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Bouzeraa L, Martin H, Plessis C, Dufour P, Marques JCS, Moore S, Cerri R, Sirard MA. Decoding epigenetic markers: implications of traits and genes through DNA methylation in resilience and susceptibility to mastitis in dairy cows. Epigenetics 2024; 19:2391602. [PMID: 39151128 DOI: 10.1080/15592294.2024.2391602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 07/25/2024] [Accepted: 08/06/2024] [Indexed: 08/18/2024] Open
Abstract
Cattle farming faces challenges linked to intensive exploitation and climate change, requiring the reinforcement of animal resilience in response to these dynamic environments. Currently, genetic selection is used to enhance resilience by identifying animals resistant to specific diseases; however, certain diseases, such as mastitis, pose difficulties in genetic prediction. This study introduced the utilization of enzymatic methyl sequencing (EM-seq) of the blood genomic DNA from twelve dairy cows to identify DNA methylation biomarkers, with the aim of predicting resilience and susceptibility to mastitis. The analysis uncovered significant differences between cows resilient and susceptible to mastitis, with 196,275 differentially methylated cytosines (DMCs) and 1,227 Differentially Methylated Regions (DMRs). Key genes associated with the immune response and morphological traits, including ENOPH1, MYL10 and KIR2DL5A, were identified by our analysis. Quantitative trait loci (QTL) were also highlighted and the body weight trait was the most targeted by DMCs and DMRs. Based on our results, the risk of developing mastitis can potentially be estimated with as few as fifty methylation biomarkers, paving the way for early animal selection. This research sets the stage for improved animal health management and economic yields within the framework of agricultural sustainability through early selection based on the epigenetic status of animals.
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Affiliation(s)
- Lotfi Bouzeraa
- Department of Animal Sciences, Faculty of Agricultural and Food Sciences, Laval University, Québec, QC, Canada
- Research Center in Reproduction, Development, Intergenerational Health (CRDSI), Québec, QC, Canada
| | - Helene Martin
- Department of Animal Sciences, Faculty of Agricultural and Food Sciences, Laval University, Québec, QC, Canada
- Research Center in Reproduction, Development, Intergenerational Health (CRDSI), Québec, QC, Canada
| | - Clement Plessis
- Department of Molecular Medicine, Faculty of Medicine, Laval University, Québec, QC, Canada
| | - Pascal Dufour
- Department of Molecular Medicine, Faculty of Medicine, Laval University, Québec, QC, Canada
| | - Jessica C S Marques
- Faculty of Land and Food Systems, University of British Columbia, Vancouver, Canada
| | - Sydney Moore
- Faculty of Land and Food Systems, University of British Columbia, Vancouver, Canada
| | - Ronaldo Cerri
- Faculty of Land and Food Systems, University of British Columbia, Vancouver, Canada
| | - Marc-Andre Sirard
- Department of Animal Sciences, Faculty of Agricultural and Food Sciences, Laval University, Québec, QC, Canada
- Research Center in Reproduction, Development, Intergenerational Health (CRDSI), Québec, QC, Canada
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2
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Pozovnikova MV, Leibova VB, Tulinova OV, Romanova EA, Dysin AP, Dementieva NV, Azovtseva AI, Sedykh SE. Comparison of miR-106b, miR-191, and miR-30d expression dynamics in milk with regard to its composition in Holstein and Ayrshire cows. Anim Biosci 2024; 37:965-981. [PMID: 38419530 PMCID: PMC11065953 DOI: 10.5713/ab.23.0427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/25/2023] [Accepted: 01/12/2024] [Indexed: 03/02/2024] Open
Abstract
OBJECTIVE Milk composition varies considerably and depends on paratypical, genetic, and epigenetic factors. MiRNAs belong to the class of small non-coding RNAs; they are one of the key tools of epigenetic control because of their ability to regulate gene expression at the post-transcriptional level. We compared the relative expression levels of miR-106b, miR-191, and miR-30d in milk to demonstrate the relationship between the content of these miRNAs with protein and fat components of milk in Holstein and Ayrshire cattle. METHODS Milk fat, protein, and casein contents were determined in the obtained samples, as well as the content of the main fatty acids (g/100 g milk), including: saturated acids, such as myristic (C14:0), palmitic (C16:0), and stearic (C18:0) acids; monounsaturated acids, including oleic (C18:1) acid; as well as long-, medium- and short-chain, polyunsaturated, and trans fatty acids. Real-time stem-loop one-tube reverse transcription polymerase chain reaction with TaqMan probes was used to measure the miRNA expression levels. RESULTS The miRNA expression levels in milk samples were found to be decreased in the first two months in Holstein breed, and in the first four months in Ayrshire breed. Correlation analysis did not reveal any dependence between changes in the expression level of miRNA and milk fat content, but showed a multidirectional relationship with individual milk fatty acids. Positive associations between the expression levels of miR-106b and miR-30d and protein and casein content were found in the Ayrshire breed. Receiver operating characteristic curve analysis showed that miR-106b and miR-30d expression levels can cause changes in fatty acid and protein composition of milk in Ayrshire cows, whereas miR-106b expression level determines the fatty acid composition in Holsteins. CONCLUSION The data obtained in this study showed that miR-106b, miR-191, and miR-30d expression levels in milk samples have peculiarities associated with breed affiliation and the lactation period.
