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Silva EFP, Gaia RC, Mulim HA, Pinto LFB, Iung LHS, Brito LF, Pedrosa VB. Genome-Wide Association Study of Conformation Traits in Brazilian Holstein Cattle. Animals (Basel) 2024; 14:2472. [PMID: 39272257 PMCID: PMC11394126 DOI: 10.3390/ani14172472] [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: 07/18/2024] [Revised: 08/12/2024] [Accepted: 08/20/2024] [Indexed: 09/15/2024] Open
Abstract
The linear conformation of animals exerts an influence on health, reproduction, production, and welfare, in addition to longevity, which directly affects the profitability of milk-producing farms. The objectives of this study were (1) to perform genome-wide association studies (GWASs) of conformation traits, namely the Rump, Feet and Legs, Mammary System, Dairy Strength, and Final Classification traits, and (2) to identify genes and related pathways involved in physiological processes associated with conformation traits in Brazilian Holstein cattle. Phenotypic and genotypic data from 2339 Holstein animals distributed across the states of Rio Grande do Sul, Paraná, São Paulo, and Minas Gerais were used. The genotypic data were obtained with a 100 K SNP marker panel. The single-step genome-wide association study (ssGWAS) method was employed in the analyses. Genes close to a significant SNP were identified in an interval of 100 kb up- and downstream using the Ensembl database available in the BioMart tool. The DAVID database was used to identify the main metabolic pathways and the STRING program was employed to create the gene regulatory network. In total, 36 significant SNPs were found on 15 chromosomes; 27 of these SNPs were linked to genes that may influence the traits studied. Fourteen genes most closely related to the studied traits were identified, as well as four genes that showed interactions in important metabolic pathways such as myogenesis, adipogenesis, and angiogenesis. Among the total genes, four were associated with myogenesis (TMOD2, TMOD3, CCND2, and CTBP2), three with angiogenesis (FGF23, FGF1, and SCG3), and four with adipogenesis and body size and development (C5H12orf4, CCND2, EMILIN1, and FGF6). These results contribute to a better understanding of the biological mechanisms underlying phenotypic variability in conformation traits in Brazilian Holstein cattle.
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Affiliation(s)
- Emanueli F P Silva
- Department of Animal Sciences, State University of Ponta Grossa, Ponta Grossa 84010-330, PR, Brazil
| | - Rita C Gaia
- Department of Animal Sciences, State University of Ponta Grossa, Ponta Grossa 84010-330, PR, Brazil
| | - Henrique A Mulim
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA
| | | | - Laiza H S Iung
- Neogen Corporation, Pindamonhangaba 12412-800, SP, Brazil
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Victor B Pedrosa
- Department of Animal Sciences, State University of Ponta Grossa, Ponta Grossa 84010-330, PR, Brazil
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA
- Neogen Corporation, Biotechnology Research, Lincoln, NE 68504, USA
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Zeng F, Li L, Yang J, Liu S, Yuan Y, Zhao C, Wang J. Transcriptomic and Proteomic Analyses Reveal New Insights into Regulatory Mechanisms of Strontium in Bovine Chondrocytes. Animals (Basel) 2023; 13:ani13081301. [PMID: 37106864 PMCID: PMC10135116 DOI: 10.3390/ani13081301] [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: 01/09/2023] [Revised: 04/07/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
Strontium (Sr) is a trace element found mainly in bone, and it performs a dual action by promoting bone formation and inhibiting bone resorption. Sr has been used to evaluate the gastrointestinal calcium (Ca) absorption capacity of dairy cows due to the similar physicochemical properties of the two elements. However, the possible effects of Sr on dairy cows remain unclear. This study aimed to explore the potential regulatory mechanism of Sr in bovine chondrocytes by performing transcriptomic and proteomic analyses. A total of 111 genes (52 up-regulated and 59 down-regulated) were identified as significantly altered (1.2-fold change and p < 0.05) between control and Sr-treated groups. Moreover, LC-MS-based proteomic analysis detected 286 changed proteins (159 up-regulated and 127 down-regulated) between the control and Sr-treated groups (1.2-fold change and p < 0.05). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations of a combination analysis of the transcriptomic and proteomic data revealed that the genes were predominantly involved in chondrocyte proliferation and differentiation, fat metabolism, the inflammation process, and immune responses. Overall, our data reveal a potential regulatory mechanism of strontium in bovine chondrocytes, thus providing further insights into the functions and application of Sr in ruminants.
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Affiliation(s)
- Fangyuan Zeng
- College of Veterinary Medicine, Northwest A&F University, Xianyang 712100, China
| | - Lan Li
- College of Veterinary Medicine, Northwest A&F University, Xianyang 712100, China
| | - Jiaqi Yang
- College of Veterinary Medicine, Northwest A&F University, Xianyang 712100, China
| | - Siqi Liu
- College of Veterinary Medicine, Northwest A&F University, Xianyang 712100, China
| | - Yang Yuan
- College of Veterinary Medicine, Northwest A&F University, Xianyang 712100, China
| | - Chenxu Zhao
- College of Veterinary Medicine, Northwest A&F University, Xianyang 712100, China
| | - Jianguo Wang
- College of Veterinary Medicine, Northwest A&F University, Xianyang 712100, China
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3
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Wang X, Xu J, Zeng H, Han Z. Enhancement of BCAT2-Mediated Valine Catabolism Stimulates β-Casein Synthesis via the AMPK-mTOR Signaling Axis in Bovine Mammary Epithelial Cells. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:9898-9907. [PMID: 35916279 DOI: 10.1021/acs.jafc.2c03629] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Valine, a kind of branched-chain amino acid, plays a regulatory role beyond that of a building block in milk protein synthesis. However, the underlying molecular mechanism through which valine stimulates β-casein synthesis has not been clarified. Therefore, our study aimed to evaluate the effect of valine on β-casein synthesis and shed light into the molecular mechanism using an in vitro model. Results showed that valine supplementation significantly increased β-casein synthesis in bovine mammary epithelial cells (BMECs). Meanwhile, the supplementation of valine resulted in high levels of branched-chain aminotransferase transaminase 2 (BCAT2), TCA-cycle intermediate metabolites, and ATP, AMP-activated protein kinase (AMPK) inhibition, and mammalian target of rapamycin (mTOR) activation. Furthermore, the inhibition of BCAT2 decreased the β-casein synthesis and downregulated the AMPK-mTOR pathway, with similar results observed for AMPK activation. Together, the present data indicate that valine promotes the synthesis of β-casein by affecting the AMPK-mTOR signaling axis and that BCAT2-mediated valine catabolism is the key target.
