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Article ; Online: The Impact of Relationship Context on Dissociation-Induced Shame Using Vignette Scenarios.

Dorahy, Martin J / McKeogh, Kate / Yogeeswaran, Kumar

2023 , Page(s) 332941231166606

Abstract: Research supports an association between dissociation and elevations in feelings of shame. Yet, some work suggests this connection may be influenced by interpersonal relationship context, with shame heightened when dissociation is experienced with a ... ...

Abstract	Research supports an association between dissociation and elevations in feelings of shame. Yet, some work suggests this connection may be influenced by interpersonal relationship context, with shame heightened when dissociation is experienced with a close friend compared to when alone or with an acquaintance. The current studies sought to further clarify the relational context in which dissociation appears to maximize shame activation. Participants read stories depicting either dissociation or sadness in different relationship contexts, and subsequently responded on measures of emotions, state shame, shame explanations, and perceived behavioral responses. Study 1 (
Language	English
Publishing date	2023-04-19
Publishing country	United States
Document type	Journal Article
ZDB-ID	205658-6
ISSN	1558-691X ; 0033-2941
ISSN (online)	1558-691X
ISSN	0033-2941
DOI	10.1177/00332941231166606
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Article ; Online: An across breed, diet and tissue analysis reveals the transcription factor NR1H3 as a key mediator of residual feed intake in beef cattle.

Keogh, Kate / Kenny, D A / Alexandre, P A / McGee, M / Reverter, A

BMC genomics

2024 Volume 25, Issue 1, Page(s) 234

Abstract: Background: Provision of feed is a major determinant of overall profitability in beef production systems, accounting for up to 75% of the variable costs. Thus, improving cattle feed efficiency, by way of determining the underlying genomic control and ... ...

Abstract	Background: Provision of feed is a major determinant of overall profitability in beef production systems, accounting for up to 75% of the variable costs. Thus, improving cattle feed efficiency, by way of determining the underlying genomic control and subsequently selecting for feed efficient cattle, provides a method through which feed input costs may be reduced. The objective of this study was to undertake gene co-expression network analysis using RNA-Sequence data generated from Longissimus dorsi and liver tissue samples collected from steers of two contrasting breeds (Charolais and Holstein-Friesian) divergent for residual feed intake (RFI), across two consecutive distinct dietary phases (zero-grazed grass and high-concentrate). Categories including differentially expressed genes (DEGs) based on the contrasts of RFI phenotype, breed and dietary source, as well as key transcription factors and proteins secreted in plasma were utilised as nodes of the gene co-expression network. Results: Of the 2,929 DEGs within the network analysis, 1,604 were reported to have statistically significant correlations (≥ 0.80), resulting in a total of 43,876 significant connections between genes. Pathway analysis of clusters of co-expressed genes revealed enrichment of processes related to lipid metabolism (fatty acid biosynthesis, fatty acid β-oxidation, cholesterol biosynthesis), immune function, (complement cascade, coagulation system, acute phase response signalling), and energy production (oxidative phosphorylation, mitochondrial L-carnitine shuttle pathway) based on genes related to RFI, breed and dietary source contrasts. Conclusions: Although similar biological processes were evident across the three factors examined, no one gene node was evident across RFI, breed and diet contrasts in both liver and muscle tissues. However within the liver tissue, the IRX4, NR1H3, HOXA13 and ZNF648 gene nodes, which all encode transcription factors displayed significant connections across the RFI, diet and breed comparisons, indicating a role for these transcription factors towards the RFI phenotype irrespective of diet and breed. Moreover, the NR1H3 gene encodes a protein secreted into plasma from the hepatocytes of the liver, highlighting the potential for this gene to be explored as a robust biomarker for the RFI trait in beef cattle.
MeSH term(s)	Cattle ; Animals ; Transcription Factors ; Diet/veterinary ; Gene Expression Regulation ; Eating/genetics ; Fatty Acids
Chemical Substances	Transcription Factors ; Fatty Acids
Language	English
Publishing date	2024-03-04
Publishing country	England
Document type	Journal Article
ZDB-ID	2041499-7
ISSN	1471-2164 ; 1471-2164
ISSN (online)	1471-2164
ISSN	1471-2164
DOI	10.1186/s12864-024-10151-2
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Article ; Online: Effect of plane of nutrition in early life on the transcriptome of visceral adipose tissue in Angus heifer calves.

