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Influence of the At-Arrival Host Transcriptome on Bovine Respiratory Disease Incidence during Backgrounding. Vet Sci 2023; 10:vetsci10030211. [PMID: 36977250 PMCID: PMC10053706 DOI: 10.3390/vetsci10030211] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/06/2023] [Accepted: 03/09/2023] [Indexed: 03/12/2023] Open
Abstract
Bovine respiratory disease (BRD) remains the leading disease within the U.S. beef cattle industry. Marketing decisions made prior to backgrounding may shift BRD incidence into a different phase of production, and the importance of host gene expression on BRD incidence as it relates to marketing strategy is poorly understood. Our objective was to compare the influence of marketing on host transcriptomes measured on arrival at a backgrounding facility on the subsequent probability of being treated for BRD during a 45-day backgrounding phase. This study, through RNA-Seq analysis of blood samples collected on arrival, evaluated gene expression differences between cattle which experienced a commercial auction setting (AUCTION) versus cattle directly shipped to backgrounding from the cow–calf phase (DIRECT); further analyses were conducted to determine differentially expressed genes (DEGs) between cattle which remained clinically healthy during backgrounding (HEALTHY) versus those that required treatment for clinical BRD within 45 days of arrival (BRD). A profound difference in DEGs (n = 2961) was identified between AUCTION cattle compared to DIRECT cattle, regardless of BRD development; these DEGs encoded for proteins involved in antiviral defense (increased in AUCTION), cell growth regulation (decreased in AUCTION), and inflammatory mediation (decreased in AUCTION). Nine and four DEGs were identified between BRD and HEALTHY cohorts in the AUCTION and DIRECT groups, respectively; DEGs between disease cohorts in the AUCTION group encoded for proteins involved in collagen synthesis and platelet aggregation (increased in HEALTHY). Our work demonstrates the clear influence marketing has on host expression and identified genes and mechanisms which may predict BRD risk.
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Scott MA, Woolums AR, Swiderski CE, Finley A, Perkins AD, Nanduri B, Karisch BB. Hematological and gene co-expression network analyses of high-risk beef cattle defines immunological mechanisms and biological complexes involved in bovine respiratory disease and weight gain. PLoS One 2022; 17:e0277033. [PMID: 36327246 PMCID: PMC9632787 DOI: 10.1371/journal.pone.0277033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
Bovine respiratory disease (BRD), the leading disease complex in beef cattle production systems, remains highly elusive regarding diagnostics and disease prediction. Previous research has employed cellular and molecular techniques to describe hematological and gene expression variation that coincides with BRD development. Here, we utilized weighted gene co-expression network analysis (WGCNA) to leverage total gene expression patterns from cattle at arrival and generate hematological and clinical trait associations to describe mechanisms that may predict BRD development. Gene expression counts of previously published RNA-Seq data from 23 cattle (2017; n = 11 Healthy, n = 12 BRD) were used to construct gene co-expression modules and correlation patterns with complete blood count (CBC) and clinical datasets. Modules were further evaluated for cross-populational preservation of expression with RNA-Seq data from 24 cattle in an independent population (2019; n = 12 Healthy, n = 12 BRD). Genes within well-preserved modules were subject to functional enrichment analysis for significant Gene Ontology terms and pathways. Genes which possessed high module membership and association with BRD development, regardless of module preservation (“hub genes”), were utilized for protein-protein physical interaction network and clustering analyses. Five well-preserved modules of co-expressed genes were identified. One module (“steelblue”), involved in alpha-beta T-cell complexes and Th2-type immunity, possessed significant correlation with increased erythrocytes, platelets, and BRD development. One module (“purple”), involved in mitochondrial metabolism and rRNA maturation, possessed significant correlation with increased eosinophils, fecal egg count per gram, and weight gain over time. Fifty-two interacting hub genes, stratified into 11 clusters, may possess transient function involved in BRD development not previously described in literature. This study identifies co-expressed genes and coordinated mechanisms associated with BRD, which necessitates further investigation in BRD-prediction research.
