Biology subjects

Rossi, S.

Publications and source records attributed to Rossi, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Towards coevolution-aware ancestral sequence reconstruction

Ancestral sequence reconstruction (ASR) is a powerful approach for studying molecular evolution and the emergence of protein function. Yet most ASR methods assume that sites evolve independently, neglecting the epistatic constraints that shape protein structure, stability, and function. This simplification affects both ancestral inference and its evaluation: maximum-a-posteriori reconstructions may over-concentrate probability into a single over-idealized sequence, whereas independent posterior sampling can generate implausible or poorly functional ancestors. Here, we introduce a coevolution-aware ASR framework that combines standard phylogenetic inference with Direct Coupling Analysis (DCA), thereby preserving site-wise ancestral uncertainty while enforcing residue-residue constraints learned from extant protein families. To benchmark the method, we develop a controlled forward-evolution framework based on a DCA evolutionary sampler, allowing reconstructed ancestors to be compared with known ground-truth sequences generated under realistic epistatic constraints. Applied to {beta}-lactamases and DNA-binding domains, the approach improves reconstruction when ancestral states are epistatically constrained, and yields ensembles of candidate ancestors that are both phylogenetically consistent and statistically compatible with natural protein families. This framework bridges the gap between single-sequence MAP reconstruction and unconstrained posterior sampling, providing a practical route toward ancestral reconstructions that better reflect the coupled nature of protein evolution. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=106 SRC="FIGDIR/small/731024v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@1248f23org.highwire.dtl.DTLVardef@13176b5org.highwire.dtl.DTLVardef@688789org.highwire.dtl.DTLVardef@9a66df_HPS_FORMAT_FIGEXP M_FIG Graphical abstract Our procedure works as follows: we take as input a Multiple Sequence Alignment of extant sequences [D]extant, and infer in parallel both a phylogenetic tree[T] (phylogenetic signal) and a Direct Coupling Analysis model of coevolution (generative model with energy EDCA). The two models are then combined to form a general, coevolution-aware framework for Ancestral Sequence Reconstruction, which can be benchmarked against in silico data generated by the DCA forward evolver. C_FIG

evolutionary biology↗

bioRxiv2026

Modeling Protein Evolution via Generative Inference From Monte Carlo Chains to Population Genetics

Generative models derived from large protein sequence alignments define complex fitness landscapes, but their utility for accurately modeling non-equilibrium evolutionary dynamics remains unclear. In this work, we perform a rigorous comparative analysis of three simulation schemes, designed to mimic evolution in silico by local sampling of the probability distribution defined by a generative model. We compare standard independent Markov Chain Monte Carlo, Monte Carlo on a phylogenetic tree, and a population genetics dynamics, benchmarking their outputs against deep sequencing data from four distinct in vitro evolution experiments. We find that standard Monte Carlo fails to reproduce the correct phylogenetic structure and generates unrealistic, gradual mutational sweeps. Performing Monte Carlo on a tree inferred from data improves phylogenetic fidelity and historical accuracy. The population genetics scheme successfully captures phylogenetic correlations, mutational abundances, and selective sweeps as emergent properties, without the need to infer additional information from data. However, the latter choice come at the price of not sampling the proper generative model distribution at long times. Our findings highlight the crucial role of phylogenetic correlations and finite-population effects in shaping evolutionary trajectories on fitness landscapes. These models therefore provide powerful tools for predicting complex adaptive paths and for reliably extrapolating evolutionary dynamics beyond current experimental limitations.

evolutionary biology↗

bioRxiv2026

Distinct cortical excitability and connectivity profiles within the human SMA complex

