Biology subjects

Malard, F.

Publications and source records attributed to Malard, F..

8 recordsLinked to original sources

bioRxiv2026

SCKAnalyzer: A Web Tool for Single-Cycle Kinetics Analysis and Simulation

Surface plasmon resonance (SPR) and biolayer interferometry (BLI) are well-established label-free analytical technologies used to determine biomolecular interaction rates (ka, kd) and equilibrium constants (KD). While assays historically rely on multi-cycle kinetics (MCK), this approach requires intermediate surface regeneration, risking sensor degradation and increasing reagent consumption. Single-cycle kinetics (SCK) avoids regeneration by sequentially injecting increasing analyte concentrations. However, implementing SCK workflows on biosensor platforms like the OctetRR8 BLI instrument (Sartorius) remains a challenge due to the lack of built-in or online data analysis tools. To address this, we introduce SCKAnalyzer, a free, user-friendly web application designed for processing and fitting SCK datasets. SCKAnalyzer accepts column-based text files and native raw BLI data (.frd format) from Sartorius instruments, performing data pre-processing and non-linear fitting to a 1:1 interaction model. Additionally, it offers advanced simulation capabilities that allow variable association and dissociation durations across sequential injection steps, a feature absent in existing platforms such as BiacoreTMSimul8. The performance of SCKAnalyzer was experimentally validated using a 3-step SCK method (SCK3) for DNA/RNA duplex formation on a Biacore T200, as well as 4-step (SCK4) and 5-step (SCK5) methods for DNA/DNA duplex formation on an OctetRR8 BLI instrument. Binding parameters (ka, kd, KD) derived from SCKAnalyzer showed excellent agreement with values from established proprietary softwares such as Biacore T200 Evaluation Software v3.2.1 and BIAevaluation v4.1.1. SCKAnalyzer provides a practical alternative to MCK, reducing probe consumption and extending SCK utility across biosensor platforms. SCKAnalyzer is available at sck.iecb.u-bordeaux.fr (source code: github.com/synthaze/sckanalyzer).

biophysics↗

bioRxiv2023

Evolutionary origin of morphologically cryptic species imprints co-occurrence and sympatry patterns

AimMorphologically cryptic species are an important part of global biodiversity, yet it remains unclear how these species contribute to and integrate into communities at different geographic scales. It is especially unclear at which scales they co-occur, and if and how their ranges overlap. To adequately protect biodiversity, an accurate understanding of the underlying processes and adequate level of protection is needed, in particularly for often overlooked cryptic species. QuestionWe analyzed patterns of syntopies (local co-occurrences) and sympatries (range overlap) to test how the evolutionary origin of cryptic species shapes biodiversity patterns at different geographic scales. We hypothesized i) that syntopies are more common among phylogenetically deeply divergent cryptic species than among close relatives, and ii) that sympatries are an outcome of phylogenetic relatedness and dispersal, with range size as a proxy of dispersal ability. LocationWestern Europe. TaxonSubterranean amphipod crustaceans of the polyphyletic Niphargus rhenorhodanensis species complex. MethodsUnilocus species delimitations (PTP, ASAP), calibrated multilocus phylogenetic analyses, co-occurrence analyses using a probabilistic model, generalized linear models (GLM). ResultsThe studied species complex comprises 37-48 molecular operational taxonomic units (MOTUs) from nine different clades. Syntopies are random or less frequent than expected, implying an insufficient between-MOTU differentiation allowing stable coexistence. GLM suggested that age of divergence does not predict species sympatries, although they emerge more frequently among MOTUs from different clades. By contrast, sympatries emerge when at least one MOTU disperses over a large geographic range. Biodiversity rich regions were found at the foothills of the Alps, the Jura and the Central Massif, regardless the inference method. Main conclusionsBiodiversity patterns of the herein studied species complex are driven mainly by dispersal and reflect geographic circumstances of speciation. While species richness on a local scale may be the outcome of competition and dispersal, regional biodiversity patterns emerged through biogeographic history on a clade-level.

ecology↗

bioRxiv2023

The diversity of splicing modifiers acting on A-1 bulged 5'-splice sites reveals rules to guide rational design

Non-physiological alternative splicing patterns are associated with numerous human diseases. Among the strategies developed to treat these diseases, small molecule splicing modifiers are emerging as a new class of RNA therapeutics. The SMN2 splicing modifier SMN-C5 was used as a prototype to understand their mode of action and discover the concept of 5-splice site bulge repair. However, different small molecules harbouring a similar activity were also identified. In this study, we combined NMR spectroscopy and computational approaches to determine the binding modes of other SMN2 and HTT splicing modifiers at the interface between U1 snRNP and an A-1 bulged 5-splice site. Our results show that the other splicing modifiers interact with the intermolecular RNA helix epitope containing an unpaired adenine within a G-2A-1G+1U+2 motif, which is essential for their biological activity. We also determined structural models of risdiplam, SMN-CX, and branaplam bound to RNA, and solved the solution structure of the most divergent SMN2 splicing modifier, SMN-CY, in complex with the RNA helix. These findings not only deepen our understanding of the chemical diversity of splicing modifiers that target A-1 bulged 5-splice sites, but also identify common pharmacophores required for modulating 5-splice site selection with small molecules.

