MinActionPath2: path generation between different conformations of large macromolecular assemblies by action minimization

International audienceRecent progress in solving macromolecular structures and assemblies by cryogenic electron microscopy techniques enables sampling of their conformations in different states that are relevant to their biological function. Knowing the transition path between these conformations would provide new avenues for drug discovery. While the experimental study of transition paths is intrinsically difficult, in-silico methods can be used to generate an initial guess for those paths. The Elastic Network Model (ENM), along with a coarse-grained representation (CG) of the structures are among the most popular models to explore such possible paths. Here we propose an update to our software platform MinActionPath that generates non-linear transition paths based on ENM and CG models, using action minimization to solve the equations of motion. The new website enables the study of large structures such as ribosomes or entire virus envelopes. It provides direct visualization of the trajectories along with quantitative analyses of their behaviors at http://dynstr.pasteur.fr/servers/minactionpath/ minactionpath2_submission

Atypical Audio-Visual Neural Synchrony and Speech Processing in children with Autism Spectrum Disorder

Background: Children with Autism Spectrum Disorders (ASD) often exhibit communication difficulties that may stem from basic auditory temporal integration impairment but also be aggravated by an audio-visual integration deficit, resulting in a lack of interest in face-to-face communication. This study addresses whether speech processing anomalies in young (mean age 3.09-year-old) children with ASD are associated with alterations of audio-visual temporal integration. Methods: We used high-density electroencephalography (HD-EEG) and eye tracking to record brain activity and gaze patterns in 31 children (6 females) with ASD and 33 typically developing (TD) children (11 females), while they watched cartoon videos. Neural responses to temporal audio-visual stimuli were analyzed using Temporal Response Functions model and phase analyses for audiovisual temporal coordination. Results: The reconstructability of speech signals from auditory responses was reduced in children with ASD compared to controls, but despite more restricted gaze patterns in ASD it was similar for visual responses in both groups. Speech reception was most strongly affected when visual speech information was also present, an interference that was not seen in TD children. These differences were associated with a broader phase angle distribution (exceeding pi/2) in the EEG theta range in autistic children, signaling reduced reliability of audio-visual temporal alignment. Conclusion: These findings show that speech processing anomalies in ASD do not stand alone and that they are associated already at a very early development stage with audio-visual imbalance with lousier auditory response encoding and disrupted audio-visual temporal coordination

Impact of socioeconomic status on healthy immune responses in humans

International audienceIndividuals with low socioeconomic status (SES) are at greater risk of contracting and developing severe disease compared with people with higher SES. Age, sex, host genetics, smoking and cytomegalovirus (CMV) serostatus are known to have a major impact on human immune responses and thus susceptibility to infection. However, the impact of SES on immune variability is not well understood or explored. Here, we used data from the Milieu Intérieur project, a study of 1000 healthy volunteers with extensive demographic and biological data, to examine the effect of SES on immune variability. We developed an Elo‐rating system using socioeconomic features such as education, income and home ownership status to objectively rank SES in the 1000 donors. We observed sex‐specific SES associations, such as females with a low SES having a significantly higher frequency of CMV seropositivity compared with females with high SES, and males with a low SES having a significantly higher frequency of active smoking compared with males with a high SES. Using random forest models, we identified specific immune genes which were significantly associated with SES in both baseline and immune challenge conditions. Interestingly, many of the SES associations were sex stimuli specific, highlighting the complexity of these interactions. Our study provides a new way of computing SES in human populations that can help identify novel SES associations and reinforces biological evidence for SES‐dependent susceptibility to infection. This should serve as a basis for further understanding the molecular mechanisms behind SES effects on immune responses and ultimately disease

MAIT cells monitor intestinal dysbiosis and contribute to host protection during colitis

International audienceIntestinal inflammation shifts microbiota composition and metabolism. How the host monitors and responds to such changes remains unclear. Here, we describe a protective mechanism by which mucosal-associated invariant T (MAIT) cells detect microbiota metabolites produced upon intestinal inflammation and promote tissue repair. At steady state, MAIT ligands derived from the riboflavin biosynthesis pathway were produced by aerotolerant bacteria residing in the colonic mucosa. Experimental colitis triggered luminal expansion of riboflavin-producing bacteria, leading to increased production of MAIT ligands. Modulation of intestinal oxygen levels suggested a role for oxygen in inducing MAIT ligand production. MAIT ligands produced in the colon rapidly crossed the intestinal barrier and activated MAIT cells, which expressed tissue-repair genes and produced barrier-promoting mediators during colitis. Mice lacking MAIT cells were more susceptible to colitis and colitis-driven colorectal cancer. Thus, MAIT cells are sensitive to a bacterial metabolic pathway indicative of intestinal inflammation

