Biology subjects

Brennan, C.

Publications and source records attributed to Brennan, C..

11 recordsLinked to original sources

bioRxiv2026

Genome-resolved ecology and evolution of the microbiome enabled by quantitative long-read metagenomics

Standard metagenomics resolves microbial communities only in relative terms and at coarse taxonomic resolution, obscuring how individual strains change in absolute abundance and evolve within a host. We present long-read quantiomics (LRQ), a quantitative metagenomics platform coupling long-read sequencing with plasmid-based internal standards to recover high-quality genomes, including from degraded or low-input stool, and measure absolute, genome-resolved strain abundances. We validate LRQ using large plasmid standards and bacterial spike-ins, then apply it to eight years of dense sampling from an individual with colonic Crohn's disease. LRQ resolves co-resident strains of the same species following opposing trajectories with inflammation. Escherichia coli, long treated as a single pathobiont, separates into two sub-populations with opposing inflammation responses; the inflammation-associated lineage carries an immune-evasion module of virulence-associated metal-acquisition, biofilm, capsule and toxin genes. We observe genome-wide adaptive sweeps on timescales matched to disease incidence. LRQ therefore converts long-read metagenomics from a genome-recovery tool into a quantitative framework providing absolute, strain-level measurement of microbial ecology and evolution.

microbiology↗

bioRxiv2026

Hypoglossal motor output is altered by C4 epidural electrical stimulation via ascending spinal and peripheral feedback pathways

After cervical spinal cord injury (cSCI), swallowing dysfunction is common and increases mortality via aspiration pneumonia. While these deficits have often been attributed to secondary damage from complications of injury management, there has recently been a greater appreciation for the modulatory role of spinal populations in swallow generation that are disrupted by injury. Here, we illustrate in a rodent model of cSCI that epidural spinal stimulation (ESS) of the phrenic motor nucleus at spinal segment C4 alters motor output at the hypoglossal motor nucleus through activation of excitatory ascending spinal pathways and inhibitory peripheral sensory feedback mechanisms. These findings highlight the importance of spinal-brainstem communication in shaping the motor program of swallow-related musculature and offer the potential for stimulation of the cervical spinal cord to be a therapeutic target for restoring swallowing function after injury. NEW & NOTEWORTHYIn two varying severity models of spinal cord injury, we demonstrate the effects of spinal cord stimulation at C4 on the distal hypoglossal motor nucleus. We show that despite being anatomically distant, electrical stimulation of the phrenic motor nucleus increases hypoglossal motor output through ascending spinal pathways and dampens it through peripheral pathways. These findings highlight the importance of spinal-brainstem communication and illustrate the ability of spinal stimulation to restore this communication after injury.

neuroscience↗

bioRxiv2026

Rearing, dissection, and temporal transcriptomic profiling protocols to study density-dependent phenotypic plasticity in Schistocerca (Insecta: Orthoptera)

This protocol generates gregarious and solitarious density-dependent phenotypes in multiple Schistocerca species under controlled environmental conditions. It describes cage setup, feeding, animal handling, and sterile dissection workflows to isolate nervous, chemosensory, gut, fat body, and female reproductive tissues from nymphs and adults. It emphasizes rapid tissue stabilization and RNase-control practices for downstream single-tissue DNA and RNA analyses. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=136 SRC="FIGDIR/small/705994v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@59afdaorg.highwire.dtl.DTLVardef@283b72org.highwire.dtl.DTLVardef@156fa13org.highwire.dtl.DTLVardef@13bf71b_HPS_FORMAT_FIGEXP M_FIG C_FIG

zoology↗

bioRxiv2025

Behavioral Thermoceptive Responses and Morphologic Correlates in Mouse Models of CMT1A, HNPP and Aging

