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

Mass-Up and Decision Peptide-Driven: two open-source applications for MALDI-TOF MS data analysis and protein quantification

Poster presentation at EUBIC Winter School 2017 (10th - 13th January 2017, Sporthotel Semmering, Austria)

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

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

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]

PileLineGUI: a desktop environment for handling genome position files in next-generation sequencing studies

Next-generation sequencing (NGS) technologies are making sequence data available on an unprecedented scale. In this context, new catalogs of Single Nucleotide Polymorphism and mutations generated by resequencing studies are usually stored in genome position files (e.g. Variant Call Format, SAMTools pileup, BED, GFF) comprising of large lists of genomic positions, which are difficult to handle by researchers. Here, we present PileLineGUI, a novel desktop application primarily designed for manipulating, browsing and analysing genome position files (GPF), with specific support to somatic mutation finding studies. The developed tool also integrates a new genome browser module specially designed for inspecting GPFs. PileLineGUI is free, multiplatform and designed to be intuitively used by biomedical researchers. PileLineGUI is available at: http://sing.ei.uvigo.es/pileline/pilelinegui.html

An RNA-seq Based Machine Learning Approach Identifies Latent Tuberculosis Patients With an Active Tuberculosis Profile.

A better understanding of the response against Tuberculosis (TB) infection is required to accurately identify the individuals with an active or a latent TB infection (LTBI) and also those LTBI patients at higher risk of developing active TB. In this work, we have used the information obtained from studying the gene expression profile of active TB patients and their infected -LTBI- or uninfected -NoTBI- contacts, recruited in Spain and Mozambique, to build a class-prediction model that identifies individuals with a TB infection profile. Following this approach, we have identified several genes and metabolic pathways that provide important information of the immune mechanisms triggered against TB infection. As a novelty of our work, a combination of this class-prediction model and the direct measurement of different immunological parameters, was used to identify a subset of LTBI contacts (called TB-like) whose transcriptional and immunological profiles are suggestive of infection with a higher probability of developing active TB. Validation of this novel approach to identifying LTBI individuals with the highest risk of active TB disease merits further longitudinal studies on larger cohorts in TB endemic areas

AIBench: a rapid application development framework for translational research in biomedicine

Applied research in both biomedical discovery and translational medicine today often requires the rapid development of fully featured applications containing both advanced and specific functionalities, for real use in practice. In this context, new tools are demanded that allowfor efficient generation, deployment and reutilization of such biomedical applications as well as their associated functionalities. In this context this paper presents AIBench, an open-source Java desktop application framework for scientific software development with the goal of providing support to both fundamental and applied research in the domain of translational biomedicine. AIBench incorporates a powerful plug-in engine, a flexible scripting platform and takes advantage of Java annotations, reflection and various design principles in order to make it easy to use, lightweight and non-intrusive. By following a basic input–processing–output life cycle, it is possible to fully develop multiplatform applications using only three types of concepts: operations, data-types and views. The framework automatically provides functionalities that are present in a typical scientific application including user parameter definition, logging facilities, multi-threading execution, experiment repeatability and user interface workflow management, among others. The proposed framework architecture defines a reusable component model which also allows assembling new applications by the reuse of libraries from past projects or third-party software.This work was partially supported by the Integrated Action Development of computational tools for cancer diagnosis using gene expression data (HP2006-0125) between Portugal (University of Minho) and Spain (University of Vigo), the project Development of biomedical applications (09VIB10) from University of Vigo and the project MEDICAL-BENCH: Platform for the development and integration of knowledge-based data mining techniques and their application to the clinical domain (TIN2009-14057-C03-02) from Ministry of Science and Innovation. D. Glez-Peria acknowledges Xunta de Galicia (Spain) for the program Maria Barbeito. We would also like to thank all those involved in the implementation of the OptFlux, @Note and GOABench applications referred to in Section 4, namely: Isabel Rocha, Analia Lourenco, Eugenio Ferreira, Pedro Evangelista, Rafael Carreira, Jose P. Pinto, Ruben Romero, Pablo Ferreiro and Jose R. Mendez

GC4S: A bioinformatics-oriented Java software library of reusable graphical user interface components

Modern bioinformatics and computational biology are fields of study driven by the availability of effective software required for conducting appropriate research tasks. Apart from providing reliable and fast implementations of different data analysis algorithms, these software applications should also be clear and easy to use through proper user interfaces, providing appropriate data management and visualization capabilities. In this regard, the user experience obtained by interacting with these applications via their Graphical User Interfaces (GUI) is a key factor for their final success and real utility for researchers. Despite the existence of different packages and applications focused on advanced data visualization, there is a lack of specific libraries providing pertinent GUI components able to help scientific bioinformatics software developers. To that end, this paper introduces GC4S, a bioinformatics-oriented collection of high-level, extensible, and reusable Java GUI elements specifically designed to speed up bioinformatics software development. Within GC4S, developers of new applications can focus on the specific GUI requirements of their projects, relying on GC4S for generalities and abstractions. GC4S is free software distributed under the terms of GNU Lesser General Public License and both source code and documentation are publicly available at http://www.sing-group.org/gc4sH. López-Fernández is supported by a post-doctoral fellowship from Xunta de Galicia (ED481B 2016/068-0). SING group thanks 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