Biology subjects

Chiari, M.

Publications and source records attributed to Chiari, M..

6 recordsLinked to original sources

bioRxiv2026

Beyond competence: a mechanistic model of avian demographic drivers in West Nile virus dynamics

BackgroundWest Nile virus (WNV) is a vector-borne zoonotic pathogen maintained in an enzootic cycle between birds and mosquitoes which is considered a significant public health concern in Europe, particularly in relation to its recent increase in reported human cases and range expansion. While a comprehensive understanding of the viruss epidemiological dynamics is essential to inform effective prevention and control strategies, to date significant knowledge gaps remain in quantifying interspecific differences within the complex avian communities involved in WNV circulation. Globally, WNV-infection has indeed been documented across more than 300 bird species, however, whether and how inter-specific differences in avian hosts traits affect the spread of WNV is still largely unknown. A substantial body of research has investigated how epidemiological traits, such as the duration of infection and competence, influence WNV dynamics. However, much less is known about the role of avian demography. Methodology/Principal findingsWe therefore investigated through mathematical modelling the role of avian demographic traits in shaping patterns of mosquito WNV infection dynamics in northern Italy (Lombardy Region, 2016-2018). We focused on the effects of annual offspring production, timing and synchrony of breeding which ultimately affect seasonal abundance of competent avian hosts. We highlighted that timing of breeding has the greatest effect on the number of infected mosquitoes, while annual offspring production influences the timing of the infection peak. Our simulations provide evidence that non-corvid species can have a key impact on WNV transmission. Conclusion/SignificanceThese results can support future research by providing priority bird species to direct further studies and by suggesting that the acknowledgment of spatio-temporal variation in the abundance of competent avian hosts plays a key role in the development of effective surveillance strategies and mosquito control actions. Author summaryWest Nile virus (WNV) is endemic in Italy and represents a significant public health threat in Europe, with increasing cases of severe neuroinvasive disease in humans in recent years. Surveillance data reveal marked spatial and temporal variability in infection dynamics, suggesting that key drivers of WNV transmission remain poorly understood. The contribution of different bird species (over 300 are implicated in the WNV cycle) is often overlooked despite evidence that species-specific traits are critical determinants of WNV infection dynamics. Few studies have examined birds demographic traits, despite their well-established importance in shaping infection dynamics across diseases. Given the challenges in collecting detailed wildlife data, we employed mechanistic models to explore transmission scenarios and test whether avian demographic traits influence bird species roles in WNV transmission and maintenance in Lombardy. Our findings demonstrate that brood size, hatching synchrony, and hatching time significantly affect estimated WNV prevalence in mosquitoes.

ecology↗

bioRxiv2026

Computational Drug Repurposing Targeting LuxS-Mediated Quorum Sensing in Fusobacterium nucleatum: A Virtual Screening and Molecular Dynamics Approach

Fusobacterium nucleatum is an anaerobic bacterium strongly associated with the development and progression of colorectal cancer (CRC). Its pathogenic mechanisms involve the LuxS/AI-2 quorum sensing (QS) system, which regulates biofilm formation, virulence factor expression, and host immune evasion. Targeting LuxS represents a promising anti-virulence strategy that could disrupt bacterial communication without inducing selective pressure for antibiotic resistance. In this study, we employed a computational drug repurposing pipeline to identify FDA-approved drugs capable of inhibiting the LuxS enzyme in F. nucleatum. We performed structure-based virtual screening of 9,466 compounds from DrugBank using AutoDock Vina against the AlphaFold-predicted LuxS structure (UniProt: A0A133NIU3). From 1,082 initial hits (binding energy [≤] - 7.0 kcal/mol), we applied ADMET filtering and composite scoring to select the top 5 candidates. Molecular dynamics simulations (10 ns each) using OpenMM with the AMBER14 force field confirmed the stability of all five protein-ligand complexes (RMSD < 2.0 [A]). The most promising candidates include Tubocurarine ({Delta}G = -16.97 kcal/mol, RMSD = 1.87 [A]), Docetaxel ({Delta}G = -13.22 kcal/mol, RMSD = 1.81 [A]), Metyrosine ({Delta}G = -13.78 kcal/mol, RMSD = 1.97 [A]), and Ergometrine ({Delta}G = -13.22 kcal/mol, RMSD = 1.92 [A]). These results constitute an exploratory computational basis that requires subsequent experimental validation through in vitro and in vivo assays, and provide candidates for testing as anti-quorum sensing agents against F. nucleatum, with potential implications for CRC prevention and treatment.