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Affiliation(s)
- Xinling Wang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Jie Xu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Hanfang Zeng
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhaoyu Han
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
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Nguyen LT, Lau LY, Fortes MRS. Proteomic Analysis of Hypothalamus and Pituitary Gland in Pre and Postpubertal Brahman Heifers. Front Genet 2022; 13:935433. [PMID: 35774501 PMCID: PMC9237413 DOI: 10.3389/fgene.2022.935433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 05/25/2022] [Indexed: 11/28/2022] Open
Abstract
The hypothalamus and the pituitary gland are directly involved in the complex systemic changes that drive the onset of puberty in cattle. Here, we applied integrated bioinformatics to elucidate the critical proteins underlying puberty and uncover potential molecular mechanisms from the hypothalamus and pituitary gland of prepubertal (n = 6) and postpubertal (n = 6) cattle. Proteomic analysis in the hypothalamus and pituitary gland revealed 275 and 186 differentially abundant (DA) proteins, respectively (adjusted p-value < 0.01). The proteome profiles found herein were integrated with previously acquired transcriptome profiles. These transcriptomic studies used the same tissues harvested from the same heifers at pre- and post-puberty. This comparison detected a small number of matched transcripts and protein changes at puberty in each tissue, suggesting the need for multiple omics analyses for interpreting complex biological systems. In the hypothalamus, upregulated DA proteins at post-puberty were enriched in pathways related to puberty, including GnRH, calcium and oxytocin signalling pathways, whereas downregulated proteins were observed in the estrogen signalling pathway, axon guidance and GABAergic synapse. Additionally, this study revealed that ribosomal pathway proteins in the pituitary were involved in the pubertal development of mammals. The reported molecules and derived protein-protein networks are a starting point for future experimental approaches that might dissect with more detail the role of each molecule to provide new insights into the mechanisms of puberty onset in cattle.
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Affiliation(s)
- Loan To Nguyen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Australia
- *Correspondence: Loan To Nguyen,
| | - Li Yieng Lau
- Agency of Science, Technology and Research, Singapore, Singapore
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Liu X, Tang Y, Wu J, Liu JX, Sun HZ. Feedomics provides bidirectional omics strategies between genetics and nutrition for improved production in cattle. ANIMAL NUTRITION (ZHONGGUO XU MU SHOU YI XUE HUI) 2022; 9:314-319. [PMID: 35600547 PMCID: PMC9097626 DOI: 10.1016/j.aninu.2022.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 02/10/2022] [Accepted: 03/15/2022] [Indexed: 06/15/2023]
Abstract
Increasing the efficiency and sustainability of cattle production is an effective way to produce valuable animal proteins for a growing human population. Genetics and nutrition are the 2 major research topics in selecting cattle with beneficial phenotypes and developing genetic potentials for improved performance. There is an inextricable link between genetics and nutrition, which urgently requires researchers to uncover the underlying molecular mechanisms to optimize cattle production. Feedomics integrates a range of omic techniques to reveal the mechanisms at different molecular levels related to animal production and health, which can provide novel insights into the relationships of genes and nutrition/nutrients. In this review, we summarized the applications of feedomics techniques to reveal the effect of genetic elements on the response to nutrition and investigate how nutrients affect the functional genome of cattle from the perspective of both nutrigenetics and nutrigenomics. We highlighted the roles of rumen microbiome in the interactions between host genes and nutrition. Herein, we discuss the importance of feedomics in cattle nutrition research, with a view to ensure that cattle exhibit the best production traits for human consumption from both genetic and nutritional aspects.
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Wang B, Sun H, Wang D, Liu H, Liu J. Constraints on the utilization of cereal straw in lactating dairy cows: A review from the perspective of systems biology. ANIMAL NUTRITION 2022; 9:240-248. [PMID: 35600542 PMCID: PMC9097690 DOI: 10.1016/j.aninu.2022.01.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 12/17/2021] [Accepted: 01/24/2022] [Indexed: 10/24/2022]
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Zhu Y, Bu D, Ma L. Integration of Multiplied Omics, a Step Forward in Systematic Dairy Research. Metabolites 2022; 12:metabo12030225. [PMID: 35323668 PMCID: PMC8955540 DOI: 10.3390/metabo12030225] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 02/07/2023] Open
Abstract
Due to their unique multi-gastric digestion system highly adapted for rumination, dairy livestock has complicated physiology different from monogastric animals. However, the microbiome-based mechanism of the digestion system is congenial for biology approaches. Different omics and their integration have been widely applied in the dairy sciences since the previous decade for investigating their physiology, pathology, and the development of feed and management protocols. The rumen microbiome can digest dietary components into utilizable sugars, proteins, and volatile fatty acids, contributing to the energy intake and feed efficiency of dairy animals, which has become one target of the basis for omics applications in dairy science. Rumen, liver, and mammary gland are also frequently targeted in omics because of their crucial impact on dairy animals’ energy metabolism, production performance, and health status. The application of omics has made outstanding contributions to a more profound understanding of the physiology, etiology, and optimizing the management strategy of dairy animals, while the multi-omics method could draw information of different levels and organs together, providing an unprecedented broad scope on traits of dairy animals. This article reviewed recent omics and multi-omics researches on physiology, feeding, and pathology on dairy animals and also performed the potential of multi-omics on systematic dairy research.
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Affiliation(s)
- Yingkun Zhu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
- School of Agriculture & Food Science, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland
| | - Dengpan Bu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
- Joint Laboratory on Integrated Crop-Tree-Livestock Systems of the Chinese Academy of Agricultural Sciences (CAAS), Ethiopian Institute of Agricultural Research (EIAR), and World Agroforestry Center (ICRAF), Beijing 100193, China
- Correspondence: (D.B.); (L.M.)
| | - Lu Ma
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
- Correspondence: (D.B.); (L.M.)
