Back to Water: Signature of Adaptive Evolution in Cetacean Mitochondrial tRNAs

Abstract The mitochondrion is the power plant of the eukaryotic cell, and tRNAs are the fundamental components of its translational machinery. In the present paper, the evolution of mitochondrial tRNAs was investigated in the Cetacea, a clade of Cetartiodactyla that retuned to water and thus had to adapt its metabolism to a different medium than that of its mainland ancestors. Our analysis focussed on identifying the factors that influenced the evolution of Cetacea tRNA double-helix elements, which play a pivotal role in the formation of the secondary and tertiary structures of each tRNA and consequently manipulate the whole translation machinery of the mitochondrion. Our analyses showed that the substitution pathways in the stems of different tRNAs were influenced by various factors, determining a molecular evolution that was unique to each of the 22 tRNAs. Our data suggested that the composition, AT-skew, and GC-skew of the tRNA stems were the main factors influencing the substitution process. In particular, the range of variation and the fluctuation of these parameters affected the fate of single tRNAs. Strong heterogeneity was observed among the different species of Cetacea. Finally, it appears that the evolution of mitochondrial tRNAs was also shaped by the environments in which the Cetacean taxa differentiated. This latter effect was particularly evident in toothed whales that either live in freshwater or are deep divers

An integrated genomic approach for the study of mandibular prognathism in the European seabass (Dicentrarchus labrax)

Skeletal anomalies in farmed fish are a relevant issue affecting animal welfare and health and causing significant economic losses. Here, a high-density genetic map of European seabass for QTL mapping of jaw deformity was constructed and a genome-wide association study (GWAS) was carried out on a total of 298 juveniles, 148 of which belonged to four full-sib families. Out of 298 fish, 107 were affected by mandibular prognathism (MP). Three significant QTLs and two candidate SNPs associated with MP were identified. The two GWAS candidate markers were located on ChrX and Chr17, both in close proximity with the peaks of the two most significant QTLs. Notably, the SNP marker on Chr17 was positioned within the Sobp gene coding region, which plays a pivotal role in craniofacial development. The analysis of differentially expressed genes in jaw-deformed animals highlighted the "nervous system development" as a crucial pathway in MP. In particular, Zic2, a key gene for craniofacial morphogenesis in model species, was significantly down-regulated in MP-affected animals. Gene expression data revealed also a significant down-regulation of Sobp in deformed larvae. Our analyses, integrating transcriptomic and GWA methods, provide evidence for putative mechanisms underlying seabass jaw deformity

Corporate board network and information flows in the Italian Stock Exchange

EnIn this work we investigate the governance models of listed companies in the Italian Stock Exchange. We use a network approach in order to investigate the interlinks among board of directors. A graph theoretical approach and the vertex centrality measures quantify the role of network and the intensity of the relationships, according to the assumption that the information conveyed by such interconnections could exert some impact on market prices. A weighted graph represent the listed companies (vertices) and their relationships (weighted edges) by using as centrality measure the flow-betweenness. It is expected that this centrality measure may give a representation of the intensity of the relationship between companies, capturing the volume of information flowing from a vertex to another one

Critical Line in Random Threshold Networks with Inhomogeneous Thresholds

We calculate analytically the critical connectivity $K_c$ of Random Threshold Networks (RTN) for homogeneous and inhomogeneous thresholds, and confirm the results by numerical simulations. We find a super-linear increase of $K_c$ with the (average) absolute threshold $|h|$, which approaches $K_c(|h|) \sim h^2/(2\ln{|h|})$ for large $|h|$, and show that this asymptotic scaling is universal for RTN with Poissonian distributed connectivity and threshold distributions with a variance that grows slower than $h^2$. Interestingly, we find that inhomogeneous distribution of thresholds leads to increased propagation of perturbations for sparsely connected networks, while for densely connected networks damage is reduced; the cross-over point yields a novel, characteristic connectivity $K_d$, that has no counterpart in Boolean networks. Last, local correlations between node thresholds and in-degree are introduced. Here, numerical simulations show that even weak (anti-)correlations can lead to a transition from ordered to chaotic dynamics, and vice versa. It is shown that the naive mean-field assumption typical for the annealed approximation leads to false predictions in this case, since correlations between thresholds and out-degree that emerge as a side-effect strongly modify damage propagation behavior.Comment: 18 figures, 17 pages revte

