Biology subjects

Casanova, C.

Publications and source records attributed to Casanova, C..

8 recordsLinked to original sources

bioRxiv2026

PCR-free, targeted genomic sequencing using Dynamically optimized reference Adaptive Sampling (DORAS)

Whole genome sequencing (WGS) has become a cornerstone of clinical microbiology, enabling comprehensive analysis of microbial genome diversity. However, WGS is often computationally intensive and time-consuming when applied to specific applications like multilocus sequence typing (MLST), where only a subset of genes is only needed for typing. This study evaluates the potential of adaptive sampling (AS), a software-based solution available on Oxford Nanopore Technologies (ONT) devices, to optimize sequencing runs for MLST by reducing the production of unnecessary reads falling outside of the target areas. We demonstrate that AS, when used directly with the target gene sequences, does not reach sufficient target coverage when compared to WGS baseline sequencing due to inefficient read recruitment. Thus, we developed a novel, PCR-free approach, termed Dynamically Optimized Reference Adaptive Sampling (DORAS), which streamlines gene-specific enrichment by targeting genomic regions of interest and their genomic vicinity. DORAS first determines the genomic context of regions of interest for each sample, and then dynamically adjusts the length of the reference sequences during live sequencing. Consensus sequences are periodically constructed and evaluated for taxonomic classification. We demonstrate that full MLST profiles can be obtained in approximately half the time required for whole-genome sequencing to achieve 30X coverage (3 vs. 6 h), with no additional hands-on library preparation time. Validation on clinical isolates from hospital outbreaks belonging to Corynebacterium diphtheriae, vancomycin-resistant Enterococci, and routine clinical E. coli isolates, demonstrated the consistent retrieval of MLST types as compared to standard WGS methods. DORAS thus offers a cost-effective, efficient solution for routine surveillance and outbreak investigations based on MLST types in the clinical setting.

genomics↗

bioRxiv2024

Estimating the effective population size across space and time in the Critically Endangered western chimpanzee in Guinea-Bissau: challenges and implications for conservation management

Effective population size (Ne) is a key concept in evolutionary and conservation biology. The western chimpanzee (Pan troglodytes verus) is a Critically Endangered taxon. In Guinea-Bissau, chimpanzees are mainly threatened by habitat loss, hunting and diseases. Guinea-Bissau is considered a key area for its conservation. Genetic tools have not yet been applied to inform management and no estimates of Ne have been obtained. In this study, we use countrys range-wide microsatellite data and five whole-genome sequences to estimate several Ne and infer the recent and ancient demographic history of populations using different methods. We also aim to integrate the different Ne estimates to improve our understanding of the evolutionary history and current demography of this great ape and to discuss strengths and limitations of each estimator and their complementarity in informing conservation decisions. Results from the PSMC method suggest a large ancestral Ne, likely due to ancient structure over the whole subspecies distribution until approximately 10-15,000 years ago. After that, a change in connectivity, a real decrease in size or a combination of both occurred, which reduced the then still large ancestral population to a smaller size (MSVAR: [~]10,000 decreasing to 1,000-6,000 individuals), possibly indicating a fragmentation into coastal and inner subpopulations. In the most recent past, contemporary Ne is below or close to 500 (GONE: 116-580, NeEstimator: 107-549), suggesting a high risk of extinction. The populations at coastal Parks may have been small or isolated for several generations whereas the Boe Park one exhibit higher long-term Ne estimates and can be considered a stronghold of chimpanzee conservation. Through combining different types of molecular markers and analytical methodologies, we try to overcome the limitations of obtaining high quality DNA sampling from wild threatened populations and estimate Ne at different temporal and spatial scales, which is crucial information to make informed conservation decisions at local and regional scales.

genomics↗

bioRxiv2024

Exposure of gut bacterial isolates to the anthelminthic drugs, ivermectin and moxidectin, leads to antibiotic-like phenotypes of growth inhibition and adaptation.

