Cytogenomics Unveil Possible Transposable Elements Driving Rearrangements in Chromosomes 2 and 4 of Solea senegalensis

Cytogenomics, the integration of cytogenetic and genomic data, has been used here to reconstruct the evolution of chromosomes 2 and 4 of Solea senegalensis. S. senegalensis is a flat fish with a karyotype comprising 2n = 42 chromosomes: 6 metacentric + 4 submetacentric + 8 subtelocentric + 24 telocentric. The Fluorescence in situ Hybridization with Bacterial Artificial Chromosomes (FISH-BAC) technique was applied to locate BACs in these chromosomes (11 and 10 BACs in chromosomes 2 and 4, respectively) and to generate integrated maps. Synteny analysis, taking eight reference fish species (Cynoglossus semilaevis, Scophthalmus maximus, Sparus aurata, Gasterosteus aculeatus, Xiphophorus maculatus, Oryzias latipes, Danio rerio, and Lepisosteus oculatus) for comparison, showed that the BACs of these two chromosomes of S. senegalensis were mainly distributed in two principal chromosomes in the reference species. Transposable Elements (TE) analysis showed significant differences between the two chromosomes, in terms of number of loci per Mb and coverage, and the class of TE (I or II) present. Analysis of TE divergence in chromosomes 2 and 4 compared to their syntenic regions in four reference fish species (C. semilaevis, S. maximus, O. latipes, and D. rerio) revealed differences in their age of activity compared with those species but less notable differences between the two chromosomes. Differences were also observed in peaks of divergence and coverage of TE families for all reference species even in those close to S. senegalensis, like S. maximus and C. semilaevis. Considered together, chromosomes 2 and 4 have evolved by Robertsonian fusions, pericentric inversions, and other chromosomal rearrangements mediated by TEs

Integrated gene mapping and synteny studies give insights into the evolution of a sex proto-chromosome in Solea senegalensis.

La evolución de los genes relacionados con el sexo y la reproducción en los peces muestra una alta plasticidad y, hasta la fecha, el sistema de determinación del sexo sólo ha sido identificado en unas pocas especies. Solea senegalensis tiene 42 cromosomas y un sistema cromosómico XX/XY para la determinación del sexo, mientras que las especies relacionadas muestran el sistema ZZ/ZW. Se han llevado a cabo técnicas de secuenciación de próxima generación (NGS), hibridación in situ con fluorescencia multicolor (mFISH) y análisis bioinformáticos, con el objetivo de revelar nueva información sobre la determinación del sexo y la reproducción en S. senegalensis. A ese Finalmente, se analizaron varios clones de cromosomas artificiales bacterianos (BAC) que contienen genes candidatos implicados en dichos procesos (dmrt1, dmrt2, dmrt3, dmrt4, sox3, sox6, sox8, sox9, lh, cyp19a1a, amh, vasa, aqp3 y nanos3). y comparado con la misma región en otras especies relacionadas. Los estudios de Synteny demostraron que la colocalización de dmrt1-dmrt2-drmt3 en el cromosoma metacéntrico más grande de S. senegalensis coincide con la encontrada en el cromosoma Z de Cynoglossus semilaevis, lo que potencialmente lo convertiría en un protocromosoma sexual. Los estudios filogenéticos muestran la estrecha proximidad de S. senegalensis a Oryzias latipes, una especie con un sistema XX/XY y un gen maestro sexual. El mapeo comparativo proporciona evidencia de la asociación preferencial de estos genes candidatos en pares de cromosomas particulares. Utilizando las técnicas NGS y mFISH se ha podido obtener un mapa genético integrado, que muestra que 15 de 21 pares de cromosomas de S. senegalensis tienen al menos un clon BAC. Este resultado es importante para distinguir aquellos pares de cromosomas de S. senegalensis que son similares en forma y tamaño. El análisis mFISH muestra las siguientes co-localizaciones en los mismos cromosomas: dmrt1-dmrt2-dmrt3, dmrt4-sox9-thrb, aqp3-sox8, cyp19a1a-fshb, igsf9b-sox3 y lysg-sox6.The evolution of genes related to sex and reproduction in fish shows high plasticity and, to date, the sex determination system has only been identified in a few species. Solea senegalensis has 42 chromosomes and an XX/XY chromosome system for sex determination, while related species show the ZZ/ZW system. Next-generation sequencing (NGS), multi-color fluorescence in situ hybridization (mFISH) techniques, and bioinformatics analysis have been carried out, with the objective of revealing new information about sex determination and reproduction in S. senegalensis. To that end, several bacterial artificial chromosome (BAC) clones that contain candidate genes involved in such processes (dmrt1, dmrt2, dmrt3, dmrt4, sox3, sox6, sox8, sox9, lh, cyp19a1a, amh, vasa, aqp3, and nanos3) were analyzed and compared with the same region in other related species. Synteny studies showed that the co-localization of dmrt1-dmrt2-drmt3 in the largest metacentric chromosome of S. senegalensis is coincident with that found in the Z chromosome of Cynoglossus semilaevis, which would potentially make this a sex protochromosome. Phylogenetic studies show the close proximity of S. senegalensis to Oryzias latipes, a species with an XX/XY system and a sex master gene. Comparative mapping provides evidence of the preferential association of these candidate genes in particular chromosome pairs. By using the NGS and mFISH techniques, it has been possible to obtain an integrated genetic map, which shows that 15 out of 21 chromosome pairs of S. senegalensis have at least one BAC clone. This result is important for distinguishing those chromosome pairs of S. senegalensis that are similar in shape and size. The mFISH analysis shows the following co-localizations in the same chromosomes: dmrt1-dmrt2-dmrt3, dmrt4-sox9-thrb, aqp3-sox8, cyp19a1a-fshb, igsf9b-sox3, and lysg-sox6.Este estudio ha contado con el apoyo del Ministerio de Ciencia e Innovación MICINN-FEDER (proyectos AGL 2011–25596 y AGL2014-51860-C2-1-P) y del proyecto AQUAGENET (SOE 2/ P1/E287) del INTERREG IVB. Programa SUDOE. SPB recibió una beca de la UCA