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Affiliation(s)
- Matthew A. Scott
- Veterinary Education, Research, and Outreach Center, Texas A&M University and West Texas A&M University, Canyon, TX, United States of America
- * E-mail:
| | - Amelia R. Woolums
- Department of Pathobiology and Population Medicine, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, United States of America
| | - Cyprianna E. Swiderski
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona, United States of America
| | - Abigail Finley
- Veterinary Education, Research, and Outreach Center, Texas A&M University and West Texas A&M University, Canyon, TX, United States of America
| | - Andy D. Perkins
- Department of Computer Science and Engineering, Mississippi State University, Mississippi State, MS, United States of America
| | - Bindu Nanduri
- Department of Comparative Biomedical Sciences, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, United States of America
| | - Brandi B. Karisch
- Department of Animal and Dairy Sciences, Mississippi State University, Mississippi State, MS, United States of America
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Integrative Analysis of the Nasal Microbiota and Serum Metabolites in Bovines with Respiratory Disease by 16S rRNA Sequencing and Gas Chromatography/Mass Selective Detector-Based Metabolomics. Int J Mol Sci 2022; 23:ijms231912028. [PMID: 36233330 PMCID: PMC9569885 DOI: 10.3390/ijms231912028] [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: 09/12/2022] [Revised: 10/01/2022] [Accepted: 10/07/2022] [Indexed: 11/17/2022] Open
Abstract
Bovine respiratory disease (BRD) continues to pose a serious threat to the cattle industry, resulting in substantial economic losses. As a multifactorial disease, pathogen infection and respiratory microbial imbalance are important causative factors in the occurrence and development of BRD. Integrative analyses of 16S rRNA sequencing and metabolomics allow comprehensive identification of the changes in microbiota and metabolism associated with BRD, making it possible to determine which pathogens are responsible for the disease and to develop new therapeutic strategies. In our study, 16S rRNA sequencing and metagenomic analysis were used to describe and compare the composition and diversity of nasal microbes in healthy cattle and cattle with BRD from different farms in Yinchuan, Ningxia, China. We found a significant difference in nasal microbial diversity between diseased and healthy bovines; notably, the relative abundance of Mycoplasma bovis and Pasteurella increased. This indicated that the composition of the microbial community had changed in diseased bovines compared with healthy ones. The data also strongly suggested that the reduced relative abundance of probiotics, including Pasteurellales and Lactobacillales, in diseased samples contributes to the susceptibility to bovine respiratory disease. Furthermore, serum metabolomic analysis showed altered concentrations of metabolites in BRD and that a significant decrease in lactic acid and sarcosine may impair the ability of bovines to generate energy and an immune response to pathogenic bacteria. Based on the correlation analysis between microbial diversity and the metabolome, lactic acid (2TMS) was positively correlated with Gammaproteobacteria and Bacilli and negatively correlated with Mollicutes. In summary, microbial communities and serum metabolites in BRD were characterized by integrative analysis. This study provides a reference for monitoring biomarkers of BRD, which will be critical for the prevention and treatment of BRD in the future.
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Scott MA, Woolums AR, Karisch BB, Harvey KM, Capik SF. Impact of preweaning vaccination on host gene expression and antibody titers in healthy beef calves. Front Vet Sci 2022; 9:1010039. [PMID: 36225796 PMCID: PMC9549141 DOI: 10.3389/fvets.2022.1010039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 08/25/2022] [Indexed: 11/13/2022] Open
Abstract
The impact of preweaning vaccination for bovine respiratory viruses on cattle health and subsequent bovine respiratory disease morbidity has been widely studied yet questions remain regarding the impact of these vaccines on host response and gene expression. Six randomly selected calves were vaccinated twice preweaning (T1 and T3) with a modified live vaccine for respiratory pathogens and 6 randomly selected calves were left unvaccinated. Whole blood samples were taken at first vaccination (T1), seven days later (T2), at revaccination and castration (T3), and at weaning (T4), and utilized for RNA isolation and sequencing. Serum from T3 and T4 was analyzed for antibodies to BRSV, BVDV1a, and BHV1. Sequenced RNA for all 48 samples was bioinformatically processed with a HISAT2/StringTie pipeline, utilizing reference guided assembly with the ARS-UCD1.2 bovine genome. Differentially expressed genes were identified through analyzing the impact of time across all calves, influence of vaccination across treatment groups at each timepoint, and the interaction of time and vaccination. Calves, regardless of vaccine administration, demonstrated an increase in gene expression over time related to specialized proresolving mediator production, lipid metabolism, and stimulation of immunoregulatory T-cells. Vaccination was associated with gene expression related to natural killer cell activity and helper T-cell differentiation, enriching for an upregulation in Th17-related gene expression, and downregulated genes involved in complement system activity and coagulation mechanisms. Type-1 interferon production was unaffected by the influence of vaccination nor time. To our knowledge, this is the first study to evaluate mechanisms of vaccination and development in healthy calves through RNA sequencing analysis.
