891 PMCID: PMC9711964 DOI: 10.1155/2022/9125242] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 09/04/2024]
Abstract
Esophageal squamous cell carcinoma (ESCC) is one of the subtypes of esophageal cancer with Chinese characteristics, and its five-year survival rate is less than 20%. Early diagnosis is beneficial to improving the survival rate of ESCC significantly. Quantitative Real-Time Polymerase Chain Reaction is a high-throughput technique that can quantify tumor-related genes for early diagnosis. Its accuracy largely depends on the stability of the reference gene. There is no systematic scientific basis to demonstrate which reference gene expression is stable in ESCC and no consensus on the selection of internal reference. Therefore, this research used four software programs (The comparative delta-Ct method, GeNorm, NormFinder, and BestKeeper) to evaluate the expression stability of eight candidate reference genes commonly used in other tumor tissues and generated a comprehensive analysis by RefFinder. Randomly selected transcriptome sequencing analysis confirmed the SPP1 gene is closely related to ESCC. It was found that the expression trend of SPP1 obtained by RPS18 and PPIA as internal reference genes were the same as that of sequencing. The results show that RPS18 and PPIA are stable reference genes, and PPIA + RPS18 are a suitable reference gene combination. This is a reference gene report that combines transcriptome sequencing analysis and only focuses on ESCC, which makes the quantification more precise, systematic, and standardized, and promotes gene regulation research and the early diagnosis of ESCC in the future.
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Affiliation(s)
- Jia Xu
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Ming Yang
- Department of General Surgery, Fifth People's Hospital of Huaian City, Huaian, China
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, China
| | - Ai-zhong Shao
- Department of Cardiothorac Surgery, Affiliated People's Hospital of Jiangsu University, Zhenjiang, China
| | - Hui-wen Pan
- Department of Cardiothoracic Surgery, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Yi-xuan Fan
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Ke-ping Chen
- School of Life Sciences, Jiangsu University, Zhenjiang, China
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Fodor CC, Fouhse J, Drouin D, Ma T, Willing BP, Guan LL, Cobo ER. Colonic innate immune defenses and microbiota alterations in acute swine dysentery. Microb Pathog 2022; 173:105873. [DOI: 10.1016/j.micpath.2022.105873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/04/2022] [Accepted: 11/05/2022] [Indexed: 11/11/2022]
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Koehler S, Springer A, Issel N, Klinger S, Wendt M, Breves G, Strube C. Effects of adult Ascaris suum and their antigens (total and trans-cuticular excretory-secretory antigen, cuticular somatic antigen) on intestinal nutrient transport in vivo. Parasitology 2022; 150:1-34. [PMID: 36274629 PMCID: PMC10090646 DOI: 10.1017/s0031182022001512] [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: 06/08/2022] [Revised: 09/20/2022] [Accepted: 10/14/2022] [Indexed: 11/05/2022]
Abstract
Ascaris suum constitutes a major problem in commercial pig farming worldwide. Lower weight gains in infected pigs probably result from impaired nutrient absorption. This study investigated intestinal nutrient transport in 4 groups of 6 pigs each, which were inoculated with 30 living adult A. suum , or antigen fractions consisting of (1) total excretory–secretory (ES) antigens of adult worms, (2) ES antigens secreted exclusively from the parasites' body surface (trans-cuticular ES) and (3) cuticular somatic antigens of A. suum , compared to placebo-treated controls. Three days after inoculation into the gastrointestinal tract, glucose, alanine and glycyl-l -glutamine transport was measured in the duodenum, jejunum and ileum using Ussing chambers. Transcription of relevant genes [sodium glucose cotransporter 1 (SGLT1), glucose transporter 1 (GLUT1), GLUT2, hypoxia-inducible factor 1-alpha (Hif1α ), interleukin-4 (IL-4), IL-13, signal transducer and activator of transcription 6 (STAT6), peptide transporter 1 (PepT1)] and expression of transport proteins [SGLT1, phosphorylated SGLT1, GLUT2, Na+/K+-ATPase, amino acid transporter A (ASCT1), PepT1] were studied. Although no significant functional changes were noted after exposure to adult A. suum , a significant downregulation of jejunal GLUT1, STAT6, Hif1α and PepT1 transcription as well as ileal GLUT2 and PepT1 expression indicates a negative impact of infection on transport physiology. Therefore, the exposure period of 3 days may have been insufficient for functional alterations to become apparent. In contrast, A. suum antigens mainly induced an upregulation of transport processes and an increase in transcription of relevant genes in the duodenum and jejunum, possibly as a compensatory reaction after a transient downregulation. In the ileum, a consistent pattern of downregulation was observed in all inoculated groups, in line with the hypothesis of impaired nutrient transport.
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Affiliation(s)
- Sarina Koehler
- Institute for Parasitology, Centre for Infection Medicine, University of Veterinary Medicine Hannover, Hanover, Germany
| | - Andrea Springer
- Institute for Parasitology, Centre for Infection Medicine, University of Veterinary Medicine Hannover, Hanover, Germany
| | - Nicole Issel
- Institute for Physiology and Cell Biology, University of Veterinary Medicine Hannover, Hanover, Germany
| | - Stefanie Klinger
- Institute for Physiology and Cell Biology, University of Veterinary Medicine Hannover, Hanover, Germany
| | - Michael Wendt
- Clinic for Swine, Small Ruminants, Forensic Medicine and Ambulatory Service, University of Veterinary Medicine Hannover, Hanover, Germany
| | - Gerhard Breves
- Institute for Physiology and Cell Biology, University of Veterinary Medicine Hannover, Hanover, Germany
| | - Christina Strube
- Institute for Parasitology, Centre for Infection Medicine, University of Veterinary Medicine Hannover, Hanover, Germany
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11
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Wu Q, Han Y, Wu X, Wang Y, Su Q, Shen Y, Guan K, Michal JJ, Jiang Z, Liu B, Zhou X. Integrated time-series transcriptomic and metabolomic analyses reveal different inflammatory and adaptive immune responses contributing to host resistance to PRRSV. Front Immunol 2022; 13:960709. [PMID: 36341362 PMCID: PMC9631489 DOI: 10.3389/fimmu.2022.960709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 10/05/2022] [Indexed: 11/20/2022] Open
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is a highly contagious disease that affects the global pig industry. To understand mechanisms of susceptibility/resistance to PRRSV, this study profiled the time-serial white blood cells transcriptomic and serum metabolomic responses to PRRSV in piglets from a crossbred population of PRRSV-resistant Tongcheng pigs and PRRSV-susceptible Large White pigs. Gene set enrichment analysis (GSEA) illustrated that PRRSV infection up-regulated the expression levels of marker genes of dendritic cells, monocytes and neutrophils and inflammatory response, but down-regulated T cells, B cells and NK cells markers. CIBERSORT analysis confirmed the higher T cells proportion in resistant pigs during PRRSV infection. Resistant pigs showed a significantly higher level of T cell activation and lower expression levels of monocyte surface signatures post infection than susceptible pigs, corresponding to more severe suppression of T cell immunity and inflammatory response in susceptible pigs. Differentially expressed genes between resistant/susceptible pigs during the course of infection were significantly enriched in oxidative stress, innate immunity and humoral immunity, cell cycle, biotic stimulated cellular response, wounding response and behavior related pathways. Fourteen of these genes were distributed in 5 different QTL regions associated with PRRSV-related traits. Chemokine CXCL10 levels post PRRSV infection were differentially expressed between resistant pigs and susceptible pigs and can be a promising marker for susceptibility/resistance to PRRSV. Furthermore, the metabolomics dataset indicated differences in amino acid pathways and lipid metabolism between pre-infection/post-infection and resistant/susceptible pigs. The majority of metabolites levels were also down-regulated after PRRSV infection and were significantly positively correlated to the expression levels of marker genes in adaptive immune response. The integration of transcriptome and metabolome revealed concerted molecular events triggered by the infection, notably involving inflammatory response, adaptive immunity and G protein-coupled receptor downstream signaling. This study has increased our knowledge of the immune response differences induced by PRRSV infection and susceptibility differences at the transcriptomic and metabolomic levels, providing the basis for the PRRSV resistance mechanism and effective PRRS control.
