Biology subjects

Simoes, P.

Publications and source records attributed to Simoes, P..

13 recordsLinked to original sources

bioRxiv2026

Connexin 30 mutation rescues high-frequency hearing, reduces gap junctional coupling and alters potassium currents in cochlear Deiters cells

The early-onset, high-frequency hearing loss phenotype of CD-1 mice is rescued by the A88V mutation of the connexin 30 gap-junctional protein, despite a reduced endocochlear potential (EP), which drives cochlear hair cell receptor potentials. The mutation enables organ of Corti (OoC) extracellular receptor potentials to be similar in size to those of sensitive-hearing CBA/J mice, presumably through increased OoC resistance, despite smaller intracellular outer hair cell (OHC) receptor potentials. Low-frequency hearing in CD-1Cx30A88V/A88V mice is impaired, compared with those of CBA/J and wild-type CD-1 mice. To investigate the cellular basis of OoC resistance increase and EP decrease, we made in situ electrophysiological measurements from Deiters cells (DCs) in the OoC of homozygous CD-1Cx30A88V/A88V mice. DCs contribute to the OHC cytoskeletal scaffold and cochlear K+ recycling, and are interconnected by syncytial junctions comprising connexins 30 and 26. Measurements from CD-1Cx30A88V/A88V mice were compared with those from wild-type CD-1 mice, with sensitive hearing below 12 kHz, and from the CBA/J strain. Syncytial junctional-coupling between DCs of CD-1Cx30A88V/A88V mice was weaker, input resistance greater, potassium current expression was modified, and voltage-sensitive activation was shifted to more negative values compared to those of CD-1 and CBA/J mice. Inactivating potassium currents dominate in DCs of CBA/J and CD-1Cx30A88V/A88V mice with excellent high-frequency hearing, and sustained currents dominate in DCs of CD-1 mice with early-onset hearing loss. These findings are discussed in relation to maintenance of OoC electrochemistry, rescue of early-onset hearing loss, impaired low-frequency hearing in CD-1Cx30A88V/A88V mice, and the basis of high-frequency hearing. KEY POINTS SUMMARYO_LIA88V mutation in gap-junctional protein Connexin 30 reshapes cochlear electrophysiology: The mutation increases organ of Corti resistance, raises Deiters cell input resistance, and weakens gap-junction coupling between supporting cells. Although it reduces endocochlear potential and low-frequency hearing, it preserves extracellular outer hair cell receptor potentials, rescuing high-frequency early-onset hearing loss in wild-type CD-1 mice. C_LIO_LIDeiters cell K+-conductances in mutants resemble those of the excellent-hearing CBA/J mice: Mutant CD-1 mice show potassium-channel properties nearly identical to CBA/J strain and distinct from wild-type CD-1 mice. These faster, more sensitive K+-conductances may enhance high-frequency hearing and support resistance to hearing loss. C_LIO_LIReduced gap-junction connectivity may protect against age-related hearing loss: Loss of heterotypic gap junctions and reduced supporting-cell connectivity may disrupt harmful feedback loops involved in noise-induced degeneration, explaining preserved high-frequency hearing in mutant CD-1 mice. C_LIO_LIOur findings provide bases for understanding mechanisms of high-frequency hearing and cochlear electrochemistry. C_LI

neuroscience↗

bioRxiv2026

Preserved CD4+ T cell helper function and coordinated antiviral immunity in people with HBV/HIV co-infection on long-term therapy

