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Vogt A, Barth K, Waiblinger S, König von Borstel U. Can a gradual weaning and separation process reduce weaning distress in dam-reared dairy calves? A comparison with the 2-step method. J Dairy Sci 2024; 107:5942-5961. [PMID: 38490545 DOI: 10.3168/jds.2024-23809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 02/12/2024] [Indexed: 03/17/2024]
Abstract
The weaning and separation phase remains one of the biggest challenges for cow-calf contact systems, but a gradual process that better mimics the naturally occurring reduction in milk intake has not yet been scientifically investigated. Therefore, the aim of our study was to compare behavioral and physiological indicators of distress in 3-mo-old dam-reared dairy calves (with previous full-time cow-calf contact) weaned and separated either via gradual reduction of contact time with the dam (GR; 1 wk of half-day contact, 1 wk of morning contact, and 1 wk of fence-line contact before complete separation, n = 18) or via 2-step weaning using a nose flap (NF, 2 wk of access to the dam with a nose flap, 1 wk of fence-line contact before complete separation, n = 18). Behavior was recorded 1 wk before (or for lying 3 wk before) weaning start and during the 3 wk weaning and separation period with direct observations on 4 d/wk or via accelerometers (locomotor play, lying behavior). Blood and fecal samples were taken twice per week from weaning start until 3 wk after weaning start. Calves were weighed weekly. Statistical analysis was conducted using (generalized) linear mixed models. Over the whole weaning and separation phase, NF calves showed a stronger decrease in the number of lying bouts, amount of locomotor play, and ADG, as well as a higher increase in TMR feeding time compared with GR calves, whereas GR calves vocalized more often and showed more searching behavior than NF calves. Also, the neutrophil:lymphocyte ratio of NF calves was elevated on d 3 after insertion of the nose flaps compared with baseline, but showed no change for GR calves on any sampling day. Overall, results point toward a favorable effect of a gradual weaning strategy on reduction of weaning and separation distress in dam-reared dairy calves, but the method requires further improvement from the protocol used in our study.
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Affiliation(s)
- Anina Vogt
- Division of Animal Husbandry, Behaviour and Welfare, Justus-Liebig-University of Giessen, 35392 Giessen, Germany.
| | - Kerstin Barth
- Institute of Organic Farming, Johann Heinrich von Thünen Institute, Federal Research Institute for Rural Areas, Forestry and Fisheries, 23847 Westerau, Germany
| | - Susanne Waiblinger
- Institute of Animal Welfare Science, University of Veterinary Medicine, 1210 Vienna, Austria
| | - Uta König von Borstel
- Division of Animal Husbandry, Behaviour and Welfare, Justus-Liebig-University of Giessen, 35392 Giessen, Germany
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Howell A, Arsic N, Griebel P. Resting and activated bovine neutrophils and eosinophils differ in their responses to adrenergic agonists. Vet Immunol Immunopathol 2024; 272:110758. [PMID: 38669937 DOI: 10.1016/j.vetimm.2024.110758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/09/2024] [Accepted: 04/19/2024] [Indexed: 04/28/2024]
Abstract
Polymorphonuclear cells (PMN) provide a rapid response to infection and tissue damage and stress can modify these critical innate immune defences. The study of adrenergic receptor (AR) expression and function in bovine PMNs is limited but both neutrophils and eosinophils express numerous AR genes but differ significantly in their expression of individual AR genes. A flow cytometric technique was developed to differentiate between bovine neutrophils and eosinophils so both neutrophil and eosinophil responses to adrenergic agonists could be analysed. Neutrophils and eosinophils displayed significantly different changes in CD11b, L-selectin, and CD44 expression when activated by bovine serum opsonized zymosan and recombinant bovine interferon gamma. The responses of activated and resting neutrophils and eosinophils were then compared following stimulation with endogenous adrenergic agonists, epinephrine (E) norepinephrine (NE), and synthetic agonists targeting α1-, α2-, or β-ARs. Both resting and activated neutrophils and eosinophils displayed differences in iROS, CD44, and L-selectin expression following stimulation with E and NE. Resting neutrophils displayed pro-inflammatory responses to both E and NE, while resting eosinophils displayed a pro-inflammatory response to only NE. No single synthetic adrenergic agonist fully recapitulated responses observed with either E or NE and responses to adrenergic agonists were dose-dependent. In conclusion, bovine eosinophils and neutrophils responded to multiple adrenergic agonists by altering expression of proteins involved in immune surveillance and pro-inflammatory responses. Significant differences in neutrophil and eosinophil responses to adrenergic agonists are consistent with their differences in AR gene expression. This highlights the importance of analysing separately these two PMN subpopulations when investigating the effects of either endogenous or synthetic AR agonists.
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Affiliation(s)
- Angela Howell
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, 120-Veterinary Road, Saskatoon, SK S7N 5E3, Canada; Global Institute for Food Security (GIFS), University of Saskatchewan, 421 Downey Rd, Saskatoon, SK S7N 4L8, Canada
| | - Natasa Arsic
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, 120-Veterinary Road, Saskatoon, SK S7N 5E3, Canada
| | - Philip Griebel
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, 120-Veterinary Road, Saskatoon, SK S7N 5E3, Canada; School of Public Health, 104 Clinic Place, University of Saskatchewan, SK S7N 2Z4, Canada.
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Treon E, Sidney T, Taiwo G, Idowu M, Leal Y, Ologunagba D, Ogunade IM. Effects of dietary supplementation of a blend of Saccharomyces cerevisiae, multiple live probiotic bacteria, and their fermentation products on performance, health, and rumen bacterial community of newly weaned beef steers during a 56-d receiving period. Transl Anim Sci 2023; 8:txad143. [PMID: 38221963 PMCID: PMC10785767 DOI: 10.1093/tas/txad143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 12/16/2023] [Indexed: 01/16/2024] Open
Abstract
We examined the effects of a blend of Saccharomyces cerevisiae, multiple live probiotic bacteria, and their fermentation products on performance, health, and the ruminal bacterial community of newly weaned beef steers during a 56-d receiving period. Forty newly weaned Angus crossbred steers (221 ± 25.6 kg BW; 180 ± 17 d of age) were stratified by body weight (BW) into four pens (10 steers per pen) such that each pen had a similar average BW at the beginning of the experiment. The pens were randomly assigned to receive a corn silage basal diet (CON; n = 20) or the basal diet supplemented with 9 g/steer/d of PRO feed additive (PRO; n = 20). The PRO additive is a blend of S. cerevisiae and the fermentation products of Enterococcus faecium, Bacillus licheniformis, B. subtilis, Lactobacillus animalis, and Propionibacterium freudenreichii. The DMI and water consumed were monitored using the GrowSafe intake nodes and custom flow meters, respectively. BWs were recorded weekly to calculate average daily gain (ADG). Before morning feeding, 10 mL of blood was taken from each steer on days 0-7, and thereafter weekly for analyses of immune cells, plasma glucose, and NEFAs. On day 56, rumen fluid samples (200 mL each) were collected from all the steers for microbiome analysis. Over the 56-d receiving period, the supplemental PRO had no effects on DMI, water intake, or ADG. However, compared to CON, beef steers fed supplemental PRO tended to have greater ADG (P = 0.08) and BW (P = 0.07) during the first 14 d of the study. There was a treatment × day interaction (P ≤ 0.05) for WBC, neutrophils and monocytes over the 56 d such that beef steers fed supplemental PRO had lower blood concentrations on certain days during the first 7 d after weaning, indicating reduced inflammation or stress response. The results of the rumen microbiome analysis revealed that the relative abundance of complex fiber degrading or obligate proton-reducing bacterial genera such as Bacteroides, Ruminococcus gauvreauii group, Desulfovibrio, Syntrophococcus, and Acetitomaculum were greater (P ≤ 0.05) in beef steers fed supplemental PRO compared to CON. This study demonstrated that dietary supplementation of PRO improved the growth performance, reduced stress or inflammatory response during the initial days after weaning, and altered the ruminal bacterial community toward increased relative abundance of bacterial genera associated with improved rumen function.
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Affiliation(s)
- Emily Treon
- Division of Animal and Nutritional Science, West Virginia University, Morgantown, WV 26505, USA
| | - Taylor Sidney
- Division of Animal and Nutritional Science, West Virginia University, Morgantown, WV 26505, USA
| | - Godstime Taiwo
- Division of Animal and Nutritional Science, West Virginia University, Morgantown, WV 26505, USA
| | - Modoluwamu Idowu
- Division of Animal and Nutritional Science, West Virginia University, Morgantown, WV 26505, USA
| | - Yarahy Leal
- Division of Animal and Nutritional Science, West Virginia University, Morgantown, WV 26505, USA
| | - Deborah Ologunagba
- Division of Animal and Nutritional Science, West Virginia University, Morgantown, WV 26505, USA
| | - Ibukun M Ogunade
- Division of Animal and Nutritional Science, West Virginia University, Morgantown, WV 26505, USA
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Turner N, Abeysinghe P, Flay H, Meier S, Sadowski P, Mitchell MD. SWATH-MS Analysis of Blood Plasma and Circulating Small Extracellular Vesicles Enables Detection of Putative Protein Biomarkers of Fertility in Young and Aged Dairy Cows. J Proteome Res 2023; 22:3580-3595. [PMID: 37830897 DOI: 10.1021/acs.jproteome.3c00406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
The development of biomarkers of fertility could provide benefits for the genetic improvement of dairy cows. Circulating small extracellular vesicles (sEVs) show promise as diagnostic or prognostic markers since their cargo reflects the metabolic state of the cell of origin; thus, they mirror the physiological status of the host. Here, we employed data-independent acquisition mass spectrometry to survey the plasma and plasma sEV proteomes of two different cohorts of Young (Peripubertal; n = 30) and Aged (Primiparous; n = 20) dairy cows (Bos taurus) of high- and low-genetic merit of fertility and known pregnancy outcomes (ProteomeXchange data set identifier PXD042891). We established predictive models of fertility status with an area under the curve of 0.97 (sEV; p value = 3.302e-07) and 0.95 (plasma; p value = 6.405e-08). Biomarker candidates unique to high-fertility Young cattle had a sensitivity of 0.77 and specificity of 0.67 (*p = 0.0287). Low-fertility biomarker candidates uniquely identified in sEVs from Young and Aged cattle had a sensitivity and specificity of 0.69 and 1.0, respectively (***p = 0.0005). Our bioinformatics pipeline enabled quantification of plasma and circulating sEV proteins associated with fertility phenotype. Further investigations are warranted to validate this research in a larger population, which may lead to improved classification of fertility status in cattle.
