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Postoperative infectious complications are extremely important to surgeons and the entire medical care team. Among these complications, surgical site infection (SSI) appears to be one of the earliest and most prevalent events and is considered an inherent complication of surgical procedures. In oncological patients submitted to resections of digestive system tumors, there is a confluence of several risk factors for SSI, making it necessary to establish measures to maximize the control of this condition to provide a better prognosis for these patients. Some risk factors for SSI are the manipulation of structures hosting the highest density of pathogenic microorganisms, such as the colon, the patient's performance status, the patient's nutritional status, the use of chemotherapy and/or radiotherapy, and the surgical procedure itself, which tends to last longer and be more complex than surgeries for benign conditions of the digestive system. Therefore, this review sought to provide a qualitative analysis and a summary of the literature regarding the SSI of postoperative tumor patients who underwent surgical resection and were well-structured postoperatively, to provide objective data on this problem, and alert about the well-structured needs of individualized pre-, peri-, and post-protocols to avoid the development of these events.
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Neoplasias del Sistema Digestivo , Infección de la Herida Quirúrgica , Humanos , Infección de la Herida Quirúrgica/etiología , Infección de la Herida Quirúrgica/prevención & control , Infección de la Herida Quirúrgica/epidemiología , Neoplasias del Sistema Digestivo/cirugía , Factores de Riesgo , Procedimientos Quirúrgicos del Sistema Digestivo/métodos , Procedimientos Quirúrgicos del Sistema Digestivo/efectos adversosRESUMEN
Bacterial relatedness measured using select chromosomal loci forms the basis of public health genomic surveillance. While approximating vertical evolution through this approach has proven exceptionally valuable for understanding pathogen dynamics, it excludes a fundamental dimension of bacterial evolution-horizontal gene transfer. Incorporating the accessory genome is the logical remediation and has recently shown promise in expanding epidemiological resolution for enteric pathogens. Employing k-mer-based Jaccard index analysis, and a novel genome length distance metric, we computed pangenome (i.e., core and accessory) relatedness for the globally important pathogen Salmonella enterica serotype Typhi (Typhi), and graphically express both vertical (homology-by-descent) and horizontal (homology-by-admixture) evolutionary relationships in a reticulate network of over 2,200 U.S. Typhi genomes. This analysis revealed non-random structure in the Typhi pangenome that is driven predominantly by the gain and loss of mobile genetic elements, confirming and expanding upon known epidemiological patterns, revealing novel plasmid dynamics, and identifying avenues for further genomic epidemiological exploration. With an eye to public health application, this work adds important biological context to the rapidly improving ways of analyzing bacterial genetic data and demonstrates the value of the accessory genome to infer pathogen epidemiology and evolution.IMPORTANCEGiven bacterial evolution occurs in both vertical and horizontal dimensions, inclusion of both core and accessory genetic material (i.e., the pangenome) is a logical step toward a more thorough understanding of pathogen dynamics. With an eye to public, and indeed, global health relevance, we couple contemporary tools for genomic analysis with decades of research on mobile genetic elements to demonstrate the value of the pangenome, known and unknown, annotated, and hypothetical, for stratification of Salmonella enterica serovar Typhi (Typhi) populations. We confirm and expand upon what is known about Typhi epidemiology, plasmids, and antimicrobial resistance dynamics, and offer new avenues of exploration to further deduce Typhi ecology and evolution, and ultimately to reduce the incidence of human disease.