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Affiliation(s)
- Marina V. Pozovnikova
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, St. Petersburg, 196625,
Russia
| | - Viktoria B. Leibova
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, St. Petersburg, 196625,
Russia
| | - Olga V. Tulinova
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, St. Petersburg, 196625,
Russia
| | - Elena A. Romanova
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, St. Petersburg, 196625,
Russia
| | - Artem P. Dysin
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, St. Petersburg, 196625,
Russia
| | - Natalia V. Dementieva
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, St. Petersburg, 196625,
Russia
| | - Anastasiia I. Azovtseva
- Russian Research Institute of Farm Animal Genetics and Breeding—Branch of the L.K. Ernst Federal Research Center for Animal Husbandry, Pushkin, St. Petersburg, 196625,
Russia
| | - Sergey E. Sedykh
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090,
Russia
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3
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Jadhav AB, Ingole SD, Bharucha SV, Yoshitha KL, Gaikwad RV, Pharande RR, Kharde SD. Milk miRNA expression in buffaloes as a potential biomarker for mastitis. BMC Vet Res 2024; 20:150. [PMID: 38643124 PMCID: PMC11031985 DOI: 10.1186/s12917-024-04002-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 04/01/2024] [Indexed: 04/22/2024] Open
Abstract
BACKGROUND Buffaloes have the highest potential for production due to a promising gene pool that is being enhanced and upgraded. Mastitis is a significant health impediment that greatly diminishes milk yield and quality, affecting rural farmers' livelihoods. The traditional gold standard used for diagnosing mastitis or subclinical mastitis is CMT, but it has the drawback of false positive or negative results. Subclinical mastitis, if not treated promptly, can lead to mammary tumors. To address the gap in early diagnosis of subclinical mastitis in CMT-negative milk of buffaloes, we performed a retrospective analysis and evaluated the milk miRNA expression profiles as potential biomarkers. RESULTS Thirty buffalo milk samples based on clinical signs and CMT were divided into normal, subclinical, and clinical mastitis. SCC evaluation showed significant differences between the groups. The data analysis demonstrated that the elevation of miR-146a and miR-383 differed substantially between normal, subclinical, and clinical mastitis milk of buffaloes with 100% sensitivity and specificity. The relationship of SCC with miR-146a and miR-383 in normal/healthy and subclinical mastitis was positively correlated. CONCLUSION The overexpression of miR-146a and miR-383 is associated with inflammation. It can be a valuable prognostic and most sensitive biomarker for early mastitis detection in buffaloes with SCC below 2 lakhs and CMT-ve, enhancing the accuracy of subclinical mastitis diagnosis.
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Affiliation(s)
- Abhishek B Jadhav
- Department of Veterinary Physiology, Mumbai Veterinary College, Maharashtra Animal and Fishery Sciences University, Mumbai, India
| | - Shailesh D Ingole
- Department of Veterinary Physiology, Mumbai Veterinary College, Maharashtra Animal and Fishery Sciences University, Mumbai, India.
| | - Simin V Bharucha
- Department of Veterinary Physiology, Mumbai Veterinary College, Maharashtra Animal and Fishery Sciences University, Mumbai, India
| | - Korsapati L Yoshitha
- Department of Veterinary Physiology, Mumbai Veterinary College, Maharashtra Animal and Fishery Sciences University, Mumbai, India
| | - Rajiv V Gaikwad
- Teaching Veterinary Clinical Complex, Mumbai Veterinary College, Maharashtra Animal and Fishery Sciences University, Mumbia, India
| | - Rajesh R Pharande
- Department of Veterinary Microbiology, Mumbai Veterinary College, Maharashtra Animal and Fishery Sciences University, Mumbai, India
| | - Shambhudeo D Kharde
- Department of Veterinary Physiology, Mumbai Veterinary College, Maharashtra Animal and Fishery Sciences University, Mumbai, India
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Salehi M, Negahdari B, Mehryab F, Shekari F. Milk-Derived Extracellular Vesicles: Biomedical Applications, Current Challenges, and Future Perspectives. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:8304-8331. [PMID: 38587896 DOI: 10.1021/acs.jafc.3c07899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Extracellular vesicles (EVs) are nano to-micrometer-sized sacs that are released by almost all animal and plant cells and act as intercellular communicators by transferring their cargos between the source and target cells. As a safe and scalable alternative to conditioned medium-derived EVs, milk-derived EVs (miEVs) have recently gained a great deal of popularity. Numerous studies have shown that miEVs have intrinsic therapeutic actions that can treat diseases and enhance human health. Additionally, they can be used as natural drug carriers and novel classes of biomarkers. However, due to the complexity of the milk, the successful translation of miEVs from benchtop to bedside still faces several unfilled gaps, especially a lack of standardized protocols for the isolation of high-purity miEVs. In this work, by comprehensively reviewing the bovine miEVs studies, we provide an overview of current knowledge and research on miEVs while highlighting their challenges and enormous promise as a novel class of theranostics. It is hoped that this study will pave the way for clinical applications of miEVs by addressing their challenges and opportunities.
