An improved microRNA annotation of the canine genome

The domestic dog, Canis familiaris, is a valuable model for studying human diseases. The publication of the latest Canine genome build and annotation, CanFam3.1 provides an opportunity to enhance our understanding of gene regulation across tissues in the dog model system. In this study, we used the latest dog genome assembly and small RNA sequencing data from 9 different dog tissues to predict novel miRNAs in the dog genome, as well as to annotate conserved miRNAs from the miRBase database that were missing from the current dog annotation. We used both miRCat and miRDeep2 algorithms to computationally predict miRNA loci. The resulting, putative hairpin sequences were analysed in order to discard false positives, based on predicted secondary structures and patterns of small RNA read alignments. Results were further divided into high and low confidence miRNAs, using the same criteria. We generated tissue specific expression profiles for the resulting set of 811 loci: 720 conserved miRNAs, (207 of which had not been previously annotated in the dog genome) and 91 novel miRNA loci. Comparative analyses revealed 8 putative homologues of some novel miRNA in ferret, and one in microbat. All miRNAs were also classified into the genic and intergenic categories, based on the Ensembl RefSeq gene annotation for CanFam3.1. This additionally allowed us to identify four previously undescribed MiRtrons among our total set of miRNAs. We additionally annotated piRNAs, using proTRAC on the same input data. We thus identified 263 putative clusters, most of which (211 clusters) were found to be expressed in testis. Our results represent an important improvement of the dog genome annotation, paving the way to further research on the evolution of gene regulation, as well as on the contribution of post-transcriptional regulation to pathological conditions

Genome-wide microRNA screening in Nile tilapia reveals pervasive isomiRs’ transcription, sex-biased arm switching and increasing complexity of expression throughout development

MicroRNAs (miRNAs) are key regulators of gene expression in multicellular organisms. The elucidation of miRNA function and evolution depends on the identification and characterization of miRNA repertoire of strategic organisms, as the fast-evolving cichlid fishes. Using RNA-seq and comparative genomics we carried out an in-depth report of miRNAs in Nile tilapia (Oreochromis niloticus), an emergent model organism to investigate evo-devo mechanisms. Five hundred known miRNAs and almost one hundred putative novel vertebrate miRNAs have been identified, many of which seem to be teleost-specific, cichlid-specific or tilapia-specific. Abundant miRNA isoforms (isomiRs) were identified with modifications in both 5p and 3p miRNA transcripts. Changes in arm usage (arm switching) of nine miRNAs were detected in early development, adult stage and even between male and female samples. We found an increasing complexity of miRNA expression during ontogenetic development, revealing a remarkable synchronism between the rate of new miRNAs recruitment and morphological changes. Overall, our results enlarge vertebrate miRNA collection and reveal a notable differential ratio of miRNA arms and isoforms influenced by sex and developmental life stage, providing a better picture of the evolutionary and spatiotemporal dynamics of miRNAs

Pengaruh Good Corporate Governance Terhadap Company Performance Pada Perusahaan Manufaktur Di Indonesia Dan Thailand

The purpose of this study is to obtain empirical evidence and to test the factors that affect company performance between Indonesia and Thailand, by using ownership concentration, managerial ownership, institutional ownership, board size, audit committee, audit type, firm size, financial leverage, and firm age variables. The firm performance is measured by using Tobin's Q. Population of this study is the manufacturing companies listed in Indonesia Stock Exchange (IDX) and Stock Exchange Thailand (SET) during 2013 to 2015. The sample is obtained by using purposive sampling method. There are 129 samples from Indonesia, and 165 samples from Thailand selected as the final samples. Hypotheses tested by using multiple regression analysis. The result of this studies indicates that board size and firm age shows impact to company performance in both country, Indonesia and Thailand. But ownership concentration, managerial ownership, institutional ownership, audit committee, audit type, firm size, and financial leverage do not have impact on company performance in Indonesia and Thailand

Escaping the trap of "blocking": A kinetic model linking economic development and political competition

In this paper we present a kinetic model with evolutive stochastic game-type interactions, analyzing the relationship between the level of political competition in a society and the degree of economic liberalization. The above issue regards the complex interactions between economy and institutional policies intended to introduce technological innovations in a society, where technological innovations are intended in a broad sense comprehending reforms critical to production [3]. A special focus is placed on the political replacement effect described in a macroscopic model by Acemoglu and Robinson (AR-model [1], henceforth), which can determine the phenomenon of innovation 'blocking', possibly leading to economic backwardness. One of the goals of our modelization is to obtain a mesoscopic dynamical model whose macroscopic outputs are qualitatively comparable with stylized facts of the AR-model and the comparison is settled in a number of case studies. A set of numerical solutions is presented showing the non monotonous relationship between economic liberalization and political competition in particular conditions, which can be considered as an emergent phenomenon of the analyzed complex socioeconomic interaction dynamics.Fil: Dolfin, M.. Universita Degli Studi Di Messina; ItaliaFil: Knopoff, Damián Alejandro. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Centro de Investigación y Estudios de Matemática. Universidad Nacional de Córdoba. Centro de Investigación y Estudios de Matemática; ArgentinaFil: Leonida, L.. University College London; Estados UnidosFil: Maimone Ansaldo Patti, D.. Universita Degli Studi Di Messina; Itali