Biology subjects

Fernandez, L.

Publications and source records attributed to Fernandez, L..

14 recordsLinked to original sources

bioRxiv2025

Behavioural and Physiological Signatures of Chronic Unpredictable Mild Stress Models in Mice

The chronic unpredictable mild stress (CUMS) paradigm is one of the most widely used preclinical models to investigate the role of stress in the neurobiology of depression and to evaluate potential antidepressant therapies, owing to its strong translational relevance. However, despite its extensive use, substantial discrepancies and concerns regarding the reproducibility of CUMS outcomes persist in the literature, with many studies reporting inconsistent or unreliable results. In the present comparative study, we implemented several CUMS protocols in mice that differed in the intensity and duration of stress exposure, and systematically evaluated the resulting pathophysiological and behavioural alterations associated with depressive- and anxiety-like phenotypes. We found that progressive escalation in stress intensity and frequency, as well as prolonged exposure, induced increasingly robust disease-related behavioural and physiological changes, including depression- and anxiety-like behaviours, adrenal hypertrophy, and reduced body weight gain.. Moreover, social isolation emerged as a major contributing factor exacerbating stress-induced deficits. Altogether, data suggest that a multidimensional assessment of the behavioural impairments is critical to reinforce the physiological changes indicative of a hyperactive hypothalamic-pituitary-adrenal axis (HPA). Differences in individual stress susceptibility, stressor intensity, frequency, and housing conditions are key determinants of CUMS outcomes. Therefore, precise, detailed, and transparent reporting of protocol parameters is critical to enhance reproducibility and enable meaningful comparisons across studies.

neuroscience↗

bioRxiv2025

Ki-67 shapes the nucleolus by anchoring chromatin via its amphiphilic properties

The nucleolus, a membrane-less organelle essential for ribosome biogenesis, adopts variable shapes across cell types and in response to environmental conditions, yet the mechanisms regulating its morphology and functional implications remain unclear. Using a high-throughput screen, we identify the proliferation marker Ki-67 as a central regulator of nucleolar shape. Ki-67 localises to the chromatinnucleolus interface, where its depletion induces nucleolar rounding and reduces chromatin enrichment within and around the nucleolus. This effect is driven by amphiphilic properties conferred by two distinct affinity domains separated by a spacer. Given that chromatin loss is a common feature of rounded nucleoli in our screen, and acute chromatin digestion also induces rounding, we propose that the chromatin environment in and around the nucleolus plays a key role in determining nucleolar shape. Our study elucidates a novel Ki-67-mediated chromatin anchoring mechanism, tightly linking nucleolar shape to genome organisation and expanding our understanding of condensate morphology.

cell biology↗

bioRxiv2024

Eosinophils promote monocyte to macrophage differentiation and anti-bacterial immunity

Chemokine receptors control cell migration within the body. Here we reveal a novel interaction between eosinophils and monocytes in the bone marrow, indirectly controlled by the atypical chemokine receptor ACKR2. We demonstrate that ACKR2 maintains eosinophil levels within the bone marrow by scavenging CCL11. In the absence of ACKR2, elevated CCL11 leads to increased egress of eosinophils from the bone marrow into the bloodstream. As a result, eosinophil and monocyte interactions are reduced within the bone marrow niche, leading to changes in monocyte gene expression. Monocytes from ACKR2-/- mice are recruited to the tissues but are fundamentally altered in their ability to differentiate into macrophages, in the lung, peritoneal cavity and cavity wall. Bacterial elimination is impaired in ACKR2-/- mice during peritoneal infection. ACKR2 is therefore a key regulator of eosinophil-driven monocyte education in the bone marrow, required for full monocyte differentiation and macrophage function within the tissues.

