Biology subjects

Silva, M. S.

Publications and source records attributed to Silva, M. S..

15 recordsLinked to original sources

bioRxiv2026

Disease-associated variants alter a novel physiological role of hnRNP H2 in neuronal development

Heterogeneous nuclear ribonucleoprotein H2 (hnRNP H2) is a member of the hnRNP family of RNA-binding proteins that regulate neuronal function through multiple aspects of RNA metabolism. Mutations in the nuclear localisation signal (NLS) and quasi-RNA recognition motifs (qRRMs) of hnRNP H2 have recently been linked to a severe developmental syndrome, termed HNRNPH2-related neurodevelopmental disorder. Despite its emerging importance, the physiological roles of hnRNP H2 in neuronal development and synaptic maturation, and how disease-associated variants alter these processes to drive pathology, remain poorly understood. Here, we show that hnRNP H2 is expressed in hippocampal neurons and localises to the synaptic compartment. Knockdown of hnRNP H2 revealed essential roles of the protein in the regulation of neuronal morphology, dendritic spine maturation, synaptic transmission, and cortical neuronal migration in vivo. Disease-associated hnRNP H2 variants altered protein localisation and activity-dependent synaptic recruitment, resulting in defects in neuronal morphology, in vivo cortical neuronal migration and laminar orientation, dendritic spine maturation, and synaptic function. Together, these findings establish hnRNP H2 as a critical regulator of neurodevelopment and identify a molecular basis for HNRNPH2-related neurodevelopmental disorder.

neuroscience↗

bioRxiv2026

NMR reveals specific remodelling of protein folding landscapes in ionic liquids

Ionic liquids (ILs) are designer solvents with tunable properties that have emerged as powerful cosolutes in protein science and biotechnology. While ILs are known to stabilize or destabilize proteins, their molecular mechanisms remain poorly defined, particularly regarding effects on the unfolded ensemble. Here, we use the metastable SH3 domain of the Drosophila adaptor protein Drk, which coexists in a slow two-state equilibrium between folded and unfolded states, as a model to dissect how ILs modulate protein conformational equilibria. Using nuclear magnetic resonance (NMR) spectroscopy, we show that cholinium glutamate ([Ch][Glu]) stabilizes the folded state by preferential exclusion from the protein surface, raising the barrier to unfolding in a manner reminiscent of osmolytes and crowding agents. In contrast, 1-butyl-3-methylimidazolium dicyanamide ([Bmim][dca]) shifts the equilibrium toward the unfolded state, not by destabilizing the native fold, but by stabilizing a compact, non-native -helical conformation within the unfolded ensemble. Notably, this concentration-dependent mechanism differs from traditional denaturants such as urea or guanidinium chloride, which promote random-coil unfolded states. Kinetic measurements further reveal that [Ch][Glu] slows unfolding, whereas [Bmim][dca] slows folding, indicating that the two ILs reshape the folding landscape in opposite directions. These findings challenge the prevailing view that cosolutes act primarily on the folded state and establish unfolded-state stabilization as a critical determinant of protein stability. More broadly, this work provides a molecular framework for understanding how ILs reshape protein folding landscapes and offers design principles for tailoring ILs as stabilizers or destabilizers in biotechnology and therapeutic applications. Significance StatementProteins exist in a delicate balance between folded and unfolded states, and cosolutes such as salts are generally viewed as acting only on the folded state. Here, we show that ionic liquids (ILs) are able to reshape this balance and uniquely modulate both folded and unfolded protein states through distinct molecular mechanisms. These results challenge the conventional view of protein stabilization/destabilization and demonstrate that unfolded-state modulation is a critical determinant of protein behavior. By establishing principles for how ILs alter protein folding landscapes, this work provides a framework for designing ILs with tailored effects, with implications for biocatalysis, protein engineering, and therapeutic formulation. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=178 SRC="FIGDIR/small/700775v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@372d3borg.highwire.dtl.DTLVardef@7a7fadorg.highwire.dtl.DTLVardef@543f4eorg.highwire.dtl.DTLVardef@1084836_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2024

POLO kinase inhibits Protein Phosphatase 1 to promote the Spindle Assembly Checkpoint and prevent aneuploidy