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Li G, Zhao H, Guo D, Liu Z, Wang H, Sun Q, Liu Q, Xu B, Guo X. Distinct molecular impact patterns of abamectin on Apis mellifera ligustica and Apis cerana cerana. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 232:113242. [PMID: 35104778 DOI: 10.1016/j.ecoenv.2022.113242] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 01/20/2022] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
The effects of insecticides on bee health are a topic of intensive research. Although abamectin is toxic to bees, the molecular impact of abamectin needs to be clarified. Here, we found that Apis cerana cerana exhibited a higher mortality rate when exposed to abamectin than Apis mellifera ligustica. In addition, A. cerana cerana had markedly higher numbers of differentially expressed genes (DEGs), differentially expressed proteins (DEPs) and differentially expressed metabolites (DEMs) than A. mellifera ligustica during exposure to abamectin. These results indicate that abamectin exposure exerts stronger effects on A. cerana cerana than on A. mellifera ligustica. In addition, six DEGs, two DEPs and two DEMs overlapped between the two bee species under abamectin exposure; however, some genes or proteins from the zinc finger protein, superoxide dismutase and peroxiredoxin families and the energy metabolism pathway were only unregulated in A. cerana cerana, which indicates a significant difference in the impact of abamectin on the two bee species. Despite these differences, several of the same gene families, such as heat shock proteins, cytochrome P450, odorant-binding proteins and cuticle proteins, and pathways, including the carbohydrate metabolism, immune system, lipid metabolism, amino acid metabolism, sensory system, locomotion and development pathways, were influenced by abamectin exposure in both A. cerana cerana and A. mellifera ligustica. Together, our results indicate that abamectin causes adverse effects on bees and thus poses a risk to bee populations and that abamectin exposure affects A. cerana cerana more strongly than A. mellifera ligustica. These findings improve our understanding of the behavioural and physiological effects of abamectin on bees.
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Affiliation(s)
- Guilin Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, PR China; College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong 271018, PR China; College of Life Sciences, Qufu Normal University, Qufu 273165, PR China
| | - Hang Zhao
- College of Life Sciences, Qufu Normal University, Qufu 273165, PR China
| | - Dezheng Guo
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, PR China
| | - Zhenguo Liu
- College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong 271018, PR China
| | - Hongfang Wang
- College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong 271018, PR China
| | - Qinghua Sun
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, PR China
| | - Qingxin Liu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, PR China
| | - Baohua Xu
- College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong 271018, PR China.
| | - Xingqi Guo
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong 271018, PR China.
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Zhang P, Li Q, Wu Y, Zhang Y, Zhang B, Zhang H. Identification of candidate genes that specifically regulate subcutaneous and intramuscular fat deposition using transcriptomic and proteomic profiles in Dingyuan pigs. Sci Rep 2022; 12:2844. [PMID: 35181733 PMCID: PMC8857214 DOI: 10.1038/s41598-022-06868-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 02/08/2022] [Indexed: 12/13/2022] Open
Abstract
Subcutaneous fat and intramuscular fat (IMF) deposition are closely related to meat production and pork quality. Dingyuan pig, as a native pig breed in China, low selection leads to obvious genetic and phenotypic differences in the population. Individuals with extreme fat content in the population are ideal models for studying the mechanism of fat deposition. In this study, we used RNA-Seq and tandem mass tags-based (TMT) proteomics to analyze the key pathways and genes that specifically regulate subcutaneous fat and IMF deposition in Dingyuan pigs. We identified 191 differentially expressed genes (DEGs) and 61 differentially abundant proteins (DAPs) in the high and low back fat thickness (HBF, LBF) groups, 85 DEGs and 12 DAPs were obtained in the high and low intramuscular fat (HIMF, LIMF) groups. The functional analysis showed that the DEGs and DAPs in the backfat groups were mainly involved in carbohydrates, amino acids, and fatty acids metabolism, whereas the IMF groups were involved in the insulin pathway, longevity, and some disease-related pathways. We found 40 candidate genes that might tissue-specifically lipids deposition for subcutaneous and intramuscular fat. Our research provides theoretical reference materials for the improvement of fat deposition traits of local pig breeds in my country.
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Affiliation(s)
- Pan Zhang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - Qinggang Li
- Institute of Animal Sciences and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, Anhui, China
| | - Yijing Wu
- Institute of Animal Sciences and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei, 230031, Anhui, China
| | - Yawen Zhang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China
| | - Bo Zhang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China.
| | - Hao Zhang
- National Engineering Laboratory for Animal Breeding, China Agricultural University, Beijing, 100193, China
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Regulation of Milk Protein Synthesis by Free and Peptide-Bound Amino Acids in Dairy Cows. BIOLOGY 2021; 10:biology10101044. [PMID: 34681143 PMCID: PMC8533557 DOI: 10.3390/biology10101044] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 10/12/2021] [Accepted: 10/12/2021] [Indexed: 11/17/2022]
Abstract
Milk protein (MP) synthesis in the mammary gland of dairy cows is a complex biological process. As the substrates for protein synthesis, amino acids (AAs) are the most important nutrients for milk synthesis. Free AAs (FAAs) are the main precursors of MP synthesis, and their supplies are supplemented by peptide-bound AAs (PBAAs) in the blood. Utilization of AAs in the mammary gland of dairy cows has attracted the great interest of researchers because of the goal of increasing MP yield. Supplying sufficient and balanced AAs is critical to improve MP concentration and yield in dairy cows. Great progress has been made in understanding limiting AAs and their requirements for MP synthesis in dairy cows. This review focuses on the effects of FAA and PBAA supply on MP synthesis and their underlying mechanisms. Advances in our knowledge in the field can help us to develop more accurate models to predict dietary protein requirements for dairy cows MP synthesis, which will ultimately improve the nitrogen utilization efficiency and lactation performance of dairy cows.
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Wang K, Qin Z, Wu S, Zhao P, Zhen C, Gao H. Antifungal Mechanism of Volatile Organic Compounds Produced by Bacillus subtilis CF-3 on Colletotrichum gloeosporioides Assessed Using Omics Technology. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:5267-5278. [PMID: 33899461 DOI: 10.1021/acs.jafc.1c00640] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Bacillus subtilis is commonly used as a biocontrol bacterium owing to its strong antifungal activity, broad-spectrum inhibition, and general safety. In this study, the inhibitory effects of volatile organic compounds (VOCs) produced by B. subtilis CF-3 on Colletotrichum gloeosporioides, a major destructive phytopathogen of litchi anthracnose, were analyzed using proteomics and transcriptomics. Differentially expressed genes (DEGs) and proteins (DEPs) indicated that the inhibition of C. gloeosporioides by B. subtilis CF-3 VOCs downregulated the expression of genes related to cell membrane fluidity, cell wall integrity, energy metabolism, and production of cell wall-degrading enzymes. Particularly, those important DEGs and DEPs related to the ergosterol biosynthetic and biosynthesis of unsaturated fatty acids are most significantly influenced. 2,4-di-tert-butylphenol, a characteristic component of B. subtilis CF-3 VOCs, also showed a similar effect on C. gloeosporioides. Our results provide a theoretical basis for the potential application of B. subtilis CF-3 in the postharvest protection of fruits and vegetables.
