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The current cheapening of next-generation sequencing has led to an enormous growth in the number of sequenced genomes and transcriptomes, allowing wet labs to get the sequences from their organisms of study. To make the most of these data, one of the first things that should be done is the functional annotation of the protein-coding genes. But it used to be a slow and tedious step that can involve the characterization of thousands of sequences. Sma3s is an accurate computational tool for annotating proteins in an unattended way. Now, we have developed a completely new version, which includes functionalities that will be of utility for fundamental and applied science. Currently, the results provide functional categories such as biological processes, which become useful for both characterizing particular sequence datasets and comparing results from different projects. But one of the most important implemented innovations is that it has now low computational requirements, and the complete annotation of a simple proteome or transcriptome usually takes around 24 hours in a personal computer. Sma3s has been tested with a large amount of complete proteomes and transcriptomes, and it has demonstrated its potential in health science and other specific projects. ; This research was supported by the Ministry of Economy and Competitiveness of the Spanish Government grant BFU2013-46923-P. ; Peer Reviewed

[Background]: The current growth in DNA sequencing techniques makes of genome annotation a crucial task in the genomic era. Traditional gene finders focus on protein-coding sequences, but they are far from being exhaustive. The number of this kind of genes continuously increases due to new experimental data and development of improved bioinformatics algorithms. ; [Results]: In this context, AnABlast represents a novel in silico strategy, based on the accumulation of short evolutionary signals identified by protein sequence alignments of low score. This strategy potentially highlights protein-coding regions in genomic sequences regardless of traditional homology or translation signatures. Here, we analyze the evolutionary information that the accumulation of these short signals encloses. Using the Drosophila melanogaster genome, we stablish optimal parameters for the accurate gene prediction with AnABlast and show that this new strategy significantly contributes to add genes, exons and pseudogenes regions, yet to be discovered in both already annotated and new genomes. ; [Conclusions]: AnABlast can be freely used to analyze genomic regions of whole genomes where it contributes to complete the previous annotation. ; This research was supported by the Ministry of Economy and Competitiveness of the Spanish Government grant BFU2016–77297-P. It has funded the PhD thesis of CC and the project where this article is integrated. ; Peer reviewed

The productivity of any scientist is affected by cumbersome, tedious and time-consuming tasks that try to make the heterogeneous web services compatible so that they can be useful in their research. MOWServ, the bioinformatic platform offered by the Spanish National Institute of Bioinformatics, was released to provide integrated access to databases and analytical tools. Since its release, the number of available services has grown dramatically, and it has become one of the main contributors of registered services in the EMBRACE Biocatalogue. The ontology that enables most of the web-service compatibility has been curated, improved and extended. The service discovery has been greatly enhanced by Magallanes software and biodataSF. User data are securely stored on the main server by an authentication protocol that enables the monitoring of current or already-finished user's tasks, as well as the pipelining of successive data processing services. The BioMoby standard has been greatly extended with the new features included in the MOWServ, such as management of additional information (metadata such as extended descriptions, keywords and datafile examples), a qualified registry, error handling, asynchronous services and service replication. All of them have increased the MOWServ service quality, usability and robustness. MOWServ is available at http://www.inab.org/MOWServ/ and has a mirror at http://www.bitlab-es.com/MOWServ/. ; The National Institute for Bioinformatics, a platform of the Genoma-España Foundation; the European Union co-funded project 'Advancing Clinico-Genomic Trials on Cancer' (contract-026996); Red de Investigación de Reacciones Adversas a Alergenos y Fármacos – Redes Tematicas de Investigación Cooperativa Sanitaria (RIFAAF – RETICS RD07/0064/0017); Ministerio de Ciencia e Innovación, proyecto I+D AGL2009-12139-C02-02; Universidad Pablo de Olavide (CABD-CSIC/JA/UPO). ; Peer Reviewed