Keogh, Kate / Kelly, Alan K / Kenny, David A

Scientific reports

2021 Volume 11, Issue 1, Page(s) 9716

Abstract: Adipose tissue represents not only an important energy storage tissue but also a major endocrine organ within the body, influencing many biochemical systems including metabolic status, immune function and energy homeostasis. The objective of this study ... ...

Abstract	Adipose tissue represents not only an important energy storage tissue but also a major endocrine organ within the body, influencing many biochemical systems including metabolic status, immune function and energy homeostasis. The objective of this study was to evaluate the effect of an enhanced dietary intake during the early calfhood period on the transcriptome of visceral adipose tissue. Artificially reared Angus × Holstein-Friesian heifer calves were offered either a high (HI, n = 15) or moderate (MOD, n = 15) plane of nutrition from 3 to 21 weeks of life. At 21 weeks of age all calves were euthanized, visceral adipose harvested and samples subsequently subjected to mRNA sequencing. Plane of nutrition resulted in the differential expression of 1214 genes within visceral adipose tissue (adj. p < 0.05; fold change > 1.5). Differentially expressed genes were involved in processes related to metabolism and energy production. Biochemical pathways including Sirtuin signalling (adj. p < 0.0001) and the adipogenesis pathways (adj. p = 0.009) were also significantly enriched, indicating greater metabolic processing and adipogenesis in the calves on the high plane of nutrition. Results from this study identify novel genes regulating the molecular response of visceral adipose tissue to an improved plane of nutrition during early calfhood.
MeSH term(s)	Animal Nutritional Physiological Phenomena ; Animals ; Cattle ; Computational Biology ; Female ; Growth ; Intra-Abdominal Fat/metabolism ; Sequence Analysis, RNA/methods ; Signal Transduction ; Transcriptome
Language	English
Publishing date	2021-05-06
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-021-89252-x
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Article ; Online: Early life nutrition affects the molecular ontogeny of testicular development in the young bull calf.

Coen, Stephen / Keogh, Kate / Lonergan, Pat / Fair, Sean / Kenny, David A

Scientific reports

2023 Volume 13, Issue 1, Page(s) 6748

Abstract: Enhanced early life nutrition accelerates sexual development in the bull calf through neuroendocrine-signalling mediated via the hypothalamic-pituitary-testicular axis. Our aim was to assess the impact of contrasting feeding regimes in bull calves during ...

Abstract	Enhanced early life nutrition accelerates sexual development in the bull calf through neuroendocrine-signalling mediated via the hypothalamic-pituitary-testicular axis. Our aim was to assess the impact of contrasting feeding regimes in bull calves during the first 12 weeks of life on the testes transcriptome and proteome. Holstein-Friesian bull calves were offered either a high (HI) or moderate (MOD) plane of nutrition, designed to support target growth rates of 1.0 and 0.5 kg/day, respectively. At 12 weeks of age all calves were euthanized, testicular parenchyma sampled, and global transcriptome (miRNAseq and mRNAseq) and proteome analyses undertaken. Bioinformatic analyses revealed 7 differentially expressed (DE) miRNA and 20 DE mRNA. There were no differentially abundant proteins between the two dietary groups. Integration of omics results highlighted a potential role for the cadherin gene, CDH13, in earlier reproductive development. Furthermore, co-regulatory network analysis of the proteomic data revealed CDH13 as a hub protein within a network enriched for processes related to insulin, IGF-1, androgen and Sertoli cell junction signalling pathways as well as cholesterol biosynthesis. Overall, results highlight a potential role for CDH13 in mediating earlier reproductive development as a consequence of enhanced early life nutrition in the bull calf.
MeSH term(s)	Cattle ; Animals ; Male ; Proteome/metabolism ; Proteomics ; Nutritional Status ; Testis/metabolism ; Diet/veterinary
Chemical Substances	Proteome
Language	English
Publishing date	2023-04-25
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-022-23743-3
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Article ; Online: Effect of breed and diet on the M. longissimus thoracis et lumborum transcriptome of steers divergent for residual feed intake.