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Affiliation(s)
- Mahsa Salehi
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran 14177-55469, Iran
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran 16635-148, Iran
| | - Babak Negahdari
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran 14177-55469, Iran
| | - Fatemeh Mehryab
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran 16635-148, Iran
- Department of Pharmaceutics and Pharmaceutical Nanotechnology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran 14155-6153, Iran
| | - Faezeh Shekari
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran 16635-148, Iran
- Advanced Therapy Medicinal Product Technology Development Center (ATMP-TDC), Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran 16635-148, Iran
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Özkan H, Keçeli HH, Kaya U, Dalkiran S, Yüksel M, Tek E, Yakan A. Considering potential roles of selected MicroRNAs in evaluating subclinical mastitis and Milk quality in California mastitis test (+) and infected bovine milk. Anim Sci J 2024; 95:e13959. [PMID: 38769761 DOI: 10.1111/asj.13959] [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: 11/07/2023] [Revised: 04/13/2024] [Accepted: 04/25/2024] [Indexed: 05/22/2024]
Abstract
This study investigates the relationships between subclinical mastitis and milk quality with selected microRNAs in cow milk. California Mastitis Test (CMT)-positive (n = 20) and negative (n = 20) samples were compared (Experiment I). Additionally, samples with CMT-positive but microbiological-negative, as well as positive for only Staphylococcus subspecies (Staph spp.) and only Streptococcus subspecies (Strep spp.) were examined (Experiment II). Four groups were formed in Experiment II: Group I (CMT and microbiological-negative) (n = 20), Group II (CMT-positive but microbiological-negative) (n = 10), Group III (Staph spp.) (n = 5), Group IV (Strep spp.) (n = 5). While electrical conductivity, somatic cell count (SCC), malondialdehyde (MDA) increased, miR-27a-3p and miR-223 upregulated and miR-125b downregulated in the CMT-positive group in Experiment I. SCC and MDA were higher in CMT-positive groups. miR-27a-3p and miR-223 upregulated in Groups III and IV. While miR-155 is upregulated, miR-125b downregulated in Group IV. Milk fat is positively correlated with miR-148a and miR-223. As miR-27a-3p positively correlated with SCC and MDA, miR-125b negatively correlated with electrical conductivity and SCC. miR-148a and MDA were positively correlated. miR-155 was correlated with fat-free dry matter, protein, lactose, and freezing point. miR-223 was positively correlated with SCC and miR-148a. Results particularly highlight miR-27a-3p and miR-223 as potential biomarkers in subclinical mastitis, especially those caused by Staph spp. and Strep spp., while miR-148a, miR-155, and miR-223 stand out in determining milk quality.
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Affiliation(s)
- Hüseyin Özkan
- Faculty of Veterinary Medicine, Department of Genetics, Hatay Mustafa Kemal University, Hatay, Turkiye
| | - Hasan Hüseyin Keçeli
- Faculty of Veterinary Medicine, Department of Genetics, Hatay Mustafa Kemal University, Hatay, Turkiye
| | - Ufuk Kaya
- Faculty of Veterinary Medicine, Department of Biostatistics, Hatay Mustafa Kemal University, Hatay, Turkiye
| | - Sevda Dalkiran
- Institute of Health Sciences, Department of Molecular Biochemistry and Genetics, Hatay Mustafa Kemal University, Hatay, Turkiye
| | - Murat Yüksel
- Faculty of Veterinary Medicine, Department of Veterinary Obstetrics and Gynecology, Hatay Mustafa Kemal University, Hatay, Turkiye
| | - Erhan Tek
- Faculty of Veterinary Medicine, Department of Microbiology, Hatay Mustafa Kemal University, Hatay, Turkiye
| | - Akın Yakan
- Faculty of Veterinary Medicine, Department of Genetics, Hatay Mustafa Kemal University, Hatay, Turkiye
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Algharib SA, Dawood AS, Huang L, Guo A, Zhao G, Zhou K, Li C, Liu J, Gao X, Luo W, Xie S. Basic concepts, recent advances, and future perspectives in the diagnosis of bovine mastitis. J Vet Sci 2024; 25:e18. [PMID: 38311330 PMCID: PMC10839174 DOI: 10.4142/jvs.23147] [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: 07/01/2023] [Revised: 10/23/2023] [Accepted: 10/23/2023] [Indexed: 02/07/2024] Open
Abstract
Mastitis is one of the most widespread infectious diseases that adversely affects the profitability of the dairy industry worldwide. Accurate diagnosis and identification of pathogens early to cull infected animals and minimize the spread of infection in herds is critical for improving treatment effects and dairy farm welfare. The major pathogens causing mastitis and pathogenesis are assessed first. The most recent and advanced strategies for detecting mastitis, including genomics and proteomics approaches, are then evaluated . Finally, the advantages and disadvantages of each technique, potential research directions, and future perspectives are reported. This review provides a theoretical basis to help veterinarians select the most sensitive, specific, and cost-effective approach for detecting bovine mastitis early.