Due to their broad-spectrum activities, ivermectin and moxidectin are widely used anthelminthics in veterinary and human medicine. However, ivermectin has recently been shown to perturbate gut-microbial growth. Given the macrolide-like structure of both ivermectin and moxidectin, there is a need to characterize the antibiotic spectrum of these anthelminthic drugs and their potential implications in the development of cross-resistance to macrolides and other families of antibiotics. Here, we incubated 59 bacterial isolates representing different clades frequently found in the gut with ivermectin and moxidectin at different concentrations for 16-72h. Further, we challenged 10 bacterial isolates with repeated and gradually increasing concentrations of these two anthelminthics and subsequently characterized their sensitivity to different antibiotics as well as ascending anthelminthic concentrations. We found, that antibacterial activity of the two anthelminthics is comparable to a selection of tested antibiotics, as observed by potency and dose dependence. Bacterial anthelminthic challenging in vitro resulted in decreased anthelminthic sensitivity. Further, adaptation to anthelminthics is associated with decreased antibiotic sensitivity towards three macrolides, a lincosamide, a fluoroquinolone, a tetracycline and two carbapenems. The observed change in bacterial sensitivity profiles is associated with - and likely caused by - repeated anthelminthic exposure. Hence, current and future large-scale administration of ivermectin and moxidectin, respectively, for the control of helminths and malaria raises serious concerns - and hence potential off-target effects should be carefully monitored.

microbiology↗

bioRxiv2024

The impact of kinship composition on social structure

The relatedness between group members is a potential driver of variation in social structure. Relatedness predicts biases in partner choice and formation of strong relationships among group members. As such, groups that differ in their percentage of non-kin dyads, i.e., in their kinship composition, should therefore differ in the structure of their social networks. Yet the relationship between kinship composition and social structure remains unclear. Here, we used long-term social and pedigree data from a population of rhesus macaques to investigate the relationship between kinship composition and the connectivity, cohesion, potential for transmission and social differentiation of the social networks of adult female macaques. We found no evidence that the social structure of groups composed of greater proportion of unrelated females differ from that of groups with a lower proportion of non-kin. To investigate this unexpected finding, we built agent-based models parameterised with the empirical data to further explore (1) the expected relationship between kinship composition and social structure and (2) why we did not find such a relationship in the empirical data. Agent-based models showed that kinship composition can influence social structure in populations similar to the one studied, but that this effect may only be detectable with a sample size even larger than ours (19 group-years) and with greater variance in kinship composition (proportion of non-kin varied between 0.830-0.922 in the empirical data). The relationship between kinship composition and social structure might be more apparent when comparing data from species that differ strongly in their social organisation, translating into marked differences in kinship composition. This further emphasises the importance of reporting existing and future kinship composition data to deepen our understanding of the evolution of sociality and highlights the potential of agent-based models to better understand empirical results.

animal behavior and cognition↗

bioRxiv2021

Corticothalamic Projections Gate Alpha Rhythms in the Pulvinar

Two types of corticothalamic (CT) terminals reach the pulvinar nucleus of the thalamus, and their distribution varies according to the hierarchical level of the cortical area they originate from. While type 2 terminals are more abundant at lower hierarchical levels, terminals from higher cortical areas mostly exhibit type 1 axons. Such terminals also evoke different excitatory postsynaptic potential dynamic profiles, presenting facilitation for type 1 and depression for type 2. As the pulvinar is involved in the oscillatory regulation between intercortical areas, fundamental questions about the role of these different terminal types in the neuronal communication throughout the cortical hierarchy are yielded. Our theoretical results support that the co-action of the two types of terminals produces different oscillatory rhythms in pulvinar neurons. More precisely, terminal types 1 and 2 produce alpha-band oscillations at a specific range of connectivity weights. Such oscillatory activity is generated by an unstable transition of the balanced state networks properties that it is found between the quiescent state and the stable asynchronous spike response state. While CT projections from areas 17 and 21a are arranged in the model as the empirical proportion of terminals types 1 and 2, the actions of these two cortical connections are antagonistic. As area 17 generates low-band oscillatory activity, cortical area 21a shifts pulvinar responses to stable asynchronous spiking activity and vice-versa when area 17 produces an asynchronous state. To further investigate such oscillatory effects through corticothalamo-cortical projections, the transthalamic pathway, we created a cortical feedforward network of two cortical areas, 17 and 21a, with CT connections to a pulvinar-like network. With this model, the transthalamic pathway propagates alpha waves from the pulvinar to area 21a. This oscillatory transfer ceases when reciprocal connections from area 21a reach the pulvinar, closing the cortico-thalamic loop. Taken together, results of our model suggest that the pulvnar shows a bi-stable spiking activity, oscillatory or regular asynchronous spiking, whose responses are gated by the different activation of cortico-pulvinar projections from lower to higher-order areas such as areas 17 and 21a.

