Biology subjects

Alves, M.

Publications and source records attributed to Alves, M..

12 recordsLinked to original sources

bioRxiv2026

Carbonic anhydrase inhibition rescues heart function in the Tg2576 Alzheimer's mouse model by ameliorating cardiac amyloid-β pathology and neurotrophic signaling impairment.

FDA-approved carbonic anhydrase inhibitors (CAIs) have shown robust efficacy in reducing amyloid- beta pathology, neurodegeneration, and cerebrovascular dysfunction in Alzheimer disease (AD) and cerebral amyloid angiopathy (CAA) models, highlighting carbonic anhydrases (CAs) as a promising, previously untapped therapeutic target for AD and the vascular contribution to dementia. We have recently shown that amyloid- beta aggregates disrupt neuro-signaling and deplete neurotrophic factors (particularly BDNF) in the heart of AD mouse models and human subjects. In this study, we present the first in-depth examination of CAI therapy (acetazolamide, ATZ) in Tg2576 mice, a well-established model of AD and CAA. We confirm that progressive cardiac fibrosis and amyloid- beta deposition in 13-month-old mice severely impair the cardiac neuro-signaling system, marked by a drastic decrease in BDNF and reductions in adrenergic fibers and regenerating nerve endings (TH and GAP-43 markers), leading to significant declines in ejection fraction and fractional shortening compared to age-matched WT littermates. Critically, this study demonstrates that long-term ATZ treatment in Tg2576 mice significantly reduces cardiac amyloid- beta burden, prevents adverse neuro-signaling remodeling, and restores heart physiological function, as assessed via speckle tracking strain echocardiography. These in vivo findings were corroborated in human cardiomyocytes, in which CA inhibition reduced human amyloid- beta40 oligomer-dependent disruption of CREB signaling, thus preserving BDNF expression. Together, these results reveal a previously unrecognized cardio-neuroprotective role for CAIs in preventing amyloid- beta-induced cardiovascular remodeling and neuro-signaling disruption in the Tg2576-AD model. Given the established benefits of CAIs on cerebrovascular function and cognition, our findings further support advancing repurposing efforts into clinical trials. CAIs such as ATZ could offer a dual-action therapy approach, addressing both the central nervous system and cardiac pathologies associated with AD and, potentially, the systemic effects of amyloidosis.

cell biology↗

bioRxiv2025

Chromosome-Scale Genome Assembly of Australian Finger Lime and Resequencing Reveal the Hidden Diversity of Oceanian Citrus

Oceanian citrus species, including wild taxa native to Australia and Papua New Guinea, form a genetically distinct clade within the Citrus L. (1753) genus. These species remain largely underexplored, despite their adaptation to diverse environments and relevance for citrus improvement. To support their use in breeding and evolutionary studies, we generated a high-quality, Chromosome-scale genome assembly of an Australian finger lime accession (SRA 1002), a natural interspecific hybrid. The genome was assembled using long-read sequencing, optical mapping, and a high-density genetic map, resulting in nine pseudomolecules covering over 97% of the genome. Using this reference, we analyzed whole-genome resequencing data from 132 accessions representing the diversity of Asian and Oceanian citrus. Variant calling across the dataset produced a high-resolution catalogue of single nucleotide polymorphisms (SNPs) and derived database of SNP fully discriminant of 20 Citrus species (DSNPs), enabling detailed exploration of inter- and intra-specific diversity. The data reveal a strong population structure within the group with clear heterozygosity variation between ancestral species and admixed accessions, reflecting their complex evolutionary history and hybridization patterns. This study provides the first integrated genomic framework for Oceanian citrus diversity, offering essential tools for downstream applications in citrus breeding, conservation, and evolutionary genomics. The resources generated lay the groundwork for future association studies and the targeted introgression of beneficial traits into cultivated citrus.

plant biology↗

bioRxiv2025

Ancient Protein Resurrection of an ancestral Arf GTPase that regulates membrane trafficking uncovers dual cellular localization and unanticipated properties of modern Arf1 proteins.