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Affiliation(s)
- Natalie Turner
- Centre for Children's Health Research (CCHR), Queensland University of Technology (QUT), 62 Graham Street, South Brisbane, Queensland 4101, Australia
| | - Pevindu Abeysinghe
- Centre for Children's Health Research (CCHR), Queensland University of Technology (QUT), 62 Graham Street, South Brisbane, Queensland 4101, Australia
| | - Holly Flay
- DairyNZ Limited, Private Bag 3221, Hamilton 3240, New Zealand
| | - Susanne Meier
- DairyNZ Limited, Private Bag 3221, Hamilton 3240, New Zealand
| | - Pawel Sadowski
- Central Analytical Research Facility (CARF), QUT, Gardens Point Campus, 2 George Street, Brisbane City, Queensland 4000, Australia
| | - Murray D Mitchell
- Centre for Children's Health Research (CCHR), Queensland University of Technology (QUT), 62 Graham Street, South Brisbane, Queensland 4101, Australia
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Naldurtiker A, Batchu P, Kouakou B, Terrill TH, McCommon GW, Kannan G. Differential gene expression analysis using RNA-seq in the blood of goats exposed to transportation stress. Sci Rep 2023; 13:1984. [PMID: 36737466 PMCID: PMC9898539 DOI: 10.1038/s41598-023-29224-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Transportation stress causes significant changes in physiological responses in goats; however, studies exploring the transcriptome of stress are very limited. The objective of this study was to determine the differential gene expressions and related pathways in the blood samples using RNA-seq procedure in Spanish goats subjected to different durations of transportation stress. Fifty-four male Spanish goats (8-mo old; BW = 29.7 ± 2.03 kg) were randomly subjected to one of three treatments (TRT; n = 18 goats/treatment): (1) transported for 180 min, (2) transported for 30 min, or (3) held in pens (control). Blood samples were collected before and after treatment for stress hormone, metabolite, and transcriptomic analysis. RNA-seq technology was used to obtain the transcriptome profiles of blood. Analysis of physiological data using SAS showed that plasma cortisol concentrations were higher (P < 0.01) in 180 min and 30 min groups compared to the control group. Enrichment analysis of DEGs related to transportation stress through Gene Ontology and KEGG databases revealed that the differentially expressed genes related to inflammatory pathways, caspases, and apoptosis such as IL1R2, CASP14, CD14, TLR4, and MAPK14 were highly enriched in the transported group of goats compared to non-transported goats. Stress in goats leads to a sequence of events at cellular and molecular levels that causes inflammation and apoptosis.
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Affiliation(s)
- Aditya Naldurtiker
- Agricultural Research Station, Fort Valley State University, 1005 State University Drive, Fort Valley, GA, 31030, USA
| | - Phaneendra Batchu
- Agricultural Research Station, Fort Valley State University, 1005 State University Drive, Fort Valley, GA, 31030, USA
| | - Brou Kouakou
- Agricultural Research Station, Fort Valley State University, 1005 State University Drive, Fort Valley, GA, 31030, USA
| | - Thomas H Terrill
- Agricultural Research Station, Fort Valley State University, 1005 State University Drive, Fort Valley, GA, 31030, USA
| | - George W McCommon
- Agricultural Research Station, Fort Valley State University, 1005 State University Drive, Fort Valley, GA, 31030, USA
| | - Govind Kannan
- Agricultural Research Station, Fort Valley State University, 1005 State University Drive, Fort Valley, GA, 31030, USA.
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Farias SDS, Dierings AC, Mufalo VC, Sabei L, Parada Sarmiento M, da Silva AN, Ferraz PA, Pugliesi G, Ribeiro CVDM, Oliveira CADA, Zanella AJ. Asinine milk mitigates stress-mediated immune, cortisol and behavioral responses of piglets to weaning: A study to foster future interventions in humans. Front Immunol 2023; 14:1139249. [PMID: 37122716 PMCID: PMC10140756 DOI: 10.3389/fimmu.2023.1139249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 03/24/2023] [Indexed: 05/02/2023] Open
Abstract
Introduction The present study assessed whether asinine milk supplementation improved the immune and behavioral responses of piglets during an early life weaning stress event as a model for its future use in humans. Methods For this, 48 piglets from 4 different litters were used. At 20 days of age, piglets were weighed and allocated with their litter and dam into group pens until 28 days of age. Four piglets from each litter were then randomly assigned to either (1) asinine milk supplementation (n = 16) (2), skimmed cow milk supplementation (n = 16) or (3) no supplementation (n = 16; control group). The supplementations were voluntarily administered for 3 days preweaning and 3 days postweaning using a baby bottle. The effects on the weaning stress response were assessed through salivary cortisol measurements; behavioral tests such as the open field, novel object end elevated plus maze tests; and gene expression of HSD11B1, NR3C1 and IL1B in PBMCs, which was determined by RT-qPCR and normalized to GAPDH and UBB. To test the effect of the supplementations on weight, milk intake, gene expression, and behavior, a randomized block design was used with repeated measurements over time by the PROC MIXED procedure. Results and discussion The effects on salivary cortisol were determined using the ratio between the morning and afternoon concentrations, considering the time before and after the weaning event. Principal component analysis (PCA) and Fisher's test were performed to evaluate the behavior test data. When comparing salivary cortisol concentrations between the pre- and postweaning periods, there was a difference (p < 0.05) between the supplementation groups in the afternoon period, suggesting that piglets fed asinine milk had lower afternoon cortisol concentrations postweaning than their counterparts. For the behavioral tests, the supplementations had no measurable effects. No difference was between groups pre- and postweaning for the expression of HSD11B2, which codes for an enzyme that breaks down cortisol. However, the expression of NR3C1, which encodes the glucocorticoid receptor, was significantly upregulated in piglets supplemented with cow milk (mean 1.245; p < 0.05). Conclusion Asinine milk downregulated 1L1B gene expression, which codes for an inflammatory cytokine. In conclusion, these results suggest that supplementation with asinine milk may represent a strategy to diminish the damage associated with an early life event by modulating IL1B expression and reducing salivary cortisol levels in piglets undergoing weaning stress. Further transcriptomic and metabolomic studies may improve our understanding of the molecular pathways that mediate this systemic immune-mediated response.
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Affiliation(s)
- Sharacely de Souza Farias
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Science, University of São Paulo, Pirassununga, São Paulo, Brazil
- *Correspondence: Sharacely de Souza Farias, ; Adroaldo José Zanella,
| | - Ana Carolina Dierings
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Science, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Vinicius Cardoso Mufalo
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Science, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Leandro Sabei
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Science, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Marisol Parada Sarmiento
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Science, University of São Paulo, Pirassununga, São Paulo, Brazil
- Faculty of Veterinary Medicine, University of Teramo, Teramo, Italy
| | - Arthur Nery da Silva
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Science, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Priscila Assis Ferraz
- Department of Animal Reproduction, School of Veterinary Medicine and Animal Science, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Guilherme Pugliesi
- Department of Animal Reproduction, School of Veterinary Medicine and Animal Science, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Claudio Vaz Di Mambro Ribeiro
- Department of Animal Science, School of Veterinary Medicine and Animal Science, Federal University of Bahia, Salvador, Brazil
| | - Chiara Albano de Araujo Oliveira
- Department of Preventive Veterinary Medicine and Animal Production, School of Veterinary Medicine and Animal Science, Federal University of Bahia, Salvador, Brazil
| | - Adroaldo José Zanella
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Science, University of São Paulo, Pirassununga, São Paulo, Brazil
- *Correspondence: Sharacely de Souza Farias, ; Adroaldo José Zanella,
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Khan RIN, Sahu AR, Malla WA, Praharaj MR, Hosamani N, Kumar S, Gupta S, Sharma S, Saxena A, Varshney A, Singh P, Verma V, Kumar P, Singh G, Pandey A, Saxena S, Gandham RK, Tiwari AK. Systems biology under heat stress in Indian cattle. Gene 2021; 805:145908. [PMID: 34411649 DOI: 10.1016/j.gene.2021.145908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 08/11/2021] [Accepted: 08/13/2021] [Indexed: 11/26/2022]
Abstract
Transcriptome profiling of Vrindavani and Tharparkar cattle (n = 5 each) revealed that more numbers of genes were dysregulated in Vrindavani than in Tharparkar. A contrast in gene expression was observed with 18.9 % of upregulated genes in Vrindavani downregulated in Tharparkar and 17.8% upregulated genes in Tharparkar downregulated in Vrindavani. Functional annotation of genes differentially expressed in Tharparkar and Vrindavani revealed that the systems biology in Tharparkar is moving towards counteracting the effects due to heat stress. Unlike Vrindavani, Tharparkar is not only endowed with higher expression of the scavengers (UBE2G1, UBE2S, and UBE2H) of misfolded proteins but also with protectors (VCP, Serp1, and CALR) of naïve unfolded proteins. Further, higher expression of the antioxidants in Tharparkar enables it to cope up with higher levels of free radicals generated as a result of heat stress. In this study, we found relevant genes dysregulated in Tharparkar in the direction that can counter heat stress.
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Affiliation(s)
- Raja Ishaq Nabi Khan
- Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Bareilly, India
| | - Amit Ranjan Sahu
- Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Bareilly, India
| | - Waseem Akram Malla
- Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Bareilly, India
| | - Manas Ranjan Praharaj
- Computational Biology and Genomics, National Institute of Animal Biotechnology, Hyderabad, India
| | - Neelima Hosamani
- Computational Biology and Genomics, National Institute of Animal Biotechnology, Hyderabad, India
| | - Shakti Kumar
- Computational Biology and Genomics, National Institute of Animal Biotechnology, Hyderabad, India
| | - Smita Gupta
- Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Bareilly, India
| | - Shweta Sharma
- Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Bareilly, India
| | - Archana Saxena
- Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Bareilly, India
| | - Anshul Varshney
- Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Bareilly, India
| | - Pragya Singh
- Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Bareilly, India
| | - Vinay Verma
- Division of Physiology and Climatology, Indian Veterinary Research Institute, Bareilly, India
| | - Puneet Kumar
- Division of Physiology and Climatology, Indian Veterinary Research Institute, Bareilly, India
| | - Gyanendra Singh
- Division of Physiology and Climatology, Indian Veterinary Research Institute, Bareilly, India
| | - Aruna Pandey
- Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Bareilly, India
| | - Shikha Saxena
- Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Bareilly, India
| | - Ravi Kumar Gandham
- Computational Biology and Genomics, National Institute of Animal Biotechnology, Hyderabad, India.
| | - Ashok Kumar Tiwari
- Division of Biological Standardization, Indian Veterinary Research Institute, Bareilly, India.