BackgroundThermoceptive dysfunction is a frequent but understudied feature of peripheral neuropathies and aging. Patients often report abnormal heat perception, yet the underlying sensory mechanisms remain unclear. This study evaluated thermoceptive behavior and corresponding structural changes in mouse models of inherited dysmyelinating neuropathy and natural aging to identify shared and divergent mechanisms. MethodsThermal preference was assessed using a user-independent gradient apparatus spanning physiological to noxious temperatures, with automated quantification of time in zone, distance traveled, and velocity. Nocifensive responses were evaluated by hot plate latency. Intraepidermal nerve fiber density (IENFD) was measured in paw pads, and TRPV1-positive dorsal root ganglion (DRG) neurons were analyzed by immunofluorescence and confocal imaging. ResultsThermal gradient testing revealed preserved temperature preference in CMT1A and HNPP mice but significantly altered behavior in aged animals, which spent less time in warmer zones. Hot plate testing showed prolonged times to nocifensive behavior in aged and CMT1A mice, whereas HNPP mice exhibited variable responses. IENFD was markedly reduced in aged mice but preserved in CMT1A and HNPP. DRG analysis revealed smaller soma diameters and reduced proportions of TRPV1-positive A{delta} neurons in aged mice, while CMT1A animals maintained normal morphology. InterpretationAging produces thermoceptive deficits through axonal degeneration and selective A{delta}-fiber vulnerability, whereas CMT1A mice display conduction-related impairment due to dysmyelination. Both models reproduce key human sensory phenotypes and provide translational platforms for studying small-fiber dysfunction and therapeutic interventions in peripheral neuropathies. Key PointsO_LIThermoceptive dysfunction is a common but understudied feature of peripheral neuropathy and aging. C_LIO_LIIn aged mice, altered thermal preference, reduced intraepidermal nerve fiber density, and smaller TRPV1-positive A{delta} neurons indicate a degenerative mechanism of sensory loss. C_LIO_LIIn CMT1A mice, delayed noxious heat responses occur despite preserved epidermal and DRG morphology, consistent with dysmyelination rather than axonal degeneration. C_LIO_LIHNPP mice showed inconsistent nocifensive responses without structural fiber loss, suggesting strain- or injury-dependent effects. C_LIO_LIThermal gradient and hot plate assays demonstrate strong reproducibility and provide relevant outcome measures for preclinical modeling of thermoceptive dysfunction. C_LI

neuroscience↗

bioRxiv2025

Whole-Proteome Screening and Multi-Modal Profiling of Antigen-Specific CD4+ T Cells at Single-Cell Resolution

Systematic whole-proteome screening and comprehensive profiling of antigen-specific CD4+ T cells are crucial for advancing our understanding of CD4+ T cell immunity, yet such efforts remain technically challenging. Here, we present a high-throughput platform that employs large-scale class II single-chain trimer libraries to detect antigen-specific CD4+ T cells, while simultaneously profiling their antigen specificity, TCR/{beta} sequences, MHC restriction, whole transcriptomes, and patient/timepoint origins at single-cell resolution. We benchmarked SCTs against conventional pMHCs and validated the SCT library-based approach in direct ex vivo identification of antigen-specific CD4+ T cells in healthy donors. We then applied the platform to screen the entire SARS-CoV-2 receptor-binding domain in a longitudinal patient cohort, identifying 2,188 antigen-specific CD4+ T cells and revealing key features that define antigen immunogenicity. Extending to cancer, we performed whole-proteome screening of HPV-16 E6/E7 for TCR repertoire profiling in a precancerous cohort, uncovering functional heterogeneity of HPV-specific TCRs. By integrating high-throughput antigen screening with high-dimensional, multi-modal cellular characterization, our approach offers an unprecedented window into CD4+ T cell immunity across diverse disease contexts and empowers the development of new therapies.

bioengineering↗

bioRxiv2025

A pathogenic subpopulation of human glioma associated macrophages linked to glioma progression