microbiology↗

bioRxiv2022

Understanding West Nile virus spread: Mathematical modelling to determine the mechanisms with the most influence on infection dynamics.

West Nile disease is a vector-borne disease caused by West Nile virus (WNV), involving mosquitoes as vectors and birds as maintenance hosts. Humans and other mammals can be infected via mosquito bites, developing symptoms ranging from mild fever to severe neurological infection. Due to the worldwide spread of WNV, human infection risk is high in several countries. Nevertheless, there are still several knowledge gaps regarding WNV dynamics. Several aspects of transmission taking place between birds and mosquitoes, such as the length of the infectious period in birds or mosquito biting rates, are still not fully understood, and precise quantitative estimates are still lacking for the European species involved. This lack of knowledge affects the precision of parameter values when modelling the infection, consequently resulting in a potential impairment of the reliability of model simulations and predictions. Further investigations are thus needed to better understand these aspects, but field studies, especially those involving several wild species, such as in the case of WNV, can be challenging. Thus, it becomes crucial to identify which mechanisms most influence the dynamics of WNV transmission. In the present work, we propose a sensitivity analysis to identify the parameters that have the largest impact on the spread of the infection. Based on a mathematical model simulating WNV spread into the Lombardy region (northern Italy), the basic reproduction number of the infection was estimated and used to quantify infection spread into mosquitoes and birds. Then, we quantified how variations in the duration of the infectious period in birds, the mosquito biting rate on birds, and the competence and susceptibility to infection of different bird species might affect WNV transmission. Our study highlights that all considered parameters can affect the spread of WNV, but the duration of the infectious period in birds and mosquito biting rate are the most impactful, highlighting the need for further studies to better estimate these parameters. In addition, our study suggests that a WNV outbreak is very likely to occur in all areas with suitable temperatures, highlighting the wide area where WNV represents a serious risk for public health. Author SummaryInfectious communicable diseases are currently one of the main burdens for human beings and public health. The comprehension of their spread and maintenance is one of the main goals to facilitate their control and eradication, but due to the complexity of their cycles and transmission mechanisms, obtaining this information is often difficult and demanding. The control of vector-borne diseases in particular represents an important and very complex challenge for public health. Mathematical models are suitable tools to investigate disease dynamics and their transmission mechanisms. To build a suitable model that can simulate transmission dynamics, a reliable and precise estimate of parameters for measuring transmission mechanisms is fundamental. We thus propose a sensitivity analysis of four unknown epidemiological parameters (bird recovery rate, mosquito biting rate, avian susceptibility to infection and avian competence to infection) that play a crucial role in driving West Nile virus (WNV) infection to determine which of them have the greatest impact on infection spread. This analysis allows us to identify the investigated parameters that need the most accurate estimate and to further investigate mechanisms that majorly affect WNV spread.

ecology↗

bioRxiv2020

EVs analysis in the COVID-19 era: insights on serum inactivation protocols towards downstream isolation and analysis

