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    Multi-omic analyses in Abyssinian cats with primary renal amyloid deposits
    (Springer Nature Limited, 2021-04-16) Genova F; Nonnis S; Maffioli E; Tedeschi G; Strillacci MG; Carisetti M; Sironi G; Cupaioli FA; Di Nanni N; Mezzelani A; Mosca E; Helps CR; Leegwater PAJ; Dorso L; 99 Lives Consortium; Longeri M
    The amyloidoses constitute a group of diseases occurring in humans and animals that are characterized by abnormal deposits of aggregated proteins in organs, affecting their structure and function. In the Abyssinian cat breed, a familial form of renal amyloidosis has been described. In this study, multi-omics analyses were applied and integrated to explore some aspects of the unknown pathogenetic processes in cats. Whole-genome sequences of two affected Abyssinians and 195 controls of other breeds (part of the 99 Lives initiative) were screened to prioritize potential disease-associated variants. Proteome and miRNAome from formalin-fixed paraffin-embedded kidney specimens of fully necropsied Abyssinian cats, three affected and three non-amyloidosis-affected were characterized. While the trigger of the disorder remains unclear, overall, (i) 35,960 genomic variants were detected; (ii) 215 and 56 proteins were identified as exclusive or overexpressed in the affected and control kidneys, respectively; (iii) 60 miRNAs were differentially expressed, 20 of which are newly described. With omics data integration, the general conclusions are: (i) the familial amyloid renal form in Abyssinians is not a simple monogenic trait; (ii) amyloid deposition is not triggered by mutated amyloidogenic proteins but is a mix of proteins codified by wild-type genes; (iii) the form is biochemically classifiable as AA amyloidosis.
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    MicroRNA and mRNA analysis of two species of New Zealand Pachycladon : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Genetics at Massey University, Manawatu, New Zealand
    (Massey University, 2014) Carr, Louise Michelle
    MicroRNAs (miRNAs) are small, non-coding RNAs important in post-transcriptional regulation. In this study, potential miRNAs from two New Zealand Pachycladon species, P. cheesemanii and P. fastigiatum, are identified and compared. Sixteen miRNAs were differentially expressed between the species, most of which have roles in flower and leaf development. Potential targets for 15 miRNAs were located in expressed sequence tag (EST) libraries for P. cheesemanii and/or P. fastigiatum, including a new potential relationship in P. cheesemanii between miR825 and MYB29 (AT5G07690), a transcription factor involved in the synthesis of methionine-derived glucosinolates. From the results of the differential expression analysis and target identification, 27 miRNAs from 21 miRNA families were chosen for pre-miRNA sequencing. Sequences of 15 P. cheesemanii miRNA hairpins and 13 P. fastigiatum miRNA hairpins were validated experimentally. Additionally, mRNA-Seq data obtained at the same time as the miRNAs were analysed. A gene ontology analysis indicated enriched terms for defence responses and miRNAs in P. fastigiatum. This study is the first investigation of the miRNAs present in Pachycladon and how their differential expression contributes to the adaptive divergence between the species.