Exchange of functional domains between a bacterial conjugative relaxase and the integrase of the human adeno-associated virus

Endonucleases of the HUH family are specialized in processing single-stranded DNA in a variety of evolutionarily highly conserved biological processes related to mobile genetic elements. They share a structurally defined catalytic domain for site-specific nicking and strand-transfer reactions, which is often linked to the activities of additional functional domains, contributing to their overall versatility. To assess if these HUH domains could be interchanged, we created a chimeric protein from two distantly related HUH endonucleases, containing the N-terminal HUH domain of the bacterial conjugative relaxase TrwC and the C-terminal DNA helicase domain of the human adeno-associated virus (AAV) replicase and site-specific integrase. The purified chimeric protein retained oligomerization properties and DNA helicase activities similar to Rep68, while its DNA binding specificity and cleaving-joining activity at oriT was similar to TrwC. Interestingly, the chimeric protein could catalyse site-specific integration in bacteria with an efficiency comparable to that of TrwC, while the HUH domain of TrwC alone was unable to catalyze this reaction, implying that the Rep68 C-terminal helicase domain is complementing the TrwC HUH domain to achieve site-specific integration into TrwC targets in bacteria. Our results illustrate how HUH domains could have acquired through evolution other domains in order to attain new roles, contributing to the functional flexibility observed in this protein superfamily.This work was supported by the Medical Research Council (MRC) grant MR/N022890/1 to EH and grant 1001764 to RML; National Institutes of Health (NIH) grant RO1-GM09285 to CRE; Spanish Ministry of Economy and competitiveness (MINECO) grant BIO2013-46414-P to ML and AFM is supported by a Doc.Mobility fellowship from the Swiss National Science Foundation. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Treatment with tocilizumab or corticosteroids for COVID-19 patients with hyperinflammatory state: a multicentre cohort study (SAM-COVID-19)

Objectives: The objective of this study was to estimate the association between tocilizumab or corticosteroids and the risk of intubation or death in patients with coronavirus disease 19 (COVID-19) with a hyperinflammatory state according to clinical and laboratory parameters. Methods: A cohort study was performed in 60 Spanish hospitals including 778 patients with COVID-19 and clinical and laboratory data indicative of a hyperinflammatory state. Treatment was mainly with tocilizumab, an intermediate-high dose of corticosteroids (IHDC), a pulse dose of corticosteroids (PDC), combination therapy, or no treatment. Primary outcome was intubation or death; follow-up was 21 days. Propensity score-adjusted estimations using Cox regression (logistic regression if needed) were calculated. Propensity scores were used as confounders, matching variables and for the inverse probability of treatment weights (IPTWs). Results: In all, 88, 117, 78 and 151 patients treated with tocilizumab, IHDC, PDC, and combination therapy, respectively, were compared with 344 untreated patients. The primary endpoint occurred in 10 (11.4%), 27 (23.1%), 12 (15.4%), 40 (25.6%) and 69 (21.1%), respectively. The IPTW-based hazard ratios (odds ratio for combination therapy) for the primary endpoint were 0.32 (95%CI 0.22-0.47; p < 0.001) for tocilizumab, 0.82 (0.71-1.30; p 0.82) for IHDC, 0.61 (0.43-0.86; p 0.006) for PDC, and 1.17 (0.86-1.58; p 0.30) for combination therapy. Other applications of the propensity score provided similar results, but were not significant for PDC. Tocilizumab was also associated with lower hazard of death alone in IPTW analysis (0.07; 0.02-0.17; p < 0.001). Conclusions: Tocilizumab might be useful in COVID-19 patients with a hyperinflammatory state and should be prioritized for randomized trials in this situatio

