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Exploring the longitudinal dynamics of herd BVD antibody test results using model-based clustering. Sci Rep 2019; 9:11353. [PMID: 31388019 PMCID: PMC6684638 DOI: 10.1038/s41598-019-47339-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 07/15/2019] [Indexed: 11/08/2022] Open
Abstract
Determining the Bovine Viral Diarrhoea (BVD) infection status of cattle herds is a challenge for control and eradication schemes. Given the changing dynamics of BVD virus (BVDV) antibody responses in cattle, classifying herds based on longitudinal changes in the results of BVDV antibody tests could offer a novel, complementary approach to categorising herds that is less likely than the present system to result in a herd's status changing from year to year, as it is more likely to capture the true exposure dynamics of the farms. This paper describes the dynamics of BVDV antibody test values (measured as percentage positivity (PP)) obtained from 15,500 bovines between 2007 and 2010 from thirty nine cattle herds located in Scotland and Northern England. It explores approaches of classifying herds based on trend, magnitude and shape of their antibody PP trajectories and investigates the epidemiological similarities between farms within the same cluster. Gaussian mixture models were used for the magnitude and shape clustering. Epidemiologically meaningful clusters were obtained. Farm cluster membership depends on clustering approach used. Moderate concordance was found between the shape and magnitude clusters. These methods hold potential for application to enhance control efforts for BVD and other infectious livestock diseases.
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Olejnik J, Suchowerska N, Herrid M, Jackson A, Jackson M, Andronicos NM, Hinch GN, Hill JR. Sensitivity of spermatogonia to irradiation varies with age in pre-pubertal ram lambs. Anim Reprod Sci 2018; 193:58-67. [PMID: 29636209 DOI: 10.1016/j.anireprosci.2018.03.037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 03/23/2018] [Accepted: 03/29/2018] [Indexed: 01/15/2023]
Abstract
Although germ cells from donor rams transplanted into irradiated recipient testes have produced donor derived offspring, efficiency is low. Further optimization of recipient irradiation protocols will add precision to the depletion of recipient spermatogonia prior to germ cell transplant. Three irradiation doses (9,12,15 Gy) were administered to ram lambs aged 14 weeks (Group 1) and 20 weeks (Group 2), then testicular biopsies were collected 1, 2 and 3 months after irradiation. At 1 month after irradiation of Group 1, only the largest dose (15 Gy) reduced spermatogonia numbers below 10% of non-irradiated controls, whereas in Group 2 lambs, each irradiation dose reduced spermatogonia below 10% of controls. In both Groups, fewer differentiated germ cells were present in seminiferous tubules compared to controls. At 2 months after irradiation, spermatogonia numbers in both Groups increased more than sixfold to be similar to controls, whereas fewer differentiated germ cells were present in the tubules of both Groups. At 3 months in Group 1, each irradiation dose reduced spermatogonia numbers to <30% of controls and fewer tubules contained differentiated germ cells. Lesser expression of spermatogonial genes, VASA and UCHL-1, was observed in the 15 Gy group. In Group 2, only 12 Gy treated tubules contained fewer spermatogonia. Knowledge of these subtle differences between age groups in the effect of irradiation doses on spermatogonia or differentiated germ cell numbers and the duration of recovery of spermatogonia numbers after irradiation will aid the timing of germ cell transplants into prepubertal recipient lambs.
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Affiliation(s)
- J Olejnik
- CSIRO Food Futures National Research Flagship, Australia; CSIRO Animal, Food and Health Sciences, F. D. McMaster Laboratory, Armidale, NSW, 2350 Australia; University of New England, Armidale, NSW, 2350, Australia
| | - N Suchowerska
- School of Physics, University of Sydney, NSW, Australia; Faculty of Medicine, University of Sydney, Sydney, NSW, Australia
| | - M Herrid
- CSIRO Food Futures National Research Flagship, Australia
| | - A Jackson
- CSIRO Food Futures National Research Flagship, Australia
| | - M Jackson
- Faculty of Medicine, University of Sydney, Sydney, NSW, Australia
| | - N M Andronicos
- CSIRO Animal, Food and Health Sciences, F. D. McMaster Laboratory, Armidale, NSW, 2350 Australia; University of New England, Armidale, NSW, 2350, Australia
| | - G N Hinch
- University of New England, Armidale, NSW, 2350, Australia
| | - J R Hill
- CSIRO Food Futures National Research Flagship, Australia; University of Queensland, School of Veterinary Science, Gatton, QLD 4343, Queensland, Australia.
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Costa ASH, Costa P, Alves SP, Alfaia CM, Prates JAM, Vleck V, Cassar-Malek I, Hocquette JF, Bessa RJB. Does growth path influence beef lipid deposition and fatty acid composition? PLoS One 2018; 13:e0193875. [PMID: 29614102 PMCID: PMC5882120 DOI: 10.1371/journal.pone.0193875] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Accepted: 02/19/2018] [Indexed: 11/18/2022] Open
Abstract
Despite the recent advances in transcriptomics, gene expression studies addressing cattle´s skeletal muscle adaptations in response to compensatory growth are warranted, particularly regarding lipid metabolism due to its impact in meat sensory and nutritional traits. In the present study, in comparison to ad libitum feeding, a period of feed restriction was used in order to understand the changes in bull´s lipid metabolism and gene expression of the adipogenic and lipogenic pathways after re-alimentation. Thus, 40 young Alentejana bulls were either fed ad libitum (CG group) from 9 to 18 months of age or subjected to food restriction from 9 to 15 months of age, and fed ad libitum until 24 months of age (DG group). The intramuscular fat (IMF) and total fatty acids (FA) contents were similar between groups. The major FA (>2%) contents were similar (16:0, 16:1c9, 18:1c9 and 18:2n-6) between treatments with the exception of 18:0 content that was 15% lower in DG than in CG and 20:4n-6 that tended to be greater on DG bulls. Regarding minor FA (<2%), the DG group presented greater proportions (P<0.01) of 17:1c9, 18:1t9, 18:1t10 (, 18:1c11), 18:1c13, 18:3n-6, 22:0, 22:4n-6 and 22:6n-3 and lower (P<0.05) proportions of 20:0, 18:1t16+c14, and branched chain FA (iso-15:0, anteiso-15:0, iso-16:0 and anteiso-17:0) than the CG group. Delta-9 desaturase activity indices were consistently greater (P<0.05) in DG, when compared to the CG group. Regarding microarray analysis, differentially expressed genes between CG and DG bulls were grouped in 5 main biological functions: lipid and nucleic acid metabolisms, small molecule biochemistry, molecular transport and translational modification. Discontinuous growth down-regulated the expression of ACACB (FC (fold-change) = 1.32), FABP3 (FC = 1.45), HADHA (FC = 1.41) and SLC37A4 (FC = 1.40) genes, when compared to the CG system (FDR<0.05). In contrast, in the CG bulls, the expression of ELOVL5 (FC = 1.58) and FASN (FC = 1.71) was down-regulated when compared to DG bulls. These results were confirmed to be significant (P<0.05) in the case of ELOVL5, FASN and SLC37A4, and almost significant for FABP3 by qRT-PCR analysis. The SCD1 and SCD5 gene expressions were not found to be affected by growth path. These results contribute to the still scarce knowledge about the mechanisms involved in fatty acid metabolism during compensatory growth which have decisive role on meat quality produced in Mediterranean areas.
