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Salichos L, Thayavally R, Kloen P, Hadjiargyrou M. Human nonunion tissues display differential gene expression in comparison to physiological fracture callus. Bone 2024; 183:117091. [PMID: 38570121 PMCID: PMC11023750 DOI: 10.1016/j.bone.2024.117091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/30/2024] [Accepted: 03/31/2024] [Indexed: 04/05/2024]
Abstract
The healing of bone fractures can become aberrant and lead to nonunions which in turn have a negative impact on patient health. Understanding why a bone fails to normally heal will enable us to make a positive impact in a patient's life. While we have a wealth of molecular data on rodent models of fracture repair, it is not the same with humans. As such, there is still a lack of information regarding the molecular differences between normal physiological repair and nonunions. This study was designed to address this gap in our molecular knowledge of the human repair process by comparing differentially expressed genes (DEGs) between physiological fracture callus and two different nonunion types, hypertrophic (HNU) and oligotrophic (ONU). RNA sequencing data revealed over ∼18,000 genes in each sample. Using the physiological callus as the control and the nonunion samples as the experimental groups, bioinformatic analyses identified 67 and 81 statistically significant DEGs for HNU and ONU, respectively. Out of the 67 DEGs for the HNU, 34 and 33 were up and down-regulated, respectively. Similarly, out of the 81 DEGs for the ONU, 48 and 33 were up and down-regulated, respectively. Additionally, we also identified common genes between the two nonunion samples; 8 (10.8 %) upregulated and 12 (22.2 %) downregulated. We further identified many biological processes, with several statistically significant ones. Some of these were related to muscle and were common between the two nonunion samples. This study represents the first comprehensive attempt to understand the global molecular events occurring in human nonunion biology. With further research, we can perhaps decipher new molecular pathways involved in aberrant healing of human bone fractures that can be therapeutically targeted.
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Affiliation(s)
- Leonidas Salichos
- Department of Biological & Chemical Sciences, New York Institute of Technology, New York, NY 10023, USA; Center for Biomedical Data Science, New York Institute of Technology, New York, NY 10023, USA
| | - Rishika Thayavally
- Department of Biological & Chemical Sciences, New York Institute of Technology, New York, NY 10023, USA; Center for Biomedical Data Science, New York Institute of Technology, New York, NY 10023, USA
| | - Peter Kloen
- Department of Orthopedic Surgery and Sports Medicine, Amsterdam UMC location, Meibergdreef 9, the Netherlands; Amsterdam Movement Sciences, (Tissue Function and Regeneration), Amsterdam, the Netherlands
| | - Michael Hadjiargyrou
- Center for Biomedical Data Science, New York Institute of Technology, New York, NY 10023, USA; Department of Biological & Chemical Sciences, New York Institute of Technology, Old Westbury, NY, 11568, USA.
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Lin Y, Sun L, Lv Y, Liao R, Zhang K, Zhou J, Zhang S, Xu J, He M, Wu C, Zhang D, Shen X, Dai J, Gao J. Transcriptomic and metabolomic dissection of skeletal muscle of crossbred Chongming white goats with different meat production performance. BMC Genomics 2024; 25:443. [PMID: 38704563 PMCID: PMC11069289 DOI: 10.1186/s12864-024-10304-3] [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: 10/07/2023] [Accepted: 04/12/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND The transcriptome and metabolome dissection of the skeletal muscle of high- and low- growing individuals from a crossbred population of the indigenous Chongming white goat and the Boer goat were performed to discover the potential functional differentially expressed genes (DEGs) and differential expression metabolites (DEMs). RESULTS A total of 2812 DEGs were detected in 6 groups at three time stages (3,6,12 Month) in skeletal muscle using the RNA-seq method. A DEGs set containing seven muscle function related genes (TNNT1, TNNC1, TNNI1, MYBPC2, MYL2, MHY7, and CSRP3) was discovered, and their expression tended to increase as goat muscle development progressed. Seven DEGs (TNNT1, FABP3, TPM3, DES, PPP1R27, RCAN1, LMOD2) in the skeletal muscle of goats in the fast-growing and slow-growing groups was verified their expression difference by reverse transcription-quantitative polymerase chain reaction. Further, through the Liquid chromatography-mass spectrometry (LC-MS) approach, a total of 183 DEMs in various groups of the muscle samples and these DEMs such as Queuine and Keto-PGF1α, which demonstrated different abundance between the goat fast-growing group and slow-growing group. Through weighted correlation network analysis (WGCNA), the study correlated the DEGs with the DEMs and identified 4 DEGs modules associated with 18 metabolites. CONCLUSION This study benefits to dissection candidate genes and regulatory networks related to goat meat production performance, and the joint analysis of transcriptomic and metabolomic data provided insights into the study of goat muscle development.
