A new class of marine Euryarchaeota group II from the mediterranean deep chlorophyll maximum

We have analyzed metagenomic fosmid clones from the deep chlorophyll maximum (DCM), which, by genomic parameters, correspond to the 16S ribosomal RNA (rRNA)-defined marine Euryarchaeota group IIB (MGIIB). The fosmid collections associated with this group add up to 4Mb and correspond to at least two species within this group. From the proposed essential genes contained in the collections, we infer that large sections of the conserved regions of the genomes of these microbes have been recovered. The genomes indicate a photoheterotrophic lifestyle, similar to that of the available genome of MGIIA (assembled from an estuarine metagenome in Puget Sound, Washington Pacific coast), with a proton-pumping rhodopsin of the same kind. Several genomic features support an aerobic metabolism with diversified substrate degradation capabilities that include xenobiotics and agar. On the other hand, these MGIIB representatives are non-motile and possess similar genome size to the MGIIA-assembled genome, but with a lower GC content. The large phylogenomic gap with other known archaea indicates that this is a new class of marine Euryarchaeota for which we suggest the name Thalassoarchaea. The analysis of recruitment from available metagenomes indicates that the representatives of group IIB described here are largely found at the DCM (ca. 50m deep), in which they are abundant (up to 0.5% of the reads), and at the surface mostly during the winter mixing, which explains formerly described 16S rRNA distribution patterns. Their uneven representation in environmental samples that are close in space and time might indicate sporadic blooms.This work was supported by projects MICROGEN (Programa CONSOLIDER-INGENIO 2010 CDS2009-00006)MEDIMAX BFPU2013-48007-P from the Spanish Ministerio de Economía y CompetitividadThe French Agence Nationale de la Recherche (ANR-08-GENM-024-001, EVOLDEEP)MaCuMBA Project 311975 of the European Commission FP7 (FEDER funds supported this project), ACOMP/2014/024 and AORG 2014/032

Evolution of neutrophil apoptosis in septic shock survivors and nonsurvivors

Producción CientíficaThe aims were to analyze the temporal evolution of neutrophil apoptosis, to determine the differences in neutrophil apoptosis among 28-day survivors and nonsurvivors, and to evaluate the use of neutrophil apoptosis as a predictor of mortality in patients with septic shock. [Materials and Methods]: Prospective multicenter observational study carried out between July 2006 and June 2009. The staining solution study included 80 patients with septic shock and 25 healthy volunteers. Neutrophil apoptosis was assessed by fluorescein isothiocyanate (FITC)-conjugated annexin V and aminoactinomycin D staining. [Results]: The percentage of neutrophil apoptosis was significantly decreased at 24 hours, 5 days, and 12 days after the diagnosis of septic shock (14.8% ± 13.4%, 13.4% ± 8.4%, and 15.4% ± 12.8%, respectively; P .05). The mortality rate at 28 days was 53.7%. The crude hazard ratio for mortality in patients with septic shock did not differ according to the percentage of apoptosis (hazard ratio, 1.006; 95% confidence interval, 0.98-1.03; P = .60). [Conclusions]: During the first 12 days of septic shock development, the level of neutrophil apoptosis decreases and does not recover normal values. No differences were observed between surviving and nonsurviving patients

Pobreza en la ocupación e instrumentos de reacción

Unión Europea,Ministerio de Economía y Competitividad y el Fondo Europeo de Desarrollo Regional DER2015-63701-C3-1-

Polyclonality of Concurrent Natural Populations of Alteromonas macleodii

We have analyzed a natural population of the marine bacterium, Alteromonas macleodii, from a single sample of seawater to evaluate the genomic diversity present. We performed full genome sequencing of four isolates and 161 metagenomic fosmid clones, all of which were assigned to A. macleodii by sequence similarity. Out of the four strain genomes, A. macleodii deep ecotype (AltDE1) represented a different genome, whereas AltDE2 and AltDE3 were identical to the previously described AltDE. Although the core genome (∼80%) had an average nucleotide identity of 98.51%, both AltDE and AltDE1 contained flexible genomic islands (fGIs), that is, genomic islands present in both genomes in the same genomic context but having different gene content. Some of the fGIs encode cell surface receptors known to be phage recognition targets, such as the O-chain of the lipopolysaccharide, whereas others have genes involved in physiological traits (e.g., nutrient transport, degradation, and metal resistance) denoting microniche specialization. The presence in metagenomic fosmids of genomic fragments differing from the sequenced strain genomes, together with the presence of new fGIs, indicates that there are at least two more A. macleodii clones present. The availability of three or more sequences overlapping the same genomic region also allowed us to estimate the frequency and distribution of recombination events among these different clones, indicating that these clustered near the genomic islands. The results indicate that this natural A. macleodii population has multiple clones with a potential for different phage susceptibility and exploitation of resources, within a seemingly unstructured habitat

