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Nicholson TL, Waack U, Fleming DS, Chen Q, Miller LC, Merkel TJ, Stibitz S. The contribution of BvgR, RisA, and RisS to global gene regulation, intracellular cyclic-di-GMP levels, motility, and biofilm formation in Bordetella bronchiseptica. Front Microbiol 2024; 15:1305097. [PMID: 38516008 PMCID: PMC10955343 DOI: 10.3389/fmicb.2024.1305097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 02/20/2024] [Indexed: 03/23/2024] Open
Abstract
Bordetella bronchiseptica is a highly contagious respiratory bacterial veterinary pathogen. In this study the contribution of the transcriptional regulators BvgR, RisA, RisS, and the phosphorylation of RisA to global gene regulation, intracellular cyclic-di-GMP levels, motility, and biofilm formation were evaluated. Next Generation Sequencing (RNASeq) was used to differentiate the global gene regulation of both virulence-activated and virulence-repressed genes by each of these factors. The BvgAS system, along with BvgR, RisA, and the phosphorylation of RisA served in cyclic-di-GMP degradation. BvgR and unphosphorylated RisA were found to temporally regulate motility. Additionally, BvgR, RisA, and RisS were found to be required for biofilm formation.
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Affiliation(s)
- Tracy L. Nicholson
- Agricultural Research Service, USDA, National Animal Disease Center, Ames, IA, United States
| | - Ursula Waack
- Agricultural Research Service, USDA, National Animal Disease Center, Ames, IA, United States
- United States Department of Energy, Oak Ridge Institute for Science and Education, Oak Ridge, TN, United States
| | - Damarius S. Fleming
- USDA, Agricultural Research Service, Beltsville Agricultural Research Center, Beltsville, MD, United States
| | - Qing Chen
- Division of Bacterial, Parasitic, and Allergenic Products, Center for Biologics Evaluation and Research, FDA, Silver Spring, MD, United States
| | - Laura C. Miller
- Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, United States
| | - Tod J. Merkel
- Division of Bacterial, Parasitic, and Allergenic Products, Center for Biologics Evaluation and Research, FDA, Silver Spring, MD, United States
| | - Scott Stibitz
- Division of Bacterial, Parasitic, and Allergenic Products, Center for Biologics Evaluation and Research, FDA, Silver Spring, MD, United States
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2
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Fleming DS, Liu F, Li RW. Differential Correlation of Transcriptome Data Reveals Gene Pairs and Pathways Involved in Treatment of Citrobacter rodentium Infection with Bioactive Punicalagin. Molecules 2023; 28:7369. [PMID: 37959788 PMCID: PMC10650703 DOI: 10.3390/molecules28217369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 11/15/2023] Open
Abstract
This study is part of the work investigating bioactive fruit enzymes as sustainable alternatives to parasite anthelmintics that can help reverse the trend of lost efficacy. The study looked to define biological and molecular interactions that demonstrate the ability of the pomegranate extract punicalagin against intracellular parasites. The study compared transcriptomic reads of two distinct conditions. Condition A was treated with punicalagin (PA) and challenged with Citrobacter rodentium, while condition B (CM) consisted of a group that was challenged and given mock treatment of PBS. To understand the effect of punicalagin on transcriptomic changes between conditions, a differential correlation analysis was conducted. The analysis examined the regulatory connections of genes expressed between different treatment conditions by statistically querying the relationship between correlated gene pairs and modules in differing conditions. The results indicated that punicalagin treatment had strong positive correlations with the over-enriched gene ontology (GO) terms related to oxidoreductase activity and lipid metabolism. However, the GO terms for immune and cytokine responses were strongly correlated with no punicalagin treatment. The results matched previous studies that showed punicalagin to have potent antioxidant and antiparasitic effects when used to treat parasitic infections in mice and livestock. Overall, the results indicated that punicalagin enhanced the effect of tissue-resident genes.