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Affiliation(s)
- Yuexia Lin
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai, 201106, China
| | - Lingwei Sun
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai, 201106, China
- Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, 201106, China
| | - Yuhua Lv
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai, 201106, China
| | - Rongrong Liao
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai, 201106, China
| | - Keqing Zhang
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai, 201106, China
| | - Jinyong Zhou
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai, 201106, China
| | - Shushan Zhang
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai, 201106, China
- Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, 201106, China
| | - Jiehuan Xu
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai, 201106, China
- Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, 201106, China
| | - Mengqian He
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai, 201106, China
- Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, 201106, China
| | - Caifeng Wu
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai, 201106, China
- Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, 201106, China
| | - Defu Zhang
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai, 201106, China
- Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, 201106, China
| | - Xiaohui Shen
- Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China.
| | - Jianjun Dai
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China.
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai, 201106, China.
- Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, 201106, China.
| | - Jun Gao
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, China.
- Shanghai Municipal Key Laboratory of Agri-Genetics and Breeding, Shanghai, 201106, China.
- Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, 201106, China.
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Reißmann M, Rajavel A, Kokov ZA, Schmitt AO. Identification of Differentially Expressed Genes after Endurance Runs in Karbadian Horses to Determine Candidates for Stress Indicators and Performance Capability. Genes (Basel) 2023; 14:1982. [PMID: 38002925 PMCID: PMC10671444 DOI: 10.3390/genes14111982] [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: 09/15/2023] [Revised: 10/13/2023] [Accepted: 10/18/2023] [Indexed: 11/26/2023] Open
Abstract
RNA sequencing makes it possible to uncover genetic mechanisms that underlie certain performance traits. In order to gain a deeper insight into the genetic background and biological processes involved in endurance performance in horses, the changes in the gene expression profiles induced by endurance runs over long (70 km) and short (15 km) distances in the blood of Kabardian horses (Equus caballus) were analyzed. For the long-distance runs, we identified 1484 up- and 691 downregulated genes, while after short-distance runs, only 13 up- and 8 downregulated genes (FC > |1.5|; p < 0.05) were found. These differentially expressed genes (DEGs) are involved in processes and pathways that are primarily related to stress response (interleukin production, activation of inflammatory system) but also to metabolism (carbohydrate catabolic process, lipid biosynthesis, NADP metabolic process). The most important genes involved in these processes therefore represent good candidates for the monitoring and evaluation of the performance of horses in order to avoid excessive demands when endurance performance is required, like ACOD1, CCL5, CD40LG, FOS, IL1R2, IL20RA, and IL22RA2, on the one hand, and, on the other hand, for assessing the suitability of a horse for endurance races, like GATA2, GYG1, HIF1A, MOGAT1, PFKFB3, PLIN5, SIK1, and STBD1.
