Biology subjects

Bernard, E.

Publications and source records attributed to Bernard, E..

15 recordsLinked to original sources

bioRxiv2026

Multi-site phenotypic characterisation of Kisumu colonies for comparison of insecticide susceptibility between testing centres

Testing of insecticides and insecticide-based vector control tools relies on the use of bioassays whereby insects are exposed and mortality, or another relevant entomological endpoint, is measured. To be able to compare results between products and across time and space standard laboratory strains are used. Insecticide-susceptible strains are often used as comparators in studies involving insecticide-resistant populations. Kisumu is a long-established, widely-used insecticide-susceptible strain of Anopheles gambiae. In this study, 16 facilities across different countries exposed their Kisumu colonies aged 3-5 days to four insecticides (permethrin, alpha-cypermethrin, DDT and pirimiphos-methyl) at a range of concentrations in WHO tube assays to assess susceptibility. Insecticide-treated filter papers were made at the Liverpool School of Tropical Medicine and sent to testing centres, along with a standard protocol and testing conditions requirements, to standardise testing as much as possible. A first observation was that DDT results were affected by the use of Risella oil, the WHO-recommended carrier oil but immiscible in acetone, leading to uneven coating of papers and increased variability in bioassay results (40x variance between colonies). Bioassay data generated by the testing facilities suggest a wide range of susceptibility to different insecticides between colonies of Kisumu: LC50 values between colonies differed, though not significantly, by up to 4x for permethrin, 6x for pirimiphos-methyl, and 15x for alpha-cypermethrin. Some colonies are classified as insecticide resistant based on the WHO definition of <98% mortality on exposure to a discriminating concentration. The assumption that Kisumu is a standard susceptible strain, consistent between facilities is challenged, which has implications when comparing results between studies. We propose genotypic analysis of the colonies to identify signs of resistance markers indicative of contamination from resistant strains or wild mosquitoes, and generation of guidance to support the maintenance and monitoring of susceptible mosquito strains.

zoology↗

bioRxiv2026

SHERLOC: An interpretable deep learning model for longitudinal circulating tumor DNA data in survival analysis

Longitudinal circulating tumor DNA (ctDNA) measurements offer a noninvasive means to monitor treatment response, but clinical trial data present substantial methodological challenges due to high-dimensional short longitudinal ctDNA sequences and limited sample sizes. We introduce SHERLOC, a deep learning framework specifically designed for survival analysis using longitudinal on-treatment ctDNA data, which integrates shared temporal representations of gene-level variant allele frequencies, feature-specific temporal trajectories of panel-level ctDNA biomarkers, and survival-aware genomic representations pre-trained on a large pan-cancer tissue-biopsy dataset (MSK-CHORD), within an interpretable Cox proportional hazards framework. Benchmarked against diverse statistical, ensemble, and deep learning approaches in a non-small-cell lung cancer cohort from the phase III IMpower150 trial, SHERLOC consistently achieved superior survival discrimination and calibration, while remaining interpretable and robust to reductions in the number of available longitudinal liquid biopsy time points per patient. The resulting ctDNA-based risk score provided prognostic information both independent of and complementary to standard radiographic response assessments, and enabled patient stratification within homogeneous RECIST response groups--highlighting its potential as an early, non-invasive decision-support tool to guide treatment adaptation and patient management.

cancer biology↗

bioRxiv2026

Reversible peptide self-assembly enables sustained drug delivery with tuneable pharmacokinetics

Therapeutic peptides combine high target specificity with potent biological activity.1 However, treatment success is often limited by rapid clearance and the need for frequent injections.2, 3 This challenge is particularly acute for therapeutic peptides used in obesity, where clinical benefit must be balanced against dose-dependent adverse effects. In nature, these constraints are overcome by storing hormones as reversible fibrils,4 but pharmacokinetic control is essential for widespread adoption of bio-inspired self-assembled depots for therapeutic peptides. Here, we show that tuneable pharmacokinetics can be achieved and modelled by mapping the fundamental chemical parameters of reversibly self-assembly in vitro. We demonstrate this approach for the amylin analogue pramlintide. Amylin analogues are under development for the next generation of diabetes and obesity treatments, with improved mechanism of action e.g. preserving lean body mass.5-8 Pramlintide is an approved drug with a well-established safety profile, however, it has a comparable half-life to native amylin.8-12 In a pilot study, we achieve in vitro-in vivo correlation, increasing the half-life of pramlintide 20-82-fold in rats, while controlling burst release. These findings demonstrate that the optimisation of pharmacokinetics can be decoupled from peptide engineering, establishing a generalisable framework for generating long-acting peptide formulations by emulating native storage mechanisms.