Cancer-on-a-chip model shows that the adenomatous polyposis coli mutation impairs T cell engagement and killing of cancer spheroids

International audienceEvaluating the ability of cytotoxic T lymphocytes (CTLs) to eliminate tumor cells is crucial, for instance, to predict the efficiency of cell therapy in personalized medicine. However, the destruction of a tumor by CTLs involves CTL migration in the extra-tumoral environment, accumulation on the tumor, antigen recognition, and cooperation in killing the cancer cells. Therefore, identifying the limiting steps in this complex process requires spatio-temporal measurements of different cellular events over long periods. Here, we use a cancer-on-a-chip platform to evaluate the impact of adenomatous polyposis coli (APC) mutation on CTL migration and cytotoxicity against 3D tumor spheroids. The APC mutated CTLs are found to have a reduced ability to destroy tumor spheroids compared with control cells, even though APC mutants migrate in the extra-tumoral space and accumulate on the spheroids as efficiently as control cells. Once in contact with the tumor however, mutated CTLs display reduced engagement with the cancer cells, as measured by a metric that distinguishes different modes of CTL migration. Realigning the CTL trajectories around localized killing cascades reveals that all CTLs transition to high engagement in the 2 h preceding the cascades, which confirms that the low engagement is the cause of reduced cytotoxicity. Beyond the study of APC mutations, this platform offers a robust way to compare cytotoxic cell efficiency of even closely related cell types, by relying on a multiscale cytometry approach to disentangle complex interactions and to identify the steps that limit the tumor destruction

Acinetobacter baumannii: Setup and characterization of pneumonia and septicemia preclinical models with longitudinal monitoring using bioluminescent strains

International audienceBacterial multidrug resistance (MDR) is responsible of up to 4.9 million deaths,with the MDR ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus,Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, andEnterobacter spp) being the leading cause of nosocomial infections worldwide.Treating these MDR bacteria represents one of the greatest challenges in clinicalpractice.Among ESKAPE pathogens, the emergence of rapidly spreading carbapenem-resistant Acinetobacter baumannii, combined to the lack of available active antibioticshas led the WHO to raise the threat level to "Urgent" and classify it in the criticalgroup of its Bacterial Priority Pathogens List (2024). These observations call for anurgent need for new anti-microbials.The goal of this study was to setup preclinical models mimicking the mainclinical infections caused by A. baumannii (bacteraemia and pneumonia) usingbioluminescent strains that allow to perform longitudinal monitoring of the bacterialdissemination and assess antibacterial candidate’s efficac

Neurones du cortex insulaire projetant vers le complex vagal : caractérisation et rôles dans le comportement et l'inflammation