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Affiliation(s)
- Samah Attia Algharib
- Engineering Laboratory for Tarim Animal Diseases Diagnosis and Control, College of Animal Science and Technology, Tarim University, Alar, Xinjiang 843300, China
- Key Laboratory of Tarim Animal Husbandry & Science Technology of Xinjiang Production & Construction Corps., Alar, Xinjiang 843300, China
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Wuhan, Hubei 430070, China
- Department of Clinical Pathology, Faculty of Veterinary Medicine, Benha University, Moshtohor, Toukh 13736, QG, Egypt
| | - Ali Sobhy Dawood
- The State Key Laboratory of Agricultural Microbiology, (HZAU), Wuhan, Hubei 430070, China
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, University of Sadat City, Sadat City 32897, Egypt
| | - Lingli Huang
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Aizhen Guo
- The State Key Laboratory of Agricultural Microbiology, (HZAU), Wuhan, Hubei 430070, China
| | - Gang Zhao
- Key Laboratory of Ministry of Education for Conservation and Utilization of Special Biological Resources in the Western China, School of Life Sciences, Ningxia University, Yinchuan, Ningxia 750021, China
| | - Kaixiang Zhou
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Wuhan, Hubei 430070, China
| | - Chao Li
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Wuhan, Hubei 430070, China
| | - Jinhuan Liu
- Engineering Laboratory for Tarim Animal Diseases Diagnosis and Control, College of Animal Science and Technology, Tarim University, Alar, Xinjiang 843300, China
| | - Xin Gao
- College of Integrated Chinese and Western Medicine, Southwest Medical University, Lu Zhou, Sichuan 646000, China
| | - Wanhe Luo
- Engineering Laboratory for Tarim Animal Diseases Diagnosis and Control, College of Animal Science and Technology, Tarim University, Alar, Xinjiang 843300, China
- Key Laboratory of Tarim Animal Husbandry & Science Technology of Xinjiang Production & Construction Corps., Alar, Xinjiang 843300, China.
| | - Shuyu Xie
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Wuhan, Hubei 430070, China
- The State Key Laboratory of Agricultural Microbiology, (HZAU), Wuhan, Hubei 430070, China.
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Smulski S, Pszczoła M, Stachowiak M, Bilińska A, Szczerbal I. Droplet digital PCR quantification of selected microRNAs in raw mastitic cow's milk from the west of Poland. J Vet Res 2023; 67:583-591. [PMID: 38130455 PMCID: PMC10730559 DOI: 10.2478/jvetres-2023-0062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 10/27/2023] [Indexed: 12/23/2023] Open
Abstract
Introduction MicroRNAs (miRNAs), a class of noncoding small RNAs, have been recognised as potential biomarkers of mammary gland conditions, including bovine mastitis diagnosis. The aim of this study was to quantify selected miRNAs in the milk of mastitic cows. Material and Methods Milk samples (n = 90) were collected from healthy and mastitic dairy cows originating from local dairy cattle farms located in the west of Poland. MicroRNAs of the miR-21a, miR-92a, miR-146a and miR-383 species were quantified using the highly sensitive droplet digital PCR method. Direct measurement of somatic cell count (SCC) was performed using a cell counter. Cows were divided into three groups: those with an SCC below 200,000/mL were designated Low (n = 25), those with an SCC between 200,000 and 999,999 were Medium (n = 34), and those with an SCC of 1,000,000 or higher were High (n = 31). Microbiological analyses were performed using standard culture testing. Results The level of miR-383 was very low and this miRNA was excluded from analysis. The miR-92a was used to normalise miR-21a and miR-146a expression levels. The obtained results of expression of miR-21a and miR-146a correlated with somatic cell number (R = 0.53 and 0.79, respectively). Conclusion These results show that ddPCR is a useful method for quantifying miRNAs in raw cow milk. It seems that miR-146a is a promising marker for bovine mastitis, although further studies are needed to select a panel of miRNAs that can be used in mastitis monitoring in Poland.
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Affiliation(s)
- Sebastian Smulski
- Department of Internal Diseases and Diagnostics, Poznan University of Life Sciences, 60-637, Poznan, Poland
| | - Marcin Pszczoła
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, 60-637, Poznan, Poland
| | - Monika Stachowiak
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, 60-637, Poznan, Poland
| | - Adrianna Bilińska
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, 60-637, Poznan, Poland
| | - Izabela Szczerbal
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, 60-637, Poznan, Poland
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8
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Leduc A, Le Guillou S, Laloë D, Herve L, Laubier J, Poton P, Faulconnier Y, Pires J, Gele M, Martin P, Leroux C, Boutinaud M, Le Provost F. MiRNome variations in milk fractions during feed restrictions of different intensities in dairy cows. BMC Genomics 2023; 24:680. [PMID: 37957547 PMCID: PMC10641998 DOI: 10.1186/s12864-023-09769-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023] Open
Abstract
BACKGROUND In dairy cows, diet is one factor that can affect their milk production and composition. However, the effect of feed restriction on milk miRNome has not yet been described. Indeed, milk is the body fluid with the highest RNA concentration, which includes numerous microRNA. Its presence in the four different milk fractions, whole milk, fat globules, mammary epithelial cells and extracellular vesicles, is still poorly documented. This study aimed to describe the effects of different feed restrictions on the miRNome composition of different milk fractions. RESULTS Two feed restrictions were applied to lactating dairy cows, one of high intensity and one of moderate intensity. 2,896 mature microRNA were identified in the different milk fractions studied, including 1,493 that were already known in the bovine species. Among the 1,096 microRNA that were sufficiently abundant to be informative, the abundance of 1,027 of them varied between fractions: 36 of those were exclusive to one milk fraction. Feed restriction affected the abundance of 155 microRNA, with whole milk and milk extracellular vesicles being the most affected, whereas milk fat globules and exfoliated mammary epithelial cells were little or not affected at all. The high intensity feed restriction led to more microRNA variations in milk than moderate restriction. The target prediction of known microRNA that varied under feed restriction suggested the modification of some key pathways for lactation related to milk fat and protein metabolisms, cell cycle, and stress responses. CONCLUSIONS This study highlighted that the miRNome of each milk fraction is specific, with mostly the same microRNA composition but with variations in abundance between fractions. These specific miRNomes were affected differently by feed restrictions, the intensity of which appeared to be a major factor modulating milk miRNomes. These findings offer opportunities for future research on the use of milk miRNA as biomarkers of energy status in dairy cows, which is affected by feed restrictions.