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Affiliation(s)
- Qingqing Wu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Yu Han
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Xianmeng Wu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Yuan Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Qiuju Su
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Yang Shen
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Kaifeng Guan
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Jennifer J. Michal
- Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA, United States
| | - Zhihua Jiang
- Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA, United States
| | - Bang Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- The Engineering Technology Research Center of Hubei Province Local Pig Breed Improvement, Huazhong Agricultural University, Wuhan, China
- *Correspondence: Xiang Zhou, ; Bang Liu,
| | - Xiang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- The Engineering Technology Research Center of Hubei Province Local Pig Breed Improvement, Huazhong Agricultural University, Wuhan, China
- *Correspondence: Xiang Zhou, ; Bang Liu,
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12
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Hasuda AL, Person E, Khoshal AK, Bruel S, Puel S, Oswald IP, Bracarense APFL, Pinton P. Deoxynivalenol induces apoptosis and inflammation in the liver: Analysis using precision-cut liver slices. Food Chem Toxicol 2022; 163:112930. [DOI: 10.1016/j.fct.2022.112930] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/28/2022] [Accepted: 03/16/2022] [Indexed: 12/22/2022]
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13
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Novak B, Lopes Hasuda A, Ghanbari M, Mayumi Maruo V, Bracarense APFRL, Neves M, Emsenhuber C, Wein S, Oswald IP, Pinton P, Schatzmayr D. Effects of Fusarium metabolites beauvericin and enniatins alone or in mixture with deoxynivalenol on weaning piglets. Food Chem Toxicol 2021; 158:112719. [PMID: 34843867 DOI: 10.1016/j.fct.2021.112719] [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: 10/21/2021] [Revised: 11/22/2021] [Accepted: 11/25/2021] [Indexed: 01/16/2023]
Abstract
The impact of the Fusarium-derived metabolites beauvericin, enniatin B and B1 (EB) alone or in combination with deoxynivalenol (DON) was investigated in 28-29 days old weaning piglets over a time period of 14 days. The co-application of EB and DON (EB + DON) led to a significant decrease in the weight gain of the animals. Liver enzyme activities in plasma were significantly decreased at day 14 in piglets receiving the EB + DON-containing diet compared to piglets receiving the control diet. All mycotoxin-contaminated diets led to moderate to severe histological lesions in the jejunum, the liver and lymph nodes. Shotgun metagenomics revealed a significant effect of EB-application on the gut microbiota. Our results provide novel insights into the harmful impact of emerging mycotoxins alone or with DON on the performance, gut health and immunological parameters in pigs.
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Affiliation(s)
- Barbara Novak
- BIOMIN Research Center, Technopark 1, 3430, Tulln, Austria.
| | - Amanda Lopes Hasuda
- Laboratory of Animal Pathology, State University of Londrina, P.O. Box 10.011, Londrina, PR, 86057-970, Brazil; Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, 31027, Toulouse, France.
| | - Mahdi Ghanbari
- BIOMIN Research Center, Technopark 1, 3430, Tulln, Austria.
| | - Viviane Mayumi Maruo
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, 31027, Toulouse, France; Universidade Federal do Tocantins, Araguaína, 77824-838, Brazil.
| | - Ana Paula F R L Bracarense
- Laboratory of Animal Pathology, State University of Londrina, P.O. Box 10.011, Londrina, PR, 86057-970, Brazil.
| | - Manon Neves
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, 31027, Toulouse, France.
| | | | - Silvia Wein
- BIOMIN Research Center, Technopark 1, 3430, Tulln, Austria.
| | - Isabelle P Oswald
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, 31027, Toulouse, France.
| | - Philippe Pinton
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRA, ENVT, INP-Purpan, UPS, 31027, Toulouse, France.
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14
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Zhao N, Xu J, Jiao L, Qiu M, Zhang J, Wei X, Fan M. Transcriptome-Based Selection and Validation of Reference Genes for Gene Expression Analysis of Alicyclobacillus acidoterrestris Under Acid Stress. Front Microbiol 2021; 12:731205. [PMID: 34512609 PMCID: PMC8430261 DOI: 10.3389/fmicb.2021.731205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 08/10/2021] [Indexed: 11/13/2022] Open
Abstract
Alicyclobacillus acidoterrestris is a major concern in fruit juice industry due to its spoilage potential of acidic fruit juice. Quantifying the expression levels of functional genes by real-time quantitative polymerase chain reaction (RT-qPCR) is necessary to elucidate the response mechanisms of A. acidoterrestris to acid stress. However, appropriate reference genes (RGs) for data normalization are required to obtain reliable RT-qPCR results. In this study, eight novel candidate RGs were screened based on transcriptome datasets of A. acidoterrestris under acid stress. The expression stability of eight new RGs and commonly used RG 16s rRNA was assessed using geNorm, NormFinder, and BestKeeper algorithms. Moreover, the comprehensive analysis using the RefFinder program and the validation using target gene ctsR showed that dnaG and dnaN were the optimal multiple RGs for normalization at pH 4.0; ytvI, dnaG, and 16s rRNA at pH 3.5; icd and dnaG at pH 3.0; and ytvI, dnaG, and spoVE at pH 2.5. This study revealed for the first time that A. acidoterrestris had different suitable RGs under different acid conditions, with implications for further deciphering the acid response mechanisms of this spoilage-causing bacterium.
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Affiliation(s)
- Ning Zhao
- College of Food Science and Engineering, Northwest A&F University, Xianyang, China
| | - Junnan Xu
- College of Food Science and Engineering, Northwest A&F University, Xianyang, China
| | - Lingxia Jiao
- School of Food Science, Henan Institute of Science and Technology, Xinxiang, China
| | - Mengzhen Qiu
- College of Food Science and Engineering, Northwest A&F University, Xianyang, China
| | - Jie Zhang
- College of Food Science and Engineering, Northwest A&F University, Xianyang, China
| | - Xinyuan Wei
- College of Food Science and Engineering, Northwest A&F University, Xianyang, China
| | - Mingtao Fan
- College of Food Science and Engineering, Northwest A&F University, Xianyang, China
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15
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Validation of the Reference Genes for the Gene Expression Studies in Different Cell Lines of Pig. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5364190. [PMID: 34458368 PMCID: PMC8390154 DOI: 10.1155/2021/5364190] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 07/20/2021] [Indexed: 11/30/2022]
Abstract
Reverse transcription quantitative real-time polymerase chain reaction is one of the important methods to investigate gene expression in cells and tissues. However, if the data cannot be normalized with appropriate reference genes, the results may be unreliable. In this study, we detected the expression of 15 reference genes in three pig cell lines. The results showed that SDHA and ALDOA were the most stable reference genes in 3D4/21 cells. TOP2B, TBP, and PPIA were the most stable reference genes in PK-15 cells. SDHA and ALDOA were the most stable reference genes in IPEC-J2 cells. In addition, each cell line only needs to use two reference genes to standardize the expression of target genes. Taken together, this study provides a reference for different pig cell lines to select reference genes and also provides a theoretical basis for the use of these cell lines in related functional researches.