Brain-body interactions are crucial for organisms survival; the brain constantly receives external and internal information that it integrates to regulate various physiological function. Notably, the nervous system closely interacts with the immune system. In the case of inflammation, the brain's features enable an optimized regulation of immune responses. These features include the brain's ability to sense environmental cues, anticipate outcomes, and transmit signals rapidly through an extensive network of neurons innervating the entire body within milliseconds. The vagus nerve, linking the brain to visceral organs, is an important support of this bidirectional communication. It is composed of sensory and motor branches. Sensory afferences carry peripheral information to the vagal complex in the brain which transmits the signals to deeper brain structures, while motor efferences mediate the generated responses to targeted organs.In processing internal information, the insular cortex emerges as a critical multimodal hub. As a sensory cortex, it receives various inputs from external-sensing systems such as somatosensory, and olfactory cortices, while also being densely interconnected with regions processing internal cues such as inflammatory threats, such as the vagal complex. This allows the insular cortex to integrate exteroceptive and interoceptive information and play a pivotal role in the salience network. Within the organism, it can optimize responses to specific situations by regulating cardiac or intestinal activity, as well as immune responses, but the underlying circuits are poorly understood. Given the role played by the vagus nerve in transmitting information between the brain and the periphery, along with the presence of projections from the insular cortex to the vagal complex (InsCtxVC), we hypothesize that some of the insular cortex functions are mediated through the vagus nerve.To investigate the role of InsCtxVC, we first characterized these neurons anatomically using viral retrograde labeling. We found that InsCtxVC are predominantly located within the posterior-intermerdiate InsCtx, mainly in layer V, and express CTIP, a downstream effector of the Fezf2 pathway. Next, we examined the connectivity of these neurons using viral labeling of outputs and inputs. Our experiments revealed that within the vagal complex, InsCtxVC neurons preferentially synapse with the medial NTS (rather than caudal NTS or DMN), and the central amygdala and parasubthalamic nucleus. Additionally, we analyzed their presynaptic inputs, highlighting a predominant innervation from sensory cortices including the insula itself, the somatosensory and olfactory cortices. Based on our anatomical findings and existing litterature, we screened various contexts likely to recruit the InsCtxVC. Through specific chemogenetic and optogenetic manipulation of these neurons, we found that InsCtxVC are not involved in anxiety behaviors or neuroimmune conditionned taste aversion. However, chemogenetic activation of InsCtxVC neurons during early LPS-induced inflammation exacerbates sickness behavior, including increased weight loss, elevated blood proinflammatory cytokines and corticosterone response. Taken together, our results characterize a previsouly undefined neuronal population linking the insular cortex to a major parasympathetic center, which regulates immune responses in the periphery.Les interactions entre le cerveau et le reste du corps sont cruciales pour la survie de l'organisme. Le cerveau reçoit et intègre une multitude d'informations externes et internes et régule diverses fonctions physiologiques en permanence. Notamment, le système nerveux interagit étroitement avec le système immunitaire. En cas d'infection, les caractéristiques uniques du cerveau permettent une régulation optimisée des réponses immunitaires. Cela inclut la capacité du cerveau à détecter les signaux environnementaux, à anticiper les situations à venir et à transmettre rapidement des signaux à travers un vaste réseau de neurones innervant l'ensemble du corps en quelques millisecondes. Le nerf vague, reliant le cerveau aux organes viscéraux, est un support important de cette communication bidirectionnelle. Il est composé de branches sensorielles et motrices. Les afférences relaient les informations périphériques au complexe vagal dans le cerveau, qui transmet les signaux aux structures cérébrales plus profondes, tandis que les efférences motrices transmettent les réponses générées vers les organes cibles. Dans le traitement des informations intéroceptives, le cortex insulaire émerge comme un hub multimodal essentiel. En tant que cortex sensoriel, il reçoit diverses entrées des systèmes de détection externes tels que les cortex somatosensoriels et olfactifs, tout en étant densément interconnecté avec les régions comme le complexe vagal, traitant les signaux internes tels que les stimuli inflammatoires. Cela permet au cortex insulaire d'intégrer les informations extéroceptives et intéroceptives et de jouer un rôle central dans le ‘salient network'. Au sein de l'organisme, il peut optimiser les réponses à des situations spécifiques en régulant l'activité cardiaque ou intestinale, ainsi que les réponses immunitaires, mais les circuits qui médient ces fonctions ne sont pas bien connus. Compte tenu de l'importance du nerf vague dans la transmission d'informations entre le cerveau et la périphérie, ainsi que l'existence de projections du cortex insulaire vers le complexe vagal (InsCtxVC), nous émettons l'hypothèse que certaines fonctions du cortex insulaire sont médiées par le nerf vague. Pour étudier le rôle de l'InsCtxVC, nous avons d'abord caractérisé ces neurones anatomiquement à l'aide d'un virus rétrograde permettant leur marquage. Nous avons constaté que les neurones InsCtxVC sont principalement situés dans le cortex insulaire postérieur-intermédiaire dans la couche V, et expriment CTIP, un effecteur en aval de la voie Fezf2. Ensuite, nous avons examiné les entrées et sorties de ces neurones en utilisant des marqueurs viraux. Nos expériences ont révélé qu'au sein du complexe vagal, les neurones InsCtxVC établissent préférentiellement des synapses avec le NTS médian (plutôt que le NTS caudal ou le DMN), ainsi qu'avec l'amygdale centrale et le noyau parasubthalamique. De plus, nous avons analysé leurs entrées présynaptiques, mettant en évidence une innervation prédominante des cortex sensoriels, y compris le cortex insulaire lui-même, et les cortex somatosensoriels et olfactifs. Sur la base de nos résultats anatomiques et de la littérature, nous avons examiné divers contextes susceptibles de recruter l'InsCtxVC. Grace à des manipulations chemogénétiques et optogénétiques spécifiques de ces neurones, nous avons constaté que l'InsCtxVC n'est pas impliqué dans les comportements anxieux ou l'aversion gustative conditionnée neuro-immunitaire. Cependant, l'activation chemogénétique des neurones InsCtxVC lors d'une inflammation induite par le LPS exacerbe le comportement de maladie, incluant une perte de poids accrue, une élévation des cytokines pro-inflammatoires et de la corticostérone dans le sang.En conclusion, nos résultats caractérisent une population neuronale non décrite précédemment reliant le cortex insulaire à un centre parasympathique majeur régulant les réponses immunitaires périphériques