A Microarray study of Carpet-Shell Clam (Ruditapes decussatus) shows common and organ-specific growth-related gene expression Differences in gills and digestive gland

Growth rate is one of the most important traits from the point of view of individual fitness and commercial production in mollusks, but its molecular and physiological basis is poorly known. We have studied differential gene expression related to differences in growth rate in adult individuals of the commercial marine clam Ruditapes decussatus. Gene expression in the gills and the digestive gland was analyzed in 5 fast-growing and five slow-growing animals by means of an oligonucleotide microarray containing 14,003 probes. A total of 356 differentially expressed genes (DEG) were found. We tested the hypothesis that differential expression might be concentrated at the growth control gene core (GCGC), i. e., the set of genes that underlie the molecular mechanisms of genetic control of tissue and organ growth and body size, as demonstrated in model organisms. The GCGC includes the genes coding for enzymes of the insulin/ insulin-like growth factor signaling pathway (IIS), enzymes of four additional signaling pathways (Raf/ Ras/ Mapk, Jnk, TOR, and Hippo), and transcription factors acting at the end of those pathways. Only two out of 97 GCGC genes present in themicroarray showed differential expression, indicating a very little contribution of GCGC genes to growth-related differential gene expression. Forty eight DEGs were shared by both organs, with gene ontology (GO) annotations corresponding to transcription regulation, RNA splicing, sugar metabolism, protein catabolism, immunity, defense against pathogens, and fatty acid biosynthesis. GO termenrichment tests indicated that genes related to growth regulation, development and morphogenesis, extracellular matrix proteins, and proteolysis were overrepresented in the gills. In the digestive gland overrepresented GO terms referred to gene expression control through chromatin rearrangement, RAS-related small GTPases, glucolysis, and energy metabolism. These analyses suggest a relevant role of, among others, some genes related to the IIS, such as the ParaHox gene Xlox, CCAR and the CCN family of secreted proteins, in the regulation of growth in bivalves.Direccion General de Investigacion Cientifica y Tecnica of the Spanish Government [AGL2010-16743, AGL2013-49144-C3-3-R]; COMPETE Program; Portuguese National Funds [PEst-255 C/MAR/LA0015/2011]; Portuguese FCT [UID/Multi/04326/2013]; Generalitat Valenciana; Ministry of Education, Culture, and Sports of the Spanish Government; Association of European Marine Biology Laboratoriesinfo:eu-repo/semantics/publishedVersio

The Islamic West in the Work of al-Muḳaddasī

In this article we are going to approach the geographical work of al-Muḳaddasī (380/990), Kitāb aḥsan al-taqāsīm fī maʿrifat al-aqālīm (The best divisions for knowledge of the regions). His geographical conception and his systematic methodology make him one of the best representative figures of the geographical literature of the 10th century. Even though, his work includes the geography of empire controlled by Muslims (mamlaka), my contribution just will focus on the Western Islamic world, of which al-Muḳaddasī offers an interesting point of view, firstly for his oriental origin, and secondly for the sources used (he didn't travel to al-Ándalus, and there are few possibilities that he did it to the Maghreb, but that doesn't diminish his work). As an intellectual of the genre al-masālik wa-l-mamālik (the paths and kingdoms), he focused on toponymies and principle western routes, which are exhaustively detailed in his work. However, his work as an expert went beyond a part of the physical geographic, so that he focused his interest also in aspects typical of the human geographic. For that reason, his work offers a lot of details about populations of the areas described (habits, food, clothes, religion etc.), providing a testimony which is unique and precise, with a huge value for who is interested in Western Islamic medieval world.En el presente artículo se hará una aproximación a la obra geográfica de al-Muqaddasī (380/990), Kitāb aḥsan al-taqāsīm fī maʿrifat al-aqālīm (La mejor división para el conocimiento de las provincias). Su concepción geográfica y su metodología sistemática lo convierten en uno de los mejores representantes de la literatura geográfica del siglo X. Aunque su obra abarca la geografía del imperio controlado por los musulmanes (mamlaka), el trabajo se centrará exclusivamente en Occidente islámico, del que al-Muqaddasī ofrece una visión muy interesante, tanto por su origen oriental como por las fuentes utilizadas (no viajó a al-Andalus y es poco probable que lo hiciera al Mágreb, lo cual no resta objetividad a su trabajo). Como cultivador del género de al-masālik wa-l-mamālik (Los caminos y los reinos), se ocupó de los topónimos y rutas principales occidentales, los cuales detalla exhaustivamente en su obra. Pero su labor de especialista fue más allá, interesándose por aspectos propios de la geografía física y humana. Por esta razón, en su obra ofrece muchos detalles sobre las poblaciones de las zonas descritas (costumbres, tipos de comida, vestimenta, religión etc...), aportando un testimonio único y preciso de gran valor para todos los interesados el Occidente islámico medieval

