Mass spectrometry‑based identification of peptides presented by major histocompatibility complex in macrophages

Immunopeptidomics is a field of research that has progressed in thelast years due to advances in sophisticated analytical techniquesbased on mass spectrometry and bioinformatics. The ability to identifymolecules to the extent of a single ion led to a step forward inimmunopeptidomics. Mass spectrometry enables the identificationof thousands of peptide sequences in a single sample, thus providinglarge-scale reliable information. The immunopeptidome is the entire group of peptides presented by the major histocompatibility complexClass-I (MHC-I), at the surface of all nucleated cells and Class II, at thesurface of professional antigen presenting cells. The MHC-bound peptidesare recognized by T cells and constitute the immunological synapse,leading to the initiation of the adaptive immune response. Underpathological conditions, peptides originating from the proteolysis ofpathogen proteins are presented to the cells of the host immune systemvia MHC. Thus, the identification of pathogen peptides throughimmunopeptidomics is an unbiased method for understanding thegeneration of adaptive immune responses against pathogens.Here we describe the establishment of a new mass spectrometrybasedimmunopeptidomics platform for peptide identification inphysiological and pathological conditions. Using the macrophage cellline with THP-1, with a known HLA-type, we were able to identify atotal of 2913 unique MHC-I bound peptides. The peptide length distribution,NetMHCpan-4.1 rank affinity, and best match HLA bindingallele for each peptide will be presented.Finally, identifying MHC-I and MHC-II peptides under physiologicaland pathological conditions could uncover the most relevant peptidesable to stimulate the right type of T-cell response for vaccine designand development.info:eu-repo/semantics/publishedVersio

Rational design of multi-functional nanomaterials

FCT-MEC project PTDC/QEQMED/2118/2014publishersversionpublishe

From Liberal Acceptance to Intolerance: Discourses on Sexual Diversity in Schools by Portuguese Young People

Purpose: This article explores different strands of educational discourse about sexual diversity in Portuguese schools, from the students’ perspectives.Method: The methodological approach consisted in conducting focus groups discussions: 36 with 232 young students (H = 106, M = 126) in 12 public secondary schools.Findings: Students reveal a polyphony of discourses that gravitate between liberal acceptance, conditional acceptance and intolerance.Research implications: Attention is drawn not only to discriminatory processes that question school as a democratic place for LGBT youth, but also to the gap between what is legally decreed and a lack of know-how in the approach to sexual diversity in school

Effectiveness of intensive physiotherapy for gait improvement in stroke: systematic review

Introduction: Stroke is one of the leading causes of functional disability worldwide. Approximately 80% of post-stroke subjects have motor changes. Improvement of gait pattern is one of the main objectives of physiotherapists intervention in these cases. The real challenge in the recovery of gait after stroke is to understand how the remaining neural networks can be modified, to be able to provide response strategies that compensate for the function of the affected structures. There is evidence that intensive training, including physiotherapy, positively influences neuroplasticity, improving mobility, pattern and gait velocity in post-stroke recovery. Objectives: Review and analyze in a systematic way the experimental studies (RCT) that evaluate the effects of Intensive Physiotherapy on gait improvement in poststroke subjects. Methodology: Were only included all RCT performed in humans, without any specific age, that had a clinical diagnosis of stroke at any stage of evolution, with sensorimotor deficits and functional gait changes. The databases used were: Pubmed, PEDro (Physiotherapy Evidence Database) and CENTRAL (Cochrane Center Register of Controlled Trials). Results: After the application of the criteria, there were 4 final studies that were included in the systematic review. 3 of the studies obtained a score of 8 on the PEDro scale and 1 obtained a score of 4. The fact that there is clinical and methodological heterogeneity in the studies evaluated, supports the realization of the current systematic narrative review, without meta-analysis. Discussion: Although the results obtained in the 4 studies are promising, it is important to note that the significant improvements that have been found, should be carefully considered since pilot studies with small samples, such as these, are not designed to test differences between groups, in terms of the effectiveness of the intervention applied. Conclusion: Intensive Physiotherapy seems to be safe and applicable in post-stroke subjects and there are indications that it is effective in improving gait, namely speed, travelled distance and spatiotemporal parameters. However, there is a need to develop more RCTs with larger samples and that evaluate the longterm resultsN/