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Behdani E, Ghaderi-Zefrehei M, Rafeie F, Bakhtiarizadeh MR, Roshanfeker H, Fayazi J. RNA-Seq Bayesian Network Exploration of Immune System in Bovine. IRANIAN JOURNAL OF BIOTECHNOLOGY 2020; 17:e1748. [PMID: 32195281 PMCID: PMC7080973 DOI: 10.29252/ijb.1748] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Background: The stress is one of main factors effects on production system. Several factors (both genetic and environmental elements) regulate immune response to stress. Objectives: In order to determine the major immune system regulatory genes underlying stress responses, a learning Bayesian network approach for those regulatory
genes was applied to RNA-Seq data from a bovine leukocyte model system. Material and Methods: The transcriptome dataset GSE37447 was used from GEO and a Bayesian network on differentially expressed genes was learned to investigate the gene regulatory network. Results: Applying the method produced a strongly interconnected network with four genes (TERF2IP, PDCD10, DDX10 and CENPE) acting as nodes,
suggesting these genes may be important in the transcriptome regulation program of stress response. Of these genes TERF2IP has been
shown previously to regulate gene expression, act as a regulator of the nuclear factor-kappa B (NF-κB) signalling, and to activate
expression of NF-κB target genes; PDCD10 encodes a conserved protein associated with cell apoptosis; DDX10 encodes a DEAD box protein
and is believed to be associated with cellular growth and division; and CENPE involves unstable spindle microtubule capture at kinetochores.
Together these genes are involved in DNA damage of apoptosis, RNA splicing, DNA repairing, and regulating cell division in the bovine genome.
The topology of the learned Bayesian gene network indicated that the genes had a minimal interrelationship with each other.
This type of structure, using the publically available computational tool, was also observed on human orthologous genes of the differentially expressed genes. Conclusions: Overall, the results might be used in transcriptomic-assisted selection and design of new drug targets to treat stress-related problems in bovines.
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Affiliation(s)
- Elham Behdani
- Department of Animal Science, Faculty of Animal and Food Science, Khuzestan Agricultural Sciences and Natural Resources University, Mollasani, Khuzestan, Iran
| | | | - Farjad Rafeie
- Department of Agricultural Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran
| | | | - Hedayatollah Roshanfeker
- Department of Animal Science, Faculty of Animal and Food Science, Khuzestan Agricultural Sciences and Natural Resources University, Mollasani, Khuzestan, Iran
| | - Jamal Fayazi
- Department of Animal Science, Faculty of Animal and Food Science, Khuzestan Agricultural Sciences and Natural Resources University, Mollasani, Khuzestan, Iran
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9
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Earley B, Arguello A, O’Riordan E, Crosson P, Cappelleri A, McGee M. Antimicrobial drug usage from birth to 180 days of age in Irish dairy calves and in suckler beef calves. JOURNAL OF APPLIED ANIMAL RESEARCH 2019. [DOI: 10.1080/09712119.2019.1665525] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- B. Earley
- Animal and Bioscience Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Dunsany, Ireland
| | - A. Arguello
- Animal and Bioscience Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Dunsany, Ireland
| | - E. O’Riordan
- Animal and Bioscience Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Dunsany, Ireland
| | - P. Crosson
- Livestock Systems Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Dunsany, Ireland
| | - A. Cappelleri
- Animal and Bioscience Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Dunsany, Ireland
| | - M. McGee
- Livestock Systems Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Dunsany, Ireland
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10
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Zhang B, Wang C, Yang W, Zhang H, Meng Q, Shi B, Shan A. Transcriptome analysis of the effect of pyrroloquinoline quinone disodium (PQQ·Na 2) on reproductive performance in sows during gestation and lactation. J Anim Sci Biotechnol 2019; 10:62. [PMID: 31406573 PMCID: PMC6685232 DOI: 10.1186/s40104-019-0369-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 06/05/2019] [Indexed: 02/07/2023] Open
Abstract
Background Pyrroloquinoline quinone (PQQ), which is a water soluble, thermo-stable triglyceride-quinone, is widely distributed in nature and characterized as a mammalian vitamin-like redox cofactor. The objective of this study was to investigate the effects of pyrroloquinoline quinone disodium (PQQ·Na2) on reproductive performance in sows. Results Dietary supplementation with PQQ·Na2 significantly increased the total number of piglets born, the number of piglets born alive and the born alive litter weight. It also increased the antioxidant status in the placenta, plasma and milk. The concentration of NO was significantly increased in the plasma and placenta. RNA-seq analysis showed that 462 unigenes were differentially expressed between the control (Con) treatment and PQQ treatment groups. Among these unigenes, 199 were upregulated, while 263 unigenes were downregulated. The assigned functions of the unigenes covered a broad range of GO categories. Reproduction (27, 7.03%) and the reproduction process (27, 7.03%) were assigned to the biological process category. By matching DEGs to the KEGG database, we identified 29 pathways. Conclusions In conclusion, dietary supplementation with PQQ·Na2 in gestating and lactating sows had positive effects on their reproductive performance. Electronic supplementary material The online version of this article (10.1186/s40104-019-0369-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Boru Zhang
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, 150030 People's Republic of China
| | - Chenxi Wang
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, 150030 People's Republic of China
| | - Wei Yang
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, 150030 People's Republic of China
| | - Hongyun Zhang
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, 150030 People's Republic of China
| | - Qingwei Meng
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, 150030 People's Republic of China
| | - Baoming Shi
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, 150030 People's Republic of China
| | - Anshan Shan
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin, 150030 People's Republic of China
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11
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McDonnell RP, O' Doherty JV, Earley B, Clarke AM, Kenny DA. Effect of supplementation with n-3 polyunsaturated fatty acids and/or β-glucans on performance, feeding behaviour and immune status of Holstein Friesian bull calves during the pre- and post-weaning periods. J Anim Sci Biotechnol 2019; 10:7. [PMID: 30719285 PMCID: PMC6350401 DOI: 10.1186/s40104-019-0317-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 01/04/2019] [Indexed: 12/25/2022] Open
Abstract
Background Previous research in both calves and other species has suggested n-3 polyunsaturated fatty acids (PUFA) and β-glucans may have positive effects on immune function. This experiment measured performance, behaviour, metabolite and immunological responses to pre-weaning supplementation of dairy bull calves with n-3 PUFA in the form of fish oil and β-glucans derived from seaweed extract. 44 Holstein Friesian bull calves, aged 13.7 ± 2.5 d and weighing 48.0 ± 5.8 kg were artificially reared using an electronic feeding system. Each calf was offered 5 L (120 g/L) per day of milk replacer (MR) and assigned to one of four treatments included in the MR, (1) Control (CON); (2) 40 g n-3 PUFA per day (FO); (3) 1 g β-glucans per day (GL) and (4) 40 g n-3 PUFA per day & 1 g/d β-glucans (FOGL) in a 2 × 2 factorial design. Milk replacer and concentrate was offered from d 0–62 (pre-weaning), while concentrate provision continued for a further 31 d post-weaning period. Individual daily feed intake and feeding behaviour was recorded throughout, while bodyweight and blood analyte data were collected at regular intervals. Results Overall mean concentrate DMI from d 0–93 was 1.39, 1.27, 1.00 and 0.72 kg/d for CON, FO, GL and FOGL calves, respectively (SEM = 0.037; P < 0.0001). Calves supplemented with GL were significantly lighter (P < 0.0001) at both weaning (d 62) and turnout to pasture (d 93) than un-supplemented calves, with a similar effect (P < 0.0001) evident for calves receiving FO compared to un-supplemented contemporaries. Supplementation with GL reduced the number of unrewarded visits where milk was not consumed (P < 0.0001) while supplementation with FO increased mean drinking speed (P < 0.0001). Supplementation with GL resulted in greater concentrations of haptoglobin (P = 0.034), greater serum osmolality (P = 0.021) and lower lymphocyte levels (P = 0.027). In addition, cells from GL supplemented calves exhibited a lower response than un-supplemented contemporaries to both Phytohaemagglutinin A stimulated IFN-γ (P = 0.019) and Concanavalin A stimulated IFN-γ (P = 0.012) following in vitro challenges. Conclusions Pre-weaning supplementation of bull calves with either n-3 PUFA or β-glucan resulted in reduced voluntary feed intake of concentrate and consequently poorer pre-weaning calf performance. There was no evidence for any beneficial effect of either supplementation strategy on calves’ immune responses.
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Affiliation(s)
- Ruairi P McDonnell
- 1School of Agriculture, Food Science and Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland.,Present address: GippsDairy, 71 Korumburra-Warragul Road, Warragul, VIC 3820 Australia
| | - John V O' Doherty
- 1School of Agriculture, Food Science and Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - Bernadette Earley
- Teagasc Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre (AGRIC), Grange, Dunsany, Co. Meath, Ireland
| | - Anne Marie Clarke
- 1School of Agriculture, Food Science and Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - David A Kenny
- 1School of Agriculture, Food Science and Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland.,Teagasc Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre (AGRIC), Grange, Dunsany, Co. Meath, Ireland
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12
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Zhang Q, Li C, Niu X, Zhang Z, Li F, Li F. An intensive milk replacer feeding program benefits immune response and intestinal microbiota of lambs during weaning. BMC Vet Res 2018; 14:366. [PMID: 30477479 PMCID: PMC6258415 DOI: 10.1186/s12917-018-1691-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 11/09/2018] [Indexed: 12/31/2022] Open
Abstract
Background Pre-weaning milk replacer (MR) feeding program is a key factor affecting the health and welfare of lambs during their weaning. Weaning stress is well known as an inducement that negatively impacts the immune system of young ruminants, whose physiological and immune state is closely linked to the community of microbiota in their intestines. This study had two objectives: 1) To evaluate the innate immune response to weaning stress at both the physiological and molecular level; 2) To investigate changes to the jejunal chyme and mucosal adhesive microbiota between the control and high plane of MR groups. Results In this experiment, the plasma concentrations of cortisol, norepinephrine (NE) and tumor necrosis factor-α (TNFα) were higher in the C than the H group (P < 0.05), as was the expression of pro-inflammatory cytokines such as TNFα and CXCL8 (P < 0.05) in plasma. In jejunal tissue, the expression of TLR4 and TNFα were also higher in the C group (P < 0.01); histopathology showed the H group had lower lymphocyte infiltration. In the C group, however, major pathological changes were associated with extensive infiltration of lymphocytes, eosinophils, and neutrophils. Principal component analysis indicated the lamb immune response was influenced by weaning stress and modulated by the MR treatments. 16S-rRNA sequencing was used to evaluate jejunal mucosa and chyme bacterial diversity and composition. The C group’s chyme had a greater alpha index (ACE: P = 0.095; Chao1: P = 0.085) than H group. In jejunal mucosa, the relative abundance of Plesiomonas was 4-fold higher (P = 0.017) in the C than the H group. Conclusions This study’s results revealed that weaning stress induced alterations to the lambs’ immune system that lasted beyond the 21 d measured, and that a long-term inflammatory response effect was evidenced by changes in their hematological and expressed pro-inflammatory cytokines. Pre-weaning with a differing MR allowance resulted in complicated biological responses and compositional changes to the lambs’ jejunal microbiota. Clearly, an intensive MR feeding program induced a milder immunity response and lower relative abundance of pathogenic bacteria when compared with the traditional feeding program.
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Affiliation(s)
- Qian Zhang
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Chong Li
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China.,College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiaolin Niu
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Zhian Zhang
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Fadi Li
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China.
| | - Fei Li
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China.