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Affiliation(s)
- Ke Wang
- School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Zhen Qin
- School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Shiyuan Wu
- School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Pengyu Zhao
- School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Chaoying Zhen
- School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Haiyan Gao
- School of Life Sciences, Shanghai University, Shanghai 200444, China
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Chew SY, Brown AJP, Lau BYC, Cheah YK, Ho KL, Sandai D, Yahaya H, Than LTL. Transcriptomic and proteomic profiling revealed reprogramming of carbon metabolism in acetate-grown human pathogen Candida glabrata. J Biomed Sci 2021; 28:1. [PMID: 33388061 PMCID: PMC7778802 DOI: 10.1186/s12929-020-00700-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 12/21/2020] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Emergence of Candida glabrata, which causes potential life-threatening invasive candidiasis, has been widely associated with high morbidity and mortality. In order to cause disease in vivo, a robust and highly efficient metabolic adaptation is crucial for the survival of this fungal pathogen in human host. In fact, reprogramming of the carbon metabolism is believed to be indispensable for phagocytosed C. glabrata within glucose deprivation condition during infection. METHODS In this study, the metabolic responses of C. glabrata under acetate growth condition was explored using high-throughput transcriptomic and proteomic approaches. RESULTS Collectively, a total of 1482 transcripts (26.96%) and 242 proteins (24.69%) were significantly up- or down-regulated. Both transcriptome and proteome data revealed that the regulation of alternative carbon metabolism in C. glabrata resembled other fungal pathogens such as Candida albicans and Cryptococcus neoformans, with up-regulation of many proteins and transcripts from the glyoxylate cycle and gluconeogenesis, namely isocitrate lyase (ICL1), malate synthase (MLS1), phosphoenolpyruvate carboxykinase (PCK1) and fructose 1,6-biphosphatase (FBP1). In the absence of glucose, C. glabrata shifted its metabolism from glucose catabolism to anabolism of glucose intermediates from the available carbon source. This observation essentially suggests that the glyoxylate cycle and gluconeogenesis are potentially critical for the survival of phagocytosed C. glabrata within the glucose-deficient macrophages. CONCLUSION Here, we presented the first global metabolic responses of C. glabrata to alternative carbon source using transcriptomic and proteomic approaches. These findings implicated that reprogramming of the alternative carbon metabolism during glucose deprivation could enhance the survival and persistence of C. glabrata within the host.
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Affiliation(s)
- Shu Yih Chew
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
| | - Alistair J. P. Brown
- MRC Centre for Medical Mycology, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD UK
| | - Benjamin Yii Chung Lau
- Proteomics and Metabolomics (PROMET) Group, Malaysian Palm Oil Board, Bandar Baru Bangi, 43000 Kajang, Selangor Malaysia
| | - Yoke Kqueen Cheah
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
| | - Kok Lian Ho
- Department of Pathology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
| | - Doblin Sandai
- Infectomics Cluster, Advanced Medical and Dental Institute, Universiti Sains Malaysia, 13200 Kepala Batas, Pulau Pinang Malaysia
| | - Hassan Yahaya
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
- Department of Medical Laboratory Science, Faculty of Allied Health Sciences, Bayero University, Kano, Nigeria
| | - Leslie Thian Lung Than
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
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Dai W, Zhao F, Liu J, Liu H. ASCT2 Is Involved in SARS-Mediated β-Casein Synthesis of Bovine Mammary Epithelial Cells with Methionine Supply. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:13038-13045. [PMID: 31597423 DOI: 10.1021/acs.jafc.9b03833] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The methionine (Met) uptake into mammary cells depends upon the corresponding amino acid (AA) transporters, which play a regulatory role in the mammary protein production beyond transport. Our previous studies have identified that seryl-tRNA synthetase (SARS) could be a novel mediator to regulate essential AA-stimulated casein synthesis in primary bovine mammary epithelial cells (BMECs). However, the regulatory mechanisms of Met in milk protein production in dairy cows remain further clarified. Here, we aimed to investigate the effects of Met on milk protein synthesis in BMECs and explore the underlying mechanism. The effects of Met on the AA transporter, casein synthesis, and the related signaling pathway were evaluated in the BMECs treated with 0.6 mM Met for 6 h combined with or without the inhibition of AA transporter (ASCT2, a neutral AA transporter) activity by the corresponding inhibitor (GPNA). Besides, the effects of SARS on the cells were mainly evaluated in the BMECs treated with 0.6 mM Met for 6 h together with or without SARS knockdown by RNAi interference. The gene expression of AA transporters and pathway-related genes were analyzed by the real-time quantitative polymerase chain reaction method, and the protein expression of related proteins were determined by the western blot assay. Results showed that 0.6 mM Met remarkably enhanced cell growth and β-casein synthesis compared to the supply of other Met concentrations. Among 13 amino acid transporters, 0.6 mM Met highly increased ASCT2 expression. This Met-stimulated ASCT2 expression and the enhanced mammary intracellular Met uptake were both decreased by the addition of 500 μM GPNA, an inhibitor of ASCT2. In the presence of 0.6 mM Met, the inhibition of ASCT2 activity (by GPNA) and SARS expression (by RNAi) both reduced β-casein synthesis. Additionally, 0.6 mM Met increased the gene expression of mTOR, S6K1, 4EBP1, and Akt; in contrast, the inhibition of ASCT2 by GPNA lowered the gene expression of these four genes. Collectively, this work suggests that ASCT2 is involved in the SARS-mediated Met stimulation of β-casein synthesis through enhancing mammary Met uptake and activating the mTOR signaling pathway in BMECs.