Introduction and aimUnderstanding brain functions increasingly relies on a network-based perspective, emphasizing interactions across distributed regions. High-order cognitive functions, like language and executive processes, engage such networks rather than isolated cortical areas, yet mapping their dynamics in humans remains challenging. The supplementary motor area (SMA) complex serves as a crucial hub, functioning as an interface between cognitive and sensorimotor processing. Navigated transcranial magnetic stimulation combined with electroencephalography (TMS-EEG) enables causal, time-resolved assessment of cortical excitability and connectivity with high temporal and spatial precision. Extending prior proof-of-concept work, this study aims to provide normative neurophysiological signatures of the SMA complex (pre-SMA and SMA). MethodsTwenty-one healthy subjects underwent a TMS-EEG session where six stimulation targets over the SMA complex (three in pre-SMA, one in the border between pre-SMA and SMA, two in SMA) were recorded. Global cortical excitability via global mean field power (GMFP) was computed over three time-windows (10-50, 50-100, and 100-200 ms) and compared across targets. Normalized power in different frequency bands (, {beta}1, {beta}2, {gamma}) and natural frequency (NF) were also computed and compared across stimulation sites. Then, we calculated tractography-derived connectivity metrics to examine corticothalamic projections from each stimulation site. Apparent fiber density (AFD)-derived connection strength quantified intra-axonal fibre volume along pathways to the whole thalamus, whereas fibre bundle capacity (FBC) assessed the aggregate intra-axonal cross-sectional area at pathway endpoints, providing an estimate of information transmission capacity to each of the 23 thalamic nuclei. ResultsCortical excitability and oscillatory properties varied significantly across TMS targets. A gradient in cortical excitability was observed, where anterior and middle portions of pre-SMA exhibited significantly lower GMFP in the early post-stimulus phase (i.e., 10-50 ms) than SMA portions; interestingly, these differences were clearly dampened in a later time-window (50-100 ms) and disappeared after this period. Furthermore, higher and lower {beta}2 power were observed in anterior pre-SMA than posterior pre-SMA portions. No differences were observed in NF. Crucially, we also observed significant differences in whole- and single-nuclei thalamic structural connectivity. DiscussionThese findings provide direct human in vivo evidence for distinct neurophysiological and structural connectivity profiles of the pre-SMA and SMA, possibly reflecting their different cytoarchitectonic, myeloarchitectonic and connectivity properties. Variations in cortical excitability, oscillatory dynamics, and FBC along the rostro-caudal axis may mirror functional specialization, with pre-SMA supporting cognitive control processes and SMA engaging motor-related thalamocortical networks. Together, the results demonstrate the sensitivity of TMS-EEG and diffusion-weighted connectomics to measure fine-grained neurophysiological differences of corticothalamic projections, which can lead to individualized neuromodulation targeting.

neuroscience↗

bioRxiv2025

ACTION ENHANCEMENT DRIVES THE EMBODIMENT OF A SUPERNUMERARY ROBOTIC DIGIT

Wearable robotic supernumerary limbs enhance motor capabilities by leveraging principles from both engineering and neuroscience. Despite extensive research, how supernumerary limbs become embodied and the relationship between embodiment and artificially enhanced action possibilities remain largely unexplored. This gap has implications for device design and clinical adoption, as embodiment likely promotes patients acceptance and daily use of their supernumerary limb. Using an adapted proprioceptive drift paradigm from rubber hand illusion research, we investigated the embodiment of a robotic Soft Sixth Finger (SSF). Participants performed grasp-to-lift actions versus mere lift actions without object interaction, wearing the SSF on two different configurations: the palm and back of the hand. The Palm condition involved achievable actions without the SSF, while the Dorsal condition enabled otherwise anatomically impossible actions, extending beyond the physiological motor repertoire. Hand proprioceptive drift was measured before and after each task. Results showed that the SSF impacted body representation only when dorsally mounted. Proprioceptive drift was significantly higher for grasp-to-lift actions in Dorsal versus Palm conditions and higher for grasp-to-lift versus mere lift in the Dorsal condition only. This proves that SSF embodiment relates to extending, rather than substituting, users action possibilities. Future research must integrate behavioral, cognitive, and neural measurements across healthy and patient populations. Our study provides an ideal model for clinical application, demonstrating how enabling otherwise impossible actions drives robotic supernumerary finger embodiment.