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13
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Sanglard LP, Nascimento M, Moriel P, Sommer J, Ashwell M, Poore MH, Duarte MDS, Serão NVL. Impact of energy restriction during late gestation on the muscle and blood transcriptome of beef calves after preconditioning. BMC Genomics 2018; 19:702. [PMID: 30253751 PMCID: PMC6156876 DOI: 10.1186/s12864-018-5089-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 09/19/2018] [Indexed: 02/03/2023] Open
Abstract
Background Maternal nutrition has been highlighted as one of the main factors affecting intra-uterine environment. The increase in nutritional requirements by beef cows during late gestation can cause nutritional deficiency in the fetus and impact the fetal regulation of genes associated with myogenesis and immune response. Methods Forty days before the expected calving date, cows were assigned to one of two diets: 100% (control) or 70% (restricted group) of the daily energy requirement. Muscle samples were collected from 12 heifers and 12 steers, and blood samples were collected from 12 steers. The objective of this work was to identify and to assess the biological relevance of differentially expressed genes (DEG) in the skeletal muscle and blood of beef calves born from cows that experienced [or not] a 30% energy restriction during the last 40 days of gestation. Results A total of 160, 164, and 346 DEG (q-value< 0.05) were identified in the skeletal muscle for the effects of diet, sex, and diet-by-sex interaction, respectively. For blood, 452, 1392, and 155 DEG were identified for the effects of diet, time, and diet-by-time interaction, respectively. For skeletal muscle, results based on diet identified genes involved in muscle metabolism. In muscle, from the 10 most DEG down-regulated in the energy-restricted group (REST), we identified 5 genes associated with muscle metabolism and development: SLCO3A1, ATP6V0D1, SLC2A1, GPC4, and RASD2. In blood, among the 10 most DEG, we found genes related to response to stress up-regulated in the REST after weaning, such as SOD3 and INO80D, and to immune response down-regulated in the REST after vaccination, such as OASL, KLRF1, and LOC104968634. Conclusion In conclusion, maternal energy restriction during late gestation may limit the expression of genes in the muscle and increase expression in the blood of calves. In addition, enrichment analysis showed that a short-term maternal energy restriction during pregnancy affects the expression of genes related to energy metabolism and muscle contraction, and immunity and stress response in the blood. Therefore, alterations in the intra-uterine environment can modify prenatal development with lasting consequences to adult life. Electronic supplementary material The online version of this article (10.1186/s12864-018-5089-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Leticia P Sanglard
- Department of Animal Science, Iowa State University, Ames, 50011, USA.,Department of Animal Science, North Carolina State University, Raleigh, 27695, USA
| | - Moysés Nascimento
- Department of Animal Science, North Carolina State University, Raleigh, 27695, USA.,Department of Statistics, Universidade Federal de Viçosa, Viçosa, 36570-000, Brazil
| | - Philipe Moriel
- Range Cattle Research and Education Center, University of Florida, Ona, Florida, 33865, USA
| | - Jeffrey Sommer
- Department of Animal Science, North Carolina State University, Raleigh, 27695, USA
| | - Melissa Ashwell
- Department of Animal Science, North Carolina State University, Raleigh, 27695, USA
| | - Matthew H Poore
- Department of Animal Science, North Carolina State University, Raleigh, 27695, USA
| | - Márcio de S Duarte
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, 36570-000, Brazil.,Instituto Nacional de Ciência e Tecnologia - Ciência Animal, Viçosa, 36570-000, Brazil
| | - Nick V L Serão
- Department of Animal Science, Iowa State University, Ames, 50011, USA. .,Department of Animal Science, North Carolina State University, Raleigh, 27695, USA.
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14
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Correia CN, McLoughlin KE, Nalpas NC, Magee DA, Browne JA, Rue-Albrecht K, Gordon SV, MacHugh DE. RNA Sequencing (RNA-Seq) Reveals Extremely Low Levels of Reticulocyte-Derived Globin Gene Transcripts in Peripheral Blood From Horses ( Equus caballus) and Cattle ( Bos taurus). Front Genet 2018; 9:278. [PMID: 30154823 PMCID: PMC6102425 DOI: 10.3389/fgene.2018.00278] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 07/09/2018] [Indexed: 12/15/2022] Open
Abstract
RNA-seq has emerged as an important technology for measuring gene expression in peripheral blood samples collected from humans and other vertebrate species. In particular, transcriptomics analyses of whole blood can be used to study immunobiology and develop novel biomarkers of infectious disease. However, an obstacle to these methods in many mammalian species is the presence of reticulocyte-derived globin mRNAs in large quantities, which can complicate RNA-seq library sequencing and impede detection of other mRNA transcripts. A range of supplementary procedures for targeted depletion of globin transcripts have, therefore, been developed to alleviate this problem. Here, we use comparative analyses of RNA-seq data sets generated from human, porcine, equine, and bovine peripheral blood to systematically assess the impact of globin mRNA on routine transcriptome profiling of whole blood in cattle and horses. The results of these analyses demonstrate that total RNA isolated from equine and bovine peripheral blood contains very low levels of globin mRNA transcripts, thereby negating the need for globin depletion and greatly simplifying blood-based transcriptomic studies in these two domestic species.
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Affiliation(s)
- Carolina N Correia
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD College of Health and Agricultural Sciences University College Dublin, Dublin, Ireland
| | - Kirsten E McLoughlin
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD College of Health and Agricultural Sciences University College Dublin, Dublin, Ireland
| | - Nicolas C Nalpas
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD College of Health and Agricultural Sciences University College Dublin, Dublin, Ireland
| | - David A Magee
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD College of Health and Agricultural Sciences University College Dublin, Dublin, Ireland
| | - John A Browne
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD College of Health and Agricultural Sciences University College Dublin, Dublin, Ireland
| | - Kevin Rue-Albrecht
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD College of Health and Agricultural Sciences University College Dublin, Dublin, Ireland
| | - Stephen V Gordon
- UCD School of Veterinary Medicine, UCD College of Health and Agricultural Sciences University College Dublin, Dublin, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research University College Dublin, Dublin, Ireland
| | - David E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD College of Health and Agricultural Sciences University College Dublin, Dublin, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research University College Dublin, Dublin, Ireland
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15
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Behdani E, Bakhtiarizadeh MR. Construction of an integrated gene regulatory network link to stress-related immune system in cattle. Genetica 2017; 145:441-454. [PMID: 28825201 DOI: 10.1007/s10709-017-9980-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 08/14/2017] [Indexed: 01/01/2023]
Abstract
The immune system is an important biological system that is negatively impacted by stress. This study constructed an integrated regulatory network to enhance our understanding of the regulatory gene network used in the stress-related immune system. Module inference was used to construct modules of co-expressed genes with bovine leukocyte RNA-Seq data. Transcription factors (TFs) were then assigned to these modules using Lemon-Tree algorithms. In addition, the TFs assigned to each module were confirmed using the promoter analysis and protein-protein interactions data. Therefore, our integrated method identified three TFs which include one TF that is previously known to be involved in immune response (MYBL2) and two TFs (E2F8 and FOXS1) that had not been recognized previously and were identified for the first time in this study as novel regulatory candidates in immune response. This study provides valuable insights on the regulatory programs of genes involved in the stress-related immune system.
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Affiliation(s)
- Elham Behdani
- Department of Animal Sciences, College of Agriculture and Natural Resources, Ramin University, Khozestan, Iran
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16
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Pošćić N, Montanari T, D’Andrea M, Licastro D, Pilla F, Ajmone-Marsan P, Minuti A, Sgorlon S. Breed and adaptive response modulate bovine peripheral blood cells' transcriptome. J Anim Sci Biotechnol 2017; 8:11. [PMID: 28149510 PMCID: PMC5264304 DOI: 10.1186/s40104-017-0143-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 01/07/2017] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Adaptive response includes a variety of physiological modifications to face changes in external or internal conditions and adapt to a new situation. The acute phase proteins (APPs) are reactants synthesized against environmental stimuli like stress, infection, inflammation. METHODS To delineate the differences in molecular constituents of adaptive response to the environment we performed the whole-blood transcriptome analysis in Italian Holstein (IH) and Italian Simmental (IS) breeds. For this, 663 IH and IS cows from six commercial farms were clustered according to the blood level of APPs. Ten extreme individuals (five APP+ and APP- variants) from each farm were selected for the RNA-seq using the Illumina sequencing technology. Differentially expressed (DE) genes were analyzed using dynamic impact approach (DIA) and DAVID annotation clustering. Milk production data were statistically elaborated to assess the association of APP+ and APP- gene expression patterns with variations in milk parameters. RESULTS The overall de novo assembly of cDNA sequence data generated 13,665 genes expressed in bovine blood cells. Comparative genomic analysis revealed 1,152 DE genes in the comparison of all APP+ vs. all APP- variants; 531 and 217 DE genes specific for IH and IS comparison respectively. In all comparisons overexpressed genes were more represented than underexpressed ones. DAVID analysis revealed 369 DE genes across breeds, 173 and 73 DE genes in IH and IS comparison respectively. Among the most impacted pathways for both breeds were vitamin B6 metabolism, folate biosynthesis, nitrogen metabolism and linoleic acid metabolism. CONCLUSIONS Both DIA and DAVID approaches produced a high number of significantly impacted genes and pathways with a narrow connection to adaptive response in cows with high level of blood APPs. A similar variation in gene expression and impacted pathways between APP+ and APP- variants was found between two studied breeds. Such similarity was also confirmed by annotation clustering of the DE genes. However, IH breed showed higher and more differentiated impacts compared to IS breed and such particular features in the IH adaptive response could be explained by its higher metabolic activity. Variations of milk production data were significantly associated with APP+ and APP- gene expression patterns.