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16
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Morales A, González F, Bernal H, Camacho RL, Arce N, Vásquez N, González-Vega JC, Htoo JK, Viana MT, Cervantes M. Effect of arginine supplementation on the morphology and function of intestinal epithelia, and serum concentrations of amino acids in pigs exposed to heat stress. J Anim Sci 2021; 99:6291043. [PMID: 34077525 DOI: 10.1093/jas/skab179] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/31/2021] [Indexed: 11/13/2022] Open
Abstract
The exposure of pigs to heat stress (HS) appears to damage their intestinal epithelia, affecting the absorption of amino acids (AA). Arg is involved in the restoration of intestinal epithelial cells but HS reduces Arg intake. The effect of dietary supplementation with Arg on morphology of intestinal epithelia, AA transporter gene expression, and serum concentration (SC) of free AA in HS pigs were analyzed. Twenty pigs (25.3 ± 2.4 kg BW) were randomly assigned to two dietary treatments: control (0.81% Arg), wheat-soybean meal diet supplemented with L-Lys, L-Thr, DL-Met and L-Trp, and the experimental diet where 0.16% free L-Arg was supplemented to a similar control diet (+Arg). All pigs were individually housed and exposed to HS, fed at libitum with full access to water. The ambient temperature, recorded at 15-min intervals during the 21-d trial, ranged on average from 29.6 to 39.4 °C within the same day. Blood samples were collected on d18 at 1600 h (ambient temperature peak); serum was separated by centrifugation. At the end of the trial, five pigs per treatment were sacrificed to collect samples of mucosa scratched from each small intestine segment. The expression of AA transporters in intestinal mucosa and the SC of AA were analyzed. Villi height was higher (P < 0.01) in duodenum, jejunum, and ileum but the crypt depth did not differ between the control and the +Arg pigs. Supplementation of L-Arg increased the mRNA coding for the synthesis of the cationic AA transporter b 0,+ (P < 0.01) and the neutral AA transporter B 0 (P < 0.05) in duodenum by approximately five-folds and three-folds, respectively, but no effect on mRNA abundance was observed in jejunum and ileum. The supplementation of L-Arg increased serum Arg, His, Met, Thr, Trp, and urea (P < 0.05); tended to increase Val (P < 0.10), but did not affect Ile, Lys, Leu, and Phe. These results indicate that supplementing 0.16% L-Arg to the control diet may help to improve the function of the small intestine epithelium, by increasing the villi height, the abundance of AA transporters, and the SC of most indispensable AA in pigs exposed to HS conditions. However, the lack of effect of supplemental Arg on both Lys SC and weight gain of pigs suggests that increasing the Lys content in the +Arg diet might be needed to improve the performance of HS pigs.
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Affiliation(s)
- A Morales
- Universidad Autónoma de Baja California, Mexicali, B. C., México
| | - F González
- Universidad Autónoma de Baja California, Mexicali, B. C., México
| | - H Bernal
- Universidad Autónoma de Nuevo León, Monterrey, México
| | - R L Camacho
- Universidad Autónoma de Baja California, Mexicali, B. C., México
| | - N Arce
- Universidad Autónoma de Baja California, Mexicali, B. C., México
| | - N Vásquez
- Universidad Autónoma de Nuevo León, Monterrey, México
| | | | - J K Htoo
- Evonik Operations GmbH, Hanau, Germany
| | - M T Viana
- Universidad Autónoma de Baja California, Mexicali, B. C., México
| | - M Cervantes
- Universidad Autónoma de Baja California, Mexicali, B. C., México
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17
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Guo Q, Zhang L, Duan Y, Wang W, Huang R, Li F. Changes in carcass traits, meat quality, muscle fiber characteristics, and liver function of finishing pigs fed high level of fish oil. CANADIAN JOURNAL OF ANIMAL SCIENCE 2021. [DOI: 10.1139/cjas-2020-0028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The study was aimed to investigate the changes in carcass traits, meat quality, muscle fiber characteristics, and liver function in pigs fed with high levels of fresh fish oil and oxidized fish oil. About 30 piglets were randomly assigned to receive basal diet plus 2% fish oil (LFO), basal diet plus 8% fish oil (HFO), or basal diet plus 8% oxidized fish oil (OFO) for 120 d. Pigs of the HFO and OFO group showed reduced carcass weight, dressing percentage, loin eye area, and increased yellowness of the longissimus dorsi muscle compared with LFO group (P < 0.05). Dietary HFO and OFO suppressed the relative expression levels of myosin heavy chain (MyHC) isoform (I and II a), glutathione peroxidase 4, and NAD(P)H: quinone oxidoreductase-1 and mitochondrial biogenesis in longissimus dorsi muscle (P < 0.05). Dietary HFO or OFO increased the serum aspartates aminotransferase, alanine aminotransferase, total bilirubin, direct bilirubin, oxidized low-density lipoprotein, liver index, and concentration of malondialdehyde (MDA) in liver (P < 0.05). In conclusion, high levels of fresh fish oil and oxidized fish oil have adverse effects on carcass traits, muscle fiber characteristics, and liver function, which may be partly due to the mitochondrial dysfunction and impaired antioxidative capacity.
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Affiliation(s)
- Qiuping Guo
- Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process; Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences; National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production; Scientific Observing and Experimental Station of Animal Nutrition and Feed Science in South-Central, Ministry of Agriculture, Changsha 410125, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Lingyu Zhang
- Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process; Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences; National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production; Scientific Observing and Experimental Station of Animal Nutrition and Feed Science in South-Central, Ministry of Agriculture, Changsha 410125, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yehui Duan
- Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process; Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences; National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production; Scientific Observing and Experimental Station of Animal Nutrition and Feed Science in South-Central, Ministry of Agriculture, Changsha 410125, China
| | - Wenlong Wang
- Laboratory of Animal Nutrition and Human Health, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, College of Life Science, Hunan Normal University, Changsha, Hunan 410081, China
| | - Ruilin Huang
- Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process; Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences; National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production; Scientific Observing and Experimental Station of Animal Nutrition and Feed Science in South-Central, Ministry of Agriculture, Changsha 410125, China
| | - Fengna Li
- Hunan Provincial Key Laboratory of Animal Nutritional Physiology and Metabolic Process; Key Laboratory of Agro-ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences; National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production; Scientific Observing and Experimental Station of Animal Nutrition and Feed Science in South-Central, Ministry of Agriculture, Changsha 410125, China
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18
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Poklukar K, Čandek-Potokar M, Vrecl M, Batorek-Lukač N, Fazarinc G, Kress K, Stefanski V, Škrlep M. Adipose Tissue Gene Expression of Entire Male, Immunocastrated and Surgically Castrated Pigs. Int J Mol Sci 2021; 22:1768. [PMID: 33578947 PMCID: PMC7916650 DOI: 10.3390/ijms22041768] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/01/2021] [Accepted: 02/06/2021] [Indexed: 12/13/2022] Open
Abstract
Differences in adipose tissue deposition and properties between pig male sex categories, i.e., entire males (EM), immunocastrates (IC) and surgical castrates (SC) are relatively well-characterized, whereas the underlying molecular mechanisms are still not fully understood. To gain knowledge about the genetic regulation of the differences in adipose tissue deposition, two different approaches were used: RNA-sequencing and candidate gene expression by quantitative PCR. A total of 83 differentially expressed genes were identified between EM and IC, 15 between IC and SC and 48 between EM and SC by RNA-sequencing of the subcutaneous adipose tissue. Comparing EM with IC or SC, upregulated genes related to extracellular matrix dynamics and adipogenesis, and downregulated genes involved in the control of lipid and carbohydrate metabolism were detected. Differential gene expression generally indicated high similarity between IC and SC as opposed to EM, except for several heat shock protein genes that were upregulated in EM and IC compared with SC. The candidate gene expression approach showed that genes involved in lipogenesis were downregulated in EM compared with IC pigs, further confirming RNA-sequencing results.