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Affiliation(s)
- Damarius S. Fleming
- USDA-ARS, Beltsville Agricultural Research Center, Animal Parasitic Diseases Laboratory, Beltsville, MD 20705, USA;
| | - Fang Liu
- Zhengzhou University, Zhengzhou 450001, China;
| | - Robert W. Li
- USDA-ARS, Beltsville Agricultural Research Center, Animal Parasitic Diseases Laboratory, Beltsville, MD 20705, USA;
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3
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Fleming DS, Miller LC, Li J, Van Geelen A, Sang Y. Transcriptomic Analysis of Liver Indicates Novel Vaccine to Porcine Reproductive and Respiratory Virus Promotes Homeostasis in T-Cell and Inflammatory Immune Responses Compared to a Commercial Vaccine in Pigs. Front Vet Sci 2022; 9:791034. [PMID: 35400088 PMCID: PMC8987227 DOI: 10.3389/fvets.2022.791034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 02/14/2022] [Indexed: 12/01/2022] Open
Abstract
One of the largest impediments for commercial swine production is the presence of Porcine Reproductive and Respiratory Syndrome Virus (PRRSV), a devastating RNA viral infection that is responsible for over $1 billion in loss in the U.S. annually. The challenge with combating PRRSV is a combination of the effect of an extraordinary rate of mutation, the ability to infect macrophages, and subversion of host immune response through a series of actions leading to both immunomodulation and immune evasion. Currently there are a handful of commercial vaccines on the market that have been shown to be effective against homologous infections, but struggle against heterologous or mixed strain infections. However, vaccination is the current best strategy for combating PRRSV, making research into new vaccine technology key. To address these issues with PRRSV and host antiviral functions a novel modified-live vaccine (MLV) able to stimulate known antiviral interferons was created and examined for its ability to potentiate effective immunity and better protection. Here, we examine gene expression in the liver of pigs vaccinated with our novel vaccine, given the liver's large role in antiviral responses and vaccine metabolism. Our study indicated that pigs administered the novel vaccine experience homeostatic gene expression consistent with less inflammation and T-cell depletion risk than pigs administered the commercial vaccine.
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Affiliation(s)
- Damarius S. Fleming
- USDA, Agricultural Research Service, Beltsville Agricultural Research Center, Animal Parasite Disease Laboratory, Beltsville, MD, United States
| | - Laura C. Miller
- USDA, Agricultural Research Service, National Animal Disease Center, Virus and Prion Research Unit, Ames, IA, United States
| | - Jiuyi Li
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, Nashville, TN, United States
| | - Albert Van Geelen
- USDA, National Animal Disease Center, Center for Veterinary Biologics: Policy, Evaluation and Licensing, Ames, IA, United States
| | - Yongming Sang
- Department of Agricultural and Environmental Sciences, College of Agriculture, Tennessee State University, Nashville, TN, United States
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4
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Miller LC, Fleming DS, Lager KM. Comparison of the Transcriptome Response within the Swine Tracheobronchial Lymphnode Following Infection with PRRSV, PCV-2 or IAV-S. Pathogens 2020; 9:pathogens9020099. [PMID: 32033425 PMCID: PMC7168592 DOI: 10.3390/pathogens9020099] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 01/29/2020] [Accepted: 02/04/2020] [Indexed: 12/16/2022] Open
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is a major respiratory pathogen of swine that has become extremely costly to the swine industry worldwide, often causing losses in production and animal life due to their ease of spread. However, the intracellular changes that occur in pigs following viral respiratory infections are still scantily understood for PRRSV, as well as other viral respiratory infections. The aim of this study was to acquire a better understanding of the PRRS disease by comparing gene expression changes that occur in tracheobronchial lymph nodes (TBLN) of pigs infected with either porcine reproductive and respiratory syndrome virus (PRRSV), porcine circovirus type 2 (PCV-2), or swine influenza A virus (IAV-S) infections. The study identified and compared gene expression changes in the TBLN of 80 pigs following infection by PRRSV, PCV-2, IAV-S, or sham inoculation. Total RNA was pooled for each group and time-point (1, 3, 6, and 14 dpi) to make 16 libraries—analyses are by Digital Gene Expression Tag Profiling (DGETP). The data underwent standard filtering to generate a list of sequence tag raw counts that were then analyzed using multidimensional and differential expression statistical tests. The results showed that PRRSV, IAV-S and PCV-2 viral infections followed a clinical course in the pigs typical of experimental infection of young pigs with these viruses. Gene expression results echoed this course, as well as uncovered genes related to intersecting and unique host immune responses to the three viruses. By testing and observing the host response to other respiratory viruses, our study has elucidated similarities and differences that can assist in the development of vaccines and therapeutics that shorten or prevent a chronic PRRSV infection.