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Affiliation(s)
- Ana S. H. Costa
- CIISA – Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, Pólo Universitário do Alto da Ajuda, Lisboa, Portugal
| | - Paulo Costa
- CIISA – Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, Pólo Universitário do Alto da Ajuda, Lisboa, Portugal
- * E-mail:
| | - Susana P. Alves
- CIISA – Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, Pólo Universitário do Alto da Ajuda, Lisboa, Portugal
| | - Cristina M. Alfaia
- CIISA – Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, Pólo Universitário do Alto da Ajuda, Lisboa, Portugal
| | - José A. M. Prates
- CIISA – Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, Pólo Universitário do Alto da Ajuda, Lisboa, Portugal
| | - Veronica Vleck
- CIPER – Faculdade de Motricidade Humana, Universidade de Lisboa, Estrada da costa, Cruz Quebrada-Dafundo, Lisboa, Portugal
| | - Isabelle Cassar-Malek
- INRA, UR 1213, Unité de Recherches sur les Herbivores (URH), Theix, Saint-Genés Champanelle, France
- Clermont Université, VetAgro Sup, UMR1213, Herbivores, Clermont-Ferrand, France
| | - Jean-François Hocquette
- INRA, UR 1213, Unité de Recherches sur les Herbivores (URH), Theix, Saint-Genés Champanelle, France
- Clermont Université, VetAgro Sup, UMR1213, Herbivores, Clermont-Ferrand, France
| | - Rui J. B. Bessa
- CIISA – Centro de Investigação Interdisciplinar em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, Pólo Universitário do Alto da Ajuda, Lisboa, Portugal
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Shukla SK, Shukla S, Chauhan A, Sarvjeet, Khan R, Ahuja A, Singh LV, Sharma N, Prakash C, Singh AV, Panigrahi M. Differential gene expression in Mycobacterium bovis challenged monocyte-derived macrophages of cattle. Microb Pathog 2017; 113:480-489. [PMID: 29170044 DOI: 10.1016/j.micpath.2017.11.030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 11/14/2017] [Accepted: 11/18/2017] [Indexed: 12/18/2022]
Abstract
A functional genomics approach was used to examine the immune response for transcriptional profiling of PBMC M. bovis infected cattle and healthy control cattle to stimulation with bovine tuberculin (purified protein derivative PPD-b). Total cellular RNA was extracted from non-challenged control and M. bovis challenged MDM for all animals at intervals of 6 h post-challenge, in response to in-vitro challenge with M. bovis (multiplicity of infection 2:1) and prepared for global gene expression analysis using the Agilent Bovine (V2) Gene Expression Microarray, 8 × 60 K. The pattern of expression of these genes in PPD bovine stimulated PBMC provides the first description of an M. bovis specific signature of infection that may provide insights into the molecular basis of the host response to infection. Analysis of these mapped reads showed 2450 genes (1291 up regulated and 1158 down regulated) 462 putative natural antisense transcripts (354 up-regulated and 108 down regulated) that were differentially expressed based on sense and antisense strand data, respectively (adjusted P-value ≤ 0.05). The results provided enrichment for genes involved top ten up regulated and down regulated panel of genes, including transcription factors proliferation of T and B lymphocytes. The highest differentially-expressed genes were associated to immune and inflammatory responses, immunity, differentiation, cell growth, apoptosis, cellular trafficking and regulation of lipolysis and thermogenesis. Microarray results were confirmed in infected cattle by RT qPCR to identify potential biomarkers TLR2, CD80, NFKB1, IL8, CXCL6 and ADORA3 of bovine tuberculosis.
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Affiliation(s)
- Sanjeev Kumar Shukla
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, U.P., India.
| | - Shubhra Shukla
- Department of Biosciences, Integral University, Lucknow, U.P., India
| | - Anuj Chauhan
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, U.P., India
| | - Sarvjeet
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, U.P., India
| | - Rehan Khan
- Division of Hematology, Mayo Clinic, Rochester, MN, United States
| | - Anuj Ahuja
- The Faculty of Medicine in the Galilee, Bar-Ilan University, Henrietta Szold St. 8, Safed, Israel
| | - Lakshya Veer Singh
- Tuberculosis Aerosol Challenge Facility Laboratory, ICGEB, Campus, New Delhi, India
| | - Naveen Sharma
- Department of Health Research, IRCS Building, New Delhi, India
| | - Chandan Prakash
- CADRAD, Indian Veterinary Research Institute, Izatnagar, Bareilly, U.P., India
| | - Ajay Vir Singh
- ICMR-National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Tajganj, Agra, U.P., India
| | - Manjit Panigrahi
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, U.P., India
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González-Calvo L, Dervishi E, Joy M, Sarto P, Martin-Hernandez R, Serrano M, Ordovás JM, Calvo JH. Genome-wide expression profiling in muscle and subcutaneous fat of lambs in response to the intake of concentrate supplemented with vitamin E. BMC Genomics 2017; 18:92. [PMID: 28095783 PMCID: PMC5240399 DOI: 10.1186/s12864-016-3405-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 12/09/2016] [Indexed: 01/20/2023] Open
Abstract
Background The objective of this study was to acquire a broader, more comprehensive picture of the transcriptional changes in the L. Thoracis muscle (LT) and subcutaneous fat (SF) of lambs supplemented with vitamin E. Furthermore, we aimed to identify novel genes involved in the metabolism of vitamin E that might also be involved in meat quality. In the first treatment, seven lambs were fed a basal concentrate from weaning to slaughter (CON). In the second treatment, seven lambs received basal concentrate from weaning to 4.71 ± 2.62 days and thereafter concentrate supplemented with 500 mg dl-α-tocopheryl acetate/kg (VE) during the last 33.28 ± 1.07 days before slaughter. Results The addition of vitamin E to the diet increased the α-tocopherol muscle content and drastically diminished the lipid oxidation of meat. Gene expression profiles for treatments VE and CON were clearly separated from each other in the LT and SF. Vitamin E supplementation had a dramatic effect on subcutaneous fat gene expression, showing general up-regulation of significant genes, compared to CON treatment. In LT, vitamin E supplementation caused down-regulation of genes related to intracellular signaling cascade. Functional analysis of SF showed that vitamin E supplementation caused up-regulation of the lipid biosynthesis process, cholesterol, and sterol and steroid biosynthesis, and it down-regulated genes related to the stress response. Conclusions Different gene expression patterns were found between the SF and LT, suggesting tissue specific responses to vitamin E supplementation. Our study enabled us to identify novel genes and metabolic pathways related to vitamin E metabolism that might be implicated in meat quality. Further exploration of these genes and vitamin E could lead to a better understanding of how vitamin E affects the oxidative process that occurs in manufactured meat products. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3405-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Elda Dervishi
- University of Alberta, 116 St and 85 Ave, Edmonton, AB, T6G 2R3, Canada
| | - Margalida Joy
- Unidad de Tecnología en Producción Animal, CITA, 59059, Zaragoza, Spain
| | - Pilar Sarto
- Unidad de Tecnología en Producción Animal, CITA, 59059, Zaragoza, Spain
| | | | | | - Jose M Ordovás
- Jean Mayer-USDA Human Nutrition Research Center on Aging at Tufts University, Boston, MA, USA
| | - Jorge H Calvo
- Unidad de Tecnología en Producción Animal, CITA, 59059, Zaragoza, Spain. .,ARAID, 50004, Zaragoza, Spain.