neuroscience↗

bioRxiv2025

Ubiquitin-dependent degradation of p21Waf1/Cip1 is mediated by AMBRA1 to limit DNA replication stress

The cell cycle is a fundamental process that orchestrates the events that lead to cell replication and division. AMBRA1 is a scaffold factor that interacts with the E3 ubiquitin ligase CRL4-DDB1 complex to regulate the stability of cyclin D-type proteins, key regulators of the G1/S phase transition. However, how cells complete S-phase and coordinate the speed of DNA synthesis is still to be fully elucidated. Here we demonstrate that AMBRA1 affects the turnover of p21Waf1/Cip1 and p27Kip1, by coupling the CRL4-DDB1 complex directly to these proteins. In the absence of AMBRA1, the increased stability of p21Waf1/Cip1, rather than p27Kip1, resulted in the accumulation of replication stress by leaving under-replicated DNA during the S phase. We also found that AMBRA1-depleted cells with consequent high p21Waf1/Cip1 are sensitive to the inhibition of lagging-strand DNA synthesis. Of clinical relevance, low levels of AMBRA1 in Sonic-Hedgehog medulloblastoma correlate with a worse prognosis, suggesting that AMBRA1 expression levels could be an informative criterion for patient stratification and treatment.

molecular biology↗

bioRxiv2025

Functional bottlenecks can emerge from non-epistatic underlying traits

Protein fitness landscapes frequently exhibit epistasis, where the effect of a mutation depends on the genetic context in which it occurs, i.e., the rest of the protein sequence. Epistasis increases landscape complexity, often resulting in multiple fitness peaks. In its simplest form, known as global epistasis, fitness is modeled as a non-linear function of an underlying additive trait. In contrast, more complex epistasis arises from a network of (pairwise or many-body) interactions between residues, which cannot be removed by a single non-linear transformation. Recent studies have explored how global and network epistasis contribute to the emergence of functional bottlenecks - fitness landscape topologies where two broad high-fitness basins, representing distinct phenotypes, are separated by a bottleneck that can only be crossed via one or a few mutational paths. Here, we introduce and analyze a stylized model of global epistasis with an additive underlying trait. We demonstrate that functional bottlenecks arise with high probability if the model is properly calibrated. Furthermore, our results underscore that a proper balance between neutral and non-neutral mutations is needed for the emergence of functional bottlenecks. Author SummaryA central challenge in the study of protein evolution is understanding how interactions between mutations in-fluence evolutionary dynamics. These interactions, collectively known as epistasis, play a key role in shaping protein fitness landscapes, representing maps between amino acid sequences and their functional performance. However, the impact of epistasis on landscape ruggedness and accessibility remains a subject of debate. Recent experiments have revealed the existence of functional bottlenecks: regions of low fitness that restrict evolutionary transitions between proteins with different functionalities. While these bottlenecks represent a significant constraint on evolutionary outcomes and are often attributed to complex networks of interacting mutations, we demonstrate that they can arise in a much simpler setting. Using a stylized model where fitness depends nonlinearly on an underlying additive trait, we show that functional bottlenecks do not require complex network epistasis. Instead, they can emerge from the inherent variability of the mutational effect distribution. Specifically, these bottlenecks arise when the mutational landscape is dominated by small, nearly neutral effects, but remains punctuated by enough strongly non-neutral mutations to create sharp fitness transitions. Our findings offer a new perspective on the constraints shaping protein evolution and highlight the critical role of mutational effect hetero-geneity in determining evolutionary accessibility.

evolutionary biology↗

bioRxiv2025

Multiple orthoflaviviruses secrete sfRNA in mosquito saliva to promote transmission by inhibiting MDA5-mediated early interferon response