[Background]: Sphingomonads are Alphaproteobacteria that belong to the Sphingomonas, Novosphingobium, Sphingopyxis or Sphingobium genera, They are physiologically diverse and broadly distributed in nature, playing important roles in oligotrophic environments and in the degradation of recalcitrant polyaromatic compounds, Sphingopyxis is a poorly studied genus of which only one representative (S. alaskensis RB2256) has been deeply characterized. In this paper we analyze the genomic features of S. granuli strain TFA (formerly Sphingomonas macrogoltabida) in comparison with the available Sphingopyxis sequenced genomes, to describe common characteristics of this genus and to highlight unique characteristics of strain TFA. [Results]: The TFA genome has been assembled in a single circular chromosome of 4.7 Mb. Genomic sequence analysis and proteome comparison re-assigned the TFA strain to the Sphingopyxis genus and the S. granuli species. Some regions of the TFA genome show high similarity (ca. 100 %) to other bacteria and several genomic islands have been detected. Pathways for aromatic compound degradation have been predicted but no growth of TFA has been detected using these as carbon or nitrogen sources. Genes for nitrate respiration have been identified as TFA exclusive. Experimental data on anaerobic growth of TFA using nitrate as a terminal electron acceptor are also provided. [Conclusions]: Sphingopyxis representatives form a compact phylogenetic group (with the exception of S. baekryungensis DSM 16222) that share several characteristics, such as being naturally resistant to streptomycin, having only one ribosomal operon, a low number of prophages and CRISPR sequences, absence of selenoproteins and presence of ectoin and other biosynthesis pathways for secondary metabolites. Moreover, the TFA genome organization shows evidence of the presence of putative integrative and conjugative elements (ICE) responsible for the acquisition of several characteristics by horizontal transfer mechanisms. Sphingopyxis representatives have been described as strict aerobes but anaerobic growth using nitrate as a terminal electron acceptor might confer an environmental advantage to the first S. granuli strain characterized at genomic level. ; This work was supported by the Spanish Ministry of Economy and Competitiveness, Grants BIO2011-24003 and BIO2014-57545-R. We also acknowledge the institutional support of the Junta de Andalucía (Andalusian Regional Government) for the CABD, and to the Research Information Resource Unit at the Consejo Superior de Investigaciones Científicas (CSIC, Higher Scientific Research Council) for the article-processing charge contribution. ; Peer Reviewed

© The Author(s) 2020. ; [Motivation]: Short bioactive peptides encoded by small open reading frames (sORFs) play important roles in eukaryotes. Bioinformatics prediction of ORFs is an early step in a genome sequence analysis, but sORFs encoding short peptides, often using non-AUG initiation codons, are not easily discriminated from false ORFs occurring by chance. ; [Results]: AnABlast is a computational tool designed to highlight putative protein-coding regions in genomic DNA sequences. This protein-coding finder is independent of ORF length and reading frame shifts, thus making of AnABlast a potentially useful tool to predict sORFs. Using this algorithm, here, we report the identification of 82 putative new intergenic sORFs in the Caenorhabditis elegans genome. Sequence similarity, motif presence, expression data and RNA interference experiments support that the underlined sORFs likely encode functional peptides, encouraging the use of AnABlast as a new approach for the accurate prediction of intergenic sORFs in annotated eukaryotic genomes. ; [Availability and implementation]: AnABlast is freely available at http://www.bioinfocabd.upo.es/ab/. The C.elegans genome browser with AnABlast results, annotated genes and all data used in this study is available at http://www.bioinfocabd.upo.es/celegans. ; This research was supported by the Ministry of Economy and Competitiveness of the Spanish Government [BFU2016-77297-P].

3 Páginas.-- 1 Tabla ; The draft genome sequences of five Lactobacillus pentosus strains isolated from biofilms on the skin of green table olives are presented here. These genome sequences will assist in revealing the potential probiotic properties of these strains, as the intake of fermented olives implicates the passage of millions of Lactobacillus spp. throughout a consumer's gastrointestinal tract. ; This work was funded by the Junta de Andalucía through the P11-AGR-7051 project and by the Spanish Government through MICIIN projects AGL2013-48300-R/ALI (OliFilm project: www.olifilm.science.com.es) and BFU2016-77297-P. B.C.-D. was the beneficiary of a PIF grant from the Junta de Andalucía, and A.B.-C. was supported by the MICIIN through a PIF grant. We thank C3UPO for the high-performance computing (HPC) support. ; Peer reviewed

Here, we report the genome sequences of six Lactobacillus pentosus strains isolated from traditional noninoculated Spanish-style green table olive brines. The total genome sizes varied between 3.77 and 4.039 Mbp. These genome sequences will assist in revealing the genes responsible for both technological and probiotic properties of these strains. ; The Junta de Andalucía supported this study through the P11-AGR-7051 project and the Spanish Government through MICIIN projects AGL2013-48300-R/ALI (OliFilm project) and BFU2016-77297-P. B.C.-D. was the beneficiary of a PIF grant from the Junta de Andalucía. We thank C3UPO for the HPC support. ; Peer Reviewed

