Biology subjects

Maillard, M.

Publications and source records attributed to Maillard, M..

3 recordsLinked to original sources

bioRxiv2025

Addressing multiple facets of ligand-receptor network inference including single-cell proteomics

Distinct ligand-receptor interaction (LRI) inference tools often produce markedly different results, and their performance can vary considerably across datasets. Indeed, performance is influenced by differences in experimental designs and dataset-specific features, making it difficult to establish a universal LRI tool. To address this challenge, we expanded our SingleCellSignalR Bioconductor package to provide an integrated framework that incorporates alternative scoring strategies and adjustable analytical depth. We motivate this choice through the analysis of two single-cell transcriptomics datasets that exemplify contrasting experimental designs. Leveraging the new framework flexibility, we present a detailed analysis of paired single-cell proteomics and transcriptomics data, providing, to our knowledge, the first direct comparison of LRI inference across these complementary modalities at single-cell resolution. Finally, we demonstrate how the same framework seamlessly accommodates additional underexplored data types from the LRI perspective, including patient-derived mouse xenografts and bulk RNA sequencing of upstream-sorted cell populations.

bioinformatics↗

bioRxiv2022

High-throughput and automatic structural and developmental root phenotyping on Arabidopsis seedlings

BackgroundHigh-throughput phenotyping is crucial for the genetic and molecular understanding of adaptive root system development. In recent years, imaging automata have been developed to acquire the root system architecture of many genotypes grown in Petri dishes to explore the Genetic x Environment (GxE) interaction. There is now an increasing interest in understanding the dynamics of the adaptive responses, such as the organ apparition or the growth rate. However, due to the increasing complexity of root architectures in development, the accurate description of the topology, geometry, and dynamics of a growing root system remains a challenge. ResultsWe designed a high-throughput phenotyping method, combining an imaging device and an automatic analysis pipeline based on registration and topological tracking, capable of accurately describing the topology and geometry of observed root systems in 2D+t. The method was tested on a challenging Arabidopsis seedling dataset, including numerous root occlusions and crossovers. Static phenes are estimated with high accuracy (R2 = 0.996 and 0, 923 for primary and second-order roots length, respectively). These performances are similar to state-of-the-art results obtained on root systems of equal or lower complexity. In addition, our pipeline estimates dynamic phenes accurately between two successive observations (R2 = 0. 938 for lateral root growth). ConclusionsWe designed a novel method of root tracking that accurately and automatically measures both static and dynamic RSA parameters from a novel high-throughput root phenotyping platform. It has been used to characterize developing patterns of root systems grown under various environmental conditions. It provides a solid basis to explore the GxE interaction controlling the dynamics of root system architecture adaptive responses. In future work, our approach will be adapted to a wider range of imaging configurations and species.

plant biology↗

bioRxiv2019

Large herbivores strongly slow down litter decomposition in temperate forests

AO_SCPCAPBSTRACTC_SCPCAPIn temperate forest ecosystems, the role of deer in litter decomposition, a key nutrient cycling process, remains debated. Deer may modify the decomposition process by affecting plant cover and thus modifying litter abundance. They can also alter litter quality through differential browsing and affect decomposer ability by changing soil abiotic properties and the nature of decomposer communities. We used two litterbag experiments in a quasi-experimental situation resulting from the introduction of Sitka black-tailed deer Odocoileus odocoileus sitkensis on forested islands of Haida Gwaii (Canada). We investigated the effects of deer on decomposition through their impacts on litter quality and on decomposer ability. After one year, the effect of deer on litter quality resulted in a lower rate of mass loss in litter from litterbags. This mass loss mainly reflected a 21 and 38 % lower rate of carbon (C) and nitrogen (N) loss, respectively. Presence of deer resulted in lower decomposer ability for the rate of carbon loss, but not for nitrogen loss. The level of C loss after one year was 5% higher for litter decomposing on an island without deer. But the change in the rate of carbon loss explained by the effect of deer on decomposer ability was outweighed by the effect deer had on litter quality. Additional effects of deer on the decomposition process through feces deposition were significant but minor. These results question the role the large increase in deer populations observed in temperate forests at continental scales may play in broad scale patterns of C and N cycling.

ecology↗