Background Subclinical intramammary infection(IMI)represents a significant problem in maintaining dairy cows’health.Disease severity and extent depend on the interaction between the causative agent,environment,and ho...Background Subclinical intramammary infection(IMI)represents a significant problem in maintaining dairy cows’health.Disease severity and extent depend on the interaction between the causative agent,environment,and host.To investigate the molecular mechanisms behind the host immune response,we used RNA-Seq for the milk somatic cells(SC)transcriptome profiling in healthy cows(n=9),and cows naturally affected by subclinical IMI from Proto-theca spp.(n=11)and Streptococcus agalactiae(S.agalactiae;n=11).Data Integration Analysis for Biomarker discov-ery using Latent Components(DIABLO)was used to integrate transcriptomic data and host phenotypic traits related to milk composition,SC composition,and udder health to identify hub variables for subclinical IMI detection.Results A total of 1,682 and 2,427 differentially expressed genes(DEGs)were identified when comparing Prototheca spp.and S.agalactiae to healthy animals,respectively.Pathogen-specific pathway analyses evidenced that Proto-theca’s infection upregulated antigen processing and lymphocyte proliferation pathways while S.agalactiae induced a reduction of energy-related pathways like the tricarboxylic acid cycle,and carbohydrate and lipid metabolism.The integrative analysis of commonly shared DEGs between the two pathogens(n=681)referred to the core-mastitis response genes,and phenotypic data evidenced a strong covariation between those genes and the flow cytometry immune cells(r2=0.72),followed by the udder health(r2=0.64)and milk quality parameters(r2=0.64).Variables with r≥0.90 were used to build a network in which the top 20 hub variables were identified with the Cytoscape cyto-hubba plug-in.The genes in common between DIABLO and cytohubba(n=10)were submitted to a ROC analysis which showed they had excellent predictive performances in terms of discriminating healthy and mastitis-affected animals(sensitivity>0.89,specificity>0.81,accuracy>0.87,and precision>0.69).Among these genes,CIITA could play a key role in regulating the animals’response to subclinical IMI.Conclusions Despite some differences in the enriched pathways,the two mastitis-causing pathogens seemed to induce a shared host immune-transcriptomic response.The hub variables identified with the integrative approach might be included in screening and diagnostic tools for subclinical IMI detection.展开更多
In the recent years, the number of endangered animals, both referred to livestock and wild species, has grown enormously. The “livestock” term refers to animals domesticated for producing commodities for man such as...In the recent years, the number of endangered animals, both referred to livestock and wild species, has grown enormously. The “livestock” term refers to animals domesticated for producing commodities for man such as food, fiber and draught. Livestock biodiversity is integral to our culture, history, environment, and economy. Thousands of livestock breeds have evolved over time to suit particular environments and farming systems. Conservation and analyses of these genetic resources rely on demographic characterization and correct breeding schemes. In addition, molecular genetic studies allow to identify and monitor the genetic diversity within and across breeds and to reconstruct their evolution history. The conservation of livestock variability is also a crucial element in order to preserve and valorise specific nutritional and nutraceutical properties of animal products. Efficient ex situ and in situ conservation strategies, as well as the creation of bio-banks and specific biotechnological and bioinformatics tools for genetic analyses and digital preservation, are obligatory requirements in order to implement an appropriate action for the conservation of animal biodiversity. The main issues concerning different species are summarised, with particular reference to the livestock biodiversity still existing. Some examples of ex situ conservation strategies, which mainly refer to cryoconservation of semen, ova, embryos or tissues, developed in Italy, are presented, and the different actions in defense of Animal Genetic Resources (AnGR) developed within the European Community are illustrated. Interestingly, the same strategies for biological and digital analyses and preservation of livestock biodiversity can be exported to wild endangered animals in order to plan a correct conservation and repopulation of the species. Furthermore, the European Union has set up the guidelines to safeguard the biodiversity and to combat the extinction of animal species, and has made the protection of biodiversity and ecosystems one of the main objectives of the Sixth Environment Action Programme.展开更多
基金the Ministero delle politiche agricole alimentari,forestali e del turismo(MIPAAF),Rome,Italy.Moreover,the study was conducted within the Agritech National Research Center and received funding from the European Union Next-GenerationEU(PIANO NAZIONALE DI RIPRESA E RESILIENZA(PNRR)-MISSIONE 4 COMPONENTE 2,INVESTIMENTO 1.4-D.D.103217/06/2022,CN00000022).
