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Ellis J, Marx J, Perumbakkam S, West K, Gow S, Lacoste S, Gururaja A, Masic A, Lappin BN, Brice C, Mahan SM. Genealogy of an in-vivo passaged isolate of western Canadian bovine respiratory syncytial virus. Can J Vet Res 2022; 86:218-228. [PMID: 35794977 PMCID: PMC9251804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 03/10/2022] [Indexed: 01/03/2023]
Abstract
Bovine respiratory syncytial virus (BRSV) is a primary respiratory pathogen in calves. Clinical infection with this pathogen has been experimentally modelled to assess vaccine efficacy using a field isolate (Asquith) of BRSV that has been sequentially passaged in vivo in neonatal calves to maintain virulence. The objective of this retrospective cumulative analysis of passages over approximately 20 years was to determine if there have been any changes in the viral genome of this isolate because of this process. Sequence analyses indicated that the Asquith isolate placed genetically in a clade comprising US and some European isolates and a recently described Chinese BRSV isolate (DQ). Furthermore, there were rare changes in bases over time in the N, G, and F gene segments examined when comparing among different passages ranging from 1996 to 2019. These results indicated the absence of significant mutations in the absence of significant adaptive immunological pressure.
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Williams Z, Perumbakkam S, Schott M, Valberg S. Combining transcriptomic and proteomic analyses to investigate the pathophysiology of muscle disease in horses. J Equine Vet Sci 2019. [DOI: 10.1016/j.jevs.2019.03.063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Valberg SJ, Soave K, Williams ZJ, Perumbakkam S, Schott M, Finno CJ, Petersen JL, Fenger C, Autry JM, Thomas DD. Coding sequences of sarcoplasmic reticulum calcium ATPase regulatory peptides and expression of calcium regulatory genes in recurrent exertional rhabdomyolysis. J Vet Intern Med 2019; 33:933-941. [PMID: 30720217 PMCID: PMC6430904 DOI: 10.1111/jvim.15425] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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: 08/07/2018] [Accepted: 01/11/2019] [Indexed: 12/12/2022] Open
Abstract
Background Sarcolipin (SLN), myoregulin (MRLN), and dwarf open reading frame (DWORF) are transmembrane regulators of the sarcoplasmic reticulum calcium transporting ATPase (SERCA) that we hypothesized played a role in recurrent exertional rhabdomyolysis (RER). Objectives Compare coding sequences of SLN, MRLN, DWORF across species and between RER and control horses. Compare expression of muscle Ca2+ regulatory genes between RER and control horses. Animals Twenty Thoroughbreds (TB), 5 Standardbreds (STD), 6 Quarter Horses (QH) with RER and 39 breed‐matched controls. Methods Sanger sequencing of SERCA regulatory genes with comparison of amino acid (AA) sequences among control, RER horses, human, mouse, and rabbit reference genomes. In RER and control gluteal muscle, quantitative real‐time polymerase chain reaction of SERCA regulatory peptides, the calcium release channel (RYR1), and its accessory proteins calsequestrin (CASQ1), and calstabin (FKBP1A). Results The SLN gene was the highest expressed horse SERCA regulatory gene with a uniquely truncated AA sequence (29 versus 31) versus other species. Coding sequences of SLN, MRLN, and DWORF were identical in RER and control horses. A sex‐by‐phenotype effect occurred with lower CASQ1 expression in RER males versus control males (P < .001) and RER females (P = .05) and higher FKBP1A (P = .01) expression in RER males versus control males. Conclusions and Clinical Importance The SLN gene encodes a uniquely truncated peptide in the horse versus other species. Variants in the coding sequence of SLN, MLRN, or DWORF were not associated with RER. Males with RER have differential gene expression that could reflect adaptations to stabilize RYR1.
