Automation Proposal for the Intermediate Steps in the 16S FFPE Samples Analysis Pipeline

Cursos e Congresos, C-155[Abstract] In the day-to-day work of bioinformatics, the use of integrated software packages, which encompass a wide range of tools, enables the development of pipelines for omics data analysis. Within the various existing pipelines, we focus on the analysis of the 16S rRNA gene as it allows for the study of diversity and taxonomy of prokaryotic microorganisms such as Bacteria and Archaea. However, these pipelines often involve a sequence of multiple tools that require intermediate steps before further processing can proceed, as in the case between Cutadapt and DADA2. In fact, in a typical pipeline, the values for DADA2 input arguments ’trunc-len-f’ and ’trunc-len-r’ are extracted from the output of Cutadapt. The best approach for selecting optimal values (aka the trimming positions) is graphically visualizing Cutadapt output and manually selecting the most accurate trimming position length. Therefore, we propose the automation of this specific intermediate step between Cutadapt and DADA2 tools, by selecting values displayed in the graphs that meet the filtering criteria. This automation has been incorporated into a custom pipeline for the analysis of the microbiome in 16S paired-end samples from colorectal cancer patients, and could potentially serve as a standardization approach in these processesThe authors of this paper extend their sincere appreciation to the collaborative efforts and contributions of the meiGAbiome Group, aswell as the entire team of medical and anatomopathologists. Finally, we are deeply grateful to the patients whose selfless donations have made this and numerous other studies possibl

Contribution of the a-baumannii A1S_0114 gene to the interaction with eukaryotic cells and virulence

Genetic and functional studies showed that some components of the Acinetobacter baumannii ATCC 17978 A1S_0112-A1S_0119 gene cluster are critical for biofilm biogenesis and surface motility. Recently, our group has shown that the A1S_0114 gene was involved in biofilm formation, a process related with pathogenesis. Confirming our previous results, microscopy images revealed that the ATCC 17978 10114 derivative lacking this gene was unable to form a mature biofilm structure. Therefore, other bacterial phenotypes were analyzed to determine the role of this gene in the pathogenicity of A. baumannii ATCC 17978. The interaction of the ATCC 17978 parental strain and the 10114 mutant with A549 human alveolar epithelial cells was quantified revealing that the A1S_0114 gene was necessary for proper attachment to A549 cells. This dependency correlates with the negative effect of the A1S_0114 deletion on the expression of genes coding for surface proteins and pili-assembly systems, which are known to play a role in adhesion. Three different experimental animal models, including vertebrate and invertebrate hosts, confirmed the role of the A1S_0114 gene in virulence. All of the experimental infection assays indicated that the virulence of the ATCC 17978 was significantly reduced when this gene was inactivated. Finally, we discovered that the A1S_0114 gene was involved in the production of a small lipopeptide-like compound herein referred to as acinetin 505 (Ac-505). Ac-505 was isolated from ATCC 17978 spent media and its chemical structure was interpreted by mass spectrometry. Overall, our observations provide novel information on the role of the A1S_0114 gene in A. baumannii’s pathobiology and lay the foundation for future work to determine the mechanisms by which Ac-505, or possibly an Ac-505 precursor, could execute critical functions as a secondary metaboliteS

Postcranial morphology of the middle Pleistocene humans from Sima de los Huesos, Spain

Current knowledge of the evolution of the postcranial skeleton in the genus Homo is hampered by a geographically and chronologically scattered fossil record. Here we present a complete characterization of the postcranium of the middle Pleistocene paleodeme from the Sima de los Huesos (SH) and its paleobiological implications. The SH hominins show the following: (i) wide bodies, a plesiomorphic char- acter in the genus Homo inherited from their early hominin ancestors; (ii) statures that can be found in modern human middle-latitude pop- ulations that first appeared 1.6–1.5 Mya; and (iii) large femoral heads in some individuals, a trait that first appeared during the middle Pleistocene in Africa and Europe. The intrapopulational size variation in SH shows that the level of dimorphism was similar to modern humans (MH), but the SH hominins were less encephalized than Ne- andertals. SH shares many postcranial anatomical features with Ne- andertals. Although most of these features appear to be either plesiomorphic retentions or are of uncertain phylogenetic polarity, a few represent Neandertal apomorphies. Nevertheless, the full suite of Neandertal-derived features is not yet present in the SH popula- tion. The postcranial evidence is consistent with the hypothesis based on the cranial morphology that the SH hominins are a sister group to the later Neandertals. Comparison of the SH postcranial skeleton to other hominins suggests that the evolution of the postcranium oc- curred in a mosaic mode, both at a general and at a detailed level

