Biology subjects

Cordelieres, F.

Publications and source records attributed to Cordelieres, F..

3 recordsLinked to original sources

bioRxiv2025

CABaNe, an automated, high content ImageJ macro for cell and neurite analysis

Measuring neurite length is crucial in neurobiology because it provides valuable insights into the growth, development, and function of neurons. In particular, neurite length is fundamental to study neuronal development and differentiation, neurons responses to drugs, neurodegenerative diseases and neuronal plasticity. Surprisingly, there is currently a lack of tools for high content neurite analysis. In this article, we present CABaNe, as an open source, high content, rule based Image J macro for cell analysis, including their neurite length. This macro possesses a graphical interface, metadata production, as well as verification means before and after analysis. Rule based and machine learning based programming have been tested for cell identification. After testing, we had better precision and adaptability using rule based cell identification. We challenged CABaNe with currently used techniques, which are manual or assisted. When tested on a small sample, CABaNe demonstrated a massive speed increase in capacity to treat dataset while maintaining or increasing precision when compared to manual measurement. When tested on a large data set, comparing different conditions, we successfully highlighted differences between conditions, in a fully automated manner. Therefore, CABaNe is viable as a high content option for cell analysis, for neurite length and other parameters. It is a base of code that can be used for other analysis or to train deep learning models. In the future, we expect this tool to be widely used in both basic and applied neurobiology research. Significance statementWhen studying neuronal cell differentiation, an important morphological parameter is neurite length. This parameter requires measuring the protrusions length of analysed cells. However, this analysis done manually can be long, as each individual cell must be measured independently. Currently, efficient single cell tools exist to assist the measurement, such as NeuronJ. However, there is currently no available automated tool for this analysis, and manual techniques suffer operator bias. In this paper, we present a macro to fully automatize neurite length and other parameters measurement, for each cell, in each image, in each condition.

neuroscience↗

bioRxiv2023

ER-to-Golgi trafficking via a dynamic intermediate cis-Golgi tubular network in Arabidopsis

Endoplasmic Reticulum (ER)-to-Golgi trafficking is a central process of the secretory system of eukaryotic cells that ensures proper spatiotemporal sorting of proteins and lipids1-5. However, the nature of the ER-Golgi Intermediate Compartments (ERGIC) and the molecular mechanisms mediating the transition between the ERGIC and the Golgi, as well as the universality of these processes amongst Eukaryotes, remain undiscovered. Here, we took advantage of the plant cell system in which the Golgi is highly dynamic and in close vicinity to the ER6-9. We discovered that the ERGIC is composed from at least two distinct subpopulations of cis-Golgi. A subpopulation is a reticulated tubulo-vesicular network mostly independent from the Golgi, highly dynamic at the ER-Golgi interface and crossed by ER-induced release of luminal cargos at early stage. Another subpopulation is more stable, cisterna-like and mostly associated to the Golgi. Our results identified that the generation and dynamics of the ER-Golgi intermediate tubulo-vesicular network is regulated by the acyl-chain length of sphingolipids as well as the contacts it establishes with existing Golgi cisternae. Our study is a major twist in the understanding of the Golgi by identifying that the ERGIC in plants is a Golgi-independent highly dynamic tubular network from which arise more stable cisternae-like Golgi structures. This novel model presents a mechanism for early secretory trafficking adapted to respond to developmental and environmental stimuli, including susceptibility or resistance to diseases, autophagy or cell-reprograming.

cell biology↗

bioRxiv2020

APP accumulates around dense-core amyloid plaques with presynaptic proteins in Alzheimer's disease brain

In Alzheimers disease (AD), a central role is given to the extracellular deposition of A{beta} peptides, remotely produced by the proteolysis of the amyloid precursor protein (APP). This contrasts with other neurodegenerative diseases which are characterized by the intraneuronal aggregation of full-length proteins such as huntingtin, -synuclein or TDP-43. Importantly, the distribution of APP around amyloid plaques is poorly characterized. Here, we combined an extensive set of methodological and analytical tools to investigate neuropathological features of APP in the human AD hippocampus and in two mouse models of AD. We report that APP remarkably accumulates in the surrounding of dense-core amyloid plaques together with the secretases necessary to produce A{beta} peptides. In addition, the Nter domain, but not the Cter domain of APP is enriched in the core of amyloid plaques uncovering a potential pathological role of the secreted APP-Nter in dense-core plaques. To investigate the subcellular compartment in which APP accumulates, we labelled neuritic and synaptic markers and report an enrichment in presynaptic proteins (Syt1, VAMP2) and phosphorylated-Tau. Ultrastructural analysis of APP accumulations reveals abundant multivesicular bodies containing presynaptic vesicles proteins and autophagosomal built-up of APP. Altogether, our data supports a role of presynaptic APP in AD pathology and highlights APP accumulations as a potential source of A{beta} and Nter peptides to fuel amyloid plaques.

neuroscience↗