Background & AimsPeople with HBV/HIV co-infection on antiretroviral therapy achieve higher rates of HBV functional cure than those with HBV mono-infection, yet the immunological basis remains poorly characterised. HBV-specific CD4+ T cell responses are critical for viral control and functional cure but have been scarcely examined in HBV/HIV co-infection. Our previous studies in HBV/HIV co-infection demonstrated preserved stem-like CD8+ T cells and NK cell functional responses, but whether CD4+ T cell helper function is similarly maintained is unknown. MethodsWe analysed CD4+ T cell responses in 72 participants (HBV n=26, HBV/HIV n=24, HIV n=22) on suppressive antiviral therapy, using multiparameter flow cytometry, virus-specific CD4+ T cell functional assays and proliferation assays. ResultsPeople with HBV/HIV co-infection had significantly higher HBV envelope- and core-specific CD4+ T cell responses, with IL-2 production particularly discriminating between groups. CD4+ T cell responses to CEF (CMV, EBV, and Influenza) were comparable, confirming antigen specificity. Granzyme B-expressing cytotoxic CD4+ T cells and TCF-1+CD127+PD-1+CD4+ T cells were enriched in co-infection. CD4+ and CD8+ T cell responses were more frequently coordinated within donors in co-infection than in mono-infection (envelope 83% vs 50%; core 94% vs 60%), where they were more often uncoupled. IL-2 producing CD4+ T cells correlated with CD8+ T cell responses and the CD4:CD8 ratio in co-infection. HBV-specific proliferative capacity was enhanced in co-infection. ConclusionsPeople with HBV/HIV co-infection mount functional HBV-specific CD4+ T helper responses that are coordinated with CD8+ T cell immunity at the individual level. Together with our prior findings of preserved NK and CD8+ T cell responses in this cohort, these data identify treated HBV/HIV co-infection as a setting of integrated, rather than compromised, antiviral immunity. Impact and ImplicationsPeople with HBV/HIV co-infection can achieve HBV functional cure more frequently than people with HBV mono-infection, but the immune mechanisms remain unclear. This study shows that treated HBV/HIV co-infection is characterised by functional HBV-specific CD4 helper responses and coordinated CD4/CD8 antiviral immunity. These responses were most strongly associated with the CD4:CD8 ratio, a routinely available clinical marker, rather than with CD4 count alone. These findings argue that people with HBV/HIV co-infection should be prioritised in, not excluded from, HBV cure immunotherapy trials. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=90 SRC="FIGDIR/small/730166v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@89be79org.highwire.dtl.DTLVardef@13836bborg.highwire.dtl.DTLVardef@1915698org.highwire.dtl.DTLVardef@cc286c_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2026

Beyond Co-Existence: α-Synuclein Sequesters Amyloid-β42 into Distinct Hybrid Assemblies

Amyloid-{beta} (A{beta}) deposits often appear in Parkinson's disease and -synuclein (-syn) pathology in Alzheimer's disease. As soluble oligomers contribute importantly to cytotoxicity, their early crosstalk is critical to understand. Using all-atom molecular dynamics, we investigated how the initial oligomeric configuration of A{beta}42 shapes its early association with -syn, simulating -syn with (i) one A{beta}42 monomer, (ii) two separated monomers, and (iii) a pre-formed dimer plus a free monomer, across 15 independent 3 s trajectories. Association patterns depended strongly on the initial configuration. With monomeric or nascent dimeric A{beta}42, -syn frequently contacted the metal-binding, central hydrophobic core (CHC), and C-terminal regions, and these contacts were temporally coordinated, most reproducibly the -syn NAC with the A{beta}42 CHC and polar regions. {beta}-hairpin sampling was reduced specifically when -syn engaged the CHC and C-terminus, an interface-dependent rather than a general effect that did not track contact duration, and coincided with more expanded conformations. With a pre-formed dimer, -syn associated mainly peripherally, while the dimer's {beta}-structured interface remained comparatively stable. First-order dihedral entropy differed only modestly between the free and associated states, indicating that association redistributed conformational populations without globally reducing local backbone diversity. Overall, -syn's early structural effect on A{beta}42 is configuration-dependent: it engages and perturbs lower-order species while associating only peripherally with the sampled dimer.

biochemistry↗

bioRxiv2026

Bigger Isn't Always Better: Comparing System Size, Hydration, and Software for Lipid Membrane Analysis

The structural and dynamic properties of membranes are known to vary with bilayer size and hydration. While Molecular Dynamic (MD) simulations are a powerful tool for studying cellular membrane systems, the results can be sensitive to the analysis work-flow and software. In this study, all-atom MD simulations (500 ns) were conducted on systems of 256, 512, and 1024 POPC lipids at 40, 80, and 160 waters per lipid. With these simulations, a two-fold study was performed: (1) to assess the convergence of structural and dynamic properties of POPC bilayers as a function of membrane size and hydration level using CPPTRAJ (CPP), including area per lipid (APL), bilayer thickness, order parameter, headgroup orientation, and lateral diffusion, and (2) to compare the analysis output and performance of four software packages: CPP, GROMACS (GRO), MDAnalysis (MDA), and LiPyphilic (LiP). For the first objective, our results show that the average values of the bilayer thickness, order parameter, and headgroup orientation are largely independent of the size and hydration levels studied. In contrast, lateral diffusion coefficient was sensitive to both size and hydration. We found that increasing the system size primarily decreased the statistical variance of the APL and thickness. For the second objective, all four packages produced consistent results for APL and thickness, with the most significant discrepancy being a known artifact from the gmx order tool when applied to unsaturated carbons. Performance bench-marks identified CPP as the fastest serial tool for all properties, whereas parallelization benefited MDA and LiP in some metrics. These findings provide a practical roadmap, demonstrating that moderately sized systems (e.g., 256L), combined with an optimized tool such as CPP, offer an efficient workflow for membrane structural property analysis.

