Evolutionary Trends in the Mitochondrial Genome of Archaeplastida: How Does the GC Bias Affect the Transition from Water to Land?

[EN] Among the most intriguing mysteries in the evolutionary biology of photosynthetic organisms are the genesis and consequences of the dramatic increase in the mitochondrial and nuclear genome sizes, together with the concomitant evolution of the three genetic compartments, particularly during the transition from water to land. To clarify the evolutionary trends in the mitochondrial genome of Archaeplastida, we analyzed the sequences from 37 complete genomes. Therefore, we utilized mitochondrial, plastidial and nuclear ribosomal DNA molecular markers on 100 species of Streptophyta for each subunit. Hierarchical models of sequence evolution were fitted to test the heterogeneity in the base composition. The best resulting phylogenies were used for reconstructing the ancestral Guanine-Cytosine (GC) content and equilibrium GC frequency (GC*) using non-homogeneous and non-stationary models fitted with a maximum likelihood approach. The mitochondrial genome length was strongly related to repetitive sequences across Archaeplastida evolution; however, the length seemed not to be linked to the other studied variables, as different lineages showed diverse evolutionary patterns. In contrast, Streptophyta exhibited a powerful positive relationship between the GC content, non-coding DNA, and repetitive sequences, while the evolution of Chlorophyta reflected a strong positive linear relationship between the genome length and the number of genes.This research was funded by the European Commission (Environment - LIFE Programme) project for the Comunidad Valenciana (Spain), LIFE05 NAT/E/000060.Pedrola-Monfort, J.; Lázaro-Gimeno, D.; Boluda, CG.; Pedrola, L.; Garmendia, A.; Soler, C.; Soriano, JM. (2020). Evolutionary Trends in the Mitochondrial Genome of Archaeplastida: How Does the GC Bias Affect the Transition from Water to Land?. Plants. 9(3):1-15. https://doi.org/10.3390/plants9030358S1159

PCIG: a web-based application to explore immune–genomics interactions across cancer types

Cancer; Application; Genomic alterationsCáncer; Aplicación; Alteraciones genómicasCàncer; Aplicació; Alteracions genòmiquesMotivation Genomic alterations can modulate the tumor immunophenotype depending on their nature and tissue of origin. Although this immune–genomic interaction may shape disease progression and response to immunotherapy, the factors governing such dynamics and the influence of each tissue-specific context remain poorly understood. Results Here, we have developed the PanCancer ImmunoGenomics (PCIG) tool, a web-based resource that provides researchers with the opportunity to mine immunome–genome relationships across several cancer types using data from the Pan-Cancer Analysis of Whole-Genomes (PCAWG) study, which comprises >2,600 samples spanning across 20 different cancer primary sites. PCIG yields an integrative analysis of the crosstalk between somatic genomic alterations and different immune features, thus helping to understand immune response-related processes.This work was supported by the Instituto de Salud Carlos III and co-funded by the European Regional Development Fund (ERDF) [CPII18/00026, PI17/01304], the CIBEREHD and CIBERNED programs from Instituto de Salud Carlos III, the Agència de Gestió d’Ajuts Universitaris i de Recerca, Generalitat de Catalunya [2017 SGR 1035], and Fundación Científica de la Asociación Española Contra el Cáncer [GCB13131592CAST]. S.L. obtained a PFIS grant from Instituto de Salud Carlos III and co-funded by the European Regional Development Fund (ERDF) [FI18/00221]. R.E.F. is supported by a doctoral training grant from MICINN/MINECO [BES-2017-081286] and a mobility grant from Fundació Universitària Agustí Pedro i Pons. This article is based upon work from COST Action [CA17118] and supported by COST (European Cooperation in Science and Technology)

Enfermedades neurológicas hereditarias: genes, mutaciones, clínica y epidemiologia genética (premio Reina Sofía 2004, de prevención de deficiencias)

Esta memoria quiere ser un resumen de los estudios y hallazgos de laboratorio y de las contribuciones científicas de la Unidad de Genética Molecular en el campo de la genética molecular de las enfermedades neurológicas, trastornos que se encuadran en el término de enfermedades raras, así como las aplicaciones en medicina clínica a las que han dado lugar, concretamente por lo que respecta al diagnóstico molecular y al consejo genético. La memoria está dividida en cuatro capítulos que hacen referencia a las ataxias hereditarias, las neuropatías periféricas hereditarias, los trastornos del movimiento y las distrofias musculares. En todos ellos se mencionan explícitamente los aspectos clínicos del diagnóstico molecular, incluidos los diagnósticos prenatal y presintomático, así como el consejo genético

