Biology subjects

de Almeida, R. F.

Publications and source records attributed to de Almeida, R. F..

4 recordsLinked to original sources

bioRxiv2026

Proteomic Profiling of Enriched Nuclei Provides a Nuclear Proteome Resource and Protein Interaction Landscape for Trypanosoma cruzi

The processes such as DNA replication, transcription, and repair are often modulated by specific nuclear proteins, protein-protein interactions (PPIs), and post-translational modifications (PTMs). In Trypanosoma cruzi, however, the nuclear proteome and interactome have not been systematically mapped, limiting the interpretation of nuclear regulatory processes. Here, we report a nuclear proteome resource generated from intact nuclei isolated from T. cruzi and analyzed by high-resolution Orbitrap LC-MS/MS, integrating proteome profiling, computational interaction network inference, and exploratory crosslinking mass spectrometry (XL-MS). Proteome profiling identified 1,734 proteins in the nuclear fraction, including 316 proteins identified with PTM-containing peptides. Subcellular localization prediction and Gene Ontology analysis support nuclear enrichment and highlight functions related to transcription, RNA metabolism, and genome maintenance. The in silico interaction network derived from STRINGDB organizes the proteins into functional clusters, including a histone-associated interaction neighborhood. In parallel, XL-MS identified 26 residue-resolved interprotein crosslinks involving 36 proteins and detected PTMs at or near linked residues. Together, these data support reuse for comparative nuclear proteomics, multi-omics integration, and prioritization of candidates for future functional studies.

microbiology↗

bioRxiv2025

SUSTAINED SYSTEMIC AND NEUROINFLAMMATION IN COGNITIVE DYSFUNCTIONAL FEMALE MICE AFTER NON-SEVERE EXPERIMENTAL MALARIA

Plasmodial infection induces systemic inflammation with great potential to contribute to the development of severe illness and lethality. It is known that the hippocampus and cortex both play a pivotal role in memory processes and are affected by the neuroinflammation associated with cerebral malaria that causes long-lasting cognitive and behavioral sequelae. Since these sequelae are also associated with the non-severe form of malaria, it is important to correlate brain morphology, particularly glial cell involvement, and neuroimmune and neuroinflammatory features with memory acquisition and consolidation processes, in this clinical presentation of malaria, the most frequent worldwide. Here, we aimed to investigate cellular and molecular neuroimmune aspects of non-severe experimental malaria-associated cognitive dysfunction. Female C57BL/6 mice were infected with Plasmodium berghei ANKA and treated with chloroquine before any clinical signs of cerebral malaria emerged. No histopathological alteration, in hematoxylin-eosin staining, or axonal damage, in Bielschowskys silver-impregnated brain sections, was observed. However, morphological alterations in GFAP+ and Iba-1+ cells suggest that: i) astrocytes in the hippocampal dentate gyrus and the cornu Ammonis 1 regions and ii) microglia in the cornu Ammonis 1 region are responding to infection. Curiously, the effect persisted only in Iba-1+ cells up to 22 days post-infection. An increase in pro-inflammatory cytokines levels and expression was observed, in both the prefrontal cortex and the hippocampus. Also, serum and spleen cytokine levels were increased at 4 days post-infection. At 22 days post-infection, infected and treated mice showed an increase in serum cytokine levels that had homeostatic levels at 155 days post-infection. This dynamic points to both an immune stimulus persistence and a cytokine autoregulation post-infection. Infected mice exhibited acquisition and consolidation memory deficits in behavioral tests early after treatment (22 days post-infection). In conclusion, in a context of sustained systemic inflammation, mild neuroinflammatory alterations of glial cells may be involved in cognitive sequelae following a single episode of non-severe experimental malaria.

immunology↗

bioRxiv2023

Barking up the wrong tree: the importance of morphology in plant molecular phylogenetic studies

Background and aimsKeraunea is a genus recently described in Convolvulaceae, though it has sat uncomfortably in this family. A recent molecular phylogenetic study suggests that its two morphologically almost identical species actually belong to different families, Malpighiaceae (Superrosids) and Ehretiaceae (Superasterids), although with little-to-no morphological evidence to support it. Material and methodsSequences of matK, rbcL, and ITS for all the 77 currently accepted genera of Malpighiaceae, K. brasiliensis and Elatinaceae (outgroup) were compiled from Genbank and analysed with Maximum Likelihood and Bayesian Inference criteria for nuclear, plastid and combined datasets. Additional database and herbarium studies were performed to locate and analyse all duplicates of the holotype of K. brasiliensis to check for misidentified or contaminated materials. Key resultsOur examination of expanded DNA datasets and herbarium sheets of all K. brasiliensis isotypes revealed that an error in tissue sampling was, in fact, what led to this species being placed in Malpighiaceae. Kews isotype had a leaf of Malpighiaceae (likely from Mascagnia cordifolia) stored in the fragment capsule, which was unfortunately sampled and sequenced instead of the actual leaves of K. brasiliensis. ConclusionsDNA sequences can be helpful in classifying taxa when morphology is conflicting or of a doubtful interpretation, with molecular phylogenetic placement becoming a popular tool that potentially accelerates the discovery of systematic relationships. However, good knowledge of plant morphology is essential for formulating the phylogenetic hypotheses to be tested and for a critical re-interpretation of the results in the context of biological information of the species or families. Thus, these techniques are, much like any others, prone to methodological errors. We highlight the crucial need to observe plant morphology alongside molecular phylogenetic results, particularly when the new hypotheses are in disagreement with the existing classification and at risk of incurring gross taxonomic mistakes.

plant biology↗

bioRxiv2022

Protein arginine and lysine methylation in Trypanosoma cruzi

Post-translational methylation of proteins, which occurs in arginines and lysines, modulates several biological processes at different levels of cell signaling. Recently, methylation has been demonstrated in the regulation beyond histones, for example, in the dynamics of protein-protein and protein-nucleic acid interactions. However, the presence and role of non-histone methylation in Trypanosoma cruzi, the etiologic agent of Chagas disease, has not yet been elucidated. Here, we applied mass spectrometry-based-proteomics (LC-MS/MS) to describe the methylproteome of T. cruzi epimastigotes. A total of 1253 methyl sites in 824 methylated proteins were identified, of these, 712 (86.4%) proteins were identified in two or more biological replicates. Our results of functional enrichment analysis, protein-protein interaction, and co-occurrence with other PTMs, show that protein methylation impacts different levels of biological processes, such translation, RNA and DNA binding, amino acid and carbohydrate metabolism. In addition, 171 methylated proteins were previously reported with phosphorylation sites in T. cruzi, including flagellar proteins and RNA binding proteins, indicating that there may be an interplay between these different modifications in non-histone proteins. Our results show that a broad spectrum of functions are affected by methylation indicating its potential to impact important processes in the biology of the parasite and other trypanosomes. Statement of the significanceTrypanosoma cruzi is a protozoan parasite that causes Chagas disease in humans and faces different environmental changes throughout its life cycle. Protein methylation is an important post-translational modification by which cells respond and adapt to the environment. We applied mass spectrometry-based proteomics and reported the first proteomic analysis of arginine and lysine methylation in T. cruzi. Our data demonstrate that protein methylation is broad and impacts different cellular processes in T. cruzi. This study represents a significant advance in the investigation of the importance of protein methylation in trypanosomes.

genomics↗