Estudios de marcado y recaptura de especies marinas

Los resultados obtenidos del marcado y posterior recaptura de los ejemplares son una herramienta muy valiosa para contribuir a mejorar el conocimiento de la biología y ecología de una especie, examinando ciertos aspectos como son: el crecimiento, los movimientos o migraciones, la mortalidad o supervivencia, la abundancia y distribución de la especie, el hábitat y diferenciación de poblaciones o stocks. Actualmente la técnica de marcado se aplica a muchas especies, tanto terrestres como marinas, pertenecientes a diversos grupos zoológicos: peces, crustáceos, reptiles, moluscos y mamíferos. Este libro repasa algunos ejemplos de marcado de especies marinas de interés comercial. No todas las especies pueden ser marcadas, porque es necesario cumplir una serie de requisitos para poder llevar a cabo con éxito un experimento de marcado. En uno de los apartados de esta guía, se describen los distintos aspectos a tener en cuenta para obtener buenos resultados. Se describen los principales proyectos de marcado actualmente en ejecución o en marcha llevados a cabo por el Instituto Español de Oceanografía (IEO). En primer lugar, se describe brevemente la especie, su distribución, crecimiento, reproducción, alimentación, etc. A continuación, se presenta la información del marcado, es decir, campañas realizadas, número de ejemplares marcados y algunos de los resultados obtenidos hasta la fecha a partir de las recapturas disponibles. En algunas especies, los programas de marcado se llevan realizando desde hace más de 20 años, como es el caso del atún rojo, por lo que la información disponible es bastante amplia. En otros casos por el contrario como la merluza, los proyectos son relativamente recientes, no obstante los resultados son bastante interesantes y prometedores.Nowadays many different marine animals are being tagged. This book summarizes recent tagging programs carried out by the Spanish Institute of Oceanography (IEO). Although the objectives of these various studies mainly depend on the species and each project in particular, the general aim is to better understand the biology and ecology of these animals the structure and dynamics of their populations and their capacity to respond to human activities. This book provides an overview of different aspects of this technique such as a brief history of tagging, the types of tags currently used, including both conventional and electronic tags, where and how to put them on the marine animals, some recommendations regarding how to perform a tagging survey and where to go or what to do if anyone recovers a tagged fish or marine animal. The book then summarizes the main species tagged by the IEO, making a short description of their biology followed by some of the results obtained from tagging studies undertaken until now. Other applications are to know the spatial distribution (spawning or feeding areas), estimate growth parameters, mortality and survival rates, longevity, the size of the population or identifying stocks. Nowadays the advances in electronics have also open new fields such us the possibility of tracking an animal and knowing its habitat preferences and behaviour. Besides some of these tags have the capacity of recording this information during long periods and sending the data from long distances even without the need to recover the animal. Tagging activities constitute a very useful tool to improve the knowledge of many species and contribute to their management and conservation. For that reason this methodology is included in many IEO projects in which other activities like the monitoring of the fishery (landings, fishing effort, fleet characteristics, fishing areas, biological sampling, etc.) are carried out. Some projects are related with coastal pelagic fisheries including anchovy, sardine and mackerel or oceanic pelagic fisheries like tuna and billfish species and pelagic sharks. Others are focused on benthic and demersal species such as hake, black spot seabream, anglerfish, flatfish, etc. Nevertheless not all species can be tagged, as they have to survive being caught and handled before being release. For this reason, tagging techniques may not easily be applied to some species.Versión del edito

Espacio y territorios: razón, pasión e imaginarios

En este caleidoscopio de acercamientos hacia lo espacial y territorial, las visiones se mueven desde aquellas románticas y existencialistas, pasando por aquellas objetivistas y positivistas, hasta las estructuralistas y postestructuralistas. Por el espacio y el territorio se interesan con enfoques diversos numerosas disciplinas, desde la psicología, la etología o la literatura, y las ciencias naturales como la biología o la ecología, hasta las ciencias sociales y políticas, como la geografía, la antropología, la economía y la sociología. Este interés multidisciplinario demuestra la importancia y la complejidad del tema espacial y territorial, y reclama la necesidad de su estudio y comprensión interdisciplinarios, como se intenta con esta publicación

