cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.17695167
title: Proteomic/peptidomic profile and <i>Escherichia coli</i> growth inhibitory effect of <i>in vitro</i> digested soya protein

description: Plant proteins contain bioactive peptides with functional properties and physiological activities. In the present work, the bioactive peptides produced during <i>in vitro</i> gastrointestinal digestion of soya protein isolate were investigated. Protein samples were subjected to simulated gastrointestinal digestion with a generation of permeate (&lt;3 kDa) and retentate (&gt;3 kDa) fractions. The permeate was analysed by nano-liquid chromatography electrospray ionisation tandem mass spectrometry (LC-nano ESI MS/MS) using a shotgun peptidomic approach, and the retentate was further digested with trypsin and analysed using a shotgun proteomic approach. Based on protein profile observed, the retentate was further tested for its potential antimicrobial activity by evaluating the inhibitory effect on <i>E. coli</i> growth. In the present study the peptidomic/proteomic characterisation of permeate and retentate fractions revealed the presence of bioactive peptides and proteins associated with antioxidant, ACE-inhibitory, anti-hypertensive and antimicrobial activities. The presence of potentially antimicrobial proteins in the retentate fraction is supported by a marked <i>E. coli</i> F18+ growth inhibitory activity of the same fraction. In particular, the growth inhibitory effect was significant from one until six hours of incubation with 0.65–2.6 mg/ml of <i>in vitro</i> digested soya. The obtained data confirmed that soya-based supplements may have potential beneficial effects after human consumption, and they may be re-cycled for animal nutrition in line with the circular economy concept.HighlightsSoya-based supplements are relevant sources of bioactive molecules.Soya based supplements could be re-cycled for animal feeding considering the circular economy concept. Soya-based supplements are relevant sources of bioactive molecules. Soya based supplements could be re-cycled for animal feeding considering the circular economy concept.
DOI: 10.6084/m9.figshare.17695167.v1
title: Proteomic/peptidomic profile and <i>Escherichia coli</i> growth inhibitory effect of <i>in vitro</i> digested soya protein

description: Plant proteins contain bioactive peptides with functional properties and physiological activities. In the present work, the bioactive peptides produced during <i>in vitro</i> gastrointestinal digestion of soya protein isolate were investigated. Protein samples were subjected to simulated gastrointestinal digestion with a generation of permeate (&lt;3 kDa) and retentate (&gt;3 kDa) fractions. The permeate was analysed by nano-liquid chromatography electrospray ionisation tandem mass spectrometry (LC-nano ESI MS/MS) using a shotgun peptidomic approach, and the retentate was further digested with trypsin and analysed using a shotgun proteomic approach. Based on protein profile observed, the retentate was further tested for its potential antimicrobial activity by evaluating the inhibitory effect on <i>E. coli</i> growth. In the present study the peptidomic/proteomic characterisation of permeate and retentate fractions revealed the presence of bioactive peptides and proteins associated with antioxidant, ACE-inhibitory, anti-hypertensive and antimicrobial activities. The presence of potentially antimicrobial proteins in the retentate fraction is supported by a marked <i>E. coli</i> F18+ growth inhibitory activity of the same fraction. In particular, the growth inhibitory effect was significant from one until six hours of incubation with 0.65–2.6 mg/ml of <i>in vitro</i> digested soya. The obtained data confirmed that soya-based supplements may have potential beneficial effects after human consumption, and they may be re-cycled for animal nutrition in line with the circular economy concept.HighlightsSoya-based supplements are relevant sources of bioactive molecules.Soya based supplements could be re-cycled for animal feeding considering the circular economy concept. Soya-based supplements are relevant sources of bioactive molecules. Soya based supplements could be re-cycled for animal feeding considering the circular economy concept.
DOI: 10.6084/m9.figshare.16699451
title: Meta-analysis to evaluate the impact of the reduction of dietary crude protein on the gut health of post-weaning pigs