The emergence of eukaryotes from their prokaryotic ancestors (eukaryogenesis) marked a fundamental shift in cellular organisation, with the appearance of intracellular compartments including the nucleus, the Golgi apparatus and endosomes. These organelles are part of the endomembrane system of eukaryotic cells, which mediates many processes, including secretion of proteins to the exterior of the cell, uptake of material by endocytosis, and compartmentalized degradation of cellular components. The period of eukaryogenesis after the merger of prokaryotic lineages but preceding the last eukaryotic common ancestor, is inferred to have involved a progressive increase in cellular complexity through expansion of organelle-specific protein machineries. However, the steps and stages of organelle emergence during this period are poorly understood as no extant organisms exist from this period, precluding the use of comparative genomics to determine the properties of ancestral proteins present. Membrane trafficking pathways linking organelles are regulated by Arf family GTPases, including Arf1 and Arf6, both present in the last eukaryotic common ancestor. Here we use ancestral sequence reconstruction and molecular cell biological characterization to explore the properties of the ancestor of the Arf1 and Arf6 GTPases. Arf1 has a major function at the Golgi apparatus in regulation of the secretory pathway, whereas Arf6 regulates endocytic pathways at the plasma membrane and endosomes. Our results indicate that the ancestral Arf1/6 protein localizes to both the Golgi and the plasma membrane. We find that localization to the plasma membrane is due to a C-terminal polybasic motif that unexpectedly is also found in a number of modern Arf1 proteins from a wide diversity of eukaryotes. Our data suggest that the ancestral Arf protein acted at both internal compartments and the cell periphery, a feature preserved in a number of modern Arf1 proteins.

evolutionary biology↗

bioRxiv2024

Direct observation of fluorescent proteins in gels: a rapid, cost-efficient and quantitative alternative to immunoblotting

The discovery of Green Fluorescent Protein (GFP) and its derivatives has revolutionized cell biology. These fluorescent proteins (FPs) have enabled the real-time observation of protein localization and dynamics within live cells. Applications of FP vary from monitoring gene/protein expression patterns, visualizing protein-protein interactions, measuring protein stability, assessing protein mobility and creating biosensors. The utility of FPs also extends to biochemical approaches through immunoblotting and proteomic analyses, aided by anti-FP antibodies and nanobodies. FPs are notoriously robust proteins with a tightly folded domain that confers a strong stability and a relative resistance to degradation and denaturation. In this study, we report that various green, orange and red FPs can be maintained in a native, fluorescent state during the entire process of protein sample extraction, incubation with sample buffer, loading and migration on SDS-PAGE with only minor adaptations of traditional protocols. This protocol results in the ability to detect and quantify in-gel fluorescence (IGF) of endogenously-expressed proteins tagged with FPs directly after migration, using standard fluorescence-imaging devices. This approach eliminates the need for antibodies and chemiluminescent reagents, as well as the time-consuming steps inherent in immunoblotting such as transfer onto a membrane and antibody incubations. Overall, IGF detection provides clearer data with less background interference, a sensitivity comparable or better to antibody-based detection, a better quantification and a broader dynamic range. After fluorescence imaging, gels can still be used for other applications such as total protein staining or immunoblotting if needed. It also expands possibilities by allowing the detection of FPs for which antibodies are not available. Our study explores the feasibility, limitations, and applications of IGF for detecting endogenously expressed proteins in cell extracts, providing insights into sample preparation, imaging conditions, and sensitivity optimizations, and potential applications such as co-immunoprecipitation experiments.