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González-Calvo L, Joy M, Alberti C, Ripoll G, Molino F, Serrano M, Calvo JH. Effect of finishing period length with α-tocopherol supplementation on the expression of vitamin E-related genes in the muscle and subcutaneous fat of light lambs. Gene 2014; 552:225-33. [PMID: 25241385 DOI: 10.1016/j.gene.2014.09.037] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 07/11/2014] [Accepted: 09/17/2014] [Indexed: 01/19/2023]
Abstract
The aim of this study was to investigate how different finishing period lengths with α-tocopherol supplementation or alfalfa grazing affect mRNA expression levels of genes related to vitamin E metabolism in L. thoracis (LT) muscle and subcutaneous fat (SF) from lambs of the Rasa Aragonesa breed. Indoors, concentrate-fed light lambs (n=48) were supplemented with 500 dl-α-tocopheryl acetate/kg concentrate for an average finishing period length of 0 (C), 10.7 (VE10d), 21.2 (VE20d) and, 32.3 (VE30d) days before slaughtering. Simultaneously, 8 lambs with their dams were alfalfa-grazed. The α-tocopherol affected in a short-term the expression of genes in LT muscle (ABCA1, LPL, APOE, and SREBP1) and SF (ABCA1, SCARB1, LPL, and PPARG). On the contrary, PPARA gene expression showed a long-term α-tocopherol effect because the highest levels of PPARA mRNA were found in the VE30d.
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Affiliation(s)
- L González-Calvo
- Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Unidad de Tecnología en Producción Animal, Avda. Montañana, 930, 50059 Zaragoza, Spain
| | - M Joy
- Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Unidad de Tecnología en Producción Animal, Avda. Montañana, 930, 50059 Zaragoza, Spain
| | - C Alberti
- Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Unidad de Tecnología en Producción Animal, Avda. Montañana, 930, 50059 Zaragoza, Spain
| | - G Ripoll
- Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Unidad de Tecnología en Producción Animal, Avda. Montañana, 930, 50059 Zaragoza, Spain
| | - F Molino
- Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Unidad de Tecnología en Producción Animal, Avda. Montañana, 930, 50059 Zaragoza, Spain
| | - M Serrano
- Departamento de Mejora Genética animal, INIA, 28040 Madrid, Spain
| | - J H Calvo
- Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Unidad de Tecnología en Producción Animal, Avda. Montañana, 930, 50059 Zaragoza, Spain; ARAID, C/ María de Luna, n° 11, 1ª planta, Edificio CEEI Aragón, 50018 Zaragoza, Spain.
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Yamada T. Genetic dissection of marbling trait through integration of mapping and expression profiling. Anim Sci J 2014; 85:349-55. [DOI: 10.1111/asj.12179] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 11/19/2013] [Indexed: 01/28/2023]
Affiliation(s)
- Takahisa Yamada
- Department of Agrobiology, Faculty of Agriculture; Niigata University; Niigata Japan
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Forage preservation (grazing vs. hay) fed to ewes affects the fatty acid profile of milk and CPT1B gene expression in the sheep mammary gland. BMC Vet Res 2012; 8:106. [PMID: 22776723 PMCID: PMC3416728 DOI: 10.1186/1746-6148-8-106] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2012] [Accepted: 07/09/2012] [Indexed: 11/23/2022] Open
Abstract
Background Alterations in lipid metabolism occur when animals are exposed to different feeding systems. In the last few decades, the characterisation of genes involved in fat metabolism and technological advances have enabled the study of the effect of diet on the milk fatty acid (FA) profile in the mammary gland and aided in the elucidation of the mechanisms of the response to diet. The aim of this study was to evaluate the effect of different forage diets (grazing vs. hay) near the time of ewe parturition on the relationship between the fatty acid profile and gene expression in the mammary gland of the Churra Tensina sheep breed. Results In this study, the forage type affected the C18:2 cis-9 trans-11 (CLA) and long-chain saturated fatty acid (LCFA) content, with higher percentages during grazing than during hay feeding. This may suggest that these FAs act as regulatory factors for the transcriptional control of the carnitine palmitoyltransferase 1B (CPT1B) gene, which was more highly expressed in the grazing group (GRE). The most highly expressed gene in the mammary gland at the fifth week of lactation is CAAT/ enhancer- binding protein beta (CEBPB), possibly due to its role in milk fat synthesis in the mammary gland. More stable housekeeping genes in the ovine mammary gland that would be appropriate for use in gene expression studies were ribosomal protein L19 (RPL19) and glyceraldehyde- 3- phosphate dehydrogenase (GAPDH). Conclusions Small changes in diet, such as the forage preservation (grazing vs. hay), can affect the milk fatty acid profile and the expression of the CPT1B gene, which is associated with the oxidation of fatty acids. When compared to hay fed indoors, grazing fresh low mountain pastures stimulates the milk content of CLA and LCFA via mammary uptake. In this sense, LCFA in milk may be acting as a regulatory factor for transcriptional control of the CPT1B gene, which was more highly expressed in the grazing group.
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Neibergs HL, Johnson KA. ALPHARMA BEEF CATTLE NUTRITION SYMPOSIUM: Nutrition and the genome1. J Anim Sci 2012; 90:2308-16. [DOI: 10.2527/jas.2011-4582] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- H. L. Neibergs
- Department of Animal Sciences, Washington State University, Pullman 99164
| | - K. A. Johnson
- Department of Animal Sciences, Washington State University, Pullman 99164
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Dervishi E, Joy M, Alvarez-Rodriguez J, Serrano M, Calvo JH. The forage type (grazing versus hay pasture) fed to ewes and the lamb sex affect fatty acid profile and lipogenic gene expression in the longissimus muscle of suckling lambs1. J Anim Sci 2012; 90:54-66. [DOI: 10.2527/jas.2011-4057] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- E. Dervishi
- Unidad de Tecnología en Producción Animal, Centro de Investigación y Tecnología Agroalimentaria (CITA), Avda Montañana 930, 50059 Zaragoza, Spain
| | - M. Joy
- Unidad de Tecnología en Producción Animal, Centro de Investigación y Tecnología Agroalimentaria (CITA), Avda Montañana 930, 50059 Zaragoza, Spain
| | - J. Alvarez-Rodriguez
- Unidad de Tecnología en Producción Animal, Centro de Investigación y Tecnología Agroalimentaria (CITA), Avda Montañana 930, 50059 Zaragoza, Spain
| | - M. Serrano
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Ctra. La Coruña 7.5, 28040 Madrid, Spain
| | - J. H. Calvo
- Unidad de Tecnología en Producción Animal, Centro de Investigación y Tecnología Agroalimentaria (CITA), Avda Montañana 930, 50059 Zaragoza, Spain
- ARAID Fundacion Agencia Aragonesa para la Investigacion y Desarrollo, 50004 Zaragoza, Spain
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Casellas J, Ibáñez-Escriche N. Bayesian recursive mixed linear model for gene expression analyses with continuous covariates. J Anim Sci 2011; 90:67-75. [PMID: 21908645 DOI: 10.2527/jas.2010-3750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The analysis of microarray gene expression data has experienced a remarkable growth in scientific research over the last few years and is helping to decipher the genetic background of several productive traits. Nevertheless, most analytical approaches have relied on the comparison of 2 (or a few) well-defined groups of biological conditions where the continuous covariates have no sense (e.g., healthy vs. cancerous cells). Continuous effects could be of special interest when analyzing gene expression in animal production-oriented studies (e.g., birth weight), although very few studies address this peculiarity in the animal science framework. Within this context, we have developed a recursive linear mixed model where not only are linear covariates accounted for during gene expression analyses but also hierarchized and the effects of their genetic, environmental, and residual components on differential gene expression inferred independently. This parameterization allows a step forward in the inference of differential gene expression linked to a given quantitative trait such as birth weight. The statistical performance of this recursive model was exemplified under simulation by accounting for different sample sizes (n), heritabilities for the quantitative trait (h(2)), and magnitudes of differential gene expression (λ). It is important to highlight that statistical power increased with n, h(2), and λ, and the recursive model exceeded the standard linear mixed model with linear (nonrecursive) covariates in the majority of scenarios. This new parameterization would provide new insights about gene expression in the animal science framework, opening a new research scenario where within-covariate sources of differential gene expression could be individualized and estimated. The source code of the program accommodating these analytical developments and additional information about practical aspects on running the program are freely available by request to the corresponding author of this article.