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Affiliation(s)
- Laura C. Miller
- Virus and Prion Research Unit, National Animal Disease Center, USDA, Agricultural Research Service, Ames, IA 50161, USA; (D.S.F.); (K.M.L.)
- Correspondence:
| | - Damarius S. Fleming
- Virus and Prion Research Unit, National Animal Disease Center, USDA, Agricultural Research Service, Ames, IA 50161, USA; (D.S.F.); (K.M.L.)
- Oak Ridge Associated Universities/Oak Ridge Institute for Science and Education, Oakridge, TN 37830, USA
| | - Kelly M. Lager
- Virus and Prion Research Unit, National Animal Disease Center, USDA, Agricultural Research Service, Ames, IA 50161, USA; (D.S.F.); (K.M.L.)
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5
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Fleming DS, Miller LC. Differentially Expressed MiRNAs and tRNA Genes Affect Host Homeostasis During Highly Pathogenic Porcine Reproductive and Respiratory Syndrome Virus Infections in Young Pigs. Front Genet 2019; 10:691. [PMID: 31428130 PMCID: PMC6687759 DOI: 10.3389/fgene.2019.00691] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 07/02/2019] [Indexed: 12/15/2022] Open
Abstract
Background: Porcine respiratory and reproductive syndrome virus (PRRSV) is a single-stranded RNA virus member that infects pigs and causes losses to the commercial industry reaching upward of a billion dollars annually in combined direct and indirect costs. The virus can be separated into etiologies that contain multiple heterologous low and highly pathogenic strains. Recently, the United States has begun to see an increase in heterologous type 2 PRRSV strains of higher virulence (HP-PRRSV). The high pathogenicity of these strains can drastically alter host immune responses and the ability of the animal to maintain homeostasis. Because the loss of host homeostasis can denote underlying changes in gene and regulatory element expression profiles, the study aimed to examine the effect PRRSV infections has on miRNA and tRNA expression and the roles they play in host tolerance or susceptibility. Results: Using transcriptomic analysis of whole blood taken from control and infected pigs at several time points (1, 3, 8 dpi), the analysis returned a total of 149 statistically significant (FDR ⫹ 0.15) miRNAs (n = 89) and tRNAs (n = 60) that were evaluated for possible pro- and anti-viral effects. The tRNA differential expression increased in both magnitude and count as dpi increased, with no statistically significant expression at 1 dpi, but increases at 3 and 8 dpi. The most abundant tRNA amino acid at 3 dpi was alanine, while glycine was the most abundant at 8 dpi. For the miRNAs, focus was put on upregulation that can inhibit gene expression. These results yielded candidates with potential anti- and pro-viral actions such as Ssc-miR-125b, which is predicted to limit PRRSV viral levels, and Ssc-miR-145-5p shown to cause alternative macrophage priming. The results also showed that both the tRNAs and miRNAs displayed expression patterns. Conclusions: The results indicated that the HP-PRRSV infection affects host homeostasis through changes in miRNA and tRNA expression and their subsequent gene interactions that target and influence the function of host immune, metabolic, and structural pathways.
