Alpha proteobacterial ancestry of the [Fe-Fe]-hydrogenases in anaerobic eukaryotes

Eukaryogenesis, a major transition in evolution of life, originated from the symbiogenic fusion of an archaea with a metabolically versatile bacterium. By general consensus, the latter organism belonged to α proteobacteria, subsequently evolving into the mitochondrial organelle of our cells. The consensus is based upon genetic and metabolic similarities between mitochondria and aerobic α proteobacteria but fails to explain the origin of several enzymes found in the mitochondria-derived organelles of anaerobic eukaryotes such as Trichomonas and Entamoeba. These enzymes are thought to derive from bacterial lineages other than α proteobacteria, e.g., Clostridium - an obligate anaerobe. [FeFe]-hydrogenase constitues the characteristic enzyme of this anaerobic metabolism and is present in different types also in Entamoeba and other anaerobic eukaryotes. Here we show that α proteobacteria derived from metagenomic studies possess both the cytosolic and organellar type of [FeFe]-hydrogenase, as well as all the proteins required for hydrogenase maturation. These organisms are related to cultivated members of the Rhodospirillales order previously suggested to be close relatives of mitochondrial ancestors. For the first time, our evidence supports an α proteobacterial ancestry for both the anaerobic and the aerobic metabolism of eukaryotes. Reviewers: This article was reviewed by William Martin and Nick Lane, both suggested by the Authors. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13062-016-0136-3) contains supplementary material, which is available to authorized users

Abundance and Diversity of Earthworms in Managed and Non- Managed Fallow Lands of Calakmul Reserve of Campeche, Mexico

In Mexico, the best preserved tropical rain forest is found in Calakmul Reserve, where fallow land management has been established. Fallow lands are developed as a consequence of a successional vegetation process after clearing the primary vegetation and milpa production. Forty-nine sites were studied, where 17 were managed fallow lands, 24 non-managed fallow lands, and 8 tropical rain forests. Earthworms were collected at the end of the raining season, and four monoliths of 25 × 25 × 30 cm were developed per site according to the TSBF method. We observed how Zapatadrilus siboney, a native species was dominant in managed and non-managed fallow lands. Earthworm’s total biomass and density were not significantly different between the managed and non-managed fallow lands. Earthworm’s species richness was significantly low in non-managed fallow lands. We observed a strong correlation between earthworm density and richness with the age of the fallow lands (r2: 0.9 and 0.7; p < 0.05, respectively). The management type of the fallow land seems to affect earthworm biomasses (r2: 0.56; p < 0.05)

Characterization of Rhizobium grahamii extrachromosomal replicons and their transfer among rhizobia

Background: Rhizobium grahamii belongs to a new phylogenetic group of rhizobia together with Rhizobium mesoamericanum and other species. R. grahamii has a broad-host-range that includes Leucaena leucocephala and Phaseolus vulgaris, although it is a poor competitor for P. vulgaris nodulation in the presence of Rhizobium etli or Rhizobium phaseoli strains. This work analyzed the genome sequence and transfer properties of R. grahamii plasmids. Results: Genome sequence was obtained from R. grahamii CCGE502 type strain isolated from Dalea leporina in Mexico. The CCGE502 genome comprises one chromosome and two extrachromosomal replicons (ERs), pRgrCCGE502a and pRgrCCGE502b. Additionally, a plasmid integrated in the CCGE502 chromosome was found. The genomic comparison of ERs from this group showed that gene content is more variable than average nucleotide identity (ANI). Well conserved nod and nif genes were found in R. grahamii and R. mesoamericanum with some differences. R. phaseoli Ch24-10 genes expressed in bacterial cells in roots were found to be conserved in pRgrCCGE502b. Regarding conjugative transfer we were unable to transfer the R. grahamii CCGE502 symbiotic plasmid and its megaplasmid to other rhizobial hosts but we could transfer the symbiotic plasmid to Agrobacterium tumefaciens with transfer dependent on homoserine lactones. Conclusion: Variable degrees of nucleotide identity and gene content conservation were found among the different R. grahamii CCGE502 replicons in comparison to R. mesoamericanum genomes. The extrachromosomal replicons from R. grahamii were more similar to those found in phylogenetically related Rhizobium species. However, limited similarities of R. grahamii CCGE502 symbiotic plasmid and megaplasmid were observed in other more distant Rhizobium species. The set of conserved genes in R. grahamii comprises some of those that are highly expressed in R. phaseoli on plant roots, suggesting that they play an important role in root colonization.Instituto de Biotecnologia y Biologia Molecula