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Affiliation(s)
- J Casellas
- Grup de Recerca en Remugants, Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.
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Wang J, Wen S, Symmans WF, Pusztai L, Coombes KR. The bimodality index: a criterion for discovering and ranking bimodal signatures from cancer gene expression profiling data. Cancer Inform 2009; 7:199-216. [PMID: 19718451 PMCID: PMC2730180 DOI: 10.4137/cin.s2846] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Motivation Identifying genes with bimodal expression patterns from large-scale expression profiling data is an important analytical task. Model-based clustering is popular for this purpose. That technique commonly uses the Bayesian information criterion (BIC) for model selection. In practice, however, BIC appears to be overly sensitive and may lead to the identification of bimodally expressed genes that are unreliable or not clinically useful. We propose using a novel criterion, the bimodality index, not only to identify but also to rank meaningful and reliable bimodal patterns. The bimodality index can be computed using either a mixture model-based algorithm or Markov chain Monte Carlo techniques. Results We carried out simulation studies and applied the method to real data from a cancer gene expression profiling study. Our findings suggest that BIC behaves like a lax cutoff based on the bimodality index, and that the bimodality index provides an objective measure to identify and rank meaningful and reliable bimodal patterns from large-scale gene expression datasets. R code to compute the bimodality index is included in the ClassDiscovery package of the Object-Oriented Microarray and Proteomic Analysis (OOMPA) suite available at the web site http;//bioinformatics.mdanderson.org/Software/OOMPA.
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Affiliation(s)
- Jing Wang
- Department of Bioinformatics and Computational Biology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030-4009, USA.
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Graugnard DE, Piantoni P, Bionaz M, Berger LL, Faulkner DB, Loor JJ. Adipogenic and energy metabolism gene networks in longissimus lumborum during rapid post-weaning growth in Angus and Angus x Simmental cattle fed high-starch or low-starch diets. BMC Genomics 2009; 10:142. [PMID: 19335898 PMCID: PMC2676302 DOI: 10.1186/1471-2164-10-142] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2008] [Accepted: 03/31/2009] [Indexed: 01/12/2023] Open
Abstract
Background Transcriptional networks coordinate adipocyte differentiation and energy metabolism in rodents. The level of fiber and starch in diets with adequate energy content fed to young cattle has the potential to alter intramuscular adipose tissue development in skeletal muscle. Post-weaning alterations in gene expression networks driving adipogenesis, lipid filling, and intracellular energy metabolism provide a means to evaluate long-term effects of nutrition on longissimus muscle development across cattle types. Results Longissimus lumborum (LL) from Angus (n = 6) and Angus × Simmental (A × S; n = 6) steer calves (155 ± 10 days age) fed isonitrogenous high-starch (HiS; 1.43 Mcal/kg diet dry matter; n = 6) or low-starch (LoS; 1.19 Mcal/kg diet dry matter; n = 6) diets was biopsied at 0, 56, and 112 days of feeding for transcript profiling of 31 genes associated with aspects of adipogenesis and energy metabolism. Intake of dietary energy (9.44 ± 0.57 Mcal/d) across groups during the study did not differ but feed efficiency (weight gain/feed intake) during the first 56 days was greater for steers fed HiS. Expression of PPARG increased ca. 2-fold by day 56 primarily due to HiS in A × S steers. Several potential PPARG-target genes (e.g., ACACA, FASN, FABP4, SCD) increased 2.5-to-25-fold by day 56 across all groups, with responses (e.g., FASN, FABP4) being less pronounced in A × S steers fed LoS. This latter group of steers had markedly greater blood plasma glucose (0.99 vs. 0.79 g/L) and insulin (2.95 vs. 1.17 μg/L) by day 112, all of which were suggestive of insulin resistance. Interactions were observed for FABP4, FASN, GPAM, SCD, and DGAT2, such that feeding A × S steers high-starch and Angus steers low-starch resulted in greater fold-changes by day 56 or 112 (GPAM). Marked up-regulation of INSIG1 (4-to-8-fold) occurred throughout the study across all groups. SREBF1 expression, however, was only greater on day 112 namely due to LoS in A × S steers. The lipogenic transcription factor THRSP was 6-to-60-fold greater by day 56 primarily due to HiS in A × S steers, constituting the greatest response among all genes. Conclusion Results involving gene markers of mature adipocytes (e.g., PPARG, THRSP, SCD) provided evidence of intramuscular adipose tissue differentiation during the early portion of the growing phase. The resulting gene networks underscored a central role for PPARG in controlling transcription of genes which are known to co-ordinately regulate adipocyte differentiation and lipid filling in non-ruminants. Unlike rodents, INSIG1 appears to play an important role in cattle muscle adipogenesis. We propose that a network of transcription regulators and nuclear receptors including PPARG-target genes, INSIG1, and THRSP, coordinate activation of adipocyte differentiation and lipid filling at an early age.
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Affiliation(s)
- Daniel E Graugnard
- Mammalian NutriPhysioGenomics, Department of Animal Sciences, University of Illinois, Urbana, Illinois, 61801, USA.
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Díaz C, Moreno-Sánchez N, Rueda J, Reverter A, Wang YH, Carabaño MJ. Model selection in a global analysis of a microarray experiment1. J Anim Sci 2009; 87:88-98. [DOI: 10.2527/jas.2007-0713] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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15
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Bruce H, Hewavitharana A, Hunter R. Creatinine and pseudouridine in plasma and urine from Brahman-cross steers fed a low, medium or high plane of nutrition. Livest Sci 2008. [DOI: 10.1016/j.livsci.2008.03.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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16
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Sharp JA, Mailer SL, Thomson PC, Lefèvre C, Nicholas KR. Identification and transcript analysis of a novel wallaby (Macropus eugenii) basal-like breast cancer cell line. Mol Cancer 2008; 7:1. [PMID: 18179684 PMCID: PMC2263075 DOI: 10.1186/1476-4598-7-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2007] [Accepted: 01/07/2008] [Indexed: 11/10/2022] Open
Abstract
Background A wide variety of animal models have been used to study human breast cancer. Murine, feline and canine mammary tumor cell lines have been studied for several decades and have been shown to have numerous aspects in common with human breast cancer. It is clear that new comparative approaches to study cancer etiology are likely to be productive. Results A continuous line of breast carcinoma cells (WalBC) was established from a primary breast cancer that spontaneously arose in a female tammar wallaby (Macropus eugenii). The primary tumor was 1.5 cm3 and although large, did not appear to invade the stroma and lacked vimentin expression. The WalBC cell line was cultured from the primary tumor and passaged for 22 months. WalBC cells displayed an epithelial morphology when grown on plastic, were not EGF responsive, stained strongly for cyto-keratin and negatively for vimentin. WalBC cells were shown to be non-invasive within a Matrigel invasion assay and failed to produce tumors following transplantation into nude mice. Gene expression profiling of WalBC cells was performed using a cDNA microarray of nearly 10,000 mammary gland cDNA clones and compared to normal primary mammary cells and profiles of human breast cancer. Seventy-six genes were down-regulated and sixty-six genes were up-regulated in WalBC cells when compared to primary mammary cells. WalBC cells exhibited expression of known markers of basal invasive human breast cancers as well as increased KRT17, KRT 14 and KRT 19, DSP, s100A4, NDRG-1, ANXA1, TK1 and AQP3 gene expression and decreased gene expression of TIMP3, VIM and TAGLN. New targets for breast cancer treatment were identified such as ZONAB, PACSIN3, MRP8 and SUMO1 which have human homologues. Conclusion This study demonstrates how novel models of breast cancer can provide new fundamental clues regarding cancer etiology which may lead to new human treatments and therapies.