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Affiliation(s)
- Monika Reißmann
- Thaer-Institute of Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany;
| | - Abirami Rajavel
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany
| | - Zaur A. Kokov
- Institute of Physics and Mathematics, Kabardino-Balkarian State University, Chernyshevsky 173, Nalchik 360004, Russia;
| | - Armin O. Schmitt
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), Georg-August University, Carl-Sprengel-Weg 1, 37075 Göttingen, Germany
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Yu X, Fang C, Liu L, Zhao X, Liu W, Cao H, Lv S. Transcriptome study underling difference of milk yield during peak lactation of Kazakh horse. J Equine Vet Sci 2021; 102:103424. [PMID: 34119198 DOI: 10.1016/j.jevs.2021.103424] [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: 11/06/2020] [Revised: 02/15/2021] [Accepted: 02/15/2021] [Indexed: 01/10/2023]
Abstract
This study was designed to provide a basis for further understanding of the mechanism of lactation based on mRNA expression differences in milk fat between different milk yields in Kazakh horses. Total RNA was extracted from the milk fat during the peak of lactation period. A total of 310 differentially expressed genes (DEGs) were identified by comparative transcriptome analysis of the high-yield and low-yield group. These DEGs regulate lactation by participated in AMPK signaling pathway, FoxO signaling pathway, ErbB signaling pathway, VEGF signaling pathway. In addition, we performed quantitative PCR to validated 5 selected DEGs and the results were in agreement with RNA-seq analysis. A new profile has been established for revealing the mechanism of equid's mammalian lactation.
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Affiliation(s)
- Xi Yu
- Xinjiang Agricultural University, Urumuqi, China
| | | | - Lingling Liu
- Xinjiang Agricultural University, Urumuqi, China
| | | | - Wujun Liu
- Xinjiang Agricultural University, Urumuqi, China.
| | - Hang Cao
- Xinjiang Agricultural University, Urumuqi, China
| | - Shipeng Lv
- Xinjiang Agricultural University, Urumuqi, China
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Denham J, McCluskey M, Denham MM, Sellami M, Davie AJ. Epigenetic control of exercise adaptations in the equine athlete: Current evidence and future directions. Equine Vet J 2020; 53:431-450. [PMID: 32671871 DOI: 10.1111/evj.13320] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 06/04/2020] [Accepted: 06/25/2020] [Indexed: 12/11/2022]
Abstract
Horses (Equus ferus caballus) have evolved over the past 300 years in response to man-made selection for particular athletic traits. Some of the selected traits were selected based on the size and horses' muscular power (eg Clydesdales), whereas other breeds were bred for peak running performance (eg Thoroughbred and Arabian). Although the physiological changes and some of the cellular adaptations responsible for athletic potential of horses have been identified, the molecular mechanisms are only just beginning to be comprehensively investigated. The purpose of this review was to outline and discuss the current understanding of the molecular mechanisms underpinning the athletic performance and cardiorespiratory fitness in athletic breeds of horses. A brief review of the biology of epigenetics is provided, including discussion on DNA methylation, histone modifications and small RNAs, followed by a summary and critical review of the current work on the exercise-induced epigenetic and transcriptional changes in horses. Important unanswered questions and currently unexplored areas that deserve attention are highlighted. Finally, a rationale for the analysis of epigenetic modifications in the context with exercise-related traits and ailments associated with athletic breeds of horses is outlined in order to help guide future research.