Characterization of Rhizobium grahamii extrachromosomal replicons and their transfer among rhizobia

Background: Rhizobium grahamii belongs to a new phylogenetic group of rhizobia together with Rhizobium mesoamericanum and other species. R. grahamii has a broad-host-range that includes Leucaena leucocephala and Phaseolus vulgaris, although it is a poor competitor for P. vulgaris nodulation in the presence of Rhizobium etli or Rhizobium phaseoli strains. This work analyzed the genome sequence and transfer properties of R. grahamii plasmids. Results: Genome sequence was obtained from R. grahamii CCGE502 type strain isolated from Dalea leporina in Mexico. The CCGE502 genome comprises one chromosome and two extrachromosomal replicons (ERs), pRgrCCGE502a and pRgrCCGE502b. Additionally, a plasmid integrated in the CCGE502 chromosome was found. The genomic comparison of ERs from this group showed that gene content is more variable than average nucleotide identity (ANI). Well conserved nod and nif genes were found in R. grahamii and R. mesoamericanum with some differences. R. phaseoli Ch24-10 genes expressed in bacterial cells in roots were found to be conserved in pRgrCCGE502b. Regarding conjugative transfer we were unable to transfer the R. grahamii CCGE502 symbiotic plasmid and its megaplasmid to other rhizobial hosts but we could transfer the symbiotic plasmid to Agrobacterium tumefaciens with transfer dependent on homoserine lactones. Conclusion: Variable degrees of nucleotide identity and gene content conservation were found among the different R. grahamii CCGE502 replicons in comparison to R. mesoamericanum genomes. The extrachromosomal replicons from R. grahamii were more similar to those found in phylogenetically related Rhizobium species. However, limited similarities of R. grahamii CCGE502 symbiotic plasmid and megaplasmid were observed in other more distant Rhizobium species. The set of conserved genes in R. grahamii comprises some of those that are highly expressed in R. phaseoli on plant roots, suggesting that they play an important role in root colonization.Instituto de Biotecnologia y Biologia Molecula

West Nile virus emergence in humans in Extremadura, Spain 2020

In Spain, the largest human West Nile virus (WNV) outbreak among humans was reported in 2020, constituting the second most important outbreak in Europe that season. Extremadura (southwestern Spain) was one of the affected areas, reporting six human cases. The first autochthonous human case in Spain was reported in Extremadura in 2004, and no other human cases were reported until 2020. In this work, we describe the first WNV human outbreak registered in Extremadura, focusing on the most important clinical aspects, diagnostic results, and control actions which followed. In 2020, from September to October, human WNV infections were diagnosed using a combination of molecular and serological methods (an in-house specific qRT-PCR and a commercial ELISA for anti-WNV IgM and IgG antibodies) and by analysing serum, urine, and/or cerebrospinal fluid samples. Serological positive serum samples were further tested using commercial kits against related flaviviruses Usutu and Tick-borne encephalitis in order to analyse serological reactivity and to confirm the results by neutralisation assays. In total, six cases of WNV infection (five with neuroinvasive disease and one with fever) were identified. Clinical presentation and laboratory findings are described. No viral RNA was detected in any of the analysed samples, but serological cross-reactivity was detected against the other tested flaviviruses. Molecular and serological methods for WNV detection in various samples as well as differential diagnosis are recommended. The largest number of human cases of WNV infection ever registered in Extremadura, Spain, occurred in 2020 in areas where circulation of WNV and other flaviviruses has been previously reported in humans and animals. Therefore, it is necessary to enhance surveillance not only for the early detection and implementation of response measures for WNV but also for other emerging flaviviruses that could be endemic in this area.This research was partially funded by the project PI19CIII/00014 from the Instituto de Salud Carlos III.S

Nodular diagnosis for ecological engineering of the symbiotic nitrogen fixation with legumes

As a major contributor to the reduced nitrogen pool in the biosphere, symbiotic nitrogen fixation by legumes plays a critical role in a sustainable production system. However this legume contribution varies with the physico-chemical and biological conditions of the nodulated-root rhizosphere. In order to assess the abiotic and biotic constrains that might limit this symbiosis at the agroecosystem level, a nodular diagnosis is proposed with common bean as a model grain-legume, and a major source of plant proteins for world human nutrition. The engineering of the legume symbiosis is addressed by participatory assessment of bean recombinant inbred lines contrasting for their efficiency in use of phosphorous for symbiotic nitrogen fixation. With this methodology, in field-sites chosen with farmers of an area of cereal-cropping in the Mediterranean basin, a large spatial and temporal variation in the legume nodulation was found. Soil P availability was a major limiting factor of the rhizobial symbiosis. In order to relate the field measurements with progress in functional genomics of the symbiosis, in situ RT-PCR on nodule sections has been implemented showing that the phytase gene is expressed in the cortex with significantly higher number of transcripts in P-efficient RILs. It is concluded that various tools and indicators are available for developing the ecological engineering of the rhizobial symbiosis, in particular for its beneficial contribution to the bio-geochemical cycle of N, and also P and C

