Predicting Specificities Under the Non-self Gametophytic Self-Incompatibility Recognition Model

Non-self gametophytic self-incompatibility (GSI) recognition system is characterized by the presence of multiple F-box genes tandemly located in the S-locus, that regulate pollen specificity. This reproductive barrier is present in Solanaceae, Plantaginacea and Maleae (Rosaceae), but only in Petunia functional assays have been performed to get insight on how this recognition mechanism works. In this system, each of the encoded S-pollen proteins (called SLFs in Solanaceae and Plantaginaceae /SFBBs in Maleae) recognizes and interacts with a sub-set of non-self S-pistil proteins, called S-RNases, mediating their ubiquitination and degradation. In Petunia there are 17 SLF genes per S-haplotype, making impossible to determine experimentally each SLF specificity. Moreover, domain –swapping experiments are unlikely to be performed in large scale to determine S-pollen and S-pistil specificities. Phylogenetic analyses of the Petunia SLFs and those from two Solanum genomes, suggest that diversification of SLFs predate the two genera separation. Here we first identify putative SLF genes from nine Solanum and 10 Nicotiana genomes to determine how many gene lineages are present in the three genera, and the rate of origin of new SLF gene lineages. The use of multiple genomes per genera precludes the effect of incompleteness of the genome at the S-locus. The similar number of gene lineages in the three genera implies a comparable effective population size for these species, and number of specificities. The rate of origin of new specificities is one per 10 million years. Moreover, here we determine the amino acids positions under positive selection, those involved in SLF specificity recognition, using 10 Petunia S-haplotypes with more than 11 SLF genes. These 16 amino acid positions account for the differences of self-incompatible (SI) behavior described in the literature. When SLF and S-RNase proteins are divided according to the SI behavior, and the positively selected amino acids classified according to hydrophobicity, charge, polarity and size, we identified fixed differences between SI groups. According to the in silico 3D structure of the two proteins these amino acid positions interact. Therefore, this methodology can be used to infer SLF/S-RNase specificity recognition.This work was financed by the project Norte-01-0145-FEDER-000008-Porto Neurosciences and Neurologic Disease Research Initiative at I3S, supported by Norte Portugal Regional Operational Programme (NORTE 2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (FEDER). SR is supported by a post-doctoral fellowship under this project. HL-F is supported by a post-doctoral fellowship from Xunta de Galicia (ED481B 2016/068-0). SING group acknowledges Consellería de Educación, Universidades e Formación Profesional (Xunta de Galicia) for the ED431C2018/55-GRC grant and CITI (Centro de Investigación, Transferencia e Innovación) from University of Vigo for hosting its IT infrastructure

ATXN1 N-terminal region explains the binding differences of wild-type and expanded forms

BACKGROUND: Wild-type (wt) polyglutamine (polyQ) regions are implicated in stabilization of protein-protein interactions (PPI). Pathological polyQ expansion, such as that in human Ataxin-1 (ATXN1), that causes spinocerebellar ataxia type 1 (SCA1), results in abnormal PPI. For ATXN1 a larger number of interactors has been reported for the expanded (82Q) than the wt (29Q) protein. METHODS: To understand how the expanded polyQ affects PPI, protein structures were predicted for wt and expanded ATXN1, as well as, for 71 ATXN1 interactors. Then, the binding surfaces of wt and expanded ATXN1 with the reported interactors were inferred. RESULTS: Our data supports that the polyQ expansion alters the ATXN1 conformation and that it enhances the strength of interaction with ATXN1 partners. For both ATXN1 variants, the number of residues at the predicted binding interface are greater after the polyQ, mainly due to the AXH domain. Moreover, the difference in the interaction strength of the ATXN1 variants was due to an increase in the number of interactions at the N-terminal region, before the polyQ, for the expanded form. CONCLUSIONS: There are three regions at the AXH domain that are essential for ATXN1 PPI. The N-terminal region is responsible for the strength of the PPI with the ATXN1 variants. How the predicted motifs in this region affect PPI is discussed, in the context of ATXN1 post-transcriptional modifications.This work was financed by the project Norte-01-0145-FEDER-000008 -Porto Neurosciences and Neurologic Disease Research Initiative at I3S, supported by Norte Portugal Regional Operational Programme (NORTE 2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (FEDER). Sara Rocha is supported by a post-doctoral fellowship under this project. Hugo López-Fernández is supported by a postdoctoral fellowship from Xunta de Galicia (ED481B 2016/068–0). SING group thanks Consellería de Educación, Universidades e Formación Profesional (Xunta de Galicia) for the ED431C2018/55-GRC grant and CITI (Centro de Investigación, Transferencia e Innovación) from University of Vigo for hosting its IT infrastructure. The funding bodies played no role in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript

