Biology subjects

Costa, R.

Publications and source records attributed to Costa, R..

16 recordsLinked to original sources

bioRxiv2026

Warming exacerbates fungal pathogenicity to drive physiological collapse and microbiome reorganization in octocorals

Corals are increasingly threatened by climate change, yet the interplay between ocean warming and fungal infection remains experimentally underexplored. Here, we demonstrate that thermal stress exacerbates the pathogenicity of the fungus Aspergillus sydowii, driving physiological collapse and functional reorganization in the octocoral Sclerophytum sp. We deployed a 34-day mesocosm heat-stress experiment and quantified performance, mortality, and taxonomic and functional microbiome shifts. Combined heat and fungal exposure proved highly lethal, causing 45% mortality compared to 7% under heat exposure alone. Re-isolation from diseased nubbins implicates A. sydowii as the causal agent. Metagenomic profiling indicated that physiological collapse was underpinned by a functional transition from mutualism to antagonism in the microbiome. Specifically, combined heat and fungal stress triggered a depletion of ankyrin- and WD40-repeat proteins - hallmarks of symbiotic stability - concurrent with a surge in genes involved in fungal cell wall degradation and secondary metabolite biosynthesis. While surviving holobionts recovered full photosynthetic efficiency after combined stress, their microbiomes did not revert to baseline. Instead, they assembled into a taxonomically distinct configuration characterized by enrichments of sulfate-reducers (Thermodesulfobacteriota) and thermotolerant phototrophs (Thermosynechococcales). This suggests that despite the rapid photosystem recovery, the holobiont retained a complex legacy of thermal and biotic stress across both its internal chemical microenvironment and its microbiome. These findings highlight the decoupled recovery processes of different holobiont components, demonstrating that even though some corals may survive severe climate-driven disease, they emerge as ecologically reorganized entities.

ecology↗

bioRxiv2026

Decellularized Small Intestine for Full Thickness Burn Wound Treatment

Treating extensive full-thickness burn wounds remains difficult in clinical practice because available donor skin is often limited, the risk of infection is high, and many standard dressings do not perform well when defects are large or structurally complex. These limitations have shifted attention to decellularized extracellular matrix (dECM) scaffolds, which can provide physical coverage while preserving biochemical cues that may support tissue repair. Based on this rationale, we designed a decellularization method that improves reagent penetration to produce a full-thickness porcine decellularized small intestine (dSI) scaffold for use in burn wound coverage. The protocol removed most cellular material while leaving low levels of detergent residue, and it maintained the native three-layer structure of the intestinal wall. Most key ECM components, such as collagen and glycosaminoglycans, were also retained. In this study, the dSI showed several properties relevant to burn care, capacity to absorb large amounts of fluid, water vapor transmission rates similar to those reported for skin, and resisted microbial penetration in vitro. From a mechanical standpoint, the scaffold retained anisotropic behaviour and remained stable under cyclic loading. This pattern indicates that it could withstand repeated deformation instead of acting like a fragile membrane. Degradation tests under enzymatic and oxidative conditions indicate that the material breaks down in a controlled way over a period that appears consistent with typical wound-healing timelines. In vitro assays indicated that the scaffold was cytocompatible, as human dermal fibroblasts and keratinocytes both attached to its surface and continued to proliferate. Cell responses differed depending on surface orientation, suggesting that preserved intestinal layers may shape cell behaviour in ways that are often missing in thinner or more uniform matrices. Overall, full-thickness dSI appears to act as a biologically active scaffold and shows mechanical properties that exceed those of many currently used burn dressings.

bioengineering↗

bioRxiv2025

BDNF-TrkB signaling promotes synaptic GluN2A-NMDA receptor expression and network hyperexcitability in cultured hippocampal neurons and during status epilepticus