Numerous orthoflaviviruses transmitted through the bites of different mosquito species infect more than 500 million people annually. Skin infection at the bite site represents a critical and conserved step in transmission and a deeper understanding of this process will promote the design of broad-spectrum interventions to address diverse orthoflavivirus health threats. Here, we identify and characterize a transmission-enhancing viral factor in mosquito saliva that is shared across orthoflaviviruses. Saliva from West Nile virus-infected Culex and Zika virus-infected Aedes contains a viral non-coding RNA, subgenomic flaviviral RNA (sfRNA), within lipid vesicles distinct from virions. Higher concentration of sfRNA in infectious saliva positively correlates with infection intensity in human cells and skin explants. Early sfRNA delivery into transmission-relevant skin cell types and human skin explant demonstrate that sfRNA is responsible for the infection enhancement. Co-inoculation of sfRNA in a mouse model of transmission enhanced skin infection and worsened disease severity, supporting the role of salivary sfRNA as a transmission-enhancer. Mechanistically, salivary sfRNA attenuates early interferon response in human skin cells and skin explants by disrupting MDA5 signaling. Our results, derived from two distinct orthoflaviviruses and supported by prior studies, establish salivary sfRNA as a pan-orthoflavivirus transmission-enhancing factor driven by a conserved viral non-coding RNA.

immunology↗

bioRxiv2024

Fluctuations and the limit of predictability in protein evolution

Protein evolution involves mutations occurring across a wide range of time scales. In analogy with disordered systems in statistical physics, this dynamical heterogeneity suggests strong correlations between mutations happening at distinct sites and times. To quantify these correlations, we examine the role of various fluctuation sources in protein evolution, simulated using a data-driven energy landscape as a proxy for protein fitness. By applying spatio-temporal correlation functions developed in the context of disordered physical systems, we disentangle fluctuations originating from the initial condition, i.e. the ancestral sequence from which the evolutionary process originated, from those driven by stochastic mutations along independent evolutionary paths. Our analysis shows that, in diverse protein families, fluctuations from the ancestral sequence predominate at shorter time scales. This allows us to identify a time scale over which ancestral sequence information persists, enabling its reconstruction. We link this persistence to the strength of epistatic interactions: ancestral sequences with stronger epistatic signatures impact evolutionary trajectories over extended periods. At longer time scales, however, ancestral influence fades as epistatically constrained sites evolve collectively. To confirm this idea, we apply a standard ancestral sequence reconstruction algorithm and verify that the time-dependent recovery error is influenced by the properties of the ancestor itself. Overall, our results reveal that the properties of ancestral sequences--particularly their epistatic constraints--influence the initial evolutionary dynamics and the performance of standard ancestral sequence reconstruction algorithms.

evolutionary biology↗

bioRxiv2024

Cytoplasmic accumulation of a splice variant of hnRNP A2/B1 contributes to FUS-associated toxicity in a mouse model of ALS

Genetic and experimental findings point to a crucial role of RNA dysfunction in the pathogenesis of Amyotrophic Lateral Sclerosis (ALS). Evidence suggests that mutations in RBPs such as FUS, a gene associated with ALS, affect the regulation of alternative splicing. We have previously shown that the overexpression of wild-type FUS in mice, a condition that induces ALS-like phenotypes, impacts the splicing of hnRNP A2/B1, a protein with key roles in RNA metabolism, suggesting that a pathological connection between FUS and hnRNP A2/B1 might promote FUS-associated toxicity. Here we report that the expression and distribution of different hnRNP A2/B1 splice variants are modified in the affected tissues of mice overexpressing wild-type FUS. Notably, degenerating motor neurons are characterized by the cytoplasmic accumulation of splice variants of hnRNP A2/B1 lacking exon 9 (hnRNP A2b/B1b). In vitro studies show that exon 9 skipping affects the nucleocytoplasmic distribution of hnRNP A2/B1, promoting its localization into stress granules (SGs), and demonstrate that cytoplasmic localization is the primary driver of hnRNP A2b recruitment into SGs and cell toxicity. Finally, boosting exon 9 skipping using splicing switching oligonucleotides exacerbates disease phenotypes in wild-type FUS mice. Altogether, these findings reveal that alterations of the nucleocytoplasmic distribution of hnRNP A2/B1, driven by FUS-induced splicing changes, likely contribute to motor neuron degeneration in ALS.