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Affiliation(s)
- Damarius S Fleming
- ORAU/ORISE, Oak Ridge, TN, United States.,Virus and Prion Diseases of Livestock Research Unit, National Animal Disease Center, USDA, Agricultural Research Service, Ames, IA, United States
| | - Laura C Miller
- Virus and Prion Diseases of Livestock Research Unit, National Animal Disease Center, USDA, Agricultural Research Service, Ames, IA, United States
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6
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Elbeltagy AR, Bertolini F, Fleming DS, Van Goor A, Ashwell CM, Schmidt CJ, Kugonza DR, Lamont SJ, Rothschild MF. Natural Selection Footprints Among African Chicken Breeds and Village Ecotypes. Front Genet 2019; 10:376. [PMID: 31139205 PMCID: PMC6518202 DOI: 10.3389/fgene.2019.00376] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Accepted: 04/09/2019] [Indexed: 01/09/2023] Open
Abstract
Natural selection is likely a major factor in shaping genomic variation of the African indigenous rural chicken, driving the development of genetic footprints. Selection footprints are expected to be associated with adaptation to locally prevailing environmental stressors, which may include diverse factors as high altitude, disease resistance, poor nutrition, oxidative and heat stresses. To determine the existence of a selection footprint, 268 birds were randomly sampled from three indigenous ecotypes from East Africa (Rwanda and Uganda) and North Africa (Baladi), and two registered Egyptian breeds (Dandarawi and Fayoumi). Samples were genotyped using the chicken Affymetrix 600K Axiom® Array. A total of 494,332 SNPs were utilized in the downstream analysis after implementing quality control measures. The intra-population runs of homozygosity (ROH) that occurred in >50% of individuals of an ecotype or in >75% of a breed were studied. To identify inter-population differentiation due to genetic structure, FST was calculated for North- vs. East-African populations and Baladi and Fayoumi vs. Dandarawi for overlapping windows (500 kb with a step-size of 250 kb). The ROH and FST mapping detected several selective sweeps on different autosomes. Results reflected selection footprints of the environmental stresses, breed behavior, and management. Intra-population ROH of the Egyptian chickens showed selection footprints bearing genes for adaptation to heat, solar radiation, ion transport and immunity. The high-altitude-adapted East-African populations' ROH showed a selection signature with genes for angiogenesis, oxygen-heme binding and transport. The neuroglobin gene (GO:0019825 and GO:0015671) was detected on a Chromosome 5 ROH of Rwanda-Uganda ecotypes. The sodium-dependent noradrenaline transporter, SLC6A2 on a Chromosome 11 ROH in Fayoumi breed may reflect its active behavior. Inter-population FST among Egyptian populations reflected genetic mechanisms for the Fayoumi resistance to Newcastle Disease Virus (NDV), while FST between Egyptian and Rwanda-Uganda populations indicated the Secreted frizzled related protein 2, SFRP2, (GO:0009314) on Chromosome 4, that contributes to melanogenic activity and most likely enhances the Dandarawi chicken adaptation to high-intensity of solar radiation in Southern Egypt. These results enhance our understanding of the natural selection forces role in shaping genomic structure for adaptation to the stressful African conditions.
