Biology subjects

Gomes, A.

Publications and source records attributed to Gomes, A..

10 recordsLinked to original sources

bioRxiv2026

Dose-additive and dose-dependent fetal testis toxicity of a nine-phthalate mixture in the rat

Phthalates (ortho-phthalic acid diesters) are used in a variety of manufacturing processes, particularly as non-covalent plasticizers in flexible polyvinyl chloride. Phthalates are male reproductive toxicants that disrupt the development of the fetal testis, resulting in malformed seminiferous cords, multinucleated germ cells (MNGs), and decreased testosterone production. We previously reported that MNGs were a sensitive, dose-dependent marker of dipentyl phthalate (DPEP) germ cell toxicity. To test whether germ cell effects of phthalates are dose-additive, we measured the induction of MNGs by a phthalate mixture. We treated timed pregnant Sprague Dawley rats with an equipotent mixture of nine phthalates, spanning a two-log dose range, from GD 17-21. We found that the phthalate mixture effects on morphogenesis of the testis, assessed through histological analysis of MNGs and seminiferous cord diameter were dose-additive. Consistent with prior results, we also found that the testosterone-reducing effect of the phthalate mixture was dose-additive and dose-dependent. Induction of MNGs had the lowest effective dose of any endpoint that we measured, with a benchmark dose (BMD10) of 9.402 (6.093, 13.13) mg ({sum} all phthalates)/kg/d, which is equivalent to a BMD10 of 3.517 (2.275, 4.919) mg DPEP/kg/d, based on relative potency factors. Quantitative analysis of phthalate metabolites in dam serum showed that the metabolites were present in approximately the same relative concentrations as the parent compounds in the dosing mixture, but with lower levels of monocyclohexyl phthalate and monobenzyl phthalate. Proteomic and spatial transcriptomic analyses showed significant decreases in expression of Leydig cell genes and proteins involved in steroid hormone biosynthesis, as well as enrichment of proteins related to metabolism of lipids and amino acids. Proteomic BMD analysis produced a lowest BMDmedian of 2.156 (0.204, 27.830) mg ({sum} all phthalates)/kg/d, which was within a 4.36-fold margin of the lowest apical endpoint BMD.

pharmacology and toxicology↗

bioRxiv2026

Carbohydrate-active enzymes of giant viruses: Molecular and biochemical characterization of glycosyl hydrolases from algae-infecting chloroviruses

Microbial hydrolases are considered to be promising enzymes for pathogen control. Bacterial and viral chitinases of the glycosyl hydrolase (GH) 18 family are important biological macromolecules with antifungal and anti-insect activity. Chloroviruses, nucleocytoplasmic large DNA viruses (NCLDVs) that infect unicellular green algae have a considerable number of genes involved in carbohydrate metabolism, including the chitinase GH18 family. In this study, we investigated the abundance and diversity of chitinases in chlorovirus genomes using a combination of silico and in vitro strategies, and characterized these enzymes at a molecular and biochemical level. Different enzymatic profiles were observed in Chlorovirus subgenera revealing the different viral machinery related to host species. We performed a comprehensive biochemical characterization of three heterologous expressed GH18 domains, which revealed their endo and exochitinase activity and thermostability. Crystallographic analysis of the GH18 domain by X-ray diffraction yielded a structure at 1.0 [A] resolution, representing the highest-resolution structure reported to date for a giant viral protein and showing lower predominancy of residue coevolution compared GH18 chitinases from other organisms. Additionally, our binding site characterization predicted high conservation in betachloroviruses and gammachloroviruses, and less so in alphachloroviruses. Lastly, these enzymes did not inhibit fungal growth of medical and agricultural importance species in vitro but exhibited high inhibitory activity against different algae at nanogram/mL range. Together, our experimental and computational data show that evolutionary events may contribute to maintaining viral chitinases enzymatic activity and specificity. These findings highlight the potential of virus-derived enzymes as promising new biotechnological tools for microbial control against different algal strains.

microbiology↗

bioRxiv2026

A TAK1-Driven NLRP1 Inflammasome Pathway Revealed by Phosphatase-Targeting Environmental Toxins