immunology↗

bioRxiv2024

Bacterial protein function prediction via multimodal deep learning

Bacterial proteins are specialized with extensive functional diversity for survival in diverse and stressful environments. A significant portion of these proteins remains functionally uncharacterized, limiting our understanding of bacterial survival mechanisms. Hence, we developed Deep Expression STructure (DeepEST), a multimodal deep learning framework designed to accurately predict protein function in bacteria by assigning Gene Ontology (GO) terms. DeepEST comprises two modules: a multi-layer perceptron that takes gene expression and gene location as input features, and a protein structure-based predictor. Within DeepEST, we integrated these modules through a learnable weighted linear combination and introduced a novel masked loss function to fine-tune the structure-based predictor for bacterial species. These modeling choices are particularly well suited for bacteria due to the spatial organization of their circular genomes. Functionally related genes frequently co-localize and are co-transcribed within operons, allowing transcription dynamics to serve as crucial, condition-dependent regulatory signals. We show that DeepEST outperforms existing protein function prediction methods on a 25-species benchmark, relying solely on amino acid sequence or protein structure. Moreover, DeepEST predicts GO terms for unclassified hypothetical proteins across 25 human bacterial pathogens, facilitating the design of experimental setups for characterization studies. By combining expression, localization, and structure information in a unified deep learning framework, DeepEST bridges organism-specific data integration and structure-based transfer learning, providing a method tailored for bacterial protein function prediction in settings with structural and multi-condition expression data. AvailabilityAccompanying code and data can be found under https://github.com/BorgwardtLab/DeepEST.

bioinformatics↗

bioRxiv2024

Disordered regions of human eIF4B orchestrate a dynamic self-association landscape

Eukaryotic translation initiation factor eIF4B is required for efficient cap-dependent translation, it is overexpressed in cancer cells, and may influence stress granule formation. Due to the high degree of intrinsic disorder, eIF4B is rarely observed in cryo-EM structures of translation complexes and only ever by its single structured RNA recognition motif domain, leaving the molecular details of its large intrinsically disordered region (IDR) unknown. By integrating experiments and simulations we demonstrate that eIF4B IDR orchestrates and fine-tunes an intricate transition from monomers to a condensed phase, in which large-size dynamic oligomers form before mesoscopic phase separation. Single-molecule spectroscopy combined with molecular simulations enabled us to characterize the conformational ensembles and underlying intra- and intermolecular dynamics across the oligomerization transition. The observed sensitivity to ionic strength and molecular crowding in the self-association landscape suggests potential regulation of eIF4B nanoscopic and mesoscopic behaviors such as driven by protein modifications, binding partners or changes to the cellular environment.

biophysics↗

bioRxiv2024

The new SH3_T domain increases the structural and functional variability among SH3b-like CBDs from staphylococcal phage endolysins

Endolysins, proteins encoded by phages to lyse their hosts and release their progeny, have evolved to adapt to the structural features of each host. The endolysins from Staphylococcus-infecting phages typically feature complex architectures with two enzymatically active domains (EADs) and one cell wall-binding domain (CBD) belonging to the bacterial SH3 (SH3b) superfamily. This study focuses on three SH3b-like CBDs from exemplary staphylococcal phage endolysins (LysRODI, LysC1C, and LysIPLA5) that were structurally and functionally characterized. While RODI_CBD and C1C_CBD were assigned to the well-known SH3_5 family, a new family, SH3b_T, was identified using the CBD from LysIPLA5 as a model. GFP-fused CBDs were created to assess their differential binding to a collection of staphylococcal strains. IPLA5_CBD showed enhanced binding to Staphylococcus epidermidis, while RODI_CBD and C1C_CBD exhibited distinct binding profiles, with RODI_CBD targeting Staphylococcus aureus specifically and C1C_CBD displaying broad binding. Sequence comparisons suggested that a few differences in key amino acids could be responsible for the latter binding difference. The CBDs modulated the activity spectrum of synthetic EAD-CBD combinations in accordance with the previous binding profiles, but in a manner that was also dependent on the EAD present in the fusion protein. These results serve as a context for the diversity and versatility of SH3b domains in staphylococcal endolysins, providing insights on how (i) the CBDs from this superfamily have diverged to adapt to diverse bacterial ligands in spite of sharing a common fold; and (ii) the evolution of specificity relies on the EAD-CBD combination rather than solely the CBD. IMPORTANCEClinical management of bacterial infections is nowadays compromised by the rise in antimicrobial resistance. The development of new antimicrobial therapies with diverse modes of action is therefore of pivotal importance to complement the current standard of care. Phage endolysins are a new class of antibacterial agents based on rapid peptidoglycan degradation. The natural reservoir of phage endolysins offers a practically infinite diversity. This works reveals a broadly spread but still unknown phage endolysin domain targeting staphylococci while providing structural-functional insights that are paramount to understand the evolution of endolysins and how they can be applied as an antimicrobial.