文摘Background Subclinical intramammary infection(IMI)represents a significant problem in maintaining dairy cows’health.Disease severity and extent depend on the interaction between the causative agent,environment,and host.To investigate the molecular mechanisms behind the host immune response,we used RNA-Seq for the milk somatic cells(SC)transcriptome profiling in healthy cows(n=9),and cows naturally affected by subclinical IMI from Proto-theca spp.(n=11)and Streptococcus agalactiae(S.agalactiae;n=11).Data Integration Analysis for Biomarker discov-ery using Latent Components(DIABLO)was used to integrate transcriptomic data and host phenotypic traits related to milk composition,SC composition,and udder health to identify hub variables for subclinical IMI detection.Results A total of 1,682 and 2,427 differentially expressed genes(DEGs)were identified when comparing Prototheca spp.and S.agalactiae to healthy animals,respectively.Pathogen-specific pathway analyses evidenced that Proto-theca’s infection upregulated antigen processing and lymphocyte proliferation pathways while S.agalactiae induced a reduction of energy-related pathways like the tricarboxylic acid cycle,and carbohydrate and lipid metabolism.The integrative analysis of commonly shared DEGs between the two pathogens(n=681)referred to the core-mastitis response genes,and phenotypic data evidenced a strong covariation between those genes and the flow cytometry immune cells(r2=0.72),followed by the udder health(r2=0.64)and milk quality parameters(r2=0.64).Variables with r≥0.90 were used to build a network in which the top 20 hub variables were identified with the Cytoscape cyto-hubba plug-in.The genes in common between DIABLO and cytohubba(n=10)were submitted to a ROC analysis which showed they had excellent predictive performances in terms of discriminating healthy and mastitis-affected animals(sensitivity>0.89,specificity>0.81,accuracy>0.87,and precision>0.69).Among these genes,CIITA could play a key role in regulating the animals’response to subclinical IMI.Conclusions Despite some differences in the enriched pathways,the two mastitis-causing pathogens seemed to induce a shared host immune-transcriptomic response.The hub variables identified with the integrative approach might be included in screening and diagnostic tools for subclinical IMI detection.
文摘In the recent years, the number of endangered animals, both referred to livestock and wild species, has grown enormously. The “livestock” term refers to animals domesticated for producing commodities for man such as food, fiber and draught. Livestock biodiversity is integral to our culture, history, environment, and economy. Thousands of livestock breeds have evolved over time to suit particular environments and farming systems. Conservation and analyses of these genetic resources rely on demographic characterization and correct breeding schemes. In addition, molecular genetic studies allow to identify and monitor the genetic diversity within and across breeds and to reconstruct their evolution history. The conservation of livestock variability is also a crucial element in order to preserve and valorise specific nutritional and nutraceutical properties of animal products. Efficient ex situ and in situ conservation strategies, as well as the creation of bio-banks and specific biotechnological and bioinformatics tools for genetic analyses and digital preservation, are obligatory requirements in order to implement an appropriate action for the conservation of animal biodiversity. The main issues concerning different species are summarised, with particular reference to the livestock biodiversity still existing. Some examples of ex situ conservation strategies, which mainly refer to cryoconservation of semen, ova, embryos or tissues, developed in Italy, are presented, and the different actions in defense of Animal Genetic Resources (AnGR) developed within the European Community are illustrated. Interestingly, the same strategies for biological and digital analyses and preservation of livestock biodiversity can be exported to wild endangered animals in order to plan a correct conservation and repopulation of the species. Furthermore, the European Union has set up the guidelines to safeguard the biodiversity and to combat the extinction of animal species, and has made the protection of biodiversity and ecosystems one of the main objectives of the Sixth Environment Action Programme.