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Affiliation(s)
- Nataliya Pošćić
- Department of Agriculture, Food, Environment and Animal Science (DI4A), University of Udine, via delle Scienze 206, 33100 Udine, Italy
| | - Tommaso Montanari
- Department of Agriculture, Food, Environment and Animal Science (DI4A), University of Udine, via delle Scienze 206, 33100 Udine, Italy
| | - Mariasilvia D’Andrea
- Department of Agricultural, Environmental and Food Sciences, University of Molise, via F. De Sanctis snc, 86100 Campobasso, Italy
| | - Danilo Licastro
- CBM S.c.r.l, SS 14 – km 163.5 AREA Science Park, 34149 Basovizza, TS Italy
| | - Fabio Pilla
- Department of Agricultural, Environmental and Food Sciences, University of Molise, via F. De Sanctis snc, 86100 Campobasso, Italy
| | - Paolo Ajmone-Marsan
- Institute of Zootechnics, Catholic University of the Sacred Heart, via Emilia Parmense 84, 29133 Piacenza, Italy
| | - Andrea Minuti
- Institute of Zootechnics, Catholic University of the Sacred Heart, via Emilia Parmense 84, 29133 Piacenza, Italy
| | - Sandy Sgorlon
- Department of Agriculture, Food, Environment and Animal Science (DI4A), University of Udine, via delle Scienze 206, 33100 Udine, Italy
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17
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De Toni L, Guidolin D, De Filippis V, Tescari S, Strapazzon G, Santa Rocca M, Ferlin A, Plebani M, Foresta C. Osteocalcin and Sex Hormone Binding Globulin Compete on a Specific Binding Site of GPRC6A. Endocrinology 2016; 157:4473-4486. [PMID: 27673554 DOI: 10.1210/en.2016-1312] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The undercarboxylated form of osteocalcin (ucOC) regulates male fertility and energy metabolism, acting through the G protein-coupled receptor (GPRC)6A, thus forming a new pancreas-bone-testis axis. Recently, GPRC6A has also been suggested to mediate the nongenomic responses of free testosterone (T). However, these data did not consider the physiological scenario, where circulating T is mainly bound to sex hormone-binding globulin (SHBG) and only a small percentage circulates freely in the blood. Here, by the use of computational modelling, we document the existence of similar structural moieties between ucOC and SHBG that are predicted to bind to GPRC6A at docking analysis. This hypothesis of competition was assessed by binding experiments on human embryonic kidney-293 cells transfected with human GPRC6A gene. Unliganded SHBG specifically bound the membrane of human embryonic kidney-293 cells transfected with GPRC6A and was displaced by ucOC when coincubated at 100-fold molar excess. Furthermore, specific downstream Erk1/2 phosphorylation after stimulation of GPRC6A with ucOC was significantly blunted by 100-fold molar excess of unliganded SHBG. Intriguingly previous incubation with unliganded SHBG, followed by incubation with T, induced Erk1/2 phosphorylation in a dose-dependent manner. Neither binding nor stimulating activities were shown for SHBG saturated with T. Experiments on mutation constructs of GPRC6A strengthened the hypothesis of a common binding site of ucOC and SHBG. Given the role of GPRC6A on energy metabolism, these data agree with epidemiological association between SHBG levels and insulin sensitivity, suggest GPRC6A as a likely SHBG receptor, and add bases for the possible regulation of androgen activity in a nonsteroidal manner.
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Affiliation(s)
- Luca De Toni
- Department of Medicine (L.D.T., M.S.R., A.F., C.F.), Unit of Andrology and Reproductive Medicine, University of Padova and Department of Laboratory Medicine (M.P.), University-Hospital, 35128 Padova, Italy; Department of Molecular Medicine (D.G.), University of Padova Medical School, 35121 Padova, Italy; Laboratory of Protein Chemistry (V.D.F., S.T.), Department of Pharmaceutical and Pharmacological Sciences, School of Medicine, University of Padova, 35131 Padova, Italy; and European Academy of Bozen/Bolzano (G.S.), Institute of Mountain Emergency Medicine, 39100 Bolzano, Italy
| | - Diego Guidolin
- Department of Medicine (L.D.T., M.S.R., A.F., C.F.), Unit of Andrology and Reproductive Medicine, University of Padova and Department of Laboratory Medicine (M.P.), University-Hospital, 35128 Padova, Italy; Department of Molecular Medicine (D.G.), University of Padova Medical School, 35121 Padova, Italy; Laboratory of Protein Chemistry (V.D.F., S.T.), Department of Pharmaceutical and Pharmacological Sciences, School of Medicine, University of Padova, 35131 Padova, Italy; and European Academy of Bozen/Bolzano (G.S.), Institute of Mountain Emergency Medicine, 39100 Bolzano, Italy
| | - Vincenzo De Filippis
- Department of Medicine (L.D.T., M.S.R., A.F., C.F.), Unit of Andrology and Reproductive Medicine, University of Padova and Department of Laboratory Medicine (M.P.), University-Hospital, 35128 Padova, Italy; Department of Molecular Medicine (D.G.), University of Padova Medical School, 35121 Padova, Italy; Laboratory of Protein Chemistry (V.D.F., S.T.), Department of Pharmaceutical and Pharmacological Sciences, School of Medicine, University of Padova, 35131 Padova, Italy; and European Academy of Bozen/Bolzano (G.S.), Institute of Mountain Emergency Medicine, 39100 Bolzano, Italy
| | - Simone Tescari
- Department of Medicine (L.D.T., M.S.R., A.F., C.F.), Unit of Andrology and Reproductive Medicine, University of Padova and Department of Laboratory Medicine (M.P.), University-Hospital, 35128 Padova, Italy; Department of Molecular Medicine (D.G.), University of Padova Medical School, 35121 Padova, Italy; Laboratory of Protein Chemistry (V.D.F., S.T.), Department of Pharmaceutical and Pharmacological Sciences, School of Medicine, University of Padova, 35131 Padova, Italy; and European Academy of Bozen/Bolzano (G.S.), Institute of Mountain Emergency Medicine, 39100 Bolzano, Italy
| | - Giacomo Strapazzon
- Department of Medicine (L.D.T., M.S.R., A.F., C.F.), Unit of Andrology and Reproductive Medicine, University of Padova and Department of Laboratory Medicine (M.P.), University-Hospital, 35128 Padova, Italy; Department of Molecular Medicine (D.G.), University of Padova Medical School, 35121 Padova, Italy; Laboratory of Protein Chemistry (V.D.F., S.T.), Department of Pharmaceutical and Pharmacological Sciences, School of Medicine, University of Padova, 35131 Padova, Italy; and European Academy of Bozen/Bolzano (G.S.), Institute of Mountain Emergency Medicine, 39100 Bolzano, Italy
| | - Maria Santa Rocca
- Department of Medicine (L.D.T., M.S.R., A.F., C.F.), Unit of Andrology and Reproductive Medicine, University of Padova and Department of Laboratory Medicine (M.P.), University-Hospital, 35128 Padova, Italy; Department of Molecular Medicine (D.G.), University of Padova Medical School, 35121 Padova, Italy; Laboratory of Protein Chemistry (V.D.F., S.T.), Department of Pharmaceutical and Pharmacological Sciences, School of Medicine, University of Padova, 35131 Padova, Italy; and European Academy of Bozen/Bolzano (G.S.), Institute of Mountain Emergency Medicine, 39100 Bolzano, Italy
| | - Alberto Ferlin
- Department of Medicine (L.D.T., M.S.R., A.F., C.F.), Unit of Andrology and Reproductive Medicine, University of Padova and Department of Laboratory Medicine (M.P.), University-Hospital, 35128 Padova, Italy; Department of Molecular Medicine (D.G.), University of Padova Medical School, 35121 Padova, Italy; Laboratory of Protein Chemistry (V.D.F., S.T.), Department of Pharmaceutical and Pharmacological Sciences, School of Medicine, University of Padova, 35131 Padova, Italy; and European Academy of Bozen/Bolzano (G.S.), Institute of Mountain Emergency Medicine, 39100 Bolzano, Italy
| | - Mario Plebani
- Department of Medicine (L.D.T., M.S.R., A.F., C.F.), Unit of Andrology and Reproductive Medicine, University of Padova and Department of Laboratory Medicine (M.P.), University-Hospital, 35128 Padova, Italy; Department of Molecular Medicine (D.G.), University of Padova Medical School, 35121 Padova, Italy; Laboratory of Protein Chemistry (V.D.F., S.T.), Department of Pharmaceutical and Pharmacological Sciences, School of Medicine, University of Padova, 35131 Padova, Italy; and European Academy of Bozen/Bolzano (G.S.), Institute of Mountain Emergency Medicine, 39100 Bolzano, Italy
| | - Carlo Foresta
- Department of Medicine (L.D.T., M.S.R., A.F., C.F.), Unit of Andrology and Reproductive Medicine, University of Padova and Department of Laboratory Medicine (M.P.), University-Hospital, 35128 Padova, Italy; Department of Molecular Medicine (D.G.), University of Padova Medical School, 35121 Padova, Italy; Laboratory of Protein Chemistry (V.D.F., S.T.), Department of Pharmaceutical and Pharmacological Sciences, School of Medicine, University of Padova, 35131 Padova, Italy; and European Academy of Bozen/Bolzano (G.S.), Institute of Mountain Emergency Medicine, 39100 Bolzano, Italy
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18
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Friedrich J, Brand B, Graunke KL, Langbein J, Schwerin M, Ponsuksili S. Adrenocortical Expression Profiling of Cattle with Distinct Juvenile Temperament Types. Behav Genet 2016; 47:102-113. [PMID: 27586633 DOI: 10.1007/s10519-016-9816-0] [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: 12/18/2015] [Accepted: 08/27/2016] [Indexed: 01/13/2023]
Abstract
Temperament affects ease of handling, animal welfare, and economically important production traits in cattle. The use of gene expression profiles as molecular traits provides a novel means of gaining insight into behavioural genetics. In this study, differences in adrenocortical expression profiles between 60 F2 cows (Charolais × German Holstein) of distinct temperament types were analysed. The cows were assessed in a novel-human test at an age of 90 days. Most of the adrenal cortex transcripts which were differentially expressed (FDR <0.05) were found between temperament types of 'fearful/neophobic-alert' and all other temperament types. These transcripts belong to several biological functions like NRF2-mediated oxidative stress response, Glucocorticoid Receptor Signalling and Complement System. Overall, the present study provides new insight into transcriptional differences in the adrenal cortex between cows of distinct temperament types. Genetic regulations of such molecular traits facilitate uncovering positional and functional gene candidates for temperament type in cattle.
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Affiliation(s)
- Juliane Friedrich
- Institute for Farm Animal Research and Technology, University of Rostock, Rostock, Germany
| | - Bodo Brand
- Institute for Genome Biology, Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Katharina Luise Graunke
- Institute for Behavioural Physiology, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany
| | - Jan Langbein
- Institute for Behavioural Physiology, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany
| | - Manfred Schwerin
- Institute for Farm Animal Research and Technology, University of Rostock, Rostock, Germany.,Institute for Genome Biology, Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Siriluck Ponsuksili
- Institute for Genome Biology, Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany.
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Sun X, Li M, Sun Y, Cai H, Li R, Wei X, Lan X, Huang Y, Lei C, Chen H. The developmental transcriptome landscape of bovine skeletal muscle defined by Ribo-Zero ribonucleic acid sequencing. J Anim Sci 2016; 93:5648-58. [PMID: 26641174 DOI: 10.2527/jas.2015-9562] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Ribonucleic acid sequencing (RNA-Seq) libraries are normally prepared with oligo(dT) selection of poly(A)+ mRNA, but it depends on intact total RNA samples. Recent studies have described Ribo-Zero technology, a novel method that can capture both poly(A)+ and poly(A)- transcripts from intact or fragmented RNA samples. We report here the first application of Ribo-Zero RNA-Seq for the analysis of the bovine embryonic, neonatal, and adult skeletal muscle whole transcriptome at an unprecedented depth. Overall, 19,893 genes were found to be expressed, with a high correlation of expression levels between the calf and the adult. Hundreds of genes were found to be highly expressed in the embryo and decreased at least 10-fold after birth, indicating their potential roles in embryonic muscle development. In addition, we present for the first time the analysis of global transcript isoform discovery in bovine skeletal muscle and identified 36,694 transcript isoforms. Transcriptomic data were also analyzed to unravel sequence variations; 185,036 putative SNP and 12,428 putative short insertions-deletions (InDel) were detected. Specifically, many stop-gain, stop-loss, and frameshift mutations were identified that probably change the relative protein production and sequentially affect the gene function. Notably, the numbers of stage-specific transcripts, alternative splicing events, SNP, and InDel were greater in the embryo than in the calf and the adult, suggesting that gene expression is most active in the embryo. The resulting view of the transcriptome at a single-base resolution greatly enhances the comprehensive transcript catalog and uncovers the global trends in gene expression during bovine skeletal muscle development.