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Affiliation(s)
- A Leduc
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, 78350, France
- PEGASE, INRAE, Institut Agro, 35590, Saint Gilles, France
- Institut de L'Elevage, 75012, Paris, France
| | - S Le Guillou
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, 78350, France
| | - D Laloë
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, 78350, France
| | - L Herve
- PEGASE, INRAE, Institut Agro, 35590, Saint Gilles, France
| | - J Laubier
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, 78350, France
| | - P Poton
- PEGASE, INRAE, Institut Agro, 35590, Saint Gilles, France
| | - Y Faulconnier
- INRAE, Université Clermont Auvergne, VetagroSup, UMRH, Saint-Genès-Champanelle, 63122, France
| | - J Pires
- INRAE, Université Clermont Auvergne, VetagroSup, UMRH, Saint-Genès-Champanelle, 63122, France
| | - M Gele
- Institut de L'Elevage, 75012, Paris, France
| | - P Martin
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, 78350, France
| | - C Leroux
- INRAE, Université Clermont Auvergne, VetagroSup, UMRH, Saint-Genès-Champanelle, 63122, France
| | - M Boutinaud
- PEGASE, INRAE, Institut Agro, 35590, Saint Gilles, France
| | - F Le Provost
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, 78350, France.
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9
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Zhou M, Barkema HW, Gao J, Yang J, Wang Y, Kastelic JP, Khan S, Liu G, Han B. MicroRNA miR-223 modulates NLRP3 and Keap1, mitigating lipopolysaccharide-induced inflammation and oxidative stress in bovine mammary epithelial cells and murine mammary glands. Vet Res 2023; 54:78. [PMID: 37710276 PMCID: PMC10503159 DOI: 10.1186/s13567-023-01206-5] [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: 05/18/2023] [Accepted: 08/12/2023] [Indexed: 09/16/2023] Open
Abstract
Bovine mastitis, the most prevalent and costly disease in dairy cows worldwide, decreases milk quality and quantity, and increases cow culling. However, involvement of microRNAs (miRNAs) in mastitis is not well characterized. The objective was to determine the role of microRNA-223 (miR-223) in regulation of the nucleotide-binding oligomerization domain-like receptor containing pyrin domain 3 (NLRP3) inflammasome and kelch like ECH-associated protein 1 (Keap1)/nuclear factor erythroid 2-related factor 2 (Nrf2) oxidative stress pathway in mastitis models induced by lipopolysaccharide (LPS) treatment of immortalized bovine mammary epithelial cells (bMECs) and murine mammary glands. In bMECs cultured in vitro, LPS-induced inflammation downregulated bta-miR-223; the latter interacted directly with the 3' untranslated region (3' UTR) of NLRP3 and Keap1. Overexpression of bta-miR-223 in bMECs decreased LPS and Adenosine 5'-triphosphate (ATP)-induced NLRP3 and its mediation of caspase 1 and IL-1β, and inhibited LPS-induced Keap1 and Nrf2 mediated oxidative stress, whereas inhibition of bta-miR-223 had opposite effects. In an in vivo murine model of LPS-induced mastitis, increased miR-223 mitigated pathology in the murine mammary gland, whereas decreased miR-223 increased inflammatory changes and oxidative stress. In conclusion, bta-miR-223 mitigated inflammation and oxidative injury by downregulating the NLRP3 inflammasome and Keap1/Nrf2 signaling pathway. This study implicated bta-miR-223 in regulation of inflammatory responses, with potential as a novel target for treating bovine mastitis and other diseases.
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Affiliation(s)
- Man Zhou
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Herman W Barkema
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Jian Gao
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Jingyue Yang
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Yue Wang
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - John P Kastelic
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Sohrab Khan
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Gang Liu
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China.
| | - Bo Han
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China.