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Affiliation(s)
- Stephanie J Valberg
- McPhail Equine Performance Center, Department of Large Animal Clinical Sciences, Michigan State University, East Lansing, Michigan
| | - Kaitlin Soave
- McPhail Equine Performance Center, Department of Large Animal Clinical Sciences, Michigan State University, East Lansing, Michigan
| | - Zoë J Williams
- McPhail Equine Performance Center, Department of Large Animal Clinical Sciences, Michigan State University, East Lansing, Michigan
| | - Sudeep Perumbakkam
- McPhail Equine Performance Center, Department of Large Animal Clinical Sciences, Michigan State University, East Lansing, Michigan
| | - Melissa Schott
- McPhail Equine Performance Center, Department of Large Animal Clinical Sciences, Michigan State University, East Lansing, Michigan
| | - Carrie J Finno
- Department of Population Health and Reproduction, University of California-Davis, Davis, California
| | - Jessica L Petersen
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, Nebraska
| | - Clara Fenger
- Equine Integrated Medicine, PLC, Lexington, Kentucky
| | - Joseph M Autry
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, Minnesota
| | - David D Thomas
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota Medical School, Minneapolis, Minnesota
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Autry JM, Svensson B, Karim CB, Perumbakkam S, Chen Z, Finno CJ, Thomas DD, Valberg SJ. Null-Sarcolipin Equine Muscle Shows Enhanced SERCA Calcium Transport Which May Potentiate the Prevalence of Exertional Rhabdomyolysis. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.1309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Gianino GM, Valberg SJ, Perumbakkam S, Henry ML, Gardner K, Penedo C, Finno CJ. Prevalence of the E321G MYH1 variant for immune-mediated myositis and nonexertional rhabdomyolysis in performance subgroups of American Quarter Horses. J Vet Intern Med 2019; 33:897-901. [PMID: 30623495 PMCID: PMC6430863 DOI: 10.1111/jvim.15393] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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: 07/03/2018] [Accepted: 11/16/2018] [Indexed: 01/30/2023] Open
Abstract
Background Immune‐mediated myositis (IMM) in American Quarter Horses (QHs) causes acute muscle atrophy and lymphocytic infiltration of myofibers. Recently, an E321G mutation in a highly conserved region of the myosin heavy chain 1 (MYH1) gene was associated with susceptibility to IMM and nonexertional rhabdomyolysis. Objectives To estimate prevalence of the E321G MYH1 variant in the QH breed and performance subgroups. Animals Three‐hundred seven elite performance QHs and 146 random registered QH controls. Methods Prospective genetic survey. Elite QHs from barrel racing, cutting, halter, racing, reining, Western Pleasure, and working cow disciplines and randomly selected registered QHs were genotyped for the E321G MYH1 variant and allele frequencies were calculated. Results The E321G MYH1 variant allele frequency was 0.034 ± 0.011 in the general QH population (6.8% of individuals in the breed) and the highest among the reining (0.135 ± 0.040; 24.3% of reiners), working cow (0.085 ± 0.031), and halter (0.080 ± 0.027) performance subgroups. The E321G MYH1 variant was present in cutting (0.044 ± 0.022) and Western Pleasure (0.021 ± 0.015) QHs at lower frequency and was not observed in barrel racing or racing QHs. Conclusions and Clinical Importance Knowing that reining and working cow QHs have the highest prevalence of the E321G MYH1 variant and that the variant is more prevalent than the alleles for hereditary equine regional dermal asthenia and hyperkalemic periodic paralysis in the general QH population will guide the use of genetic testing for diagnostic and breeding purposes.