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Peffers MJ, Goljanek-Whysall K, Collins J, Fang Y, Rushton M, Loughlin J, Proctor C, Clegg PD. Decoding the Regulatory Landscape of Ageing in Musculoskeletal Engineered Tissues Using Genome-Wide DNA Methylation and RNASeq. PLoS One 2016; 11:e0160517. [PMID: 27533049 PMCID: PMC4988628 DOI: 10.1371/journal.pone.0160517] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 07/20/2016] [Indexed: 12/11/2022] Open
Abstract
Mesenchymal stem cells (MSC) are capable of multipotent differentiation into connective tissues and as such are an attractive source for autologous cell-based regenerative medicine and tissue engineering. Epigenetic mechanisms, like DNA methylation, contribute to the changes in gene expression in ageing. However there was a lack of sufficient knowledge of the role that differential methylation plays during chondrogenic, osteogenic and tenogenic differentiation from ageing MSCs. This study undertook genome level determination of the effects of DNA methylation on expression in engineered tissues from chronologically aged MSCs. We compiled unique DNA methylation signatures from chondrogenic, osteogenic, and tenogenic engineered tissues derived from young; n = 4 (21.8 years ± 2.4 SD) and old; n = 4 (65.5 years±8.3SD) human MSCs donors using the Illumina HumanMethylation 450 Beadchip arrays and compared these to gene expression by RNA sequencing. Unique and common signatures of global DNA methylation were identified. There were 201, 67 and 32 chondrogenic, osteogenic and tenogenic age-related DE protein-coding genes respectively. Findings inferred the nature of the transcript networks was predominantly for 'cell death and survival', 'cell morphology', and 'cell growth and proliferation'. Further studies are required to validate if this gene expression effect translates to cell events. Alternative splicing (AS) was dysregulated in ageing with 119, 21 and 9 differential splicing events identified in chondrogenic, osteogenic and tenogenic respectively, and enrichment in genes associated principally with metabolic processes. Gene ontology analysis of differentially methylated loci indicated age-related enrichment for all engineered tissue types in 'skeletal system morphogenesis', 'regulation of cell proliferation' and 'regulation of transcription' suggesting that dynamic epigenetic modifications may occur in genes associated with shared and distinct pathways dependent upon engineered tissue type. An altered phenotype in engineered tissues was observed with ageing at numerous levels. These changes represent novel insights into the ageing process, with implications for stem cell therapies in older patients. In addition we have identified a number of tissue-dependant pathways, which warrant further studies.
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Affiliation(s)
- Mandy Jayne Peffers
- Institute of Ageing and Chronic Disease, University of Liverpool, Leahurst, Chester High Road, Neston, Wirral, UK, CH64 7TE
| | - Katarzyna Goljanek-Whysall
- Institute of Ageing and Chronic Disease, University of Liverpool, Leahurst, Chester High Road, Neston, Wirral, UK, CH64 7TE
| | - John Collins
- Thurston Arthritis Research Centre, School Of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA, 27599
| | - Yongxiang Fang
- Centre for Genomic Research, Institute of Integrative Biology, Biosciences Building, Crown Street, University of Liverpool, Liverpool, UK, L69 7ZB
| | - Michael Rushton
- Musculoskeletal Research Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK, NE2 4HH
| | - John Loughlin
- Musculoskeletal Research Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK, NE2 4HH
| | - Carole Proctor
- Musculoskeletal Research Group, Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK, NE2 4HH
- Newcastle University Institute for Ageing, Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne, UK, NE4 5PL
| | - Peter David Clegg
- Institute of Ageing and Chronic Disease, University of Liverpool, Leahurst, Chester High Road, Neston, Wirral, UK, CH64 7TE
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Characterisation of the Whole Blood mRNA Transcriptome in Holstein-Friesian and Jersey Calves in Response to Gradual Weaning. PLoS One 2016; 11:e0159707. [PMID: 27479136 PMCID: PMC4968839 DOI: 10.1371/journal.pone.0159707] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 07/07/2016] [Indexed: 12/11/2022] Open
Abstract
Weaning of dairy calves is an early life husbandry management practice which involves the changeover from a liquid to a solid feed based diet. The objectives of the study were to use RNA-seq technology to examine the effect of (i) breed and (ii) gradual weaning, on the whole blood mRNA transcriptome of artificially reared Holstein-Friesian and Jersey calves. The calves were gradually weaned over 14 days (day (d) -13 to d 0) and mRNA transcription was examined one day before gradual weaning was initiated (d -14), one day after weaning (d 1), and 8 days after weaning (d 8). On d -14, 550 genes were differentially expressed between Holstein-Friesian and Jersey calves, while there were 490 differentially expressed genes (DEG) identified on d 1, and 411 DEG detected eight days after weaning (P < 0.05; FDR < 0.1). No genes were differentially expressed within breed, in response to gradual weaning (P > 0.05). The pathways, gene ontology terms, and biological functions consistently over-represented among the DEG between Holstein-Friesian and Jersey were associated with the immune response and immune cell signalling, specifically chemotaxis. Decreased transcription of several cytokines, chemokines, immunoglobulin-like genes, phagocytosis-promoting receptors and g-protein coupled receptors suggests decreased monocyte, natural killer cell, and T lymphocyte, chemotaxis and activation in Jersey compared to Holstein-Friesian calves. Knowledge of breed-specific immune responses could facilitate health management practices better tailored towards specific disease sensitivities of Holstein-Friesian and Jersey calves. Gradual weaning did not compromise the welfare of artificially-reared dairy calves, evidenced by the lack of alterations in the expression of any genes in response to gradual weaning.
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Yi H, Jiang D, Zhang L, Xiong H, Han F, Wang Y. Developmental expression of STATs, nuclear factor-κB and inflammatory genes in the jejunum of piglets during weaning. Int Immunopharmacol 2016; 36:199-204. [PMID: 27160867 DOI: 10.1016/j.intimp.2016.04.032] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Revised: 04/15/2016] [Accepted: 04/20/2016] [Indexed: 01/05/2023]
Abstract
The signal transducer and activator of transcription (STAT) proteins play essential roles in apoptosis, proliferation and survival. However, the role of STATs in intestinal inflammation during weaning is unclear. This study aimed to investigate developmental expression of STATs, nuclear factor-κB (NF-κB) and inflammatory genes in the jejunum of piglets during weaning. Thirty-two piglets were weaned at 21d and sacrificed at 0, 1, 7, or 14d (n=8) after weaning. Villus height and the villus height/crypt depth ratio were decreased, whereas crypt depth was increased in the jejunum at 7 and 14d after weaning. In addition, the mRNA levels of interferon-γ (IFN-γ), inducible nitric oxide synthase (iNOS), IL-6, IL-8, IL-12 and IL-22 were increased in the jejunum at 7 and 14d after weaning, whereas transforming growth factor-β (TGF-β), suppressor of cytokine signaling 3 (SCOS3) and arginase-1 was decreased. Neutrophil infiltration was increased in the mucosa of the jejunum after weaning. Moreover, phosphorylation of IκB-α, NF-κB, AKT and STAT-3 was increased. However, the phosphorylation of STAT-1 (at 7 and 14d) and STAT-6 (at 1 and 7d) was suppressed in the jejunum after weaning. Treatment of porcine jejunal epithelial (IPEC-J2) cells with the STAT inhibitors fludarabine, niclosamide and teriflunomide, which inhibit the phosphorylation of STAT-1, STAT-3 and STAT-6, respectively, weakened the defense capacity of these cells against bacterial infection. In conclusion, weaning caused severe inflammation associated with activation of the NF-κB and STAT-3 pathways and suppression of STAT-1 and STAT-6 in the jejunum of piglets.
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Affiliation(s)
- Hongbo Yi
- Laboratory of Animal Nutrition and Feed Science, Department of Animal Science, Zhejiang University, Hangzhou, Zhejiang Province 310058, China
| | - Denghu Jiang
- Laboratory of Animal Nutrition and Feed Science, Department of Animal Science, Zhejiang University, Hangzhou, Zhejiang Province 310058, China
| | - Lin Zhang
- Laboratory of Animal Nutrition and Feed Science, Department of Animal Science, Zhejiang University, Hangzhou, Zhejiang Province 310058, China
| | - Haitao Xiong
- Laboratory of Animal Nutrition and Feed Science, Department of Animal Science, Zhejiang University, Hangzhou, Zhejiang Province 310058, China
| | - Feifei Han
- Laboratory of Animal Nutrition and Feed Science, Department of Animal Science, Zhejiang University, Hangzhou, Zhejiang Province 310058, China
| | - Yizhen Wang
- Laboratory of Animal Nutrition and Feed Science, Department of Animal Science, Zhejiang University, Hangzhou, Zhejiang Province 310058, China.
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Feng YZ, Wang L, Fu JM, Wuyun TN, Du HY, Tan XF, Zou F, Li FD. Transcriptome sequencing discovers genes related to fatty acid biosynthesis in the seeds of Eucommia ulmoides. Genes Genomics 2016. [DOI: 10.1007/s13258-015-0362-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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McGettigan PA, Browne JA, Carrington SD, Crowe MA, Fair T, Forde N, Loftus BJ, Lohan A, Lonergan P, Pluta K, Mamo S, Murphy A, Roche J, Walsh SW, Creevey CJ, Earley B, Keady S, Kenny DA, Matthews D, McCabe M, Morris D, O'Loughlin A, Waters S, Diskin MG, Evans ACO. Fertility and genomics: comparison of gene expression in contrasting reproductive tissues of female cattle. Reprod Fertil Dev 2016; 28:11-24. [DOI: 10.1071/rd15354] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
To compare gene expression among bovine tissues, large bovine RNA-seq datasets were used, comprising 280 samples from 10 different bovine tissues (uterine endometrium, granulosa cells, theca cells, cervix, embryos, leucocytes, liver, hypothalamus, pituitary, muscle) and generating 260 Gbases of data. Twin approaches were used: an information–theoretic analysis of the existing annotated transcriptome to identify the most tissue-specific genes and a de-novo transcriptome annotation to evaluate general features of the transcription landscape. Expression was detected for 97% of the Ensembl transcriptome with at least one read in one sample and between 28% and 66% at a level of 10 tags per million (TPM) or greater in individual tissues. Over 95% of genes exhibited some level of tissue-specific gene expression. This was mostly due to different levels of expression in different tissues rather than exclusive expression in a single tissue. Less than 1% of annotated genes exhibited a highly restricted tissue-specific expression profile and approximately 2% exhibited classic housekeeping profiles. In conclusion, it is the combined effects of the variable expression of large numbers of genes (73%–93% of the genome) and the specific expression of a small number of genes (<1% of the transcriptome) that contribute to determining the outcome of the function of individual tissues.
