Evolution of overlapping reading frames in virus genomes

Viruses are formidable pathogens that represent the majority of biological entities in our planet, and their genomes are a source of interesting enigmas. One feature in which virus genomes are usually rich, is the presence of overlapping reading frames (OvRFs) — portions of the genome where the same nucleotide sequence encodes more than one protein. OvRFs are hypothesized to be used by viruses to encode proteins more compactly and to regulate transcription. In addition, OvRFs might be a source of gene novelty, facilitating the creation of new open reading frames (ORF) within the transcriptional context of existing ones. To characterize the distribution OvRFs in viruses, I analyzed 12,609 reference genomes from the NCBI virus database and discovered that, while the number of OvRFs increases the genome length, the overlapping regions tend to be shorter in longer genomes. I also demonstrated that dif- ferent frameshifts have distinct patterns in OvRFs. For example, +2 frameshifts are predominantly found in dsDNA viruses, whereas +0 frameshifts in RNA viruses tend to involve longer overlaps, which may increase the selective burden of the same nucleotide positions within codons. Further, I retrieved n = 8, 586 protein-coding sequences from n = 1, 224 reference genomes, and used an alignment-free method to cluster these sequences within virus families. I used these clusters to develop a new network-based representation of the distribution of OvRFs, which provides a means of visualizing and analyzing these genome features for each virus family. I also used these net- works to generate a high-level visualization of how overlapping genes are distributed among virus genomes in the same family. Evolution in overlapping genes is complicated because the effect of a nucleotide substitution has multiple contexts. To unravel the effects of OvRFs on virus evolution, I developed HexSE, a simulation model of nucleotide sequence evolution along a phylogeny that tracks the substitution rates at every nucleotide site. In HexSE, I implemented a customized data structure to efficiently track the substitution rates at every nucleotide site. These rates are determined by the stationary nucleotide frequencies, transition bias, and the distribution of selection biases (dN and dS) in the respective reading frames. Next, I compared HexSE simulations under varying settings to an alignment of actual hepatitis B virus (HBV) genomes, which revealed consistent drops in synonymous substitution rates (dS) in association with overlapping regions of an ORF. This thesis explores the cryptic information contained in viral genomes to help explain the evolutionary processes that shape them. In particular, understanding the impact of OvRFs on the evolution of virus genomes will provide us with crucial pieces of a significant puzzle — under- standing the origin of new genes in virus genomes, and thereby virus diversity

Genome sequencing of two iBell pepper endornavirus/i (BPEV) variants infecting iCapsicum annuum/i in Colombia

Transcriptome analysis of chili and bell pepper samples from commercial plots in the municipalities of Santa Fe de Antioquia and El Penol in the province of Antioquia revealed the presence of viral sequences with significant similarity to genomes of members of the genus Endornavirus. Assembly of the chili and bell pepper transcriptomes resulted in consensus sequences of 14,727 nt and 14,714 nt that were identified as Bell pepper endornavirus (BPEV). Both sequences were nearly identical by 99.9 % at both nucleotide and amino acid levels. The presence of BPEV was confirmed by RT-qPCR, RT-PCR and Sanger sequencing using RdRp-specific primers designed from the assembled sequences in ten independent random samples taken from the investigated bell pepper stands. The phylogenetic analysis of both BPEV variants and their affiliation within the genus Endornavirus is discussed. For our knowledge, this is the first study on this group of viruses in Colombia

Hypothalamic endocannabinoids inversely correlate with the development of diet-induced obesity in male and female mice

The endocannabinoid (eCB) system regulates energy homeostasis and is linked to obesity development. However, the exact dynamic and regulation of eCBs in the hypothalamus during obesity progression remain incompletely described and understood. Our study examined the time course of responses in two hypothalamic eCBs, 2-arachidonoylglycerol (2-AG) and arachidonoylethanolamine (AEA), in male and female mice during diet-induced obesity and explored the association of eCB levels with changes in brown adipose tissue (BAT) thermogenesis and body weight. We fed mice a high-fat diet (HFD), which induced a transient increase (substantial at 7 days) in hypothalamic eCBs, followed by a progressive decrease to basal levels with a long-term HFD. This transient rise at early stages of obesity is considered a physiologic compensatory response to BAT thermogenesis, which is activated by diet surplus. The eCB dynamic was sexually dimorphic: hypothalamic eCBs levels were higher in female mice, who became obese at later time points than males. The hypothalamic eCBs time course positively correlated with thermogenesis activation, but negatively matched body weight, leptinemia, and circulating eCB levels. Increased expression of eCB-synthetizing enzymes accompanied the transient hypothalamic eCB elevation. Icv injection of eCB did not promote BAT thermogenesis; however, administration of thermogenic molecules, such as central leptin or a peripheral β3-adrenoreceptor agonist, induced a significant increase in hypothalamic eCBs, suggesting a directional link from BAT thermogenesis to hypothalamic eCBs. This study contributes to the understanding of hypothalamic regulation of obesity. Keywords: hypothalamus, sexual dimorphism, brown adipose tissu