Protein phosphatase 1 (PP1) is essential for spindle assembly checkpoint (SAC) silencing and mitotic exit, but its regulation during mitosis remains ill-defined. Here, we demonstrate in vitro and in Drosophila cells that the mitotic kinase POLO phosphorylates PP187B at a conserved residue (T286) within a pocket implicated in the recognition of RVxF-containing target proteins. Phosphorylation of T286 inhibits PP187B binding to the RVxF motif of the SAC kinase MPS1, dampening the dephosphorylation of MPS1 T-loop. Phosphorylation of T286 is dynamically regulated during mitosis. It occurs at unattached/tensionless kinetochores and decreases as chromosomes congress. Expression of phosphomimetic PP187BT286D prevents MPS1 inactivation in metaphase and causes a SAC-dependent delay of anaphase onset. Conversely, an unphosphorylatable PP187BT286A mutant impairs MPS1 activation at unattached kinetochores and weakens the SAC. In vivo, larval neuroblasts expressing PP187BT286 phosphomutants exhibit frequent chromosome mis-segregation and aneuploidy. Thus, our findings identify POLO-mediated phosphorylation of PP187B as a critical regulatory strategy that fine-tunes phosphatase activity to ensure a robust and timely SAC and prevent genome instability.

cell biology↗

bioRxiv2024

Classifying Genetic Interactions Using an HIV Experimental Study

Current methods of addressing novel viruses remain predominantly reactive and reliant on empirical strategies. To develop more proactive methodologies for the early identification and treatment of diseases caused by viruses like HIV and Sars-CoV-2, we focus on host targeting, which requires identifying and altering human genetic host factors that are crucial to the life cycle of these viruses. To this end, we present three classification models to pinpoint host genes of interest. For each one, we thoroughly analyze the current predictive accuracy, susceptibility to modifications of the input space, and potential for further optimization. Our methods rely on the exploration of different gene representations, including graph-based embeddings and large foundation transformer models, to establish a set of baseline classification models. Subsequently, we introduce an order-invariant Siamese neural network that exhibits more robust pattern recognition with sparse datasets while ensuring that the representation does not capture unwanted patterns, such as the directional relationship of genetic interactions. Through these models, we generate biological features that predict pairwise gene interactions, with the intention of extrapolating this proactive therapeutic approach to other virus families.

bioinformatics↗

bioRxiv2024

Early mechanisms of aortic failure in a zebrafish model for thoracic aortic dissection and rupture

Thoracic aortic aneurysm and dissection (TAAD) associates with a high mortality rate. Despite the existence of different mouse models for TAAD, the underlying disease mechanisms remain elusive. Treatment options are limited and mainly consist of surgical repair at critical aortic diameters as current pharmacological interventions are unable to stop disease progression. In humans, loss of function (LOF) of SMAD3 and SMAD6 impairs vascular homeostasis, increasing the risk for TAAD. We developed a zebrafish model for thoracic aortic dissection/rupture by targeting both ohnologs of smad3 and smad6. At 10 days post fertilization, we found an increased diameter of the ventral aorta in smad3a-/-;smad3b-/- double knockout zebrafish, while smad6a-/-;smad6b-/- double knockout zebrafish have a reduced aortic diameter associated with early mortality. We discovered that a smad3a-/-;smad3b-/-;smad6a-/-;smad6b-/- quadruple knockout (qKO) zebrafish model is viable and survives to adulthood, although exposure to stress leads to sudden death. Histological analysis of the adult ventral aorta shows medial elastolysis, aortic dissections and ruptures at sites exposed to high biomechanical stress. RNA-sequencing of 5 days post fertilization qKO zebrafish indicates a profile of reduced negative regulation of proteolysis and upregulation of melanogenesis, a previously unaddressed pathway in this pathology. We confirm that pharmacological modulation of tyrosinase, the enzyme responsible for the production of melanin, influences aortic morphology. Overall, the qKO mutant, thus far the only known zebrafish model of thoracic aortic dissection and rupture, reveals novel SMAD3/6-dependent pathways that impact thoracic aortic homeostasis, in this way opening avenues for the development of novel treatments in TAAD.

developmental biology↗

bioRxiv2023

A unique chaperoning mechanism in Class A JDPs recognizes and stabilizes mutant p53.