Human NLRP1 is highly sensitive to phosphorylation-dependent activation, indicating a need for tight phosphatase control to prevent excessive inflammasome activity. In this study, we identified the phosphatases PP1 and PP2A as negative regulators of the NLRP1 inflammasome in human keratinocytes. Accordingly, exposure to the environmental toxins Dinophysistoxin, Okadaic acid, and Cantharidin, which inhibit PP1 and PP2A, triggered NLRP1 inflammasome activation. Notably, this toxin-induced activation process relied on hyperactivation of the MAP3 kinase TAK1. Mechanistically, both TAK1 and its downstream effectors p38 kinases phosphorylated and activated the NLRP1 inflammasome. Further studies underscored that TAK1 also contributed to the NLRP1 inflammasome activation during double-stranded RNA stimulation and viral infection. Finally, human native skins exposed to environmental toxins underlined the role of the PP1/PP2A-regulated TAK1/p38 axis in the development of skin dermatitis. Thus, these findings reveal a novel pathway of phosphorylation-driven NLRP1 activation and expand our understanding of its regulation in epithelial immunity. One Sentence SummaryPP1/PP2A phosphatases restrict TAK1-driven NLRP1 inflammasome response. O_FIG O_LINKSMALLFIG WIDTH=146 HEIGHT=200 SRC="FIGDIR/small/701233v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@128de37org.highwire.dtl.DTLVardef@151fbdorg.highwire.dtl.DTLVardef@d6b98aorg.highwire.dtl.DTLVardef@12f419d_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstractC_FLOATNO Schematic representation of the phosphorylation-driven hNLRP1 inflammasome response upon exposure to environmental toxins and to dsRNA/viral infection. C_FIG

immunology↗

bioRxiv2025

Brazil Seed Transfer Zones: Supporting Seed Sourcing for Climate-Resilient Ecosystem Restoration

O_LIEcosystem restoration is key to jointly address the biodiversity, climate, and social inequality crises. In Brazil, large-scale seed-based restoration is gaining momentum, but a national framework to match seed sources with planting sites is still lacking, undermining long-term success. C_LIO_LIWe developed the first Seed Transfer Zones (STZs) for Brazil using 25 environmental variables. We assessed restoration supply and demand within each STZ and projected the zones into the future under contrasting climate change scenarios. C_LIO_LIWe identified 48 STZs, distributed across Brazils six major vegetation regions (Amazon, Cerrado, Atlantic Forest, Caatinga, Pantanal, and Pampa). Overlaying the STZs with data on seed collection capacity and restoration opportunities revealed priority regions where seed supply is unlikely to meet demand (e.g., Cerrado). Future climate projections also indicate substantial reshaping of STZs, with 51-88% of Brazils land area expected to experience mismatches between current and future seed zones. C_LIO_LIThe creation of Brazils first STZs provides a scalable framework to guide seed sourcing for restoration, aligning supply with demand, and future-proofing projects to deliver lasting benefits for biodiversity, climate, and society. C_LI Societal Impact StatementTens of millions of hectares of degraded land in Brazil are in need of ecosystem restoration to achieve national and global biodiversity and climate goals. Sowing genetically diverse native seeds is key to restoring degraded lands to climate-resilient landscapes, but we still lack guidance on how to effectively match seed sources to restoration sites across broad geographic scales, within the context of a changing climate. We addressed this by identifying 48 Seed Transfer Zones (STZs) based on current and expected future climatic conditions. These zones will help ensure that the right seeds are used in the right places, enabling more effective and climate-smart restoration for nature and people.

ecology↗

bioRxiv2025

Tissue-Specific Regulatory and Expression Patterns of CDG-causative genes account to Phenotypic Variability

Congenital disorders of glycosylation (CDGs) are rare metabolic diseases caused by impaired addition of glycans to proteins and lipids. They display wide clinical variability, but the molecular basis remains unclear. Using healthy transcriptomic data from the GTEx project (bulk: 2,833 samples across 36 tissues; single-nucleus: 209,126 nuclei from 25 samples spanning 8 tissue types and 44 cell types), we investigated the expression and regulatory landscapes of 12 CDG-causative genes. CDG-causative genes were broadly but heterogeneously expressed, with both high and low expression aligning with clinical features. Interindividual variability in expression may contribute to phenotypic diversity in CDG. VPS13B was broadly expressed in fibroblasts, supporting their use in patient-derived models, while other genes showed more tissue-restricted expression, underscoring the importance of cellular context. Several genes exhibited tissue-specific deviations from balanced biallelic expression. Five allelic expression types across individuals - biallelic balanced or biased, tissue-specific or constitutive monoallelic, and autosomal random monoallelic - suggest a role for allelic regulation in phenotypic heterogeneity. Tissue-specific eQTLs highlighted regulatory complexity, with many variants located in intronic enhancers of unrelated genes. Finally, gene expression-immune cell correlations recapitulated known immune phenotypes and suggested context-dependent immune roles. Together, these findings reveal how genetic, regulatory, and immune factors shape CDG heterogeneity and provide a framework for future research.