neuroscience↗

bioRxiv2024

Temperature effects on interspecific eavesdropping in the wild

Mating signals are targets of conspecific signal recognition and sexual selection, but are also subject to abiotic temperature effects and to biotic interspecific eavesdroppers. In crickets, the male calling song becomes faster at warmer temperatures, and female crickets recognition of male song tracks temperature in a coordinated manner, termed temperature coupling. But female crickets are not the only ecologically relevant listeners: some cricket species are parasitized by Ormia ochracea, a parasitoid fly which finds its cricket hosts by eavesdropping on male cricket song. How temperature affects parasitoid fly phonotaxis to song is largely unexplored, with only one previous study conducted under field conditions. Here we explore six possible patterns of thermal effects on fly responses to cricket song, including temperature coupling, using field playbacks of synthetic Gryllus lineaticeps songs designed to be species-typical at various temperatures. We find that temperature does affect fly response, but that the temperature deviation of songs from ambient does not impact numbers of flies caught. We extend this finding by comparing the temperatures of the air and ground to show that temperature coupling is unlikely to be effective given microhabitat variation and differential rates of cooling in the evening hours when flies are most active. Our results can be interpreted more broadly to suggest (i) temperature effects on intraspecific communication systems may be more tightly coupled than are effects on interspecific eavesdropping, and (ii) variation in thermal microhabitats in the field make it difficult to translate laboratory physiological responses to natural selection in the wild. Lay SummaryMating signals and signal recognition change with temperature, and sometimes mating signals are intercepted by predators or parasites. By using playbacks of cricket song in the wild, we show that temperature changes do affect the response of a parasitoid fly to cricket song. However, parasitoid responses are not tightly coupled to temperature induced changes in cricket song, in part due to unpredictable variation in microhabitat temperatures typical of crickets and flies.

animal behavior and cognition↗

bioRxiv2023

A subset of CD4+ effector memory T cells limit immunity to pulmonary viral infection and prevent tissue pathology via activation of latent TGFβ

A rapid immune response to pathogen re-exposure underpins immunological memory, with protection against divergent pathogens such as heterologous or novel viral strains requiring cross-reactive memory T cells. Understanding the pathways that control memory T cell function is therefore important for the rational design of viral vaccines and will aid the discovery of therapies to boost anti-viral immunity. Here, we identify a sub-population of memory T cells that limit secondary immune responses to viral re-infection, which is crucial in preventing host tissue damage. We show that a population of CD4+ effector memory T (TEM) cells activate the important immunoregulatory cytokine TGF{beta}, via expression of an integrin, v{beta}8. Integrin v{beta}8 expression marks a transcriptionally distinct sub-population of CD4+ TEM, enriched for anti-inflammatory pathways. Loss of integrin v{beta}8 on murine CD4+ TEM, but not Foxp3+ regulatory T cells (TREG), led to exacerbated virus-specific CD8+ T cell responses following secondary influenza A virus (IAV) infection, which was associated with enhanced viral clearance. However, although accelerating clearance, loss of integrin v{beta}8 expression on CD4+ TEM resulted in enhanced lung pathology following secondary IAV infection, which was completely reversed by adoptive transfer of v{beta}8+ CD4+ TEM cells. These data highlight a new pathway by which a distinct CD4+ memory T cell subset restrains anti-viral immunity to prevent host tissue damage during secondary viral infection. Such pathways could be targeted therapeutically to either boost memory T-cell-mediated immunity or restrain host tissue damage during viral infection.