description: Weaning transition is often associated with the occurrence of the post-weaning diarrhoea syndrome (PWDS). The reduction of dietary crude protein (CP) has been intensively used as a strategy for controlling PWDS. The aim of the present meta-analysis was to report the effect of the reduction of dietary CP on the intestinal parameters related to the gut health, growth and diarrhoea of post-weaning piglets. A literature review of the articles published from 2006 to 2019 produced 48 articles and, of these 26 were selected. Parameters (bacterial metabolites, pH, microbiota diversity, intestinal morphology, inflammation markers, growth, faecal score) were extracted, expressed as a percentage of the control diet and analysed using a general linear model which included the study, reduction in points of dietary CP, and the ratio of digestible Lysine and dietary CP (dLys/CP) as factors. The reduction of dietary CP decreased ammonia (<i>p</i> &lt; .0001), pH (<i>p</i> = .039), total short-chain fatty acids (SCFAs) (<i>p</i> = .027), biogenic amines including cadaverine (<i>p</i> = .034) and putrescine (<i>p</i> = .030) and the expression of <i>TLR4</i> (<i>p</i> &lt; .0001) in the intestine and also reduced the faecal score (<i>p</i> = .002). The dLys/CP ratio increased the level of <i>Lactobacilli</i> and the expression of <i>TLR4</i> (<i>p</i> &lt; .05), and tended to increase acetic acid (<i>p</i> &lt; .1). Crypt depth, villus height, microbiota diversity and growth remained unchanged. In conclusion, this study confirmed that a reduction of dietary CP could reduce bacterial protein fermentation and the production of potentially toxic metabolites. In turn, this could result in lower intestinal inflammation and a decreased risk of diarrhoea in weaning piglets.HighlightsReducing the dietary crude protein can decrease the fermentation of undigested dietary protein, especially in the large intestine.Lowering undigested dietary protein results in a reduction of the intestinal pH and potentially toxic metabolites, including ammonia and amines.Diets with lower crude protein reduce inflammation of the intestinal mucosa and the post-weaning diarrhoea of piglets without compromising performance. Reducing the dietary crude protein can decrease the fermentation of undigested dietary protein, especially in the large intestine. Lowering undigested dietary protein results in a reduction of the intestinal pH and potentially toxic metabolites, including ammonia and amines. Diets with lower crude protein reduce inflammation of the intestinal mucosa and the post-weaning diarrhoea of piglets without compromising performance.
DOI: 10.6084/m9.figshare.16699451.v1
title: Meta-analysis to evaluate the impact of the reduction of dietary crude protein on the gut health of post-weaning pigs

description: Weaning transition is often associated with the occurrence of the post-weaning diarrhoea syndrome (PWDS). The reduction of dietary crude protein (CP) has been intensively used as a strategy for controlling PWDS. The aim of the present meta-analysis was to report the effect of the reduction of dietary CP on the intestinal parameters related to the gut health, growth and diarrhoea of post-weaning piglets. A literature review of the articles published from 2006 to 2019 produced 48 articles and, of these 26 were selected. Parameters (bacterial metabolites, pH, microbiota diversity, intestinal morphology, inflammation markers, growth, faecal score) were extracted, expressed as a percentage of the control diet and analysed using a general linear model which included the study, reduction in points of dietary CP, and the ratio of digestible Lysine and dietary CP (dLys/CP) as factors. The reduction of dietary CP decreased ammonia (<i>p</i> &lt; .0001), pH (<i>p</i> = .039), total short-chain fatty acids (SCFAs) (<i>p</i> = .027), biogenic amines including cadaverine (<i>p</i> = .034) and putrescine (<i>p</i> = .030) and the expression of <i>TLR4</i> (<i>p</i> &lt; .0001) in the intestine and also reduced the faecal score (<i>p</i> = .002). The dLys/CP ratio increased the level of <i>Lactobacilli</i> and the expression of <i>TLR4</i> (<i>p</i> &lt; .05), and tended to increase acetic acid (<i>p</i> &lt; .1). Crypt depth, villus height, microbiota diversity and growth remained unchanged. In conclusion, this study confirmed that a reduction of dietary CP could reduce bacterial protein fermentation and the production of potentially toxic metabolites. In turn, this could result in lower intestinal inflammation and a decreased risk of diarrhoea in weaning piglets.HighlightsReducing the dietary crude protein can decrease the fermentation of undigested dietary protein, especially in the large intestine.Lowering undigested dietary protein results in a reduction of the intestinal pH and potentially toxic metabolites, including ammonia and amines.Diets with lower crude protein reduce inflammation of the intestinal mucosa and the post-weaning diarrhoea of piglets without compromising performance. Reducing the dietary crude protein can decrease the fermentation of undigested dietary protein, especially in the large intestine. Lowering undigested dietary protein results in a reduction of the intestinal pH and potentially toxic metabolites, including ammonia and amines. Diets with lower crude protein reduce inflammation of the intestinal mucosa and the post-weaning diarrhoea of piglets without compromising performance.
DOI: 10.6084/m9.figshare.17695173.v1
title: An association analysis between a polymorphism in the <i>SEC24A</i> gene and lipid traits recorded in Duroc pigs

