Biology subjects

Conte, D.

Publications and source records attributed to Conte, D..

6 recordsLinked to original sources

bioRxiv2025

Symmetry breaking and avalanche shapes in modular neural networks

Modularity is as a key characteristic of structural and functional brain networks across species and spatial scales. We investigate the stochastic Wilson-Cowan model on a modular network in which synaptic strengths differ between intra-module and inter-module connections. The system exhibits a rich phase diagram comprising symmetric (SL and SH) and "broken symmetry" (B1, B2, ...) phases. The phase SL (SH) is characterized by the same low (high) activity in all the modules, while the Bm phases are characterized by a high activity in m modules and low activity in the remaining modules. Between SL and SH, and between SL and B1, there are two lines of critical points, where the system shows a critical behaviour, with power law distributions in the avalanches. Along these lines, avalanche shapes differ systematically: they are symmetric or right-skewed at the SL-SH transition, but can become left-skewed over intermediate durations along the SL-B1 critical line. These results provide a theoretical framework that accounts for both symmetric and left-skewed neural avalanche shapes observed experimentally, linking modular organization to critical brain dynamics.

neuroscience↗

bioRxiv2024

Inferring global exponents in subsampled neural systems

In systems displaying an activity charaterized by avalanches, critical exponents may give informations on the mechanisms underlying the observed behaviour or on the topology of the connections. However, when only a small fraction of the units composing the system are observed and sampled, the measured exponents may differ significantly from the true ones. In this study, using Branching Process and (2+1)D Directed Percolation we show that some of the exponents, namely the ones governing the power spectrum and the detrended fluctuation analysis (DFA) of the system activity, are more robust and are unaffected in some intervals of frequencies by the subsampling. This robustness derives from the preservation of long-time correlations in the subsampled signal, even though large avalanches can be fragmented into smaller ones. These results dont depend on the specific model and may be used therefore to extract in a simple and unbiased way some of the exponents of the unobserved full system.

neuroscience↗

bioRxiv2020

PIE-1 promotes SUMOylation and activation of HDAC1 during the C. elegans oogenesis

Germlines shape and balance heredity, integrating and regulating information from both parental and foreign sources. Insights into how the germline handles information have come from the identification of factors that specify or maintain the germline fate. In early C. elegans embryos, the CCCH zinc-finger protein PIE-1 localizes to the germline where it prevents somatic differentiation programs. Here we show that PIE-1 also functions in the meiotic ovary where it becomes SUMOylated and engages the SUMO-conjugating machinery. Using whole-proteome mass spectrometry to detect SUMO-conjugated proteins, we identify HDAC SUMOylation as a target of PIE-1. Our findings suggest that SUMOylation activates HDAC, lowering histone acetylation and enhancing Argonaute-mediated surveillance in the germline.

molecular biology↗

bioRxiv2020

HDAC1 SUMOylation promotes Argonaute directed transcriptional silencing in C. elegans

Eukaryotic cells use guided search to coordinately control dispersed genetic elements. The transitive effectors of these mechanisms, Argonaute proteins and their small-RNA co-factors, engage nascent RNAs and chromatin-associated proteins to direct transcriptional silencing. The small ubiquitin-like modifier (SUMO) has been shown to promote the induction and maintenance of silent chromatin (called heterochromatin) in yeast, plants, and animals. Here we show that Argonaute-directed transcriptional silencing in C. elegans requires SUMOylation of the type 1 histone deacetylase HDA-1. SUMOylation of HDA-1 promotes interactions with components of the nucleosome remodeling and deacetylase (NuRD) complex and with the nuclear Argonaute HRDE-1/WAGO-9. Our findings suggest how HDAC1 SUMOylation promotes the association of HDAC and other chromatin remodeling factors with a nuclear Argonaute in order to initiate de novo heterochromatin silencing.

molecular biology↗

bioRxiv2020

The RNA phosphatase PIR-1 regulates endogenous small RNA pathways in C. elegans

Eukaryotic cells regulate 5 triphosphorylated (ppp-) RNAs to promote cellular functions and prevent recognition by antiviral RNA sensors. For example, RNA capping enzymes possess triphosphatase domains that remove the {gamma} phosphates of ppp-RNAs during RNA capping. Members of the closely related PIR1 family of RNA polyphosphatases remove both the {beta} and {gamma} phosphates from ppp-RNAs. Here we show that C. elegans PIR-1 dephosphorylates ppp-RNAs made by cellular RdRPs and is required for the maturation of 26G-RNAs, Dicer-dependent small RNAs that regulate thousands of genes during spermatogenesis and embryogenesis. PIR-1 also regulates the CSR-1 22G-RNA pathway and has critical functions in both somatic and germline development. Our findings suggest that PIR-1 modulates both Dicer-dependent and - independent Argonaute pathways, and provide insight into how cells and viruses use a conserved RNA phosphatase to regulate and respond to ppp-RNA species.

molecular biology↗

bioRxiv2020

Diversity of Antimicrobial-Resistant Aeromonas Species Isolated from Aquatic Environments in Brazil

In the present study, we characterized antimicrobial resistance profile and genetic relatedness of Aeromonas spp. isolated from healthcare and urban effluents, wastewater treatment plant (WWTP), and river water. We detected the presence of genes responsible for the resistance to {beta}-lactam, quinolone, and aminoglycoside. Enterobacterial Repetitive Intergenic Consensus PCR and multilocus sequence typing (MLST) were carried out to differentiate the strains and multilocus phylogenetic analysis (MLPA) was used to identify species. A total of 28 Aeromonas spp. cefotaxime-resistant strains were identified that carried a variety of resistance determinants, including uncommon GES-type {beta}-lactamases. Multidrug-resistant Aeromonas spp. were found in hospital wastewater, WWTP, and sanitary effluent. Among these isolates, we detected A. caviae producing GES-1 or GES-5, as well as A. veronii harboring GES-7 or GES-16. We successfully identified Aeromonas spp. by using MLPA and found that A. caviae was the most prevalent species (85.7%). In contrast, it was not possible to determine sequence type of all isolates, suggesting incompleteness of the Aeromonas spp. MLST database. Our findings reinforce the notion about the ability of Aeromonas spp. to acquire determinants of antimicrobial resistance from the environment. Such ability can be enhanced by the release of untreated healthcare effluents, in addition to the presence of antimicrobials, recognized as potential factors for the spread of resistance. Thus, Aeromonas spp. could be included as priority pathogens under the One Health concept. IMPORTANCEAeromonas species are native bacteria in aquatic ecosystems worldwide. However, they have also been isolated from humans and animals. Globally, aquatic environments have been affected by anthropogenic activities. For example, the excessive use of antimicrobials in medical and veterinary practice causes the development of bacterial resistance. In addition, eliminated hospital and sanitary effluents can also serve as potential sources of bacteria carrying antimicrobial resistance genes. Thereby, impacted environments play an important role in the transmission of these pathogens, their evolution, and dissemination of genes conferring resistance to antimicrobials. Aeromonas spp. have been reported as a reservoir of antimicrobial resistance genes in the environment. In this study, we identified a great repertoire of antimicrobial resistance genes in Aeromonas spp. from diverse aquatic ecosystems, including those that encode enzymes degrading broad-spectrum antimicrobials widely used to treat healthcare-associated infections. These are a public health threat as they may spread in the population.

microbiology↗