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Affiliation(s)
- Wenting Dai
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, People's Republic of China
| | - Fengqi Zhao
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, People's Republic of China
- Department of Animal and Veterinary Sciences, University of Vermont, Burlington, Vermont 05405, United States
| | - Jianxin Liu
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, People's Republic of China
| | - Hongyun Liu
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, People's Republic of China
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Sun HZ, Zhou M, Wang O, Chen Y, Liu JX, Guan LL. Multi-omics reveals functional genomic and metabolic mechanisms of milk production and quality in dairy cows. Bioinformatics 2020; 36:2530-2537. [PMID: 31873721 DOI: 10.1093/bioinformatics/btz951] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 11/04/2019] [Accepted: 12/20/2019] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Enhancing the utilization of human-inedible crop by-products by ruminants to produce high-quality milk for human consumption is an emerging global task. We performed a multi-omics-based study to decipher the regulatory biological processes of milk production when cows fed low-quality crop by-products with the aim to improve their utilization. RESULTS Seven types of different high-throughput omics data were generated across three central organs [rumen, liver and mammary gland (MG)] and biofluids (rumen fluid and blood) that involved in milk production. The integrated multi-omics analysis including metabolomics, metagenomics and transcriptomics showed altered microbiome at compositional and functional levels, microbial metabolites in the rumen, down-regulated genes and associated functions in liver and MG. These changes simultaneously contributed to down-regulated three key metabolic nodes (propionate, glucose and amino acid) across these organs and biofluids that led to lowered milk yield and quality when cows consumed corn stover (CS). Hippuric acid was identified as a biomarker that led to low milk production in CS-fed cows, suggesting a future evaluation parameter related to the metabolic mechanism of low-quality forage utilization. This study unveils the milk production-related biological mechanism across different biofluids and tissues under a low-quality forage diet, which provides a novel understanding and potential improvement strategies for future crop by-products utilization and sustainable ruminant production. AVAILABILITY AND IMPLEMENTATION The raw files of metagenomics, metabolomics, and transcriptomics data can be accessed at NCBI SRA (No. SRR5028206), EMBI-EBI (No. MTBLS411), and GEO (NO. GSE78524) databases respectively. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Hui-Zeng Sun
- Institute of Dairy Science, MoE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou 310058, P. R. China.,Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Mi Zhou
- Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Ou Wang
- Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Yanhong Chen
- Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Jian-Xin Liu
- Institute of Dairy Science, MoE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Le Luo Guan
- Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
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15
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Comparative transcriptomic and proteomic analyses provide insights into functional genes for hypoxic adaptation in embryos of Tibetan chickens. Sci Rep 2020; 10:11213. [PMID: 32641697 PMCID: PMC7343830 DOI: 10.1038/s41598-020-68178-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 04/22/2020] [Indexed: 12/11/2022] Open
Abstract
The Tibetan chicken is a unique breed that has adapted to the high-altitude hypoxic conditions of the Tibetan plateau. A number of positively selected genes have been reported in these chickens; however, the mechanisms of gene expression for hypoxia adaptation are not fully understood. In the present study, eggs from Tibetan and Chahua chickens were incubated under hypoxic and normoxic conditions, and vascularization in the chorioallantoic membrane (CAM) of embryos was observed. We found that the vessel density index in the CAM of Tibetan chickens was lower than in Chahua chickens under hypoxia conditions. Transcriptomic and proteomic analyses of CAM tissues were performed in Tibetan and Chahua chicken embryos under hypoxic incubation using RNA-Seq and iTRAQ. We obtained 160 differentially expressed genes and 387 differentially expressed proteins that were mainly enriched in angiogenesis, vasculature development, blood vessel morphogenesis, blood circulation, renin-angiotensin system, and HIF-1 and VEGF signaling pathways. Twenty-six genes involved in angiogenesis and blood circulation, two genes involved in ion transport, and six genes that regulated energy metabolism were identified as candidate functional genes in regulating hypoxic adaptation of chicken embryos. This research provided insights into the molecular mechanism of hypoxia adaptation in Tibetan chickens.
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Tandem Mass Tag (TMT)-based quantitative proteomics reveals potential targets associated with onset of Sub-clinical Mastitis in cows. Sci Rep 2020; 10:9321. [PMID: 32518370 PMCID: PMC7283279 DOI: 10.1038/s41598-020-66211-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 05/08/2020] [Indexed: 12/14/2022] Open
Abstract
Bovine milk is vital for infant nutrition and is a major component of the human diet. Bovine mastitis is a common inflammatory disease of mammary gland in cattle. It alters the immune profile of the animal and lowers the quality and yield of milk causing huge economic losses to dairy industry. The incidence of sub-clinical mastitis (SCM) is higher (25-65% worldwide) than clinical mastitis (CM) (>5%), and frequently progresses to clinical stage due to lack of sensitive and specific detection method. We used quantitative proteomics to identify changes in milk during sub-clinical mastitis, which may be potential biomarkers for developing rapid, non-invasive, sensitive detection methods. We performed comparative proteome analysis of the bovine milk, collected from the Indian hybrid cow Karan Fries. The differential proteome in the milk of Indian crossbred cows during sub-acute and clinical intramammary gland infection has not been investigated to date. Using high-resolution mass spectrometry-based quantitative proteomics of the bovine whey proteins, we identified a total of 1459 and 1358 proteins in biological replicates, out of which 220 and 157 proteins were differentially expressed between normal and infected samples. A total of 82 proteins were up-regulated and 27 proteins were down-regulated, having fold changes of ≥2 and ≤0.8 respectively. Among these proteins, overexpression of CHI3L1, LBP, GSN, GCLC, C4 and PIGR proteins was positively correlated with the events that elicit host defence system, triggering production of cytokines and inflammatory molecules. The appearance of these potential biomarkers in milk may be used to segregate affected cattle from the normal herd and may support mitigation measures for prevention of SCM and CM.