Keogh, Kate / McKenna, Clare / Waters, Sinead M / Porter, Richard K / Fitzsimons, Claire / McGee, Mark / Kenny, David A

Scientific reports

2023 Volume 13, Issue 1, Page(s) 9034

Abstract: Improving cattle feed efficiency through selection of residual feed intake (RFI) is a widely accepted approach to sustainable beef production. A greater understanding of the molecular control of RFI in various breeds offered contrasting diets is ... ...

Abstract	Improving cattle feed efficiency through selection of residual feed intake (RFI) is a widely accepted approach to sustainable beef production. A greater understanding of the molecular control of RFI in various breeds offered contrasting diets is necessary for the accurate identification of feed efficient animals and will underpin accelerated genetic improvement of the trait. The aim of this study was to determine genes and biological processes contributing to RFI across varying breed type and dietary sources in skeletal muscle tissue. Residual feed intake was calculated in Charolais and Holstein-Friesian steers across multiple dietary phases (phase-1: high concentrate (growing-phase); phase-2: zero-grazed grass (growing-phase); phase-3: high concentrate (finishing-phase). Steers divergent for RFI within each breed and dietary phase were selected for muscle biopsy collection, and muscle samples subsequently subjected to RNAseq analysis. No gene was consistently differentially expressed across the breed and diet types examined. However, pathway analysis revealed commonality across breeds and diets for biological processes including fatty acid metabolism, immune function, energy production and muscle growth. Overall, the lack of commonality of individual genes towards variation in RFI both within the current study and compared to the published literature, suggests other genomic features warrant further evaluation in relation to RFI.
MeSH term(s)	Cattle/genetics ; Animals ; Transcriptome ; Animal Feed/analysis ; Plant Breeding ; Eating/genetics ; Diet/veterinary
Language	English
Publishing date	2023-06-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-35661-z
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Article ; Online: Genome-wide association study reveals candidate markers related to field fertility and semen quality traits in Holstein-Friesian bulls.

Abril-Parreño, Laura / Carthy, Tara R / Keogh, Kate / Štiavnická, Miriama / O'Meara, Ciara / Lonergan, Patrick / Kenny, David A / Fair, Sean

Animal : an international journal of animal bioscience

2023 Volume 17, Issue 6, Page(s) 100841

Abstract: In vitro assessment of bull semen quality is routinely used in bull semen processing centres in order to ensure that semen destined to be used in the field has passed minimum standards. Despite these stringent quality control checks, individual bulls ... ...

Abstract	In vitro assessment of bull semen quality is routinely used in bull semen processing centres in order to ensure that semen destined to be used in the field has passed minimum standards. Despite these stringent quality control checks, individual bulls that pass the quality control checks can still vary in field fertility by up to 25%. A genome-wide association study was undertaken to determine genetic markers associated with prefreeze and post-thaw bull sperm quality traits as well as field fertility. Genome-wide association analysis was performed using a single nucleotide polymorphism (SNP) regression mixed linear model in WOMBAT. Genes within a 250 Kb span of a suggestive (P ≤ 1 × 10
MeSH term(s)	Male ; Cattle/genetics ; Animals ; Semen Analysis/veterinary ; Genome-Wide Association Study/veterinary ; Semen ; Sperm Motility/genetics ; Spermatozoa ; Genetic Markers
Chemical Substances	Genetic Markers
Language	English
Publishing date	2023-04-28
Publishing country	England
Document type	Journal Article
ZDB-ID	2257920-5
ISSN	1751-732X ; 1751-7311
ISSN (online)	1751-732X
ISSN	1751-7311
DOI	10.1016/j.animal.2023.100841
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Article ; Online: Gene co-expression networks contributing to the expression of compensatory growth in metabolically active tissues in cattle.

Keogh, Kate / Kenny, David A / Waters, Sinead M

Scientific reports

2019 Volume 9, Issue 1, Page(s) 6093

Abstract: Compensatory growth (CG) is an accelerated growth phenomenon which occurs in animals upon re-alimentation following a period of dietary restriction. The objective of this study was to perform gene co-expression analysis on metabolic tissues of animals ... ...