Incidence of peripheral arterial disease in the ARTPER population cohort after 5 years of follow-up

To know the epidemiology (prevalence, incidence, progression and morbidity and mortality associated) of peripheral artery disease in general population and the factors associated with this progression is essential to know the evolution of atherosclerosis and develop preventive strategies. The aim of the study was to determine the incidence of PAD after 5 years of follow-up population-based cohort ARTPER, and the evolution of Ankle brachial Index (ABI) in this period. Peripheral artery disease incidence analysis after 5 years of follow-up of 3786 subjects > 50 years old. Peripheral artery disease incident when the second cross section Ankle brachial Index was <0.9 in any of the lower limbs, with normal baseline (0.9 to 1.4). Between 2012 and 2013 2762 individuals (77 % participation) were re-examined. Finally analyzed 2256 subjects (after excluding pathological Ankle brachial Index) followed for 4.9 years (range 3.8 to 5.8 years), totalling 11,106 person-years. Peripheral artery disease 95 new cases were detected, representing an incidence of 4.3 % at 5 years and 8.6 per 1000 person-years (95 % CI 6.9 to 10.5) being higher in men (10.2, 95 % CI 7.4 to 13.5) than in women (7.5, 95 % CI 5.5 to 9.9). Linear correlation between the baseline Ankle brachial Index and the second cross section was low (r = 0.23). The incidence of peripheral artery disease in ARTPER cohort was 8.6 cases per 1000 person-years, being higher in men, especially <65 years. The correlation between two measures Ankle brachial Index after 5 years of follow-up was low. One might consider whether Ankle brachial Index repeated measures could improve the correlation

Factors associated with implementation of the 5A's smoking cessation model

Background: several health organizations have adopted the 5A's brief intervention model (Ask, Advise, Assess, Assist, Arrange), based on evidence-based guidelines for smoking cessation. We examine individual, cognitive, behavioral, and organizational factors associated with the 5A's performance among clinical healthcare workers in Catalonia. We also investigate how these factors interact and potentially predict the implementation of each component of the 5A's. Methods: a cross-sectional survey was conducted among clinical health workers enrolled in an online smoking cessation training course (n = 580). The survey included questions about individual characteristics as well as cognitive, behavioral, and organizational factors previously identified in research. We assessed self-reported performance of the 5A's, assessed on a scale from 0 to 10, and used Multivariate regression to examine factors associated with its performance. Results: the performance means (standard deviation) were moderate for the first 3A's [Ask: 6.4 (3.1); Advise: 7.1 (2.7); Assess: 6.3 (2.8)] and low for the last 2A's [Assist: 4.4 (2.9); Arrange: 3.2 (3.3)]. We observed a high correlation between Assist and Arrange (r = 0.704, p < 0.001). Having positive experiences and feeling competent were positively associated with performing the 5A's model and having organizational support with Assist and Arrange. Personal tobacco use among healthcare workers was negatively associated with Advice and Arrange. Conclusions: our study found that clinical healthcare workers do not perform the 5A's completely. The main barriers identified suggest the need of training and making available practical guidelines in healthcare services. Organizational support is essential for moving towards the implementation of Assist and Arrange