A Single-Run Next-Generation Sequencing (NGS) Assay for the Simultaneous Detection of Both Gene Mutations and Large Chromosomal Abnormalities in Patients with Myelodysplastic Syndromes (MDS) and Related Myeloid Neoplasms

Chromosomal abnormalities and somatic mutations are found in patients with myelodysplastic syndromes (MDS) and myelodysplastic/myeloproliferative neoplasms (MDS/MPN) in around 50-80% of cases. The identification of these alterations is important for the accurate diagnosis and prognostic classification of these patients. Often, an apparently normal or failed karyotype might lead to an inadequate estimation of the prognostic risk, and several strategies should be combined to solve these cases. The aim of this study was to introduce a novel next-generation sequencing (NGS)-based strategy for the simultaneous detection of all the clinically relevant genetic alterations associated with these disorders. We validated this approach on a large cohort of patients by comparing our findings with those obtained with standard-of-care methods (i.e., karyotype and SNP-arrays). We show that our platform represents a significant improvement on current strategies in defining diagnosis and risk stratification of patients with MDS and myeloid-related disorders. Myelodysplastic syndromes (MDS) and myelodysplastic/myeloproliferative neoplasms are clonal disorders that share most of their cytogenetic and molecular alterations. Despite the increased knowledge of the prognostic importance of genetics in these malignancies, next-generation sequencing (NGS) has not been incorporated into clinical practice in a validated manner, and the conventional karyotype remains mandatory in the evaluation of suspected cases. However, non-informative cytogenetics might lead to an inadequate estimation of the prognostic risk. Here, we present a novel targeted NGS-based assay for the simultaneous detection of all the clinically relevant genetic alterations associated with these disorders. We validated this platform in a large cohort of patients by performing a one-to-one comparison with the lesions from karyotype and single-nucleotide polymorphism (SNP) arrays. Our strategy demonstrated an approximately 97% concordance with standard clinical assays, showing sensitivity at least equivalent to that of SNP arrays and higher than that of conventional cytogenetics. In addition, this NGS assay was able to identify both copy-neutral loss of heterozygosity events distributed genome-wide and copy number alterations, as well as somatic mutations within significant driver genes. In summary, we show a novel NGS platform that represents a significant improvement to current strategies in defining diagnosis and risk stratification of patients with MDS and myeloid-related disorder

Establecimiento del tamaño de raciones de consumo de frutas y hortalizas para su uso en guías alimentarias en el entorno español: propuesta del Comité Científico de la Asociación 5 al día