Abstract	Compensatory growth (CG) is an accelerated growth phenomenon which occurs in animals upon re-alimentation following a period of dietary restriction. The objective of this study was to perform gene co-expression analysis on metabolic tissues of animals undergoing CG, in order to elucidate the molecular control governing this phenomenon. Thirty Holstein Friesian bulls were fed a restricted diet for 125 days, after which they received feed ad libitum. Following 55 days of ad libitum feeding all animals were slaughtered. RNAseq and gene co-expression analyses were performed on tissue samples collected at slaughter including liver, rumen papillae and jejunum epithelium tissues. A period of CG resulted in 15 networks of co-expressed genes. One network of genes, involved in proteasome core complex, signal transduction and protein synthesis was found to be similar across liver and jejunum tissue datasets (r = 0.68, P = 0.04). Results from this study also showed that a large portion of co-expressed genes had not previously been implicated in the expression of CG, thus this study identifies novel genes involved in controlling CG across tissues, with hub genes holding potential for use as biomarkers for the selection of animals with a greater propensity to display CG.
MeSH term(s)	Animal Nutritional Physiological Phenomena ; Animals ; Cattle/growth & development ; Diet/veterinary ; Epithelium/metabolism ; Food Deprivation ; Gene Regulatory Networks ; Jejunum/metabolism ; Liver/metabolism ; Male ; RNA-Seq ; Rumen/metabolism ; Transcriptome
Language	English
Publishing date	2019-04-15
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-019-42608-w
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Article ; Online: A high plane of nutrition during early life alters the hypothalamic transcriptome of heifer calves.

Sánchez, José M / Keogh, Kate / Kelly, Alan K / Byrne, Colin J / Lonergan, Pat / Kenny, David A

Scientific reports

2021 Volume 11, Issue 1, Page(s) 13978

Abstract: The aim was to examine the effect of rapid body weight gain during early calfhood consistent with earlier sexual development on the transcriptional profile of the hypothalamus. Angus X Holstein-Friesian heifer calves (19 ± 5 days of age) were offered a ... ...

Abstract	The aim was to examine the effect of rapid body weight gain during early calfhood consistent with earlier sexual development on the transcriptional profile of the hypothalamus. Angus X Holstein-Friesian heifer calves (19 ± 5 days of age) were offered a high (HI, n = 14) or moderate (MOD, n = 15) plane of nutrition from 3 to 21 weeks of age to achieve a growth rate of 1.2 kg/d and 0.5 kg/d, respectively. Following euthanasia at 21 weeks, the arcuate nucleus (ARC) region was separated from the remainder of the hypothalamus and both were subjected to RNA-Seq. HI calves exhibited altered expression of 80 and 39 transcripts in the ARC and the remaining hypothalamus, respectively (P < 0.05) including downregulation of AGRP and NPY and upregulation of POMC, previously implicated in precocious sexual development. Stress-signaling pathways were amongst the most highly dysregulated. Organ morphology, reproductive system development and function, and developmental disorder were amongst the networks derived from differentially expressed genes (DEGs) in the ARC. Gene co-expression analysis revealed DEGs within the ARC (POMC, CBLN2, CHGA) and hypothalamus (PENK) as hub genes. In conclusion, enhanced nutrition during early calfhood alters the biochemical regulation of the hypothalamus consistent with advanced sexual development in the prepubertal heifer.
MeSH term(s)	Age Factors ; Animal Nutritional Physiological Phenomena ; Animals ; Arcuate Nucleus of Hypothalamus/metabolism ; Cattle ; Computational Biology ; Gene Expression Profiling ; Gene Expression Regulation ; Gene Regulatory Networks ; Hypothalamus/metabolism ; Transcriptome
Language	English
Publishing date	2021-07-07
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-021-93080-4
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Article ; Online: Transcriptome assisted label free proteomics of hepatic tissue in response to both dietary restriction and compensatory growth in cattle

Mullins, Yvonne / Keogh, Kate / Blackshields, Gordon / Kenny, David A. / Kelly, Alan K. / Waters, Sinéad M.

Journal of Proteomics. 2021 Feb., v. 232 p.104048-

2021

Abstract: Compensatory growth (CG) is a naturally occurring phenomenon where, following a period of under nutrition, an animal exhibits accelerated growth upon re-alimentation. The objective was to identify and quantify hepatic proteins involved in the regulation ... ...