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Affiliation(s)
- Klavdija Poklukar
- Agricultural Institute of Slovenia, Hacquetova ulica 17, 1000 Ljubljana, Slovenia; (K.P.); (M.Č.-P.); (N.B.-L.)
| | - Marjeta Čandek-Potokar
- Agricultural Institute of Slovenia, Hacquetova ulica 17, 1000 Ljubljana, Slovenia; (K.P.); (M.Č.-P.); (N.B.-L.)
- Faculty of Agriculture and Life Sciences, University of Maribor, Pivola 10, 2311 Hoče, Slovenia
| | - Milka Vrecl
- Institute of Preclinical Sciences, Veterinary Faculty, University of Ljubljana, Gerbičeva ulica 60, 1000 Ljubljana, Slovenia; (M.V.); (G.F.)
| | - Nina Batorek-Lukač
- Agricultural Institute of Slovenia, Hacquetova ulica 17, 1000 Ljubljana, Slovenia; (K.P.); (M.Č.-P.); (N.B.-L.)
| | - Gregor Fazarinc
- Institute of Preclinical Sciences, Veterinary Faculty, University of Ljubljana, Gerbičeva ulica 60, 1000 Ljubljana, Slovenia; (M.V.); (G.F.)
| | - Kevin Kress
- Behavioural Physiology of Livestock, Institute of Animal Science, University of Hohenheim, Garbenstrasse 17, 70599 Stuttgart, Germany; (K.K.); (V.S.)
| | - Volker Stefanski
- Behavioural Physiology of Livestock, Institute of Animal Science, University of Hohenheim, Garbenstrasse 17, 70599 Stuttgart, Germany; (K.K.); (V.S.)
| | - Martin Škrlep
- Agricultural Institute of Slovenia, Hacquetova ulica 17, 1000 Ljubljana, Slovenia; (K.P.); (M.Č.-P.); (N.B.-L.)
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19
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Zhao X, Zhu R, Wang Y, Qi J, Wang J, Bai L, Wang H, Wu Y, Hu H. Differentiation proliferative capacity of skeletal muscle satellite cells from Dapulian and Landrace pigs. ITALIAN JOURNAL OF ANIMAL SCIENCE 2020. [DOI: 10.1080/1828051x.2020.1769511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Xueyan Zhao
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Rongsheng Zhu
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yanping Wang
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Jing Qi
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Jiying Wang
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Liya Bai
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Huaizhong Wang
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Ying Wu
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Hongmei Hu
- Shandong Provincial Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
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20
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Feng X, Cao X, Zhu R, Huang J. Selection and validation of reference genes for RT-qPCR in adipose and longissimus dorsi muscle tissues of buffalo. Anim Biotechnol 2020; 33:526-535. [DOI: 10.1080/10495398.2020.1811715] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Xue Feng
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Xiaodan Cao
- College of Life Sciences, Xinyang Normal University, Xinyang, China
| | - Ruirui Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
| | - Jieping Huang
- College of Life Sciences, Xinyang Normal University, Xinyang, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, China
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21
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Luo Y, Wang G, Wang C, Gong Y, Bian Y, Zhou Y. Selection and Validation of Reference Genes for qRT-PCR in Lentinula edodes under Different Experimental Conditions. Genes (Basel) 2019; 10:genes10090647. [PMID: 31461882 PMCID: PMC6770232 DOI: 10.3390/genes10090647] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 08/17/2019] [Accepted: 08/22/2019] [Indexed: 12/04/2022] Open
Abstract
Lentinula edodes is the most consumed mushroom in Asia due to its nutritional and medicinal values, and the optimal reference gene is crucial for normalization of its gene expression analysis. Here, the expression stability of 18 candidate reference genes (CRGs) in L. edodes was analyzed by three statistical algorithms (geNorm, NormFinder and BestKeeper) under different stresses (heat, cadmium excess and Trichoderma atroviride infection), different substrates (straw, sawdust and corn stalk) and different development stages (mycelia, primordia and fruit bodies). Among the 18 CRGs, 28S, Actin and α-tub exhibited the highest expression stability in L. edodes under all conditions, while GPD, SPRYP and MSF showed the least stable expression. The best reference gene in different conditions was different. The pairwise variation values showed that two genes would be sufficient for accurate normalization under different conditions of L. edodes. This study will contribute to more accurate estimation of the gene relative expression levels under different conditions using the optimal reference gene in qRT-PCR (quantitative reverse transcription polymerase chain reaction) analysis.
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Affiliation(s)
- Yi Luo
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Gangzheng Wang
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
- State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Open Laboratory of Applied Microbiology, Guangdong Institute of Microbiology, Guangzhou 510070, China
| | - Chen Wang
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yuhua Gong
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yinbing Bian
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Yan Zhou
- Institute of Applied Mycology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
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22
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Validation of Reference Genes for Gene Expression Normalization in RAW264.7 Cells under Different Conditions. BIOMED RESEARCH INTERNATIONAL 2019; 2019:6131879. [PMID: 31223620 PMCID: PMC6541955 DOI: 10.1155/2019/6131879] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 03/03/2019] [Accepted: 04/03/2019] [Indexed: 12/17/2022]
Abstract
RAW264.7 is a macrophage strain derived from mice tumour and shows a significant ability in antigen uptake. Real-time quantitative PCR (RT-qPCR) is one of the most commonly used methods in gene studies and requires suitable reference genes to normalize and quantitate the expression of gene of interest with sensitivity and specificity. However, suitable reference genes in RAW264.7 cells have not yet been identified for accurate gene expression quantification. In the current study, we evaluated expression levels of ten candidate reference genes in RAW264.7 cells under different conditions. RT-qPCR results indicated significant differences in the expression levels among the ten reference genes. Statistical analyses were carried out using geNorm, NormFinder, and BestKeeper software to further investigate the stability of the reference genes. Integrating the results from the three analytical methods, cytochrome c-1 and hydroxymethylbilane synthase were found to be the most stable and therefore more suitable reference genes, while ribosomal protein L4 and cyclophilin A were the least stable. This study emphasises the importance of identifying and selecting the most stable reference genes for normalization and provides a basis for future gene expression studies using RAW264.7 cells.