genomics↗

bioRxiv2023

Unmasking Hidden Systemic Effects of Neurodegenerative Diseases: A Two-Pronged Approach to Biomarker Discovery

Identification of reliable blood biomarkers for neurodegenerative diseases (NDs) is crucial for translational and clinical research. However, conventional omics struggle with blood samples complexity, hindering desired outcomes. In this work the potential of High Molecular Weight (HMW) fractionation under non-denaturing conditions as a complementary approach to the conventional proteomics for identifying serum biomarkers in NDs was explored. A cohort of 58 serum samples of Alzheimers disease (AD), Parkinsons disease (PD) patients and control (CT) individuals was used to compare the two proteomics strategies: i) direct analysis of whole serum and ii) non-denaturing fractionation using 300 kDa cut-off filters (HMW serum). Although both approaches quantified a similar set of proteins, each approach captured a distinct subset of differentially altered proteins, suggesting that HMW fractionation identified additional types of alterations beyond conventional protein level changes. A discriminant model combining altered proteins from both datasets effectively distinguished between the three groups (AUC = 0.999 and median sensitivity and specificity of 97.4% and 91.7%, respectively). Importantly, this performance surpassed that of any model created using each method individually. Altogether, this work demonstrated that HMW fractionation can be a valuable complementary method to direct serum analysis and could enhance biomarker discovery. The 10 proteins included in the model (5 from each strategy), comprise clear evidence for the contribution of apolipoproteins for the diagnosis of NDs, revealing potential changes within lipid metabolism and the organization of macromolecules and their complexes, thereby uncovering effects that remain hidden from a conventional serum proteome analysis.

biochemistry↗

bioRxiv2022

Men in menopause? Experimental verification of the mate choice theory of menopause with Drosophila melanogaster

Various hypotheses regarding the origin of menopause have been proposed, and although the kin-selection-based theory appears promising, it involves population genetic processes that are insufficient to compensate for loss of fitness. The grandmother hypothesis and its variation the live long hypothesis are untenable; the former requires "climbing a steep fitness hill", as grandmothers share only 25% of their genes with their grandchildren, compared to 50% with their direct offspring, while the latter proposes a prolongation of the post-menopausal lifespan through selection, which is impossible in a population of non-reproducing females. The mate choice theory explains menopause as the result of asymmetric mating involving younger females and older males that leads to an accumulation of infertility mutations and the evolution of menopause in older females. In this study, we investigated the mate choice theory using an infertility mutation accumulation experiment with Drosophila melanogaster that involved mating between individuals of different age groups. After 70 generations of asymmetric mating, the results showed that younger females who were paired with older males showed declining fertility in old age. The same trend was noted with younger males when mated with older females; the fertility of the males declined in old age. These results support the mate choice theory and indicate that menopause is not a life history trait of females but of the sex of the younger mate. Mate choice theory treats the evolution of menopause and post-menopausal lifespan as independent traits that are driven by the mate choices exercised by older males. Menopause may be an atypical process because the evolutionary mechanism (age-restricted asymmetric mating) involved is rarely observed.

evolutionary biology↗

bioRxiv2022

Functional characterization of Atlantic salmon (Salmo salar L.) PepT2 transporters