Brain-derived neurotrophic factor (BDNF) is a key modulator of synaptic function, acting through activation of TrkB receptors. This neurotrophic factor mediates synaptic plasticity and plays an important role in epileptogenesis, but the underlying molecular mechanisms have not been fully elucidated. In this work, we investigated the role of BDNF-TrkB signaling in the regulation of synaptic GluN2A-containing NMDA receptors (NMDAR), and the impact on network synchronization in cultured hippocampal neurons. Incubation with BDNF increased the synaptic surface expression of GluN2A-containing NMDAR in rat hippocampal synaptoneurosomes and in cultured hippocampal neurons. The effect in the latter preparation was time-dependent and required new protein synthesis. Mechanistically, we identified a signaling cascade involving hnRNPK, the non-receptor tyrosine kinase Pyk2, and protein kinase C (PKC) as essential for mediating BDNF-induced upregulation in the synaptic expression of GluN2A-containing NMDAR. Knockdown of hnRNPK or Pyk2, pharmacological inhibition of PKC, or expression of a phosphorylation -deficient Pyk2 mutant abolished BDNF-induced synaptic surface accumulation of Glu2A. Moreover, Pyk2 phosphorylation at Y402 was necessary for both basal and BDNF-induced synaptic GluN2A expression. Functional multielectrode array (MEA) recordings showed that endogenous BDNF and GluN2A-containing NMDAR contributed to the increase in network activity in cultured hippocampal neurons evoked by stimulation with a cocktail including bicuculline, 4-aminopyridine, and glycine. Importantly, BDNF-TrkB signaling also mediated the upregulation in the hippocampal synaptic surface expression of GluN2A-containing NMDAR, as determined in rats subjected to the pilocarpine model of temporal lobe epilepsy, where increased GluN2A synaptic expression was observed and shown to be TrkB-dependent. These findings unveil a crucial BDNF/TrkB-PKC-Pyk2-hnRNPK signaling axis that regulates synaptic GluN2A levels and network excitability, offering novel insights into the molecular basis of synaptic plasticity.

neuroscience↗

bioRxiv2025

Cold-sensing TRP channels and temperature preference modulate ovarian development in the model organism Drosophila melanogaster

Temperature is perceived primarily via Transient Receptor Potential (TRP) channels, which are integral to the molecular machinery sensing environmental and cellular signals. Functional evidence of TRP channels involvement in regulating cold-induced developmental/reproductive responses remains scarce. Here we show that mutations affecting cold-sensing TRP channels antagonize the reduction of ovarian development induced by low temperatures (reproductive dormancy) in Drosophila melanogaster. More specifically, mutants for brv1, trp, and trpl significantly lowered dormancy levels at 12{degrees}C, and exhibited well-developed oocytes characterized by advanced vitellogenesis. Similarly, functional knockouts for norpA, a gene encoding a phospholipase C acting downstream to Trp and Trpl, exhibited a reduced dormancy response, suggesting that Ca2+ signalling is key to relaying cold-sensing stimuli during dormancy induction and maintenance. Finally, mutants with altered temperature preference (i.e. exhibiting impaired cold or warm avoidance) differentially responded to cold, either lowering or increasing dormancy levels. In summary, our phenotypic analysis provides functional evidence of developmental/reproductive modulation by specific cold-sensing TRP channels in Drosophila melanogaster, and indicates that temperature preference affects developmental processes. As the studied genes are highly conserved and have mammalian homologues, the potential implications of our findings for human metabolism and drug development are also discussed.

developmental biology↗

bioRxiv2024

Synaptic accumulation of GluN2B-containing NMDA receptors mediates the effects of BDNF-TrkB signalling on synaptic plasticity and in epileptogenesis