immunology↗

bioRxiv2021

Heat Stress Regulates the Expression of TPK1 Gene at Transcriptional and Post-Transcriptional Levels in Saccharomyces cerevisiae

In Saccharomyces cerevisiae, cAMP regulates a number of different cellular processes, such as cell growth, metabolism, stress resistance and gene transcription. The intracellular target for this second messenger in yeast cells is the cAMP-dependent protein kinase (PKA). The way in which a broad specificity protein kinase mediates one right physiological response after cAMP increase indicates that specificity is highly regulated in the cAMP / PKA system. Here we address the mechanism through which cAMP-PKA signalling mediates its response to heat shock thermotolerance in Saccharomyces cerevisiae. Yeast PKA is a tetrameric holoenzyme composed of a regulatory (Bcy1) subunit dimer and two catalytic subunits (Tpk1, Tpk2 and Tpk3). PKA subunits are differentially expressed under certain stress conditions. In the present study we show that, although the mRNA levels of TPK1 are upregulated upon heat shock at 37{degrees}C, no change is detected in Tpk1 protein levels. The half-life of TPK1 mRNA increases and this mRNA condensates in cytoplasmic foci upon thermal stress. The resistance of TPK1 mRNA foci to cycloheximide-induced disassembly, together with the polysome profiling analysis suggest that TPK1 mRNA is impaired for entry into translation. TPK1 mRNA foci and TPK1 expression were also evaluated during thermotolerance. The crosstalk of cAMP-PKA pathway and cell wall integrity (CWI) signalling was also studied. Wsc3 sensor and other components of the CWI pathway are necessary for the upregulation of TPK1 mRNA upon heat shock conditions. The assembly in cytoplasmic foci upon thermal stress shows to be dependent of Wsc3. Finally, evidence of an increase in the abundance of Tpk1 in the PKA holoenzyme in response to heat shock is presented, suggesting that a recurrent stress enhanced the fitness for the coming favorable conditions The results indicate the existence of a mechanism that exclusively regulates Tpk1 subunit expression and therefore contributing to the specificity of cAMP-PKA. SUMMARY STATEMENTPKA subunits are differentially expressed under heat-shock conditions. The mRNA of the TPK1 subunit is upregulated upon heat-shock at 37{degrees}C and thermotolerance, the half-life increases upon heat-stress and also this transcript condensates in cytoplasmic foci upon thermal stress and thermotolerance. The resistance to cycloheximide treatment of TPK1 mRNA foci together with the analysis by polysome profiling suggest that TPK1 mRNA is impaired for entry into translation upon thermal stress. An increase in Tpk1 protein and PKA activity was detected after the heat stress treatments. Cell Wall Integrity pathway, through Wsc3 sensor, is involved in TPK1 expression. Heat-stress regulates TPK1 expression through this pathway from an intermediate step of the cascade and independently of the upstream elements of the CWI pathway activation. These results demonstrate a new crosstalk between the two signalling pathways. The increment in Tpk1-dependent PKA activity during cell adaptation to heat stress might contribute to the overall cellular fitness when more favorable environmental conditions are restored. The results indicate the existence of a mechanism that exclusively regulates TPK1 subunit expression and therefore contributing to the specificity of cAMP-PKA.

molecular biology↗

bioRxiv2021

Sex-specific tuning of modular muscle activation patterns for locomotion in young and older adults