Link Invariants for Flows in Higher Dimensions

Linking numbers in higher dimensions and their generalization including gauge fields are studied in the context of BF theories. The linking numbers associated to $n$-manifolds with smooth flows generated by divergence-free p-vector fields, endowed with an invariant flow measure are computed in different cases. They constitute invariants of smooth dynamical systems (for non-singular flows) and generalizes previous results for the 3-dimensional case. In particular, they generalizes to higher dimensions the Arnold's asymptotic Hopf invariant for the three-dimensional case. This invariant is generalized by a twisting with a non-abelian gauge connection. The computation of the asymptotic Jones-Witten invariants for flows is naturally extended to dimension n=2p+1. Finally we give a possible interpretation and implementation of these issues in the context of string theory.Comment: 21+1 pages, LaTeX, no figure

Omic Insights into Molecular Mechanisms at the Intestinal Level

PM003/2016). Support was also provided by Bioisi MassSpec Facility. Publisher Copyright: © 2024 by the authors.High blood cholesterol levels are a major risk factor for cardiovascular diseases. A purified aqueous extract of Fucus vesiculosus, rich in phlorotannins and peptides, has been described for its potential to inhibit cholesterol biosynthesis and intestinal absorption. In this work, the effect of this extract on intestinal cells’ metabolites and proteins was analysed to gain a deeper understanding of its mode of action on lipids’ metabolism, particularly concerning the absorption and transport of exogenous cholesterol. Caco-2 cells, differentiated into enterocytes, were exposed to the extract, and analysed by untargeted metabolomics and proteomics. The results of the metabolomic analysis showed statistically significant differences in glutathione content of cells exposed to the extract compared to control cells, along with an increased expression of fatty acid amides in exposed cells. A proteomic analysis showed an increased expression in cells exposed to the extract compared to control cells of FAB1 and NPC1, proteins known to be involved in lipid metabolism and transport. To the extent of our knowledge, this study is the first use of untargeted metabolomics and a proteomic analysis to investigate the effects of F. vesiculosus on differentiated Caco-2 cells, offering insights into the molecular mechanism of the extract’s compounds on intestinal cells.publishersversionpublishe

Photo-Organocatalysis, Photo-Redox, and Electro- Organocatalysis Processes

The research involving photo-organocatalysis, photoredox, and electro-organocatalysis processes is revised in this chapter. Modern synthetic processes enable the formation of large arrays of organic molecules with precise control over their three-dimensional structure, which is important in a variety of fields ranging from pharmaceutical to materials science. Photochemical reactions may have a substantial impact on these fields by affording direct access to specific structural motifs that are difficult to construct otherwise. The conjugate structural feature shown by most of the photo-organocatalysts seems to enable the production of free radicals or radical ions in an easy fashion. Electro-organocatalysis has also received recent interest from both academia and industry. In this chapter, we mainly review recent remarkable advancements in organocatalysis involving photo-, photoredox, and electrochemical processes with particular emphasis on asymmetric protocols

Native rodent species are unlikely sources of infection for Leishmania (Viannia) braziliensis along the Transoceanic Highway in Madre de Dios, Peru.