A new approach to bacterial colony morphotyping by matrix-assisted laser desorption ionization time of flight-based mass spectrometry

Matrix assisted laser desorption ionization time of flight mass spectrometry has been explored as a tool to bacterial colony morphotyping.To this end,four colony morphotypes of Pseudomonas aeruginosa and four of Staphylococcus aureus were analysed using intact bacteria.Results suggest that mass spectrometry of intact bacteria could,in some extent,be used to complement the classical morphological classification of bacteria.Financial support from IBB-CEB and Fundacao para a Ciencia e Tecnologia (FCT) and European Community fund FEDER, through Program COMPETE, in the ambit of the FCT project "PTDC/SAU-SAP/113196/2009/ FCOMP-01-0124-FEDER-016012" and Ana Margarida Sousa PhD grant (SFRH/BD/72551/2010), is gratefully acknowledged. Authors also thank Portugal-Spain cooperation action sponsored by the Foundation of Portuguese Universities [E 48/11] and the Spanish Ministry of Science and Innovation [AIB2010PT-00353]

Multiple independent L-gulonolactone oxidase (GULO) gene losses and vitamin C synthesis reacquisition events in non-Deuterostomian animal species

Background: L-ascorbate (Vitamin C) is an important antioxidant and co-factor in eukaryotic cells, and in mammals it is indispensable for brain development and cognitive function. Vertebrates usually become L-ascorbate auxothrophs when the last enzyme of the synthetic pathway, an L-gulonolactone oxidase (GULO), is lost. Since Protostomes were until recently thought not to have a GULO gene, they were considered to be auxothrophs for Vitamin C. Results: By performing phylogenetic analyses with tens of non-Bilateria and Protostomian genomes, it is shown, that a GULO gene is present in the non-Bilateria Placozoa, Myxozoa (here reported for the first time) and Anthozoa groups, and in Protostomians, in the Araneae family, the Gastropoda class, the Acari subclass (here reported for the first time), and the Priapulida, Annelida (here reported for the first time) and Brachiopoda phyla lineages. GULO is an old gene that predates the separation of Animals and Fungi, although it could be much older. We also show that within Protostomes, GULO has been lost multiple times in large taxonomic groups, namely the Pancrustacea, Nematoda, Platyhelminthes and Bivalvia groups, a pattern similar to that reported for Vertebrate species. Nevertheless, we show that Drosophila melanogaster seems to be capable of synthesizing L-ascorbate, likely through an alternative pathway, as recently reported for Caenorhabditis elegans. Conclusions: Non-Bilaterian and Protostomians seem to be able to synthesize Vitamin C either through the conventional animal pathway or an alternative pathway, but in this animal group, not being able to synthesize L-ascorbate seems to be the exception rather than the rule.This work is financed by the project Norte-01-0145-FEDER-000008 - Porto Neurosciences and Neurologic Disease Research Initiative at I3S, supported by Norte Portugal Regional Operational Programme (NORTE 2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (FEDER). S. F. Henriques is supported by a post-doctoral fellowship also funded by the above mentioned project. SING group is supported by the Consellería de Educación, Universidades e Formación Pro-fesional (Xunta de Galicia) by the ED431C2018/55-GRC grant. H. López-Fer-nández is supported by a post-doctoral fellowship from Xunta de Galicia (ED481B 2016/068–0). The funding bodies played no role in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript

The extracellular proteins of Lactobacillus acidophilus DSM 20079T display anti-inflammatory effect in both in piglets, healthy human donors and Crohns Disease patients