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Affiliation(s)
- Giuliana M Gianino
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California
| | - Stephanie J Valberg
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, Michigan
| | - Sudeep Perumbakkam
- McPhail Equine Neuromuscular Diagnostic and Research Laboratory, McPhail Equine Performance Center, College of Veterinary Medicine, Michigan State University, East Lansing, Michigan
| | - Marisa L Henry
- McPhail Equine Neuromuscular Diagnostic and Research Laboratory, McPhail Equine Performance Center, College of Veterinary Medicine, Michigan State University, East Lansing, Michigan
| | - Keri Gardner
- McPhail Equine Neuromuscular Diagnostic and Research Laboratory, McPhail Equine Performance Center, College of Veterinary Medicine, Michigan State University, East Lansing, Michigan
| | - Cecilia Penedo
- Service Department, Veterinary Genetics Lab (Penedo), University of California, Davis, California
| | - Carrie J Finno
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California
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Valberg SJ, Perumbakkam S, McKenzie EC, Finno CJ. Proteome and transcriptome profiling of equine myofibrillar myopathy identifies diminished peroxiredoxin 6 and altered cysteine metabolic pathways. Physiol Genomics 2018; 50:1036-1050. [PMID: 30289745 PMCID: PMC6337024 DOI: 10.1152/physiolgenomics.00044.2018] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [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] [Indexed: 01/08/2023] Open
Abstract
Equine myofibrillar myopathy (MFM) causes exertional muscle pain and is characterized by myofibrillar disarray and ectopic desmin aggregates of unknown origin. To investigate the pathophysiology of MFM, we compared resting and 3 h postexercise transcriptomes of gluteal muscle and the resting skeletal muscle proteome of MFM and control Arabian horses with RNA sequencing and isobaric tags for relative and absolute quantitation analyses. Three hours after exercise, 191 genes were identified as differentially expressed (DE) in MFM vs. control muscle with >1 log2 fold change (FC) in genes involved in sulfur compound/cysteine metabolism such as cystathionine-beta-synthase ( CBS, ↓4.51), a cysteine and neutral amino acid membrane transporter ( SLC7A10, ↓1.80 MFM), and a cationic transporter (SLC24A1, ↓1.11 MFM). In MFM vs. control at rest, 284 genes were DE with >1 log2 FC in pathways for structure morphogenesis, fiber organization, tissue development, and cell differentiation including > 1 log2 FC in cardiac alpha actin ( ACTC1 ↑2.5 MFM), cytoskeletal desmoplakin ( DSP ↑2.4 MFM), and basement membrane usherin ( USH2A ↓2.9 MFM). Proteome analysis revealed significantly lower antioxidant peroxiredoxin 6 content (PRDX6, ↓4.14 log2 FC MFM), higher fatty acid transport enzyme carnitine palmitoyl transferase (CPT1B, ↑3.49 MFM), and lower sarcomere protein tropomyosin (TPM2, ↓3.24 MFM) in MFM vs. control muscle at rest. We propose that in MFM horses, altered cysteine metabolism and a deficiency of cysteine-containing antioxidants combined with a high capacity to oxidize fatty acids and generate ROS during aerobic exercise causes chronic oxidation and aggregation of key proteins such as desmin.
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Affiliation(s)
- Stephanie J Valberg
- McPhail Equine Performance Center, Department of Large Animal Clinical Sciences, Michigan State University, East Lansing, Michigan.,Department of Population Sciences, University of Minnesota , St. Paul, Minnesota
| | - Sudeep Perumbakkam
- Department of Large Animal Clinical Sciences, Michigan State University , East Lansing, Michigan
| | - Erica C McKenzie
- Department of Clinical Sciences, Carlson College of Veterinary Medicine, Oregon State University , Corvallis, Oregon
| | - Carrie J Finno
- Department of Population Health and Reproduction, University of California Davis , Davis, California
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Valberg SJ, Henry ML, Perumbakkam S, Gardner KL, Finno CJ. An E321G MYH1 mutation is strongly associated with nonexertional rhabdomyolysis in Quarter Horses. J Vet Intern Med 2018; 32:1718-1725. [PMID: 30079499 PMCID: PMC6189380 DOI: 10.1111/jvim.15299] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 07/02/2018] [Accepted: 07/17/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND An E321G mutation in MYH1 was recently identified in Quarter Horses (QH) with immune-mediated myositis (IMM) defined by a phenotype of gross muscle atrophy and myofiber lymphocytic infiltrates. HYPOTHESIS/OBJECTIVES We hypothesized that the MYH1 mutation also was associated with a phenotype of nonexertional rhabdomyolysis. The objective of this study was to determine the prevalence of the MYH1 mutation in QH with exertional (ER) and nonexertional (nonER) rhabdomyolysis. ANIMALS Quarter Horses: 72 healthy controls, 85 ER-no atrophy, 56 ER-atrophy, 167 nonER horses selected regardless of muscle atrophy. METHODS Clinical and histopathologic information and DNA was obtained from a database for (1) ER > 2 years of age, with or without atrophy and (2) nonER creatine kinase (CK) ≥ 5000 U/L, <5 years of age. Horses were genotyped for E321G MYH1 by pyrosequencing. RESULTS The MYH1 mutation was present in a similar proportion of ER-no atrophy (1/56; 2%) and in a higher proportion of ER-atrophy (25/85; 29%) versus controls (4/72; 5%). The MYH1 mutation was present in a significantly higher proportion of nonER (113/165; 68%) than controls either in the presence (39/42; 93%) or in absence (72/123; 59%) of gross atrophy. Lymphocytes were present in <18% of muscle samples with the MYH1 mutation. CONCLUSIONS AND CLINICAL IMPORTANCE Although not associated with ER, the MYH1 mutation is associated with atrophy after ER. The MYH1 mutation is highly associated with nonER regardless of whether muscle atrophy or lymphocytic infiltrates are present. Genetic testing will enhance the ability to diagnose MYH1 myopathies (MYHM) in QH.