Since the outbreak of COVID-19 crisis, the handling of biological samples from confirmed or suspected SARS-CoV-2 positive individuals demanded the use of inactivation protocols to ensure laboratory operators safety. While not standardized, these practices can be roughly divided in two categories, namely heat inactivation and solvent-detergent treatments. As such, these routine procedures should also apply to samples intended for Extracellular Vesicles (EVs) analysis. Assessing the impact of virus inactivating pre-treatments is therefore of pivotal importance, given the well-known variability introduced by different pre-analytical steps on downstream EVs isolation and analysis. Arguably, shared guidelines on inactivation protocols tailored to best address EVs-specific requirements will be needed among the EVs community, yet deep investigations in this direction havent been reported so far. In the attempt of sparking interest on this highly relevant topic, we here provide preliminary insights on SARS-CoV-2 inactivation practices to be adopted prior serum EVs analysis by comparing solvent/detergent treatment vs. heat inactivation. Our analysis entailed the evaluation of EVs recovery and purity along with biochemical, biophysical and biomolecular profiling by means of Nanoparticle Tracking Analysis, Western Blotting, Atomic Force Microscopy, miRNA content (digital droplet PCR) and tetraspanin assessment by microarrays. Our data suggest an increase in ultracentrifugation (UC) recovery following heat-treatment, however accompanied by a marked enrichment in EVs-associated contaminants. On the contrary, solvent/detergent treatment is promising for small EVs (< 150 nm range), yet a depletion of larger vesicular entities was detected. This work represents a first step towards the identification of optimal serum inactivation protocols targeted to EVs analysis.

biochemistry↗

bioRxiv2020

SARS-CoV-2 epitope mapping on microarrays highlights strong immune-response to N protein region

A workflow for SARS-CoV-2 epitope discovery on peptide microarrays is herein reported. The process started with a proteome-wide screening of immunoreactivity based on the use of a high-density microarray followed by a refinement and validation phase on a restricted panel of probes using microarrays with tailored peptide immobilization through a click-based strategy. Progressively larger, independent cohorts of Covid-19 positive sera were tested in the refinement processes, leading to the identification of immunodominant regions on SARS-CoV-2 Spike (S), Nucleocapsid (N) protein and Orf1ab polyprotein. A summary study testing 50 serum samples highlighted an epitope of the N protein (region 155-171) providing 92% sensitivity and 100% specificity of IgG detection in Covid-19 samples thus being a promising candidate for rapid implementation in serological tests.

biochemistry↗

bioRxiv2020

Non-Langmuir kinetics of DNA surface hybridization

Hybridization of complementary single strands of DNA represents a very effective natural molecular recognition process widely exploited for diagnostic, biotechnology and nanotechnology applications. A common approach relies on the immobilization on a surface of single stranded DNA probes that bind complementary targets in solution. However, despite the deep knowledge on DNA interactions in bulk solution, the modelling of the same interactions on a surface are still challenging and perceived as strongly system-dependent. Here we show that a two dimensional analysis of the kinetics of hybridization, performed at different target concentration and probe surface density by a label-free optical biosensor, reveals peculiar features inconsistent with an ideal Langmuir-like behaviour. We propose a simple non-Langmuir kinetic model accounting for an enhanced electrostatic repulsion originating from the surface immobilization of nucleic acids and for steric hindrance close to full hybridization of the surface probes. The analysis of the kinetic data by the model enables to quantify the repulsive potential at the surface, as well as to retrieve the kinetic parameters of isolated probes. We show that the strength and the kinetics of hybridization at large probe density can be improved by a 3D immobilization strategy of probe strands with a double stranded linker. Statement of SignificanceHybridization of nucleic acids strands with complementary sequences is a fundamental biological process and is also widely exploited for diagnostic purposes. Despite the availability of effective models for the equilibrium strength of freely diffusing strands, a general predictive model for surface hybridization is still missing. Moreover, the kinetics of hybridization is not fully understood neither in solution nor on a surface. In this work we show that the analysis of the kinetics of hybridization on a surface reveals and enables to quantify two main additional contributions: electrostatic repulsion and steric hindrance. These are general effects expected to occur not only on a surface but in any condition with large density of nucleic acids, comparable to that of the cellular nucleus.

biophysics↗