biophysics↗

bioRxiv2025

Molecular Surveillance Identifies Evidence of Getah Virus (GETV) in Mosquito Vectors in Alabama, USA

The Getah virus (GETV) is a mosquito-borne RNA virus in the Togaviridae family and the Alphavirus genus, associated with severe disease outbreaks in livestock across Asia-Pacific regions. Since its first isolation in Malaysia in 1955, GETV has been reported in Eurasia and the South Pacific, yet documented cases in the United States remain exceptionally rare, leaving major gaps in regional vector competence and surveillance data. To evaluate the potential of local mosquito populations as GETV carriers, field collections were conducted in Montgomery and Pike Road neighborhoods of Alabama from 2023 to 2024, capturing multiple mosquito species for molecular screening. Initial real-time qPCR assays on 200 pooled and individual samples suggested that approximate 30% of specimens demonstrated possible GETV carriage potential. To validate viral presence, two distinct primer sets were designed to amplify viral genome fragments. Mosquito RNA was reverse-transcribed into cDNA, followed by conventional PCR. The first PCR, targeting [~]280 bp, produced single or multiple amplicon bands in 32% of samples via gel electrophoresis. These positive cDNAs were re-amplified with a second primer pair targeting a [~]430 bp fragment from a separate genomic region, yielding confirmatory bands in 30% of specimens. Amplified products were purified and Sanger sequenced, revealing approximate 95% nucleotide similarity to the wild-type GETV reference genome. This study delivers the first field-based molecular evidence supporting GETV detection in Alabama mosquitoes, signaling either localized emergence or potential introduction of the virus. These findings underscore the need for expanded vector competence profiling, arboviral surveillance, and livestock disease preparedness in the southeastern United States, strengthening both public health readiness and state-level vector monitoring strategies.

microbiology↗

bioRxiv2025

Ambecovirus, a novel Betacoronavirus subgenus circulating in neotropical bats sheds new light on bat-borne coronaviruses evolution

Understanding the viral diversity harboured by wildlife is essential for effective prediction and prevention of future zoonotic outbreaks. Bats, in particular, are recognized as natural reservoirs for several zoonotic viral pathogens of high impact on public health, including coronaviruses responsible for SARS, the rabies virus, Marburg, Ebola, Nipah and Hendra viruses. However, the large extent of bat viruses remains unexplored, especially in highly biodiverse regions of the Neotropics such as Brazil. We used a meta-transcriptomic to characterize new virus genomes found in blood, oral and anal samples collected from cave- and non-cave bats from Northeast Brazil. From a total of 19 coronavirus-positive bats, we have assembled two complete genomes of a new Betacoronavirus subgenus, named Ambecovirus (American betacoronavirus). The subgenus herein described is phylogenetically placed between the Sarbeco-/Hibeco-/Nebecovirus and the Merbeco-/Embecovirus clades, being basal to the former. While the conserved S2 region of the spike protein retained hallmark domains, including HR1 and HR2, the S1/S2 cleavage site and the furin cleavage site, the S1 region consistently displayed only the N-terminal domain. The receptor-binding domain could not be identified due to high dissimilarity relative to known congeneres. The detection of Ambercovirus in sympatric Pteronotus gymnonotus and Carollia perspicillata bats suggests interspecies transmission. Longitudinal sampling confirmed persistent Ambecovirus infection in P. gymnonotus over multiple years and virus dispersion at a minimum distance of 270 km between caves. The present study confirms that viral diversity in neotropical hosts remains largely unknown not just in Brazil but, likely, in the other countries of the region, supporting the need for a systematic approach to virome exploration and analysis followed by in vitro experimentation to assess zoonotic potential.

evolutionary biology↗

bioRxiv2025

Three-dimensional fossils of a Cretaceous collared carpet shark (Parascylliidae, Orectolobiformes) shed light on skeletal evolution in galeomorphs