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Affiliation(s)
- Joshua Denham
- RMIT University, School of Health and Biomedical Sciences, Melbourne, VIC, Australia
| | | | | | - Maha Sellami
- Qatar University, College of Arts and Sciences (CAS), Sport Science Program (SSP), Doha, Qatar
| | - Allan J Davie
- Australian Equine Racing and Research Centre (AERR), Ballina, NSW, Australia
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Khummuang S, Lee HG, Joo SS, Park JW, Choi JY, Oh JH, Kim KH, Youn HH, Kim M, Cho BW. Comparison for immunophysiological responses of Jeju and Thoroughbred horses after exercise. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2019; 33:424-435. [PMID: 31480163 PMCID: PMC7054627 DOI: 10.5713/ajas.19.0260] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 07/12/2019] [Indexed: 11/27/2022]
Abstract
OBJECTIVE The study was conducted to investigate variations in the immunophysiological responses to exercise-induced stress in Jeju and Thoroughbred horses. METHODS Blood samples were collected from the jugular veins of adult Jeju (n = 5) and Thoroughbred (n = 5) horses before and after 30 min of exercise. The hematological, biochemical, and immunological profiles of the blood samples were analyzed. Blood smears were stained and observed under a microscope. The concentration of cell-free (cf) DNA in the plasma was determined using real time polymerase chain reaction (PCR). Peripheral blood mononuclear cells (PBMCs) and polymorphonuclear cells were separated using Polymorphprep, and the expression of various stress-related and chemokine receptor genes was measured using reverse transcriptase (RT) and real-time PCR. RESULTS After exercise, Jeju and Thoroughbred horses displayed stress responses with significantly increased rectal temperatures, cortisol levels, and muscle catabolism-associated metabolites. Red blood cell indices were significantly higher in Thoroughbred horses than in Jeju horses after exercise. In addition, exercise-induced stress triggered the formation of neutrophil extracellular traps (NETs) and reduced platelet counts in Jeju horses but not in Thoroughbred horses. Heat shock protein 72 and heat shock protein family A (Hsp70) member 6 expression is rapidly modulated in response to exercise-induced stress in the PBMCs of Jeju horses. The expression of CXC chemokine receptor 4 in PBMCs was higher in Thoroughbred horses than in Jeju horses after exercise. CONCLUSION In summary, the different immunophysiological responses of Jeju and Thoroughbred horses explain the differences in the physiological and anatomical properties of the two breeds. The physiology of Thoroughbred horses makes them suitable for racing as they are less sensitive to exercise-induced stress compared to that of Jeju horses. This study provides a basis for investigating the link between exercise-induced stresses and the physiological alteration of horses. Hence, our findings show that some of assessed parameters could be used to determine the endurance performance of horses.
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Affiliation(s)
- Saichit Khummuang
- Department of Animal Science, College of Natural Resources and Life Sciences, Pusan National University, Miryang 50463, Korea
| | - Hyo Gun Lee
- Department of Animal Science, College of Natural Resources and Life Sciences, Pusan National University, Miryang 50463, Korea
| | - Sang Seok Joo
- Department of Animal Science, College of Natural Resources and Life Sciences, Pusan National University, Miryang 50463, Korea
| | - Jeong-Woong Park
- Department of Animal Science, College of Natural Resources and Life Sciences, Pusan National University, Miryang 50463, Korea
| | - Jae-Young Choi
- Department of Animal Science, College of Natural Resources and Life Sciences, Pusan National University, Miryang 50463, Korea
| | - Jin Hyeog Oh
- Department of Animal Science, College of Natural Resources and Life Sciences, Pusan National University, Miryang 50463, Korea
| | - Kyoung Hwan Kim
- Department of Animal Science, College of Natural Resources and Life Sciences, Pusan National University, Miryang 50463, Korea
| | - Hyun-Hee Youn
- Department of Animal Science, College of Natural Resources and Life Sciences, Pusan National University, Miryang 50463, Korea
| | - Myunghoo Kim