Personalized monitoring of circulating tumor DNA with a specific signature of trackable mutations after chimeric antigen receptor T-cell therapy in follicular lymphoma patients

BackgroundCART therapy has produced a paradigm shift in the treatment of relapsing FL patients. Strategies to optimize disease surveillance after these therapies are increasingly necessary. This study explores the potential value of ctDNA monitoring with an innovative signature of personalized trackable mutations.MethodEleven FL patients treated with anti-CD19 CAR T-cell therapy were included. One did not respond and was excluded. Genomic profiling was performed before starting lymphodepleting chemotherapy to identify somatic mutations suitable for LiqBio-MRD monitoring. The dynamics of the baseline mutations (4.5 per patient) were further analyzed on 59 cfDNA follow-up samples. PET/CT examinations were performed on days +90, +180, +365, and every six months until disease progression or death.ResultsAfter a median follow-up of 36 months, all patients achieved a CR as the best response. Two patients progressed. The most frequently mutated genes were CREBBP, KMT2D and EP300. Simultaneous analysis of ctDNA and PET/CT was available for 18 time-points. When PET/CT was positive, two out of four ctDNA samples were LiqBio-MRD negative. These two negative samples corresponded to women with a unique mesenteric mass in two evaluations and never relapsed. Meanwhile, 14 PET/CT negative images were mutation-free based on our LiqBio-MRD analysis (100%). None of the patients had a negative LiqBio-MRD test by day +7. Interestingly, all durably responding patients had undetectable ctDNA at or around three months after infusion. Two patients presented discordant results by PET/CT and ctDNA levels. No progression was confirmed in these cases. All the progressing patients were LiqBio-MRD positive before progression.ConclusionThis is a proof-of-principle for using ctDNA to monitor response to CAR T-cell therapy in FL. Our results confirm that a non-invasive liquid biopsy MRD analysis may correlate with response and could be used to monitor response. Harmonized definitions of ctDNA molecular response and pinpointing the optimal timing for assessing ctDNA responses are necessary for this setting. If using ctDNA analysis, we suggest restricting follow-up PET/CT in CR patients to a clinical suspicion of relapse, to avoid false-positive results

Regulatory sites for splicing in human basal ganglia are enriched for disease-relevant information

Genome-wide association studies have generated an increasing number of common genetic variants associated with neurological and psychiatric disease risk. An improved understanding of the genetic control of gene expression in human brain is vital considering this is the likely modus operandum for many causal variants. However, human brain sampling complexities limit the explanatory power of brain-related expression quantitative trait loci (eQTL) and allele-specific expression (ASE) signals. We address this, using paired genomic and transcriptomic data from putamen and substantia nigra from 117 human brains, interrogating regulation at different RNA processing stages and uncovering novel transcripts. We identify disease-relevant regulatory loci, find that splicing eQTLs are enriched for regulatory information of neuron-specific genes, that ASEs provide cell-specific regulatory information with evidence for cellular specificity, and that incomplete annotation of the brain transcriptome limits interpretation of risk loci for neuropsychiatric disease. This resource of regulatory data is accessible through our web server, http://braineacv2.inf.um.es/

Identification of novel risk loci, causal insights, and heritable risk for Parkinson's disease: a meta-analysis of genome-wide association studies

Background Genome-wide association studies (GWAS) in Parkinson's disease have increased the scope of biological knowledge about the disease over the past decade. We aimed to use the largest aggregate of GWAS data to identify novel risk loci and gain further insight into the causes of Parkinson's disease. Methods We did a meta-analysis of 17 datasets from Parkinson's disease GWAS available from European ancestry samples to nominate novel loci for disease risk. These datasets incorporated all available data. We then used these data to estimate heritable risk and develop predictive models of this heritability. We also used large gene expression and methylation resources to examine possible functional consequences as well as tissue, cell type, and biological pathway enrichments for the identified risk factors. Additionally, we examined shared genetic risk between Parkinson's disease and other phenotypes of interest via genetic correlations followed by Mendelian randomisation. Findings Between Oct 1, 2017, and Aug 9, 2018, we analysed 7·8 million single nucleotide polymorphisms in 37 688 cases, 18 618 UK Biobank proxy-cases (ie, individuals who do not have Parkinson's disease but have a first degree relative that does), and 1·4 million controls. We identified 90 independent genome-wide significant risk signals across 78 genomic regions, including 38 novel independent risk signals in 37 loci. These 90 variants explained 16–36% of the heritable risk of Parkinson's disease depending on prevalence. Integrating methylation and expression data within a Mendelian randomisation framework identified putatively associated genes at 70 risk signals underlying GWAS loci for follow-up functional studies. Tissue-specific expression enrichment analyses suggested Parkinson's disease loci were heavily brain-enriched, with specific neuronal cell types being implicated from single cell data. We found significant genetic correlations with brain volumes (false discovery rate-adjusted p=0·0035 for intracranial volume, p=0·024 for putamen volume), smoking status (p=0·024), and educational attainment (p=0·038). Mendelian randomisation between cognitive performance and Parkinson's disease risk showed a robust association (p=8·00 × 10−7). Interpretation These data provide the most comprehensive survey of genetic risk within Parkinson's disease to date, to the best of our knowledge, by revealing many additional Parkinson's disease risk loci, providing a biological context for these risk factors, and showing that a considerable genetic component of this disease remains unidentified. These associations derived from European ancestry datasets will need to be followed-up with more diverse data. Funding The National Institute on Aging at the National Institutes of Health (USA), The Michael J Fox Foundation, and The Parkinson's Foundation (see appendix for full list of funding sources)