Global genomics of Aedes aegypti unveils widespread and novel infectious viruses capable of triggering a small RNA response

International audienceThe mosquito Aedes aegypti is a prominent vector for arboviruses, but the breadth of mosquito viruses that infects this specie is not fully understood. In the broadest global survey to date of over 200 Ae. aegypti small RNA samples, we detected viral small interfering RNAs (siRNAs) and Piwi interacting RNAs (piRNAs) arising from mosquito viruses. We confirmed that most academic laboratory colonies of Ae. aegypti lack persisting viruses, yet two commercial strains were infected by a novel tombus-like virus. Ae. aegypti from North to South American locations were also teeming with multiple insect viruses, with Anphevirus and a bunyavirus displaying geographical boundaries from the viral small RNA patterns. Asian Ae. aegypti small RNA patterns indicate infections by similar mosquito viruses from the Americas and reveal the first wild example of dengue virus infection generating viral small RNAs. African Ae. aegypti also contained various viral small RNAs including novel viruses only found in these African substrains. Intriguingly, viral long RNA patterns can differ from small RNA patterns, indicative of viral transcripts evading the mosquitoes’ RNA interference (RNAi) machinery. To determine whether the viruses we discovered via small RNA sequencing were replicating and transmissible, we infected C6/36 and Aag2 cells with Ae. aegypti homogenates. Through blind passaging, we generated cell lines stably infected by these mosquito viruses which then generated abundant viral siRNAs and piRNAs that resemble the native mosquito viral small RNA patterns. This mosquito small RNA genomics approach augments surveillance approaches for emerging infectious diseases

Minimal perturbation analysis of mRNA degradation rates with Tet-off and RT-qPCR

Messenger RNA stability is an important variable in gene expression and its dynamics. High stability ensures a constant level of synthesized protein, whereas mRNA instability can be critical for regulatory processes in which protein production needs to be stopped, such as development, inflammation or adaptation to stress. Accurate measurements of RNA degradation rates are important for understanding how RNA features and RNA binding proteins affect the post-transcriptional life of an mRNA. As an alternative to global transcriptional inhibition methods, the use of a Tet-off repressible promoter has the advantage that cells are minimally perturbed by the addition of doxycyclin during the assay. We illustrate the use of a reporter mRNA expressed from a plasmid in Saccharomyces cerevisiae cells, but similar methods can be applied to other regulated promoters, on plasmids or by genome editing, and in other organisms. RNA levels are measured by reverse transcription followed by quantitative PCR. An exponential decay law is then used to estimate how well the measurements follow this expected trend for the simplest possible mechanism of RNA degradation, where the decay is proportional to the amount of RNA present at any given time

Nonlinear network-based quantitative trait prediction from biological data

International audienceAbstract Quantitatively predicting phenotypic variables using biomarkers is a challenging task for several reasons. First, the collected biological observations might be heterogeneous and correspond to different biological mechanisms. Second, the biomarkers used to predict the phenotype are potentially highly correlated since biological entities (genes, proteins, and metabolites) interact through unknown regulatory networks. In this paper, we present a novel approach designed to predict multivariate quantitative traits from biological data which address the 2 issues. The proposed model performs well on prediction but it is also fully parametric, with clusters of individuals and regulatory networks, which facilitates the downstream biological interpretation