description: By regulating the expression of low-density lipoprotein receptors (LDLR), the SEC24A protein modulates the clearance of plasma cholesterol in mice. The whole-genome sequencing of five Duroc boars that sired a Duroc purebred experimental population (LIPGEN population, 350 individuals) revealed the segregation of one putative nonsense mutation located at the <i>SEC24A</i> (rs336401826, c.44G&gt;A) gene. Genotyping of this polymorphic site in the LIPGEN population highlighted the existence of a significant departure from the Hardy Weinberg equilibrium (<i>χ</i><sup>2</sup> = 5.05, <i>p</i>-value = 0.024527). Despite the fact that SEC24A inactivation should affect serum lipid concentrations, we did not observe an association between <i>SEC24A</i> genotype and such traits. A thorough revision of the annotation of the <i>SEC24A</i> rs336401826 SNP revealed that this polymorphism is probably located in the 5’UTR of the <i>SEC24A</i> gene, rather than at the beginning of the first exon, hence not introducing the predicted premature stop codon that could truncate the SEC24A protein. Given that the annotation of loss-of-function mutations in pigs is far from perfect, careful manual curation of such mutations is recommended before undertaking the analysis of their effects at the experimental level.HIGHLIGHTSOne mutation (c.44 G&gt;A) predicted to disrupt the SEC24A protein segregates in a Duroc pig population.This polymorphism is not associated with serum lipid levels despite its expected effect on such traits.Manual curation of the annotation of this putative nonsense polymorphism has revealed that it maps to the 5’UTR of the <i>SEC24A</i> gene. One mutation (c.44 G&gt;A) predicted to disrupt the SEC24A protein segregates in a Duroc pig population. This polymorphism is not associated with serum lipid levels despite its expected effect on such traits. Manual curation of the annotation of this putative nonsense polymorphism has revealed that it maps to the 5’UTR of the <i>SEC24A</i> gene.
DOI: 10.6084/m9.figshare.16826491
title: Linear and non-linear regression model fitting of testicular three-dimensional growth in Miranda donkeys

description: In endangered donkey populations, reproductive performance is one the most important areas to study, provided its connection with conservation opportunities. Among reproductive traits, testicular dimensions, their relationship with body weight and seminal qualitative and quantitative parameters is particularly notable. The aim of the present study was to model the evolution of body weight, testicular length, width and height, volume and gonadosomatic index in Miranda donkeys using in vivo ultrasonography. Data on the aforementioned variables of 23 Miranda donkeys, from 4 to 259 months of age, were fitted to eleven linear and nonlinear models. Cubic function modelling reported the best-fitting properties for almost all variables, except for body weight (sigmoid curve model). Cubic model presented a higher ability to capture interindividual variability (Adj. R<sup>2</sup> from 0.795 to 0.922) for testicular height, width, length and volume measurements than the rest of fucntions tested. Bayesian information criterion (BIC) values suggest in vivo ultrasonography may be a rather efficient and accurate tool when predicting for the evolution of testicular volume or gonadosomatic index than three-dimensional testicular measurements.HighlightsCubic functions efficiently model testicular dimensions, volume and composite indices evolution.Ultrasonography objectively, accurately and reproducibly determines testicular volume.Testicular asymmetry physiologically occurs to balance bilateral testicular activity. Cubic functions efficiently model testicular dimensions, volume and composite indices evolution. Ultrasonography objectively, accurately and reproducibly determines testicular volume. Testicular asymmetry physiologically occurs to balance bilateral testicular activity.
DOI: 10.6084/m9.figshare.16826491.v1
title: Linear and non-linear regression model fitting of testicular three-dimensional growth in Miranda donkeys