An estimated 2.3 million disability-adjusted life years are lost globally from leishmaniasis. In Peru's Amazon region, the department of Madre de Dios (MDD) rises above the rest of the country in terms of the annual incidence rates of human leishmaniasis. Leishmania (Viannia) braziliensis is the species most frequently responsible for the form of disease that results in tissue destruction of the nose and mouth. However, essentially nothing is known regarding the reservoirs of this vector-borne, zoonotic parasite in MDD. Wild rodents have been suspected, or proven, to be reservoirs of several Leishmania spp. in various ecosystems and countries. Additionally, people who live or work in forested terrain, especially those who are not regionally local and whose immune systems are thus naïve to the parasite, are at most risk for contracting L. (V.) braziliensis. Hence, the objective of this study was to collect tissues from wild rodents captured at several study sites along the Amazonian segment of the newly constructed Transoceanic Highway and to use molecular laboratory techniques to analyze samples for the presence of Leishmania parasites. Liver tissues were tested via polymerase chain reaction from a total of 217 rodents; bone marrow and skin biopsies (ear and tail) were also tested from a subset of these same animals. The most numerous rodent species captured and tested were Oligoryzomys microtis (40.7%), Hylaeamys perenensis (15.7%), and Proechimys spp. (12%). All samples were negative for Leishmania, implying that although incidental infections may occur, these abundant rodent species are unlikely to serve as primary reservoirs of L. (V.) braziliensis along the Transoceanic Highway in MDD. Therefore, although these rodent species may persist and even thrive in moderately altered landscapes, we did not find any evidence to suggest they pose a risk for L. (V.) braziliensis transmission to human inhabitants in this highly prevalent region

Identification of genomic loci associated with genotypic and phenotypic variation among Pseudomonas aeruginosa clinical isolates from pneumonia

In this work, a genotype-phenotype survey of a highly diversified Pseudomonas aeruginosa collection was conducted, aiming to detail pathogen-associated scenarios that clinicians face nowadays. Genetic relation based on RAPD-PCR of 705 isolates, retrieved from 424 patients and several clinical contexts, reported an almost isolate-specific molecular-pattern. Pneumonia-associated isolates HB13 and HB15, clustered in the same RAPD-PCR group, were selected to evaluate the genomic background underlying their contrasting antibiotic resistance and virulence. The HB13 genome harbors antibiotic-inactivating enzymes-coding genes (e.g. aac(3)-Ia, arr, blaVIM-2) and single-nucleotide variations (SNVs) in antibiotic targets, likely accounting for its pan-resistance, whereas HB15 susceptibility correlated to predicted dysfunctional alleles. Isolate HB13 showed the unprecedented rhl-cluster absence and variations in other pathogen competitiveness contributors. Conversely, HB15 genome comprises exoenzyme-coding genes and SNVs linked to increased virulence. Secretome analysis identified signatures features with unknown function as potential novel pathogenic (e.g. a MATE-protein in HB13, a protease in HB15) and antibiotic resistance (a HlyD-like secretion protein in HB13) determinants. Detection of active prophages, proteases (including protease IV and alkaline metalloproteinase), a porin and a peptidase in HB15 highlights the secreted arsenal likely essential for its virulent behavior. The presented phenotype-genome association will contribute to the current knowledge on Pseudomonas aeruginosa pathogenomics.This work was supported by the strategic programme UID/BIA/0050/2013 (POCI-01-0145-FEDER-007569) funded by national funds through FCT I.P., by ERDF through the COMPETE2020 - Programa Operacional Competitividade e Internacionalização (POCI) and through a PhD grant (SFRH/BD/98558/2013) attributed to C.S.M. The facility for Biological Mass Spectrometry Isabel Moura was funded by Proteomass Scientific Society. H.M.S. is funded by the FCT 2015 Investigator Program (IF/00007/2015)

Impacts of environmental issues on health and well-being: a global pollution challenge

Every 2 years, the environmental, chemical, and health research communities meet in Costa de Caparica, Portugal to showcase the latest technologies, methodologies and research advances in pollution detection, contamination control, remediation, and related health issues. Since its inception in 2015, the International Caparica Conference on Pollution Metal Ions and Molecules (PTIM) has become a biennial global forum to hear from those who protect the land, the water, and the air at all environmental scales. During past PTIM editions, we have learned about numerous efforts to develop new recovery and clean-up processes to restore the natural equilibria of our planet. Soil, land, water, and air are the key focus of efforts that will require deeper understanding and better control.publishersversionpublishe