biochemistry↗

bioRxiv2024

Arf family GTPases are present in Asgard archaea

The emergence of eukaryotes from their prokaryotic ancestors is one of the most fundamental evolutionary events in the history of life. Little is robustly known about how eukaryogenesis occurred, but a major breakthrough came with the identification of the Asgardarchaeota, the closest prokaryotic lineage to eukaryotes yet discovered. Endomembrane organelles, and the capacity to transport material between them, are major hallmarks of eukaryotic cells. The Arf family GTPases are crucial regulators of organelle dynamics in eukaryotes, functioning in vesicle budding, membrane tethering and membrane-cytoskeleton interactions. Although an expanded GTPase complement has been reported in the Asgardarchaeota, the specific origins of the Arf family remain elusive. Here we report a new group of prokaryotic GTPases, the ArfRs. Widely present in Asgardarchaeota and almost exclusive to them, it is the clade from which all eukaryotic Arf family proteins are derived. Heterologous expression of representative Asgardarchaeota ArfR proteins in the model eukaryote Saccharomyces cerevisiae and X-ray crystallographic studies demonstrate that ArfR GTPases possess the mechanism of membrane binding and structural features unique to Arf family proteins. Our results show that Arf family GTPases are present in Asgardarchaeota, and strongly suggest that they originated in the archaeal contributor to eukaryogenesis, providing support for nascent endomembrane system capacity evolving early in eukaryogenesis.

evolutionary biology↗

bioRxiv2023

Human enteric glia diversity in health and disease: new avenues for the treatment of Hirschsprung disease

Hirschsprung disease (HSCR) is caused by an absence of the enteric nervous system (ENS), which is crucial for intestinal function. The ENS is composed of enteric neurons and glia, and is mostly derived from migrating vagal neural crest cells. Trunk-derived Schwann cells also play a significant role in postnatal maintenance of the ENS. However, the diversity of the ENS in health and disease remains largely unknown. Here, we performed single cell RNA sequencing on pediatric controls and HSCR individuals, and identified two major classes of enteric glia, being canonical and Schwann-like enteric glia. We show that the latter are the main contributors of enteric glia heterogeneity after birth and importantly, that they are preserved in aganglionic segments of HSCR individuals. In a zebrafish model of HSCR, which also shows preservation of Schwann-like enteric glia, enteric neurogenesis could be stimulated, demonstrating a potential novel therapy for HSCR.

pathology↗

bioRxiv2021

An early Shh-H2O2 feedback loop controls the progression of the regenerative program during adult zebrafish fin regeneration

Reactive oxygen species (ROS), originally classified as toxic molecules, have attracted increasing interest given their actions in cell signaling. Among these molecules, Hydrogen peroxide (H2O2) is the major ROS produced by cells and acts as a second messenger to modify redox-sensitive proteins or lipids. After amputation, tight spatiotemporal regulation of ROS is required first for wound healing and later to initiate the regenerative program. However, the mechanisms carrying out this sustained ROS production and their integration with signaling pathways are still poorly understood. We focused on the early dialog between H2O2 and Sonic Hedgehog (Shh) during fin regeneration. We demonstrate that H2O2 controls Shh expression and that Shh in turn regulates the H2O2 level via a canonical pathway. Moreover, this tightly controlled feedback loop changes during the successive phases of the regenerative program. Dysregulation of the Hedgehog pathway has been implicated in several developmental syndromes, diabetes and cancer. These data support the existence of a very early feedback loop between Shh and H2O2 that might be more generally involved in various physiological or pathological processes. These new findings pave the way to improve regenerative processes, particularly in vertebrates.

developmental biology↗

bioRxiv2020

High concordance between hippocampal transcriptome of the intraamygdala kainic acid model and human temporal lobe epilepsy