Pinturas murales de la casa de Ariadna (Pompeya, Italia): un estudio multidisciplinar de su estado actual enfocado a una futura restauración y conservación preventiva

[EN] This paper deals with the development of a multidisciplinary study on the current state of conservation of Ariadne’s house (Pompeii, Italy), a domus of great archaeological value. The aim of this study is to undertake the preventive conservation actions required and increase the knowledge about its conservation and to generate discussions and points of view for a future restoration. Environmental studies, electromagnetic radiation measurements, study of materials and a photographical study were carried out. Those studies revealed that the rooftops covering the analyzed rooms resulting in adverse weather conditions causing grave damage to the conservation of the wall paintings. Thus, between 2009-2010 the rooftops were changed and new environmental studies were conducted. Studies of materials showed that the paintings match in execution and composition with those reported by other authors. The salts from modern mortars from previous restorations were affecting frescoes, also it is described a thin grayish surface layer from environmental contaminants.[ES] Este trabajo desarrolla un estudio multidisciplinar sobre el actual estado de conservación de la casa de Ariadna (Pompeya, Italia), domus de gran valor arqueológico. El objetivo es aumentar el conocimiento del estado actual de conservación de la casa para la discusión de una futura restauración. Para ello se realizaron estudios ambientales, mediciones de radiación electromagnética, estudio de materiales y un estudio fotográfico. Los estudios revelaron que los tejados que cubrían las salas analizadas estaban originando unas condiciones climatológicas adversas que se traducían en un grave daño para la conservación de las pinturas murales. Entre 2009-2010 se cambiaron las cubiertas y los estudios ambientales fueron repetidos. Los estudios de materiales demostraron que las pinturas coinciden en ejecución y composición con las señaladas por otros autores. Las sales procedentes de morteros modernos de anteriores restauraciones afectaban a las pinturas, también se describe una fina capa superficial de tonalidad grisácea procedente de contaminantes ambientales.This work was partially supported by the Spanish "Ministerio de Ciencia e Innovacion" under projects HAR2010-21944-C02-01 and HAR2010-21944-C02-02. The authors are grateful to J. Minguez for his English grammar corrections.Pérez García, MDC.; García Diego, FJ.; Merello Giménez, P.; D'antoni, P.; Fernández Navajas, A.; Ribera I Lacomba, A.; Ferrazza, L.... (2013). Ariadne's house (Pompeii, Italy) wall paintings: A multidisciplinary study of its present state focused on a future restoration and preventive conservation. Materiales de Construcción. 63(311):449-467. https://doi.org/10.3989/mc.2012.00812S4494676331

Primary care randomized clinical trial: manual therapy effectiveness in comparison with TENS in patients with neck pain

This study investigated effectiveness of manual therapy (MT) with transcutaneous electrical nerve stimulation (TENS) to reduce pain intensity in patients with mechanical neck disorder (MND). A randomized multi-centered controlled clinical trial was performed in 12 Primary Care Physiotherapy Units in Madrid Region. Ninety patients were included with diagnoses of subacute or chronic MND without neurological damage, 47 patients received MT and 43 TENS. The primary outcome was pain intensity measured in millimeters using the Visual Analogue Scale (VAS). Also disability, quality of life, adverse effects and sociodemographic and prognosis variables were measured. Three evaluations were performed (before, when the procedure ?nished and six months after). Seventy-one patients (79%) completed the follow-up measurement at six months. In more than half of the treated patients the procedure had a clinically relevant ?short term? result after having ended the intervention, when either MT or TENS was used. The success rate decreased to one-third of the patients 6 months after the intervention. No differences can be found in the reduction of pain, in the decrease of disability nor in the quality of life between both therapies. Both analyzed physiotherapy techniques produce a short-term pain reduction that is clinically relevant.Ministerio de SanidadInstituto de Salud Carlos II

Targeted Next-Generation Sequencing in a Large Cohort of Genetically Undiagnosed Patients with Neuromuscular Disorders in Spain