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Affiliation(s)
- Julie A Sharp
- CRC for Innovative Dairy Products, Department of Zoology, University of Melbourne, VIC 3010, Australia.
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Byrne KA, Wang YH, Lehnert SA, Harper GS, McWilliam SM, Bruce HL, Reverter A. Gene expression profiling of muscle tissue in Brahman steers during nutritional restriction. J Anim Sci 2007; 83:1-12. [PMID: 15583036 DOI: 10.2527/2005.8311] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Expression profiling using microarrays allows for the detailed characterization of the gene networks that regulate an animal's response to environmental stresses. During nutritional restriction, processes such as protein turnover, connective tissue remodeling, and muscle atrophy take place in the skeletal muscle of the animal. These processes and their regulation are of interest in the context of managing livestock for optimal production efficiency and product quality. Here we expand on recent research applying complementary DNA (cDNA) microarray technology to the study of the effect of nutritional restriction on bovine skeletal muscle. Using a custom cDNA microarray of 9,274 probes from cattle muscle and s.c. fat libraries, we examined the differential gene expression profile of the LM from 10 Brahman steers under three different dietary treatments. The statistical approach was based on mixed-model ANOVA and model-based clustering of the BLUP solutions for the gene x diet interaction effect. From the results, we defined a transcript profile of 156 differentially expressed array elements between the weight loss and weight gain diet substrates. After sequence and annotation analyses, the 57 upregulated elements represented 29 unique genes, and the 99 downregulated elements represented 28 unique genes. Most of these co-regulated genes cluster into groups with distinct biological function related to protein turnover and cytoskeletal metabolism and contribute to our mechanistic understanding of the processes associated with remodeling of muscle tissue in response to nutritional stress.
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Affiliation(s)
- K A Byrne
- Cooperative Research Centre for Cattle and Beef Quality, CSIRO Livestock Industries, Queensland Bioscience Precinct, St. Lucia, Queensland 4067, Australia
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Reecy JM, Spurlock DM, Stahl CH. Gene expression profiling: insights into skeletal muscle growth and development. J Anim Sci 2007; 84 Suppl:E150-4. [PMID: 16582087 DOI: 10.2527/2006.8413_supple150x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Microarray technology is now available for many livestock species, and animal scientists are beginning to utilize the technology to address issues of importance to animal agriculture. This review discusses how microarray technology has been applied to study global gene expression changes in skeletal muscle. For example, microarrays have been used to elucidate gene function in knockout mice, evaluate breed differences, evaluate the effects of hormone administration, and evaluate the effects of diet. Data generated from these global gene expression studies are providing new insights to stimulate future hypothesis-driven research.
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Affiliation(s)
- J M Reecy
- Department of Animal Science, Iowa State University, Ames, 50011-3150, USA.
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Lu Y, He X, Zhong S. Cross-species microarray analysis with the OSCAR system suggests an INSR->Pax6->NQO1 neuro-protective pathway in aging and Alzheimer's disease. Nucleic Acids Res 2007; 35:W105-14. [PMID: 17545194 PMCID: PMC1933158 DOI: 10.1093/nar/gkm408] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
OSCAR is a web platform for cluster and cross-species analysis of microarray data. It provides a comprehensive but friendly environment to both users and algorithm developers. For users, OSCAR provides cluster tools for both single and multiple species data, together with interactive analysis features. For single species data, OSCAR currently provides Hierarchical Clustering, K-means, partition around medoids (PAM), Self-Organizing Map (SOM), Tight Clustering and a novel algorithm called ‘Consensus Tight-clustering’. The new Consensus Tight-clustering algorithm delivers robust gene clusters and its result is more resistant to false positives than other state-of-the-art algorithms. For cross-species data analysis, OSCAR provides two novel computational tools: ‘coherentCluster’, ‘coherentSubset’ and a novel visualization tool: ‘comparative heatmap’. Applying the coherentCluster algorithm to human and fly aging data, we identified several coherent clusters of genes, which share co-regulation patterns that are highly correlated with the aging process in both of the two species. One coherent cluster suggests insulin receptor (INSR) may regulate Pax6 in both species and across different tissues. Further analysis with human brain expression and pathological data suggests an INSR->Pax6->quinone oxidoreductase (NQO1)->detoxification neuro-protective pathway might be present in aging or diseased brain. For algorithm developers, OSCAR is a plug-and-play platform. With little effort, developers can plug their own algorithms into the OSCAR server without revealing the source codes, which will equip their command line executables with user-friendly interface and interactive analysis capability. In summary, OSCAR initiates an open platform for development and application of clustering and cross-species analysis programs. OSCAR stands for an open system for cluster analysis of microarray data. It is available at: http://biocomp.bioen.uiuc.edu/oscar
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Affiliation(s)
- Yue Lu
- Department of Computer Science, Department of Bioengineering and Department of Statistics, University of Illinois at Urbana-Champaign, IL, USA
| | - Xin He
- Department of Computer Science, Department of Bioengineering and Department of Statistics, University of Illinois at Urbana-Champaign, IL, USA
| | - Sheng Zhong
- Department of Computer Science, Department of Bioengineering and Department of Statistics, University of Illinois at Urbana-Champaign, IL, USA
- *To whom correspondence should be addressed.
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Wu X, Wang J, Cui X, Maianu L, Rhees B, Rosinski J, So WV, Willi SM, Osier MV, Hill HS, Page GP, Allison DB, Martin M, Garvey WT. The effect of insulin on expression of genes and biochemical pathways in human skeletal muscle. Endocrine 2007; 31:5-17. [PMID: 17709892 DOI: 10.1007/s12020-007-0007-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/1999] [Revised: 11/30/1999] [Accepted: 11/30/1999] [Indexed: 11/24/2022]
Abstract
To study the insulin effects on gene expression in skeletal muscle, muscle biopsies were obtained from 20 insulin sensitive individuals before and after euglycemic hyperinsulinemic clamps. Using microarray analysis, we identified 779 insulin-responsive genes. Particularly noteworthy were effects on 70 transcription factors, and an extensive influence on genes involved in both protein synthesis and degradation. The genetic program in skeletal muscle also included effects on signal transduction, vesicular traffic and cytoskeletal function, and fuel metabolic pathways. Unexpected observations were the pervasive effects of insulin on genes involved in interacting pathways for polyamine and S-adenoslymethionine metabolism and genes involved in muscle development. We further confirmed that four insulin-responsive genes, RRAD, IGFBP5, INSIG1, and NGFI-B (NR4A1), were significantly up-regulated by insulin in cultured L6 skeletal muscle cells. Interestingly, insulin caused an accumulation of NGFI-B (NR4A1) protein in the nucleus where it functions as a transcription factor, without translocation to the cytoplasm to promote apoptosis. The role of NGFI-B (NR4A1) as a new potential mediator of insulin action highlights the need for greater understanding of nuclear transcription factors in insulin action.
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Affiliation(s)
- Xuxia Wu
- Department of Nutrition Sciences, University of Alabama at Birmingham, 1675 University Boulevard, Birmingham, AL 35294-3360, USA.