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10
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Sánchez-Visedo A, Gallego-Martínez B, Royo LJ, Soldado A, Valledor M, Campo JC, Ferrero FJ, Costa-Fernández JM, Fernández-Argüelles MT. MNAzymes and gold nanoparticles as isothermal signal amplification strategy for visual detection of miRNA. Mikrochim Acta 2023; 190:292. [PMID: 37458796 PMCID: PMC10352400 DOI: 10.1007/s00604-023-05868-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 06/08/2023] [Indexed: 07/20/2023]
Abstract
MicroRNAs (miRNAs) represent a class of small noncoding RNAs that are considered a novel emerging class of disease biomarkers in a variety of afflictions. Sensitive detection of miRNA is typically achieved using hybridization-based methods coupled with genetic amplification techniques. Although their sensitivity has improved, amplification techniques often present erroneous results due to their complexity. In addition, the use of these techniques is usually linked to the application of protein enzymes, the activity of which is dependent on the temperature and pH of the medium. To address these drawbacks, an alternative genetic enzyme for the highly sensitive detection of miRNAs is proposed in this work. Multicomponent nucleic acid enzymes (MNAzymes), coupled with the use of DNA-functionalized gold nanoparticles (AuNPs), were used in this study to develop an isothermal signal amplification strategy for visual genetic detection. miR146a, a biomarker of bovine mastitis present in milk, was selected as a model analyte. The developed methodology is easily carried out in 80 min at 50 °C, generating a low visual limit of detection of 250 pM based on the observation of a color change. The methodology was successfully applied to the detection of miR146a in raw cow milk samples.
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Affiliation(s)
- Adrián Sánchez-Visedo
- Department of Physical and Analytical Chemistry, University of Oviedo, Avenida Julian Clavería 8, 33006, Oviedo, Asturias, Spain
| | - Borja Gallego-Martínez
- Health Research Institute of Asturias, ISPA, Avenida Hospital Universitario, s/n 33011, Oviedo, Asturias, Spain
| | - Luis José Royo
- Department of Functional Biology, Genetics, University of Oviedo, Avenida Julián Claveria, s/n 33006, Oviedo, Asturias, Spain
| | - Ana Soldado
- Department of Physical and Analytical Chemistry, University of Oviedo, Avenida Julian Clavería 8, 33006, Oviedo, Asturias, Spain
| | - Marta Valledor
- Department of Electrical, Electronic, Communications and Systems Engineering, University of Oviedo, Campus of Gijón, 33204, Gijón, Spain
| | - Juan Carlos Campo
- Department of Electrical, Electronic, Communications and Systems Engineering, University of Oviedo, Campus of Gijón, 33204, Gijón, Spain
| | - Francisco Javier Ferrero
- Department of Electrical, Electronic, Communications and Systems Engineering, University of Oviedo, Campus of Gijón, 33204, Gijón, Spain.
| | - José Manuel Costa-Fernández
- Department of Physical and Analytical Chemistry, University of Oviedo, Avenida Julian Clavería 8, 33006, Oviedo, Asturias, Spain
| | - María Teresa Fernández-Argüelles
- Department of Physical and Analytical Chemistry, University of Oviedo, Avenida Julian Clavería 8, 33006, Oviedo, Asturias, Spain.
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11
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MacLeay M, Banos G, Donadeu FX. Association of plasma miRNAs with early life performance and aging in dairy cattle. PLoS One 2023; 18:e0288343. [PMID: 37428722 DOI: 10.1371/journal.pone.0288343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 06/25/2023] [Indexed: 07/12/2023] Open
Abstract
Early life performance traits in dairy cattle can have important influences on lifetime productivity. Poor health and fertility are of great economical and animal welfare concern. Circulating miRNAs have been linked to several livestock traits, including resistance to infection, fertility, and muscle development. This study aimed to identify circulating miRNAs associated with early life performance traits and aging in dairy cattle. Plasma samples from female calves (n = 12) identified retrospectively as differing in health, growth, and fertility outcomes prior to first calving were analyzed using PCR arrays detecting 378 miRNAs. Levels of 6 miRNAs differed significantly in calves with poor growth/fertility relative to controls (t-test: P<0.05). Additionally, general(ized) (non)linear mixed models identified 1 miRNA associated with average daily gain until weaning, 22 with live bodyweight at one year of age, 47 with age at first service, and 19 with number of infections before first calving. Out of 85 distinct miRNAs that were associated with at least one animal trait, 9 miRNAs were validated by RT-qPCR in a larger cohort (n = 91 animals), which included longitudinal plasma samples (calf, heifer, first lactation cow). Significant associations (P<0.05) involving individual miRNAs or ratios between miRNAs and early-life performance traits were identified, but did not retain significance after multiple testing adjustment. However, levels of 8 plasma miRNAs (miR-126-3p, miR-127, miR-142-5p, miR-154b, miR-27b, miR-30c-5p, miR-34a, miR-363) changed significantly with age, most prominently during the calf-to-heifer transition. Comparative RT-qPCR analyses of these miRNAs across 19 calf tissues showed that most were ubiquitously expressed. Online database mining identified several pathways involved in metabolism and cell signaling as putative biological targets of these miRNAs. These results suggest that miR-126-3p, miR-127, miR-142-5p, miR-154b, miR-27b, miR-30c-5p, miR-34a, miR-363 are involved in regulating growth and development from birth to first lactation (~2 years old) and could provide useful biomarkers of aging in cattle.