This article belongs to the Special Issue Genetic Advances in Neuromuscular Disorders: From Gene Identification to Gene Therapy.The term neuromuscular disorder (NMD) includes many genetic and acquired diseases and differential diagnosis can be challenging. Next-generation sequencing (NGS) is especially useful in this setting given the large number of possible candidate genes, the clinical, pathological, and genetic heterogeneity, the absence of an established genotype-phenotype correlation, and the exceptionally large size of some causative genes such as TTN, NEB and RYR1. We evaluated the diagnostic value of a custom targeted next-generation sequencing gene panel to study the mutational spectrum of a subset of NMD patients in Spain. In an NMD cohort of 207 patients with congenital myopathies, distal myopathies, congenital and adult-onset muscular dystrophies, and congenital myasthenic syndromes, we detected causative mutations in 102 patients (49.3%), involving 42 NMD-related genes. The most common causative genes, TTN and RYR1, accounted for almost 30% of cases. Thirty-two of the 207 patients (15.4%) carried variants of uncertain significance or had an unidentified second mutation to explain the genetic cause of the disease. In the remaining 73 patients (35.3%), no candidate variant was identified. In combination with patients’ clinical and myopathological data, the custom gene panel designed in our lab proved to be a powerful tool to diagnose patients with myopathies, muscular dystrophies and congenital myasthenic syndromes. Targeted NGS approaches enable a rapid and cost-effective analysis of NMD- related genes, offering reliable results in a short time and relegating invasive techniques to a second tier.This study was granted by FIS PI15/01898, funded by ISCIII and FEDER, ‘Una manera de hacer Europa’ and by Fundación Mutua Madrileña in the “Convocatoria de ayudas a la Investigación en Salud 2015”. It was also funded by an ACCI grant from CIBERER. Daniel Natera-de Benito is the recipient of a grant from the Instituto de Salud Carlos III (Contrato Rio Hortega, CM17/00044)

Making waves: collaboration in the time of SARS-CoV-2 - rapid development of an international co-operation and wastewater surveillance database to support public health decision-making

The presence of SARS-CoV-2 RNA in wastewater was first reported in March 2020. Over the subsequent months, the potential for wastewater surveillance to contribute to COVID-19 mitigation programmes has been the focus of intense national and international research activities, gaining the attention of policy makers and the public. As a new application of an established methodology, focused collaboration between public health practitioners and wastewater researchers is essential to developing a common understanding on how, when and where the outputs of this non-invasive community-level approach can deliver actionable outcomes for public health authorities. Within this context, the NORMAN SCORE "SARS-CoV-2 in sewage" database provides a platform for rapid, open access data sharing, validated by the uploading of 276 data sets from nine countries to-date. Through offering direct access to underpinning meta-data sets (and describing its use in data interpretation), the NORMAN SCORE database is a resource for the development of recommendations on minimum data requirements for wastewater pathogen surveillance. It is also a tool to engage public health practitioners in discussions on use of the approach, providing an opportunity to build mutual understanding of the demand and supply for data and facilitate the translation of this promising research application into public health practice. [Abstract copyright: Copyright © 2021 Elsevier Ltd. All rights reserved.

Relación entre la grasa corporal y la expresión de ira en personas que realizan ejercicio regularmente

La actividad física proporciona benecios, tanto a la población sana como enferma, pero también puede derivar en problemas psicológicos y emocionales como respuesta al estrés. Además, aquellos atletas con menor peso corporal presentan indicadores más elevados de depresión e ira. Se plantea determinar la relación de la grasa corporal sobre la expresión de ira y entender la relación entre distintos comportamientos psicológicos, en personas físicamente activas. 264 sujetos cumplimentaron el Inventario de Expresión de Ira Estado-Rasgo, versión 2, para el estudio sobre las características de la ira y sus efectos en la salud mental y física. Se tomaron medidas antropométricas (peso, talla, IMC, porcentaje de grasa corporal, masa libre de grasa). Se calcularon distintos percentiles en función del género y edad, clasicando a los participantes en tres grupos: percentil <45, entre 45 y 55 y >55 de grasa corporal. Se analizaron distintos comportamientos en relación al STAXI-2 y a los distintos percentiles, pero sin encontrar diferencias significativas entre la ira y los tres grupos.