ObjectivePharmacoresistance and the lack of disease-modifying actions of current anti-seizure drugs persist as major challenges in the treatment of epilepsy. Experimental models of chemoconvulsant-induced status epilepticus remain the models of choice to discover potential anti-epileptogenic drugs but doubts remain as to the extent to which they model human pathophysiology. The aim of the present study was to compare the molecular landscape of the intraamygdala kainic acid model of status epilepticus in mice with findings in resected brain tissue from patients with drug-resistant temporal lobe epilepsy (TLE). MethodsStatus epilepticus was induced via intraamygdala microinjection of kainic acid in C57BL/6 mice and gene expression analysed via microarrays in hippocampal tissue at acute and chronic time-points. Results were compared to reference datasets in the intraperitoneal pilocarpine and intrahippocampal kainic acid model and to human resected brain tissue (hippocampus and cortex) from patients with drug-resistant TLE. ResultsIntraamygdala kainic acid injection in mice triggered extensive dysregulation of gene expression which was [~]3-fold greater shortly after status epilepticus (2729 genes) when compared to epilepsy (412). Comparison to samples of patients with TLE revealed a particular high correlation of gene dysregulation during established epilepsy. Pathway analysis found suppression of calcium signalling to be highly conserved across different models of epilepsy and patients. CREB was predicted as one of the main up-stream transcription factors regulating gene expression during acute and chronic phases and inhibition of CREB reduced seizure severity in the intraamygdala kainic acid model. SignificanceOur findings suggest the intraamygdala kainic acid model faithfully replicates key molecular features of human drug-resistant temporal lobe epilepsy and provides potential rationale target approaches for disease-modification through new insights into the unique and shared gene expression landscape in experimental epilepsy. Key point boxO_LIMore genes show expression changes shortly following intraamygdala kainic acid-induced status epilepticus when compared to established epilepsy. C_LIO_LIThe intraamygdala kainic acid mouse model mimics closely the gene expression landscape in the brain of patients with temporal lobe epilepsy. C_LIO_LISupressed calcium signalling in the brain as common feature across experimental models of epilepsy and patients with temporal lobe epilepsy. C_LIO_LICREB is a major up-stream transcription factor during early changes following status epilepticus and once epilepsy is established. C_LI

neuroscience↗

bioRxiv2019

Large-scale changes to mRNA polyadenylation in temporal lobe epilepsy

The molecular mechanisms that shape the gene expression landscape during the development and maintenance of chronic states of brain hyperexcitability are incompletely understood. Here we show that cytoplasmic mRNA polyadenylation, a posttranscriptional mechanism for regulating gene expression, undergoes widespread reorganisation in temporal lobe epilepsy. Specifically, over 25% of the hippocampal transcriptome displayed changes in their poly(A) tail in mouse models of epilepsy, particular evident in the chronic phase. The expression of cytoplasmic polyadenylation binding proteins (CPEB1-4) was found to be altered in the hippocampus in mouse models of epilepsy and temporal lobe epilepsy patients and CPEB4 target transcripts were over-represented among those showing poly(A) tail changes. Supporting an adaptive function, CPEB4-deficiency leads to an increase in seizure severity and neurodegeneration in mouse models of epilepsy. Together, these findings reveal an additional layer of gene expression control during epilepsy and point to novel targets for seizure control and disease-modification in epilepsy.

neuroscience↗

bioRxiv2019

Multi-enhancer transcriptional hubs confer phenotypic robustness

We had previously shown in Drosophila melanogaster embryos that low-affinity Ultrabithorax (Ubx)-responsive shavenbaby (svb) enhancers drive robust expression using localized transcriptional environments and that active svb enhancers tended to colocalize, even when placed on different chromosomes (Tsai et al., 2017). Here, we test the hypothesis that these multi-enhancer \"hubs\" improve robustness by increasing transcription factor retention near transcription sites. Deleting a redundant enhancer from the svb locus led to reduced trichome numbers in embryos raised at elevated temperatures. Using high-resolution fluorescence microscopy, we observed lower Ubx concentration and transcriptional output in this deletion allele. Transcription sites of the full svb cis-regulatory region inserted into a different chromosome colocalized with the svb locus, increasing Ubx concentration, the transcriptional output of svb, and partially rescuing the phenotype. Thus, multiple enhancers could reinforce a local transcriptional hub to buffer against environmental stresses and genetic perturbations, providing a mechanism for phenotypical robustness.\n\nImpact statementMultiple enhancers in physical proximity can reinforce shared transcriptional \"hubs\" to retain transcription factors, providing a buffer during environmental stresses and genetic perturbations to preserve phenotypic robustness.