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Affiliation(s)
- Ahmed R Elbeltagy
- Department of Animal Science, Iowa State University, Ames, IA, United States.,Department of Animal Biotechnology, Animal Production Research Institute, Giza, Egypt
| | - Francesca Bertolini
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Damarius S Fleming
- Department of Animal Science, Iowa State University, Ames, IA, United States.,Virus and Prion Diseases of Livestock Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, United States
| | - Angelica Van Goor
- Department of Animal Science, Iowa State University, Ames, IA, United States.,Institute of Food Production and Sustainability, National Institute of Food and Agriculture, United States Department of Agriculture, Washington, DC, United States
| | - Chris M Ashwell
- Department of Poultry Science, North Carolina State University, Raleigh, NC, United States
| | - Carl J Schmidt
- Department of Animal and Food Sciences, University of Delaware, Newark, DE, United States
| | - Donald R Kugonza
- Department of Agricultural Production, Makerere University, Kampala, Uganda
| | - Susan J Lamont
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Max F Rothschild
- Department of Animal Science, Iowa State University, Ames, IA, United States
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7
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Fleming DS, Anderson SJ, Miller LC. Identification of Coding and Non-coding RNA Classes Expressed in Swine Whole Blood. J Vis Exp 2018. [PMID: 30582594 DOI: 10.3791/58689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
The advent of innovative and increasingly powerful next generation sequencing techniques has opened new avenues into the ability to examine the underlying gene expression related to biological processes of interest. These innovations not only allow researchers to observe expression from the mRNA sequences that code for genes that effect cellular function, but also the non-coding RNA (ncRNA) molecules that remain untranslated, but still have regulatory functions. Although researchers have the ability to observe both mRNA and ncRNA expression, it has been customary for a study to focus on one or the other. However, when studies are interested in both mRNA and ncRNA expression, many times they use separate samples to examine either coding or non-coding RNAs due to the difference in library preparations. This can lead to the need for more samples which can increase time, consumables, and animal stress. Additionally, it may cause researchers to decide to prepare samples for only one analysis, usually the mRNA, limiting the number of biological questions that can be investigated. However, ncRNAs span multiple classes with regulatory roles that effect mRNA expression. Because ncRNA are important to fundamental biologic processes and disorder of these processes in during infection, they may, therefore, make attractive targets for therapeutics. This manuscript demonstrates a modified protocol for the generation mRNA and non-coding RNA expression libraries, including viral RNA, from a single sample of whole blood. Optimization of this protocol, improved RNA purity, increased ligation for recovery of methylated RNAs, and omitted size selection, to allow capture of more RNA species.
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Affiliation(s)
- Damarius S Fleming
- Virus and Prion Research Unit, National Animal Disease Center, USDA, Agricultural Research Service; ORAU/ORISE
| | - Sarah J Anderson
- Virus and Prion Research Unit, National Animal Disease Center, USDA, Agricultural Research Service
| | - Laura C Miller
- Virus and Prion Research Unit, National Animal Disease Center, USDA, Agricultural Research Service;
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8
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Miller LC, Fleming DS, Harhay GP, Kehrli ME, Lager KM. Transcriptome Responses to Respiratory Virus Infection of Pigs within the Tracheobronchial Lymphnode Following Infection with PRRSV, PCV2 or IAV. The Journal of Immunology 2018. [DOI: 10.4049/jimmunol.200.supp.59.14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Abstract
Porcine reproductive and respiratory syndromevirus (PRRSV) is a major respiratory pathogen of swine that has become extremely costly to the swine industry worldwide, often causing losses in production and animal life due to their ease of spread. However, the intracellular changes that occur in pigs following viral respiratory infections are still scantily understood for PRRSV, as well as, other viral respiratory infections. The aim of this study was to acquire a better understanding of PRRS disease by comparing gene expression changes that occur in tracheobronchial lymph nodes (TBLN) of pigs infected with either porcine reproductive and respiratory syndrome virus (PRRSV), porcine circovirus type 2 (PCV2), or swine influenza virus (IAV) infections. The study identified and compared gene expression changes in the TBLN of 16 pigs following infection by PRRSV, PCV2, IAV, or sham inoculation. Total RNA was pooled for each group and time-point (1, 3, 6, and14 DPI) to make 16 libraries, for analysis by Digital Gene Expression Tag Profiling (DGETP). The data underwent standard filtering to generate a list of sequence tag raw counts that were then analyzed using multidimensional and differential expression statistical tests. The results showed that PRRSV, IAV and PCV-2 infections followed a clinical course typical of experimental infection of young pigs with these viruses. Gene expression results echoed this course, as well as, uncovered genes related to shared and unique host immune responses to the 3 viruses. By testing and observing the host response to other respiratory viruses, our study has elucidated similarities and differences that can assist in development of vaccine and therapeutics that shorten or prevent a chronic PRRSV infection.