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23
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Wang S, Wang B, He H, Sun A, Guo C. A new set of reference housekeeping genes for the normalization RT-qPCR data from the intestine of piglets during weaning. PLoS One 2018; 13:e0204583. [PMID: 30256841 PMCID: PMC6157878 DOI: 10.1371/journal.pone.0204583] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Accepted: 09/11/2018] [Indexed: 01/09/2023] Open
Abstract
The intestinal mucosal development of piglets (Sus scrofa) during the weaning stage is important to their disease susceptibility and later growth. Quantitative real-time PCR (RT-qPCR) is commonly used to screen for differentially expressed genes and, for accurate results, proper reference housekeeping genes are essential. Here we assessed the mRNA expression of 18 well-known candidate reference genes at different parts of the gastrointestinal tract (GIT) of piglets during the weaning process by RT-qPCR assay. GeNorm analysis revealed that B2M/HMBS/HPRT1 were the three most stable reference genes and GAPDH was the least stable gene in the duodenum, jejunum, ileum, colon, and whole GIT. BestKeeper analysis found that B2M/HMBS/PGK11, HMBS/B2M/HPRT1, B2M/HMBS/HSPCB, B2M/HPRT1/HMBS, and B2M/HMBS/HPRT1 were the most stable genes in the duodenum, jejunum, ileum, colon, and whole GIT, respectively, whereas GAPDH, B-actin, and 18S rRNA were the least stable genes at different parts of the GIT. To confirm the crucial role of appropriate housekeeping genes in obtaining reliable results, we analyzed the expression of ALP using each of the 18 reference genes to normalize the RT-qPCR data. We found that the expression levels of ALP normalized using the most stable reference genes (B2M/HMBS/HPRT1) differed greatly from the expression levels obtained when the data were normalized using the least stable genes (GAPDH, B-actin, and 18S). We concluded that B2M/HMBS/HPRT1 were the optimal reference genes for gene expression analysis by RT-qPCR in the intestinal mucosal development stages of piglets at weaning. Our findings provide a set of porcine housekeeping reference genes for studies of mRNA expression in different parts of the pig intestine.
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Affiliation(s)
- Shujin Wang
- College of Life Science and Technology, Southwest Miznu University, Chengdu, China.,Department of Molecular Genetics and Cell Biology, Maastricht University, Maastricht, The Netherlands
| | - Binxing Wang
- College of Life Science and Technology, Southwest Miznu University, Chengdu, China.,Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, China
| | - Huan He
- College of Life Science and Technology, Southwest Miznu University, Chengdu, China.,Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, China
| | - Aomin Sun
- Department of Molecular Genetics and Cell Biology, Maastricht University, Maastricht, The Netherlands
| | - Chunhua Guo
- College of Life Science and Technology, Southwest Miznu University, Chengdu, China.,Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education, Southwest Minzu University, China
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24
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Lorenzetti WR, Ibelli AMG, Peixoto JDO, Mores MAZ, Savoldi IR, do Carmo KB, de Oliveira HC, Ledur MC. Identification of endogenous normalizing genes for expression studies in inguinal ring tissue for scrotal hernias in pigs. PLoS One 2018; 13:e0204348. [PMID: 30235332 PMCID: PMC6147718 DOI: 10.1371/journal.pone.0204348] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 09/06/2018] [Indexed: 02/06/2023] Open
Abstract
The use of reference genes is required for relative quantification in gene expression analysis and since the stability of these genes could be variable depending on the experimental design, it has become indispensable to test the reliability of endogenous genes. Therefore, this study evaluated 10 reference candidate genes in two different experimental conditions in order to obtain stable genes to be used as reference in expression studies related to scrotal hernias in pigs. Two independent experiments were performed: one with 30 days-old MS115 pigs and the other with 60 days-old Landrace pigs. The inguinal ring/canal was collected, frozen and further submitted to real-time PCR analysis (qPCR). For the reference genes stability evaluation, four tools were used: GeNorm in the SLqPCR, BestKeeper, NormFinder and Comparative CT. A general ranking was generated using the BruteAggreg function of R environment. In this study, the RPL19 was one of the most reliable endogenous genes for both experiments. The breed/age effects influenced the expression stability of candidate reference genes evaluated in the inguinal ring of pigs. Therefore, this study reinforces the importance of evaluating the stability of several endogenous genes previous their use, since a consensual set of reference genes is not easily obtained. Here, two sets of genes are recommended: RPL19, RPL32 and H3F3A for 30-days MS115 and PPIA and RPL19 for the 60 days-old Landrace pigs. This is the first study using the inguinal ring tissue and the results can be useful as an indicative for other studies working with gene expression in this tissue.
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Affiliation(s)
- William Raphael Lorenzetti
- Programa de Pós-graduação em Zootecnia, Centro de Educação Superior do Oeste (CEO), Universidade do Estado de Santa Catarina, UDESC, Chapecó, Santa Catarina, Brazil
- Embrapa Suínos e Aves, Concórdia, Santa Catarina, Brazil
| | | | | | | | | | | | | | - Mônica Corrêa Ledur
- Programa de Pós-graduação em Zootecnia, Centro de Educação Superior do Oeste (CEO), Universidade do Estado de Santa Catarina, UDESC, Chapecó, Santa Catarina, Brazil
- Embrapa Suínos e Aves, Concórdia, Santa Catarina, Brazil
- * E-mail:
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25
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Liu H, Xue Q, Cao W, Yang F, Ma L, Liu W, Zhang K, Liu X, Zhu Z, Zheng H. Foot-and-mouth disease virus nonstructural protein 2B interacts with cyclophilin A, modulating virus replication. FASEB J 2018; 32:fj201701351. [PMID: 29906248 DOI: 10.1096/fj.201701351] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Foot-and-mouth disease (FMD) is a highly contagious virus that affects cloven-hoofed animals. To understand better the role of nonstructural protein 2B of the causative agent FMD virus (FMDV) in the process of virus replication, we identified a porcine host protein, cyclophilin A (CypA), which interacts with FMDV 2B. The 2B-CypA interaction was confirmed by coimmunoprecipitation and GST pull-down assays. CypA showed antiviral functions during FMDV infection. Overexpression of CypA decreased FMDV leader protein (Lpro) and 3A at protein levels. CypA-induced reduction of Lpro enhanced the synthesis of host proteins and increased the integrality of host eukaryotic translation initiation factor (eIF)-4γ (eIF4G). The reduction of Lpro and 3A was dependent on the proteasome pathway. No interaction was identified between CypA and Lpro or 3A. However, CypA-induced reduction of Lpro and 3A was suppressed by 2B, and disruption of 2B-CypA interaction impaired this inhibitive effect induced by 2B. In summary, our findings identify the antiviral role of CypA against FMDV and provide key insights into how FMDV antagonizes host antiviral response by 2B protein.-Liu, H., Xue, Q., Cao, W., Yang, F., Ma, L., Liu, W., Zhang, K., Liu, X., Zhu, Z., Zheng, H. Foot-and-mouth disease virus nonstructural protein 2B interacts with cyclophilin A, modulating virus replication.
