Selection among site-dependent structurally constrained substitution models of protein evolution by approximate Bayesian computation

Motivation The selection among substitution models of molecular evolution is fundamental for obtaining accurate phylogenetic inferences. At the protein level, evolutionary analyses are traditionally based on empirical substitution models but these models make unrealistic assumptions and are being surpassed by structurally constrained substitution (SCS) models. The SCS models often consider site-dependent evolution, a process that provides realism but complicates their implementation into likelihood functions that are commonly used for substitution model selection. Results We present a method to perform selection among site-dependent SCS models, also among empirical and site-dependent SCS models, based on the approximate Bayesian computation (ABC) approach and its implementation into the computational framework ProteinModelerABC. The framework implements ABC with and without regression adjustments and includes diverse empirical and site-dependent SCS models of protein evolution. Using extensive simulated data, we found that it provides selection among SCS and empirical models with acceptable accuracy. As illustrative examples, we applied the framework to analyze a variety of protein families observing that SCS models fit them better than the corresponding best-fitting empirical substitution models. Availability and implementation ProteinModelerABC is freely available from https://github.com/DavidFerreiro/ProteinModelerABC, can run in parallel and includes a graphical user interface. The framework is distributed with detailed documentation and ready-to-use examples.Agencia Estatal de Investigación | Ref. PID2019-107931GA-I00Xunta de Galicia | Ref. ED481A-2020/192Universidade de Vigo/CISU

An internal ribosome entry site element directs the synthesis of the 80 kDa isoforms of protein 4.1R

<p>Abstract</p> <p>Background</p> <p>In red blood cells, protein 4.1 (4.1R) is an 80 kDa protein that stabilizes the spectrin-actin network and anchors it to the plasma membrane through its FERM domain. While the expression pattern of 4.1R in mature red cells is relatively simple, a rather complex array of 4.1R protein isoforms varying in N-terminal extensions, internal sequences and subcellular locations has been identified in nucleated cells. Among these, 135 kDa and 80 kDa isoforms have different N-terminal extensions and are expressed either from AUG1- or AUG2-containing mRNAs, respectively. These two types of mRNAs, varying solely by presence/absence of 17 nucleotides (nt) which contain the AUG1 codon, are produced by alternative splicing of the 4.1R pre-mRNA. It is unknown whether the 699 nt region comprised between AUG1 and AUG2, kept as a 5' untranslated region in AUG2-containing mRNAs, plays a role on 4.1R mRNA translation.</p> <p>Results</p> <p>By analyzing the <it>in vitro </it>expression of a panel of naturally occurring 4.1R cDNAs, we observed that all AUG1/AUG2-containing cDNAs gave rise to both long, 135 kDa, and short, 80 kDa, 4.1R isoforms. More importantly, similar results were also observed in cells transfected with this set of 4.1R cDNAs. Mutational studies indicated that the short isoforms were not proteolytic products of the long isoforms but products synthesized from AUG2. The presence of a cryptic promoter in the 4.1R cDNA sequence was also discounted. When a 583 nt sequence comprised between AUG1 and AUG2 was introduced into bicistronic vectors it directed protein expression from the second cistron. This was also the case when ribosome scanning was abolished by introduction of a stable hairpin at the 5' region of the first cistron. Deletion analysis of the 583 nt sequence indicated that nucleotides 170 to 368 are essential for expression of the second cistron. The polypyrimidine tract-binding protein bound to the 583 nt active sequence but not to an inactive 3'-fragment of 149 nucleotides.</p> <p>Conclusion</p> <p>Our study is the first demonstration of an internal ribosome entry site as a mechanism ensuring the production of 80 kDa isoforms of protein 4.1R. This mechanism might also account for the generation of 60 kDa isoforms of 4.1R from a downstream AUG3. Our results reveal an additional level of control to 4.1R gene expression pathways and will contribute to the understanding of the biology of proteins 4.1R and their homologues, comprising an ample family of proteins involved in cytoskeletal organization.</p

Waste clay materials as pozzolanic additions

En: 1st Spanish National Conference on Advances in Materials Recycling and Eco – Energy Madrid, 12-13 November 2009.-- Editors: F. A. López, F. Puertas, F. J. Alguacil and A. Guerrero.-- 4 pages, 3 figures.The building materials industries have made improvements in manufacturing processes. However, with the implementation of quality systems, more compliance, with new standard more restrictive, and especially by the competition between products, it is inevitable that industries deemed a rejection of material unsuitable for marketing or materials waste. The wastes from the ceramic industry (ceramic waste) may have characteristics suitable for use as pozzolanic materials, as it is known that the first materials used as pozzolans were heat-treated clays, material like clay products.This research was funded by a Science and Technology Commission (CICYT) (Research Project AMB96-1095).Peer reviewe

New insight on vertebral anomalies in cultured Senegalese sole (Solea senegalensis, Kaup) at early stages of development