molecular biology↗

bioRxiv2023

Early delta cortical tracking to non-verbal auditory stimuli predicts reading skills: A one-year longitudinal study

The precision of cortical tracking of auditory rhythmic stimuli in low frequency ranges coding for prosodic (delta) and syllabic (theta) amplitude modulations in the speech signal has been proposed to contribute to the development of phonological processing and reading acquisition. The present study investigates the role of low frequency cortical tracking of non-verbal auditory stimuli in reading acquisition through a longitudinal design from before the onset of formal reading instruction until one year afterwards. At time one, 40 prereading children performed a passive listening task of amplitude modulated white noise presented in the delta (2 Hz) and theta (4 Hz) frequency bands, while their neural activity was recorded via EEG. At time two, at the end of first grade, childrens reading skills were assessed. Results show significant cortical tracking in prereading children at both frequencies, with larger responses for theta than for delta rate non-verbal auditory stimuli. Importantly, only pre-reding cortical tracking measures for delta rate stimuli predicted reading acquisition one year later. These findings underscore the role of early neural synchronization to delta rate rhythmic auditory stimuli to reading acquisition and support the potential important role of early prosodic processing for the development of future reading skills.

neuroscience↗

bioRxiv2023

Experimental and computational analysis of REM sleep distributed cortical activity in mice

Although classically Rapid-Eye Movement (REM) sleep is thought to generate desynchronized activity similar to wakefulness, it was found that some brain regions can express Slow Wave activity (SWA), a pattern which is normally typical of slow-wave sleep. To investigate possible underlying mechanisms, we analyze experimental recordings and introduce a computational model of mice cerebral cortex in REM sleep. We characterized the patterns of slow-wave activity across somatosensory and motor areas, and find that the most prominent REM-related SWA is present in the primary (S1) and secondary (S2) somatosensory areas, more rarely seen in motor cortex, and absent from prefrontal cortex or hippocampus. The SWA also tends to be synchronized in S1 and S2. We next investigated possible mechanisms by using a computational model of the mouse brain consisting of adaptive Exponential (AdEx) mean-fields connected together according to the mouse connectome. To compare with experimental data, the local field potential is calculated in each mouse brain region. To reproduce the experiments, we had to assume a heterogeneous level of adaptation in different cortical regions during REM sleep. In these conditions, the model reproduces some of the experimental observations in the somato-motor areas and the other cortical areas. We then used the model to test how the presence of SWA affects cortical responsiveness. Indeed, we find that the areas expressing SWA have diminished evoked responses, which may participate to a diminished responsiveness during REM sleep.

neuroscience↗

bioRxiv2022

Utilising TMS-EEG to assess the response to cerebellar-brain inhibition

BackgroundCerebellar-brain inhibition (CBI) is a transcranial magnetic stimulation (TMS) paradigm indexing excitability of cerebellar projections to motor cortex (M1). Stimulation involved with CBI is often considered to be uncomfortable, and alternative ways to index connectivity between cerebellum and the cortex would be valuable. Utilising electroencephalography in conjunction with TMS (combined TMS-EEG) to record the response to CBI has the potential to achieve this, but has not been attempted previously. ObjectiveTo investigate the utility of TMS-EEG for characterising cerebellar-cortical interactions recruited by CBI. MethodsA total of 33 volunteers (25.7 {+/-} 4.9 years, 20 females) participated across three experiments. These investigated EEG responses to CBI induced with a figure-of-eight (F8; experiment 1) or double cone (DC; experiment 2) conditioning coil over cerebellum, in addition to multisensory sham stimulation (experiment 3). ResultsBoth F8 and DC coils suppressed early TMS-evoked EEG potentials (TEPs) produced by TMS to M1 (P < 0.05). Furthermore, the TEP produced by CBI stimulation was related to the motor inhibitory response to CBI recorded in a hand muscle (P < 0.05), but only when using the DC coil. Multisensory sham stimulation failed to modify the M1 TEP. ConclusionsCerebellar conditioning produced changes in the M1 TEP that were not apparent following sham stimulation, and that were related to the motor inhibitory effects of CBI. Our findings therefore suggest it is possible to index the response to CBI using TMS-EEG. In addition, while both F8 and DC coils appear to recruit cerebellar projections, the nature of these may be different.