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Genoma Bacteriano , Secuencias Repetitivas Esparcidas , Salmonella typhi , Salmonella typhi/genética , Genoma Bacteriano/genética , Secuencias Repetitivas Esparcidas/genética , Plásmidos/genética , Evolución Molecular , Humanos , Filogenia , Fiebre Tifoidea/microbiología , Fiebre Tifoidea/epidemiologíaRESUMEN
INTRODUCTION: Laparoscopic major hepatectomy (LMH) remains restricted to a few specialized centers and poses a challenge to surgeons performing laparoscopic resections. Laparoscopic extended resections are even more complex and rarely conducted. METHODS: From a single-institution database, we compared the short-term outcomes of patients who underwent major and extended laparoscopic resections, stratifying the entire retrospective cohort into four groups: right hepatectomy, left hepatectomy, right extended hepatectomy, and left extended hepatectomy. Patient demographics, tumor characteristics, operative variables, and especially postoperative outcomes were evaluated. RESULTS: 250 patients underwent major and extended laparoscopic liver resections, including 160 right, 31 right extended, 36 left, and 23 left extended laparoscopic hepatectomies. The most common indication for resection was colorectal liver metastases (64%). Laparoscopic extended hepatectomy (LEH) showed significantly longer operative time, more blood loss, need for Pringle maneuver, conversion to open surgery, higher rates of liver failure, postoperative ascites, and intra-abdominal hemorrhage, R1 margins and length of stay when compared with the LMH group. Mortality rates were similar between groups. Multivariate analysis revealed intraoperative blood transfusion (OR = 5.1[CI-95%: 1.15-6.79]; p = 0.02) as an independent predictor for major complications. CONCLUSIONS: LEH showed to be feasible, however with higher blood loss and significantly associated to major complications.
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Hepatectomía , Laparoscopía , Neoplasias Hepáticas , Tempo Operativo , Complicaciones Posoperatorias , Humanos , Hepatectomía/métodos , Hepatectomía/efectos adversos , Hepatectomía/mortalidad , Laparoscopía/efectos adversos , Masculino , Femenino , Estudios Retrospectivos , Persona de Mediana Edad , Resultado del Tratamiento , Anciano , Factores de Tiempo , Neoplasias Hepáticas/cirugía , Neoplasias Hepáticas/mortalidad , Neoplasias Hepáticas/secundario , Complicaciones Posoperatorias/etiología , Factores de Riesgo , Bases de Datos Factuales , Tiempo de Internación , Pérdida de Sangre Quirúrgica , Adulto , Transfusión Sanguínea/estadística & datos numéricosRESUMEN
Lecanosticta acicola is the causal agent for brown spot needle blight that affects pine trees across the northern hemisphere. Based on marker genes and microsatellite data, two distinct lineages have been identified that were introduced into Europe on two separate occasions. Despite their overall distinct geographic distribution, they have been found to coexist in regions of northern Spain and France. Here, we present the first genome-wide study of Lecanosticta acicola, including assembly of the reference genome and a population genomics analysis of 70 natural isolates from northern Spain. We show that most of the isolates belong to the southern lineage but show signs of introgression with northern lineage isolates, indicating mating between the two lineages. We also identify phenotypic differences between the two lineages based on the activity profiles of 20 enzymes, with introgressed strains being more phenotypically similar to members of the southern lineage. In conclusion, we show undergoing genetic admixture between the two main lineages of L. acicola in a region of recent expansion. IMPORTANCE: Lecanosticta acicola is a fungal pathogen causing severe defoliation, growth reduction, and even death in more than 70 conifer species. Despite the increasing incidence of this species, little is known about its population dynamics. Two divergent lineages have been described that have now been found together in regions of France and Spain, but it is unknown how these mixed populations evolve. Here we present the first reference genome for this important plant pathogenic fungi and use it to study the population genomics of 70 isolates from an affected forest in the north of Spain. We find signs of introgression between the two main lineages, indicating that active mating is occurring in this region which could propitiate the appearance of novel traits in this species. We also study the phenotypic differences across this population based on enzymatic activities on 20 compounds.