Introduction: Food servings are standard amounts of food stuffs or drinks to help dietetic advice to promote and preserve health. The aim is to establish the serving size of fruits and vegetables (FH) to be used in food based dietary guidelines (FBDG). Material and Methods: Methodology of the United States Department of Agriculture (USDA) was adapted to establish serving sizes for FBDG, along of the followed by the food exchange system. Data was collected from the FH portion sizes reported in nutritional surveys and common sizes available in the Spanish market, and they were adjusted to an easily recognisable quantities of food with equivalence on key nutrients: the compliance with public health goals for FH consumption was evaluated. Results: Portion sizes typically reported in Spanish nutrition surveys are scarce and not homogeneous, and no data published in scientific journals on portion sizes were available. The Spanish FBDG, in spite of showing a range of serving size for FH, do not assure that they are interchangeable nor specify the method to obtein them.The serving of vegetables was 139,44g (DS:+/- 21.98, CV:0.16), 137,68g (DS:+/- 49,61, CV:0,36) for fruits and 28.00g (DS:+/- 7,53, CV:0.27) for dried fruits. Conclusions: With the established servings, the recommendation of consuming "at least 5 servings of FH a day" would allow reaching the Public Health goals for FH established in 600g (net weight)/person/day. It is recommended that the Spanish Agency for Consumers, Food Safety and Nutrition (AECOSAN) uses this methodology to establish serving sizes for the rest of food groups that make up the FBDG for the Spanish population.Introducción: Las raciones de consumo son cantidades estándar de alimentos o bebidas sugeri-das para asesorar sobre la cantidad de alimento a consumir para preservar un estado de salud adecuado. El objetivo principal de este trabajo es establecer los tamaños de ración de consumo de frutas y hortalizas (FH) para uso en guías alimentarias.Material y Métodos: Se adaptó la metodología de la United States Department of Agriculture (USDA) para el establecimiento de los tamaños de ración de consumo para guías, y la del Sistema de Intercambios. Se recopilaron datos de porción reportados en encuestas y calibres comunes en el mercado, se ajustó a cantidades de alimento fácilmente reconocibles y con equivalencia de nutrientes clave y se evaluó el grado de cumplimiento de los objetivos de salud pública para el consumo de FH. Resultados: Los tamaños de porción típicamente reportados en encuestas españolas son escasos y poco homogéneos, y no se encontraron datos publicados en revistas científicas sobre los cali-bres. Las guías alimentarias españolas, a pesar de mostrar un rango de tamaño de ración para FH no aseguran que sean intercambiables ni especifican el método para llegar a las mismas. La ración de hortalizas obtenida ha sido de 139,44g (DS:±21,98; CV:0,16), de 137,68g (DS:±49,61; CV:0,36) para frutas y 28,00g (DS:±7,53; CV:0,27) para frutas desecadas. . Conclusiones: Con las raciones establecidas, el mensaje “consume al menos 5 raciones entre FH al día” permitiría alcanzar los objetivo de Salud Pública para FH establecidos en 600g (peso neto)/persona/día. Se recomienda a la Agencia Española de Consumo, Seguridad Alimentaria y Nutrición (AECOSAN) que use esta misma metodología para el establecimiento de raciones en el resto de grupos de alimentos que configuran la Guía Dietética Basada en Alimentos para la población española

The burden of mental disorders, substance use disorders and self-harm among young people in Europe, 1990-2019 : Findings from the Global Burden of Disease Study 2019

Background Mental health is a public health issue for European young people, with great heterogeneity in resource allocation. Representative population-based studies are needed. The Global Burden of Disease (GBD) Study 2019 provides internationally comparable information on trends in the health status of populations and changes in the leading causes of disease burden over time. Methods Prevalence, incidence, Years Lived with Disability (YLDs) and Years of Life Lost (YLLs) from mental disorders (MDs), substance use disorders (SUDs) and self-harm were estimated for young people aged 10-24 years in 31 European countries. Rates per 100,000 population, percentage changes in 1990-2019, 95% Uncertainty Intervals (UIs), and correlations with Sociodemographic Index (SDI), were estimated. Findings In 2019, rates per 100,000 population were 16,983 (95% UI 12,823 - 21,630) for MDs, 3,891 (3,020 4,905) for SUDs, and 89.1 (63.8 - 123.1) for self-harm. In terms of disability, anxiety contributed to 647.3 (432 -912.3) YLDs, while in terms of premature death, self-harm contributed to 319.6 (248.9-412.8) YLLs, per 100,000 population. Over the 30 years studied, YLDs increased in eating disorders (14.9%;9.4-20.1) and drug use disorders (16.9%;8.9-26.3), and decreased in idiopathic developmental intellectual disability (-29.1%;23.8-38.5). YLLs decreased in self-harm (-27.9%;38.3-18.7). Variations were found by sex, age-group and country. The burden of SUDs and self-harm was higher in countries with lower SDI, MDs were associated with SUDs. Interpretation Mental health conditions represent an important burden among young people living in Europe. National policies should strengthen mental health, with a specific focus on young people. Funding The Bill and Melinda Gates Foundation Copyright (C) 2022 The Author(s). Published by Elsevier Ltd. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/)Peer reviewe

Trayectorias de un viaje por la investigación educativa desde el sentipensar de los maestros y maestras : experiencias en desarrollo del programa de pensamiento crítico

428 páginasEste libro reúne 19 experiencias que continúan el acompañamiento en la fundamentación, desarrollo y estructuración de estrategias de tipo pedagógico y didáctico dentro de la ruta sentipensante en el Nivel II: Experiencias en desarrollo. Igualmente, en estas experiencias se hace una ampliación de referentes, técnicas e instrumentos para recoger información de los 19 textos presentados. De tal manera, estas experiencias son fruto de este acompañamiento que ha realizado el Instituto para la Investigación Educativa y el Desarrollo Pedagógico IDEP, que servirán de base y referente para seguir aportando en la configuración y consolidación de comunidades de saber y práctica pedagógica, así como en la conformación de colectivos y redes de maestros y maestras