Labour and social security law in Spain in 2015

El informe ha sido elaborado por la Sección Juvenil de la Asociación Española de Derecho del Trabajo y Seguridad SocialEste Informe deja constancia de los cambios normativos más relevantes y de las tendencias judiciales más paradigmáticas del ordenamiento laboral en 2015. En él se observa el imparable dinamismo del Derecho del Trabajo y de la Seguridad Social en España. El documento, consciente de tal mutabilidad, recoge una minuciosa selección de cuestiones esenciales, a juicio de las personas que abordan cada una de las materias, de las que son especialistas; los autores y las autoras, que forman parte de la Sección Juvenil de la Asociación Española de Derecho del Trabajo y de la Seguridad Social, se adscriben a los grupos temáticos por afinidad con sus principales líneas de investigación y su labor docente universitaria. En síntesis, en el Informe “El Derecho del Trabajo y de la Seguridad Social en España en 2015” se puede encontrar información muy útil para los profesionales del iuslaboralismo en materia de derechos fundamentales inespecíficos, contratación laboral y empleo, vicisitudes del contrato de trabajo, derechos colectivos, igualdad y corresponsabilidad, Seguridad Social o prevención de riesgos laborales.This report has as aim leaving a record of the most relevant normative changes and the most paradigmatic judicial trends in Labour Law in 2015. One can easily observe the unstoppable dynamismof Labour and Social Security Law in Spain. The document, conscious of that mutability, collects a thorough selection of key issues, according to the judgement of the authors, all of them specialists and all of them members of the Young Scholars’ Section of the Spanish Association for Labour and Social Security Law. They are part of thematic groups, linked to their main research lines and their teaching task. Summing up, in this report “Labour and Social Security Law in Spain in 2015”, one can easily find useful information for labour lawyers in subjects such as unspecific fundamental rights, work contracts and employment, issues of the labour relationship, collective rights, equality and co-responsibility, Social Security or occupational risk prevention

El Derecho del Trabajo y de la Seguridad Social en España en 2015. Sección Juvenil de la Asociación Española de Derecho del Trabajo y de la Seguridad Social.

Este Informe deja constancia de los cambios normativos más relevantes y de las tendencias judiciales más paradigmáticas del ordenamiento laboral en 2015. En él se observa el imparable dinamismo del Derecho del Trabajo y de la Seguridad Social en España. El documento, consciente de tal mutabilidad, recoge una minuciosa selección de cuestiones esenciales, a juicio de las personas que abordan cada una de las materias, de las que son especialistas; los autores y las autoras, que forman parte de la Sección Juvenil de la Asociación Española de Derecho del Trabajo y de la Seguridad Social, se adscriben a los grupos temáticos por afinidad con sus principales líneas de investigación y su labor docente universitaria. En síntesis, en el Informe “El Derecho del Trabajo y de la Seguridad Social en España en 2015” se puede encontrar información muy útil para los profesionales del iuslaboralismo en materia de derechos fundamentales inespecíficos, contratación laboral y empleo, vicisitudes del contrato de trabajo, derechos colectivos, igualdad y corresponsabilidad, Seguridad Social o prevención de riesgos laborales. This report has as aim leaving a record of the most relevant normative changes and the most paradigmatic judicial trends in Labour Law in 2015. One can easily observe the unstoppable dynamismof Labour and Social Security Law in Spain. The document, conscious of that mutability, collects a thorough selection of key issues, according to the judgement of the authors, all of them specialists and all of them members of the Young Scholars’ Section of the Spanish Association for Labour and Social Security Law. They are part of thematic groups, linked to their main research lines and their teaching task. Summing up, in this report “Labour and Social Security Law in Spain in 2015”, one can easily find useful information for labour lawyers in subjects such as unspecific fundamental rights, work contracts and employment, issues of the labour relationship, collective rights, equality and co-responsibility, Social Security or occupational risk prevention