Biology subjects

Joyce, L.

Publications and source records attributed to Joyce, L..

7 recordsLinked to original sources

bioRxiv2026

A single-channel EEG classification system for multiscale characterization of mouse vigilance state

Long-term analysis of mouse sleep is constrained by the dependence of conventional scoring on expert interpretation of electroencephalographic (EEG) and electromyographic (EMG) recordings. We developed a channel-agnostic, EEG-only framework that combines cross-animal sleep-stage classification, causal temporal organization, and probabilistic hypnodensity analysis from a single cortical EEG signal. Motor, somatosensory, and visual cortical recordings were treated independently by a convolutional-recurrent classifier, and generalization was evaluated using nested leave-one-mouse-out cross-validation in eight mice, with each test animal excluded from training, normalization, and model selection. The primary model achieved 0.897 {+/-} 0.058 accuracy and 0.856 {+/-} 0.076 macro-F1 across previously unseen animals while preserving the principal features of expert EEG/EMG-supported sleep architecture. Causal temporal smoothing reduced fragmented predictions and restored physiologically coherent episode durations, counts, and transition structure. Beyond categorical staging, the 4-s causal EEG window was advanced in 1-s steps to generate continuous Wake, NREM, and REM hypnodensity profiles. This representation preserved overall classification performance while revealing increased probability ambiguity and state mixing around expert-defined sleep transitions. The framework was subsequently deployed without supervised adaptation in six additional mice with 32-33 recorded days per animal, where it retained organized daily sleep architecture and probabilistic sleep structure over extended recordings while remaining sensitive to changes in recording conditions. Together, these results establish a single-channel EEG framework for robust cross-animal sleep staging, physiologically structured long-term analysis, and second-by-second characterization of sleep-state probabilities in mice.

neuroscience↗

bioRxiv2026

Characterizing Transition State in Mouse Vigilance with EEG-EMG Hypnodensity

Study ObjectivesVigilance-state transitions are continuous biological processes, yet conventional rodent sleep scoring relies on discrete epochs that obscure intermediate states. As no standardized framework exists for characterizing these intermediate states in rodents, this study aimed to characterize the temporal dynamics of transitions in mice and validate a machine-learning approach for objective detection. MethodsChronic EEG and EMG recordings were obtained from male C57BL/6N mice. We extracted 56-second windows containing stable transitions between Wakefulness (WAKE), Non-Rapid Eye Movement Sleep (NREMS), and Rapid Eye Movement Sleep (REMS). Eight trained experts manually annotated the onset and duration of transitions to establish ground truth and assess inter-rater reliability. Using quantitative EEG/EMG features (e.g., spectral power, complexity, EMG variance) derived from stable states, Support Vector Machine (SVM) classifiers were trained to predict transition midpoints in independent test animals. ResultsInter-rater agreement among experts was moderate to low, particularly for WAKE to NREMS and NREMS to REMS transitions, reflecting inherent ambiguity in manual scoring. Temporal analysis revealed distinct dynamics across transition types; NREMS to REMS transitions were significantly longer than all others, while REMS to NREMS transitions were the most abrupt. Despite the variability in human scoring, SVM models trained only on stable-state features successfully predicted expert-defined transition midpoints. ConclusionsOur approach not only characterized the recognizable dynamics across transition types in mice, but also provides a reproducible framework for quantifying sleep-wake transitions, which is crucial for studying arousal stability and related impairments in disease. Statement of SignificanceTraditional sleep scoring enforces discrete boundaries between vigilance states, overlooking transitional dynamics that may be critical for understanding arousal regulation. We developed a novel hypnodensity-based framework to systematically identify and characterize intermediate vigilance states in mice using EEG-EMG recordings. By combining expert annotations with machine learning, we revealed that transitions between sleep and wake involve continuous processes with mixed state features, rather than instantaneous switches. This approach provides the first standardized method for quantifying transitional vigilance states in rodents, enabling deeper investigation of arousal instability in neurological disorders. Our framework advances automated sleep analysis beyond classical three-state classification

neuroscience↗

bioRxiv2026

The DUF998 family protein DrmA modulates cationic glycolipid levels and the emergence of high-level daptomycin resistance in Enterococcus faecalis