A rich fossil record of teeth shows that many living shark families origins lie deep in the Mesozoic. Skeletal fossils of the sharks to whom these teeth belonged are far rarer and when they are preserved are often flattened, hindering understanding of the evolutionary radiation of living shark groups. Here we use computed tomography to describe two articulated Upper Cretaceous shark skeletons from the Chalk of the UK preserving three- dimensional neurocrania, visceral cartilages, pectoral skeletons and vertebrae. These fossils display skeletal anatomies characteristic of the Parascylliidae, a family of Orectolobiformes now endemic to Australia and the Indo Pacific. However, they differ in having a more heavily mineralised braincase and a tri-basal pectoral fin endoskeleton, while their teeth can be attributed to a new species of the problematic taxon Pararhincodon. Phylogenetic analysis of these new fossils confirms that Pararhincodon is a stem-group parascylliid, providing insight into the evolution of parascylliids distinctive anatomy during the late Mesozoic-Cenozoic shift in orectolobiform biodiversity from the Northern Atlantic to the Indo Pacific. Meanwhile both Pararhincodon and extant parascylliids have a distinctive vertebral morphology previously described only in Carcharhiniformes, contributing a skeletal perspective to the picture emerging from macroevolutionary analyses of coastal, small-bodied origins for galeomorphs.

paleontology↗

bioRxiv2025

Delayed Trp53 activation protects Dnmt3a-mutant hematopoietic stem cells from inflammatory attrition.

Hematopoietic stem cells (HSCs) accumulate somatic mutations over time, some conferring a fitness advantage that can lead to clonal hematopoiesis (CH). Mutations in DNMT3A, particularly at hotspot R882, are the most prevalent in CH and carry an increased risk of acute myeloid leukemia (AML). Although DNMT3A R882 mutations are linked to global DNA hypomethylation, the mechanisms underlying their selective advantage remain unclear. Here, we show that Dnmt3a-R882H mutant HSCs exhibit resilience under inflammatory and genotoxic stress. During IL-1{beta}-induced emergency granulopoiesis, Dnmt3a R882H/+ HSCs uncouple increased proliferation from stem cell exhaustion. In contrast, wild-type HSCs rapidly progress to terminal differentiation. We link this phenotype to a delayed activation of the p53-p21-DREAM axis, that allows mutant HSCs to avoid attrition, despite increased replication stress. Similarly, mutant HSCs exhibit delayed Trp53 activation following irradiation, but eventually recover a physiological Trp53 response. Analysis of patient data reveals shared phenotypic features between DNMT3A and monoallelic TP53 mutations in CH and myeloid neoplasms, highlighting potential functional similarities. Collectively, these findings suggest that the expansion of DNMT3A-mutant clones is affected by impaired TP53 signaling, which confers resilience against stressors. Therapeutic strategies targeting inflammatory pathways or the p53-p21-DREAM axis may reduce DNMT3A-CH expansion and/or progression and its associated risks.

molecular biology↗

bioRxiv2023

In situ characterization of late Chikungunya virus replication organelle

Chikungunya virus (CHIKV) is a mosquito-borne pathogen responsible for an acute musculo-skeletal disease in humans. The viral RNA genome replication occurs in membrane spherules named replication organelles (ROs). In this work, we investigate the native structural organization of CHIKV ROs in their cellular context using in situ cryogenic-electron microscopy approaches at late replication stage. We observed previously unreported diameter heterogeneity of ROs at the plasma membrane of infected human cells. CHIKV ROs were only marginally detected in cytopathic vacuoles where they are homogeneous in size, suggesting a finely regulated internalization process. Our data show that ROs maintained at the plasma membrane beyond the first viral cycle are dynamically active both in viral RNA replication, in its export to the cell cytosol, but also in the production of viral proteins. We suggest that late CHIKV ROs have an amplifying role or represent an alternative pathway in the production of infectious viral particles. All these observations bring new insight into the CHIKV life cycle in human cells.

molecular biology↗

bioRxiv2022

The virome of bats inhabiting Brazilian biomes: knowledge gaps and biases towards zoonotic viruses