© 2021 The Authors. ; Inflammation is a hallmark of aging and is negatively affecting female fertility. In this study, we evaluate the role of the NLRP3 inflammasome in ovarian aging and female fertility. Age-dependent increased expression of NLRP3 in the ovary was observed in WT mice during reproductive aging. High expression of NLRP3, caspase-1, and IL-1β was also observed in granulosa cells from patients with ovarian insufficiency. Ablation of NLRP3 improved the survival and pregnancy rates and increased anti-Müllerian hormone levels and autophagy rates in ovaries. Deficiency of NLRP3 also reduced serum FSH and estradiol levels. Consistent with these results, pharmacological inhibition of NLRP3 using a direct NLRP3 inhibitor, MCC950, improved fertility in female mice to levels comparable to those of Nlrp3−/− mice. These results suggest that the NLRP3 inflammasome is implicated in the age-dependent loss of female fertility and position this inflammasome as a potential new therapeutic target for the treatment of infertility. ; This study was supported by a grant from the Andalusian regional government (Grupo de Investigacion Junta de Andalucia CTS113, Consejería de Salud de la Junta de Andalucia: PI-0036-2014) and European funding in Region Centre-Val de Loire (FEDER N° 2016-00110366 BIO-TARGET and EX005756 BIO-TARGET II). G.M. is supported by NIH/NIAMS AR068972 and AR076758 grants. A

While NLRP3-inflammasome has been implicated in cardiovascular diseases, its role in physiological cardiac aging is largely unknown. During aging, many alterations occur in the organism, which are associated with progressive impairment of metabolic pathways related to insulin resistance, autophagy dysfunction, and inflammation. Here, we investigated the molecular mechanisms through which NLRP3 inhibition may attenuate cardiac aging. Ablation of NLRP3-inflammasome protected mice from age-related increased insulin sensitivity, reduced IGF-1 and leptin/adiponectin ratio levels, and reduced cardiac damage with protection of the prolongation of the age-dependent PR interval, which is associated with atrial fibrillation by cardiovascular aging and reduced telomere shortening. Furthermore, old NLRP3 KO mice showed an inhibition of the PI3K/AKT/mTOR pathway and autophagy improvement, compared with old wild mice and preserved Nampt-mediated NAD+ levels with increased SIRT1 protein expression. These findings suggest that suppression of NLRP3 prevented many age-associated changes in the heart, preserved cardiac function of aged mice and increased lifespan. ; Andalusian regional government; Consejería de Salud de la Junta de Andalucia, Grant/ Award Number: PI‐0036‐2014; Ministerio de economía y competitividad, Grant/Award Number: SAF2017‐84494‐C2‐1‐R ; Sí

The requirement for Cas nucleases to recognize a specific PAM is a major restriction for genome editing. SpCas9 variants SpG and SpRY, recognizing NGN and NRN PAMs, respectively, have contributed to increase the number of editable genomic sites in cell cultures and plants. However, their use has not been demonstrated in animals. Here we study the nuclease activity of SpG and SpRY by targeting 40 sites in zebrafish and C. elegans. Delivered as mRNA-gRNA or ribonucleoprotein (RNP) complexes, SpG and SpRY were able to induce mutations in vivo, albeit at a lower rate than SpCas9 in equivalent formulations. This lower activity was overcome by optimizing mRNA-gRNA or RNP concentration, leading to mutagenesis at regions inaccessible to SpCas9. We also found that the CRISPRscan algorithm could help to predict SpG and SpRY targets with high activity in vivo. Finally, we applied SpG and SpRY to generate knock-ins by homology-directed repair. Altogether, our results expand the CRISPR-Cas targeting genomic landscape in animals. ; This study at Cerón Lab has been funded by Ministerio de Ciencia, Innovación y Universidades, which is part of Agencia Estatal de Investigación (AEI), through the Retos grant, number PID2020-114986RB-100. This work was also supported by Ramon y Cajal (RyC-2017-23041) and MDM-2016-0687 programs (Spanish Ministerio de Ciencia, Innovación y Universidades), Universidad Pablo de Olavide (UPO) Research and the Springboard programs from UPO and CABD, respectively and has been co-funded by the Fondo Europeo de Desarrollo Regional (FEDER) and Consejería de Transformación Económica, Industria, Conocimiento y Universidades de la Junta de Andalucía, within the operative program FEDER Andalucía 2014-2020 (01 - Refuerzo de la investigación, el desarrollo tecnológico y la innovación, grant P20_00866) (M.A.M.-M.). The Moreno-Mateos lab is supported by PGC2018-097260-B-I00 grant from Spanish Ministerio de Ciencia, Innovación y Universidades and European Union. J.V. had an INPhINIT PhD fellowship from "la Caixa" ...