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Bowyer JF, Tranter KM, Hanig JP, Crabtree NM, Schleimer RP, George NI. Evaluating the Stability of RNA-Seq Transcriptome Profiles and Drug-Induced Immune-Related Expression Changes in Whole Blood. PLoS One 2015; 10:e0133315. [PMID: 26177368 PMCID: PMC4503719 DOI: 10.1371/journal.pone.0133315] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 06/24/2015] [Indexed: 12/01/2022] Open
Abstract
Methods were developed to evaluate the stability of rat whole blood expression obtained from RNA sequencing (RNA-seq) and assess changes in whole blood transcriptome profiles in experiments replicated over time. Expression was measured in globin-depleted RNA extracted from the whole blood of Sprague-Dawley rats, given either saline (control) or neurotoxic doses of amphetamine (AMPH). The experiment was repeated four times (paired control and AMPH groups) over a 2-year span. The transcriptome of the control and AMPH-treated groups was evaluated on: 1) transcript levels for ribosomal protein subunits; 2) relative expression of immune-related genes; 3) stability of the control transcriptome over 2 years; and 4) stability of the effects of AMPH on immune-related genes over 2 years. All, except one, of the 70 genes that encode the 80s ribosome had levels that ranked in the top 5% of all mean expression levels. Deviations in sequencing performance led to significant changes in the ribosomal transcripts. The overall expression profile of immune-related genes and genes specific to monocytes, T-cells or B-cells were well represented and consistent within treatment groups. There were no differences between the levels of ribosomal transcripts in time-matched control and AMPH groups but significant differences in the expression of immune-related genes between control and AMPH groups. AMPH significantly increased expression of some genes related to monocytes but down-regulated those specific to T-cells. These changes were partially due to changes in the two types of leukocytes present in blood, which indicate an activation of the innate immune system by AMPH. Thus, the stability of RNA-seq whole blood transcriptome can be verified by assessing ribosomal protein subunits and immune-related gene expression. Such stability enables the pooling of samples from replicate experiments to carry out differential expression analysis with acceptable power.
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Affiliation(s)
- John F. Bowyer
- Division of Neurotoxicology, National Center for Toxicological Research, United States Food and Drug Administration, Jefferson, Arkansas, United States of America
- * E-mail:
| | - Karen M. Tranter
- Division of Neurotoxicology, National Center for Toxicological Research, United States Food and Drug Administration, Jefferson, Arkansas, United States of America
| | - Joseph P. Hanig
- Center for Drug Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Nathaniel M. Crabtree
- Division of Neurotoxicology, National Center for Toxicological Research, United States Food and Drug Administration, Jefferson, Arkansas, United States of America
| | - Robert P. Schleimer
- Division of Allergy and Immunology, Northwestern Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Nysia I. George
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, United States Food and Drug Administration, Jefferson, Arkansas, United States of America
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Abdelfattah EM, Karousa MM, Schutz MM, Lay DC, Marchant JN, Eicher SD. Acute phase cytokines, TAC1, and toll-like receptor4 mRNA expression and health associated with group size in veal calves. Vet Immunol Immunopathol 2015; 164:118-26. [PMID: 25746346 DOI: 10.1016/j.vetimm.2015.01.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 01/27/2015] [Accepted: 01/30/2015] [Indexed: 12/16/2022]
Abstract
Chronic stressors are a major health and well-being issue in animals. Immune status of animals under chronic stress is compromised, thus reducing disease resistance and compromising well-being of the animal. The objective of this study was to determine the influence of group size of veal calves on immune status and leukocyte mRNA expression of acute phase cytokines, toll-like receptor 4 (TLR4) and tachykinin 1 (TAC1) over a five-month finishing period. Holstein bull calves (n=168), 44±3 days of age were assigned to one of three treatments; 2, 4, or 8 calves/pen (pen space allowance of 1.82m(2)/calf). Jugular blood samples were collected at the day of grouping and then monthly for 4 months. The differential leukocyte counts were determined and mRNA was extracted from the leukocytes. Reverse transcription-qPCR was used to measure the gene expression of interleukin-1 (IL-1β), IL-1 receptor antagonist (IL-1Ra), tumor necrosis factor (TNF-α), TLR4, and TAC1 in leukocytes. Health was evaluated before grouping and monthly for 4 months. On the 1st month after grouping, veal calves that were housed in groups of 8 have greater expression of IL-1β mRNA than calves housed in groups of 4 or 2 (treatment×month, P=0.04). Also at 1 month, groups of 8 had greater TAC1 expression (P<0.05) than calves housed in groups of 4 or 2. However, the expression of IL-1Ra, TNF-α, and TLR4 were not influenced by group size. In the first month of the trial, calves in groups of 8 coughed more (P<0.05) than calves in groups of 2 and coughed more than calves in groups of 4 and 2 during the 2nd month (treatment×month, P=0.03). Calves housed in groups of 8 tended to have greater neutrophil percentage (P=0.09), neutrophil to lymphocyte ratio (P=0.06), and had lower lymphocyte percentage (P=0.06) than those housed in groups of 4 or 2. In conclusion, the number of veal calves in a group, given the same space during the finishing period did not alter IL-1Ra, TNF-α, and TLR4 mRNA expression. However, housing of calves in groups of 8 was associated with greater expression of IL-1β and TAC1 mRNA in peripheral blood leukocytes, and coughing during the first 2 months after grouping. Therefore, housing of veal calves in larger groups may lead to greater susceptibility to respiratory disease and stress.
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Affiliation(s)
- E M Abdelfattah
- Department of Animal Hygiene, Behavior and Management, Faculty of Veterinary Medicine, Benha University, Qalyubia, Moshtohor 13736, Egypt
| | - M M Karousa
- Department of Animal Hygiene, Behavior and Management, Faculty of Veterinary Medicine, Benha University, Qalyubia, Moshtohor 13736, Egypt
| | - M M Schutz
- Purdue University, Department of Animal Sciences, West Lafayette, IN 47907, USA
| | - D C Lay
- USDA-ARS, Livestock Behavior Research Unit, West Lafayette, IN 47907, USA
| | - J N Marchant
- USDA-ARS, Livestock Behavior Research Unit, West Lafayette, IN 47907, USA
| | - S D Eicher
- USDA-ARS, Livestock Behavior Research Unit, West Lafayette, IN 47907, USA.
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The effects of short term dietary restriction on haematological responses and leukocyte gene expression of anovulatory and ovulatory beef heifers. Res Vet Sci 2015; 98:145-53. [DOI: 10.1016/j.rvsc.2014.11.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 10/14/2014] [Accepted: 11/10/2014] [Indexed: 11/20/2022]
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Biomarker responses to weaning stress in beef calves. Res Vet Sci 2014; 97:458-63. [DOI: 10.1016/j.rvsc.2014.06.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 05/29/2014] [Accepted: 06/08/2014] [Indexed: 12/11/2022]
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Shin H, Shannon CP, Fishbane N, Ruan J, Zhou M, Balshaw R, Wilson-McManus JE, Ng RT, McManus BM, Tebbutt SJ. Variation in RNA-Seq transcriptome profiles of peripheral whole blood from healthy individuals with and without globin depletion. PLoS One 2014; 9:e91041. [PMID: 24608128 PMCID: PMC3946641 DOI: 10.1371/journal.pone.0091041] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 02/08/2014] [Indexed: 12/21/2022] Open
Abstract
Background The molecular profile of circulating blood can reflect physiological and pathological events occurring in other tissues and organs of the body and delivers a comprehensive view of the status of the immune system. Blood has been useful in studying the pathobiology of many diseases. It is accessible and easily collected making it ideally suited to the development of diagnostic biomarker tests. The blood transcriptome has a high complement of globin RNA that could potentially saturate next-generation sequencing platforms, masking lower abundance transcripts. Methods to deplete globin mRNA are available, but their effect has not been comprehensively studied in peripheral whole blood RNA-Seq data. In this study we aimed to assess technical variability associated with globin depletion in addition to assessing general technical variability in RNA-Seq from whole blood derived samples. Results We compared technical and biological replicates having undergone globin depletion or not and found that the experimental globin depletion protocol employed removed approximately 80% of globin transcripts, improved the correlation of technical replicates, allowed for reliable detection of thousands of additional transcripts and generally increased transcript abundance measures. Differential expression analysis revealed thousands of genes significantly up-regulated as a result of globin depletion. In addition, globin depletion resulted in the down-regulation of genes involved in both iron and zinc metal ion bonding. Conclusions Globin depletion appears to meaningfully improve the quality of peripheral whole blood RNA-Seq data, and may improve our ability to detect true biological variation. Some concerns remain, however. Key amongst them the significant reduction in RNA yields following globin depletion. More generally, our investigation of technical and biological variation with and without globin depletion finds that high-throughput sequencing by RNA-Seq is highly reproducible within a large dynamic range of detection and provides an accurate estimation of RNA concentration in peripheral whole blood. High-throughput sequencing is thus a promising technology for whole blood transcriptomics and biomarker discovery.