doi.org/10.1371/journal. pone.0250796

The aim was to analyze the characteristics and predictors of unfavorable outcomes in solid organ transplant recipients (SOTRs) with COVID-19. We conducted a prospective observational cohort study of 210 consecutive SOTRs hospitalized with COVID-19 in 12 Spanish centers from 21 February to 6 May 2020. Data pertaining to demographics, chronic underlying diseases, transplantation features, clinical, therapeutics, and complications were collected. The primary endpoint was a composite of intensive care unit (ICU) admission and/or death. Logistic regression analyses were performed to identify the factors associated with these unfavorable outcomes. Males accounted for 148 (70.5%) patients, the median age was 63 years, and 189 (90.0%) patients had pneumonia. Common symptoms were fever, cough, gastrointestinal disturbances, and dyspnea. The most used antiviral or host-targeted therapies included hydroxychloroquine 193/200 (96.5%), lopinavir/ritonavir 91/200 (45.5%), and tocilizumab 49/200 (24.5%). Thirty-seven (17.6%) patients required ICU admission, 12 (5.7%) suffered graft dysfunction, and 45 (21.4%) died. A shorter interval between transplantation and COVID-19 diagnosis had a negative impact on clinical prognosis. Four baseline features were identified as independent predictors of intensive care need or death: advanced age, high respiratory rate, lymphopenia, and elevated level of lactate dehydrogenase. In summary, this study presents comprehensive information on characteristics and complications of COVID-19 in hospitalized SOTRs and provides indicators available upon hospital admission for the identification of SOTRs at risk of critical disease or death, underlining the need for stringent preventative measures in the early post-transplant periodThis study was supported by Plan Nacional de I+D+i 2013-2016 and Instituto de Salud Carlos III, Subdirección General de Redes y Centros de Investigación Cooperativa, Ministerio de Ciencia, Innovación y Universidades, Spanish Network for Research in Infectious Diseases (REIPI RD16/0016); co-financed by European Development Regional Fund “A way to achieve Europe”, Operative Program Intelligence Growth 2014-2020. EC and JSC received grants from the Instituto de Salud Carlos III, Ministerio de Ciencia e Innovación, Proyectos de Investigación sobre el SARSCoV-2 y la enfermedad COVID-19 (COV20/ 00370; COV20/00580). JSC is a researcher belonging to the program “Nicola´s Monardes”(C0059–2018), Servicio Andaluz de Salud, Junta de Andalucía, Spain. SS-A is supported by a grant from the Instituto de Salud Carlos III, Ministerio de Ciencia e Innovación, Proyectos de Investigación sobre el SARS-Co

Genero e inclusión en educación superior: desarrollo de una línea permanente de innovación educativa en la Universidad de Málaga

El grupo permanente de innovación educativa sobre género e inclusión en educación superior (GpIE 22-031 de la Universidad de Málaga) tiene como objetivo el desarrollo de pautas de diagnóstico y actualización de las programaciones docentes a través de una rúbrica para evaluación de indicadores de perspectiva de género (lenguaje inclusivo, visibilización de autoras y contenidos con descripción y diferenciación por sexo) y un protocolo de actualización de las programaciones docentes (actividades prácticas) consecuente con tal evaluación. Partiendo de una primera tarea que cada participante del proyecto desarrolla en las actividades prácticas en su aula y materia, pretendemos avanzar en el diseño y validación de un protocolo de actualización. Se espera que la aplicación práctica de dicho protocolo derivará en una mayor adecuación de estas actividades a la realidad social actual y al desarrollo de competencias procedimentales en el alumnado e incluso en el profesorado. Se ha comenzado una aplicación piloto en las asignaturas vinculadas con el proyecto y previsiblemente el segundo año se podrán incorporar otras cuyo profesorado se muestre interesado. Para promover estas nuevas incorporaciones, es preciso que se procure la difusión de los productos que se elaboren en este proyecto a lo cual servirán: a) espacio web para dar a conocer los instrumentos y las actividades que se realicen y b) seminarios para intercambio de experiencias desarrolladas en el proyecto, abiertos al profesorado del departamento y al profesorado de otros centros de la universidad.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Enfoque de género e inclusión en educación superior: experiencia de innovación en la Universidad de Málaga.