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9
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Fleming DS, Miller LC. Identification of small non-coding RNA classes expressed in swine whole blood during HP-PRRSV infection. Virology 2018; 517:56-61. [PMID: 29429554 DOI: 10.1016/j.virol.2018.01.027] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 01/30/2018] [Indexed: 02/06/2023]
Abstract
It has been established that reduced susceptibility to porcine reproductive and respiratory syndrome virus (PRRSV) has a genetic component. This genetic component may take the form of small non-coding RNAs (sncRNA), which are molecules that function as regulators of gene expression. Various sncRNAs have emerged as having an important role in the immune system in humans. The study uses transcriptomic read counts to profile the type and quantity of both well and lesser characterized sncRNAs, such as microRNAs and small nucleolar RNAs to identify and quantify the classes of sncRNA expressed in whole blood between healthy and highly pathogenic PRRSV-infected pigs. Our results returned evidence on nine classes of sncRNA, four of which were consistently statistically significantly different based on Fisher's Exact Test, that can be detected and possibly interrogated for their effect on host dysregulation during PRRSV infections.
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Affiliation(s)
- Damarius S Fleming
- ORAU/ORISE, Oak Ridge, TN, USA; Virus and Prion Diseases of Livestock Research Unit, National Animal Disease Center, USDA, Agricultural Research Service, P.O. Box 70, Ames, IA 50010-0070, USA
| | - Laura C Miller
- Virus and Prion Diseases of Livestock Research Unit, National Animal Disease Center, USDA, Agricultural Research Service, P.O. Box 70, Ames, IA 50010-0070, USA.
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10
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Miller LC, Fleming DS, Li X, Bayles DO, Blecha F, Sang Y. Comparative analysis of signature genes in PRRSV-infected porcine monocyte-derived cells to different stimuli. PLoS One 2017; 12:e0181256. [PMID: 28727780 PMCID: PMC5519058 DOI: 10.1371/journal.pone.0181256] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 06/28/2017] [Indexed: 01/18/2023] Open
Abstract
Monocyte-derived DCs (mDCs) are major target cells in porcine reproductive and respiratory syndrome virus (PRRSV) pathogenesis; however, the plasticity of mDCs in response to activation stimuli and PRRSV infection remains unstudied. In this study, we polarized mDCs, and applied genome-wide transcriptomic analysis and predicted protein-protein interaction networks to compare signature genes involved in mDCs activation and response to PRRSV infection. Porcine mDCs were polarized with mediators for 30 hours, then mock-infected, infected with PRRSV strain VR2332, or a highly pathogenic PRRSV strain (rJXwn06), for 5 h. Total RNA was extracted and used to construct sequencing libraries for RNA-Seq. Comparisons were made between each polarized and unpolarized group (i.e. mediator vs. PBS), and between PRRSV-infected and uninfected cells stimulated with the same mediator. Differentially expressed genes (DEG) from the comparisons were used for prediction of interaction networks affected by the viruses and mediators. The results showed that PRRSV infection inhibited M1-prone immune activity, downregulated genes, predicted network interactions related to cellular integrity, and inflammatory signaling in favor of M2 activity. Additionally, the number of DEG and predicted network interactions stimulated in HP-PRRSV infected mDCs was superior to the VR-2332 infected mDCs and conformed with HP-PRRSV pathogenicity.