molecular biology↗

bioRxiv2022

Structural transitions in TCTP tumor protein upon Mcl-1 binding

SummaryTranslationally Controlled Tumour Protein (TCTP) is a pro-survival factor in tumor cells. TCTP inhibits the mitochondrial apoptosis pathway by potentiating the anti-apoptotic Bcl-2 family members Mcl-1 and Bcl-xL. Specifically, TCTP binds Bcl-xL and inhibits the Bax-dependent Bcl-xL-induced cytochrome c release and TCTP reduces Mcl-1 turnover by inhibiting its ubiquitinylation, thus resulting in decreased Mcl-1 mediated apoptosis. TCTP owns a BH3-like motif forming a {beta}-strand buried in the globular domain of the protein. The crystal structure of TCTP BH3-like peptide in complex with Bcl-xL highlighted the -helical conformation of TCTP BH3-like motif, suggesting major changes in TCTP structure upon complex formation. However, the structural impact of the interaction on the full-length TCTP and the structural description of TCTP/Mcl-1 interaction are still lacking. Here using biophysical/biochemical methods (NMR, SAXS, circular dichroism, limited proteolysis), we provide an in-depth description of the TCTP/Mcl-1 complex. We demonstrate that full length TCTP binds to the BH3 binding groove of Mcl-1 via its BH3-like motif which interconverts between different binding modes at the micro- to milli-second timescale. As a consequence of the engagement of the BH3-like motif in the interface, the TCTP globular domain is destabilized into a molten-globule state. We also establish that the residue D16 in TCTP BH3-like motif is crucial for the stability and dynamics of the intermolecular interface. As a conclusion, we reveal here in details the structural plasticity of TCTP and discuss its implications for TCTP biology and for future anticancer drug design strategies aiming at targeting TCTP complexes. ContactEwen Lescop, ewen.lescop@cnrs.fr. Supplementary InformationSupplementary figures, tables and files.

biochemistry↗

bioRxiv2022

The cancer-associated RBM39 bridges the pre-mRNA, U1 and U2 snRNPs to regulate alternative splicing

Pharmacologic depletion of RNA-binding motif 39 (RBM39) using aryl sulfonamides represents a promising anti-cancer therapy. However, its efficiency correlates with the expression level of DCAF15 which acts at the interface between RBM39, the drug and the E3-ubiquitin ligase. Consequently, the identification of alternative approaches to deplete RBM39 independently of DCAF15 is required. Here, we combined transcriptomic analysis, functional assays, and structural biology to elucidate the molecular mechanisms governing RBM39 homeostasis. Our data revealed that RBM39 autoregulates the splicing of its own pre-mRNA by triggering the inclusion of a poison exon. During this process, RBM39 selects the 3-splice site of the toxic exon, helps the recruitment of U1 snRNP on its weak 5-splice site and bridges the 3-splice site recognition machinery. The elucidation of the molecular mechanisms controlling RBM39 homeostasis provides unprecedented insights into alternative 3-splice site selection and a solid frame to design alternative anti-cancer therapies.

molecular biology↗

bioRxiv2021

Dynamic structural cell responses in the thymus to acute injury, regeneration, and age

The thymus is essential for establishing adaptive immunity yet undergoes age-related atrophy leading to compromised immune responsiveness. The thymus is also extremely sensitive to acute insult and although capable of regeneration, this capacity declines with age. Focusing on non-hematopoietic stromal cells, and using single-cell and spatial transcriptomics, lineage-tracing, and advanced imaging, we discovered two atypical thymic epithelial cell (TEC) states that emerged with age. Age-associated (aa)TECs formed atypical high-density epithelial clusters that were devoid of thymocytes, an accretion of non-functional thymic tissue that worsened with age and exhibited features of partial epithelial-to-mesenchymal transition (EMT). In silico interaction analysis revealed that aaTEC emergence drew tonic signals from other TEC populations at baseline, acting as a sink for TEC growth factors. Following damage, aaTEC expanded substantially, further perturbing trophic pathways, and correlating with defective regeneration of the involuted thymus. These findings define a unique feature of thymic involution linked to immune aging.

immunology↗

bioRxiv2021

EpyNN: Educational python for Neural Networks

SummaryArtificial Neural Networks (ANNs) have achieved unequaled performance for numerous problems in many areas of Science, Business, Public Policy, and more. While experts are familiar with performance-oriented software and underlying theory, ANNs are difficult to comprehend for non-experts because it requires skills in programming, background in mathematics and knowledge of terminology and concepts. In this work, we release EpyNN, an educational python resource meant for a public willing to understand key concepts and practical implementation of scalable ANN architectures from concise, homogeneous and idiomatic source code. EpyNN contains an educational Application Programming Interface (API), educational workflows from data preparation to ANN training and a documentation website setting side-by-side code, mathematics, graphical representation and text to facilitate learning and provide teaching material. Overall, EpyNN provides basics for python-fluent individuals who wish to learn, teach or develop from scratch. AvailabilityEpyNN documentation is available at https://epynn.net and repository can be retrieved from https://github.com/synthaze/epynn. ContactStephanie Olivier-Van-Stichelen, solivier@mcw.edu. Supplementary InformationSupplementary files and listings.

scientific communication and education↗

bioRxiv2020

Bedrock radioactivity influences the rate and spectrum of mutation

All organisms on Earth are exposed to low doses of natural radioactivity but some habitats are more radioactive than others. Yet, documenting the influence of natural radioactivity on the evolution of biodiversity is challenging. Here, we addressed whether organisms living in naturally more radioactive habitats accumulate more mutations across generations using 14 species of waterlice living in subterranean habitats with contrasted levels of radioactivity. We found that the mitochondrial and nuclear mutation rates across a waterlouse species genome increased on average by 60 and 30%, respectively, when radioactivity increased by a factor of three. We also found a positive correlation between the level of radioactivity and the probability of G to T (and complementary C to A) mutations, a hallmark of oxidative stress. We conclude that even low doses of natural bedrock radioactivity influence the mutation rate through the likely accumulation of oxidative damage, in particular in the mitochondrial genome.

evolutionary biology↗