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Affiliation(s)
- Stephanie J. Valberg
- McPhail Equine Performance Center, Department of Large Animal Clinical SciencesMichigan State UniversityEast LansingMichigan
| | - Marisa L. Henry
- McPhail Equine Performance Center, Department of Large Animal Clinical SciencesMichigan State UniversityEast LansingMichigan
| | - Sudeep Perumbakkam
- McPhail Equine Performance Center, Department of Large Animal Clinical SciencesMichigan State UniversityEast LansingMichigan
| | - Keri L. Gardner
- McPhail Equine Performance Center, Department of Large Animal Clinical SciencesMichigan State UniversityEast LansingMichigan
| | - Carrie J. Finno
- Department of Population Health and ReproductionUniversity of California‐DavisDavisCalifornia
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Perumbakkam S, Hunt HD, Cheng HH. Differences in CD8αα and cecal microbiome community during proliferation and late cytolytic phases of Marek's disease virus infection are associated with genetic resistance to Marek's disease. FEMS Microbiol Ecol 2016; 92:fiw188. [PMID: 27604255 DOI: 10.1093/femsec/fiw188] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2016] [Indexed: 12/12/2022] Open
Abstract
Marek's disease (MD) is an important neoplastic disease of chickens caused by Marek ': s disease virus (MDV), a highly oncogenic alphaherpesvirus. In this study using two chicken lines, one resistant and another susceptible to MD, splenic T cells and cecal microbiome were profiled to gain a better understanding of primary differences in these lines. The percent of splenic CD4+ T cells were similar regardless of MDV challenge status in both bird lines. In contrast, CD8αα profiles were different (P < 0.005) between chicken lines under naïve status and under MDV challenge, suggesting that CD8αα T cells play a key role in mediating MDV infection. Microbiome composition was different between naïve resistant (Blautia spp.) and susceptible birds (Streptococcus spp.) (P < 0.05) during initial colonization. With MDV challenge, both chicken lines showed lower numbers of beneficial Faecalibacterium spp. and increased number of Lactobacillus spp. Metabolic profiles between naïve chicken types were similar but with MDV challenge, there were differences in metabolism in both chicken lines, with amino acid metabolism impacted in resistant birds and lipid metabolism in susceptible birds. These results provide insights into immune response and potential interplay with the microbiome during infection with an oncogenic virus.
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Affiliation(s)
- Sudeep Perumbakkam
- USDA, ARS, Avian Diseases and Oncology Laboratory, East Lansing, MI 48823, USA Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Henry D Hunt
- USDA, ARS, Avian Diseases and Oncology Laboratory, East Lansing, MI 48823, USA
| | - Hans H Cheng
- USDA, ARS, Avian Diseases and Oncology Laboratory, East Lansing, MI 48823, USA
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Cheng HH, Perumbakkam S, Pyrkosz AB, Dunn JR, Legarra A, Muir WM. Fine mapping of QTL and genomic prediction using allele-specific expression SNPs demonstrates that the complex trait of genetic resistance to Marek's disease is predominantly determined by transcriptional regulation. BMC Genomics 2015; 16:816. [PMID: 26481588 PMCID: PMC4617451 DOI: 10.1186/s12864-015-2016-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 10/04/2015] [Indexed: 11/30/2022] Open
Abstract
