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]

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)

Neutron-proton pairing in the BCS approach

We investigate the BCS treatment of neutron-proton pairing involving time-reversed orbits. We conclude that an isospin-symmetric hamiltonian, treated with the help of the generalized Bogolyubov transformation, fails to describe the ground state pairing properties correctly. In order for the np isovector pairs to coexist with the like-particle pairs, one has to break the isospin symmetry of the hamiltonian by artificially increasing the strength of np pairing interaction above its isospin symmetric value. We conjecture that the np isovector pairing represents part (or most) of the congruence energy (Wigner term) in nuclear masses.Comment: 9 pages, RevTex, submitted to Phys. Rev.

A schematic model for QCD I: Low energy meson states

A simple model for QCD is presented, which is able to reproduce the meson spectrum at low energy. The model is a Lipkin type model for quarks coupled to gluons. The basic building blocks are pairs of quark-antiquarks coupled to a definite flavor and spin. These pairs are coupled to pairs of gluons with spin zero. The multiplicity problem, which dictates that a given experimental state can be described in various manners, is removed when a particle-mixing interaction is turned on. In this first paper of a series we concentrates on the discussion of meson states at low energy, the so-called zero temperature limit of the theory. The treatment of baryonic states is indicated, also.Comment: 29 pages, 6 figures. submitted to Phys. Rev.