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Affiliation(s)
- Madison MacLeay
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, United Kingdom
| | - Georgios Banos
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, United Kingdom
- Department of Animal and Veterinary Sciences, Scotland's Rural College (SRUC), Roslin Institute Building, Midlothian, United Kingdom
| | - Francesc Xavier Donadeu
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, United Kingdom
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12
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Regulatory Role of microRNA of Milk Exosomes in Mastitis of Dairy Cows. Animals (Basel) 2023; 13:ani13050821. [PMID: 36899678 PMCID: PMC10000098 DOI: 10.3390/ani13050821] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/06/2023] [Accepted: 02/20/2023] [Indexed: 03/12/2023] Open
Abstract
The aim of this study was to compare the cargos of miRNA in exosomes isolated from the milk of healthy (H) cows, cows at risk of mastitis (ARM), and cows with subclinical mastitis (SCM). Based on the number of somatic cells and the percentage of polymorphonuclear cells, 10 cows were assigned to group H, 11 to group ARM, and 11 to group SCM. After isolating exosomes in milk by isoelectric precipitation and ultracentrifugation, the extracted RNA was sequenced to 50 bp long single reads, and these were mapped against Btau_5.0.1. The resulting 225 miRNAs were uploaded to the miRNet suite, and target genes for Bos taurus were identified based on the miRTarBase and miRanda databases. The list of differentially expressed target genes resulting from the comparisons of the three groups was enriched using the Function Explorer of the Kyoto Encyclopedia of Genes and Genomes. A total of 38, 18, and 12 miRNAs were differentially expressed (DE, p < 0.05) in the comparisons of H vs. ARM, ARM vs. SCM, and H vs. SCM, respectively. Only 1 DE miRNA was shared among the three groups (bta-mir-221), 1 DE miRNA in the H vs. SCM comparison, 9 DE miRNAs in the ARM vs. SCM comparison, and 21 DE miRNAs in the H vs. ARM comparison. A comparison of the enriched pathways of target genes from the H, SCM, and ARM samples showed that 19 pathways were differentially expressed in the three groups, while 56 were expressed in the H vs. SCM comparison and 57 in the H vs. ARM comparison. Analyzing milk exosome miRNA cargos can be considered as a promising approach to study the complex molecular machinery set in motion in response to mastitis in dairy cows.
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13
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Ojo OE, Kreuzer-Redmer S. MicroRNAs in Ruminants and Their Potential Role in Nutrition and Physiology. Vet Sci 2023; 10:vetsci10010057. [PMID: 36669058 PMCID: PMC9867202 DOI: 10.3390/vetsci10010057] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/09/2022] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
The knowledge of how diet choices, dietary supplements, and feed intake influence molecular mechanisms in ruminant nutrition and physiology to maintain ruminant health, is essential to attain. In the present review, we focus on the role of microRNAs in ruminant health and disease; additionally, we discuss the potential of circulating microRNAs as biomarkers of disease in ruminants and the state of technology for their detection, also considering the major difficulties in the transition of biomarker development from bench to clinical practice. MicroRNAs are an inexhaustible class of endogenous non-protein coding small RNAs of 18 to 25 nucleotides that target either the 3' untranslated (UTR) or coding region of genes, ensuring a tight post-transcriptionally controlled regulation of gene expression. The development of new "omics" technologies facilitated a fresh perspective on the nutrition-to-gene relationship, incorporating more extensive data from molecular genetics, animal nutrition, and veterinary sciences. MicroRNAs might serve as important regulators of metabolic processes and may present the inter-phase between nutrition and gene regulation, controlled by the diet. The development of biomarkers holds the potential to revolutionize veterinary practice through faster disease detection, more accurate ruminant health monitoring, enhanced welfare, and increased productivity. Finally, we summarize the latest findings on how microRNAs function as biomarkers, how technological paradigms are reshaping this field of research, and how platforms are being used to identify novel biomarkers. Numerous studies have demonstrated a connection between circulating microRNAs and ruminant diseases such as mastitis, tuberculosis, foot-and-mouth disease, fasciolosis, and metabolic disorders. Therefore, the identification and analysis of a small number of microRNAs can provide crucial information about the stage of a disease, etiology, and prognosis.
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Differences in the microRNAs Levels of Raw Milk from Dairy Cattle Raised under Extensive or Intensive Production Systems. Vet Sci 2022; 9:vetsci9120661. [PMID: 36548822 PMCID: PMC9783024 DOI: 10.3390/vetsci9120661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/15/2022] [Accepted: 11/21/2022] [Indexed: 11/29/2022] Open
Abstract
Studying microRNA (miRNAs) in certain agri-food products is attractive because (1) they have potential as biomarkers that may allow traceability and authentication of such products; and (2) they may reveal insights into the products' functional potential. The present study evaluated differences in miRNAs levels in fat and cellular fractions of tank milk collected from commercial farms which employ extensive or intensive dairy production systems. We first sequenced miRNAs in three milk samples from each production system, and then validated miRNAs whose levels in the cellular and fat fraction differed significantly between the two production systems. To accomplish this, we used quantitative PCR with both fractions of tank milk samples from another 20 commercial farms. Differences in miRNAs were identified in fat fractions: overall levels of miRNAs, and, specifically, the levels of bta-mir-215, were higher in intensive systems than in extensive systems. Bovine mRNA targets for bta-miR-215 and their pathway analysis were performed. While the causes of these miRNAs differences remain to be elucidated, our results suggest that the type of production system could affect miRNAs levels and potential functionality of agri-food products of animal origin.