Background Marek’s disease (MD) is a lymphoproliferative disease of poultry induced by Marek’s disease virus (MDV), a highly oncogenic alphaherpesvirus. Identifying the underlying genes conferring MD genetic resistance is desired for more efficacious control measures including genomic selection, which requires accurately identified genetic markers throughout the chicken genome. Methods Hypothesizing that variants located in transcriptional regulatory regions are the main mechanism underlying this complex trait, a genome-wide association study was conducted by genotyping a ~1,000 bird MD resource population derived from experimental inbred layers with SNPs containing 1,824 previously identified allele-specific expression (ASE) SNPs in response to MDV infection as well as 3,097 random SNPs equally spaced throughout the chicken genome. Based on the calculated associations, genomic predictions were determined for 200 roosters and selected sires had their progeny tested for Marek’s disease incidence. Results Our analyses indicate that these ASE SNPs account for more than 83 % of the genetic variance and exhibit nearly all the highest associations. To validate these findings, 200 roosters had their genetic merit predicted from the ASE SNPs only, and the top 30 and bottom 30 ranked roosters were reciprocally mated to random hens. The resulting progeny showed that after only one generation of bidirectional selection, there was a 22 % difference in MD incidence and this approach gave a 125 % increase in accuracy compared to current pedigree-based estimates. Conclusions We conclude that variation in transcriptional regulation is the major driving cause for genetic resistance to MD, and ASE SNPs identify the underlying genes and are sufficiently linked to the causative polymorphisms that they can be used for accurate genomic prediction as well as help define the underlying molecular basis. Furthermore, this approach should be applicable to other complex traits. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2016-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hans H Cheng
- USDA, ARS, Avian Disease and Oncology Laboratory, East Lansing, MI, 48823, USA.
| | - Sudeep Perumbakkam
- USDA, ARS, Avian Disease and Oncology Laboratory, East Lansing, MI, 48823, USA.,Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA
| | | | - John R Dunn
- USDA, ARS, Avian Disease and Oncology Laboratory, East Lansing, MI, 48823, USA
| | - Andres Legarra
- INRA, Animal Genetics, GenPhySE, Castanet Tolosan, 31326, France
| | - William M Muir
- Department of Animal Sciences, Purdue University, West Lafayette, IN, 47907, USA
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Perumbakkam S, Hunt HD, Cheng HH. Marek's disease virus influences the core gut microbiome of the chicken during the early and late phases of viral replication. FEMS Microbiol Ecol 2014; 90:300-12. [PMID: 25065611 DOI: 10.1111/1574-6941.12392] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [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: 03/25/2014] [Revised: 07/17/2014] [Accepted: 07/19/2014] [Indexed: 11/30/2022] Open
Abstract
Marek's disease (MD) is an important neoplastic disease of chickens caused by the Marek's disease virus (MDV), an oncogenic alphaherpesvirus. In this study, dysbiosis induced by MDV on the core gut flora of chicken was assessed using next generation sequence (NGS) analysis. Total fecal and cecum-derived samples from individual birds were used to estimate the influence of MDV infection on the gut microbiome of chicken. Our analysis shows that MDV infection alters the core gut flora in the total fecal samples relatively early after infection (2-7 days) and in the late phase of viral infection (28-35 days) in cecal samples, corresponding well with the life cycle of MDV. Principle component analyses of total fecal and cecal samples showed clustering at the early and late time points, respectively. The genus Lactobacillus was exclusively present in the infected samples in both total fecal and cecal bird samples. The community colonization of core gut flora was altered by viral infection, which manifested in the enrichment of several genera during the early and late phases of MDV replication. The results suggest a relationship between viral infection and microbial composition of the intestinal tract that may influence inflammation and immunosuppression of T and B cells in the host.
