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 synthesi...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.展开更多
In this paper,we describe the data management practices and services developed for making FAIR compliant a scientific archive of Scanning Tunneling Microscopy(STM)images.As a first step,we extracted the instrument met...In this paper,we describe the data management practices and services developed for making FAIR compliant a scientific archive of Scanning Tunneling Microscopy(STM)images.As a first step,we extracted the instrument metadata of each image of the dataset to create a structured database.We then enriched these metadata with information on the structure and composition of the surface by means of a pipeline that leverages human annotation,machine learning techniques,and instrument metadata filtering.To visually explore both images and metadata,as well as to improve the accessibility and usability of the dataset,we developed"STM explorer"as a web service integrated within the Trieste Advanced Data services(TriDAS)website.On top of these data services and tools,we propose an implementation of the W3C PROV standard to describe provenance metadata of STM images.展开更多
基金funded by the Italian Ministry of Education,University and Research(PRIN GEN2PHEN)
文摘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.
基金supported by funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No.857650EOSC-Pillar project and European Union's Horizon 2020 research and innovation programme under grant agreement No.101007417 within the framework of the NFFA-Europe Pilot Joint Activities。
文摘In this paper,we describe the data management practices and services developed for making FAIR compliant a scientific archive of Scanning Tunneling Microscopy(STM)images.As a first step,we extracted the instrument metadata of each image of the dataset to create a structured database.We then enriched these metadata with information on the structure and composition of the surface by means of a pipeline that leverages human annotation,machine learning techniques,and instrument metadata filtering.To visually explore both images and metadata,as well as to improve the accessibility and usability of the dataset,we developed"STM explorer"as a web service integrated within the Trieste Advanced Data services(TriDAS)website.On top of these data services and tools,we propose an implementation of the W3C PROV standard to describe provenance metadata of STM images.