J-domain proteins (JDPs) constitute a large family of molecular chaperones that bind a broad spectrum of substrates, targeting them to Hsp70, thus determining the specificity and activating the entire chaperone functional cycle. The malfunction of JDPs is therefore inextricably linked to myriad human disorders. Here we uncover a novel mechanism by which chaperones recognize misfolded clients, present in class-A JDPs. Through a newly-identified {beta}-hairpin site, these chaperones detect changes in protein dynamics at the initial stages of misfolding, prior to exposure of hydrophobic regions or large structural rearrangements. The JDPs then sequester misfolding-prone proteins into large oligomeric assemblies, protecting them from aggregation. Through this mechanism, class-A JDPs bind destabilized p53 mutants, preventing clearance of these oncoproteins by Hsp70-mediated degradation, thus promoting cancer progression. Removal of the {beta}-hairpin abrogates this protective activity while minimally affecting other chaperoning functions. This suggests the class-A JDP {beta}-hairpin as a highly specific target for cancer therapeutics.

biochemistry↗

bioRxiv2023

Cell-specific alpha-tubulin TBA-6 and pan-ciliary IFT cargo RAB-28 generate a non-canonical transition zone

The transition zone (TZ) regulates cilia composition and function. Canonical TZs with 9 doublet microtubules (MTs) are common but non-canonical TZs that vary from 9 MT symmetry also occur and arise through unknown mechanisms. Cilia on the quadrant inner labial type 2 (IL2Q) neurons of C. elegans have a specialized non-canonical TZ with fewer than 9 doublet MTs. We previously showed that non-canonical TZs in IL2Q cilia arise via MT loss and reorganization of canonical TZs. Here, we identify structural events and mechanisms that generate non-canonical TZs. Cell-specific -tubulin TBA-6 and pan-ciliary IFT cargo RAB-28 regulate IL2QTZ MT loss without affecting ciliary assembly. Our results reveal a role for the tubulin code in generating non-canonical TZs and contribute towards understanding ciliary functional specialization. Author summaryCiliary microtubules are exquisitely diverse in arrangements and composition. Studies on how ciliary ultrastructural diversity is generated are essential to our understanding of cilia function in diverse healthy and pathological contexts. Despite its clinical relevance, the ultrastructural diversity of the transition zone and its microtubules remains understudied. Here, we uncover mechanisms contributing to generating ultrastructural diversity in the transition zone and in cilia. A subset of sensory cilia in C. elegans contain a non-canonical transition zone with 7 and fewer doublet microtubules. We previously showed that this distinct transition zone is generated through microtubule loss in a canonical transition zone with 9 doublet microtubules, a process that occurs asynchronously during animal development. Here, we identify roles for the tubulin code and for an IFT cargo in generating a distinct transition zone. Sculpting of the distinct transition zone occurs in fully assembled cilia and transition zones and is independent of general ciliogenesis mechanisms. Our results demonstrate how specialized transition zones can be generated from canonical transition zones and provide insight into mechanisms of ciliary ultrastructural diversity and post-ciliogenesis restructuring. Such mechanisms hold the key to understanding ciliary function and to restoration of function in ciliopathies with ciliary ultrastructural defects.

cell biology↗

bioRxiv2022

Computationally restoring the potency of a clinical antibody against SARS-CoV-2 Omicron subvariants

The COVID-19 pandemic underscored the promise of monoclonal antibody-based prophylactic and therapeutic drugs1-3, but also revealed how quickly viral escape can curtail effective options4, 5. With the emergence of the SARS-CoV-2 Omicron variant in late 2021, many clinically used antibody drug products lost potency, including EvusheldTM and its constituent, cilgavimab4, 6. Cilgavimab, like its progenitor COV2-2130, is a class 3 antibody that is compatible with other antibodies in combination4 and is challenging to replace with existing approaches. Rapidly modifying such high-value antibodies with a known clinical profile to restore efficacy against emerging variants is a compelling mitigation strategy. We sought to redesign COV2-2130 to rescue in vivo efficacy against Omicron BA.1 and BA.1.1 strains while maintaining efficacy against the contemporaneously dominant Delta variant. Here we show that our computationally redesigned antibody, 2130-1-0114-112, achieves this objective, simultaneously increases neutralization potency against Delta and many variants of concern that subsequently emerged, and provides protection in vivo against the strains tested, WA1/2020, BA.1.1, and BA.5. Deep mutational scanning of tens of thousands pseudovirus variants reveals 2130-1-0114-112 improves broad potency without incurring additional escape liabilities. Our results suggest that computational approaches can optimize an antibody to target multiple escape variants, while simultaneously enriching potency. Because our approach is computationally driven, not requiring experimental iterations or pre-existing binding data, it could enable rapid response strategies to address escape variants or pre-emptively mitigate escape vulnerabilities.

microbiology↗

bioRxiv2022

A Computational Pipeline to Identify Potential Drug Targets and Interacting Chemotypes in SARS-CoV-2