Daptomycin resistance (DAP-R) in enterococci is associated with alterations in the membrane lipid composition. The membrane-bound protein MprF is responsible for the synthesis of amino acid-modified lipids in bacteria, and these modified lipids contribute to DAP-R in some Gram-positive pathogens. In enterococci, MprF synthesizes three lysine-modified lipids: the phospholipid lysyl-phosphatidylglycerol (Lys-PG), and the newly identified cationic glycolipids lysyl-diglucosyl-diacylglycerol (Lys-Glc2-DAG) and lysyl-glucosyl-diacylglycerol (Lys-Glc-DAG). Given the recent discovery of cationic glycolipids in enterococci, we re-examined a collection of laboratory-evolved DAP-R E. faecalis to investigate whether these lipids contribute to DAP-R. We found that levels of Lys-Glc2-DAG were strikingly reduced in DAP-R variants with high-level resistance. The dramatic alterations in Lys-Glc2-DAG levels were temporally coupled with the emergence of loss-of-function mutations in the gene drmA, which encodes a DUF998 family protein of unknown function. DrmA is a membrane protein with six predicted transmembrane helices and is widely distributed among Gram-positive and Gram-negative bacteria, including plant and animal pathogens. Complementation of the DAP-R strains with wild-type E. faecalis drmA significantly lowered their DAP MIC, reversing their trajectory to high-level DAP-R. Using genetic and lipidomic approaches in the natively DAP-sensitive strain OG1RF, we conclusively linked drmA loss-of-function with significantly reduced Lys-Glc2-DAG levels as well as a small but significant increase in Lys-PG levels. Yet, drmA inactivation in OG1RF did not alter its DAP MIC. We conclude that drmA loss-of-function confers elevated DAP MIC on the background of preceding mutations in the DAP-R evolutionary trajectory, most likely mutations in cls1. The recurrence of drmA mutations in multiple studies underscores its importance in DAP-R evolution. Overall, our work identifies a role for the DUF998 family in cellular lipid homeostasis and confirms its significant role in the evolution of DAP-R.

microbiology↗

bioRxiv2026

Immediate methane and carbon dioxide release from exposed permafrost at an active retrogressive thaw slump in the Canadian Arctic

The Arctic is warming rapidly, causing permafrost thaw and accelerating the release of greenhouse gases. Rapid thaw features such as retrogressive thaw slumps are increasing in frequency and severity across the Arctic; however, their associated greenhouse gas emissions are poorly constrained. Current estimates of emissions from retrogressive thaw slumps rely largely on laboratory incubations and carbon stock estimates rather than in-situ field measurements. Here we directly quantify methane and carbon dioxide fluxes from the exposed headwall of an active retrogressive thaw slump. We show that thaw immediately releases biogenic methane and carbon dioxide, originating from gases trapped within the frozen soil matrix. Microbial transcription of methyl-coenzyme M reductase suggests archaea carrying out methanogenesis at subzero temperatures are the source of trapped methane. Carbon emissions varied by an order of magnitude among cryostratigraphic units, reflecting differences in geomorphologic history, organic carbon and nitrogen content, and microbial community composition. Carbon emissions were highest from organic-rich paleo cryosols from the Late Holocene that contained abundant methanogenic archaea. We estimate that [~]300 kg C (CO2 equivalents) is emitted annually from the headwall of this small thaw slump (surface area of [~]1200 m2). Considering the thousands of active slumps and extensive coastal permafrost erosion across the northern continuous permafrost zone, such features may represent a growing natural source of GHG emissions. These findings indicate that current permafrost carbon feedback models underestimate GHG release by omitting the direct release of trapped gases stored in permafrost.

ecology↗

bioRxiv2025

A murine model of adult gastrointestinal colonization by Group B Streptococcus

Group B Streptococcus (Streptococcus agalactiae, GBS) is a leading cause of invasive infections in neonates and adults. The adult gastrointestinal (GI) tract represents an understudied site of asymptomatic carriage with potential relevance for both transmission and disease. Here, we establish a murine model of GBS colonization in the adult GI tract, which provides a tractable system for probing host-microbe interactions within this niche. Using this model, we establish that GI carriage is generalizable to diverse GBS isolates and leverage transposon sequencing (Tn-Seq) to identify candidate GBS factors important for GI colonization. Informed by these TN-Seq data, we identify GBS capsule as a critical colonization factor of the adult murine GI tract. Taken together, this work highlights the GI tract as a reservoir for GBS and introduces a new experimental framework for investigating the bacterial and host determinants of GBS GI carriage.