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21
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22
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Lehnert SA, Byrne KA, Reverter A, Nattrass GS, Greenwood PL, Wang YH, Hudson NJ, Harper GS. Gene expression profiling of bovine skeletal muscle in response to and during recovery from chronic and severe undernutrition1. J Anim Sci 2006; 84:3239-50. [PMID: 17093216 DOI: 10.2527/jas.2006-192] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Gene expression profiles of LM from beef cattle that underwent significant postweaning undernutrition were studied using complementary DNA (cDNA) microarrays. After 114 d of undernutrition, the RNA from LM showed 2- to 6-fold less expression of many genes from the classes of muscle structural proteins, muscle metabolic enzymes, and extracellular matrix compared with animals on a rapid growth diet. The expression levels of these genes had mostly returned to pretreatment levels after 84 d of realimentation. The gene expression changes associated with undernutrition and BW loss showed an emphasis on downregulation of gene expression specific to fast-twitch fibers, typical of starving mammals, with a preferential atrophy of glycolytic fast-twitch fibers. We also identified a small group of genes that showed 2- to 5-fold elevated expression in LM after 114 d of undernutrition. Putative roles for these genes in atrophying skeletal muscle are regulation of myogenic differentiation (CSRP3), maintenance of mesenchymal stem cells (CYR61), modulation of membrane function (TM4SF2), prevention of oxidative damage (SESN1), and regulation of muscle protein degradation (SQSTM1). A significant increase in stearoyl-CoA desaturase (SCD) gene expression was observed in atrophying muscle, suggesting either that increased fatty acid synthesis is part of the tissue response to caloric restriction, or that SCD plays another role in energy metabolism in the mixed cellular environment of bovine skeletal muscle.
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Affiliation(s)
- S A Lehnert
- Cooperative Research Centre for Cattle and Beef Quality, Australia.
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23
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Reverter A, Wang YH, Byrne KA, Tan SH, Harper GS, Lehnert SA. Joint analysis of multiple cDNA microarray studies via multivariate mixed models applied to genetic improvement of beef cattle. J Anim Sci 2006; 82:3430-9. [PMID: 15537761 DOI: 10.2527/2004.82123430x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In functional genomic laboratories, it is common to use the same microarray slide across studies, each investigating a unique biological question, and each analyzed separately due to computational limitations and/or because there is no hybridization of samples from different studies on one slide. However, the question of analyzing data from multiple studies is a major current issue in microarray data analysis because there are gains to be made in the accuracy of estimated effects by exploiting a covariance structure between gene expression data across studies. We propose an approach for combining multiple studies using multivariate mixed models, with the assumption of a nonzero correlation among genes across experiments, while imposing a null residual covariance. We applied this method to jointly analyze three experiments in genetics of cattle with a total of 54 arrays, each with 19,200 spots and 7,638 elements. The resulting seven-variate model contains 752,476 equations and 56 covariances. To identify differentially expressed genes, we applied model-based clustering to a linear combination of the random gene x variety interaction effect. We enhanced the biological interpretation of the results by applying an iterative algorithm to identify the gene ontology classes that significantly changed in each experiment. We found 118 elements with coordinate expression that clustered into distinct biological functions such as adipogenesis and protein turnover. These results contribute to our understanding of the mechanistic processes involved in adipogenesis and nutrient partitioning.
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Affiliation(s)
- A Reverter
- The Cooperative Research Centre for Cattle and Beef Quality, CSIRO Livestock Industries, Queensland Bioscience Precinct, St. Lucia, Queensland 4067, Australia.
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Reverter A, Hudson NJ, Wang Y, Tan SH, Barris W, Byrne KA, McWilliam SM, Bottema CDK, Kister A, Greenwood PL, Harper GS, Lehnert SA, Dalrymple BP. A gene coexpression network for bovine skeletal muscle inferred from microarray data. Physiol Genomics 2006; 28:76-83. [PMID: 16985009 DOI: 10.1152/physiolgenomics.00105.2006] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
We present the application of large-scale multivariate mixed-model equations to the joint analysis of nine gene expression experiments in beef cattle muscle and fat tissues with a total of 147 hybridizations, and we explore 47 experimental conditions or treatments. Using a correlation-based method, we constructed a gene network for 822 genes. Modules of muscle structural proteins and enzymes, extracellular matrix, fat metabolism, and protein synthesis were clearly evident. Detailed analysis of the network identified groupings of proteins on the basis of physical association. For example, expression of three components of the z-disk, MYOZ1, TCAP, and PDLIM3, was significantly correlated. In contrast, expression of these z-disk proteins was not highly correlated with the expression of a cluster of thick (myosins) and thin (actin and tropomyosins) filament proteins or of titin, the third major filament system. However, expression of titin was itself not significantly correlated with the cluster of thick and thin filament proteins and enzymes. Correlation in expression of many fast-twitch muscle structural proteins and enzymes was observed, but slow-twitch-specific proteins were not correlated with the fast-twitch proteins or with each other. In addition, a number of significant associations between genes and transcription factors were also identified. Our results not only recapitulate the known biology of muscle but have also started to reveal some of the underlying associations between and within the structural components of skeletal muscle.
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Affiliation(s)
- Antonio Reverter
- Bioinformatics Group, Commonwealth Scientific and Industrial Research Organisation Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Road, St. Lucia, QLD 4067, Australia.
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25
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Mullen A, Stapleton P, Corcoran D, Hamill R, White A. Understanding meat quality through the application of genomic and proteomic approaches. Meat Sci 2006; 74:3-16. [DOI: 10.1016/j.meatsci.2006.04.015] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2006] [Revised: 04/25/2006] [Accepted: 04/25/2006] [Indexed: 10/24/2022]
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Tan SH, Reverter A, Wang Y, Byrne KA, McWilliam SM, Lehnert SA. Gene expression profiling of bovine in vitro adipogenesis using a cDNA microarray. Funct Integr Genomics 2006; 6:235-49. [PMID: 16470362 DOI: 10.1007/s10142-005-0016-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2005] [Revised: 10/04/2005] [Accepted: 10/08/2005] [Indexed: 12/16/2022]
Abstract
The gene expression profile of bovine bone marrow stromal cells undergoing adipogenesis was established using a custom cDNA microarray. Cells that were treated with adipogenic stimulants and those that were not were collected at each of the six time points, and gene expression differences between the treated and untreated samples within each time point were compared using a microarray. Statistical analyses revealed that 158 genes showed a minimum fold change of 2 in at least one of the five post-differentiation time points. These genes are involved in various cellular pathways and functions, including lipogenesis, glycolysis, cytoskeleton remodelling, extracellular matrix, transcription as well as various signalling pathways such as insulin, calcium and wingless signalling. The experiment also identified 17 differentially expressed (DE) microarray elements with no assigned function. Quantitative real-time PCR was employed to validate eight DE genes, and the PCR data were found to reproduce the microarray data for these eight genes. Subsequent gene ontology annotation was able to provide a global overview of the molecular function of DE genes during adipogenesis. This analysis was able to indicate the importance of different gene categories at various stages of adipogenic conversion, thereby providing further insights into the molecular changes during bovine adipogenesis.
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Affiliation(s)
- Siok Hwee Tan
- The Cooperative Research Center for Cattle and Beef Quality, CSIRO Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Road, St. Lucia, Qld 4067, Australia.
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27
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Lehnert SA, Wang YH, Tan SH, Reverter A. Gene expression-based approaches to beef quality research. ACTA ACUST UNITED AC 2006. [DOI: 10.1071/ea05226] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Advances in mammalian genomics have permitted the application of gene expression profiling approaches to gene discovery for meat quality traits in cattle. The first custom cDNA microarray based on the transcriptome of bovine muscle and fat tissue was developed and applied to animal experimentation and cell culture experimentation between 1999 and 2005. Complementary DNA microarray tools for beef quality research were developed in parallel with bioinformatics tools that permit the analysis of microarray data obtained from complex experimental designs commonly encountered in large animal research. In addition, tools were designed to link gene expression data with gene function in the bovine, such as in vitro models of bovine adipogenesis and bioinformatics tools to map gene networks from expression data. The application of these genomics tools to the study of beef quality has yielded novel knowledge of genes and molecules involved in the processes of intramuscular adipogenesis and protein turnover. This review summarises the current state of knowledge and important lessons derived from bovine genomics initiatives in Australia and around the world.
