Biology subjects

Bilodeau, G.

Publications and source records attributed to Bilodeau, G..

3 recordsLinked to original sources

bioRxiv2026

A Bidirectional Neural Interface With Direct On-Device Neuromorphic Decoding for Closed-Loop Optogenetics

Bidirectional interfaces combined with neural de-coding algorithms are essential for closed-loop (CL) neuromodulation, enabling simultaneous neural monitoring and responsive optogenetic stimulation. However, implementing these capabilities in compact wireless headstages for freely moving animals remains challenging, as most existing platforms rely on tethered setups and external processors to execute computationally intensive decoders. This work presents the design and optimization of a neural decoder integrated into a bidirectional wireless system for CL optogenetic experiments in rodents. The proposed platform combines 32-channel electrophysiological recording with neuromorphic feature extraction, dimensionality reduction, and a nonlinear support vector machine (NL-SVM) decoder implemented on a resource-constrained Spartan-6 FPGA. Temporal dynamics are captured using spike-count features and leaky integrators, while principal component analysis (PCA) reduces the feature space to six components, enabling sub-millisecond inference with minimal memory and power requirements. Model size is further reduced using k-means clustering during training to limit the number of support vectors. Decoder performance was validated using datasets from non-human primate and rat motor cortex recordings. The proposed decoder achieved accuracy comparable to convolutional neural networks (R2 =0.85 vs. 0.87) and outperformed Wiener filters (R2 = 0.81) while requiring significantly fewer computational resources. The full system was further demonstrated in vivo through wireless closed-loop optogenetic stimulation in rats, achieving a variance accounted for (VAF) of 0.9148. Overall, this work introduces a versatile, fully self-contained, and resource-efficient platform for real-time untethered closed-loop neuroscience experiments.

neuroscience↗

bioRxiv2024

A qPCR assay for the detection of Phytophthora abietivora, an emerging pathogen on fir species cultivated as Christmas trees

Emerging species of the Phytophthora genus are among the most important threats to global plant biodiversity. For instance, Phytophthora root rot (PRR) of Christmas trees is responsible for 10% of the observed mortality rate in nurseries. Diagnosis of PRR involves isolation followed by morphological and molecular identification of the causal agents. However, these methods are rarely adapted to larger scale experiments such as in situ detection. For these applications, molecular detection of environmental DNA (eDNA) provides the high-throughput and the fast result generation needed. Phytophthora abietivora was associated to PRR in firs cultivated as Christmas trees in the province of Quebec (Canada). This study focused on developing a sensitive and specific qPCR assay targeting P. abietivora and validating its efficiency on eDNA samples. A set of primers and probe was designed for this assay, and parameters such as the limit of detection (LoD95%) and limit of quantification (LoQ) were measured. The assay was tested on eDNA obtained from healthy-looking and PRR symptomatic firs. The assay was shown to be semi-specific because it cross-reacted with P. abietivora, and four phylogenetically close species unrelated to fir diseases. The limit of detection (LOD95%) was estimated at 10 copies per reaction (Cq of 35.7). The assay showed reliable detection down to 33 P. abietivora oospores per gram of soil. Out of 488 eDNA samples from soil, 68 tested positive for P. abietivora. While factors such as the tree species, the sampled region or the year of sampling did not affect the proportion of positive results, samples from trees showing PRR-like symptoms had significantly higher odds of testing positive compared to healthy-looking trees. This assay will be useful for rapid diagnostics of P. abietivora infected trees and as a prospecting tool to better characterize the natural distribution and dissemination of the disease.

molecular biology↗

bioRxiv2019

In Situ Processing and Efficient Environmental Detection (iSPEED) of pests and pathogens of trees using point-of-use real-time pcr

The increase in global trade is responsible for a surge in foreign invasive species introductions across the world. Early detection and surveillance activities are essential to prevent future invasions. Molecular diagnostics by DNA testing has become an integral part of this process. However, for environmental applications, there is a need for cost-effective and efficient point-of-use DNA testing that would allow for the collection of results in real-time away from laboratory facilities. To achieve this requires the development of simple and fast sample processing and DNA extraction, room-temperature stable reagents and a portable instrument. We conducted a series of tests using a crude buffer-based DNA extraction protocol and lyophilized, pre-made, reactions to address the first two requirements. We chose to demonstrate the use of this approach with organisms that cover a broad spectrum of known undesirable insects and pathogens: the ascomycete Sphaerulina musiva, the oomycete Phytophthora ramorum, the basidiomycetes Cronartium ribicola and Cronartium comandrae and the insect Lymantria dispar. Tests performed from either infected leaf material or spores (pathogens), or legs and antenna (insects). We were able to obtain positive amplification for the targeted species in all the samples tested. The shelf-life of the lyophilized reactions was assessed, confirming the stability of over a year at room temperature. Finally, successful tests conducted with portable thermocyclers and disposable plastics, demonstrating the suitability of the method, named in Situ Processing and Efficient Environment Detection (iSPEED), for field testing. This kit is ideally adapted to field testing as it fits in a backpack and can be carried to remote locations.

plant biology↗