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Affiliation(s)
- Laura C. Miller
- Virus and Prion Diseases of Livestock Research Unit, National Animal Disease Center, USDA-ARS, 1920 Dayton Ave, Ames, United States of America
- * E-mail: (LCM); (YS)
| | - Damarius S. Fleming
- Virus and Prion Diseases of Livestock Research Unit, National Animal Disease Center, USDA-ARS, 1920 Dayton Ave, Ames, United States of America
| | - Xiangdong Li
- National Research Center for Veterinary Medicine, Cuiwei Rd, High-Tech District, Luoyang, Henan, China
| | - Darrell O. Bayles
- Infectious Bacterial Diseases Research Unit, National Animal Disease Center, USDA-ARS, 1920 Dayton Ave, Ames, United States of America
| | - Frank Blecha
- Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, United States of America
| | - Yongming Sang
- Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, United States of America
- Department of Agricultural and Environmental Sciences, College of Agriculture, Human and Natural Sciences, Tennessee State University, 3500 John A. Merritt Boulevard, Nashville, United States of America
- * E-mail: (LCM); (YS)
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11
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Fleming DS, Koltes JE, Fritz-Waters ER, Rothschild MF, Schmidt CJ, Ashwell CM, Persia ME, Reecy JM, Lamont SJ. Single nucleotide variant discovery of highly inbred Leghorn and Fayoumi chicken breeds using pooled whole genome resequencing data reveals insights into phenotype differences. BMC Genomics 2016; 17:812. [PMID: 27760519 PMCID: PMC5070165 DOI: 10.1186/s12864-016-3147-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 10/05/2016] [Indexed: 11/22/2022] Open
Abstract
Background Analyses of sequence variants of two distinct and highly inbred chicken lines allowed characterization of genomic variation that may be associated with phenotypic differences between breeds. These lines were the Leghorn, the major contributing breed to commercial white-egg production lines, and the Fayoumi, representative of an outbred indigenous and robust breed. Unique within- and between-line genetic diversity was used to define the genetic differences of the two breeds through the use of variant discovery and functional annotation. Results Downstream fixation test (FST) analysis and subsequent gene ontology (GO) enrichment analysis elucidated major differences between the two lines. The genes with high FST values for both breeds were used to identify enriched gene ontology terms. Over-enriched GO annotations were uncovered for functions indicative of breed-related traits of pathogen resistance and reproductive ability for Fayoumi and Leghorn, respectively. Conclusions Variant analysis elucidated GO functions indicative of breed-predominant phenotypes related to genomic variation in the lines, showing a possible link between the genetic variants and breed traits. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3147-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - J E Koltes
- Iowa State University, Ames, IA, USA.,Department of Animal Science, University of Arkansas, Fayetteville, AR, 72701, USA
| | | | | | | | - C M Ashwell
- North Carolina State University, Raleigh, NC, USA
| | - M E Persia
- Virginia Polytechnic and State University, Blacksburg, VA, USA
| | - J M Reecy
- Iowa State University, Ames, IA, USA
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12
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Fleming DS, Miller LC. Leading edge analysis of transcriptomic changes during pseudorabies virus infection. Genom Data 2016; 10:104-106. [PMID: 27766207 PMCID: PMC5066188 DOI: 10.1016/j.gdata.2016.09.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 09/29/2016] [Indexed: 11/15/2022]
Abstract
Eight RNA samples taken from the tracheobronchial lymph nodes (TBLN) of pigs that were either infected or non-infected with a feral isolate of porcine pseudorabies virus (PRV) were used to investigate changes in gene expression related to the pathogen. The RNA was processed into fastq files for each library prior to being analyzed using Illumina Digital Gene Expression Tag Profiling sequences (DGETP) which were used as the downstream measure of differential expression. Analyzed tags consisted of 21 base pair sequences taken from time points 1, 3, 6, and 14 days' post infection (dpi) that generated 1,927,547 unique tag sequences. Tag sequences were analyzed for differential transcript expression and gene set enrichment analysis (GSEA) to uncover transcriptomic changes related to PRV pathology progression. In conjunction with the DGETP and GSEA, the study also incorporated use of leading edge analysis to help link the TBLN transcriptome data to clinical progression of PRV at each of the sampled time points. The purpose of this manuscript is to provide useful background on applying the leading edge analysis to GSEA and expression data to help identify genes considered to be of high biological interest. The data in the form of fastq files has been uploaded to the NCBI Gene Expression Omnibus (GEO) (GSE74473) database.