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Ascomicetos , Pinus , Humanos , Estudio de Asociación del Genoma Completo , Pinus/genética , Ascomicetos/genética , GenómicaRESUMEN
As the reconstruction of Genome-Scale Metabolic Models (GEMs) becomes standard practice in systems biology, the number of organisms having at least one metabolic model is peaking at an unprecedented scale. The automation of laborious tasks, such as gap-finding and gap-filling, allowed the development of GEMs for poorly described organisms. However, the quality of these models can be compromised by the automation of several steps, which may lead to erroneous phenotype simulations. Biological networks constraint-based In Silico Optimisation (BioISO) is a computational tool aimed at accelerating the reconstruction of GEMs. This tool facilitates manual curation steps by reducing the large search spaces often met when debugging in silico biological models. BioISO uses a recursive relation-like algorithm and Flux Balance Analysis (FBA) to evaluate and guide debugging of in silico phenotype simulations. The potential of BioISO to guide the debugging of model reconstructions was showcased and compared with the results of two other state-of-the-art gap-filling tools (Meneco and fastGapFill). In this assessment, BioISO is better suited to reducing the search space for errors and gaps in metabolic networks by identifying smaller ratios of dead-end metabolites. Furthermore, BioISO was used as Meneco's gap-finding algorithm to reduce the number of proposed solutions for filling the gaps.
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Algoritmos , Genoma , Genoma/genética , Simulación por Computador , Redes y Vías Metabólicas/genética , Biología de Sistemas/métodos , Modelos Biológicos , Programas InformáticosRESUMEN
Plasmids are mobile genetic elements found in many clades of Archaea and Bacteria. They drive horizontal gene transfer, impacting ecological and evolutionary processes within microbial communities, and hold substantial importance in human health and biotechnology. To support plasmid research and provide scientists with data of an unprecedented diversity of plasmid sequences, we introduce the IMG/PR database, a new resource encompassing 699 973 plasmid sequences derived from genomes, metagenomes and metatranscriptomes. IMG/PR is the first database to provide data of plasmid that were systematically identified from diverse microbiome samples. IMG/PR plasmids are associated with rich metadata that includes geographical and ecosystem information, host taxonomy, similarity to other plasmids, functional annotation, presence of genes involved in conjugation and antibiotic resistance. The database offers diverse methods for exploring its extensive plasmid collection, enabling users to navigate plasmids through metadata-centric queries, plasmid comparisons and BLAST searches. The web interface for IMG/PR is accessible at https://img.jgi.doe.gov/pr. Plasmid metadata and sequences can be downloaded from https://genome.jgi.doe.gov/portal/IMG_PR.
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Metagenoma , Microbiota , Humanos , Metadatos , Programas Informáticos , Bases de Datos Genéticas , Plásmidos/genéticaRESUMEN
Optoacoustic (OA) imaging is based on optical excitation of biological tissues with nanosecond-duration laser pulses and detection of ultrasound (US) waves generated by thermoelastic expansion following light absorption. The image quality and fidelity of OA images critically depend on the extent of tomographic coverage provided by the US detector arrays. However, full tomographic coverage is not always possible due to experimental constraints. One major challenge concerns an efficient integration between OA and pulse-echo US measurements using the same transducer array. A common approach toward the hybridization consists in using standard linear transducer arrays, which readily results in arc-type artifacts and distorted shapes in OA images due to the limited angular coverage. Deep learning methods have been proposed to mitigate limited-view artifacts in OA reconstructions by mapping artifactual to artifact-free (ground truth) images. However, acquisition of ground truth data with full angular coverage is not always possible, particularly when using handheld probes in a clinical setting. Deep learning methods operating in the image domain are then commonly based on networks trained on simulated data. This approach is yet incapable of transferring the learned features between two domains, which results in poor performance on experimental data. Here, we propose a signal domain adaptation network (SDAN) consisting of i) a domain adaptation network to reduce the domain gap between simulated and experimental signals and ii) a sides prediction network to complement the missing signals in limited-view OA datasets acquired from a human forearm by means of a handheld linear transducer array. The proposed method showed improved performance in reducing limited-view artifacts without the need for ground truth signals from full tomographic acquisitions.