Brain-derived neurotrophic factor (BDNF) is a key mediator of synaptic plasticity and memory formation in the hippocampus. However, the BDNF-induced alterations in the glutamate receptors coupled to the plasticity of glutamatergic synapses in the hippocampus have not been elucidated. In this work we investigated the putative role of GluN2B-containing NMDA receptors in the plasticity of glutamatergic synapses induced by BDNF. Stimulation of hippocampal synaptoneurosomes with BDNF led to a significant time-dependent increase in the synaptic surface expression of GluN2B-containing NMDA receptors as determined by immunocytochemistry with colocalization with pre- (vesicular glutamate transporter) and post-synaptic markers (PSD95). Similarly, BDNF induced the synaptic accumulation of GluN2B-containing NMDA receptors at the synapse in cultured hippocampal neurons, by a mechanism sensitive to the PKC inhibitor G[O]6983. The effects of PKC may be mediated by phosphorylation of Pyk2, as suggested by western blot experiments analyzing the phosphorylation of the kinase on Tyrosine 402. GluN2B-containing NMDA receptors mediated the effects of BDNF in the facilitation of the early phase of long-term potentiation (LTP) of hippocampal CA1 synapses induced by {theta}-burst stimulation, since the effect of the neurotrophin was abrogated in the presence of the GluN2B inhibitor Co 101244. In the absence of BDNF, the GluN2B inhibitor did not effect LTP. Surface accumulation of GluN2B-containing NMDA receptors was also observed in hippocampal synaptoneurosomes isolated from rats subjected to the pilocarpine model of temporal lobe epilepsy, after reaching Status epilepticus, an effect that was inhibited by administration of the TrkB receptor inhibitor ANA-12. Together, these results show that the synaptic accumulation of GluN2B-containing NMDA receptors mediate the effects of BDNF in the plasticity of glutamatergic synapses in the hippocampus.

neuroscience↗

bioRxiv2024

Segregated basal ganglia output pathways correspond to genetically divergent neuronal subclasses

The basal ganglia control multiple sensorimotor behaviors though anatomically segregated and topographically organized subcircuits with outputs to specific downstream circuits. However, it is unclear how the anatomical organization of basal ganglia output circuits relates to the molecular diversity of cell types. Here, we demonstrate that the major output nucleus of the basal ganglia, the substantia nigra pars reticulata (SNr) is comprised of transcriptomically distinct subclasses that reflect its distinct progenitor lineages. We show that these subclasses are topographically organized within SNr, project to distinct targets in the midbrain and hindbrain, and receive inputs from different striatal subregions. Finally, we show that these mouse subclasses are also identifiable in human SNr neurons, suggesting that the genetic organization of SNr is evolutionarily conserved. These findings provide a unifying logic for how the developmental specification of diverse SNr neurons relates to the anatomical organization of basal ganglia circuits controlling specialized downstream brain regions.

neuroscience↗

bioRxiv2024

Chaotic dynamics for homeostatic hematopoiesis

Homeostatic hematopoiesis is a dynamical process, characterized by large variations (e.g., with coefficients of variation larger than 1) of cell quantities, cell proliferation rates, and extensive correlations/anticorrelations between cell types within the myeloid/lymphoid lineage, and between lineages. All cell types exhibit rare but synchronized bursts of proliferation in the bone marrow, blood and spleen. Through longitudinal study of the blood contents of healthy mice, we found that leukocyte fluctuations are ergodic yet subject to chaotic behaviors characterized by a broad spectrum of characteristic timescales. We then built a minimal mathematical model to capture these dynamical features of hematopoiesis (fluctuations, correlations, and chaos) and explain how the accumulation of B cells (e.g. during lymphoma development) would transition the blood cell dynamics from chaos to oscillations as observed clinically. Finally, we demonstrated the ubiquity of the correlated blood cell fluctuations by comparing mouse cohorts of different genetic backgrounds and ages.

immunology↗

bioRxiv2023

Cohesin complex oligomerization maintains end-tethering at DNA double-strand breaks

DNA double-strand breaks (DSB) must be repaired to ensure genome stability. Crucially, DSB ends must be kept together for timely repair. In Saccharomyces cerevisiae, two poorly understood pathways mediate DSB end-tethering. One employs the Mre11-Rad50-Xrs2 (MRX) complex to physically bridge DSB ends. Another requires the conversion of DSB ends into single-strand DNA (ssDNA) by Exo1, but the bridging proteins are unknown. We uncover that cohesin, its loader and Smc5/6 act with Exo1 to tether DSB ends. Remarkably, cohesin specifically impaired in oligomerization fails to tether DSB ends, revealing a new function for cohesin oligomerization. In addition to the known importance of sister chromatid cohesion, microscopy-based microfluidic experiments unveil a new role for cohesin in repair by ensuring DSB end-tethering. Altogether, our findings demonstrate that oligomerization of cohesin prevents DSB end separation and promotes DSB repair, revealing a novel mode of action and role for cohesin in safeguarding genome integrity.