Mapping the human genetic architecture of COVID-19

Matters Arising to this article was published on 03 August 2022, available online at: https://doi.org/10.1038/s41586-022-04826-7 . A second Matters Arising to this article was published on 06 September 2023, available online at: https://doi.org/10.1038/s41586-023-06355-3 .Data availability: Summary statistics generated by the COVID-19 HGI are available at https://www.covid19hg.org/results/r5/ and are available in the GWAS Catalog (study code GCST011074). The analyses described here include the freeze-5 data. COVID-19 HGI continues to regularly release new data freezes. Summary statistics for non-European ancestry samples are not currently available due to the small individual sample sizes of these groups, but results for lead variants of 13 loci are reported in Supplementary Table 3. Individual level data can be requested directly from contributing studies, listed in Supplementary Table 1. We used publicly available data from GTEx (https://gtexportal.org/home/), the Neale lab (https://www.nealelab.is/uk-biobank/), Finucane lab (https://www.finucanelab.org), the FinnGen Freeze 4 cohort (https://www.finngen.fi/en/access_results) and the eQTL catalogue release 3 (https://www.ebi.ac.uk/eqtl/).Code availability: The code for summary statistics lift-over, the projection PCA pipeline including precomputed loadings and meta-analyses are available on GitHub (https://github.com/covid19-hg/) and the code for the Mendelian randomization and genetic correlation pipeline is available on GitHub at https://github.com/marcoralab/MRcovid.Reporting summary: Further information on research design is available in the Nature Research Reporting Summary linked to this paper online at: https://www.nature.com/articles/s41586-021-03767-x#MOESM2 .Supplementary information is available onlne at: https://www.nature.com/articles/s41586-021-03767-x#Sec24 .Extended data figures and tables are available online at: https://www.nature.com/articles/s41586-021-03767-x#Sec23 .Copyright © The Author(s) 2021. The genetic make-up of an individual contributes to the susceptibility and response to viral infection. Although environmental, clinical and social factors have a role in the chance of exposure to SARS-CoV-2 and the severity of COVID-191,2, host genetics may also be important. Identifying host-specific genetic factors may reveal biological mechanisms of therapeutic relevance and clarify causal relationships of modifiable environmental risk factors for SARS-CoV-2 infection and outcomes. We formed a global network of researchers to investigate the role of human genetics in SARS-CoV-2 infection and COVID-19 severity. Here we describe the results of three genome-wide association meta-analyses that consist of up to 49,562 patients with COVID-19 from 46 studies across 19 countries. We report 13 genome-wide significant loci that are associated with SARS-CoV-2 infection or severe manifestations of COVID-19. Several of these loci correspond to previously documented associations to lung or autoimmune and inflammatory diseases3–7. They also represent potentially actionable mechanisms in response to infection. Mendelian randomization analyses support a causal role for smoking and body-mass index for severe COVID-19 although not for type II diabetes. The identification of novel host genetic factors associated with COVID-19 was made possible by the community of human genetics researchers coming together to prioritize the sharing of data, results, resources and analytical frameworks. This working model of international collaboration underscores what is possible for future genetic discoveries in emerging pandemics, or indeed for any complex human disease

Mapping the human genetic architecture of COVID-19

The genetic make-up of an individual contributes to the susceptibility and response to viral infection. Although environmental, clinical and social factors have a role in the chance of exposure to SARS-CoV-2 and the severity of COVID-19(1,2), host genetics may also be important. Identifying host-specific genetic factors may reveal biological mechanisms of therapeutic relevance and clarify causal relationships of modifiable environmental risk factors for SARS-CoV-2 infection and outcomes. We formed a global network of researchers to investigate the role of human genetics in SARS-CoV-2 infection and COVID-19 severity. Here we describe the results of three genome-wide association meta-analyses that consist of up to 49,562 patients with COVID-19 from 46 studies across19 countries. We report 13 genome-wide significant loci that are associated with SARS-CoV-2 infection or severe manifestations of COVID-19. Several of these loci correspond to previously documented associations to lung or autoimmune and inflammatory diseases(3-7). They also represent potentially actionable mechanisms in response to infection. Mendelian randomization analyses support a causal role for smoking and body-mass index for severe COVID-19 although not for type II diabetes. The identification of novel host genetic factors associated with COVID-19 was made possible by the community of human genetics researchers coming together to prioritize the sharing of data, results, resources and analytical frameworks. This working model of international collaboration underscores what is possible for future genetic discoveries in emerging pandemics, or indeed for any complex human disease.Radiolog

Urban transit infrastructure: Spatial mismatch and labor market power

This paper estimates the effects of a subway expansion on labor market outcomes in Santiago, Chile. First, we estimate these effects through a reduced-form analysis. We find changes in work locations and wages consistent with a reduction in firms' labor market power in areas where the subway expanded. We then lay out a model with labor market oligopsonies to calculate the welfare gains from the subway expansion. The model allows decomposition of welfare gains into i) efficiency gains from improved worker-firm matching and ii) gains from reducing labor misallocation due to labor market power. We analyze the distributional implications of the subway expansion. We find that workers benefit as firms see reduced profits. In a model with labor market power these welfare gains are larger than in a competitive model

Statistical methodology to predict reaction time of water-rock experiments under quasi-steady state conditions

Edited by Ignacio S. Torres-Alvarado.Water-rock interaction experiments have provided important results in mineral dissolution studies although the steady state conditions are rarely attained. These experiments are usually costly, tedious, and time consuming. Among the controlling factors, the reaction time has been identified as a key parameter for designing optimized water-rock experiments. Moreover large discrepancies actually exist defining the reaction time needed to reach steady state conditions. We propose a statistical methodology to predict the reaction time needed to approach a quasi-steady state in water-rock experiments. The method was successfully applied for the cation exchange reaction in feldspars using experimental data already published (granite-water interaction at 200 °C, 50 MPa, fluid/rock ratio=2). Logarithmic regression models were used for fitting fluid composition [log(Na/K)] and reaction time (t). For the most probable fluid composition under unknown steady-state conditions, the log(Na/K) value inferred from Na/K geothermometers was assumed. We found that a reaction time between 3520 and 4996 hours would be required to approach the quasi-steady state in the example experiment.Peer reviewe