description: In endangered donkey populations, reproductive performance is one the most important areas to study, provided its connection with conservation opportunities. Among reproductive traits, testicular dimensions, their relationship with body weight and seminal qualitative and quantitative parameters is particularly notable. The aim of the present study was to model the evolution of body weight, testicular length, width and height, volume and gonadosomatic index in Miranda donkeys using in vivo ultrasonography. Data on the aforementioned variables of 23 Miranda donkeys, from 4 to 259 months of age, were fitted to eleven linear and nonlinear models. Cubic function modelling reported the best-fitting properties for almost all variables, except for body weight (sigmoid curve model). Cubic model presented a higher ability to capture interindividual variability (Adj. R<sup>2</sup> from 0.795 to 0.922) for testicular height, width, length and volume measurements than the rest of fucntions tested. Bayesian information criterion (BIC) values suggest in vivo ultrasonography may be a rather efficient and accurate tool when predicting for the evolution of testicular volume or gonadosomatic index than three-dimensional testicular measurements.HighlightsCubic functions efficiently model testicular dimensions, volume and composite indices evolution.Ultrasonography objectively, accurately and reproducibly determines testicular volume.Testicular asymmetry physiologically occurs to balance bilateral testicular activity. Cubic functions efficiently model testicular dimensions, volume and composite indices evolution. Ultrasonography objectively, accurately and reproducibly determines testicular volume. Testicular asymmetry physiologically occurs to balance bilateral testicular activity.
DOI: 10.6084/m9.figshare.17695173
title: An association analysis between a polymorphism in the <i>SEC24A</i> gene and lipid traits recorded in Duroc pigs

description: By regulating the expression of low-density lipoprotein receptors (LDLR), the SEC24A protein modulates the clearance of plasma cholesterol in mice. The whole-genome sequencing of five Duroc boars that sired a Duroc purebred experimental population (LIPGEN population, 350 individuals) revealed the segregation of one putative nonsense mutation located at the <i>SEC24A</i> (rs336401826, c.44G&gt;A) gene. Genotyping of this polymorphic site in the LIPGEN population highlighted the existence of a significant departure from the Hardy Weinberg equilibrium (<i>χ</i><sup>2</sup> = 5.05, <i>p</i>-value = 0.024527). Despite the fact that SEC24A inactivation should affect serum lipid concentrations, we did not observe an association between <i>SEC24A</i> genotype and such traits. A thorough revision of the annotation of the <i>SEC24A</i> rs336401826 SNP revealed that this polymorphism is probably located in the 5’UTR of the <i>SEC24A</i> gene, rather than at the beginning of the first exon, hence not introducing the predicted premature stop codon that could truncate the SEC24A protein. Given that the annotation of loss-of-function mutations in pigs is far from perfect, careful manual curation of such mutations is recommended before undertaking the analysis of their effects at the experimental level.HIGHLIGHTSOne mutation (c.44 G&gt;A) predicted to disrupt the SEC24A protein segregates in a Duroc pig population.This polymorphism is not associated with serum lipid levels despite its expected effect on such traits.Manual curation of the annotation of this putative nonsense polymorphism has revealed that it maps to the 5’UTR of the <i>SEC24A</i> gene. One mutation (c.44 G&gt;A) predicted to disrupt the SEC24A protein segregates in a Duroc pig population. This polymorphism is not associated with serum lipid levels despite its expected effect on such traits. Manual curation of the annotation of this putative nonsense polymorphism has revealed that it maps to the 5’UTR of the <i>SEC24A</i> gene.
DOI: 10.6084/m9.figshare.15002457
title: Age-related linear and nonlinear modelling of semen quality parameters in Miranda donkeys