biophysics↗

bioRxiv2025

RT-qPCR Validation of Candidate Genes Underlying Thermal Adaptation in Drosophila subobscura

Understanding the genetic basis of thermal adaptation is essential in the face of global climate change. In this study, we validate candidate genes implicated in thermal adaptation previously identified through RNA-seq analysis of Drosophila subobscura populations experimentally evolved under a progressive warming regime. Using RT-qPCR, we assessed the directionality of gene expression changes--up- or downregulation--across warming and control populations from two latitudinal origins. Out of 27 candidate gene tests, 33.3% showed consistent expression patterns between RNA-seq and RT-qPCR. Our results suggest that effect size, rather than expression level alone, is a key factor driving successful validation. This should be considered when interpreting whole-transcriptome data, which can yield many candidate genes. Future studies should examine how different log2 fold-change thresholds between populations relate to the success rate of validating RNA-seq differential expression results, in order to improve the reliability of candidate gene lists.

evolutionary biology↗

bioRxiv2025

Long-term laboratory Drosophila populations prefer ancestral nutritional cues from the environment

Plasticity can help populations cope with environmental changes namely by exploring different ecological niches. Addressing plasticity for nutritional responses in a range of fruit hosts potentially used by Drosophila may be essential in predicting the capacity of insects to colonize new environments or return to ancestral ones. Here we test for differences in oviposition performance, reproductive success and juvenile viability in different host fruits in the colonizing species Drosophila subobscura Collin, and compare them with those of the laboratory maintenance medium to which populations adapted for [~]150 generations. We question: does Drosophila subobscura show plasticity associated with different fruit hosts? Is performance better in the long-term maintenance (control) medium? We observed a higher fecundity, reproductive success and juvenile viability of flies maintained in the fruit media versus the control, but no differences between fruits. Our experiment shows that long-term lab populations of Drosophila subobscura can still assess environmental cues of new substrates allowing for flexible adaptive plasticity to occur through increased fecundity and reproductive success in fruit hosts relative to the control conditions. Importantly, this ability was not lost during long-term evolution in a benign, homogeneous environment. Furthermore, the high performance across fruits reinforces its status as a generalist species and further attests its potential to colonize different ecological settings.

ecology↗

bioRxiv2024

Monandrous flies do remate: plastic and evolutionary consequences of heat exposure on mating behaviour and fertility in Drosophila subobscura

Recent work has reinforced the importance of fertility in predicting population persistence under global warming, especially male fertility. However, most studies on mating and reproductive performance have used as model organism polyandrous species, remaining unclear if and how will monandrous species respond. This is unfortunate as one could expect monandrous species to be particularly susceptible, given their inability to use sperm from multiple males to prevent reduced progeny production due to male sterility. It could be that monandrous females can overcome this toll in fertility by plastically changing their mating rate, or that monandrous populations evolve the ability to remate upon repeated exposure to heat. To test this, we studied the real-time evolution as well as the thermal plastic response of two geographically distinct populations of the monandrous species Drosophila subobscura after 45 generations evolving under a warming scenario. We assessed the impact of heat on male mating behaviour and fertility, as well as the impact of reduced male fertility on female mating behaviour and fertility. We found that in males the toll in mating behaviour due to heat can be recovered with time, whereas that in reproductive success cannot. On the other hand, females exposed to heat-stressed males significantly increased their remating rate, allowing to recover considerably their own reproductive success. Interestingly, most responses were plastic, with no striking effect of adaptation to warming nor of geographical origin. Our work brings new insights into the effects of heat on monandrous species and establishes a model to study how a shift in mating system may affect species ability to respond to climate change.

evolutionary biology↗

bioRxiv2024

Long-term dynamics of adaptation to a warming environment is dependent on historical background

