Biology subjects

Boyer, J.

Publications and source records attributed to Boyer, J..

5 recordsLinked to original sources

bioRxiv2026

Bifurcation dynamics in a shared network beyond sensory areas characterize conscious auditory perception independently of report

The neural correlates of conscious perception remain debated, particularly regarding the role of extra-sensory regions such as the prefrontal cortex. One promising approach is to study the dynamical properties of neural processing in task-related and task-free contexts. A previous EEG study showed that conscious perception is associated with all-or-none late activations, giving rise to bifurcation dynamics even without a task. Here we used fMRI and near-threshold auditory stimulation to ask which brain networks give rise to these bifurcations, and how they differ depending on task. In both contexts, stimulus intensity modulated activity within broad networks spanning sensory and extra-sensory regions, including the prefrontal cortex. These networks showed both shared and distinct components. Single-trial modelling further revealed bifurcation dynamics beyond primary sensory cortices and enabled single-trial prediction of conscious perception in both contexts. These findings resolve previous conflicting results and reveal common networks and dynamics underlying conscious perception irrespective of task.

neuroscience↗

bioRxiv2026

Low-input proteomics enables proteome and phosphoproteome-scale molecular phenotyping of separase-deficient oocytes

We performed a comprehensive quantitative proteomic analysis of mouse oocytes using as few as 40 oocytes per condition, comparing wild-type and separase knockout oocytes at metaphase I and metaphase II. To this end, we generated a deep proteomic library spanning oocyte cell cycle stages, enabling the identification of numerous phosphosites without phosphopeptide enrichment. We further combined data-dependent (DDA) and data-independent (DIA) acquisition strategies, analyzed through multiple software pipelines in both library-based and library-free modes. Our results reveal extensive proteome remodeling during the metaphase I to metaphase II transition in wild-type oocytes, consistent with dynamic regulation of meiotic processes. As a proof of concept for our workflow, we asked whether separase knockout oocytes--unable to separate chromosomes in meiosis I--progress into meiosis II. Direct comparison of wild-type and separase knockout oocytes at the metaphase II stage revealed minimal global differences, supporting the idea that both conditions converge toward a comparable metaphase II-like cellular state despite distinct chromosomal configurations. However, at a finer scale, specific alterations were detected among chromosome-associated proteins. Notably, Meikin was enriched in separase-deficient metaphase II oocytes, consistent with defective separase-dependent cleavage and subsequent turnover. More broadly, several proteins involved in chromosome organization displayed behavior similar to Meikin, suggesting that separase activity regulates multiple substrates to orchestrate chromosome segregation during female meiosis.

Cell Biology↗

bioRxiv2025

Liver Lymphatic Dysfunction as a Driver of Fibrosis and Cirrhosis Progression

The liver lymphatic system plays a critical role in maintaining interstitial fluid balance and immune regulation. Efficient lymphatic drainage is essential for liver homeostasis, but its role in liver disease progression remains poorly understood. In cirrhosis, lymphangiogenesis initially compensates for increased lymph production, but impaired lymphatic drainage in advanced stages may lead to complications such as ascites and portal hypertension. This study aimed to evaluate how liver lymphatic dysfunction affects disease progression and to assess therapeutic strategies. Using a surgical model to block liver lymphatic outflow, we found that impaired drainage accelerates liver injury, fibrosis, and immune cell infiltration, even in healthy livers. Mechanistically, enhanced TGF-{beta} signaling in liver lymphatic endothelial cells (LyECs) contributed to reduced lymphatic vessel (LV) density and function in late-stage decompensated cirrhosis. This dysfunction was linked to the progression from compensated to decompensated cirrhosis, particularly in patients with primary sclerosing cholangitis (PSC). Conversely, liver-specific overexpression of VEGF-C via AAV8 improved lymphatic drainage, restored LV density, reduced fibrosis, mitigated liver injury, and alleviated portal hypertension in cirrhotic rats. These findings establish impaired liver lymphatic function as a pivotal driver of cirrhosis progression and identify VEGF-C as a promising therapeutic target to prevent decompensation.

pathology↗

bioRxiv2024

Analysis of the potential of environmental Burkholderia sensu lato isolates to cause infection in a zebrafish embryo model

Burkholderia sensu lato (s.l.) regroups several genera of closely related bacterial species with remarkable diversity in metabolic features. They can be free-living or have mutualistic or pathogenic interactions with different host organisms, including insects, plants and animals. Burkholderia s.l. species display numerous characteristics that can be beneficial for agronomical and biotechnological applications, including promotion of plant growth and bioremediation; however, many of the species are known human pathogens. Several recent taxonomical reclassifications of the Burkholderia genus resulted in its separation into 7 distinct genera. Burkholderia sensu stricto (s.s.), which includes the Burkholderia cepacia complex and the pseudomallei group, regroups most of the species that have been shown to cause infection in humans and plants. Little is known about the pathogenic potential of species belonging to the other 6 genera; however there have been occasional reports of human infections. Here, the vertebrate zebrafish embryo was used to analyse the behaviour of a panel of environmental isolates belonging to different species of the Burkholderia cepacia complex (5), Paraburkholderia (5) and Caballeronia (1). Burkholderia cepacia P14-NS, Burkholderia orbicola P21-NS, and Paraburkholderia sp. ABIP659 (closest to P. tropica, and further named tropica-like) each caused a low percentage (2%) of embryo mortality. While the other strains had not killed the embryos during the 4-day time span of the experiments, overall, Paraburkholderia and Burkholderia s.s. strains persisted equally well in this vertebrate host. Unexpectedly, P. tropica-like showed the highest increase in bacterial burden during infection, and induced the strongest pro-inflammatory response, including abscess formation, and poor prognosis at the endpoint of the experiment. Our study emphasizes that in vivo infection studies are needed to gain more insight into potential pathogenicity of the different Burkholderia s.l. species.

microbiology↗

bioRxiv2018

Low genetic variation is associated with low mutation rate in the giant duckweed

Mutation rate and effective population size (Ne) jointly determine intraspecific genetic diversity, but the role of mutation rate is often ignored. We investigate genetic diversity, spontaneous mutation rate and Ne in the giant duckweed (Spirodela polyrhiza). Despite its large census population size, whole-genome sequencing of 68 globally sampled individuals revealed extremely low within-species genetic diversity. Assessed under natural conditions, the genome-wide spontaneous mutation rate is at least seven times lower than estimates made for other multicellular eukaryotes, whereas Ne is large. These results demonstrate that low genetic diversity can be associated with large-Ne species, where selection can reduce mutation rates to very low levels, and accurate estimates of mutation rate can help to explain seemingly counterintuitive patterns of genome-wide variation.\n\nOne Sentence SummaryThe low-down on a tiny plant: extremely low genetic diversity in an aquatic plant is associated with its exceptionally low mutation rate.

genetics↗