Biology subjects

Felicori, L.

Publications and source records attributed to Felicori, L..

5 recordsLinked to original sources

bioRxiv2026

The Glycoproteome of Loxosceles Venom Reveals an Expanded Landscape of Animal Toxins

Spider venoms of the genus Loxosceles constitute a complex mixture of bioactive proteins and peptides associated with the major clinical manifestations of loxoscelism. Although significant advances have been made in the proteomic characterization of these toxins, studies addressing post-translational modifications, particularly glycosylation, and their potential impact on venom properties remain scarce. Here, we investigated the occurrence and characteristics of N-glycosylation in the venoms of Loxosceles gaucho, Loxosceles intermedia, and Loxosceles laeta. Using two-dimensional electrophoresis combined with glycoprotein-specific staining and LC-MS/MS, we identified glycosylation in different proteins biologically relevant to envenomation, predominantly belonging to the phospholipase D family, with distinct profiles among the species analyzed. Bottom-up glycoproteomic analysis of crude venoms using Byonic and a customized sequence database identified 88 N-glycosylated peptide sequences, primarily associated with lyases and hydrolases. Extensive microheterogeneity was detected at individual glycosylation sites, with paucimannosidic structures predominating alongside oligomannose and hybrid/complex N-glycans. Complementary enzyme-linked lectin assays supported the presence of distinct carbohydrate epitopes, including mannose, galactose, and N-acetylgalactosamine containing structures, and revealed 2,6-sialic acid-reactive motifs in two species. These findings establish N-glycosylation as an additional layer of molecular heterogeneity in Loxosceles venoms and provide a foundation for investigating its potential contribution to toxin properties and venom diversity.

biochemistry↗

bioRxiv2022

Yclon: Ultrafast clustering of B cell clones from high-throughput immunoglobulin repertoire sequencing data

MotivationThe next-generation sequencing technologies have transformed our understanding of immunoglobulin (Ig) profiles in various immune states. Clonotyping, which groups Ig sequences into B cell clones, is crucial in investigating the diversity of repertoires and changes in antigen exposure. Despite its importance, there is no widely accepted method for clonotyping, and existing methods are computationally intensive for large sequencing datasets. ResultsTo address this challenge, we introduce YClon, a fast and efficient approach for clonotyping Ig repertoire data. YClon uses a hierarchical clustering approach, similar to other methods, to group Ig sequences into B cell clones in a highly sensitive and specific manner. Notably, our approach outperforms other methods by being more than 30 to 5000 times faster in processing the repertoires analyzed. Astonishingly, YClon can effortlessly handle up to 2 million Ig sequences on a standard laptop computer. This enables in-depth analysis of large and numerous antibody repertoires. Availability and implementationYClon was implemented in Python3 and is freely available on GitHub (https://github.com/jao321/YClon.git) Contact: joaodgervasio@gmail.com, liza@icb.ufmg.br

bioinformatics↗

bioRxiv2022

Validation of a colorimetric LAMP to detect Loxosceles experimental envenomation

Diagnostic tests for brown spider accidents are unavailable and impact treatment decisions, increasing costs and patient risks. In this work, we used for the first time a fast, simple, and visual method based on the loop-mediated isothermal amplification assay (LAMP) to detect Loxosceles envenomation. Using the DNA from L. similis legs, we observed a high sensitivity using this test since as low as 0.32 pg of DNA could be detected. This pH-dependent colorimetric assay was 64 times more sensitive than PCR to detect spider DNA. The test was specific for Loxosceles once no cross-reaction was observed when testing DNA from different agents that cause similar dermonecrotic injuries. The test allowed the detection of Loxosceles intermedia DNA from hair, serum, and swab samples obtained from experimentally-envenomed rabbit within 72 h. The method sensitivity varied according to the sample and the collection time, reaching 100% sensitivity in serum and hair, respectively, 1 h and 24 h after the experimental envenomation. Due to its ease of execution, speed, sensitivity, and specificity, LAMP presents an excellent potential for identifying Loxosceles spp. envenomation. This can reduce the burden on the Health System and the morbidity for the patient by implementing the appropriate therapy immediately.In addition, this work opens up the perspective to other venomous animal accident identification using LAMP. Highlights* Using 28S primers it was possible to identify L. similis DNA with high sensitivity; * LAMP was 62-fold more sensitive than PCR and detected as low as 0.32 pg of DNA; * LAMP detected L. intermedia DNA from hair, serum, and exudate from experimentally-envenomed rabbits; * LAMP presents an excellent potential for identifying Loxosceles spp. envenomation.

molecular biology↗

bioRxiv2021

New insights of glycosylation role on variable domain of antibody structures

N-glycosylation at antibody variable domain (FvN-glyco) has emerged as an important modification for antibody function such as stability and antigen recognition, but it is also associated with autoimmune disease and IgE-mediated hypersensitivity reaction. However, the information related to its role and regulation is still scarce. Therefore, we investigated new insights in this regarding using solved antibodies structures presenting in the Protein Data Bank (PDB). From 130 FvN-glyco structures, we observed significant findings as a higher prevalence of N-glycosylation in human and mouse antibodies containing IGHV1-8 and IGHV2-2 germline genes, respectively. We also speculate the influence of activation-induced cytidine deaminase (AID) in introducing N-glycosylation sites during somatic hypermutation, specifically on threonine to asparagine substitution. Moreover, we highlight the enrichment of anti-HIV antibodies containing N-glycosylation at antibody variable domain and where we showed a possible important role of N-glycosylation, besides to antigen-antibody interactions, in antibody chain pair and antibody-antibody interactions. These could be a positive secondary effect of glycosylation to enhance antigen binding and further neutralization, including an additional mechanism to form Fab-dimers. Overall, our findings extend the knowledge on the characteristics and diverse role of N-glycosylation at antibody variable domain. Key PointsO_LIPrevalence of FvN-glyco in human IGHV1-8 and mouse IGHV2-2 germline genes. C_LIO_LIEnrichment of antibody FvN-glyco against virus, especially anti-HIV-1. C_LIO_LIFvN-glyco in the interface with antigen, antibody pair chain, and another antibody. C_LI

immunology↗

bioRxiv2018

PEPOP: new approaches to mimic non-continous epitopes

Bioinformatics methods are helpful to identify new molecules for diagnostic or therapeutic applications. For example, the use of peptides capable of mimicking binding sites has several benefits as replacing a protein difficult to produce, or toxic. Using peptides is less expensive. Peptides are easier to manipulate, and can be used as drugs. Continuous epitope predicted by bioinformatics tools are commonly used and these sequential epitopes are used as such in further experiments. Numerous discontinuous epitope predictors have been developed but only two bioinformatics tools proposed so far to predict peptide sequences: Superficial and PEPOP. PEPOP can generate series of peptide sequences that can replace continuous or discontinuous epitopes in their interaction with their cognate antibody. We have developed an improved version of PEPOP dedicated to answer to the experimentalists need for a tool able to handle proteins and to turn them into peptides. The PEPOP web site has been reorganized by peptide prediction category and is therefore better formulated to experimental designs. Since the first version of PEPOP, 32 new methods of peptide design were developed. In total, PEPOP proposes 35 methods in which 34 deal specifically with discontinuous epitopes, the most represented epitope type in nature.\n\nWe present the user-friendly, well-structured web-site of PEPOP and its validation through the use of predicted immunogenic or antigenic peptides mimicking discontinuous epitopes in different experimental ways. PEPOP proposes 35 methods of peptide design to guide experimentalists in using peptides potentially capable of replacing the cognate protein in its interaction with an Ab.

bioinformatics↗