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Affiliation(s)
- Sudeep Perumbakkam
- Avian Diseases and Oncology Laboratory, USDA, ARS, East Lansing, MI, USA; Department of Animal Science, Purdue University, West Lafayette, IN, USA
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Perumbakkam S, Muir WM, Black-Pyrkosz A, Okimoto R, Cheng HH. Comparison and contrast of genes and biological pathways responding to Marek's disease virus infection using allele-specific expression and differential expression in broiler and layer chickens. BMC Genomics 2013; 14:64. [PMID: 23363372 PMCID: PMC3599046 DOI: 10.1186/1471-2164-14-64] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 01/22/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Marek's disease (MD) is a commercially important neoplastic disease of chickens caused by the Marek's disease virus (MDV), a naturally occurring oncogenic alphaherpesvirus. Enhancing MD genetic resistance is desirable to augment current vaccines and other MD control measures. High throughput sequencing was used to profile splenic transcriptomes from individual F1 progeny infected with MDV at 4 days of age from both outbred broilers (meat-type) and inbred layer (egg-type) chicken lines that differed in MD genetic resistance. The resulting information was used to identify SNPs, genes, and biological pathways exhibiting allele-specific expression (ASE) in response to MDV infection in each type of chicken. In addition, we compared and contrasted the results of pathway analyses (ASE and differential expression (DE)) between chicken types to help inform on the biological response to MDV infection. RESULTS With 7 individuals per line and treatment group providing high power, we identified 6,132 single nucleotide polymorphisms (SNPs) in 4,768 genes and 4,528 SNPs in 3,718 genes in broilers and layers, respectively, that exhibited ASE in response to MDV infection. Furthermore, 548 and 434 genes in broilers and layers, respectively, were found to show DE following MDV infection. Comparing the datasets, only 72 SNPs and 850 genes for ASE and 20 genes for DE were common between the two bird types. Although the chicken types used in this study were genetically different, at the pathway level, both TLR receptor and JAK/STAT signaling pathways were enriched as well as exhibiting a high proportion of ASE genes, especially at the beginning of both above mentioned regulatory pathways. CONCLUSIONS RNA sequencing with adequate biological replicates is a powerful approach to identify high confidence SNPs, genes, and pathways that are associated with transcriptional response to MDV infection. In addition, the SNPs exhibiting ASE in response to MDV infection provide a strong foundation for determining the extent to which variation in expression influences MD incidence plus yield genetic markers for genomic selection. However, given the paucity of overlap among ASE SNP sets (broilers vs. layers), it is likely that separate screens need to be incorporated for each population. Finally, comparison of gene lists obtained between these two diverse chicken types indicate the TLR and JAK/STAT signaling are conserved when responding to MDV infection and may be altered by selection of genes exhibiting ASE found at the start of each pathway.
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Affiliation(s)
- Sudeep Perumbakkam
- Department of Animal Science, Purdue University, West Lafayette, IN, 47907, USA
| | - William M Muir
- Department of Animal Science, Purdue University, West Lafayette, IN, 47907, USA
| | | | - Ron Okimoto
- Cobb-Vantress, Siloam Springs, AR, 72761, USA
| | - Hans H Cheng
- Avian Diseases and Oncology Laboratory, USDA, ARS, East Lansing, MI, 48823, USA
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Perumbakkam S, Craig AM. Biochemical and Microbial Analysis of Ovine Rumen Fluid Incubated with 1,3,5-Trinitro-1,3,5-triazacyclohexane (RDX). Curr Microbiol 2012; 65:195-201. [DOI: 10.1007/s00284-012-0144-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Accepted: 04/28/2012] [Indexed: 11/24/2022]
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Abstract
Two new primer sets based on the rpoB gene were designed and evaluated with bovine and ovine rumen samples. The newly developed rpoB-DGGE primer set was used along with the 16S rRNA gene-V3, and another (old) rpoB-DGGE-based primer set from a previous study to in vitro compare the bovine and ovine rumen ecosystems. The results indicate a significant (P<0.001) difference in the microbial population between the two ruminants irrespective of the primers used in the analysis. Qualitative comparison of the data provides evidence for the presence of similar phyla profiles between the 16S rRNA gene and the newly developed rpoB primers. A comparison between the two rpoB-based primer sets (old and new) showed that the old rpoB-based primers failed to amplify phylum Bacteroidetes (a common phylum in the rumen) in both bovine and ovine rumen samples. The old and new rpoB-DGGE-based primers amplified a large number of clones belonging to phylum Proteobacteria, providing a useful insight into the microbial structure of the rumen. ChaoI, ACE, Simpson, and Shannon-Weaver index analysis estimated the bovine rumen to be more diverse than the ovine rumen for all three primer sets. These results provide a new insight into the community structure among ruminants using the newly developed primers in this study.
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Affiliation(s)
- Sudeep Perumbakkam
- Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA.