A Comprehensive Integrated Genetic Map of the Complete Karyotype of Solea senegalensis (Kaup 1858)

Solea senegalensis aquaculture production has experienced a great increase in the last decade and, consequently, the genome knowledge of the species is gaining attention. In this sense, obtaining a high-density genome mapping of the species could offer clues to the aquaculture improvement in those aspects not resolved so far. In the present article, a review and new processed data have allowed to obtain a high-density BAC-based cytogenetic map of S. senegalensis beside the analysis of the sequences of such BAC clones to achieve integrative data. A total of 93 BAC clones were used to localize the chromosome complement of the species and 588 genes were annotated, thus almost reaching the 2.5% of the S. senegalensis genome sequences. As a result, important data about its genome organization and evolution were obtained, such as the lesser gene density of the large metacentric pair compared with the other metacentric chromosomes, which supports the theory of a sex proto-chromosome pair. In addition, chromosomes with a high number of linked genes that are conserved, even in distant species, were detected. This kind of result widens the knowledge of this species' chromosome dynamics and evolution

In Silico Detection and FISH Analysis to Determine Location of miRNAs in Solea Senegalensis Chromosomes Using BACs

MicroRNAs (miRNAs) are small, non-coding RNAs that play a very important role in gene expression by regulating mRNA cleavage and translation. The Senegalese sole, Solea senegalensis (Kaup 1858), is a flatfish species that shows great potential for marine aquaculture. Nevertheless, the existence of sexual dysfunction of males reared in captivity, high larval mortality, and diseases have hampered its production. The integration of sequence information with data on chromosomal physical location is useful for understanding genetic processes and is essential for comparative analysis, quantitative trait locus (QTL) mapping, and positional cloning of gene

A chromosome-level genome assembly enables the identification of the follicule stimulating hormone receptor as the master sex-determining gene in the flatfish Solea senegalensis

Sex determination (SD) shows huge variation among fish and a high evolutionary rate, as illustrated by the Pleuronectiformes (flatfishes). This order is characterized by its adaptation to demersal life, compact genomes and diversity of SD mechanisms. Here, we assembled the Solea senegalensis genome, a flatfish of great commercial value, into 82 contigs (614 Mb) combining long- and short-read sequencing, which were next scaffolded using a highly dense genetic map (28,838 markers, 21 linkage groups), representing 98.9% of the assembly. Further, we established the correspondence between the assembly and the 21 chromosomes by using BAC-FISH. Whole genome resequencing of six males and six females enabled the identification of 41 single nucleotide polymorphism variants in the follicle stimulating hormone receptor (fshr) consistent with an XX/XY SD system. The observed sex association was validated in a broader independent sample, providing a novel molecular sexing tool. The fshr gene displayed differential expression between male and female gonads from 86 days post-fertilization, when the gonad is still an undifferentiated primordium, concomitant with the activation of amh and cyp19a1a, testis and ovary marker genes, respectively, in males and females. The Y-linked fshr allele, which included 24 nonsynonymous variants and showed a highly divergent 3D protein structure, was overexpressed in males compared to the X-linked allele at all stages of gonadal differentiation. We hypothesize a mechanism hampering the action of the follicle stimulating hormone driving the undifferentiated gonad toward testisEuropean Union's Horizon 2020 research and innovation programme under grant agreement (AQUA-FAANG). Grant Number: 81792. Junta de Andalucía-FEDER Grant. Grant Number: P20-00938. Spanish Ministry of Economy and Competitiveness, FEDER Grants. Grant Numbers: RTI2018-096847-B-C21, RTI2018-096847-B-C22S