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Tomografía Computarizada por Rayos X , Tomografía , Humanos , Tomografía/métodos , Ultrasonografía/métodos , Artefactos , Transductores , Procesamiento de Imagen Asistido por Computador/métodos , Fantasmas de ImagenRESUMEN
BACKGROUND: Molar-incisor hypomineralisation (MIH) is the most common developmental abnormality observed in teeth. Being a relatively new condition, its treatment can present a challenge for the dentist. There is currently no study available that has evaluated the knowledge of Mexican dental personnel. This study aimed to evaluate the knowledge, experience, and perceptions of dental surgeons regarding the detection, assessment, and treatment of MIH in the metropolitan area of Mexico City. METHODS: A cross-sectional study was designed. Dentists from Mexico City and its metropolitan area were invited through social networks to answer a questionnaire of 30 questions related to MIH. Participants were classified into general practice dentists, paediatric dentists, and other speciality dentists. Pearson's chi-square test was used for data analysis. RESULTS: The questionnaire was answered by 391 dentists. A total of 86% (338 out of 391) of them identified MIH lesions, while 84% of them reported having observed MIH lesions in their practice. The most frequently observed lesions were yellow-brown opacities which accounted for 47% of the lesions, 46% were white opacities, while only 7% were observed as post-eruptive fractures in the enamel as part of the manifestations of MIH. The most frequently reported problem in the management of teeth with MIH was insufficient training for treating children with MIH. A total of 84% of dentists stated that they would like more information on the treatment of MIH lesions. CONCLUSIONS: Most of the surveyed dentists recognised MIH and reported having observed MIH lesions in their practice. Most of the dentists indicated that the main problem for the management of the MIH is the lack of training.
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Hipoplasia del Esmalte Dental , Hipomineralización Molar , Niño , Humanos , Estudios Transversales , Hipoplasia del Esmalte Dental/terapia , Hipoplasia del Esmalte Dental/diagnóstico , México , Diente Molar/patología , Odontólogos , Percepción , PrevalenciaRESUMEN
In response to the threat of increasing antimicrobial resistance, we must increase the amount of available high-quality genomic data gathered on antibiotic-resistant bacteria. To this end, we developed an integrated pipeline for high-throughput long-read sequencing, assembly, annotation and analysis of bacterial isolates and used it to generate a large genomic data set of carbapenemase-producing Enterobacterales (CPE) isolates collected in Spain. The set of 461 isolates were sequenced with a combination of both Illumina and Oxford Nanopore Technologies (ONT) DNA sequencing technologies in order to provide genomic context for chromosomal loci and, most importantly, structural resolution of plasmids, important determinants for transmission of antimicrobial resistance. We developed an informatics pipeline called Assembly and Annotation of Carbapenem-Resistant Enterobacteriaceae (AACRE) for the full assembly and annotation of the bacterial genomes and their complement of plasmids. To explore the resulting genomic data set, we developed a new database called inCREDBle that not only stores the genomic data, but provides unique ways to filter and compare data, enabling comparative genomic analyses at the level of chromosomes, plasmids and individual genes. We identified a new sequence type, ST5000, and discovered a genomic locus unique to ST15 that may be linked to its increased spread in the population. In addition to our major objective of generating a large regional data set, we took the opportunity to compare the effects of sample quality and sequencing methods, including R9 versus R10 nanopore chemistry, on genome assembly and annotation quality. We conclude that converting short-read and hybrid microbial sequencing and assembly workflows to the latest nanopore chemistry will further reduce processing time and cost, truly enabling the routine monitoring of resistance transmission patterns at the resolution of complete chromosomes and plasmids.