developmental biology↗

bioRxiv2019

Comparison Between Normobaric Hypoxia Altitude Simulation Test and Altitude Hypoxia Predictive Equations in Cystic Fibrosis Patients

BackgroundThe Hypoxia Altitude Simulation Test (HAST) is the Gold Standard to evaluate hypoxia in response to altitude and to decide on in-flight requirements for oxygen supplementation. Several equations are available to predict PaO2 in altitude (PaO2alt), but it remains unclear whether their predictive value is equivalent. We aimed to compare the results obtained by the available methods in a population of cystic fibrosis (CF) adults.\n\nMethodsEighty-eight adults (58 healthy controls and 30 CF patients) performed a spirometry followed by an HAST. HAST results were compared with the predicted PaO2alt made by five equations: 1st: PaO2alt= 0,410 x PaO2ground + 1,7652; 2nd: PaO2alt= 0,519 x PaO2ground + 11,855 x FEV1 (L) - 1,760; 3rd: PaO2alt= 0,453 x PaO2ground + 0,386 x FEV1 (%) + 2,44; 4th: PaO2alt= 0,88 + 0,68 x PaO2ground; 5th: PaO2alt= PaO2ground - 26,6.\n\nResultsNone of the controls required in-flight oxygen neither by HAST or by the five predictive equations. Eleven CF-patients had PaO2alt < 50 mmHg, accessed by HAST. The positive predictive value was 50% (1st), 87.5% (2nd and 3rd), 77.78% (4th) and 58.33% (5th). Areas under the curve were 78.95% (1st), 84.69% (2nd), 88.04% (3rd) and 78.95% (4th and 5th). FEV1 and PaO2ground were correlated with HAST results.\n\nConclusionsThe 3rd equation gave the best predictions in comparison with results obtained by HAST. However, because the individual differences found were substantial for all equations, we still recommend performing a HAST whenever possible to confidently access in-flight hypoxia and the need for oxygen.

pathology↗

bioRxiv2019

Impact of pterygium on the ocular surface and meibomian glands

PurposeTo analyze how ocular surface parameters correlate to pterygium and investigate the possible impact on tear film and meibomian glands.\n\nMethodswe investigated objective parameters of the ocular surface such as conjunctival hyperemia, tear film stability and volume, meibomian gland dysfunction, dry eye disease, corneal topography comparing healthy individuals and correlating with the pterygium clinical presentation.\n\nResultsA total of 83 patients were included. Corneal astigmatism induction was 2.65 {+/-} 2.52 D (0.4-11.8). The impact of pterygium on the ocular surface parameters compared to matched controls was seen in: conjunctival hyperemia (control 1.55{+/-}0.39/pterygium 2.14{+/-}0.69; p=0.0001), tear meniscus height (control 0.24{+/-}0.05 mm/pterygium 0.36{+/-}0.14mm; p 0.0002), meiboscore lower eyelid (control 0.29{+/-}0.64/pterygium 1.38{+/-}0.95; p 0.0001) and meiboscore upper eyelid (control 0.53{+/-}0.62/pterygium 0.98{+/-}0.75; p=0.0083). We found a high number of pterygium patients (88%) presented meibomian gland alterations. Interestingly, meibomian gland loss was coincident to the localization of the pterygium in 54% of the upper and 77% lower lids.\n\nConclusionPterygium greatly impacts on ocular surface by inducing direct alterations in the pattern of meibomian glands besides corneal irregularities, conjunctival hyperemia and lacrimal film alterations, inducing significant symptoms and potential signs of dysfunction.

epidemiology↗