molecular biology↗

bioRxiv2022

A neural model of proximity to reward

Throughout learning, refinement of cortical activity in cortex, a process termed "credit assignment", underlies the refinement of behavioral actions leading to reward. While previous research shows striatums role in linking behavior to reward, striatums role in linking the underlying behaviorally-relevant cortical activity to reward remains unclear. Leveraging a neuroprosthetic task while recording from the rat cortex and striatum, we demonstrate that the striatum encodes the dynamics of the proximity of cortical activity to reward. Such encoding was independent from external task feedback and emerged as cortical activity consolidated over learning, with dorsal and ventral striatum playing complementary yet distinct roles. Striatal activity thus constitutes a neural model of cortical progress towards reward, suggesting one mechanism by which the brain implements credit assignment to refine behavior.

neuroscience↗

bioRxiv2021

Ancestral contributions to contemporary European complex traits

The contemporary European genetic makeup formed in the last 8000 years as the combination of three main genetic components: the local Western Hunter-Gatherers, the incoming Neolithic Farmers from Anatolia and the Bronze Age component from the Pontic Steppes. When meeting into the post-Neolithic European environment, the genetic variants accumulated during their three distinct evolutionary histories mixed and came into contact with new environmental challenges. Here we investigate how this genetic legacy reflects on the complex trait landscape of contemporary European populations, using the Estonian Biobank as a case study. For the first time we directly connect the phenotypic information available from biobank samples with the genetic similarity to these ancestral groups, both at a genome-wide level and focusing on genomic regions associated with each of the 27 complex traits we investigated. We also found SNPs connected to pigmentation, cholesterol, sleep, diastolic blood pressure, and body mass index (BMI) to show signals of selection following the post Neolithic admixture events. We recapitulate existing knowledge about pigmentation traits, corroborate the connection between Steppe ancestry and height and highlight novel associations. Among others, we report the contribution of Hunter Gatherer ancestry towards high BMI and low blood cholesterol levels. Our results show that the ancient components that form the contemporary European genome were differentiated enough to contribute ancestry-specific signatures to the phenotypic variability displayed by contemporary individuals in at least 11 out of 27 of the complex traits investigated here.

genomics↗

bioRxiv2021

Differences between intrinsic and acquired nucleoside analogue resistance in acute myeloid leukaemia cells

BackgroundSAMHD1 mediates resistance to anti-cancer nucleoside analogues, including cytarabine, decitabine, and nelarabine that are commonly used for the treatment of leukaemia, through cleavage of their triphosphorylated forms. Hence, SAMHD1 inhibitors are promising candidates for the sensitisation of leukaemia cells to nucleoside analogue-based therapy. Here, we investigated the effects of the cytosine analogue CNDAC, which has been proposed to be a SAMHD1 substrate, in the context of SAMHD1. MethodsCNDAC was tested in 13 acute myeloid leukaemia (AML cell lines), in 26 acute lymphoblastic leukaemia cell lines, ten AML sublines adapted to various antileukaemic drugs, 24 single cell-derived clonal AML sublines, and primary leukaemic blasts from 24 AML patients. Moreover, 24 CNDAC-resistant sublines of the AML cell lines HL-60 and PL-21 were established. The SAMHD1 gene was disrupted using CRISPR/Cas9 and SAMHD1 depleted using RNAi, and the viral Vpx protein. Forced DCK expression was achieved by lentiviral transduction. SAMHD1 promoter methylation was determined by PCR after treatment of genomic DNA with the methylation-sensitive HpaII endonuclease. Nucleoside (analogue) triphosphate levels were determined by LC-MS/MS. CNDAC interaction with SAMHD1 was analysed by an enzymatic assay and by crystallisation. ResultsAlthough the cytosine analogue CNDAC was anticipated to inhibit SAMHD1, SAMHD1 mediated intrinsic CNDAC resistance in leukaemia cells. Accordingly, SAMHD1 depletion increased CNDAC triphosphate (CNDAC-TP) levels and CNDAC toxicity. Enzymatic assays and crystallisation studies confirmed CNDAC-TP to be a SAMHD1 substrate. In 24 CNDAC-adapted acute myeloid leukaemia (AML) sublines, resistance was driven by DCK (catalyses initial nucleoside phosphorylation) loss. CNDAC-adapted sublines displayed cross-resistance only to other DCK substrates (e.g. cytarabine, decitabine). Cell lines adapted to drugs not affected by DCK or SAMHD1 remained CNDAC sensitive. In cytarabine-adapted AML cells, increased SAMHD1 and reduced DCK levels contributed to cytarabine and CNDAC resistance. ConclusionIntrinsic and acquired resistance to CNDAC and related nucleoside analogues are driven by different mechanisms. The lack of cross-resistance between SAMHD1/ DCK substrates and non-substrates provides scope for next-line therapies after treatment failure.