There is increasing evidence that including sex as a biological variable is of crucial importance to promote rigorous, repeatable and reproducible science. In spite of this, the body of literature that accounts for the sex of participants in human locomotion studies is small and often produces controversial results. Here, we investigated the modular organization of muscle activation patterns for human locomotion using the concept of muscle synergies with a double purpose: i) uncover possible sex-specific characteristics of motor control and ii) assess whether these are maintained in older age. We recorded electromyographic activities from 13 ipsilateral muscles of the lower limb in young and older adults of both sexes walking (young and old) and running (young) on a treadmill. The data set obtained from the 215 participants was elaborated through non-negative matrix factorization to extract the time-independent (i.e., motor modules) and time-dependent (i.e., motor primitives) coefficients of muscle synergies. We found sparse sex-specific modulations of motor control. Motor modules showed a different contribution of hip extensors, knee extensors and foot dorsiflexors in various synergies. Motor primitives were wider (i.e., lasted longer) in males in the propulsion synergy for walking (but only in young and not in older adults) and in the weight acceptance synergy for running. Moreover, the complexity of motor primitives was similar in younger adults of both sexes, but lower in older females as compared to older males. In essence, our results revealed the existence of small but defined sex-specific differences in the way humans control locomotion and that these strategies are not entirely maintained in older age.

neuroscience↗

bioRxiv2021

A warmer growing season triggers earlier following spring phenology

Under global warming, advances in spring phenology due to the rising temperature have been widely reported. However, the physiological mechanisms underlying the warming-induced earlier spring phenology remain poorly understood. Here, using multiple long-term and large-scale phenological datasets between 1951 and 2018, we show that warmer temperatures during the previous growing season between May and September led to earlier spring phenology in the Northern Hemisphere. We also found that warming-induced increases in maximum photosynthetic rate in the previous year advanced spring phenology, with an average of 2.50 days {degrees}C-1. Furthermore, we found a significant decline in the advancing effect of warming during the previous growing season on spring phenology from cold to warm periods over the past decades. Our results suggest that the observed warming-induced earlier spring phenology may be driven by increased photosynthetic carbon assimilation in the previous season, while the slowdown in the advanced spring phenology arise likely from decreased carbon assimilation when warming exceeding the optimal temperatures for photosynthesis. Our study highlights the vital role of photosynthetic carbon assimilation during growing season in spring phenology under global warming.

ecology↗

bioRxiv2021

Shifts in leaf senescence across the Northern Hemisphere in response to seasonal warming

Shifts in plant phenology under ongoing warming affect global vegetation dynamics and carbon assimilation of the biomes. The response of leaf senescence to climate is crucial for predicting changes in the physiological processes of trees at ecosystem scale. We used long-term ground observations, phenological metrics derived from PhenoCam, and satellite imagery of the Northern Hemisphere to show that the timings of leaf senescence can advance or delay in case of warming occurring at the beginning (before June) or during (after June) the main growing season, respectively. Flux data demonstrated that net photosynthetic carbon assimilation converted from positive to negative at the end of June. These findings suggest that leaf senescence is driven by carbon assimilation and nutrient resorption at different growth stages of leaves. Our results provide new insights into understanding and modelling autumn phenology and carbon cycling under warming scenarios.

ecology↗

bioRxiv2019

Cortical auditory distance representation based on direct-to-reverberant energy ratio