The high-affinity/low-capacity system Slc15a2 (PepT2) is responsible for the reuptake of di/tripeptides from the renal proximal tubule, but it also operates in many other tissues/organs. Information regarding PepT2 in teleost fish is limited and to date functional data are available from the zebrafish (Danio rerio) only. Here, we report the identification of two slc15a2 genes in the Atlantic salmon (Salmo salar) genome, namely slc15a2a and slc15a2b. The two encoded PepT2 proteins share 87% identity and resemble both structurally and functionally to the canonical vertebrate PepT2 system. The mRNA tissue distribution analyses reveal a widespread distribution of slc15a2a transcripts, being more abundant in the brain and gills, while slc15a2b transcripts are mainly expressed in kidney and distal part of gastrointestinal tract. The function of the two transporters was investigated by heterologous expression in Xenopus laevis oocytes and two- electrode voltage-clamp recordings of transport and presteady-state currents. Both PepT2a and PepT2b in the presence of Gly-Gln elicit pH-dependent and Na+ independent inward currents. The biophysical and kinetic analysis of the recorded currents defined the transport properties, confirming that the two Atlantic salmon PepT2 proteins behave as high-affinity/low-capacity transporters. The recent structures and the previous kinetic schemes of rat and human PepT2 qualitatively account for the characteristics of the two Atlantic salmon proteins. This study is the first to report on the functional expression of two PepT2-type transporters that operate in the same vertebrate organism as a result of (a) gene duplication process(es). Key points summaryO_LITwo slc15a2-type genes, slc15a2a and slc15a2b coding for PepT2-type peptide transporters were found in the Atlantic salmon. C_LIO_LIslc15a2a transcripts, widely distributed in the fish tissues, are abundant in brain and gills, while slc15a2b transcripts are mainly expressed in kidney and distal gastrointestinal tract. C_LIO_LIAmino acids involved in vertebrate Slc15 transport function are conserved in PepT2a and PepT2b proteins. C_LIO_LIDetailed kinetic analysis indicates that both PepT2a and PepT2b operate as high-affinity transporters. C_LIO_LIThe kinetic schemes and structures proposed for the mammalian models of PepT2 are suitable to explain the function of the two Atlantic salmon transporters. C_LI

physiology↗

bioRxiv2021

Cytotoxic CD4+ T cells driven by T-cell intrinsic IL-18R/MyD88 signaling predominantly infiltrate Trypanosoma cruzi-infected hearts

Increasing attention has been directed to cytotoxic CD4+ T cells (CD4CTLs) in different pathologies, both in humans and mice. The impact of CD4CTLs in immunity and the mechanisms controlling their generation, however, remain poorly understood. Here, we show that CD4CTLs abundantly differentiate during mouse infection with the intracellular parasite Trypanosoma cruzi. CD4CTLs display parallel kinetics to Th1 cells in the spleen, mediate specific cytotoxicity against cells presenting pathogen-derived antigens and express immunoregulatory and/or exhaustion markers. We demonstrate that CD4CTL absolute numbers and activity are severely reduced in both Myd88-/- and Il18ra-/- mice. Of note, the infection of mixed-bone marrow chimeras revealed that WT but not Myd88-/- cells transcribe the CD4CTL gene signature and that Il18ra-/- and Myd88-/- CD4+ T cells phenocopy each other. Moreover, adoptive transfer of WT CD4+GzB+ T cells to infected Il18ra-/- mice extended their survival. Importantly, cells expressing the CD4CTL phenotype predominate among CD4+ T cells infiltrating the infected mouse cardiac tissue and are increased in the blood of Chagas patients, in which the frequency of CD4CTLs correlates with the severity of cardiomyopathy. Our findings describe CD4CTLs as a major player in immunity to a relevant human pathogen and disclose T-cell intrinsic IL-18R/MyD88 signaling as a key pathway controlling the magnitude of the CD4CTL response.

immunology↗

bioRxiv2021

Toxoplasma gondii Toxolysin 4 contributes to efficient parasite egress from host cells

Egress from host cells is an essential step in the lytic cycle of T. gondii and other apicomplexan parasites; however, only a few parasite secretory proteins are known to affect this process. The putative metalloproteinase Toxolysin 4 (TLN4) was previously shown to be an extensively processed microneme protein, but further characterization was impeded by the inability to genetically ablate TLN4. Herein we show that TLN4 has the structural properties of an M16 family metalloproteinase, that it possesses proteolytic activity on a model substrate, and that genetic disruption of TLN4 reduces the efficiency of egress from host cells. Complementation of the knockout strain with the TLN4 coding sequence significantly restored egress competency, affirming that the phenotype of the {Delta}tln4 parasite was due to the absence of TLN4. This work identifies TLN4 as the first metalloproteinase and the second microneme protein to function in T. gondii egress. The study also lays a foundation for future mechanistic studies defining the precise role of TLN4 in parasite exit from host cells. IMPORTANCEAfter replicating within infected host cells, the single celled parasite Toxoplasma gondii must rupture out of such cells in a process termed egress. Although it is known that T. gondii egress is an active event that involves disruption of host-derived membranes surrounding the parasite, very few proteins that are released by the parasite are known to facilitate egress. In this study we identify a parasite secretory protease that is necessary for efficient and timely egress, thus laying the foundation for understanding precisely how this protease facilitates T. gondii exit from host cells.

microbiology↗