1Minimizing the human and economic costs of the COVID-19 pandemic and of future pandemics requires the ability to develop and deploy effective treatments for novel pathogens as soon as possible after they emerge. To this end, we introduce a unique, computational pipeline for the rapid identification and characterization of binding sites in the proteins of novel viruses as well as the core chemical components with which these sites interact. We combine molecular-level structural modeling of proteins with clustering and cheminformatic techniques in a computationally efficient manner. Similarities between our results, experimental data, and other computational studies provide support for the effectiveness of our predictive framework. While we present here a demonstration of our tool on SARS-CoV-2, our process is generalizable and can be applied to any new virus, as long as either experimentally solved structures for its proteins are available or sufficiently accurate homology models can be constructed.

bioinformatics↗

bioRxiv2021

Viral route of infection determines the effect of Drosophila melanogaster gut bacteria on host resistance and tolerance to disease.

The microbial community interacting with a host can modulate the outcome of pathogenic infections. For instance, Wolbachia, one of the most prevalent invertebrate endosymbionts, strongly increases resistance of Drosophila melanogaster and other insect hosts, to many RNA viruses. D. melanogaster is also in continuous association with gut bacteria, whose role in antiviral immunity is poorly characterized. Here we asked how gut-colonizing bacteria impact viral titres and host survival, and how these interact with route of infection or Wolbachia presence. We compared germ-free flies and flies associated with two gut bacteria species recently isolated from wild flies (Acetobacter thailandicus and Lactobacillus brevis). We found that Wolbachia-conferred protection to both DCV or FHV is not affected by the presence or absence of these gut bacteria. Flies carrying A. thailandicus have lower DCV loads than germ-free flies, upon systemic infection, but reduced survival, indicating that these bacteria increase resistance to virus and decrease disease tolerance. Association with L. brevis, alone or in combination with A. thailandicus, did not lead to changes in survival to systemic infection. In contrast to the effect on systemic infection, we did not observe an impact of these bacteria on survival or viral loads after oral infection. Overall, the impact of gut-associated bacteria in resistance and tolerance to viruses was mild, when compared with Wolbachia. These results indicate that the effect of gut-associated bacteria to different viral infections, and different routes of infection, is complex and understanding it requires a detailed characterization of several parameters of infection.

immunology↗

bioRxiv2021

Sensory cilia act as a specialized venue for regulated EV biogenesis and signaling

Extracellular vesicles play major roles in intercellular signaling, yet fundamental aspects of their biology remain poorly understood. Ciliary EV shedding is evolutionary conserved. Here we use super resolution, real time imaging of fluorescent-protein tagged EV cargo combined with in vivo bioassays to study signaling EVs in C. elegans. We find that neuronal sensory cilia shed the TRP polycystin-2 channel PKD-2::GFP-carrying EVs from two distinct sites - the ciliary tip and the ciliary base. Ciliary tip shedding requires distal ciliary enrichment of PKD-2 by the myristoylated coiled-coil protein CIL-7. Kinesin-3 KLP-6 and intraflagellar transport (IFT) kinesin-2 motors are also required for ciliary tip EV shedding. Blocking ciliary tip shedding results in excessive EV shedding from the base. Finally, we demonstrate that C. elegans male ciliated neurons modulate EV cargo composition in response to sensory stimulation by hermaphrodite mating partners. Overall, our study indicates that the cilium and its trafficking machinery act as a specialized venue for regulated EV biogenesis and signaling.

cell biology↗

bioRxiv2020

Diurnal transcript profiling of the diatom Seminavisrobusta reveals adaptations to a benthic lifestyle

1Coastal regions contribute an estimated 20% of annual gross primary production in the oceans, despite occupying only 0.03% of their surface area. Diatoms frequently dominate coastal sediments, where they experience large variations in light regime resulting from the interplay of diurnal and tidal cycles. Here, we report on an extensive diurnal transcript profiling experiment of the motile benthic diatom Seminavis robusta. Nearly 90% (23,328) of expressed protein-coding genes and 66.9% (1124) of expressed long intergenic non-coding RNAs (lincRNAs) showed significant expression oscillations and are predominantly phasing at night with a periodicity of 24h. Phylostratigraphic analysis found that rhythmic genes are enriched in deeply conserved genes, while diatom-specific genes are predominantly associated with midnight expression. Integration of genetic and physiological cell cycle markers with silica depletion data revealed potential new silica cell wall associated gene families specific to diatoms. Additionally, we observed 1752 genes with a remarkable semidiurnal (12-h) periodicity, while the expansion of putative circadian transcription factors may reflect adaptations to cope with highly unpredictable external conditions. Taken together, our results provide new insights into the adaptations of diatoms to the benthic environment and serve as a valuable resource for diurnal regulation in photosynthetic eukaryotes. O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

systems biology↗

bioRxiv2020

Humic acids enrich the plant microbiota with bacterial candidates for the suppression of pathogens