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Affiliation(s)
- Huisheng Liu
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Qiao Xue
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Weijun Cao
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Fan Yang
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Linna Ma
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Wenjie Liu
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Keshan Zhang
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xiangtao Liu
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Zixiang Zhu
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Haixue Zheng
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Diseases Reference Laboratory, Key Laboratory of Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
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26
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Yang SC, Yu GE, Ha J, Kwon S, Hwang JH, Park DH, Kang DG, Kim TW, Park HC, An SM, Kim CW. Association between an electron transfer flavoprotein alpha subunit polymorphism (rs321948383) and the meat quality of Berkshire pigs. JOURNAL OF APPLIED ANIMAL RESEARCH 2018. [DOI: 10.1080/09712119.2018.1481856] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Seung Chang Yang
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, South Korea
| | - Go Eun Yu
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, South Korea
| | - Jeongim Ha
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, South Korea
| | - Seulgi Kwon
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, South Korea
| | - Jung Hye Hwang
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, South Korea
| | - Da Hye Park
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, South Korea
| | - Deok Gyeong Kang
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, South Korea
| | - Tae Wan Kim
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, South Korea
| | | | - Sang Mi An
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, South Korea
| | - Chul Wook Kim
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, South Korea
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27
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Hur JW, Hwang JH, Kwon SG, Park DH, Kim TW, Kang DG, Yu GE, An SM, Kim IS, Park HC, Ha J, Kim CW. A non-synonymous single nucleotide polymorphism in the paraoxonase 3 gene regulates meat quality in Berkshire pigs. ANIMAL PRODUCTION SCIENCE 2018. [DOI: 10.1071/an16573] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The paraoxonase (Pon) gene family contains three members: Pon1, Pon2, and Pon3. Pon3 modulates superoxide production and prevents apoptosis. The role of Pon3 has not been fully elucidated in the pig. This study is the first to investigate the association between Pon3 and meat quality in the Berkshire pig. We identified a single nucleotide polymorphism in the Pon3 gene (c.227A > G) that resulted in a change in histidine to arginine at position 76. To elucidate the role of this non-synonymous single nucleotide polymorphism in the Pon3 gene, we analysed the Pon3 genotype and meat quality traits in 434 Berkshire pigs. The results of a codominant model show that carcass weight, meat colour (lightness), cooking loss, and the Warner–Bratzler shear force were significantly associated with the Pon3 genotype. Furthermore, the 24-h post-mortem pH had the strongest relationship with the Pon3 genotype. The G allele decreased cooking loss and fat content, whereas the A allele increased the 24-h post-mortem pH and decreased backfat thickness, which contribute to meat storage life and M. longissimus dorsi depth respectively. In conclusion, the non-synonymous single nucleotide polymorphism in the Pon3 gene showed a close correlation with meat quality traits in the Berkshire pig.
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28
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Yao H, Kang J, Li W, Liu J, Xie R, Wang Y, Liu S, Wang DA, Ren L. Novel
β
-TCP/PVA bilayered hydrogels with considerable physical and bio-functional properties for osteochondral repair. Biomed Mater 2017; 13:015012. [DOI: 10.1088/1748-605x/aa8541] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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29
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Hwang JH, An SM, Kwon S, Park DH, Kim TW, Kang DG, Yu GE, Kim IS, Park HC, Ha J, Kim CW. DNA methylation patterns and gene expression associated with litter size in Berkshire pig placenta. PLoS One 2017; 12:e0184539. [PMID: 28880934 PMCID: PMC5589248 DOI: 10.1371/journal.pone.0184539] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 08/26/2017] [Indexed: 11/18/2022] Open
Abstract
Increasing litter size is of great interest to the pig industry. DNA methylation is an important epigenetic modification that regulates gene expression, resulting in livestock phenotypes such as disease resistance, milk production, and reproduction. We classified Berkshire pigs into two groups according to litter size and estimated breeding value: smaller (SLG) and larger (LLG) litter size groups. Genome-wide DNA methylation and gene expression were analyzed using placenta genomic DNA and RNA to identify differentially methylated regions (DMRs) and differentially expressed genes (DEGs) associated with litter size. The methylation levels of CpG dinucleotides in different genomic regions were noticeably different between the groups, while global methylation pattern was similar, and excluding intergenic regions they were found the most frequently in gene body regions. Next, we analyzed RNA-Seq data to identify DEGs between the SLG and LLG groups. A total of 1591 DEGs were identified: 567 were downregulated and 1024 were upregulated in LLG compared to SLG. To identify genes that simultaneously exhibited changes in DNA methylation and mRNA expression, we integrated and analyzed the data from bisulfite-Seq and RNA-Seq. Nine DEGs positioned in DMRs were found. The expression of only three of these genes (PRKG2, CLCA4, and PCK1) was verified by RT-qPCR. Furthermore, we observed the same methylation patterns in blood samples as in the placental tissues by PCR-based methylation analysis. Together, these results provide useful data regarding potential epigenetic markers for selecting hyperprolific sows.
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Affiliation(s)
- Jung Hye Hwang
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, South Korea
| | - Sang Mi An
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, South Korea
| | - Seulgi Kwon
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, South Korea
| | - Da Hye Park
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, South Korea
| | - Tae Wan Kim
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, South Korea
| | - Deok Gyeong Kang
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, South Korea
| | - Go Eun Yu
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, South Korea
| | - Il-Suk Kim
- Department of Animal Resource Technology, Gyeongnam National University of Science & Technology, Jinju, South Korea
| | | | - Jeongim Ha
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, South Korea
- * E-mail: (JH); (CWK)
| | - Chul Wook Kim
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, South Korea
- * E-mail: (JH); (CWK)
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30
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Wang YK, Li X, Song ZQ, Yang CX. Methods of RNA preparation affect mRNA abundance quantification of reference genes in pig maturing oocytes. Reprod Domest Anim 2017; 52:722-730. [PMID: 28407308 DOI: 10.1111/rda.12972] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 02/25/2017] [Indexed: 11/28/2022]
Abstract
To ensure accurate normalization and quantification of target RNA transcripts using reverse transcription quantitative polymerase chain reaction (RT-qPCR), most studies focus on the identification of stably expressed gene(s) as internal reference. However, RNA preparation methods could also be an important factor, especially for test samples of limited quantity (e.g. oocytes). In this study, we aimed to select appropriate reference gene(s), and evaluate the effect of RNA preparation methods on gene expression quantification in porcine oocytes and cumulus cells during in vitro maturation. Expression profiles of seven genes (GAPDH, 18S, YWHAG, BACT, RPL4, HPRT1 and PPIA) were examined, on RNA samples extracted from cumulus cells (RNeasy Kit) and oocytes (RNeasy Kit and Lysis Kit) during in vitro maturation, respectively. Interestingly, different RNA preparation methods were found to potentially affect the quantification of reference gene expression in pig oocytes cultured in vitro. After geNorm analyses, the most suitable genes for normalization were identified, GAPDH/18S for cumulus cells and YWHAG/BACT for oocytes, respectively. Thus, our results provide useful data and information on the selection of better reference genes and RNA preparation method for related functional studies.