neuroscience↗

bioRxiv2020

Assessing cerebellar-cortical connectivity using concurrent TMS-EEG: A Feasibility Study

BackgroundCombined single-pulse transcranial magnetic stimulation (TMS) and electroencephalography (EEG) has been used to probe the features of local networks in the cerebral cortex. Here we investigate whether we can use this approach to explore long-range connections between the cerebellum and cerebral cortex. ObjectiveTo assess the feasibility of using cerebellar TMS-EEG for the exploration of cerebellar-cerebral network dynamics. MethodsTen healthy adults received single-pulse suprathreshold TMS to the cerebellum and an occipital/parietal control site with double-cone and figure-of-eight coils while cerebral activity was recorded. A multisensory electrical control condition was used to simulate the sensation of the double-cone coil at the cerebellar site. Two cleaning pipelines were compared, and the spatiotemporal relationships of the EEG output between conditions were examined at sensor and source levels. ResultsCerebellar stimulation with the double-cone coil resulted in large artefacts in the EEG trace. The addition of SOUND filtering to the cleaning pipeline improved the signal such that further analyses could be undertaken. The cortical potentials evoked by the active TMS conditions showed strong relationships with the responses to the multisensory control condition after ~50 ms. A distinct parietal component at ~42 ms was found following cerebellar double-cone stimulation. ConclusionsCerebellar double-cone stimulation produces large artefacts in the EEG. Cerebellar-specific responses could not be reliably differentiated from sensory evoked potentials after ~50 ms. While evoked potentials differed across conditions at early latencies, it is unclear as to whether these represented TMS-related network activation of the cerebellarthalamocortical tract, or whether components were dominated by sensory contamination and/or coil-driven artefacts. Further work will be required to clarify the specific contribution of cerebellar-cortical connectivity to the observed early latency signals.

neuroscience↗

bioRxiv2020

Ancestral function of Inhibitors-of-kappaB regulates Caenorhabditis elegans development

Mammalian I{kappa}B proteins (I{kappa}Bs) exert their main function as negative regulators of NF-{kappa}B, a central signaling pathway controlling immunity and inflammation. An alternative chromatin role for I{kappa}Bs has been shown to affect stemness and cell differentiation. However, the involvement of NF-{kappa}B in this function has not been excluded. NFKI-1 and IKB-1 are I{kappa}B homologs in Caenorhabditis elegans, which lacks NF-{kappa}B nuclear effectors. We found that nfki-1 and ikb-1 mutants display developmental defects that phenocopy mutations in Polycomb and UTX-1 histone demethylase, suggesting a role for C. elegans I{kappa}Bs in chromatin regulation. Further supporting this possibility (i) we detected NFKI-1 in the nucleus of cells; (ii) NFKI-1 and IKB-1 bind to histones and Polycomb proteins, (iii) and associate with chromatin in vivo, and (iv) mutations in nfki-1 and ikb-1 alter chromatin marks. Based on these results, we propose that ancestral I{kappa}B inhibitors modulate Polycomb activity at specific gene subsets with an impact on development.

developmental biology↗

bioRxiv2019

Quadriceps and hamstrings coactivation in exercises used in prevention and rehabilitation of hamstring strain injury in young soccer players

This study aimed to study the co-activation of hamstring-quadriceps muscles during submaximal strength exercises without the use of maximum voluntary isometric contraction testing and compare (i) the inter-limb differences in muscle activation, (ii) the intra-muscular group activation pattern, and (iii) the activation during different phases of the exercise. Muscle activation was recorded by surface electromyography of 19 elite male youth players. Participants performed five repetitions of the Bulgarian squat, lunge and the squat with an external load of 10 kg. Electrical activity was recorded for the rectus femoris, vastus medialis, vastus lateralis, biceps femoris and semitendinosus. No significant inter-limb differences were found (F1, 13=619; p=0.82; partial {eta}2=0.045). Significant differences were found in the muscle activation between different muscles within the muscle group (quadriceps and hamstrings) for each of the exercises: Bulgarian squat (F1,18=331: p<0.001; partial {eta}2=0.80), lunge (F4,72=114.5; p<0.001; partial {eta}2=0.86) and squat (F1,16=247.31; p<0.001; partial {eta}2=0.93).Differences were found between the concentric, isometric and eccentric phases of each of the exercises (F2, 26=52.27; p=0.02; partial {eta}2=0.80). The existence of an activation pattern of each of the muscles in the three proposed exercises could be used for muscle assessment and as a tool for injury recovery.