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Perumbakkam S, Mitchell EA, Craig AM. Changes to the rumen bacterial population of sheep with the addition of 2,4,6-trinitrotoluene to their diet. Antonie Van Leeuwenhoek 2010; 99:231-40. [PMID: 20607404 DOI: 10.1007/s10482-010-9481-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Accepted: 06/24/2010] [Indexed: 11/27/2022]
Abstract
Previous work has shown that bacterial isolates from the sheep rumen are capable of detoxifying 2,4,6-trinitrotoluene (TNT) into polar constituents. In this study, the dietary effects of TNT on the sheep rumen microbial community were evaluated using molecular microbiology ecology tools. Rumen samples were collected from sheep fed with and without TNT added to their diet, genomic DNA was extracted, and the 16S rRNA-V3 gene marker was used to quantify changes in the microbial population in the rumen. Control and treatment samples yielded 533 sequences. Phylogenetic analyses were performed to determine the microbial changes between the two conditions. Results indicated the predominant bacterial populations present in the rumen were comprised of the phyla Firmicutes and Bacteroidetes, irrespective of presence/absence of TNT in the diet. Significant differences (P < 0.001) were found between the community structure of the bacteria under TNT (-) and TNT (+) diets. Examination of the TNT (+) diet showed an increase in the clones belonging to family Ruminococcaceae, which have previously been shown to degrade TNT in pure culture experiments.
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Affiliation(s)
- Sudeep Perumbakkam
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA
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Rattray RM, Perumbakkam S, Smith F, Craig AM. Microbiomic comparison of the intestine of the earthworm Eisenia fetida fed ergovaline. Curr Microbiol 2010; 60:229-35. [PMID: 19924482 DOI: 10.1007/s00284-009-9530-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2009] [Accepted: 10/22/2009] [Indexed: 10/20/2022]
Abstract
Tall fescue toxicosis and ergot alkaloids cost U.S. livestock producers approximately one billion dollars in annual livestock production loss annually. Ergovaline (EV) is the tall fescue alkaloid primarily responsible for clinical disease in livestock. Since native ruminal microorganisms have not been attributed to the detoxification of EV, finding detoxifying microbes from other environments is desirable. One possible source for potential microorganisms that can degrade EV is the anaerobic gut of the earthworm, Eisenia fetida. This study describes a comparative microbial analysis of earthworm digestive tracts receiving 10,000 ppb EV (E+ treatment) when compared with a control treatment with no detectable amounts of EV (E- treatment). An HPLC assay determined a 25% loss of EV from the E+ treatment was microbial in nature. A community microbiomic approach of constructing 16S-rRNA gene clone libraries was used to compare the microbes affected by the two treatments. RDPII tools such as Classifier and Libcompare were used in the analysis of 16S sequences. DOTUR analysis was used to examine the richness and diversity of the two microbial populations in these experiments. The results indicate there are few significant differences in the microbial community structure between the two microbiomes.
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Affiliation(s)
- Rogan M Rattray
- Department of Microbiology, Oregon State University, 139 Oak Creek Building, 97331 Corvallis, OR, USA
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Perumbakkam S, Hess TF, Crawford RL. A bioremediation approach using natural transformation in pure-culture and mixed-population biofilms. Biodegradation 2006; 17:545-57. [PMID: 16477353 DOI: 10.1007/s10532-005-9025-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2005] [Accepted: 09/27/2005] [Indexed: 10/25/2022]
Abstract
Bacterial transformation by naked DNA is thought to contribute to gene transfer and microbial evolution within natural environments. In nature many microbial communities exist as complex assemblages known as biofilms where genetic exchange is facilitated. It may be possible to take advantage of natural transformation processes to modify the phenotypes of biofilm communities giving them specific and desirable functions. Work described here shows that biofilms composed of either pure cultures or mixed populations can be transformed with specific catabolic genes such that the communities acquire the ability to degrade a particular xenobiotic compound. Biofilms were transformed by plasmids bearing genes encoding green fluorescent protein (mut2) and/or atrazine chlorohydrolase (atzA). Confocal microscopy was used to quantify the number of transformants expressing mut2 in the biofilms. Degradation of atrazine by expressed atzA was quantified by tandem mass spectrometry. PCR analysis was performed to confirm the presence of atzA in transformed biofilms. These results indicate that it should be possible to use natural transformation to enhance bioremediation processes performed by biofilms.
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Affiliation(s)
- Sudeep Perumbakkam
- Department of Microbiology, Molecular Biology & Biochemistry, University of Idaho, Life Science 142, P.O.Box 443052, Moscow, ID, 83844-3052, USA
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