Mortality and pulmonary complications in patients undergoing surgery with perioperative SARS-CoV-2 infection: an international cohort study

Background: The impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on postoperative recovery needs to be understood to inform clinical decision making during and after the COVID-19 pandemic. This study reports 30-day mortality and pulmonary complication rates in patients with perioperative SARS-CoV-2 infection. Methods: This international, multicentre, cohort study at 235 hospitals in 24 countries included all patients undergoing surgery who had SARS-CoV-2 infection confirmed within 7 days before or 30 days after surgery. The primary outcome measure was 30-day postoperative mortality and was assessed in all enrolled patients. The main secondary outcome measure was pulmonary complications, defined as pneumonia, acute respiratory distress syndrome, or unexpected postoperative ventilation. Findings: This analysis includes 1128 patients who had surgery between Jan 1 and March 31, 2020, of whom 835 (74·0%) had emergency surgery and 280 (24·8%) had elective surgery. SARS-CoV-2 infection was confirmed preoperatively in 294 (26·1%) patients. 30-day mortality was 23·8% (268 of 1128). Pulmonary complications occurred in 577 (51·2%) of 1128 patients; 30-day mortality in these patients was 38·0% (219 of 577), accounting for 81·7% (219 of 268) of all deaths. In adjusted analyses, 30-day mortality was associated with male sex (odds ratio 1·75 [95% CI 1·28–2·40], p\textless0·0001), age 70 years or older versus younger than 70 years (2·30 [1·65–3·22], p\textless0·0001), American Society of Anesthesiologists grades 3–5 versus grades 1–2 (2·35 [1·57–3·53], p\textless0·0001), malignant versus benign or obstetric diagnosis (1·55 [1·01–2·39], p=0·046), emergency versus elective surgery (1·67 [1·06–2·63], p=0·026), and major versus minor surgery (1·52 [1·01–2·31], p=0·047). Interpretation: Postoperative pulmonary complications occur in half of patients with perioperative SARS-CoV-2 infection and are associated with high mortality. Thresholds for surgery during the COVID-19 pandemic should be higher than during normal practice, particularly in men aged 70 years and older. Consideration should be given for postponing non-urgent procedures and promoting non-operative treatment to delay or avoid the need for surgery. Funding: National Institute for Health Research (NIHR), Association of Coloproctology of Great Britain and Ireland, Bowel and Cancer Research, Bowel Disease Research Foundation, Association of Upper Gastrointestinal Surgeons, British Association of Surgical Oncology, British Gynaecological Cancer Society, European Society of Coloproctology, NIHR Academy, Sarcoma UK, Vascular Society for Great Britain and Ireland, and Yorkshire Cancer Research

Reducing the environmental impact of surgery on a global scale: systematic review and co-prioritization with healthcare workers in 132 countries

Abstract Background Healthcare cannot achieve net-zero carbon without addressing operating theatres. The aim of this study was to prioritize feasible interventions to reduce the environmental impact of operating theatres. Methods This study adopted a four-phase Delphi consensus co-prioritization methodology. In phase 1, a systematic review of published interventions and global consultation of perioperative healthcare professionals were used to longlist interventions. In phase 2, iterative thematic analysis consolidated comparable interventions into a shortlist. In phase 3, the shortlist was co-prioritized based on patient and clinician views on acceptability, feasibility, and safety. In phase 4, ranked lists of interventions were presented by their relevance to high-income countries and low–middle-income countries. Results In phase 1, 43 interventions were identified, which had low uptake in practice according to 3042 professionals globally. In phase 2, a shortlist of 15 intervention domains was generated. In phase 3, interventions were deemed acceptable for more than 90 per cent of patients except for reducing general anaesthesia (84 per cent) and re-sterilization of ‘single-use’ consumables (86 per cent). In phase 4, the top three shortlisted interventions for high-income countries were: introducing recycling; reducing use of anaesthetic gases; and appropriate clinical waste processing. In phase 4, the top three shortlisted interventions for low–middle-income countries were: introducing reusable surgical devices; reducing use of consumables; and reducing the use of general anaesthesia. Conclusion This is a step toward environmentally sustainable operating environments with actionable interventions applicable to both high– and low–middle–income countries

Video-Juego ADNito aprende en la Isla de la Genética. Encuentro con Mendel.