Abstract	Compensatory growth (CG) is a naturally occurring phenomenon where, following a period of under nutrition, an animal exhibits accelerated growth upon re-alimentation. The objective was to identify and quantify hepatic proteins involved in the regulation of CG in cattle. Forty Holstein Friesian bulls were equally assigned to one of four groups. Groups; A1 and A2 had ad libitum access to feed for 125 days, groups R1 and R2 were feed restricted. Following this, R1 and A1 animals were slaughtered. Remaining animals (R2 and A2) were slaughtered following ad libitum feeding for a successive 55 days. At slaughter hepatic tissue samples were collected and label-free quantitative proteomics undertaken with spectra searched against a custom built transcriptome database specific to the animals in this study. 24 differentially abundant proteins were identified during CG (R2 vs. R1) including; PSPH, ASNS and GSTM1, which are involved in nutrient metabolism, immune response and cellular growth. Proteins involved in biochemical pathways related to nutrient metabolism were down-regulated during CG, indicating a possible adaptive response by the liver to a period of fluctuating nutrient availability. The livers ability to regulate its metabolic activity may have profound effects on the efficiency of whole body energy utilization during CG. This study is the first to unravel the effect of compensatory growth on the hepatic proteome of cattle using transcriptome-assisted shot gun proteomics. Proteins identified as being affected by dietary restriction and subsequent expression of compensatory growth in this study may, following appropriate validation, contribute to the identification of functional genetic variants. Such information could be harnessed within the context of genomic selection in cattle breeding programs to identify animals with a greater genetic potential to undergo compensatory growth, thus increasing the profitability of the beef sector and accelerating genetic gain.
Keywords	Holstein ; ad libitum feeding ; beef ; biochemical pathways ; cattle ; cell growth ; compensatory growth ; databases ; dietary restriction ; energy ; genetic improvement ; genetic traits ; immune response ; liver ; marker-assisted selection ; metabolism ; nutrient availability ; nutrition ; profitability ; proteome ; proteomics ; slaughter ; transcriptome
Language	English
Dates of publication	2021-02
Publishing place	Elsevier B.V.
Document type	Article ; Online
Note	NAL-AP-2-clean ; Use and reproduction
ZDB-ID	2400835-7
ISSN	1876-7737 ; 1874-3919
ISSN (online)	1876-7737
ISSN	1874-3919
DOI	10.1016/j.jprot.2020.104048
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Label-free quantitative proteomic analysis of M. longissimus dorsi from cattle during dietary restriction and subsequent compensatory growth.

Mullins, Yvonne / Keogh, Kate / Kenny, David A / Kelly, Alan / O' Boyle, Padraig / Waters, Sinéad M

Scientific reports

2020 Volume 10, Issue 1, Page(s) 2613

Abstract: Compensatory growth (CG) is a naturally occurring physiological process whereby an animal has the ability to undergo enhanced growth following a period of restricted feeding. This studies objective was to identify key proteins involved in the expression ... ...

Abstract	Compensatory growth (CG) is a naturally occurring physiological process whereby an animal has the ability to undergo enhanced growth following a period of restricted feeding. This studies objective was to identify key proteins involved in the expression of CG. Forty Holstein Friesian bulls were equally assigned to one of four groups. R1 and R2 groups were subjected to restricted feed allowance for 125 days (Period 1). A1 and A2 animals had ad libitum access to feed in Period 1. Following Period 1, all animals from R1 and A1 were slaughtered. Remaining animals (R2 and A2) were slaughtered following ad libitum access to feed for successive 55 days (Period 2). M. longissimus dorsi samples were collected at slaughter from all animals. Proteins were isolated from samples and subjected to label-free mass spectrometry proteomic quantification. Proteins which were differentially abundant during CG (n = 39) were involved in cellular binding processes, oxidative phosphorylation and mitochondrial function. There was also evidence for up regulation of three pathways involved in nucleotide biosynthesis. Genetic variants in or regulating genes pertaining to proteins identified in this study may hold potential for use as DNA based biomarkers for genomic selection of animals with a greater ability to undergo CG.
MeSH term(s)	Animal Feed/analysis ; Animal Nutritional Physiological Phenomena ; Animals ; Cattle/genetics ; Cattle/growth & development ; Cattle/physiology ; Diet/veterinary ; Food Deprivation ; Male ; Muscle, Skeletal/growth & development ; Muscle, Skeletal/physiology ; Proteins/analysis ; Proteins/genetics ; Proteins/metabolism ; Transcriptome
Chemical Substances	Proteins
Language	English
Publishing date	2020-02-13
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-020-59412-6
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