neuroscience↗

bioRxiv2021

Light-mediated planar polarization of cone photoreceptorcilia contributes to visual acuity in mammals

The coordinated spatial arrangement of organelles within a tissue plane, generally referred to as Planar Cell Polarity (PCP), is critical for various processes ranging from organogenesis to sensory detection. Mechanistically, planar cell polarity is typically set-up by gradients of morphogens and their receptors, but whether non-molecular cues, akin to phototropism in plants, might play a part in setting up PCP in animals remains unknown. Here we report that the basal body of newborn photoreceptor cells in the mouse retina is centrally positioned, but then moves laterally around the first post-natal week, thereby generating cell-intrinsic asymmetry. During the second postnatal week, when eyes open, the basal bodies of cone photoreceptor cilia, but not rods, become coordinated across the tissue plane to face the center of the retina. Mechanistically, we show that light is required during a critical window in development, triggering a non-canonical cascade whereby cone transducin interacts with the G- protein signaling modulator protein 2 (GPSM2), which is in turn necessary for cone PCP. This work uncovers a non-canonical PCP pathway initiated by light.

cell biology↗

bioRxiv2021

Dynamical processing of orientation precision in the primary visual cortex

In our daily visual environment, the primary visual cortex (V1) processes distributions of oriented features as the basis of our visual computations. Changes of the global, median orientation of such inputs form the basis of our canonical knowledge about V1. However, another overlooked but defining characteristic of these sensory variables is their precision, which characterizes the level of variance in the input to V1. Such variability is an intrinsic part of natural images, yet it remains unclear if and how V1 accounts for the changes in orientation precision to achieve its robust orientation recognition performances. Here, we used naturalistic stimuli to characterize the response of V1 neurons to quantified variations of orientation precision. We found that about thirty percent of the recorded neurons showed a form of invariant responses to input precision. While feedforward mechanisms failed to account for the existence of these resilient neurons, neuronal competition within V1 explained the extent to which a neuron is invariant to precision. Using a decoding algorithm, we showed that the existence of such neurons in the population response of V1 can serve to encode both the orientation and its precision in the V1 population activity, which improves the robustness of the overall neural code. These precision-specific neurons operate with slow recurrent cortical dynamics, which supports the notion of predictive precisionweighted processes in V1.

neuroscience↗

bioRxiv2019

A sample-to-report solution for taxonomic identification of cultured bacteria in the clinical setting based on nanopore sequencing

Amplicon sequencing of 16S rRNA gene is commonly used for the identification of bacterial isolates in diagnostic laboratories, and mostly relies on the Sanger sequencing method. The latter, however, suffers from a number of limitations with the most significant being the inability to resolve mixed amplicons when closely related species are co-amplified from a mixed culture. This often leads to either increased turnover time or absence of usable sequence data. Short-read NGS technologies could address the mixed amplicon issue, but would lack both cost efficiency at low throughput and fast turnaround times. Nanopore sequencing developed by Oxford Nanopore Technologies (ONT) could solve those issues by enabling flexible number of samples per run and adjustable sequencing time. Here we report on the development of a standardized laboratory workflow combined with a fully automated analysis pipeline LORCAN (Long Read Consensus ANalysis), which together provide a sample-to-report solution for amplicon sequencing and taxonomic identification of the resulting consensus sequences. Validation of the approach was conducted on a panel of reference strains and on clinical samples consisting of single or mixed rRNA amplicons associated with various bacterial genera by direct comparison to the corresponding Sanger sequences. Additionally, artificial read mixtures of closely related species were used to assess LORCANs behaviour when dealing with samples with known cross-contamination level. We demonstrate that by combining ONT amplicon sequencing results with LORCAN, the accuracy of Sanger sequencing can be closely matched (>99.6% sequence identity) and that mixed samples can be resolved at the single base resolution level. The presented approach has the potential to significantly improve the flexibility, reliability and availability of amplicon sequencing in diagnostic settings.

microbiology↗