description: In endangered donkey populations, reproductive performance is one the most important areas to study, provided its connection with conservation opportunities. Among reproductive traits, the knowledge on the evolution of seminal qualitative and quantitative parameters may achieve a particular relevance given its implication with improved or more efficient fertility and fecundation chances. The aim of the present study was to model the gonadosomatic index and the quantitative and qualitative seminal parameters along age in Miranda donkeys. Forty semen collections from 8 Miranda donkeys from 2.8 and 21.6 years of age, were fitted to eleven linear and nonlinear models. Cubic function modelling reported the best-fitting properties for almost all variables, except for sperm concentration (exponential model). Cubic model presented a slightly higher ability to capture interindividual variability than less parametrically complex models and more computationally complex models, such as exponential or logarithmic. Senility may course with and larger numbers of abnormal morphology spermatozoa, and also reduced sperm concentration and motility.HighlightsTestis reach mature size rapidly which may be ascribed to a breed factor.Age promotes ejaculate volume increase and concentration reduction.Reduced motility may ascribe to increased abnormal morphology spermatozoa.Major age-related changes are linked to testicular functions degeneration. Testis reach mature size rapidly which may be ascribed to a breed factor. Age promotes ejaculate volume increase and concentration reduction. Reduced motility may ascribe to increased abnormal morphology spermatozoa. Major age-related changes are linked to testicular functions degeneration.
DOI: 10.6084/m9.figshare.15002457.v1
title: Age-related linear and nonlinear modelling of semen quality parameters in Miranda donkeys

description: In endangered donkey populations, reproductive performance is one the most important areas to study, provided its connection with conservation opportunities. Among reproductive traits, the knowledge on the evolution of seminal qualitative and quantitative parameters may achieve a particular relevance given its implication with improved or more efficient fertility and fecundation chances. The aim of the present study was to model the gonadosomatic index and the quantitative and qualitative seminal parameters along age in Miranda donkeys. Forty semen collections from 8 Miranda donkeys from 2.8 and 21.6 years of age, were fitted to eleven linear and nonlinear models. Cubic function modelling reported the best-fitting properties for almost all variables, except for sperm concentration (exponential model). Cubic model presented a slightly higher ability to capture interindividual variability than less parametrically complex models and more computationally complex models, such as exponential or logarithmic. Senility may course with and larger numbers of abnormal morphology spermatozoa, and also reduced sperm concentration and motility.HighlightsTestis reach mature size rapidly which may be ascribed to a breed factor.Age promotes ejaculate volume increase and concentration reduction.Reduced motility may ascribe to increased abnormal morphology spermatozoa.Major age-related changes are linked to testicular functions degeneration. Testis reach mature size rapidly which may be ascribed to a breed factor. Age promotes ejaculate volume increase and concentration reduction. Reduced motility may ascribe to increased abnormal morphology spermatozoa. Major age-related changes are linked to testicular functions degeneration.
DOI: 10.6084/m9.figshare.14825023
title: An application of nuclear magnetic resonance spectroscopy to study faecal canine metabolome

description: Metabolomics provides a description of the phenotype of an organism and complementary biochemical information to genomics and proteomics. The purpose of this research was to depict the metabolite profile of faecal samples from dogs fed three different diets through NMR spectroscopy analysis. Samples were collected from 14 dogs fed a commercial extruded diet, 18 dogs fed a homemade diet and 16 dogs fed a raw meat-based diet. The average BCS for all dogs was 4–5 and the average Faecal Score was 2–3. Only healthy animals were considered, as assessed from the clinical evaluation of the veterinarians. Faecal samples were prepared using phosphate buffer (pH 7.1) combined with deuterated water and analysed with NMR spectroscopy using a Bruker Avance III HD 400 MHz spectrometer. Principal component analysis of the spectra signals demonstrated clustering of dogs according to diet, with 57.8% of the variance explained by the first three components. Targeted metabolome analysis was also performed on 56 metabolites of interest, selected from a database of 558 metabolites. Our data suggest that metabolome analysis using NMR is a promising approach to describe the phenotypic variation that occurs among dogs fed different diets.The metabolomic approach is becoming always more important in the evaluation of the functional responses of animals to dietary intervention.NMR-metabolomics has emerged as a non-destructive technique that allows a simpler data interpretation compared to other techniques.NMR metabolome analysis resulted to be a promising approach to describe the phenotypic variation that occurs among dogs fed different diets. The metabolomic approach is becoming always more important in the evaluation of the functional responses of animals to dietary intervention. NMR-metabolomics has emerged as a non-destructive technique that allows a simpler data interpretation compared to other techniques. NMR metabolome analysis resulted to be a promising approach to describe the phenotypic variation that occurs among dogs fed different diets.