pharmacology and toxicology↗

bioRxiv2021

Sir3 Heterochromatin Protein Promotes NHEJ by Direct Inhibition of Sae2

Heterochromatin is a conserved feature of eukaryotic chromosomes, with central roles in gene expression regulation and maintenance of genome stability. How heterochromatin proteins regulate DNA repair remains poorly described. In Saccharomyces cerevisiae, the Silent Information Regulator (SIR) complex assembles heterochromatin-like chromatin at subtelomeres. SIR-mediated repressive chromatin limits double strand break (DSB) resection protecting damaged chromosome ends during HR. As resection initiation marks the cross-road between repair by non-homologous end joining (NHEJ) or HR, we asked whether SIR- mediated heterochromatin regulates NHEJ. We show that SIRs promote NHEJ through two pathways, one depending on repressive chromatin assembly, and the other relying on Sir3 in a manner that is independent of its heterochromatin-promoting function. Sir3 physically interacts with Sae2 and this interaction impairs Sae2-dependent MRX functions. As a consequence, Sir3 limits Mre11-mediated resection, delays MRX removal from DSB ends and promotes NHEJ.

genetics↗

bioRxiv2020

Expression of Castanea crenata Allene Oxide Synthase in Arabidopsis Improves the Defense to Phytophthora cinnamomi

Allene oxide synthase (AOS) is a key enzyme of the jasmonic acid (JA) signaling pathway. The AOS gene was previously found to be upregulated in an Asian chestnut species resistant to infection by the oomycete Phytophthora cinnamomi (Castanea crenata), while lower expression values were detected in the susceptible European chestnut (Castanea sativa). Here, we report a genetic and functional characterization of the C. crenata AOS (CcAOS) upon its heterologous gene expression in a susceptible ecotype of Arabidopsis thaliana, which contains a single AOS gene. It was found that Arabidopsis plants expressing CcAOS delay pathogen progression and exhibit more vigorous growth in its presence. They also show upregulation of jasmonic acid and salicylic acid-related genes. As in its native species, heterologous CcAOS localized to plastids, as revealed by confocal imaging of the CcAOS-eGFP fusion protein in transgenic Arabidopsis roots. This observation was confirmed upon transient expression in Nicotiana benthamiana leaf epidermal cells. To further confirm a specific role of CcAOS in the defense mechanism against the pathogen, we performed crosses between transgenic CcAOS plants and an infertile Arabidopsis AOS knockout mutant line. It was found that plants expressing CcAOS exhibit normal growth, remain infertile but are significantly more tolerant to the pathogen than wild type plants. Together, our results indicate that CcAOS is an important player in plant defense responses against oomycete infection and that its expression in susceptible varieties may be a valuable tool to mitigate biotic stress responses. One-sentence summaryHeterologous expression of the Castanea crenata allene oxide synthase gene in Arabidopsis thaliana improves the defense response to the pathogen Phytophthora cinnamomi.