Senegalese sole (Solea senegalensis, Kaup) is a promising flatfish species in aquaculture. However, skeletal anomalies are still a great concern in sole farming. Investigation of this issue is crucial to improving larval quality and optimizing production. The aim of this study was to thoroughly assess anomalies in the rachis of reared sole at early developmental stages. Sole (n = 507) were sampled at 31 or 32 days after hatching (dah). The specimens were stained with alcian blue and alizarin red and evaluated for the detection of vertebral deformities. Most fish presented 9:34:3 vertebrae in abdominal, caudal and caudal complex regions, respectively. Remarkably, all specimens showed at least one spinal anomaly. Alterations of neural/haemal elements, as well as deformities of hypurals, parhypural and epural, were recurrent. Vertebral body anomalies and/or vertebral column deviations were identified in 52% of the individuals. Vertebral deformations and fusions were common, especially in caudal complex. ‘Minor’ anomalies were predominant, and some of the detected disorders might be a result of non-/low-pathological processes. These results contribute a new insight into the main skeletal anomalies affecting cultured sole larvae. Further research is required to determine their impact on fish welfare and external appearances at commercial stagesConselleria de Economía e Industria - Xunta de Galicia (10MMA020E) Programa de Consolidación e Estructuración de Unidades de InvestigaciónCompetitivas GPC2015/034 A.M. de Azevedo held a University Professorship Formation (FPU) grant from the Spanish Ministry of Education.S

La importancia de la competencia social en jóvenes que cumplen medida judicial educativa en medio abierto

Introducción: Definir la competencia social no es tarea fácil, debido a su naturaleza pluriconceptual, recogiendo diversas acepciones que hacen referencia a este mismo concepto (CORONEL, LEVIN, & MEJAIL, 2011). Esta puede definirse como un conglomerado de habilidades diversas que se emplean con distintos fines (KELLY, 2002). También hace referencia al conjunto de las habilidades sociales, cognitivas y emocionales necesarias para una inclusión significativa en el grupo social (GARRIDO, 2005) (...

Estilos educativos familiares como factor de riesgo en jóvenes con medida judicial

Introducción: El objeto de estudio de este trabajo es la comprobación empírica de la presencia de ciertos factores familiares, tanto de riesgo como de protección que están presentes en la familia de jóvenes en situación de conflicto social. Este estudio trata de conocer, la implicación de los distintos estilos educativos parentales, comprobando en qué medida el perfil resultante se ve avalado por las conclusiones a las que llegaron algunos de los estudios con mayor reconocimiento en este ámbito. Al mismo tiempo que con la mirada puesta en adecuación de las intervenciones socioeducativas que se llevan a cabo en el cumplimiento de las medidas educativas en medio abierto que cumple la juventud en conflicto social tras resolución judicial

Skeletal Anomalies in Senegalese Sole (Solea senegalensis, Kaup) Fed with Different Commercial Enriched Artemia: A Study in Postlarvae and Juveniles

The high incidence of skeletal anomalies in Senegalese sole (Solea senegalensis) still constitutes a bottleneck constraining its production. There are diverse commercially available products for the enrichment of live preys, but few reports of their influence on skeletogenesis in Senegalese sole. This study evaluated the presence of vertebral anomalies in postlarvae and juvenile Senegalese sole fed with Artemia spp. metanauplii enriched with four commercial products (EA, EB, EC, and ED) in a fish farm. The most frequent alterations consisted of deformations of the neural/haemal arches and spines and fusions and deformations of hypurals, epural, or parhypural. The correspondence analysis ordered fish from each age in separated semiaxis, indicating the presence of different anomaly patterns for the two sampled stages. The results showed only very light changes in the frequency of vertebral abnormalities among tested enrichment products, i.e., individuals from EC and EA lots displayed less vertebral body anomalies and/or vertebral column deviations at 31 and 105 days after hatching, respectively. The existence of a large shared malformation pattern in all the experimental groups leads to impute to the rearing conditions as the main driving factor of the onset of such group of anomalies, probably masking some dietary effectThis research was funded by “Consellería de Economía e Industria” of Xunta de Galicia (10MMA020E) and Stolt Sea Farm and by “Programa de Consolidación e Estructuración de Unidades de Investigación Competitivas GPC2015/034”, SpainS

Segurança alimentar e sustentabilidade: o caso do setor do arroz no Vale do Tejo e Sorraia - perceção e práticas