scientific communication and education↗

bioRxiv2018

The Integrative Conjugative Element (ICE) of Mycoplasma agalactiae: key elements involved in horizontal dissemination and influence of co-resident ICEs

The discovery of integrative conjugative elements (ICEs) in wall-less mycoplasmas and the demonstration of their role in massive gene flows within and across species has shed new light on the evolution of these minimal bacteria. Of these, ICEA of the ruminant pathogen Mycoplasma agalactiae represents a prototype and belongs to a new clade of the Mutatorlike superfamily that has no preferential insertion site and often occurs as multiple chromosomal copies. Here, functional genomics and mating experiments were combined to address ICEA functions and define the minimal ICEA chassis conferring conjugative properties to M. agalactiae. Data further indicated a complex interaction among co-resident ICEAs, since the minimal ICEA structure was influenced by the occurrence of additional ICEA copies that can trans-complement conjugative-deficient ICEAs. However, this cooperative behavior was limited to the CDS14 surface lipoprotein, which is constitutively expressed by co-resident ICEAs, and did not extend to other ICEA proteins including the cis-acting DDE recombinase and components of the mating channel whose expression was only sporadically detected. Remarkably, conjugative-deficient mutants containing a single ICEA copy knocked-out in cdsl4 can be complemented by neighboring cells expressing CDS14. This result, together with the conservation of CDS14 functions in closely related species, may suggest a way for mycoplasma ICEs to extend their interaction outside of their chromosomal environment. Overall, this study provides a first model of conjugative transfer in mycoplasmas and offers valuable insights towards the understanding of horizontal gene transfer in this highly adaptive and diverse group of minimal bacteria.\n\nIMPRTANCEIntegrative conjugative elements (ICEs) are self-transmissible mobile genetic elements that are key mediators of horizontal gene flow in bacteria. Recently, a new category of ICEs has been identified that confer conjugative properties to mycoplasmas, a highly adaptive and diverse group of wall-less bacteria with reduced genomes. Unlike classical ICEs, these mobile elements have no preferential insertion specificity and multiple mycoplasma ICE copies can be found randomly integrated into the host chromosome. Here, the prototype ICE of Mycoplasma agalactiae was used to define the minimal conjugative machinery and propose the first model of ICE transfer in mycoplasmas. This model unveils the complex interactions taking place among co-resident ICEs and suggests a way for these elements to extend their influence outside of their chromosomal environment. These data pave the way for future studies aiming at deciphering chromosomal transfer, an unconventional mechanism of DNA swapping that has been recently associated with mycoplasma ICEs.

microbiology↗

bioRxiv2018

HIV-1 specifically traps and depletes CD9 and CD81 tetraspanins during egress

HIV-1 assembly specifically alters both partitioning and dynamics of the tetraspanins CD9 and CD81 forming enriched areas where the virus buds. Importantly the presence of these proteins at exit sites and in viral particles inhibits virus-induced membrane fusion. To get molecular insights into tetraspanins partitioning in this viral context, we correlated nanoscale CD9 mapping obtained by super resolution microscopy to membrane topography probed by Atomic Force Microscopy (AFM). We demonstrated that CD9 is specifically trapped within the nascent viral particles, especially at buds tips, and that Gag mediate CD9 and CD81 depletion from cellular surfaces, even in the absence of Vpu and Nef, resulting from tetraspanins escaping from the plasma membrane during HIV-1 release. In addition, we showed that CD9 is organized as small membrane assemblies of few tens of nanometers that can coalesce upon Gag expression. Our results support a functional redundancy among tetraspanins during HIV release.

microbiology↗