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Wang YH, Byrne KA, Reverter A, Harper GS, Taniguchi M, McWilliam SM, Mannen H, Oyama K, Lehnert SA. Transcriptional profiling of skeletal muscle tissue from two breeds of cattle. Mamm Genome 2005; 16:201-10. [PMID: 15834637 DOI: 10.1007/s00335-004-2419-8] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2004] [Accepted: 11/18/2004] [Indexed: 12/16/2022]
Abstract
We used a 9.6 K cattle muscle/fat cDNA microarray to study gene expression differences between the longuissimus dorsi (LD) muscle of Japanese Black (JB) and Holstein (HOL) cattle. JB cattle exhibit an unusual ability to accumulate intramuscular adipose tissue with fat melting points lower than that in other breeds. The LD biopsies from three JB (Tajima strain) and three HOL animals were used in this breed comparison. Seventeen genes were identified as preferentially expressed in LD samples from JB and seven genes were found to be expressed more highly in HOL. The expression of six selected differentially expressed genes was confirmed by quantitative real-time PCR. The genes more highly expressed in JB are associated with unsaturated fatty acid synthesis, fat deposition, and the thyroid hormone pathway. These results are consistent with the increased amounts and proportions of monounsaturated fatty acids observed in the muscle of JB animals. By discovering as yet uncharacterized genes that are differentially regulated in this comparison, the work may lead us to a better understanding of the regulatory pathways involved in the development of intramuscular adipose tissue.
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Affiliation(s)
- Yong-Hong Wang
- Cooperative Research Center for Cattle and Beef Quality, CSIRO Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Rd., St. Lucia, Brisbane, Queensland, 4067, Australia.
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Wilson HL, Aich P, Roche FM, Jalal S, Hodgson PD, Brinkman FSL, Potter A, Babiuk LA, Griebel PJ. Molecular analyses of disease pathogenesis: application of bovine microarrays. Vet Immunol Immunopathol 2005; 105:277-87. [PMID: 15808306 PMCID: PMC7112672 DOI: 10.1016/j.vetimm.2005.02.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The molecular analysis of disease pathogenesis in cattle has been limited by the lack of availability of tools to analyze both host and pathogen responses. These limitations are disappearing with the advent of methodologies such as microarrays that facilitate rapid characterization of global gene expression at the level of individual cells and tissues. The present review focuses on the use of microarray technologies to investigate the functional pathogenomics of infectious disease in cattle. We discuss a number of unique issues that must be addressed when designing both in vitro and in vivo model systems to analyze host responses to a specific pathogen. Furthermore, comparative functional genomic strategies are discussed that can be used to address questions regarding host responses that are either common to a variety of pathogens or unique to individual pathogens. These strategies can also be applied to investigations of cell signaling pathways and the analyses of innate immune responses. Microarray analyses of both host and pathogen responses hold substantial promise for the generation of databases that can be used in the future to address a wide variety of questions. A critical component limiting these comparative analyses will be the quality of the databases and the complete functional annotation of the bovine genome. These limitations are discussed with an indication of future developments that will accelerate the validation of data generated when completing a molecular characterization of disease pathogenesis in cattle.
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Affiliation(s)
- Heather L Wilson
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, Sask., Canada S7N 5E3
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McGuire K, Glass EJ. The expanding role of microarrays in the investigation of macrophage responses to pathogens. Vet Immunol Immunopathol 2005; 105:259-75. [PMID: 15808305 DOI: 10.1016/j.vetimm.2005.02.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
In the last few years, microarray technology has emerged as the method of choice for large-scale gene expression studies. It provides an efficient and rapid method to investigate the entire transcriptome of a cell. No research field has benefited more from microarray technology than the study of the exquisite interplay between pathogens and hosts. Numerous microarray studies have now been published in this field, which have provided insights into the mechanisms of host defence and the tactics employed by pathogens to circumvent these protection strategies. These studies have led to a more comprehensive understanding of the host immune response and identified new avenues of research for potential control strategies against pathogens. In the past, research has concentrated on human and mouse microarrays to investigate host-pathogen interactions, regardless of the host species. This trend is changing with the ever-expanding sequence resources now available for many pathogen and host species, including livestock animals. The use of species-specific microarrays has furthered our understanding of host-pathogen interactions for particular organisms and aided in the annotation of unknown genes. Macrophages play a central role in the host's innate and adaptive immune responses to pathogens. These cells are in the first line of defence and interact with a wide range of pathogens; many of which have evolved strategies to circumvent the macrophage defence mechanisms and survive within these cells. In this report, we review the wealth of studies using microarray technology to investigate the response of macrophages to pathogens. These studies illustrate how microarray technology has expanded our understanding of the dialogue between macrophage and pathogen and provide examples of the benefits and pitfalls of using this technique. Furthermore, we discuss the resources available to use microarray analysis to study the immune response of a non-human, non-rodent species, the cow.
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Affiliation(s)
- Kirsty McGuire
- Department of Genetics and Genomics, Roslin Institute, Roslin, Midlothian, Edinburgh EH25 9PS, UK.
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Everts RE, Band MR, Liu ZL, Kumar CG, Liu L, Loor JJ, Oliveira R, Lewin HA. A 7872 cDNA microarray and its use in bovine functional genomics. Vet Immunol Immunopathol 2005; 105:235-45. [PMID: 15808303 DOI: 10.1016/j.vetimm.2005.02.003] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The strategy used to create and annotate a 7872 cDNA microarray from cattle placenta and spleen cDNA sequences is described. This microarray contains approximately 6300 unique genes, as determined by BLASTN and TBLASTX similarity search against the human and mouse UniGene and draft human genome sequence databases (build 34). Sequences on the array were annotated with gene ontology (GO) terms, thereby facilitating data analysis and interpretation. A total of 3244 genes were annotated with GO terms. The array is rich in sequences encoding transcription factors, signal transducers and cell cycle regulators. Current research being conducted with this array is described, and an overview of planned improvements in our microarray platform for cattle functional genomics is presented.
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Affiliation(s)
- Robin E Everts
- Department of Animal Sciences, University of Illinois, 206 Edward R. Madigan Laboratory, 1201 West Gregory Drive, Urbana, IL 61801, USA
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32
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Moser RJ, Reverter A, Kerr CA, Beh KJ, Lehnert SA. A mixed-model approach for the analysis of cDNA microarray gene expression data from extreme-performing pigs after infection with Actinobacillus pleuropneumoniae. J Anim Sci 2005; 82:1261-71. [PMID: 15144065 DOI: 10.2527/2004.8251261x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We proposed a novel statistical approach for the analysis of cDNA experiments based on mixed-model methodology combined with mixtures of distributions. Our objective was to detect genes that may be involved in conferring heritable differences in susceptibility to common infections in intensive pig production. We employed a microarray expression profiling strategy and a mixed-model approach to the analysis of the expression data. A cDNA microarray of pig with 6,420 probes from immune tissues and cells was used to compare gene expression in peripheral blood leukocytes of two pigs showing extreme performance in their response to infection with Actinobacillus pleuropneumoniae. Principal components analyses were used to identify the two most extreme-performing pigs after infection (i.e., pigs whose measured responses to infection fell at the extremes). Blood samples and expression profiles from 0 to 24 h after infection were compared using a bivariate, mixed-model approach, in which the effect gene x immunological status interaction was treated as a random effect. Bayesian model-based clustering via mixtures of normal distributions of the resulting BLUP of the random interaction was approached and resulted in a list of 307 differentially expressed genes, of which 179 were down-regulated in the susceptible pig. The majority of the differentially expressed genes were derived from a cDNA library of leukocytes of A. pleuropneumoniae-challenged pigs that were subtracted against leukocytes before the challenge. These results provide evidence that the proposed statistical approach was useful in enhancing the knowledge of the mechanisms involved in the genetics of the immune response.