O artigo apresenta as perceções e práticas de sustentabilidade do setor do arroz no Vale do Tejo e Sorraia, um território que se destaca pela importância do setor agro-alimentar em termos nacionais e europeus. O estudo de caso envolveu atores fundamentais da cadeia de valor do arroz no território (orizicultores, associações socioprofissionais, cooperativa, indústrias e investigadores de melhoramento genético). O cultivo de arroz no Vale do Tejo e Sorraia com preocupações de sustentabilidade contribui para a manutenção dos orizicultores e de empresas industriais no território, promovendo a biodiversidade e a segurança alimentar.L'article présente les perceptions e pratiques de développement durable dans le sector du riz dans le Vale do Tejo et Sorraia, un territoire qui se détache pour l'importance du secteur agro-alimentaire national et européen. L'étude de cause á englobé acteurs fondamentaux de la chaine de valeur do riz dans le territoire (riziculteurs, associations socioprofessionnelles, coopérative, industries et investigateurs de développement génétique). La cultivation de riz dans le Vale do Tejo et Sorraia avec des préoccupations de développement contribue à la manutention des riziculteurs e des entreprises industrielles dans le territoire, développent la biodiversité et le sécurité alimentaire.El artículo presenta las percepciones y prácticas del sector del arroz en el Vale del Tajo y Sorraia, un territorio en el cual se destaca la importancia del sector agroalimentario a nivel nacional e europeo. El estudio de caso ha envuelto factores fundamentales de la cadena de valor del arroz en el territorio (productores de arroz, asociaciones socio profesionales, cooperativas, industrias e investigadores de mejoramiento genético). El cultivo del arroz en el Vale del Tajo y Sorraia con preocupaciones de sustentabilidad, contribuí para la manutención de los productores de arroz y compañías industriáis en el territorio, promoviendo la biodiversidad y seguridad alimentar.The paper presents sustainability perceptions and pratics of the rice sector in the case of Vale do Tejo e Sorraia, a territory with an important presence of agro-food industry in national and European contexts. The case study involved key actors in the value chain (farmers, industry, socioprofissional associations, a cooperative, and research centres). Sustainable practices in rice cultivation helps to ensure the maintainance of farmers and industry in this territory, promoting biodiversity and food security

Skeletal anomalies in reared Senegalese sole Solea senegalensis juveniles: a radiographic approach

Reared Senegalese sole Solea senegalensis Kaup show a high incidence of vertebral anomalies; however, little is known about its skeletal anomaly profile in the later farming phases. The purpose of this study was to provide a detailed description and quantification of the most common skeletal anomalies in reared Senegalese sole in the juvenile stage by means of computed radiography. A total of 374 Senegalese sole were classified according to the external morphology of the fish as normal or altered and then radiographed in latero-lateral and in dorso-ventral projections. Radiographic evaluation of anomalies focused especially on vertebral body anomalies (VBA) and vertebral column deviations (VCD). The 2 orthogonal projections provided a more complete visualization of the skeleton. Approximately 75% of the individuals showed at least 1 anomaly, while VBA and/or VCD were detected in 48.9% of the specimens. Regarding external morphology, 88% of the fish were categorized as normal, although about 72% of these normal fish displayed abnormalities in radiographies. The most frequent anomalies consisted of deformations of the caudal complex plates (hypurals, parhypural and epural), preurals and caudal vertebrae. Scoliosis was the most prevalent among VCD, affecting the caudal area in almost 15% of the individuals. The anomaly profile at the juvenile stages showed some differences compared to what has been reported previously in earlier stages of development. In light of these results, further investigation into the progression of skeletal anomalies over time and the causative factors at later stages is requiredThis work was supported by Consellería de Economía e Industria of Xunta de Galicia (10MMA020E) and Programa de Consolidación e Estructuración de Unidades de Investigación Competitivas GPC2015/034, Spain. A.M.A. held a University Professorship Formation (FPU) grant from the Spanish Ministry of EducationS

Developmental genoarchitectonics as a key tool to interpret the mature anatomy of the chondrichthyan hypothalamus according to the prosomeric model

The hypothalamus is a key vertebrate brain region involved in survival and physiological functions. Understanding hypothalamic organization and evolution is important to deciphering many aspects of vertebrate biology. Recent comparative studies based on gene expression patterns have proposed the existence of hypothalamic histogenetic domains (paraventricular, TPa/PPa; subparaventricular, TSPa/PSPa; tuberal, Tu/RTu; perimamillary, PM/PRM; and mamillary, MM/RM), revealing conserved evolutionary trends. To shed light on the functional relevance of these histogenetic domains, this work aims to interpret the location of developed cell groups according to the prosomeric model in the hypothalamus of the catshark Scyliorhinus canicula, a representative of Chondrichthyans (the sister group of Osteichthyes, at the base of the gnathostome lineage). To this end, we review in detail the expression patterns of ScOtp, ScDlx2, and ScPitx2, as well as Pax6-immunoreactivity in embryos at stage 32, when the morphology of the adult catshark hypothalamus is already organized. We also propose homologies with mammals when possible. This study provides a comprehensive tool to better understand previous and novel data on hypothalamic development and evolutionThis work was supported by Ministerio de Economía, Industria y Competitividad – Agencia Estatal de Investigación (grant No. BFU2017-89861-P) partially financed by the European Social Fund, and by Xunta de Galicia (grant No. ED431C 2021/18)S