microbiology↗

bioRxiv2020

Streptococcus pneumoniae, S. mitis, and S. oralis produce a phosphatidylglycerol-dependent, ltaS-independent glycerophosphate-linked glycolipid

Lipoteichoic acid (LTA) is a cell surface polymer of Gram-positive bacteria. LTA participates in host-microbe interactions including modulation of host immune reactions. It was previously reported that the major human pathogen Streptococcus pneumoniae and the closely related oral commensals S. mitis and S. oralis produce Type IV LTAs. Herein, using liquid chromatography/mass spectrometry (LC/MS)-based lipidomic analysis, we found that in addition to Type IV LTA biosynthetic precursors, S. mitis, S. oralis, and S. pneumoniae also produce glycerophosphate (Gro-P)-linked dihexosyl-diacylglycerol (DAG), which is a biosynthetic precursor of Type I LTA. Mutants in cdsA and pgsA produce dihexosyl-DAG but lack (Gro-P)-dihexosyl-DAG, indicating that the Gro-P moiety is derived from phosphatidylglycerol (PG), whose biosynthesis requires these genes. S. mitis, but neither S. pneumoniae nor S. oralis, encodes an ortholog of the PG-dependent Type I LTA synthase, ltaS. By heterologous expression analyses, we confirmed that S. mitis ltaS confers poly-(Gro-P) synthesis in both Escherichia coli and Staphylococcus aureus, and that S. mitis ltaS can rescue the severe growth defect of a S. aureus ltaS mutant. However, despite these observations, we do not detect a poly-(Gro-P) polymer in S. mitis using an anti-Type I LTA antibody. Moreover, (Gro-P)-linked dihexosyl-DAG is still synthesized by a S. mitis ltaS mutant, demonstrating that S. mitis LtaS does not catalyze the transfer of Gro-P from PG to dihexosyl-DAG. Finally, a S. mitis ltaS mutant has increased sensitivity to human serum, demonstrating that ltaS confers a beneficial but currently undefined function in S. mitis. Overall, our results demonstrate that S. mitis, S. pneumoniae, and S. oralis produce a (Gro-P)-linked glycolipid via a PG-dependent, ltaS-independent mechanism. ImportanceLTA is an important cell wall component synthesized by Gram-positive bacteria. Disruption of LTA production can confer severe physiological defects and attenuation of virulence. We report here the detection of a biosynthetic precursor of Type I LTA, in addition to the previously characterized Type IV LTA, in the total lipid extracts of S. pneumoniae, S. oralis, and S. mitis. Our results indicate that a novel mechanism is responsible for producing the Type I LTA intermediate. Our results are significant because they identify a novel feature of S. pneumoniae, S. oralis, and S. mitis glycolipid biology.

microbiology↗

bioRxiv2019

Phosphatidylcholine biosynthesis in Mitis group streptococci via a host metabolite scavenging pathway

The Mitis group streptococci include the major human pathogen Streptococcus pneumoniae and the opportunistic pathogens S. mitis and S. oralis which are human oral cavity colonizers and agents of bacteremia and infective endocarditis in immunocompromised patients. Bacterial membrane lipids play crucial roles in microbe-host interactions, yet for many pathogens, the composition of the membrane is poorly understood. In this study, we characterized the lipidomes of selected species of Mitis group streptococci and investigated the mechanistic basis for biosynthesis of the phospholipid phosphatidylcholine (PC). PC is a major lipid in eukaryotic cellular membranes, but it is considered to be comparatively rare in bacterial taxa. Using liquid chromatography/mass spectrometry (LC/MS) in conjunction with stable isotope tracing, we determined that Mitis group streptococci synthesize PC via the rare host metabolite scavenging pathway, the glycerophosphocholine (GPC) pathway, which is largely uncharacterized in bacteria. Our work demonstrates that Mitis group streptococci including S. pneumoniae remodel their membrane in response to the major human metabolites GPC and lysoPC.\n\nImportanceWe lack fundamental information about the composition of the cellular membrane even for the best studied pathogens of critical significance for human health. The Mitis group streptococci are closely linked to humans in health and disease, yet their membrane biology is poorly understood. Here, we demonstrate that these streptococci scavenge major human metabolites and use them to synthesize the membrane phospholipid phosphatidylcholine. Our work is significant because it identifies a mechanism by which the major human pathogen S. pneumoniae and the primary human oral colonizers S. mitis and S. oralis remodel their membrane in response to host metabolites.

microbiology↗