Bats are hosts of a large variety of viruses including some that may infect other vertebrates and humans. Research on bat-borne viruses attracted significant attention in recent years mainly due to epizootics caused by viruses having bats as hosts. The characterization of the viral communities of bats was then prioritized, but despite increasing efforts, there are large disparities in the geographical ranges covered and the methodologies employed around the world. As a result, large gaps remain in our current understanding of bat viromes and their role in disease emergence. This is particularly true for megadiverse regions in Latin America. This review aims to summarize the current understanding about bat-viruses that inhabit Brazilian biomes, one of the most bat species-rich and diverse regions of the globe. Taking into account all known bat-associated viral families studied in Brazilian biomes, we found that almost half of all bat species (86/181 species) were not investigated for viruses at all. Moreover, only a small fraction of viral lineages or families have been studied more in depth, usually employing targeted methods with limited power to characterize a broad virus diversity. Additionally, these studies relied on limited spatio-temporal sampling and small sample sizes. Therefore, our current understanding of bat viral communities in the Brazilian biomes is limited and biased at different levels, limiting zoonotic risk assessments of bat-borne viruses. Considering these limitations, we propose strategies to bridge the existing gaps in the near future.

microbiology↗

bioRxiv2021

Bioacoustics for in situ validation of species distribution modelling: An example with bats in Brazil

Species distribution modelling (SDM) gained importance on biodiversity distribution and conservation studies worldwide, including prioritizing areas for public policies and international treaties. Useful for large-scale approaches and estimates, is a plus considering that a minor fraction of the planet is adequately sampled. However, SDM needs to be as reliable as possible. Minimizing errors is challenging, but essential, considering the uses and consequences of such models. In situ validation of the SDM outputs should be a key-step - in some cases, urgent. Bioacoustics can be used to validate and refine those outputs, especially if the focal species vocalizations are conspicuous and species-specific. This is the case of echolocating bats. Here, we used extensive acoustic monitoring (>120 validation points, covering >758,000 km2, and >300,000 sound files) to validate MaxEnt outputs for six neotropical bat species in a poorly-sampled region of Brazil. Based on in situ validation, we evaluated four threshold-dependent theoretical evaluation metrics ability in predicting models performance. We also assessed the performance of three widely used thresholds to convert continuous SDMs into presence/absence maps. We demonstrated that MaxEnt produces very different outputs, requiring a careful choice on thresholds and modeling parameters. Although all theoretical evaluation metrics studied were positively correlated with accuracy, we empirically demonstrated that metrics based on specificity-sensitivity and sensitivity-precision are better for testing models, considering that most SDMs are based on unbalanced data. Without independent field validation, we found that using an arbitrary threshold for modelling can be a precarious approach with many possible outcomes, even after getting good evaluation scores. Bioacoustics proved to be important for validating SDMs for the six bat species analyzed, allowing a better refinement of SDMs in large and under-sampled regions, with relatively low sampling effort. Regardless of species assessing method used, our research highlighted the vital necessity of in situ validation for SDMs.

ecology↗

bioRxiv2020

A genome-wide CRISPR/Cas9 knock-out screen identifies the DEAD box RNA helicase DDX42 as a broad antiviral inhibitor

Genome-wide screens are powerful approaches to unravel new regulators of viral infections. Here, we used a CRISPR/Cas9 screen to reveal new HIV-1 inhibitors. This approach led us to identify the RNA helicase DDX42 as an intrinsic antiviral inhibitor. DDX42 was previously described as a non-processive helicase, able to bind RNA secondary structures such as G-quadruplexes, with no clearly defined function ascribed. Our data show that depletion of endogenous DDX42 significantly increased HIV-1 DNA accumulation and infection in cell lines and primary cells. DDX42 overexpression inhibited HIV-1, whereas a dominant-negative mutant increased infection. Importantly, DDX42 also restricted retrotransposition of LINE-1, infection with other retroviruses and positive-strand RNA viruses, including CHIKV and SARS-CoV-2. However, DDX42 did not inhibit infection with three negative-strand RNA viruses, arguing against a general, unspecific effect on target cells, which was confirmed by RNA-seq analysis. DDX42 was found in the vicinity of viral elements by proximity ligation assays, and cross-linking RNA immunoprecipitation confirmed a specific interaction of DDX42 with RNAs from sensitive viruses. This strongly suggested a direct mode of action of DDX42 on viral ribonucleoprotein complexes. Taken together, our results show for the first time a new and important role of DDX42 in intrinsic antiviral immunity.

microbiology↗

bioRxiv2019

Implications of TP53 Allelic State for Genome Stability, Clinical Presentation and Outcomes in Myelodysplastic Syndromes