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Bhat SA, Ahmad SM, Ibeagha-Awemu EM, Mobashir M, Dar MA, Mumtaz PT, Shah RA, Dar TA, Shabir N, Bhat HF, Ganai NA. Comparative milk proteome analysis of Kashmiri and Jersey cattle identifies differential expression of key proteins involved in immune system regulation and milk quality. BMC Genomics 2020; 21:161. [PMID: 32059637 PMCID: PMC7023774 DOI: 10.1186/s12864-020-6574-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 02/10/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Exploration of the bioactive components of bovine milk has gained global interest due to their potential applications in human nutrition and health promotion. Despite advances in proteomics profiling, limited studies have been carried out to fully characterize the bovine milk proteome. This study explored the milk proteome of Jersey and Kashmiri cattle at day 90 of lactation using high-resolution mass spectrometry based quantitative proteomics nano-scale LC-MS/Q-TOF technique. Data are available via ProteomeXchange with identifier PXD017412. RESULTS Proteins from whey were fractionated by precipitation into high and low abundant proteins. A total of 81 high-abundant and 99 low-abundant proteins were significantly differentially expressed between Kashmiri and Jersey cattle, clearly differentiating the two breeds at the proteome level. Among the top differentiating proteins, the Kashmiri cattle milk proteome was characterised by increased concentrations of immune-related proteins (apelin, acid glycoprotein, CD14 antigen), neonatal developmental protein (probetacellulin), xenobiotic metabolising enzyme (flavin monooxygenase 3 (FMO3), GLYCAM1 and HSP90AA1 (chaperone) while the Jersey milk proteome presented higher concentrations of enzyme modulators (SERPINA1, RAC1, serine peptidase inhibitor) and hydrolases (LTF, LPL, CYM, PNLIPRP2). Pathway analysis in Kashmiri cattle revealed enrichment of key pathways involved in the regulation of mammary gland development like Wnt signalling pathway, EGF receptor signalling pathway and FGF signalling pathway while a pathway (T-cell activation pathway) associated with immune system regulation was significantly enriched in Jersey cattle. Most importantly, the high-abundant FMO3 enzyme with an observed 17-fold higher expression in Kashmiri cattle milk seems to be a characteristic feature of the breed. The presence of this (FMO3) bioactive peptide/enzyme in Kashmiri cattle could be economically advantageous for milk products from Kashmiri cattle. CONCLUSION In conclusion, this is the first study to provide insights not only into the milk proteome differences between Kashmiri and Jersey cattle but also provides potential directions for application of specific milk proteins from Kashmiri cattle in special milk preparations like infant formula.
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Affiliation(s)
- Shakil A. Bhat
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, SKUAST-Kashmir, Srinagar, India
| | - Syed M. Ahmad
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, SKUAST-Kashmir, Srinagar, India
| | - Eveline M. Ibeagha-Awemu
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, Quebec Canada
| | - Mohammad Mobashir
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institute, Novels väg 16, 17165 Solna, Stockholm, Sweden
| | - Mashooq A. Dar
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, SKUAST-Kashmir, Srinagar, India
| | - Peerzada T. Mumtaz
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, SKUAST-Kashmir, Srinagar, India
| | - Riaz A. Shah
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, SKUAST-Kashmir, Srinagar, India
| | - Tanveer A. Dar
- Department of Clinical Biochemistry, University of Kashmir, Srinagar, J & K India
| | - Nadeem Shabir
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, SKUAST-Kashmir, Srinagar, India
| | - Hina F. Bhat
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, SKUAST-Kashmir, Srinagar, India
| | - Nazir A. Ganai
- Division of Animal Genetics and Breeding, Faculty of Veterinary Sciences and Animal Husbandry, SKUAST-Kashmir, Srinagar, India
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18
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Seryl-tRNA synthetase is involved in methionine stimulation of β-casein synthesis in bovine mammary epithelial cells. Br J Nutr 2019; 123:489-498. [PMID: 31711551 PMCID: PMC7015878 DOI: 10.1017/s0007114519002885] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Despite the well-characterised mechanisms of amino acids (AA) regulation of milk protein synthesis in mammary glands (MG), the underlying specific AA regulatory machinery in bovine MG remains further elucidated. As methionine (Met) is one of the most important essential and limiting AA for dairy cows, it is crucial to expand how Met exerts its regulatory effects on dairy milk protein synthesis. Our previous work detected the potential regulatory role of seryl-tRNA synthetase (SARS) in essential AA (EAA)-stimulated bovine casein synthesis. Here, we investigated whether and how SARS participates in Met stimulation of casein production in bovine mammary epithelial cells (BMEC). With or without RNA interference against SARS, BMEC were treated with the medium in the absence (containing all other EAA and devoid of Met alone)/presence (containing 0·6 mm of Met in the medium devoid of Met alone) of Met. The protein abundance of β-casein and members of the mammalian target of rapamycin (mTOR) and general control nonderepressible 2 (GCN2) pathways was determined by immunoblot assay after 6 h treatment, the cell viability and cell cycle progression were determined by cell counting and propidium iodide-staining assay after 24 h treatment, and protein turnover was determined by l-[ring-3H5]phenylalanine isotope tracing assay after 48 h treatment. In the absence of Met, there was a general reduction in cell viability, total protein synthesis and β-casein production; in contrast, total protein degradation was enhanced. SARS knockdown strengthened these changes. Finally, SARS may work to promote Met-stimulated β-casein synthesis via affecting mTOR and GCN2 routes in BMEC.
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19
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Plasma Protein Comparison between Dairy Cows with Inactive Ovaries and Estrus. Sci Rep 2019; 9:13709. [PMID: 31548586 PMCID: PMC6757064 DOI: 10.1038/s41598-019-49785-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 08/29/2019] [Indexed: 01/11/2023] Open
Abstract
To screen differentially expressed proteins in the blood dairy cows with inactive ovaries caused by a negative energy balance and to determine the roles of the identified proteins in the development of inactive ovaries.Holstein cows at 14 to 21 days postpartum in an intensive dairy farm were examined for their energy balance (EB) status by blood β-hydroxybutyrate (BHBA) and assigned to the inactive ovary (IO) group (n = 50) and the normal oestrus control (CON) group (n = 50) at 60 to 90 days postpartum by means of the oestrus manifestation, rectal examination and B-ultrasound examination. Fourteen differentially expressed proteins from 61 proteins in the plasma of dairy cows with IOs were identified by iTRAQ/LC-MS/MS and GO, KEGG, and PATHWAY analysis. Eleven expressed proteins were upregulated, and 3 expressed proteins were downregulated. Among the 10 differentially expressed proteins verified by Western blot or ELISA, the relative expression levels of ALDOB, IGFBP2, ITIH3 and LDHB in mixed samples and single samples were consistent with the proteomic protein results. PKM2, GPX3, ALDOB, RBP4 and AHSG were significantly different between the two groups (P < 0.05); APOA4 and SPAM1 were not significantly different (P > 0.05) but were still downregulated in the ovarian resting group. This study confirmed that 14 plasma differential proteins in the inactive ovaries of postpartum dairy cows were associated with follicular development, and these findings provide a foundation for further research on the mechanism and prevention of inactive ovaries in dairy cows.
