Biology subjects

Deloulme, J.-C.

Publications and source records attributed to Deloulme, J.-C..

4 recordsLinked to original sources

bioRxiv2023

Evaluation of Kernel Low-Rank Compressed Sensing in preclinical Diffusion Magnetic Resonance Imaging

Compressed Sensing (CS) is widely used to accelerate clinical diffusion MRI acquisitions, but it remains under-utilized in preclinical settings. In this study, we optimized and compared several CS reconstruction methods for diffusion imaging. Different undersampling patterns and two reconstruction approaches were evaluated: conventional CS, based on Berkeley Advanced Reconstruction Toolbox (BART-CS) toolbox, and a new Kernel Low-Rank (KLR)-CS, based on Kernel Principal Component Analysis and low-resolution-phase maps. 3D CS acquisitions were performed at 9.4T using a 4-element cryocoil on mice (wild type and a MAP6 knockout). Comparison metrics were error and Structural Similarity Index Measure (SSIM) on fractional anisotropy (FA) and mean diffusivity (MD), as well as reconstructions of the anterior commissure and fornix. Acceleration factors (AF) up to 6 were considered. In the case of retrospective undersampling, the proposed KLR-CS outperformed BART-CS up to AF=6 for FA and MD maps and tractography. For instance, for AF=4, the maximum errors were respectively 8.0% for BART-CS and 4.9% for KLR-CS, considering both FA and MD in the corpus callosum. Regarding undersampled acquisitions, these maximum errors became respectively 10.5% for BART-CS and 7.0% for KLR-CS. This difference between simulations and acquisitions arose mainly from repetition noise, but also from differences in resonance frequency drift, signal-to-noise ratio, and in reconstruction noise. Despite this increased error, fully sampled and AF=2 yielded comparable results for FA, MD and tractography, and AF=4 showed minor faults. Altogether, KLR-CS based on low-resolution-phase maps seems a robust approach to accelerate preclinical diffusion MRI.

neuroscience↗

bioRxiv2020

AutoNeuriteJ: An ImageJ plugin for measurement and classification of neuritic extensions

Morphometry characterization is an important procedure in describing neuronal cultures and identifying phenotypic differences. This task usually requires labor-intensive measurements and the classification of numerous neurites from large numbers of neurons in culture. To automate these measurements, we wrote AutoNeuriteJ, an imageJ/Fiji plugin that measures and classifies neurites from a very large number of neurons. We showed that AutoNeuriteJ is able to detect variations of neuritic growth induced by several compounds known to affect the neuronal growth. In these experiments measurement of more than 5000 mouse neurons per conditions was obtained within a few hours. Moreover, by analyzing mouse neurons deficient for the microtubule associated protein 6 (MAP6) and wild type neurons we illustrate that AutoNeuriteJ is capable to detect subtle phenotypic difference in axonal length. Overall the use of AutoNeuriteJ will provide rapid, unbiased and accurate measurement of neuron morphologies.

bioinformatics↗

bioRxiv2020

Presynaptic APP levels and synaptic homeostasis are regulated by Akt phosphorylation of Huntingtin

Studies have suggested that amyloid precursor protein (APP) regulates synaptic homeostasis, but the evidence has not been consistent. In particular, signaling pathways controlling APP transport to the synapse in axons and dendrites remain to be identified. Having previously shown that Huntingtin (HTT), the scaffolding protein involved in Huntingtons disease, regulates neuritic transport of APP, we used a microfluidic corticocortical neuronal network-on-a-chip to examine APP transport and localization to the pre- and post-synaptic compartments. We found that HTT, upon phosphorylation by the Ser/Thr kinase Akt, regulates APP transport in axons but not dendrites. Expression of an unphosphorylatable HTT decreased axonal anterograde transport of APP, reduced presynaptic APP levels, and increased synaptic density. Ablating in vivo HTT phosphorylation in APPPS1 mice, which overexpress APP, reduced presynaptic APP levels, restored synapse number and improved learning and memory. The Akt-HTT pathway and axonal transport of APP thus regulate APP presynaptic levels and synapse homeostasis.

neuroscience↗

bioRxiv2018

Neuronal integration in the adult olfactory bulb is a non-selective addition process

Adult neurogenesis is considered a competition in which neurons scramble during a critical period for integration and survival. Moreover, newborn neurons are thought to replace preexisting ones that die. Despite a wealth of evidence supporting this model, systematic in vivo observations of the process are still scarce. We used 2-photon imaging to study neuronal integration and survival directly in the olfactory bulb (OB) of living mice. Long-term tracking of over 1400 neurons demonstrated that cell-loss in the OB is virtually absent. Neuronal death resembling a critical period was induced by standard doses of BrdU or EdU, but disappeared when low doses of EdU were used, demonstrating toxicity. Finally, we demonstrate that the OB grows throughout life. This shows that neuronal selection during OB-neurogenesis does not occur during integration and argues against the existence of a critical period. Moreover, the OB is not a \"turnover\" system but shows lifelong neuronal addition.

neuroscience↗