Video-juego desarrollado con e-learning sobre Genética. El personaje principal llamado ADNito, es un niño con aspecto de super-héroe que quiere aprender Genética porque es muy importante para él. Para ello, anima al jugador a que le acompañe por una Isla donde hay diferentes puntos de referencia o “estaciones” donde tendrá encuentros con personajes y situaciones relacionados con los principales hitos en los descubrimientos de la Genética y la Evolución. Cuando el protagonista entra en un escenario (punto de la Isla), le recibe un personaje histórico del mundo de la Genética (n esta versión el encuentro es con Mendel) y le dice que necesita un ayudante, pero para ello quiere saber si está preparado en conocimientos y en actitud (en esta primera versión se trabajan las leyes de Mendel). Cuando el protagonista accede a pasar las pruebas, pasa por un lugar de aprendizaje (tipo biblioteca) donde encuentra los recursos (libros) para aprender (repasar) y empezar el juego. A partir de ese punto, va pasando dentro de esa historia por una serie de escenarios por los que otros personajes (secundarios) le plantean una serie de preguntas sobre el tema estudiado en la biblioteca. Si pasa por esos otros escenarios y responde adecuadamente, termina finalmente con un encuentro con el personaje principal de ese punto de la Isla, dándole la enhorabuena por haber llegado allí y demostrarle que está preparado para ayudarle durante un tiempo y poder seguir por tanto viajando por la Isla para obtener más conocimientos y entrenamiento.Video-juego de e-learning de Genética. En este juego, se pretende que el jugador/estudiante vaya aprendiendo diferentes contenidos de Genética y vaya recorriendo cada una de las historias y escenarios que se muestran en un mapa de una Isla, respondiendo preguntas de Genética de diferentes personajes históricos relacionados con dicho área de conocimiento. En esta versión está disponible el encuentro con Mendel. Mediante esta metodología, se pueden enseñar tantos conceptos teóricos como queramos así como aprender protocolos de prácticas de Genética. Conforme va pasando las pruebas, el protagonista de la historia (ADNito) va avanzando en el juego hasta encontrarse finalmente con el personaje principal de ese escenario donde se le dará la enhorabuena por haber conseguido terminarlo y haber avanzado en su conocimiento de la Genética

Simulador de cruzamientos de Genética en hoja de cálculo

En esta hoja de cálculo programada con macros, el usuario puede simular cruzamientos entre dos individuos para dos genes independientes con 2 alelos cada uno presentando dominancia y obtener las proporciones fenotípicas de la descendencia. Además puede simular que los genes presenten interacción (Epistásica o no Epistásica) variando de esta manera las proporciones fenotípicas observadas. En este caso, el usuario puede elegir en más de 5 opciones diferentes simplemente pulsando los botones habilitados para ello en el programa.En esta hoja de cálculo con macros, el usuario simula cruzamientos entre dos individuos para dos genes independientes con 2 alelos cada uno y obtener las proporciones fenotípicas de la descendencia según se trate de interacción epistásica, no epistásica o sin interacción

Análisis de ligamiento genético a partir de resultados de cruzamientos prueba y F2.

En este simulador realizado en una hoja de cálculo se puede saber si dos genes están ligados en el genoma o por si el contrario son independientes. Este ejercicio sirve para completar la información sobre mapas genéticos en general y mapas de ligamiento en particular. Se parte de datos de individuos descendientes de cruzamientos prueba y F2 para dos caracteres cualitativos controlados por dos genes con dos alelos cada uno presentando dominancia. El programa calcula si las frecuencias obtenidas en la descendencia se ajustan a lo esperado en el caso de genes independientes. En el caso de que no lo sean, el programa determina si alguno de los genes está segregando mal según las leyes de Mendel y si no es así, determina el ligamiento y la distancia entre los genes en un mapa de ligamiento.En este material docente se determina la independencia o ligamiento entre dos genes. Se parte de datos de una descendencia obtenida a partir de cruzamientos prueba y F2 para dos caracteres cualitativos controlados por dos genes con dos alelos cada uno presentando dominancia