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20
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Hasan MS, Feugang JM, Liao SF. A Nutrigenomics Approach Using RNA Sequencing Technology to Study Nutrient-Gene Interactions in Agricultural Animals. Curr Dev Nutr 2019; 3:nzz082. [PMID: 31414073 PMCID: PMC6686084 DOI: 10.1093/cdn/nzz082] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 06/08/2019] [Accepted: 07/08/2019] [Indexed: 11/15/2022] Open
Abstract
Thorough understanding of animal gene expression driven by dietary nutrients can be regarded as a bottom line of advanced animal nutrition research. Nutrigenomics (including transcriptomics) studies the effects of dietary nutrients on cellular gene expression and, ultimately, phenotypic changes in living organisms. Transcriptomics can be applied to investigate animal tissue transcriptomes at a defined nutritional state, which can provide a holistic view of intracellular RNA expression. As a novel transcriptomics approach, RNA sequencing (RNA-Seq) technology can monitor all gene expressions simultaneously in response to dietary intervention. The principle and history of RNA-Seq are briefly reviewed, and its 3 principal steps are described in this article. Application of RNA-Seq in different areas of animal nutrition research is summarized. Lastly, the application of RNA-Seq in swine science and nutrition is also reviewed. In short, RNA-Seq holds significant potential to be employed for better understanding the nutrient-gene interactions in agricultural animals.
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Affiliation(s)
- M Shamimul Hasan
- Department of Animal and Dairy Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Jean M Feugang
- Department of Animal and Dairy Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Shengfa F Liao
- Department of Animal and Dairy Sciences, Mississippi State University, Mississippi State, MS, USA
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21
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Faehnrich B, Nemaz P, Schabauer A. Essential oil-bearing supplementation of dairy cows
– in vivo experiments elucidating factors
and co-factors influencing parameters of feed efficiency. JOURNAL OF ANIMAL AND FEED SCIENCES 2019. [DOI: 10.22358/jafs/110413/2019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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22
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Sun HZ, Plastow G, Guan LL. Invited review: Advances and challenges in application of feedomics to improve dairy cow production and health. J Dairy Sci 2019; 102:5853-5870. [PMID: 31030919 DOI: 10.3168/jds.2018-16126] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Accepted: 03/02/2019] [Indexed: 12/22/2022]
Abstract
Dairy cattle science has evolved greatly over the past century, contributing significantly to the improvement in milk production achieved today. However, a new approach is needed to meet the increasing demand for milk production and address the increased concerns about animal health and welfare. It is now easy to collect and access large and complex data sets consisting of molecular, physiological, and metabolic data as well as animal-level data (such as behavior). This provides new opportunities to better understand the mechanisms regulating cow performance. The recently proposed concept of feedomics could help achieve this goal by increasing our understanding of interactions between the different components or levels and their impact on animal production. Feedomics is an emerging field that integrates a range of omics technologies (e.g., genomics, epigenomics, transcriptomics, proteomics, metabolomics, metagenomics, and metatranscriptomics) to provide these insights. In this way, we can identify the best strategies to improve overall animal productivity, product quality, welfare, and health. This approach can help research communities elucidate the complex interactions among nutrition, environment, management, animal genetics, metabolism, physiology, and the symbiotic microbiota. In this review, we summarize the outcomes of the most recent research on omics in dairy cows and highlight how an integrated feedomics approach could be applied in the future to improve dairy cow production and health. Specifically, we focus on 2 topics: (1) improving milk yield and milk quality, and (2) understanding metabolic physiology in transition dairy cows, which are 2 important challenges faced by the dairy industry worldwide.
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Affiliation(s)
- H Z Sun
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada, T6G 2P5
| | - G Plastow
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada, T6G 2P5
| | - L L Guan
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada, T6G 2P5.
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23
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Clancey E, Kiser JN, Moraes JGN, Dalton JC, Spencer TE, Neibergs HL. Genome-wide association analysis and gene set enrichment analysis with SNP data identify genes associated with 305-day milk yield in Holstein dairy cows. Anim Genet 2019; 50:254-258. [PMID: 30994194 DOI: 10.1111/age.12792] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2018] [Indexed: 11/29/2022]
Abstract
Milk production traits, such as 305-day milk yield (305MY), have been under direct selection to improve production in dairy cows. Over the past 50 years, the average milk yield has nearly doubled, and over 56% of the increase is attributable to genetic improvement. As such, additional improvements in milk yield are still possible as new loci are identified. The objectives of this study were to detect SNPs and gene sets associated with 305MY in order to identify new candidate genes contributing to variation in milk production. A population of 781 primiparous Holstein cows from six central Washington dairies with records of 305MY and energy corrected milk were used to perform a genome-wide association analysis (GWAA) using the Illumina BovineHD BeadChip (777 962 SNPs) to identify QTL associated with 305MY (P < 1.0 × 10-5 ). A gene set enrichment analysis with SNP data (GSEA-SNP) was performed to identify gene sets (normalized enrichment score > 3.0) and leading edge genes (LEGs) influencing 305MY. The GWAA identified three QTL comprising 34 SNPs and 30 positional candidate genes. In the GSEA-SNP, five gene sets with 58 unique and 24 shared LEGs contributed to 305MY. Identification of QTL and LEGs associated with 305MY can provide additional targets for genomic selection to continue to improve 305MY in dairy cattle.