Al-Ándalus y el Mágreb desde Oriente: aproximación a la obra geográfica de al-Muqaddasī (s. IV / X)

Trabajo de grado. Grado en Estudios Árabes e Islámicos. Curso 2018-2019[ES]El presente trabajo aborda la obra del geógrafo al-Muqaddasī (380/990), autor del Kitāb aḥsan al-taqāsīm fī maʿrifat al-aqālīm (La mejor división para el conocimiento de las pro-vincias), y la visión que ofrece del Mágreb y al-Ándalus. Al-Muqaddasī se vincula al llamado género de al-masālik wa-l-mamālik (los caminos y los reinos). Su concepción territorial sigue la escuela de al-Baljī (322/934), pero plantea un número distinto de provincias (aqālīm) con particularidades y paralelismos o elementos comunes que forman el dominio espacial del islam (mamlakat al-islām). Esta concepción y su metodología sistemática lo convierten quizá en el mejor representante de este tipo de literatura geográfica. En el trabajo se ofrece la traducción anotada de los fragmentos dedicados al Mágreb y al-Ándalus, en los cuales, al-Muqaddasī, además de ocuparse de los principales topónimos, se ocupa asimismo de las curiosidades, las características, las costumbres, la lengua, etc. de una zona geográfica que no conoció de un modo directo.[EN]This essay presents the work of the geographer al-Muqaddasī (380/990), the author of Kitāb aḥsan al-taqāsīm fī maʿrifat al-aqālīm (The best divisions for knowledge of the regions), and the point of view that he provides of the Maghreb and al-Andalus. Al-Muqaddasī belongs to the genre called al-masālik wa-l-mamālik (the paths and kingdoms). His territorial’s con-ception follows the al-Balkhī school (322/934), although he sets out a different number of provinces (aqālīm) with peculiarities and correspondences or common elements that form the land of islam (mamlakat al-islām). This conception and his systematic methodology maybe make him the best representative of this type of geographic literature. In this essay we provide the commented translation of the passages related to al-Maghreb and al-Andalus, in which, al-Muqaddasī, besides dealing with the main toponymies, focuses on some curiosities, features, customs, languages, etc. of a geographic area that he never knew in a direct way

Preventing the deterioration of bank loan portfolio quality: a focus on unlikely-to-pay loans

This study examines determinants of: (a) new flows of unlikely-to-pay loans (UTPs), comparing them to determinants of bad loans; and (b) out-flows from UTPs to performing and bad loans. A novel panel data-set covering the period 2010–2016 is used to test hypotheses relating to lending policy, bank capitalization, bad management, and procyclical credit policy. Determinants identified by the existing literature on the wider category of all non-performing loans are in part confirmed for UTPs and in part rejected. The main findings show: (i) a positive relationship exists between bank capitalization and new flows of both UTPs and bad loans; (ii) reducing cost efficiency increases both new flows of UTPs and the worsening of UTPs towards bad loans; and (iii) having a specific unit/office to manage impaired loans increases flows from UTPs to performing loans, but does not decrease flows to bad loans. Our study is useful for banks seeking to prevent new impaired exposures, to accelerate the transition from UTPs to performing loans, and to prevent UTPs worsening to bad loans. The findings reveal the importance of sound and proactive UTP management, given the need for banks to increase provisions for covering UTPs in the near future