TP53 mutations are associated with poor clinical outcomes and treatment resistance in myelodysplastic syndromes. However, the biological and clinical relevance of the underlying mono- or bi-allelic state of the mutations is unclear. We analyzed 3,324 MDS patients for TP53 mutations and allelic imbalances of the TP53 locus and found that 1 in 3 TP53-mutated patients had mono-allelic targeting of the gene whereas 2 in 3 had multiple hits consistent with bi-allelic targeting. The established associations for TP53 with complex karyotype, high-risk presentation, poor survival and rapid leukemic transformation were specific to patients with multi-hit state only. TP53 multi-hit state predicted risk of death and leukemic transformation independently of the Revised International Prognostic Scoring System, while mono-allelic patients did not differ from TP53 wild-type patients. The separation by allelic state was retained in therapy-related MDS. Findings were validated in a cohort of 1,120 patients. Ascertainment of TP53 allelic state is critical for diagnosis, risk estimation and prognostication precision in MDS, and future correlative studies of treatment response should consider TP53 allelic state.

genomics↗

bioRxiv2019

Oncologic Therapy Shapes the Fitness Landscape of ClonalHematopoiesis

Clonal hematopoiesis (CH) is frequent in cancer patients and associated with increased risk of therapy related myeloid neoplasms (tMN). To define the relationship between CH, oncologic therapy, and tMN progression, we studied 24,439 cancer patients. We show that previously treated patients have increased rates of CH, with enrichment of mutations in DNA Damage Response (DDR) genes (TP53, PPM1D, CHEK2). Exposure to radiation, platinum and topoisomerase II inhibitors have the strongest association with CH with evidence of dose-dependence and gene-treatment interactions. We validate these associations in serial sampling from 525 patients and show that exposure to cytotoxic and radiation therapy imparts a selective advantage specifically in hematopoietic cells with DDR mutations. In patients who progressed to tMN, the clone at CH demarcated the dominant clone at tMN diagnosis. CH mutational features predict risk of therapy-related myeloid neoplasm in solid tumor patients with clinical implications for early detection and treatment decisions.

genetics↗

bioRxiv2019

What threatens Brazilian endangered species and how they are Red-Listed

Brazil is a continental-sized megadiverse country with high rates of habitat loss and degradation. Part of the Brazilian biodiversity - including endemic species - is recognized as threatened. By following the IUCN standards, we review the classification of all the 1172 endangered species in Brazil, analyzing differences among categories and groups. Based on a subsample of all 464 terrestrial vertebrates we identified 1036 records of threats affecting them. Criterion B was the most used (56% overall; 70% for CR species; 75% for EN), mainly related to reductions in their habitat area, extent and/or quality due to deforestation. Data on population declines (criterion A), number of reproductive individuals (criterion C), and population sizes (criterion D) are available for only a small fraction of the Brazilian fauna. Criterion E (probability of extinction in the wild) was used for only one species. Birds and mammals had the highest diversity of used criteria, while marine fish the lowest (90% related to declining populations). Two out of three of the 464 vertebrate species analyzed were negatively impacted by agribusiness. Other major threats are hunting, urban sprawl, rural settlements, and the construction of hydroelectric dams. Birds and mammals experience more co-occurrence of threats. Some threats are clearly underestimated in Brazil: climate change was indicated for only 2% species analyzed, but included no birds or amphibians. The main threats identified are linked to the patterns of economic development in Brazil and the current political and economic context points to a worrisome conservation scenario in the near future.

ecology↗

bioRxiv2017

Kernel multitask regression for toxicogenetics

The development of high-throughput in vitro assays to study quantitatively the toxicity of chemical compounds on genetically characterized human-derived cell lines paves the way to predictive toxicogenetics, where one would be able to predict the toxicity of any particular compound on any particular individual. In this paper we present a machine learning-based approach for that purpose, kernel multitask regression (KMR), which combines chemical characterizations of molecular compounds with genetic and transcriptomic characterizations of cell lines to predict the toxicity of a given compound on a given cell line. We demonstrate the relevance of the method on the recent DREAM8 Toxicogenetics challenge, where it ranked among the best state-of-the-art models, and discuss the importance of choosing good descriptors for cell lines and chemicals.

bioinformatics↗