Global warming is leading to worldwide biodiversity decline at a fast pace. Evolutionary responses may be crucial in allowing organisms to cope with prolonged effects of climate change. This urges the need for a better understanding of the dynamics of adaptation to warming environments. In particular, addressing how reproductive success evolves in deteriorating environments is extremely relevant, as this trait is more likely constrained at lower temperatures than upper physiological thermal limits. Experimental evolution under a warming environment can elucidate the potential of populations to respond to rapid environmental changes. The few studies following such framework lack analysis of long-term response. We here focus on the long-term thermal evolution of two Drosophila subobscura populations, from different European latitudes, under warming temperatures. We estimated the reproductive success of these populations in two test environments: the ancestral (control) and the warming environment after 39 and 52 generations of thermal evolution. We found that a relevant long-term adaptive response to warming temperatures can occur, but the pace of such response is slow. In addition, we observed contrasting responses in the ancestral environmental and differences in the evolutionary dynamics between populations of distinct histories, with those originally from higher latitude only showing an adaptive response under the to the warming environment regime in at a later generation. This study reinforces the need for long-term evolution experiments to fully reveal the potential for thermal response. It also highlights that the scrutiny of several populations in this context is needed for a measure of variation within a species. Accounting for these sources of variation - both temporal and spatial - will allow for more robust assessments of climate change responses.

evolutionary biology↗

bioRxiv2022

Biogeographical history shapes evolution of reproduction in a global warming scenario

Adaptive evolution might be critical for animal populations to thrive on the fast-changing natural environments. Ectotherms are particularly vulnerable to global warming and, although their limited coping ability has been suggested, few real-time evolution experiments have directly accessed their evolutionary potential. Here, we report a long-term experimental evolution study addressing the evolution of thermal reaction norms, after [~]30 generations under different thermal environments. We analyzed the evolutionary dynamics of Drosophila subobscura populations as a function of the thermally variable environments in which they evolved and their distinct biogeographical background. Our results showed clear differences between the historically differentiated populations: while the northern D. subobscura populations showed a temporal increase in performance at higher temperatures, their southern counterparts presented the opposite pattern. This suggests that the northern populations might be better equipped to cope with the current rising temperatures. Remarkably, no effect of thermal selection was found. The lack of a clear long-term adaptive response at higher temperatures after evolution under a global warming scenario raises concerns about the evolutionary potential of ectotherms. Our results highlight the complex nature of thermal responses in face of environmental heterogeneity and emphasize the importance of considering intra-specific variation in thermal evolution studies.

evolutionary biology↗

bioRxiv2021

A gap-junction mutation in the mouse cochlea reveals cochlear amplification is driven by outer hair cell extracellular receptor potentials

Cochlear amplification, whereby cochlear responses to low-to-moderate sound levels are amplified and compressed to loud sounds, is attributed to outer hair cell (OHC) electromotility driven by voltage changes across the OHC basolateral membranes due to sound-induced receptor-current modulation. Cochlear operation at high acoustic frequencies is enigmatic because the OHC intracellular receptor potential (RP) is severely attenuated at these frequencies. Clues to understanding the voltage control of OHC electromotility at different frequencies was provided by measurements from CD-1 mice with an A88V mutation of the gap-junction (GJ) protein connexin 30 (Cx30), which with Cx26, form heterogeneous GJs between supporting cells in the organ of Corti (OoC) and stria vascularis. The A88V mutation results in a smaller GJ conductance which may explain why the resistance across the OoC in CD-1Cx30A88V/A88V mutants is higher compared with wild-type mice. The endocochlear potential, which drives the OHC receptor current and, consequently, the OHC RPs, is smaller in CD-1Cx30A88V/A88V mutants. Even so, their high-frequency hearing sensitivity equals that of wild-type mice. Preservation of high-frequency hearing correlates with similar amplitude of extracellular receptor potentials (ERPs), measured immediately adjacent to the OHCs. ERPs are generated through OHC receptor current flow across the OoC electrical resistance, which is larger in CD-1Cx30A88V/A88V than in wild-type mice. Thus, smaller OHC receptor currents flowing across a larger OoC resistance in CD-1Cx30A88V/A88V mice may explain why their ERP magnitudes are similar to wild-type mice. It is proposed that the ERPs, which are not subject to low-pass electrical filtering, drive high-frequency cochlear amplification. Significance StatementCochlear amplification, whereby responses to low-to-moderate sound levels are amplified and those to loud sounds are compressed, is attributed to outer hair cell (OHC) electromotility. Electromotility is driven by voltage changes across the OHC basolateral membranes due to modulation of receptor current flow during sound-induced sensory hair bundle displacement. Mechanisms of high-frequency cochlear amplification remain to be elucidated. A mutation of the gap-junction protein connexin 30 decreases OHC intracellular receptor potentials in CD-1 mice. Instead of decreasing auditory sensitivity, the mutation rescues high-frequency hearing by causing OHC extracellular receptor potentials to be similar in amplitude to those of sensitive wild-type mice. It is proposed extracellular, not intracellular, potentials drive high-frequency OHC motility and cochlear amplification at high acoustic frequencies.