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Affiliation(s)
- Heesun Shin
- NCE CECR PROOF Centre of Excellence, Vancouver, British Columbia, Canada
- UBC Department of Medicine (Division of Respiratory Medicine), University of British Columbia, Vancouver, British Columbia, Canada
- UBC James Hogg Research Centre & Institute for HEART + LUNG Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Casey P. Shannon
- NCE CECR PROOF Centre of Excellence, Vancouver, British Columbia, Canada
| | - Nick Fishbane
- NCE CECR PROOF Centre of Excellence, Vancouver, British Columbia, Canada
- UBC Department of Statistics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jian Ruan
- NCE CECR PROOF Centre of Excellence, Vancouver, British Columbia, Canada
- UBC James Hogg Research Centre & Institute for HEART + LUNG Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Mi Zhou
- NCE CECR PROOF Centre of Excellence, Vancouver, British Columbia, Canada
| | - Robert Balshaw
- NCE CECR PROOF Centre of Excellence, Vancouver, British Columbia, Canada
- UBC Department of Statistics, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Raymond T. Ng
- NCE CECR PROOF Centre of Excellence, Vancouver, British Columbia, Canada
- UBC Department of Computer Science, University of British Columbia, Vancouver, British Columbia, Canada
| | - Bruce M. McManus
- NCE CECR PROOF Centre of Excellence, Vancouver, British Columbia, Canada
- UBC Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- UBC James Hogg Research Centre & Institute for HEART + LUNG Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Scott J. Tebbutt
- NCE CECR PROOF Centre of Excellence, Vancouver, British Columbia, Canada
- UBC Department of Medicine (Division of Respiratory Medicine), University of British Columbia, Vancouver, British Columbia, Canada
- UBC James Hogg Research Centre & Institute for HEART + LUNG Health, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
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Waters SM, Coyne GS, Kenny DA, Morris DG. Effect of dietary n-3 polyunsaturated fatty acids on transcription factor regulation in the bovine endometrium. Mol Biol Rep 2014; 41:2745-55. [PMID: 24449365 DOI: 10.1007/s11033-014-3129-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Accepted: 01/11/2014] [Indexed: 11/25/2022]
Abstract
Dietary n-3 polyunsaturated fatty acid (n-3 PUFA) supplementation is postulated to have positive effects on fertility. The impact of dietary n-3 PUFA supplementation on physiological and biochemical processes involved in reproduction is likely to be associated with significant alterations in gene expression in key reproductive tissues which is in turn regulated by transcription factors. Beef heifers were supplemented with a rumen protected source of either a saturated fatty acid or high n-3 PUFA diet per animal per day for 45 days and uterine endometrial tissue was harvested post slaughter. A microarray analysis was conducted and bioinformatic tools were employed to evaluate the effect of n-3 PUFA supplementation on gene expression in the bovine endometrium. Clustering of microarray gene expression data was performed to identify co-expressed genes. Functional annotation of each cluster of genes was carried out using Ingenuity Pathway Analysis. Furthermore, oPOSSUM was employed to identify transcription factors involved in gene expression changes due to supplementary PUFA. Gene functions which showed a significant response to n-3 PUFA supplementation included tissue development, immune function and reproductive function. Numerous transcription factors such as FOXD1, FOXD3, NFKB1, ESR1, PGR, FOXA2, NKX3-1 and PPARα were identified as potential regulators of gene expression in the endometrium of cattle supplemented with n-3 PUFA. This study demonstrates the complex nature of the alterations in the transcriptional regulation process in the uterine endometrium of cattle following dietary supplementation which may positively influence the uterine environment.
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Affiliation(s)
- Sinéad M Waters
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, Co. Meath, Ireland,
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Weikard R, Hadlich F, Kuehn C. Identification of novel transcripts and noncoding RNAs in bovine skin by deep next generation sequencing. BMC Genomics 2013; 14:789. [PMID: 24225384 PMCID: PMC3833843 DOI: 10.1186/1471-2164-14-789] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 11/04/2013] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Deep RNA sequencing (RNAseq) has opened a new horizon for understanding global gene expression. The functional annotation of non-model mammalian genomes including bovines is still poor compared to that of human and mouse. This particularly applies to tissues without direct significance for milk and meat production, like skin, in spite of its multifunctional relevance for the individual. Thus, applying an RNAseq approach, we performed a whole transcriptome analysis of pigmented and nonpigmented bovine skin to describe the comprehensive transcript catalogue of this tissue. RESULTS A total of 39,577 unique primary skin transcripts were mapped to the bovine reference genome assembly. The majority of the transcripts were mapped to known transcriptional units (65%). In addition to the reannotation of known genes, a substantial number (10,884) of unknown transcripts (UTs) were discovered, which had not previously been annotated. The classification of UTs was based on the prediction of their coding potential and comparative sequence analysis, subsequently followed by meticulous manual curation. The classification analysis and experimental validation of selected UTs confirmed that RNAseq data can be used to amend the annotation of known genes by providing evidence for additional exons, untranslated regions or splice variants, by approving genes predicted in silico and by identifying novel bovine loci. A large group of UTs (4,848) was predicted to potentially represent long noncoding RNA (lncRNA). Predominantly, potential lncRNAs mapped in intergenic chromosome regions (4,365) and therefore, were classified as potential intergenic lncRNA. Our analysis revealed that only about 6% of all UTs displayed interspecies conservation and discovered a variety of unknown transcripts without interspecies homology but specific expression in bovine skin. CONCLUSIONS The results of our study demonstrate a complex transcript pattern for bovine skin and suggest a possible functional relevance of novel transcripts, including lncRNA, in the modulation of pigmentation processes. The results also indicate that the comprehensive identification and annotation of unknown transcripts from whole transcriptome analysis using RNAseq data remains a tremendous future challenge.
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Affiliation(s)
- Rosemarie Weikard
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Genome Biology, Dummerstorf 18196, Germany.
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Demasius W, Weikard R, Hadlich F, Müller KE, Kühn C. Monitoring the immune response to vaccination with an inactivated vaccine associated to bovine neonatal pancytopenia by deep sequencing transcriptome analysis in cattle. Vet Res 2013; 44:93. [PMID: 24099437 PMCID: PMC3851820 DOI: 10.1186/1297-9716-44-93] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 09/24/2013] [Indexed: 11/18/2022] Open
Abstract
Bovine neonatal pancytopenia (BNP) is a new fatal, alloimmune/alloantibody mediated disease of new-born calves induced by ingestion of colostrum from cows, which had been vaccinated with a specific vaccine against the Bovine Virus Diarrhoea Virus (BVDV). The hypothesis of pathogenic MHC class I molecules in the vaccine had been put up, but no formal proof of specific causal MHC class I alleles has been provided yet. However, the unique features of the vaccine obviously result in extremely high specific antibody titres in the vaccinated animals, but apparently also in further molecules inducing BNP. Thus, a comprehensive picture of the immune response to the vaccine is essential. Applying the novel approach of next generation RNA sequencing (RNAseq), our study provides a new holistic, comprehensive analysis of the blood transcriptome regulation after vaccination with the specific BVDV vaccine. Our RNAseq approach identified a novel cytokine-like gene in the bovine genome that is highly upregulated after vaccination. This gene has never been described before in any other species and might be specific to ruminant immune response. Furthermore, our data revealed a very coordinated immune response to double-stranded (ds) RNA or a dsRNA analogue after vaccination with the inactivated single-stranded (ss) RNA vaccine. This would suggest either a substantial contamination of the vaccine with dsRNA from host cells after virus culture or a dsRNA analogue applied to the vaccine. The first option would highlight the potential risks associated with virus culture on homologous cells during vaccine production; the latter option would emphasise the potential risks associated with immune stimulating adjuvants used in vaccine production.
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Affiliation(s)
- Wiebke Demasius
- Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany.
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Caswell JL. Failure of respiratory defenses in the pathogenesis of bacterial pneumonia of cattle. Vet Pathol 2013; 51:393-409. [PMID: 24021557 DOI: 10.1177/0300985813502821] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The respiratory system is well defended against inhaled bacteria by a dynamic system of interacting layers, including mucociliary clearance, host defense factors including antimicrobial peptides in the epithelial lining fluid, proinflammatory responses of the respiratory epithelium, resident alveolar macrophages, and recruited neutrophils and monocytes. Nevertheless, these manifold defenses are susceptible to failure as a result of stress, glucocorticoids, viral infections, abrupt exposure to cold air, and poor air quality. When some of these defenses fail, the lung can be colonized by bacterial pathogens that are equipped to evade the remaining defenses, resulting in the development of pneumonia. This review considers the mechanisms by which these predisposing factors compromise the defenses of the lung, with a focus on the development of bacterial pneumonia in cattle and supplemented with advances based on mouse models and the study of human disease. Deepening our understanding of how the respiratory defenses fail is expected to lead to interventions that restore these dynamic immune responses and prevent disease.
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Affiliation(s)
- J L Caswell
- Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada.
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Peffers M, Liu X, Clegg P. Transcriptomic signatures in cartilage ageing. Arthritis Res Ther 2013; 15:R98. [PMID: 23971731 PMCID: PMC3978620 DOI: 10.1186/ar4278] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 08/23/2013] [Indexed: 12/29/2022] Open
Abstract
Introduction Age is an important factor in the development of osteoarthritis. Microarray studies provide insight into cartilage aging but do not reveal the full transcriptomic phenotype of chondrocytes such as small noncoding RNAs, pseudogenes, and microRNAs. RNA-Seq is a powerful technique for the interrogation of large numbers of transcripts including nonprotein coding RNAs. The aim of the study was to characterise molecular mechanisms associated with age-related changes in gene signatures. Methods RNA for gene expression analysis using RNA-Seq and real-time PCR analysis was isolated from macroscopically normal cartilage of the metacarpophalangeal joints of eight horses; four young donors (4 years old) and four old donors (>15 years old). RNA sequence libraries were prepared following ribosomal RNA depletion and sequencing was undertaken using the Illumina HiSeq 2000 platform. Differentially expressed genes were defined using Benjamini-Hochberg false discovery rate correction with a generalised linear model likelihood ratio test (P < 0.05, expression ratios ± 1.4 log2 fold-change). Ingenuity pathway analysis enabled networks, functional analyses and canonical pathways from differentially expressed genes to be determined. Results In total, the expression of 396 transcribed elements including mRNAs, small noncoding RNAs, pseudogenes, and a single microRNA was significantly different in old compared with young cartilage (± 1.4 log2 fold-change, P < 0.05). Of these, 93 were at higher levels in the older cartilage and 303 were at lower levels in the older cartilage. There was an over-representation of genes with reduced expression relating to extracellular matrix, degradative proteases, matrix synthetic enzymes, cytokines and growth factors in cartilage derived from older donors compared with young donors. In addition, there was a reduction in Wnt signalling in ageing cartilage. Conclusion There was an age-related dysregulation of matrix, anabolic and catabolic cartilage factors. This study has increased our knowledge of transcriptional networks in cartilage ageing by providing a global view of the transcriptome.
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Alsaif M, Haenisch F, Guest PC, Rahmoune H, Bahn S. Challenges in drug target discovery in bipolar disorder. Expert Opin Ther Targets 2013; 17:565-77. [PMID: 23419165 DOI: 10.1517/14728222.2013.771169] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
INTRODUCTION Misdiagnosis and subsequent inappropriate treatment of patients with bipolar disorder (BD) can worsen their clinical condition and outcome. AREAS COVERED This review focuses on the therapeutic targets which have been implicated in BD, including the glycogen synthase kinase 3 (GSK-3) and phosphoinositide signaling pathways. In addition, evidence is presented for potential new molecular strategies which involve targeting neuropeptide-converting endopeptidases, glutamatergic excitotoxicity, insulin signaling and dysfunctions in mitochondrial metabolism. Current limitations in study design, molecular platforms, preclinical and cellular models in the context of BD drug target discovery, suggest that there are many areas for improvement. EXPERT OPINION For the future outlook, this review outlines the importance of developments such as the use of BD patient-derived cellular models for providing better understanding of the BD etiology and robust translational drug screening tools in combination with developments in the fields of bioinformatics and systems biology.
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Affiliation(s)
- Murtada Alsaif
- University of Cambridge, Institute of Biotechnology, Department of Chemical Engineering and Biotechnology , Tennis Court Road, Cambridge, CB2 1QT, Cambridgeshire, UK
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