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Affiliation(s)
- R J Moser
- CSIRO Livestock Industries, Queensland Bioscience Precinct, St. Lucia, Queensland 4067, Australia
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33
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Sudre K, Leroux C, Cassar-Malek I, Hocquette JF, Martin P. A collection of bovine cDNA probes for gene expression profiling in muscle. Mol Cell Probes 2005; 19:61-70. [PMID: 15652221 DOI: 10.1016/j.mcp.2004.07.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2004] [Revised: 06/10/2004] [Accepted: 07/30/2004] [Indexed: 11/26/2022]
Abstract
Array technology has been increasingly used to monitor global gene expression patterns in various tissues and cell types. However, applications to muscle development and pathology as well as meat production in livestock species have been hampered by the lack of appropriate cDNA collections. To overcome this problem, a directed cDNA library was constructed starting from 23 muscles of meat-producing bovines to derive a collection of 3573 clones. A preliminary sequence characterization of this collection indicated that the most abundant transcripts correspond to genes encoding proteins involved in energy metabolism (COX and NADH dehydrogenase subunits) and belonging to the contractile apparatus (myosin chains and troponin isoforms). From this cDNA library, we selected a set of 435 clones representing 340 unique genes, of which 24 were novel. This collection was subsequently completed with 75 specific cDNA probes for genes of interest already studied in our laboratory. The bovine 'muscle' cDNA repertoire thus designed was spotted onto a nylon membrane (macroarray) in order to test its utility to further investigate the transcriptome of bovine muscles in relation to meat quality traits. It is also anticipated that this type of collection might be useful for the study of chronic myologic diseases in other mammalian species, including humans.
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Affiliation(s)
- K Sudre
- INRA, Unité de Recherches sur les Herbivores, Centre de Recherches de Clermont-Ferrand/Theix, 63122 St Genès-Champanelle, France
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34
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Wang YH, Reverter A, Mannen H, Taniguchi M, Harper GS, Oyama K, Byrne KA, Oka A, Tsuji S, Lehnert SA. Transcriptional profiling of muscle tissue in growing Japanese Black cattle to identify genes involved with the development of intramuscular fat. ACTA ACUST UNITED AC 2005. [DOI: 10.1071/ea05058] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Japanese Black cattle are characterised by a unique ability to deposit intramuscular fat with lower melting temperature. In this study, 3 consecutive biopsies from Longissimus muscle tissue were taken and RNA isolated from 3 Japanese Black (Tajima strain) and 3 Holstein animals at age 11–20 months. The gene expression changes in these samples were analysed using a bovine fat/muscle cDNA microarray. A mixed-ANOVA model was fitted to the intensity signals. A total of 335 (4.8%) array elements were identified as differentially expressed genes in this breed × time comparison study. Genes preferentially expressed in Japanese Black are associated with mono-unsaturated fatty acid synthesis, fat deposition, adipogenesis development and muscle regulation, while examples of genes preferentially expressed in Holstein come from functional classes involved in connective tissue and skeletal muscle development. The gene expression differences detected between the Longissimus muscle of the 2 breeds give important clues to the molecular basis for the unique features of the Japanese Black breed, such as the onset and rate of adipose tissue development, metabolic differences, and signalling pathways involved in converting carbohydrate to lipid during lipogenesis. These findings will impact on industry management strategies designed to manipulate intramuscular adipose development at different development stages to gain maximum return for beef products.
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Reverter A, Barris W, Moreno-Sánchez N, McWilliam S, Wang YH, Harper GS, Lehnert SA, Dalrymple BP. Construction of gene interaction and regulatory networks in bovine skeletal muscle from expression data. ACTA ACUST UNITED AC 2005. [DOI: 10.1071/ea05039] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We propose a data-driven reverse engineering approach to isolate the components of a gene interaction and regulatory network. We apply this method to the construction of a network for bovine skeletal muscle. Key nodes in the network include muscle-specific genes and transcription factors. muscle-specific genes are identified from data mining the USA National Cancer Institute, Cancer Genome Anatomy Project database, while transcription factors are predicted by accurate function annotation. A total of 5 microarray studies spanning 78 hybridisations and 23 different experimental conditions provided raw expression data. A recently-reported analytical method based on multivariate mixed-model equations is used to compute gene co-expression measures across 624 genes. The resulting network included 102 genes (of which 40 were muscle-specific genes and 7 were transcription factors) that clustered in 7 distinct modules with clear biological interpretation.
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36
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Burrow HM, Bindon BM. Genetics research in the Cooperative Research Centre for Cattle and Beef Quality. ACTA ACUST UNITED AC 2005. [DOI: 10.1071/ea05069] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In its first 7-year term, the Cooperative Research Centre (CRC) for the Cattle and Beef Industry (Meat Quality) identified the genetic and non-genetic factors that impacted on beef eating quality. Following this, the CRC for Cattle and Beef Quality was established in 1999 to identify the consequences of improving beef eating quality and feed efficiency by genetic and non-genetic means on traits other than carcass and beef quality. The new CRC also had the responsibility to incorporate results from the first Beef CRC in national schemes such as BREEDPLAN (Australia’s beef genetic evaluation scheme) and Meat Standards Australia (Australia’s unique meat grading scheme that guarantees the eating quality of beef). This paper describes the integrated research programs and their results involving molecular and quantitative genetics, meat science, growth and nutrition and industry economics in the Beef CRC’s second phase (1999–2006) and the rationale for the individual genetics programs established. It summarises the planned scientific and beef industry outcomes from each of these programs and also describes the development and/or refinement by CRC scientists of novel technologies targeting increased genetic gains through enhanced measurement and recording in beef industry herds, thereby ensuring industry use of CRC results.
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Reverter A, Barris W, McWilliam S, Byrne KA, Wang YH, Tan SH, Hudson N, Dalrymple BP. Validation of alternative methods of data normalization in gene co-expression studies. Bioinformatics 2004; 21:1112-20. [PMID: 15564293 DOI: 10.1093/bioinformatics/bti124] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
MOTIVATION Clusters of genes encoding proteins with related functions, or in the same regulatory network, often exhibit expression patterns that are correlated over a large number of conditions. Protein associations and gene regulatory networks can be modelled from expression data. We address the question of which of several normalization methods is optimal prior to computing the correlation of the expression profiles between every pair of genes. RESULTS We use gene expression data from five experiments with a total of 78 hybridizations and 23 diverse conditions. Nine methods of data normalization are explored based on all possible combinations of normalization techniques according to between and within gene and experiment variation. We compare the resulting empirical distribution of gene x gene correlations with the expectations and apply cross-validation to test the performance of each method in predicting accurate functional annotation. We conclude that normalization methods based on mixed-model equations are optimal.
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Affiliation(s)
- Antonio Reverter
- Bioinformatics Group, CSIRO Livestock Industries, Queensland Bioscience Precinct, St Lucia, QLD 4067, Australia.
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Lehnert SA, Wang YH, Byrne KA. Development and application of a bovine cDNA microarray for expression profiling of muscle and adipose tissue. ACTA ACUST UNITED AC 2004. [DOI: 10.1071/ea03238] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In order to gain new knowledge of the genetic control of biochemical and developmental processes that contribute to beef quality, we constructed a bovine microarray of 9600 elements comprising about 2000 expressed sequence tags (ESTs) and 7300 anonymous cDNA clones from muscle and fat-derived cDNA libraries. The microarray was used in 2 animal experiments aimed at uncovering gene expression differences associated with adipogenesis and protein turnover. The results obtained so far show that expression profiling of bovine muscle using the microarray can reliably identify differentially expressed genes and confirm existing hypotheses. Moreover, the technique can provide new evidence on the detailed involvement of well-characterised genes and can identify genes that have not previously been described as having a role in these processes.
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