- Department of Animal Science, College of Natural Resources and Life Sciences, Pusan National University, Miryang 50463, Korea
| | - Byung-Wook Cho
- Department of Animal Science, College of Natural Resources and Life Sciences, Pusan National University, Miryang 50463, Korea
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Genome-wide association analysis for body weight identifies candidate genes related to development and metabolism in rainbow trout (Oncorhynchus mykiss). Mol Genet Genomics 2019; 294:563-571. [PMID: 30635785 DOI: 10.1007/s00438-018-1518-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 12/03/2018] [Indexed: 01/12/2023]
Abstract
Growth is one of the most important traits from both a physiological and economic perspective in aquaculture species. Thus, identifying the genomic regions and genes underpinning genetic variation for this trait is of particular interest in several fish species, including rainbow trout. In this work, we perform a genome-wide association study (GWAS) to identify the genomic regions associated with body weight at tagging (BWT) and at 18 months (BW18M) using a dense SNP panel (57 k) and 4596 genotyped rainbow trout from 105 full-sib families belonging to a Chilean breeding population. Analysis was performed by means of single-step GBLUP approach. Genetic variance explained by 20 adjacent SNP windows across the whole genome is reported. To further explore candidate genes, we focused on windows that explained the highest proportion of genetic variance in the top 10 chromosomes for each trait. The main window from the top 10 chromosomes was explored by BLAST using the first and last SNP position of each window to determine the target nucleotide sequence. As expected, the percentage of genetic variance explained by windows was relatively low, due to the polygenic nature of body weight. The most important genomic region for BWT and BW18M were located on chromosomes 15 and 24 and they explained 2.14% and 3.02% of the genetic variance for each trait, respectively. Candidate genes including several growth factors, genes involved in development of skeletal muscle and bone tissue and nutrient metabolism were identified within the associated regions for both traits BWT and BW18M. These results indicate that body weight is polygenic in nature in rainbow trout, with the most important loci explaining as much as 3% of the genetic variance for the trait. The genes identified here represent good candidates for further functional validation to uncover biological mechanisms underlying variation for growth in rainbow trout.
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Elolimy AA, Moisá SJ, Brennan KM, Smith AC, Graugnard D, Shike DW, Loor JJ. Skeletal muscle and liver gene expression profiles in finishing steers supplemented with Amaize. Anim Sci J 2018; 89:1107-1119. [PMID: 29808540 DOI: 10.1111/asj.13041] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 04/04/2018] [Indexed: 12/23/2022]
Abstract
Our main objective was to evaluate the effects of feeding α-amylase (Amaize, Alltech Inc., Nicholasville, KY, USA) for 140 days on skeletal muscle and liver gene transcription in beef steers. Steers fed Amaize had lower average daily gain (p = .03) and gain:feed ratio (p = .05). No differences (p > .10) in serum metabolites or carcass traits were detected between the two groups but Amaize steers tended (p < .15) to have increased 12th rib fat depth. Microarray analysis of skeletal muscle revealed 21 differentially expressed genes (DEG), where 14 were up-regulated and seven were down-regulated in Amaize-fed steers. The bioinformatics analysis indicated that metabolic pathways involved in fat formation and deposition, stress response, and muscle function were activated, while myogenesis was inhibited in Amaize-fed steers. The quantitative PCR results for liver revealed a decrease (p < .01) in expression of fatty acid binding protein 1 (FABP1) and 3-hydroxybutyrate dehydrogenase 1 (BDH1) with Amaize. Because these genes are key for intracellular fatty acid transport, oxidation and ketone body production, data suggest a reduction in hepatic lipid catabolism. Future work to investigate potential positive effects of Amaize on cellular stress response, muscle function, and liver function in beef cattle appears warranted.