Microbial Diversity in the Midguts of Field and Lab-Reared Populations of the European Corn Borer Ostrinia nubilalis

Background: Insects are associated with microorganisms that contribute to the digestion and processing of nutrients. The European Corn Borer (ECB) is a moth present world-wide, causing severe economical damage as a pest on corn and other crops. In the present work, we give a detailed view of the complexity of the microorganisms forming the ECB midgut microbiota with the objective of comparing the biodiversity of the midgut-associated microbiota and explore their potential as a source of genes and enzymes with biotechnological applications. Methodological/Principal Findings: A high-throughput sequencing approach has been used to identify bacterial species, genes and metabolic pathways, particularly those involved in plant-matter degradation, in two different ECB populations (field-collected vs. lab-reared population with artificial diet). Analysis of the resulting sequences revealed the massive presence of Staphylococcus warneri and Weissella paramesenteroides in the lab-reared sample. This enabled us to reconstruct both genomes almost completely. Despite the apparently low diversity, 208 different genera were detected in the sample, although most of them at very low frequency. By contrast, the natural population exhibited an even higher taxonomic diversity along with a wider array of cellulolytic enzyme families. However, in spite of the differences in relative abundance of major taxonomic groups, not only did both metagenomes share a similar functional profile but also a similar distribution of non-redundant genes in different functional categories. Conclusions/Significance: Our results reveal a highly diverse pool of bacterial species in both O. nubilalis populations, with major differences: The lab-reared sample is rich in gram-positive species (two of which have almost fully sequenced genomes) while the field sample harbors mainly gram-negative species and has a larger set of cellulolytic enzymes. We have found a clear relationship between the diet and the midgut microbiota, which reveals the selection pressure of food on the community of intestinal bacteria. © 2011 Belda et al.The research was funded by the Spanish Ministerio de Ciencia e Innovacion, under grant agreement CIT-010000-2008-5 and by a MICINN (Ministerio de Ciencia e Innovacion) TIN2009-12359 ArtBioCom project. Arnau Montagud acknowledges Generalitat Valenciana grant BFPI/2007/283. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Belda Cuesta, EA.; Pedrola, L.; Peretó Magraner, J.; Martinez Blanch, JF.; Montagud Aquino, A.; Navarro-Peris, E.; Urchueguía Schölzel, JF.... (2011). Microbial Diversity in the Midguts of Field and Lab-Reared Populations of the European Corn Borer Ostrinia nubilalis. PLoS ONE. 6(6):21751-21751. https://doi.org/10.1371/journal.pone.0021751S21751217516

Famílies botàniques de plantes medicinals

Facultat de Farmàcia, Universitat de Barcelona. Ensenyament: Grau de Farmàcia, Assignatura: Botànica Farmacèutica, Curs: 2013-2014, Coordinadors: Joan Simon, Cèsar Blanché i Maria Bosch.Els materials que aquí es presenten són els recull de 175 treballs d’una família botànica d’interès medicinal realitzats de manera individual. Els treballs han estat realitzat per la totalitat dels estudiants dels grups M-2 i M-3 de l’assignatura Botànica Farmacèutica durant els mesos d’abril i maig del curs 2013-14. Tots els treballs s’han dut a terme a través de la plataforma de GoogleDocs i han estat tutoritzats pel professor de l’assignatura i revisats i finalment co-avaluats entre els propis estudiants. L’objectiu principal de l’activitat ha estat fomentar l’aprenentatge autònom i col·laboratiu en Botànica farmacèutica

The Transcriptome Analysis of Strongyloides stercoralis L3i Larvae Reveals Targets for Intervention in a Neglected Disease