neuroscience↗

bioRxiv2021

No evidence for short-term evolutionary response to a warming environment in Drosophila

Adaptive evolution is key in mediating responses to climate change. Such evolution will expectedly lead to changes in the populations thermal reaction norm and improve their ability to cope with stressful conditions. Conversely, constraints of different nature might limit the adaptive response. Here, we test these expectations by performing a real-time evolution experiment in historically differentiated Drosophila subobscura populations. We address the phenotypic changes of flies evolving for nine generations in a daily fluctuating environment with average constant temperature, or a warming environment with increasing average and amplitude temperature across generations. Our results showed that (1) evolution under a global warming scenario has not led, so far, to a noticeable change in the thermal response; (2) historical background appears to be affecting the responses of populations under the warming environment, particularly at higher temperatures; (3) thermal reaction norms are trait-dependent: while lifelong exposure to low temperature decreases fecundity and productivity but not viability, high temperature causes negative transgenerational effects on productivity and viability, even though fecundity remains high. These findings raise concerns about the short-term efficiency of adaptive responses to the current changing climate.

evolutionary biology↗

bioRxiv2020

High developmental temperature leads to low reproduction despite adult temperature

Phenotypic plasticity can be an important tool in helping organisms to cope with changing thermal conditions and it may show an interdependency between life-stages. For instance, exposure to stressful temperatures during development can trigger a positive plastic response in adults. In this study, we analyse the thermal plastic response of laboratory populations of Drosophila subobscura, derived from two contrasting latitudes of the European cline. We measured fecundity characters in the experimental populations after exposure to five thermal treatments, with different combinations of developmental and adult temperatures (14{degrees}C, 18{degrees}C or 26{degrees}C). We ask whether (1) adult performance is enhanced (or reduced) by exposing flies to higher (or lower) temperatures during development only; (2) flies raised at lower temperatures outperform those developed at higher ones, supporting the "colder is better" hypothesis; (3) there is a cumulative effect on adult performance of exposing both juveniles and adults to higher (or lower) temperatures; (4) there is any evidence for historical effects on adult performance. Our main findings show that (1) higher developmental temperatures led to low reproductive performance regardless of adult temperature, while at lower temperatures reduced performance only occurred when cold conditions were persistent across juvenile and adult stage; (2) flies raised at lower temperatures did not always outperform those developed at other temperatures; (3) there was no (negative) cumulative effect of exposing both juveniles and adults to higher temperatures; (4) both latitudinal populations showed similar thermal plasticity patterns. The negative effect of high developmental temperature on reproductive performance, regardless of adult temperature, highlights the developmental stage as a critical and most vulnerable stage to climate change and associated heat waves.

evolutionary biology↗

bioRxiv2019

How phenotypic convergence arises in experimental evolution

Evolutionary convergence is a core issue in the study of adaptive evolution, as well as a highly debated topic at present. Few studies have analyzed this issue using a \"real-time\" or evolutionary trajectory approach. Do populations that are initially differentiated converge to a similar adaptive state when experiencing a common novel environment? Drosophila subobscura populations founded from different locations and years showed initial differences and variation in evolutionary rates in several traits during short-term ([~]20 generations) laboratory adaptation. Here we extend that analysis to 40 more generations to analyze (1) how differences in evolutionary dynamics between populations change between shorter and longer time spans, and (2) whether evolutionary convergence occurs after sixty generations of evolution in a common environment. We found substantial variation in longer-term evolutionary trajectories and differences between short and longer-term evolutionary dynamics. Though we observed pervasive patterns of convergence towards the character values of long-established populations, populations still remain differentiated for several traits at the final generations analyzed. This pattern might involve transient divergence, as we report in some cases, indicating that more generations should lead to final convergence. These findings highlight the importance of longer-term studies for understanding convergent evolution.

evolutionary biology↗