Lactobacillus genus includes both probiotic and representative strains of the human gut microbiota. Independent studies have reported on the anti-inflammatory properties of different Lactobacillus strains, although we are far from understanding the underlying molecular interplay. In this work we show that a daily administration of Lactobacillus acidophilus DSM20079T (DSM20079) to healthy piglets resulted in plasmatic increases of the anti-inflammatory IL10, whilst IL12 and the pro-inflammatory ratio IL12+TNF/IL10 decreased. The extracellular protein fraction of DSM20079 was identified as the responsible for the crosstalk interaction that elicited these tolerogenic effects. This strain was able to activate innate immune pathways in dendritic cells and to decrease the production of pro-inflammatory cytokines in both CD4+/CD8+ T cell subsets in healthy donors and in Crohns Disease patients. The tolerogenic effect exerted by the extracellular proteins of this strain suggests their potential use as coadjutant for therapeutic applications targeting chronic inflammatory illnesses.Our work is supported by the Spanish “Programa Estatal de Investigación, Desarrollo e Inovación Orientada a los Retos de la Sociedad” (grant AGL2016-78311-R); the Asociación Española Contra el Cancer (“Obtención de péptidos bioactivos contra el Cáncer ColoRectal a partir de secuencias genéticas de microbiomas intestinales”, Grant PS-2016) and by the Asturias Regional Plan I+D+i for research groups (FYCYT-IDI/2018/000236). This study was also supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UID/BIO/04469/2013 unit and COMPETE 2020 (POCI-01-0145-FEDER006684). SING group thanks CITI (Centro de Investigación, Transferencia e Innovación) from University of Vigo for hosting its IT infrastructure. LJR was supported by the Principado de Asturias, PCTI 2018–2020 (GRUPIN: IDI2018-000237) and FEDER. This work was partially supported by the Consellería de Educación, Universidades e Formación Profesional (Xunta de Galicia) under the scope of the strategic funding of ED431C2018/55-GRC Competitive Reference Group.info:eu-repo/semantics/publishedVersio

A spam filtering mult-iobjective optimization study covering parsimony maximization and three-way classification

The file attached to this record is the author's final peer reviewed version. The Publisher's final version can be found by following the DOI link.Classifier performance optimization in machine learning can be stated as a multi-objective optimization problem. In this context, recent works have shown the utility of simple evolutionary multi-objective algorithms (NSGA-II, SPEA2) to conveniently optimize the global performance of different anti-spam filters. The present work extends existing contributions in the spam filtering domain by using three novel indicator-based (SMS-EMOA, CH-EMOA) and decomposition-based (MOEA/D) evolutionary multi-objective algorithms. The proposed approaches are used to optimize the performance of a heterogeneous ensemble of classifiers into two different but complementary scenarios: parsimony maximization and e-mail classification under low confidence level. Experimental results using a publicly available standard corpus allowed us to identify interesting conclusions regarding both the utility of rule-based classification filters and the appropriateness of a three-way classification system in the spam filtering domain

The extracellular proteins of Lactobacillus acidophilus DSM 20079T display anti-inflammatory effect in both in piglets, healthy human donors and Crohn’s Disease patients

Lactobacillus genus includes both probiotic and representative strains of the human gut microbiota. Independent studies have reported on the anti-inflammatory properties of different Lactobacillus strains, although we are far from understanding the underlying molecular interplay. In this work we show that a daily administration of Lactobacillus acidophilus DSM20079T (DSM20079) to healthy piglets resulted in plasmatic increases of the anti-inflammatory IL10, whilst IL12 and the pro-inflammatory ratio IL12+TNFα/IL10 decreased. The extracellular protein fraction of DSM20079 was identified as the responsible for the crosstalk interaction that elicited these tolerogenic effects. This strain was able to activate innate immune pathways in dendritic cells and to decrease the production of pro-inflammatory cytokines in both CD4+/CD8+ T cell subsets in healthy donors and in Crohn’s Disease patients. The tolerogenic effect exerted by the extracellular proteins of this strain suggests their potential use as coadjutant for therapeutic applications targeting chronic inflammatory illnesses.Asociación Española Contra el Cancer | Ref. PS-2016Fundação para a Ciência e a Tecnologia | | Ref. UID/BIO/04469/2013Agencia Estatal de Investigación | Ref. AGL2016-78311-RPrincipado de Asturias | Ref. PCTI 2018–2020Xunta de Galicia | Ref. ED431C2018/5

Learning Object Repositories with Federated Searcher over the Cloud

The education sector is a significant generator, consumer and depository for educational content. Educators and Learners have access to technologies that allow them to obtain information ubiquitously on demand. The problems arising from the integration of educational content are usually caused by the vast amount of educational content distributed among several repositories. This work presents a proposal for an architecture based on a cloud computing paradigm that will permit the evolution of current learning resource repositories by means of cloud computing paradigm and the integration of federated search system