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Affiliation(s)
- Y-K Wang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - X Li
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Z-Q Song
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - C-X Yang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
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31
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Simon Á, Jávor A, Bai P, Oláh J, Czeglédi L. Reference gene selection for reverse transcription quantitative polymerase chain reaction in chicken hypothalamus under different feeding status. J Anim Physiol Anim Nutr (Berl) 2017; 102:286-296. [DOI: 10.1111/jpn.12690] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 01/12/2017] [Indexed: 01/19/2023]
Affiliation(s)
- Á. Simon
- Department of Animal Science; Faculty of Agricultural and Food Sciences and Environmental Management; University of Debrecen; Debrecen Hungary
| | - A. Jávor
- Department of Animal Science; Faculty of Agricultural and Food Sciences and Environmental Management; University of Debrecen; Debrecen Hungary
| | - P. Bai
- Department of Medical Chemistry; Faculty of Medicine; University of Debrecen; Debrecen Hungary
- MTA-DE Lendület Laboratory of Cellular Metabolism Research Group; Debrecen Hungary
- Research Centre for Molecular Medicine; Faculty of Medicine; University of Debrecen; Debrecen Hungary
| | - J. Oláh
- Department of Animal Science; Faculty of Agricultural and Food Sciences and Environmental Management; University of Debrecen; Debrecen Hungary
| | - L. Czeglédi
- Department of Animal Science; Faculty of Agricultural and Food Sciences and Environmental Management; University of Debrecen; Debrecen Hungary
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32
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Niu G, Yang Y, Zhang Y, Hua C, Wang Z, Tang Z, Li K. Identifying suitable reference genes for gene expression analysis in developing skeletal muscle in pigs. PeerJ 2016; 4:e2428. [PMID: 27994956 PMCID: PMC5157201 DOI: 10.7717/peerj.2428] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 08/11/2016] [Indexed: 11/20/2022] Open
Abstract
The selection of suitable reference genes is crucial to accurately evaluate and normalize the relative expression level of target genes for gene function analysis. However, commonly used reference genes have variable expression levels in developing skeletal muscle. There are few reports that systematically evaluate the expression stability of reference genes across prenatal and postnatal developing skeletal muscle in mammals. Here, we used quantitative PCR to examine the expression levels of 15 candidate reference genes (ACTB, GAPDH, RNF7, RHOA, RPS18, RPL32, PPIA, H3F3, API5, B2M, AP1S1, DRAP1, TBP, WSB, and VAPB) in porcine skeletal muscle at 26 different developmental stages (15 prenatal and 11 postnatal periods). We evaluated gene expression stability using the computer algorithms geNorm, NormFinder, and BestKeeper. Our results indicated that GAPDH and ACTB had the greatest variability among the candidate genes across prenatal and postnatal stages of skeletal muscle development. RPS18, API5, and VAPB had stable expression levels in prenatal stages, whereas API5, RPS18, RPL32, and H3F3 had stable expression levels in postnatal stages. API5 and H3F3 expression levels had the greatest stability in all tested prenatal and postnatal stages, and were the most appropriate reference genes for gene expression normalization in developing skeletal muscle. Our data provide valuable information for gene expression analysis during different stages of skeletal muscle development in mammals. This information can provide a valuable guide for the analysis of human diseases.
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Affiliation(s)
- Guanglin Niu
- The Key Laboratory for Domestic Animal Genetic Resources and Breeding of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.,Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yalan Yang
- The Key Laboratory for Domestic Animal Genetic Resources and Breeding of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.,Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - YuanYuan Zhang
- The Key Laboratory for Domestic Animal Genetic Resources and Breeding of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chaoju Hua
- The Key Laboratory for Domestic Animal Genetic Resources and Breeding of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zishuai Wang
- The Key Laboratory for Domestic Animal Genetic Resources and Breeding of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhonglin Tang
- The Key Laboratory for Domestic Animal Genetic Resources and Breeding of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.,Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Kui Li
- The Key Laboratory for Domestic Animal Genetic Resources and Breeding of Ministry of Agriculture of China, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.,Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
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Chen R, Yu S, Ren F, Lv XY, Pan CY. Detection of one large insertion/deletion (indel) and two novel SNPs within the <i>SPEF2</i> gene and their associations with male piglet reproduction traits. Arch Anim Breed 2016. [DOI: 10.5194/aab-59-275-2016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Abstract. The sperm flagella 2 (SPEF2) gene is essential for normal sperm tail development and male fertility. To fully characterize the structure of the mutation and to further study the function of the pig SPEF2 gene, we explored the insertion/deletion (indel) and novel single-nucleotide polymorphisms (SNPs) within the pig SPEF2 gene, and tested their associations with the testicular sizes in male Large White (LW) and Landrace (LD) pigs from China. Herein, a large insertion located at the SPEF2 gene in chromosome 16 was found, and two alleles of "I" (insertion) and "D" (deletion) were designated. Allele "D" was dominant in all analyzed pigs. Two novel SNPs (namely (NC_010458) g.19642G > A, resulting in AfaI aCRS PCR–PFLP, and g.19886C > G, resulting in EcoRI aCRS PCR–PFLP) were found in LW and LD pigs. Association testing revealed that g.19886C > G was significantly associated with the testis long circumference (TLC) in LW pigs (P < 0.05), suggesting that this SNP would be the DNA marker for the marker-assisted selection (MAS) in reproduction traits. This preliminary result indicates that the pig SPEF2 gene had significant effects on male reproduction traits. These findings could not only extend the spectrum of genetic variations in the pig SPEF2 gene but also contribute to implementing MAS in genetics and breeding in pigs.
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Liu Y, Zhang Y, Jiang Q, Rao M, Sheng Z, Zhang Y, Du W, Hao H, Zhao X, Xu Z, Liu J, Zhu H. Identification of Valid Housekeeping Genes for Real-Time Quantitative PCR Analysis of Collapsed Lung Tissues of Neonatal Somatic Cell Nuclear Transfer-Derived Cattle. Cell Reprogram 2016; 17:360-7. [PMID: 26393896 DOI: 10.1089/cell.2015.0024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Cloned calves produced by somatic cell nuclear transfer frequently suffer alveolar collapse as newborns. To study the underlying pathophysiological mechanisms responsible for this phenomenon, the expression profiles of numerous genes involved in lung development need to be investigated. Quantitative real-time PCR is commonly adopted in gene expression analysis. However, selection of an appropriate reference gene for normalization is critical for obtaining reliable and accurate results. Seven housekeeping genes-β-glucuronidase (GUSB), phosphoglycerate kinase 1 (PGK1), β-2-microglobolin (B2M), peptidylprolyl isomerase A (PPIA), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), TATA-box binding protein (TBP), and 5.8S ribosomal RNA (5.8S rRNA)-were selected and evaluated as candidates. Their gene expression levels in the collapsed lungs of deceased neonate cloned calves and normal lung derived from normal calves were assessed. The ranking of gene expression stability was estimated by the geNorm, NormFinder, and BestKeeper programs. 5.8S rRNA and PPIA were determined to be the most stable reference genes by geNorm and BestKeeper, whereas the combination of GAPDH and TBP was suggested as reference genes by NormFinder. Taking these results into account, we conclude that 5.8S rRNA and PPIA could be the most reliable reference genes for studying the genes involved in alveolar collapse. Moreover, 5.8S rRNA could be represented as a uniform reference gene in similar cases.