plant biology↗

bioRxiv2020

Targeting pentose phosphate pathway for SARS-CoV-2 therapy

It becomes more and more obvious that deregulation of host metabolism play an important role in SARS-CoV-2 pathogenesis with implication for increased risk of severe course of COVID-19. Furthermore, it is expected that COVID-19 patients recovered from severe disease may experience long-term metabolic disorders. Thereby understanding the consequences of SARS-CoV-2 infection on host metabolism can facilitate efforts for effective treatment option. We have previously shown that SARS-CoV-2-infected cells undergo a shift towards glycolysis and that 2-deoxy-D-glucose (2DG) inhibits SARS-CoV-2 replication. Here, we show that also pentose phosphate pathway (PPP) is remarkably deregulated. Since PPP supplies ribonucleotides for SARS-CoV-2 replication, this could represent an attractive target for an intervention. On that account, we employed the transketolase inhibitor benfooxythiamine and showed dose-dependent inhibition of SARS-CoV-2 in non-toxic concentrations. Importantly, the antiviral efficacy of benfooxythiamine was further increased in combination with 2DG.

microbiology↗

bioRxiv2020

Isolation and genome sequencing of 14 Spongia sp. bacterial associates expands the taxonomic and functional breadth of the cultivatable marine sponge microbiome

Marine sponges live with complex microbial consortia, which have been considered as potential sources of novel natural products. However, the usual recalcitrance of host-associated microorganisms to cultivation makes studying sponge symbionts challenging. To tackle this complexity, exploration of cultivated sponge-associated bacteria and their coding potential is unavoidable. In this study, we isolate and report the draft genome sequences of 14 bacterial strains from the marine sponge Spongia sp. using R2A and VXA media. The strains belong to the classes Actinobacteria, Gammaproteobacteria, Alphaproteobacteria, and Cytophagia spanning 11 formally described genera plus two potentially novel genera in the Rhodobacteraceae family and one potentially novel family in the Cytophagales order. Functional genomics revealed presumed symbiosis factors typical of specific taxonomic groups (i.e. taurine metabolism genes among the Alphaproteobacteria, chitinase encoding genes and eukaryotic-like proteins in the Cytophagia genome) while multidrug efflux pumps, also important in host-microbe interactions, were common across all genomes. Moreover, we detected 76 secondary-metabolite biosynthetic gene clusters putatively involved in the production of drug-like compounds or signalling molecules across all genomes, warranting future biotechnologically driven research into their coding potential.

microbiology↗

bioRxiv2018

Transient fibrosis resolves via fibroblast inactivation in the regenerating zebrafish heart

In the zebrafish (Danio rerio), regeneration and fibrosis after cardiac injury are not mutually exclusive responses. Upon cardiac cryoinjury, collagen and other extracellular matrix (ECM) proteins accumulate at the injury site. However, in contrast to the situation in mammals, fibrosis is transient in zebrafish and its regression is concomitant with regrowth of the myocardial wall. Little is known about the cells producing this fibrotic tissue or how it resolves. Using novel genetic tools to mark periostin b- and collagen 1alpha2 (col1a2)-expressing cells in combination with transcriptome analysis, we explored the sources of activated fibroblasts and traced their fate. We describe that during fibrosis regression, fibroblasts are not fully eliminated, but become inactivated. Unexpectedly, limiting the fibrotic response by genetic ablation of col1a2-expressing cells impaired cardiomyocyte proliferation. We conclude that ECM-producing cells are key players in the regenerative process and suggest that anti-fibrotic therapies might be less efficient than strategies targeting fibroblast inactivation.\n\nSCIENTIFIC STATEMENTAfter myocardial infarction in the mammalian heart, millions of cardiomyocytes are lost and replaced by fibrotic scar tissue. While fibrosis is persistent in adult mammals, there are some vertebrates, including zebrafish, with the capacity for regeneration. This process does not occur in the absence of fibrosis. Here we studied subpopulations of collagen producing cells and analyzed their fate after complete regeneration of the zebrafish myocardium. Our data show that fibroblasts persisted in the regenerated heart, but shut down the profibrotic program. While fibrosis could be considered as detrimental to the regeneration process, our study reveals a positive effect on cardiomyocyte proliferation. Accordingly, a fibrotic response can be beneficial for heart regeneration.

developmental biology↗