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15
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Zong W, Zhang T, Chen B, Lu Q, Cao X, Wang K, Yang Z, Chen Z, Yang Y. Emerging roles of noncoding micro RNAs and circular RNAs in bovine mastitis: Regulation, breeding, diagnosis, and therapy. Front Microbiol 2022; 13:1048142. [DOI: 10.3389/fmicb.2022.1048142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 10/28/2022] [Indexed: 11/17/2022] Open
Abstract
Bovine mastitis is one of the most troublesome and costly problems in the modern dairy industry, which is not only difficult to monitor, but can also cause economic losses while having significant implications on public health. However, efficacious preventative methods and therapy are still lacking. Moreover, new drugs and therapeutic targets are in increasing demand due to antibiotic restrictions. In recent years, noncoding RNAs have gained popularity as a topic in pathological and genetic studies. Meanwhile, there is growing evidence that they play a role in regulating various biological processes and developing novel treatment platforms. In light of this, this review focuses on two types of noncoding RNAs, micro RNAs and circular RNAs, and summarizes their characterizations, relationships, potential applications as selection markers, diagnostic or treatment targets and potential applications in RNA-based therapy, in order to shed new light on further research.
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16
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Variation of miRNA Content in Cow Raw Milk Depending on the Dairy Production System. Int J Mol Sci 2022; 23:ijms231911681. [PMID: 36232984 PMCID: PMC9569736 DOI: 10.3390/ijms231911681] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/22/2022] [Accepted: 09/27/2022] [Indexed: 11/23/2022] Open
Abstract
Pasture-based milk presents several advantages over milk from intensive industrial farming in terms of human health, the environment, animal welfare, and social aspects. This highlights the need for reliable methods to differentiate milk according to its origin on the market. Here, we explored whether miRNA profiles could serve as a marker of milk production systems. We compared levels of previously described miRNAs in milk from four production systems (altogether 112 milk samples): grazing, zero grazing, grass silage or corn silage. Total RNA was extracted from the fat phase, and miRNAs levels were quantified by real-time quantitative PCR. The levels of the miRNAs bta-miR-155 and bta-miR-103 were higher in the grazing system than in corn silage farms. The levels of bta-miR-532, bta-miR-103 and bta-miR-7863 showed differences between different farm managements. The miRNAs bta-miR-155 and bta-miR-103 were predicted to participate in common functions related to fat metabolism and fatty acid elongation. All four differentially expressed miRNAs were predicted to participate in transport, cell differentiation, and metabolism. These results suggest that the dairy production system influences the levels of some miRNAs in milk fat, and that bta-miR-155 and bta-miR-103 may be potential biomarkers to identify milk from pasture-managed systems.
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17
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Oyelami FO, Usman T, Suravajhala P, Ali N, Do DN. Emerging Roles of Noncoding RNAs in Bovine Mastitis Diseases. Pathogens 2022; 11:pathogens11091009. [PMID: 36145441 PMCID: PMC9501195 DOI: 10.3390/pathogens11091009] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 08/26/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
Non-coding RNAs (ncRNAs) are an abundant class of RNA with varying nucleotide lengths. They have been shown to have great potential in eutherians/human disease diagnosis and treatments and are now gaining more importance for the improvement of diseases in livestock. To date, thousands of ncRNAs have been discovered in the bovine genome and the continuous advancement in deep sequencing technologies and various bioinformatics tools has enabled the elucidation of their roles in bovine health. Among farm animals' diseases, mastitis, a common inflammatory disease in cattle, has caused devastating economic losses to dairy farmers over the last few decades. Here, we summarize the biology of bovine mastitis and comprehensively discuss the roles of ncRNAs in different types of mastitis infection. Based on our findings and relevant literature, we highlighted various evidence of ncRNA roles in mastitis. Different approaches (in vivo versus in vitro) for exploring ncRNA roles in mastitis are emphasized. More particularly, the potential applications of emerging genome editing technologies, as well as integrated omics platforms for ncRNA studies and implications for mastitis are presented.
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Affiliation(s)
- Favour Oluwapelumi Oyelami
- The John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia
| | - Tahir Usman
- College of Veterinary Sciences & Animal Husbandry, Abdul Wali Khan University, Mardan 23200, KP, Pakistan
| | - Prashanth Suravajhala
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana 690525, Kerala, India
| | - Nawab Ali
- Department of Zoology, Abdul Wali Khan University, Mardan 23200, KP, Pakistan
| | - Duy N. Do
- Faculty of Veterinary Medicine, Viet Nam National University of Agriculture, Hanoi 100000, Vietnam
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS B2N 5E3, Canada
- Correspondence: ; Tel.: +1-9029578789
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