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Affiliation(s)
- E Clancey
- Department of Animal Sciences, Center for Reproductive Biology, Washington State University, PO Box 646310, Pullman, WA, 99164-6310, USA
| | - J N Kiser
- Department of Animal Sciences, Center for Reproductive Biology, Washington State University, PO Box 646310, Pullman, WA, 99164-6310, USA
| | - J G N Moraes
- Division of Animal Sciences, S158A Animal Sciences Research Center, University of Missouri, Columbia, MO, 65211, USA
| | - J C Dalton
- Department of Animal and Veterinary Sciences, Caldwell Research and Extension Center, University of Idaho, 1904 E Chicago St, Suite A, B, Caldwell, ID, 83605, USA
| | - T E Spencer
- Division of Animal Sciences, S158A Animal Sciences Research Center, University of Missouri, Columbia, MO, 65211, USA
| | - H L Neibergs
- Department of Animal Sciences, Center for Reproductive Biology, Washington State University, PO Box 646310, Pullman, WA, 99164-6310, USA
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Zhang J, Shi H, Li S, Cao Z, Yang H, Wang Y. Integrative hepatic metabolomics and proteomics reveal insights into the mechanism of different feed efficiency with high or low dietary forage levels in Holstein heifers. J Proteomics 2019; 194:1-13. [DOI: 10.1016/j.jprot.2018.12.026] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 12/18/2018] [Accepted: 12/23/2018] [Indexed: 01/18/2023]
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25
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Dai W, White R, Liu J, Liu H. Seryl-tRNA synthetase-mediated essential amino acids regulate β-casein synthesis via cell proliferation and mammalian target of rapamycin (mTOR) signaling pathway in bovine mammary epithelial cells. J Dairy Sci 2018; 101:10456-10468. [DOI: 10.3168/jds.2018-14568] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Accepted: 07/25/2018] [Indexed: 01/14/2023]
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26
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Sun HZ, Wang DM, Liu HY, Liu JX. Metabolomics Integrated with Transcriptomics Reveals a Subtle Liver Metabolic Risk in Dairy Cows Fed Different Crop By-products. Proteomics 2018; 18:e1800122. [DOI: 10.1002/pmic.201800122] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 06/11/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Hui-Zeng Sun
- Institute of Dairy Science, MoE Key Laboratory of Molecular Animal Nutrition; College of Animal Sciences; Zhejiang University; Hangzhou 310058 P. R. China
| | - Di-Ming Wang
- Institute of Dairy Science, MoE Key Laboratory of Molecular Animal Nutrition; College of Animal Sciences; Zhejiang University; Hangzhou 310058 P. R. China
| | - Hong-Yun Liu
- Institute of Dairy Science, MoE Key Laboratory of Molecular Animal Nutrition; College of Animal Sciences; Zhejiang University; Hangzhou 310058 P. R. China
| | - Jian-Xin Liu
- Institute of Dairy Science, MoE Key Laboratory of Molecular Animal Nutrition; College of Animal Sciences; Zhejiang University; Hangzhou 310058 P. R. China
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27
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Transcriptomic profiles of the bovine mammary gland during lactation and the dry period. Funct Integr Genomics 2017; 18:125-140. [PMID: 29275436 DOI: 10.1007/s10142-017-0580-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 12/06/2017] [Accepted: 12/08/2017] [Indexed: 01/22/2023]
Abstract
The initiation and maintenance of lactation are complex phenomena governed by biochemical and endocrine processes in the mammary gland (MG). Although DNA-based approaches have been used to study the onset of lactation, more comprehensive RNA-based techniques may be critical in furthering our understanding of gene alterations that occur to support lactation in the bovine MG. To further determine how gene profiles vary during lactation compared with the dry period, RNA-seq transcriptomic analysis was used to identify differentially expressed genes (DEG) in bovine MG tissues from animals that were lactating and not lactating. A total of 881 DEG (605 upregulated and 276 downregulated) were identified in MG of 3 lactating Chinese Holstein dairy cows versus the 3 dry cows. The subcellular analysis showed that the upregulated genes were most abundantly located in "integral to membrane" and "mitochondrion," and the top number of downregulated genes existed in "nucleus" and "cytoplasm." The functional analysis indicated that the DEG were primarily associated with the support of lactation processes. The genes in higher abundance were most related to "metabolic process," "oxidation-reduction process," "transport" and "signal transduction," protein synthesis-related processes (transcription, translation, protein modifications), and some MG growth-associated processes (cell proliferation/cycle/apoptosis). The downregulated genes were mainly involved in immune-related processes (inflammatory/immune/defense responses). The KEGG analysis suggested that protein synthesis-related pathways (such as protein digestion and absorption; protein processing in endoplasmic reticulum; and glycine, serine, and threonine metabolism) were highly and significantly enriched in the bovine MG of lactating cows compared to dry cows. The results suggested that the dry cows had decreased capacity for protein synthesis, energy generation, and cell growth but enhanced immune response. Collectively, this reduced capacity in dry cows supports the physiological demands of the next lactation and the coordinated metabolic changes that occur to support these demands. A total of 51 identified DEG were validated by RT-PCR, and consistent results were found between RT-PCR and the transcriptomic analysis. This work provides a profile of gene-associated changes that occur during lactation and can be used to facilitate further investigation of the mechanisms underlying lactation in dairy cows.
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Laodim T, Elzo MA, Koonawootrittriron S, Suwanasopee T, Jattawa D. Identification of SNP markers associated with milk and fat yields in multibreed dairy cattle using two genetic group structures. Livest Sci 2017. [DOI: 10.1016/j.livsci.2017.10.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Li S, Wang Q, Lin X, Jin X, Liu L, Wang C, Chen Q, Liu J, Liu H. The Use of "Omics" in Lactation Research in Dairy Cows. Int J Mol Sci 2017; 18:ijms18050983. [PMID: 28475129 PMCID: PMC5454896 DOI: 10.3390/ijms18050983] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 04/17/2017] [Accepted: 04/25/2017] [Indexed: 02/07/2023] Open
Abstract
“Omics” is the application of genomics, transcriptomics, proteomics, and metabolomics in biological research. Over the years, tremendous amounts of biological information has been gathered regarding the changes in gene, mRNA and protein expressions as well as metabolites in different physiological conditions and regulations, which has greatly advanced our understanding of the regulation of many physiological and pathophysiological processes. The aim of this review is to comprehensively describe the advances in our knowledge regarding lactation mainly in dairy cows that were obtained from the “omics” studies. The “omics” technologies have continuously been preferred as the technical tools in lactation research aiming to develop new nutritional, genetic, and management strategies to improve milk production and milk quality in dairy cows.
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Affiliation(s)
- Shanshan Li
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Quanjuan Wang
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Xiujuan Lin
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Xiaolu Jin
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Lan Liu
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Caihong Wang
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Qiong Chen
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Jianxin Liu
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Hongyun Liu
- Institute of Dairy Science, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China.
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