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Affiliation(s)
- Damarius S Fleming
- Virus and Prion Research Unit, National Animal Disease Center, USDA, Agricultural Research Service, Ames, IA, USA
| | - Laura C Miller
- Virus and Prion Research Unit, National Animal Disease Center, USDA, Agricultural Research Service, Ames, IA, USA
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Fleming DS, Koltes JE, Markey AD, Schmidt CJ, Ashwell CM, Rothschild MF, Persia ME, Reecy JM, Lamont SJ. Genomic analysis of Ugandan and Rwandan chicken ecotypes using a 600 k genotyping array. BMC Genomics 2016; 17:407. [PMID: 27230772 PMCID: PMC4882793 DOI: 10.1186/s12864-016-2711-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2016] [Accepted: 05/06/2016] [Indexed: 02/07/2023] Open
Abstract
Background Indigenous populations of animals have developed unique adaptations to their local environments, which may include factors such as response to thermal stress, drought, pathogens and suboptimal nutrition. The survival and subsequent evolution within these local environments can be the result of both natural and artificial selection driving the acquisition of favorable traits, which over time leave genomic signatures in a population. This study’s goals are to characterize genomic diversity and identify selection signatures in chickens from equatorial Africa to identify genomic regions that may confer adaptive advantages of these ecotypes to their environments. Results Indigenous chickens from Uganda (n = 72) and Rwanda (n = 100), plus Kuroilers (n = 24, an Indian breed imported to Africa), were genotyped using the Axiom® 600 k Chicken Genotyping Array. Indigenous ecotypes were defined based upon location of sampling within Africa. The results revealed the presence of admixture among the Ugandan, Rwandan, and Kuroiler populations. Genes within runs of homozygosity consensus regions are linked to gene ontology (GO) terms related to lipid metabolism, immune functions and stress-mediated responses (FDR < 0.15). The genes within regions of signatures of selection are enriched for GO terms related to health and oxidative stress processes. Key genes in these regions had anti-oxidant, apoptosis, and inflammation functions. Conclusions The study suggests that these populations have alleles under selective pressure from their environment, which may aid in adaptation to harsh environments. The correspondence in gene ontology terms connected to stress-mediated processes across the populations could be related to the similarity of environments or an artifact of the detected admixture. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2711-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - J E Koltes
- Iowa State University, Ames, IA, USA.,University of Arkansas, Fayetteville, AR, USA
| | | | | | - C M Ashwell
- North Carolina State University, Raleigh, NC, USA
| | | | - M E Persia
- Virginia Polytechnic University, Blacksburg, VA, USA
| | - J M Reecy
- Iowa State University, Ames, IA, USA
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Abstract
The study purpose was to examine the relationship between sex, age, body mass index (BMI), and fitness level on the body image of 388 middle school children. Participants completed affective (social physique anxiety) and subjective evaluation (body dissatisfaction) body image measures and the 1-mile run/walk as an objective fitness measure. It was found that: (a) the females reported more social physique anxiety and body dissatisfaction than the males; (b) body dissatisfaction, especially for the females, was prevalent, (c) BMI was positively related to the body image measures; (d) for the males only, age was negatively related to the body image measures; (e) body dissatisfaction was negatively related to fitness levels; and (f) after controlling for BMI (and age for the males), fitness level was not a significant predictor of body dissatisfaction. The results indicate that body dissatisfaction was prevalent and early interventions with youth may be required.
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Affiliation(s)
- H A Hausenblas
- University of Florida, Gainesville, Florida 32611-8205, USA.
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Fleming DS, Papra J, Stoffels MA, Havir R. Salmonella typhimurium gastroenteritis. Statewide outbreak. Minn Med 1973; 56:722-3. [PMID: 4582113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Perlman LV, Isenberg EL, Donovan I, Fleming DS, Hammarsten JF. Public health nurses and the prevention of recurrences of congestive heart failure. Geriatrics (Basel) 1969; 24:82-9. [PMID: 5811750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
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Fleming DS. Community measles clinics and the physician. Minn Med 1968; 51:1457-60. [PMID: 5697889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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Fleming DS. Correspondence. Can Med Assoc J 1949; 60:529. [PMID: 20324460 PMCID: PMC1591432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
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Fleming DS. Diphtheria: A Problem of the Future. Can Med Assoc J 1944; 50:466-471. [PMID: 20323109 PMCID: PMC1581704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
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