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Affiliation(s)
- Ahmed A Elolimy
- Mammalian NutriPhysioGenomics, Department of Animal Sciences, University of Illinois, Urbana, Illinois.,Department of Animal Sciences, University of Illinois, Urbana, Illinois
| | - Sonia J Moisá
- Mammalian NutriPhysioGenomics, Department of Animal Sciences, University of Illinois, Urbana, Illinois.,Department of Animal Sciences, University of Illinois, Urbana, Illinois.,Department of Animal Sciences, Auburn University, Auburn, Alabama
| | - Kristen M Brennan
- Alltech Center for Nutrigenomics and Applied Animal Nutrition, Nicholasville, Kentucky
| | - Allison C Smith
- Alltech Center for Nutrigenomics and Applied Animal Nutrition, Nicholasville, Kentucky
| | - Daniel Graugnard
- Alltech Center for Nutrigenomics and Applied Animal Nutrition, Nicholasville, Kentucky
| | - Daniel W Shike
- Department of Animal Sciences, University of Illinois, Urbana, Illinois
| | - Juan J Loor
- Mammalian NutriPhysioGenomics, Department of Animal Sciences, University of Illinois, Urbana, Illinois.,Department of Animal Sciences, University of Illinois, Urbana, Illinois.,Division of Nutritional Sciences, Illinois Informatics Institute, University of Illinois, Urbana, Illinois
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Ghosh M, Sharma N, Singh AK, Gera M, Pulicherla KK, Jeong DK. Transformation of animal genomics by next-generation sequencing technologies: a decade of challenges and their impact on genetic architecture. Crit Rev Biotechnol 2018; 38:1157-1175. [PMID: 29631431 DOI: 10.1080/07388551.2018.1451819] [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: 12/22/2022]
Abstract
For more than a quarter of a century, sequencing technologies from Sanger's method to next-generation high-throughput techniques have provided fascinating opportunities in the life sciences. The continuing upward trajectory of sequencing technologies will improve livestock research and expedite the development of various new genomic and technological studies with farm animals. The use of high-throughput technologies in livestock research has increased interest in metagenomics, epigenetics, genome-wide association studies, and identification of single nucleotide polymorphisms and copy number variations. Such studies are beginning to provide revolutionary insights into biological and evolutionary processes. Farm animals, such as cattle, swine, and horses, have played a dual role as economically and agriculturally important animals as well as biomedical research models. The first part of this study explores the current state of sequencing methods, many of which are already used in animal genomic studies, and the second part summarizes the state of cattle, swine, horse, and chicken genome sequencing and illustrates its achievements during the last few years. Finally, we describe several high-throughput sequencing approaches for the improved detection of known, unknown, and emerging infectious agents, leading to better diagnosis of infectious diseases. The insights from viral metagenomics and the advancement of next-generation sequencing will strongly support specific and efficient vaccine development and provide strategies for controlling infectious disease transmission among animal populations and/or between animals and humans. However, prospective sequencing technologies will require further research and in-field testing before reaching the marketplace.
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Affiliation(s)
- Mrinmoy Ghosh
- a Department of Animal Biotechnology , Jeju National University , Jeju-Do , Republic of Korea
| | - Neelesh Sharma
- b Department of Veterinary Science and Animal Husbandry , Sher-e-Kashmir University of Agricultural Sciences and Technology , R.S. Pura , India
| | - Amit Kumar Singh
- a Department of Animal Biotechnology , Jeju National University , Jeju-Do , Republic of Korea
| | - Meeta Gera
- a Department of Animal Biotechnology , Jeju National University , Jeju-Do , Republic of Korea
| | | | - Dong Kee Jeong
- a Department of Animal Biotechnology , Jeju National University , Jeju-Do , Republic of Korea
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McKenzie E. Current status of myopathies affecting athletic horses. COMPARATIVE EXERCISE PHYSIOLOGY 2017. [DOI: 10.3920/cep170005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Muscular disorders rank among the most prevalent problems of horses competing in a broad variety of athletic disciplines, including track racing, dressage, endurance racing and Western riding disciplines. As described in this review, active scientific investigation is continuing to elucidate the different mechanisms underlying specific muscular disorders in horses, and is discovering and defining new disorders, and new methods of diagnosis, treatment and management. The flourishing field of equine rehabilitation and regenerative medicine is also driving the progressive application of a variety of modalities to the treatment and management of musculoskeletal conditions in horses. However, it is essential that this be accompanied by appropriate scientific investigation to verify the efficacy of recommended modalities and treatment protocols.
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Affiliation(s)
- E. McKenzie
- Department of Clinical Sciences, College of Veterinary Medicine, Oregon State University, 227 Magruder Hall, Corvallis, OR 97331, USA
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