Auditory distance perception and its neuronal mechanisms are poorly understood, mainly because 1) it is difficult to separate distance processing from intensity processing, 2) multiple intensity-independent distance cues are often available, and 3) the cues are combined in a context-dependent way. A recent fMRI study identified human auditory cortical area representing intensity-independent distance for sources presented along the interaural axis (Kopco et al., PNAS, 109, 11019-11024). For these sources, two intensity-independent cues are available, interaural level difference (ILD) and direct-to-reverberant energy ratio (DRR). Thus, the observed activations may have been contributed by not only distance-related, but also direction-encoding neuron populations sensitive to ILD. Here, the paradigm from the previous study was used to examine DRR-based distance representation for sounds originating in front of the listener, where ILD is not available. In a virtual environment, we performed behavioral and fMRI experiments, combined with computational analyses to identify the neural representation of distance based on DRR. The stimuli varied in distance (15-100 cm) while their received intensity was varied randomly and independently of distance. Behavioral performance showed that intensity-independent distance discrimination is accurate for frontal stimuli, even though it is worse than for lateral stimuli. fMRI activations for sounds varying in frontal distance, as compared to varying only in intensity, increased bilaterally in the posterior banks of Heschl's gyri, the planum temporale, and posterior superior temporal gyrus regions. Taken together, these results suggest that posterior human auditory cortex areas contain neuron populations that are sensitive to distance independent of intensity and of binaural cues relevant for directional hearing.\n\nHighlightsO_LIPosterior auditory cortices (AC) are sensitive to frontally presented distance cues\nC_LIO_LIThese effects are independent of intensity- and direction-related binaural cues\nC_LIO_LIfMRI activations to frontal distance cues are found in the right and left AC\nC_LIO_LIThe frontal reverberation-related auditory distance cues are behaviorally relevant\nC_LI

neuroscience↗

bioRxiv2019

Interleukin (IL)-17/IL-36 axis participates to the crosstalk between endothelial cells and keratinocytes during inflammatory skin responses

In inflammatory skin conditions, such as psoriasis, vascular enlargement is associated with endothelial cell proliferation, release of cytokines and adhesion molecule expression. Interleukin (IL)-17A is a pro-inflammatory cytokine mainly secreted by T helper-17 cells that is critically involved in psoriasis pathogenesis. IL-36, IL-36{beta} and IL-36{gamma} are also inflammatory cytokines up-regulated in psoriasis and induced by various stimuli, including IL-17A. In this study, we found that human keratinocytes are the main source of IL-36, in particular of IL-36{gamma}. This cytokine was strongly induced by IL-17A and efficiently activated human dermal microvascular endothelial cells (HDMECs), which expressed both IL-17 and IL-36 receptors, by inducing a molecular signaling, such as phosphorylation of ERK1/2 and NF-{kappa}B P65 subunit. We highlighted the intense IL-17A- and IL-36{gamma}-dependent interplay between keratinocytes and HDMECs, likely active in the psoriatic lesions and leading to the establishment of a cytokine network responsible for the development and maintenance of the inflamed state. On HDMECs, IL-17A or IL-36{gamma} showed a synergic activity with TNF-, potently inducing inflammatory cytokine/chemokine release and ICAM-1 expression. We also investigated the involvement of IL-36{gamma} and VEGF-A, substantially reduced in lesional skin of psoriatic patients pharmacologically treated with the anti-IL-17A antibody Secukinumab. Importantly, keratinocyte-derived IL-36{gamma} represented an additional pro-angiogenic mediator of IL-17A. We observed that keratinocyte-derived VEGF-A influenced proliferation but not reduced inflammatory responses of HDMECs. On the other hand, inhibition of IL-36{gamma} released by IL-17A-treated keratinocytes impaired ICAM-1 expression in HDMECs. Taken together, our data demonstrated that IL-17A and IL-36{gamma} are highly involved in endothelial cells/keratinocytes crosstalk in inflammatory skin conditions.

cell biology↗

bioRxiv2019

Label-free, real-time on-chip sensing of living cancer cell via grating-coupled surface plasmon resonance

The application of nanotechnologies to address biomedical questions is a key strategy for innovation in biomedical research. Among others, a key point consists in the availability of nanotechnologies for monitoring cellular processes in a real-time and label-free approach. Here, we focused on a grating-coupled Surface Plasmon Resonance (GC-SPR) sensor exploiting phase interrogation. This sensor can be integrated in a microfluidic chamber that ensures cell viability and avoids cell stress. We report the calibration of the sensor response as a function of cell number and its application to monitor cell adhesion kinetics as well as cell response to an external stimulus. Our results show that GC-SPR sensors can offer a valuable alternative to prism-coupled or imaging SPR devices, amenable for microfluidic implementation.

biophysics↗