Con la constitución como grupo permanente de innovación educativa*, nuestro objetivo será el desarrollo de pautas de diagnóstico y actualización de las programaciones docentes a través de una rúbrica para evaluación de indicadores de perspectiva de género (lenguaje inclusivo, descripción diferenciada por sexo, etc.) y un protocolo de actualización de las programaciones docentes (actividades prácticas) consecuente con tal evaluación. Partiendo de una primera tarea que cada cual desarrolla en las actividades prácticas que lleva a cabo en su aula y materia, pretendemos avanzar en el diseño y validación de un protocolo de actualización de cuya aplicación se derive una mayor adecuación de estas actividades a la realidad social actual y al desarrollo de competencias procedimentales en el alumnado e incluso en el profesorado. Comenzaremos su aplicación piloto en las asignaturas vinculadas con el proyecto y previsiblemente el segundo año se podrán incorporar otras cuyo profesorado se muestre interesado. Para promover estas nuevas incorporaciones, es preciso que se procure la difusión de los productos que se elaboren en este proyecto a lo cual servirán: a) espacio web para dar a conocer los instrumentos y las actividades que se realicen y b) dos seminarios del proyecto para intercambio de experiencias desarrolladas en el proyecto, abiertos al profesorado del departamento a final de curso 22-23 (seminario intermedio) y al profesorado de la facultad a final del 23-24 (seminario final), respectivamente. *El Grupo Permanente de innovación Educativa en Género e Inclusión en la Educación Superior (GpIE-UMA 22-031) es un proyecto financiado por el Servicio de Formación e Innovación del Vicerrectorado de Personal Docente e Investigador de la Universidad de Málaga.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Risk factors for unfavorable outcome and impact of early post-transplant infection in solid organ recipients with COVID-19: A prospective multicenter cohort study

The aim was to analyze the characteristics and predictors of unfavorable outcomes in solid organ transplant recipients (SOTRs) with COVID-19. We conducted a prospective observational cohort study of 210 consecutive SOTRs hospitalized with COVID-19 in 12 Spanish centers from 21 February to 6 May 2020. Data pertaining to demographics, chronic underlying diseases, transplantation features, clinical, therapeutics, and complications were collected. The primary endpoint was a composite of intensive care unit (ICU) admission and/or death. Logistic regression analyses were performed to identify the factors associated with these unfavorable outcomes. Males accounted for 148 (70.5%) patients, the median age was 63 years, and 189 (90.0%) patients had pneumonia. Common symptoms were fever, cough, gastrointestinal disturbances, and dyspnea. The most used antiviral or host-targeted therapies included hydroxychloroquine 193/200 (96.5%), lopinavir/ritonavir 91/200 (45.5%), and tocilizumab 49/200 (24.5%). Thirty-seven (17.6%) patients required ICU admission, 12 (5.7%) suffered graft dysfunction, and 45 (21.4%) died. A shorter interval between transplantation and COVID-19 diagnosis had a negative impact on clinical prognosis. Four baseline features were identified as independent predictors of intensive care need or death: advanced age, high respiratory rate, lymphopenia, and elevated level of lactate dehydrogenase. In summary, this study presents comprehensive information on characteristics and complications of COVID-19 in hospitalized SOTRs and provides indicators available upon hospital admission for the identification of SOTRs at risk of critical disease or death, underlining the need for stringent preventative measures in the early post-transplant period

Systematic Collaborative Reanalysis of Genomic Data Improves Diagnostic Yield in Neurologic Rare Diseases

Altres ajuts: Generalitat de Catalunya, Departament de Salut; Generalitat de Catalunya, Departament d'Empresa i Coneixement i CERCA Program; Ministerio de Ciencia e Innovación; Instituto Nacional de Bioinformática; ELIXIR Implementation Studies (CNAG-CRG); Centro de Investigaciones Biomédicas en Red de Enfermedades Raras; Centro de Excelencia Severo Ochoa; European Regional Development Fund (FEDER).Many patients experiencing a rare disease remain undiagnosed even after genomic testing. Reanalysis of existing genomic data has shown to increase diagnostic yield, although there are few systematic and comprehensive reanalysis efforts that enable collaborative interpretation and future reinterpretation. The Undiagnosed Rare Disease Program of Catalonia project collated previously inconclusive good quality genomic data (panels, exomes, and genomes) and standardized phenotypic profiles from 323 families (543 individuals) with a neurologic rare disease. The data were reanalyzed systematically to identify relatedness, runs of homozygosity, consanguinity, single-nucleotide variants, insertions and deletions, and copy number variants. Data were shared and collaboratively interpreted within the consortium through a customized Genome-Phenome Analysis Platform, which also enables future data reinterpretation. Reanalysis of existing genomic data provided a diagnosis for 20.7% of the patients, including 1.8% diagnosed after the generation of additional genomic data to identify a second pathogenic heterozygous variant. Diagnostic rate was significantly higher for family-based exome/genome reanalysis compared with singleton panels. Most new diagnoses were attributable to recent gene-disease associations (50.8%), additional or improved bioinformatic analysis (19.7%), and standardized phenotyping data integrated within the Undiagnosed Rare Disease Program of Catalonia Genome-Phenome Analysis Platform functionalities (18%)