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Enterobacteriaceae Resistentes a los Carbapenémicos , Carbapenémicos , Carbapenémicos/farmacología , Enterobacteriaceae Resistentes a los Carbapenémicos/genética , Flujo de Trabajo , Genómica/métodos , Antibacterianos/farmacologíaRESUMEN
Cephalopods are emerging animal models and include iconic species for studying the link between genomic innovations and physiological and behavioral complexities. Coleoid cephalopods possess the largest nervous system among invertebrates, both for cell counts and brain-to-body ratio. Octopus vulgaris has been at the center of a long-standing tradition of research into diverse aspects of cephalopod biology, including behavioral and neural plasticity, learning and memory recall, regeneration, and sophisticated cognition. However, no chromosome-scale genome assembly was available for O. vulgaris to aid in functional studies. To fill this gap, we sequenced and assembled a chromosome-scale genome of the common octopus, O. vulgaris. The final assembly spans 2.8 billion basepairs, 99.34% of which are in 30 chromosome-scale scaffolds. Hi-C heatmaps support a karyotype of 1n = 30 chromosomes. Comparisons with other octopus species' genomes show a conserved octopus karyotype and a pattern of local genome rearrangements between species. This new chromosome-scale genome of O. vulgaris will further facilitate research in all aspects of cephalopod biology, including various forms of plasticity and the neural machinery underlying sophisticated cognition, as well as an understanding of cephalopod evolution.
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Octopodiformes , Animales , Octopodiformes/genética , Genoma , Genómica , Sistema Nervioso , Cromosomas/genéticaRESUMEN
The use of machine learning for predicting ecotoxicological outcomes is promising, but underutilized. The curation of data with informative features requires both expertise in machine learning as well as a strong biological and ecotoxicological background, which we consider a barrier of entry for this kind of research. Additionally, model performances can only be compared across studies when the same dataset, cleaning, and splittings were used. Therefore, we provide ADORE, an extensive and well-described dataset on acute aquatic toxicity in three relevant taxonomic groups (fish, crustaceans, and algae). The core dataset describes ecotoxicological experiments and is expanded with phylogenetic and species-specific data on the species as well as chemical properties and molecular representations. Apart from challenging other researchers to try and achieve the best model performances across the whole dataset, we propose specific relevant challenges on subsets of the data and include datasets and splittings corresponding to each of these challenge as well as in-depth characterization and discussion of train-test splitting approaches.
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Benchmarking , Ecotoxicología , Animales , Peces , Aprendizaje Automático , FilogeniaRESUMEN
The pearly razorfish (Xyrichtys novacula), commonly known as raor in the Balearic Islands, is a wrasse within the family Labridae. This fish species has particular biological and socio-cultural characteristics making it an ideal model organism in the fields of behavioural ecology, molecular ecology and conservation biology. In this study, we present the first annotated chromosome-level assembly for this species. Sequencing involved a combination of long reads with Oxford Nanopore Technologies, Illumina paired-end short reads (2â ×â 151 bp), Hi-C and RNA-seq from different tissues. The nuclear genome assembly has a scaffold N50 of 34.33 Mb, a total assembly span of 775.53 Mb and 99.63% of the sequence assembled into 24 superscaffolds, consistent with its known karyotype. Quality metrics revealed a consensus accuracy (QV) of 42.92 and gene completenessâ >â 98%. The genome annotation resulted in 26,690 protein-coding genes and 12,737 non-coding transcripts. The coding regions encoded 39,613 unique protein products, 93% of them with assigned function. Overall, the publication of the X. novacula's reference genome will broaden the scope and impact of genomic research conducted on this iconic and colourful species.