Humic acids (HAs) stimulate the growth of several plant species by regulating their hormonal and redox metabolisms. Nevertheless, studies on the relationship of these substances with the plant-associated microbiota are almost nonexistent. Here, we hypothesized that the effect of HAs occurs in parallel with the regulation of the plant-associated bacterial community. Our results show the positive influence of HAs on the growth of rice and its stimulation of the root system. Metataxonomics revealed that the structure and composition of root bacterial communities were affected upon the application of HAs. Chitinophaga and Mucilaginibacter were the predominant genera in HA-treated roots. These bacteria produce enzymes that degrade compounds like those present in the wall of fungi, oomycetes, and nematode eggs. Pseudomonas and the Gp 1 group of Acidobacteria, both siderophore-producers and plant-growth promoters were also enriched, although with lower abundances. Given these results, we suggest that plants recruit these microorganisms in response to the stress caused by the HA-root interaction. For the first time, our findings indicate that HA-stimulated plants adopt the ecological strategy of recruiting members of the bacterial community that are candidates for the suppression of pathogens and, therefore, involved in plant defense.

microbiology↗

bioRxiv2020

Sodium Diethyldithiocarbamate antiparasitic activity against different Trypanosoma cruzi strains: Insights of its biological activity

BackgroundChagas disease is caused by the protozoan Trypanosoma cruzi, a neglected tropical disease that affects thousands of people, mainly in Latin America. The drugs currently used in therapy are toxic and have therapeutic limitations during treatment. In addition, the genetic diversity of T. cruzi represents an important variable and challenge with regard to the pathogenesis of the infection, the epidemiological profile of the cases, and the therapeutic control of the infection. Sodium diethyldithiocarbamate (DETC) is a compound of high pharmacological versatility acting as metal chelators and producing reactive oxygen species. Thus, the objective of this work is to characterize the antiparasitic action of DETC against different strains and evolutionary forms of T. cruzi, as well as the characterization of the mechanism of antiparasitic action. Methodology/Principal findingsThe different strains and evolutionary forms of T. cruzi were grown in LIT medium. To evaluate the antiparasitic activity of DETC, the evolutionary forms epimastigote and trypomastigote of T. cruzi were used by resazurin reduction methods and by counting under optical microscopy. Different response patterns were obtained between the strains and an IC50 of DETC ranging from 9.44 {+/-} 3,181{micro}M to 60.49 {+/-} 7.62 {micro}M. Cell cytotoxicity against cell lines 3T3 and RAW and evaluated by MTT, demonstrated that DETC in high concentration (2222 {micro}M) reduces around 60% the cell capacity of MTT reduction. The antiparasitic activity of DETC has been demonstrated through damage caused in the mitochondria of T. cruzi, a reduction of up to 80% in the mitochondrial potential of the parasites, as well as through damage caused in the membrane of the parasite. ConclusionIn this study we can conclude that DETC has antiparasitic activity against different genotypes and evolutionary forms of T. cruzi, representing a promising molecule as a drug for the treatment of Chagas disease.

pharmacology and toxicology↗

bioRxiv2018

Cell type-specific structural plasticity of the ciliary transition zone in C. elegans

Background informationThe current consensus on cilia development posits that the ciliary transition zone (TZ) is formed via extension of nine centrosomal microtubules. In this model, TZ structure remains unchanged in microtubule number throughout the cilium life cycle. This model does not however explain structural variations of TZ structure seen in nature, and could also lend itself to the misinterpretation that deviations from nine-doublet microtubule ultrastructure represent an abnormal phenotype. Thus, a better understanding of events that occur at the TZ in vivo during metazoan development is required.\n\nResultsTo address this issue, we characterized ultrastructure of two types of sensory cilia in developing Caenorhabditis elegans. We discovered that, in cephalic male (CEM) and inner labial quadrant (IL2Q) sensory neurons, ciliary TZs are structurally plastic and remodel from one structure to another during animal larval development. The number of microtubules doublets forming the TZ can be increased or decreased over time, depending on cilia type. Both cases result in structural TZ intermediates different from TZ in adult cilia. In CEM cilia, axonemal extension and maturation occurs concurrently with TZ structural maturation.\n\nConclusions and SignificanceOur work extends the current model to include the structural plasticity of metazoan transition zone, which can be structurally delayed, maintained or remodeled in cell type-specific manner.

cell biology↗