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Affiliation(s)
- Yan Liu
- 1 Institute of Animal Sciences, Chinese Academy of Agricultural Sciences , Beijing, 100193, China .,4 These authors contributed equally to this work
| | - Yunhai Zhang
- 2 Anhui Provincial Laboratory of Local Livestock and Poultry Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University , Hefei 230036, China .,4 These authors contributed equally to this work
| | - Qiuling Jiang
- 1 Institute of Animal Sciences, Chinese Academy of Agricultural Sciences , Beijing, 100193, China
| | - Man Rao
- 3 Geno-Ming Bioscience , Beijing, 101101, China
| | - Zheya Sheng
- 3 Geno-Ming Bioscience , Beijing, 101101, China
| | - Yu Zhang
- 2 Anhui Provincial Laboratory of Local Livestock and Poultry Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University , Hefei 230036, China
| | - Weihua Du
- 1 Institute of Animal Sciences, Chinese Academy of Agricultural Sciences , Beijing, 100193, China
| | - Haisheng Hao
- 1 Institute of Animal Sciences, Chinese Academy of Agricultural Sciences , Beijing, 100193, China
| | - Xueming Zhao
- 1 Institute of Animal Sciences, Chinese Academy of Agricultural Sciences , Beijing, 100193, China
| | - Zhe Xu
- 1 Institute of Animal Sciences, Chinese Academy of Agricultural Sciences , Beijing, 100193, China
| | - Jianning Liu
- 1 Institute of Animal Sciences, Chinese Academy of Agricultural Sciences , Beijing, 100193, China
| | - Huabin Zhu
- 1 Institute of Animal Sciences, Chinese Academy of Agricultural Sciences , Beijing, 100193, China
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Kwon SG, Hwang JH, Park DH, Kim TW, Kang DG, Kang KH, Kim IS, Park HC, Na CS, Ha J, Kim CW. Identification of Differentially Expressed Genes Associated with Litter Size in Berkshire Pig Placenta. PLoS One 2016; 11:e0153311. [PMID: 27078025 PMCID: PMC4831801 DOI: 10.1371/journal.pone.0153311] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 03/28/2016] [Indexed: 01/24/2023] Open
Abstract
Improvement in litter size has become of great interest in the pig industry because fecundity is directly related to sow reproductive life. Improved reproduction has thus been achieved by elucidating the molecular functions of genes associated with fecundity. In the present study, we identified differentially expressed genes (DEGs) via transcriptomic analysis using RNA-sequencing (RNA-Seq) in Berkshire pig placentas from larger (LLG, mean litter size >12) and smaller (SLG, mean litter size < 6.5) litter size groups. In total 588 DEGs were identified (p < 0.05, > 1.5-fold change), of which 98 were upregulated, while 490 were downregulated in the LLG compared with the SLG. Gene Ontology (GO) enrichment was also performed. We concluded that 129 of the 588 DEGs were closely related to litter size according to reproduction related genes selected based on previous reports, as 110 genes were downregulated and 19 upregulated in the LLG compared with the SLG. RT-qPCR utilizing specific primers targeting the early growth response 2 (EGR2), pheromaxein c subunit (PHEROC) and endothelial lipase (LIPG) genes showed high accordance with RNA-Seq results. Furthermore, we investigated the upstream regulators of these three genes in the placenta. We found that WNT9B, a Wnt signaling pathway molecule, and IL-6, known inducers of EGR2 and LIPG, respectively, were significantly increased in LLG compared with SLG. We believe that the induction of IL-6 and LIPG may play an important role in increasing nutrition supply through the placenta from the sow to the piglet during gestation. These results provide novel molecular insights into pig reproduction.
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Affiliation(s)
- Seul Gi Kwon
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, South Korea
| | - Jung Hye Hwang
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, South Korea
| | - Da Hye Park
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, South Korea
| | - Tae Wan Kim
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, South Korea
| | - Deok Gyeong Kang
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, South Korea
| | - Kyung Hee Kang
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, South Korea
| | - Il-Suk Kim
- Department of Animal Resource Technology, Gyeongnam National University of Science & Technology, Jinju, South Korea
| | | | - Chong-Sam Na
- Department of Animal Biotechnology, Chonbuk National University, Jeonju, South Korea
| | - Jeongim Ha
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, South Korea
- * E-mail: (JH); (CWK)
| | - Chul Wook Kim
- Swine Science and Technology Center, Gyeongnam National University of Science & Technology, Jinju, South Korea
- * E-mail: (JH); (CWK)
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Verification of suitable and reliable reference genes for quantitative real-time PCR during adipogenic differentiation in porcine intramuscular stromal-vascular cells. Animal 2016; 10:947-52. [PMID: 26781521 DOI: 10.1017/s1751731115002748] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Intramuscular fat (IMF) is an important trait influencing meat quality, and intramuscular stromal-vascular cell (MSVC) differentiation is a key factor affecting IMF deposition. Quantitative real-time PCR (qPCR) is often used to screen the differentially expressed genes during differentiation of MSVCs, where proper reference genes are essential. In this study, we assessed 31 of previously reported reference genes for their expression suitability in porcine MSVCs derived form longissimus dorsi with qPCR. The expression stability of these genes was evaluated using NormFinder, geNorm and BestKeeper algorithms. NormFinder and geNorm uncovered ACTB, ALDOA and RPS18 as the most three stable genes. BestKeeper identified RPL13A, SSU72 and DAK as the most three stable genes. GAPDH was found to be the least stable gene by all of the three software packages, indicating it is not an appropriate reference gene in qPCR assay. These results might be helpful for further studies in pigs that explore the molecular mechanism underlying IMF deposition.
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Chapman JR, Waldenström J. With Reference to Reference Genes: A Systematic Review of Endogenous Controls in Gene Expression Studies. PLoS One 2015; 10:e0141853. [PMID: 26555275 PMCID: PMC4640531 DOI: 10.1371/journal.pone.0141853] [Citation(s) in RCA: 198] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 10/13/2015] [Indexed: 12/20/2022] Open
Abstract
The choice of reference genes that are stably expressed amongst treatment groups is a crucial step in real-time quantitative PCR gene expression studies. Recent guidelines have specified that a minimum of two validated reference genes should be used for normalisation. However, a quantitative review of the literature showed that the average number of reference genes used across all studies was 1.2. Thus, the vast majority of studies continue to use a single gene, with β-actin (ACTB) and/or glyceraldehyde 3-phosphate dehydrogenase (GAPDH) being commonly selected in studies of vertebrate gene expression. Few studies (15%) tested a panel of potential reference genes for stability of expression before using them to normalise data. Amongst studies specifically testing reference gene stability, few found ACTB or GAPDH to be optimal, whereby these genes were significantly less likely to be chosen when larger panels of potential reference genes were screened. Fewer reference genes were tested for stability in non-model organisms, presumably owing to a dearth of available primers in less well characterised species. Furthermore, the experimental conditions under which real-time quantitative PCR analyses were conducted had a large influence on the choice of reference genes, whereby different studies of rat brain tissue showed different reference genes to be the most stable. These results highlight the importance of validating the choice of normalising reference genes before conducting gene expression studies.
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Affiliation(s)
- Joanne R. Chapman
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
- * E-mail:
| | - Jonas Waldenström
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
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