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Genoma , Perciformes , Animales , Anotación de Secuencia Molecular , Perciformes/genética , Genómica/métodos , Cromosomas , FilogeniaRESUMEN
The Mediterranean lizard Podarcis lilfordi is an emblematic species of the Balearic Islands. The extensive phenotypic diversity among extant isolated populations makes the species a great insular model system for eco-evolutionary studies, as well as a challenging target for conservation management plans. Here we report the first high-quality chromosome-level assembly and annotation of the P. lilfordi genome, along with its mitogenome, based on a mixed sequencing strategy (10X Genomics linked reads, Oxford Nanopore Technologies long reads and Hi-C scaffolding) coupled with extensive transcriptomic data (Illumina and PacBio). The genome assembly (1.5 Gb) is highly contiguous (N50 = 90 Mb) and complete, with 99% of the sequence assigned to candidate chromosomal sequences and >97% gene completeness. We annotated a total of 25,663 protein-coding genes translating into 38,615 proteins. Comparison to the genome of the related species Podarcis muralis revealed substantial similarity in genome size, annotation metrics, repeat content, and a strong collinearity, despite their evolutionary distance (~18-20 MYA). This genome expands the repertoire of available reptilian genomes and will facilitate the exploration of the molecular and evolutionary processes underlying the extraordinary phenotypic diversity of this insular species, while providing a critical resource for conservation genomics.
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Cromosomas , Lagartos , Animales , España , Anotación de Secuencia Molecular , Genoma , Lagartos/genéticaRESUMEN
Plasmids are universally present in bacteria and play key roles in the dissemination of genes such as antibiotic resistance determinants. Major concepts in Plasmid Biology derive from the efforts to classify plasmids. Here, we review the main plasmid classification systems, starting by phenotype-based methods, such as fertility inhibition and incompatibility, followed by schemes based on a single gene (replicon type and MOB class), and finishing with recently developed approaches that use genetic distances between whole plasmid sequences. A comparison of the latter highlights significant differences between them. We further discuss the need for an operational definition of plasmid species that reveals their biological features, akin to plasmid taxonomic units (PTUs).
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Antibacterianos , Bacterias , Plásmidos/genética , Bacterias/genética , Antibacterianos/farmacología , Transferencia de Gen HorizontalRESUMEN
Cyanobacteria are prokaryotic organisms that capture energy from sunlight using oxygenic photosynthesis and transform CO2 into products of interest such as fatty acids. Synechococcus elongatus PCC 7942 is a model cyanobacterium efficiently engineered to accumulate high levels of omega-3 fatty acids. However, its exploitation as a microbial cell factory requires a better knowledge of its metabolism, which can be approached by using systems biology tools. To fulfill this objective, we worked out an updated, more comprehensive, and functional genome-scale model of this freshwater cyanobacterium, which was termed iMS837. The model includes 837 genes, 887 reactions, and 801 metabolites. When compared with previous models of S. elongatus PCC 7942, iMS837 is more complete in key physiological and biotechnologically relevant metabolic hubs, such as fatty acid biosynthesis, oxidative phosphorylation, photosynthesis, and transport, among others. iMS837 shows high accuracy when predicting growth performance and gene essentiality. The validated model was further used as a test-bed for the assessment of suitable metabolic engineering strategies, yielding superior production of non-native omega-3 fatty acids such as α-linolenic acid (ALA). As previously reported, the computational analysis demonstrated that fabF overexpression is a feasible metabolic target to increase ALA production, whereas deletion and overexpression of fabH cannot be used for this purpose. Flux scanning based on enforced objective flux, a strain-design algorithm, allowed us to identify not only previously known gene overexpression targets that improve fatty acid synthesis, such as Acetyl-CoA carboxylase and ß-ketoacyl-ACP synthase I, but also novel potential targets that might lead to higher ALA yields. Systematic sampling of the metabolic space contained in iMS837 identified a set of ten additional knockout metabolic targets that resulted in higher ALA productions. In silico simulations under photomixotrophic conditions with acetate or glucose as a carbon source boosted ALA production levels, indicating that photomixotrophic nutritional regimens could be potentially exploited in vivo to improve fatty acid production in cyanobacteria. Overall, we show that iMS837 is a powerful computational platform that proposes new metabolic engineering strategies to produce biotechnologically relevant compounds, using S. elongatus PCC 7942 as non-conventional microbial cell factory.