BackgroundStrongyloidiasis is one of the most neglected diseases distributed worldwide with endemic areas in developed countries, where chronic infections are life threatening. Despite its impact, very little is known about the molecular biology of the parasite involved and its interplay with its hosts. Next generation sequencing technologies now provide unique opportunities to rapidly address these questions.Principal FindingsHere we present the first transcriptome of the third larval stage of S. stercoralis using 454 sequencing coupled with semi-automated bioinformatic analyses. 253,266 raw sequence reads were assembled into 11,250 contiguous sequences, most of which were novel. 8037 putative proteins were characterized based on homology, gene ontology and/or biochemical pathways. Comparison of the transcriptome of S. strongyloides with those of other nematodes, including S. ratti, revealed similarities in transcription of molecules inferred to have key roles in parasite-host interactions. Enzymatic proteins, like kinases and proteases, were abundant. 1213 putative excretory/secretory proteins were compiled using a new pipeline which included non-classical secretory proteins. Potential drug targets were also identified.ConclusionsOverall, the present dataset should provide a solid foundation for future fundamental genomic, proteomic and metabolomic explorations of S. stercoralis, as well as a basis for applied outcomes, such as the development of novel methods of intervention against this neglected parasite

High-Throughput Sequencing of RNA Silencing-Associated Small RNAs in Olive (Olea europaea L.)

Small RNAs (sRNAs) of 20 to 25 nucleotides (nt) in length maintain genome integrity and control gene expression in a multitude of developmental and physiological processes. Despite RNA silencing has been primarily studied in model plants, the advent of high-throughput sequencing technologies has enabled profiling of the sRNA component of more than 40 plant species. Here, we used deep sequencing and molecular methods to report the first inventory of sRNAs in olive (Olea europaea L.). sRNA libraries prepared from juvenile and adult shoots revealed that the 24-nt class dominates the sRNA transcriptome and atypically accumulates to levels never seen in other plant species, suggesting an active role of heterochromatin silencing in the maintenance and integrity of its large genome. A total of 18 known miRNA families were identified in the libraries. Also, 5 other sRNAs derived from potential hairpin-like precursors remain as plausible miRNA candidates. RNA blots confirmed miRNA expression and suggested tissue- and/or developmental-specific expression patterns. Target mRNAs of conserved miRNAs were computationally predicted among the olive cDNA collection and experimentally validated through endonucleolytic cleavage assays. Finally, we use expression data to uncover genetic components of the miR156, miR172 and miR390/TAS3-derived trans-acting small interfering RNA (tasiRNA) regulatory nodes, suggesting that these interactive networks controlling developmental transitions are fully operational in olive

Art pop i curtmetratges a una biblioteca penitenciària: tallers de dinamització cultural a la Biblioteca del Centre Penitenciari de Joves de Barcelona

Se describen y analizan dos actividades de extensión cultural realizadas en la Biblioteca del Centre Penitenciari de Joves de Barcelona a partir de una colaboración externa. Se incluye una descripción del Centro, de la Biblioteca y del perfil del usuario al que van destinadas las actividades. Seguidamente, se resumen las diferentes fases de preparación de la actividad, su desarrollo y valoración posterior. Las actividades se presentaron como talleres y estaban centradas en el hecho visual y de la imagen: pintura de estética art pop y cineforum de un cortometraje

Art pop i curtmetratges a una biblioteca penitenciària : tallers de dinamització cultural a la Biblioteca del Centre Penitenciari de Joves de Barcelona

Es descriuen i s’analitzen dues activitats d’extensió cultural dutes a terme a la Biblioteca del Centre Penitenciari de Joves de Barcelona a partir d’una col·laboració externa. S’inclou una descripció del Centre, de la Biblioteca i del perfil d’usuari a qui s’han dirigit les activats. Seguidament, es resumeixen els diferents passos duts a terme per a la confecció de les activitats, com s’han desenvolupat i la posterior valoració. Les activitats es van presentar com a tallers i se centraven en el fet visual i de la imatge: pintura d’estètica art pop i cinefòrum d’un curtmetratge.Two activities of cultural extension are described and analysed. These were carried out, with external collaboration, at the library of the Juvenile Penitentiary Centre of Barcelona. The description covers the Centre, the library, and the profile of the users to whom the activities are directed. The article then explains the different steps undertaken to set up the activities, how they developed, and their subsequent evaluation. The activities took the form of workshops centred on visual happenings and images: pop art style painting and a forum on a short-length movie.Se describen y analizan dos actividades de extensión cultural realizadas en la Biblioteca del Centre Penitenciari de Joves de Barcelona a partir de una colaboración externa. Se incluye una descripción del Centro, de la Biblioteca y del perfil del usuario al que van destinadas las actividades. Seguidamente, se resumen las diferentes fases de preparación de la actividad, su desarrollo y valoración posterior. Las actividades se presentaron como talleres y estaban centradas en el hecho visual y de la imagen: pintura de estética art pop y cineforum de un cortometraje