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Affiliation(s)
- Matthew A. Scott
- Veterinary Education, Research, and Outreach Center, Texas A&M University and West Texas A&M University, Canyon, TX, United States
| | - Amelia R. Woolums
- Department of Pathobiology and Population Medicine, Mississippi State University, Mississippi State, MS, United States
| | - Brandi B. Karisch
- Department of Animal and Dairy Sciences, Mississippi State University, Mississippi State, MS, United States
| | - Kelsey M. Harvey
- Prairie Research Unit, Mississippi State University, Prairie, MS, United States
| | - Sarah F. Capik
- Texas A&M AgriLife Research, Texas A&M University System, Amarillo, TX, United States
- Department of Veterinary Pathobiology, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, United States
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Rickert CA, Lieleg O. Machine learning approaches for biomolecular, biophysical, and biomaterials research. BIOPHYSICS REVIEWS 2022; 3:021306. [PMID: 38505413 PMCID: PMC10914139 DOI: 10.1063/5.0082179] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 05/12/2022] [Indexed: 03/21/2024]
Abstract
A fluent conversation with a virtual assistant, person-tailored news feeds, and deep-fake images created within seconds-all those things that have been unthinkable for a long time are now a part of our everyday lives. What these examples have in common is that they are realized by different means of machine learning (ML), a technology that has fundamentally changed many aspects of the modern world. The possibility to process enormous amount of data in multi-hierarchical, digital constructs has paved the way not only for creating intelligent systems but also for obtaining surprising new insight into many scientific problems. However, in the different areas of biosciences, which typically rely heavily on the collection of time-consuming experimental data, applying ML methods is a bit more challenging: Here, difficulties can arise from small datasets and the inherent, broad variability, and complexity associated with studying biological objects and phenomena. In this Review, we give an overview of commonly used ML algorithms (which are often referred to as "machines") and learning strategies as well as their applications in different bio-disciplines such as molecular biology, drug development, biophysics, and biomaterials science. We highlight how selected research questions from those fields were successfully translated into machine readable formats, discuss typical problems that can arise in this context, and provide an overview of how to resolve those encountered difficulties.
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Chai J, Capik SF, Kegley B, Richeson JT, Powell JG, Zhao J. Bovine respiratory microbiota of feedlot cattle and its association with disease. Vet Res 2022; 53:4. [PMID: 35022062 PMCID: PMC8756723 DOI: 10.1186/s13567-021-01020-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 12/06/2021] [Indexed: 12/15/2022] Open
Abstract
Bovine respiratory disease (BRD), as one of the most common and costly diseases in the beef cattle industry, has significant adverse impacts on global food security and the economic stability of the industry. The bovine respiratory microbiome is strongly associated with health and disease and may provide insights for alternative therapy when treating BRD. The niche-specific microbiome communities that colonize the inter-surface of the upper and the lower respiratory tract consist of a dynamic and complex ecological system. The correlation between the disequilibrium in the respiratory ecosystem and BRD has become a hot research topic. Hence, we summarize the pathogenesis and clinical signs of BRD and the alteration of the respiratory microbiota. Current research techniques and the biogeography of the microbiome in the healthy respiratory tract are also reviewed. We discuss the process of resident microbiota and pathogen colonization as well as the host immune response. Although associations between the microbiota and BRD have been revealed to some extent, interpreting the development of BRD in relation to respiratory microbial dysbiosis will likely be the direction for upcoming studies, which will allow us to better understand the importance of the airway microbiome and its contributions to animal health and performance.
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Affiliation(s)
- Jianmin Chai
- Division of Agriculture, Department of Animal Science, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Sarah F Capik
- Texas A&M AgriLife Research and Department of Veterinary Pathobiology, Texas A&M College of Veterinary Medicine and Biomedical Sciences, Canyon, TX, 79015, USA
| | - Beth Kegley
- Division of Agriculture, Department of Animal Science, University of Arkansas, Fayetteville, AR, 72701, USA
| | - John T Richeson
- Department of Agricultural Sciences, West Texas A&M University, Canyon, TX, 79016, USA
| | - Jeremy G Powell
- Division of Agriculture, Department of Animal Science, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Jiangchao Zhao
- Division of Agriculture, Department of Animal Science, University of Arkansas, Fayetteville, AR, 72701, USA.
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