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Introduction: gastrointestinal involvement in COVID-19 occurs in approximately 20% of patients and may include nausea, vomiting, abdominal pain, diarrhea or abnormal liver function tests. In our country, the characteristics of gastrointestinal involvement in COVID-19 patients have not been studied. Objectives: to determine the prevalence of gastrointestinal and liver involvement in patients with COVID-19 treated at two hospitals in Bogotá, Colombia. To determine the association between COVID-19 gastrointestinal involvement and length of hospital stay, severity and mortality. Design and methodology: a cross-sectional study carried out at two hospitals in a hospital subnetwork in Bogotá, Colombia from February 2020 to March 2021. Results: a total of 1,176 patients with a positive reverse transcription polymerase chain reaction (RT-PCR) were included. Gastrointestinal manifestations occurred in 50% (95%CI 47-52%), with the most frequent being diarrhea in 18.4%, odynophagia in 17.6%, anorexia in 14.7% and abdominal pain in 8.8%. An association was found between diarrhea during hospitalization and prolonged hospitalization (OR 1.93 95%CI 1.19-3.13), and between gastrointestinal bleeding on admission and death (OR 3.13, 95%CI 1.1-9.1), among others. Abnormal liver function tests occurred in 46% (95%CI 43-49%) and were more frequent in patients with severe disease and those who died. Conclusions: the prevalence of gastrointestinal manifestations in patients with COVID-19 was 50%. Diarrhea was associated with a longer hospital stay, and gastrointestinal bleeding was associated with respiratory failure and death. Forty-six percent of patients had abnormal liver function tests, with elevated transaminases being the most frequent. Elevated aspartate transaminase (AST) on admission was associated with greater mortality. (Acta Med Colomb 2022; 48. DOI:https://doi.org/10.36104/amc.2023.2729).
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Language models (LM) have grown non-stop in the last decade, from sequence-to-sequence architectures to attention-based Transformers. However, regularization is not deeply studied in those structures. In this work, we use a Gaussian Mixture Variational Autoencoder (GMVAE) as a regularizer layer. We study its advantages regarding the depth where it is placed and prove its effectiveness in several scenarios. Experimental result demonstrates that the inclusion of deep generative models within Transformer-based architectures such as BERT, RoBERTa, or XLM-R can bring more versatile models, able to generalize better and achieve improved imputation score in tasks such as SST-2 and TREC or even impute missing/noisy words with richer text.
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Lenguaje , Procesamiento de Lenguaje Natural , Distribución NormalRESUMEN
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 testis.
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Peces Planos , Receptores de HFE , Femenino , Masculino , Animales , Receptores de HFE/genética , Receptores de HFE/metabolismo , Genoma/genética , Cromosomas , Peces Planos/genética , Hormonas/metabolismoRESUMEN
[This corrects the article DOI: 10.1371/journal.pntd.0009145.].
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PURPOSE: The purpose of this study is to determine the incidence of gastric tube abnormalities after SG and its relationship with esophagitis progression. METHODS: Retrospective study which included 459 patients in the postoperative period of SG who underwent an esophagogastroduodenoscopy in both pre- and postoperative periods. The main studied variables were presence of gastric tube abnormalities (dilation, neofundus, twist, and hiatal hernia) and esophagitis progression. RESULTS: Among the 459 patients who underwent SG, 393 (85.6%) were women, and 66 (14.4%) men, with mean age of 40.4 years. Mean preoperative BMI was 39.70 kg/m2. In total, 20.3% of the sample presented progression of esophagitis after surgery. Among the whole sample, 130 (28.3%) presented with an abnormality of the remnant gastric tube. The most common alteration was gastric dilation, which occurred in 16.1% of the patients, followed by gastric twist (10.7%), neofundus (7.4%), and hiatal hernia (0.2%). Patients who presented with any abnormality of the gastric tube were significantly prone to presenting esophagitis progression (p = 0.013). When analyzing each morphological abnormality isolated, there was no statistically significant correlation. CONCLUSION: Abnormalities of the gastric tube are not uncommon after SG and seems to contribute partially to the relevant rates of GERD and esophagitis after this surgery.