Malignant gliomas follow two distinct natural histories: de novo high grade tumors such as glioblastoma, or lower grade tumors with a propensity to transform into high grade disease. Despite differences in tumor genotype, both entities converge on a common histologically aggressive phenotype, and the basis for this progression is unknown. Glioma associated macrophages (GAM) have been implicated in this process, however GAMs are ontologically and transcriptionally diverse, rendering isolation of pathogenic subpopulations challenging. Since macrophage contextual gene programs are orchestrated by transcription factors acting on cis-acting promoters and enhancers in gene regulatory networks (GRN), we hypothesized that functional populations of GAMs can be resolved through GRN inference. Here we show via parallel single cell RNA and ATAC sequencing that a subpopulation of human GAMs can be defined by a GRN centered around the Activator Protein-1 transcription factor FOSL2 preferentially enriched in high grade tumors. Using this GRN we nominate ANXA1 and HMOX1 as surrogate cell surface markers for activation, thus permitting prospective isolation and functional validation in human GAMs. These cells, termed malignancy associated GAMs (mGAMs) are pro-invasive, pro-angiogenic, pro-proliferative, possess intact antigen presentation but skew T-cells towards a CD4+FOXP3+ phenotype under hypoxia. Ontologically, mGAMs share somatic mitochondrial mutations with peripheral blood monocytes, and their presence correlates with high grade disease irrespective of underlying tumor mutation status. Furthermore, spatio-temporally mGAMs occupy distinct metabolic niches; mGAMs directly induce proliferation and mesenchymal transition of low grade glioma cells and accelerate tumor growth in vivo upon co-culture. Finally mGAMs are preferentially enriched in patients with newly transformed regions in human gliomas, supporting the view that mGAMs play a pivotal role in glioma progression and may represent a plausible therapeutic target in human high-grade glioma.

cancer biology↗

bioRxiv2024

A three-country analysis of the gut microbiome indicates taxon associations with diet vary by location and strain

Emerging research suggests that diet plays a vital role in shaping the composition and function of the gut microbiota. While significant efforts have been made to identify general patterns linking diet to the gut microbiome, much of this research lacks representation from low- and middle-income countries such as Mexico. Additionally, both diet and the gut microbiome have highly complex and individualized configurations, and there is growing evidence that tailoring diets to individual gut microbiota profiles may optimize the path toward improving or maintaining health and preventing disease. Using fecal metagenomic data from 1,291 individuals across three countries, we examine two bacterial genera prevalent in the human gut, Prevotella and Faecalibacterium, which have gained significant attention due to their potential roles in human health. We find that they show significant associations with many aspects of diet, but that these associations vary in scale and direction, depending on the level of metagenomic resolution and the contextual population. These results highlight the growing importance of assembling metagenomic datasets that are standardized, comprehensive, and representative of diverse populations to increase our ability to tease apart the complex relationship between diet and the microbiome.

microbiology↗

bioRxiv2024

Human untargeted metabolomics in the gut microbiome era: ethanol vs methanol

Untargeted metabolomics is frequently performed on human fecal samples in conjunction with sequencing to unravel gut microbiome functionality. As sample collection efforts rapidly expand, with individuals often collecting specimens at home, metabolomics experiments should adapt to accommodate the safety and needs of bulk off-site collections. Here, we show that a 95% ethanol, safe to be shipped and handled, extraction pipeline recovers comparable amounts of metabolites as a validated 50% methanol extraction, preserving metabolic profiles differences between subjects. Additionally, the fecal metabolome remains relatively stable when stored in 95% ethanol for up to a week at room temperature. Finally, we suggest a metabolomics data analysis workflow using robust centered log ratio transformation, which removes variance introduced by different sample weights, allowing for reliable and integration-ready untargeted metabolomics experiments in gut microbiome studies.

biochemistry↗

bioRxiv2021

Evaluation of plasma N-terminal pro-B-type natriuretic peptide levels in healthy North American Salukis with normal echocardiographic measurements.

Measurement of N-terminal pro-B-type natriuretic peptide (NT-proBNP) levels has been shown to have clinical significance for diagnosis and management of heart disease in dogs. Evaluation of current reference limits for specific breeds is necessary to ensure the test can accurately distinguish between healthy and diseased animals. The objective of this study is to evaluate the adequacy of currently established NT-proBNP reference limits for clinical use in healthy Salukis. Cardiac health of 33 clinically healthy Salukis was evaluated via echocardiography using available breed standards. Plasma concentrations of NT-proBNP were measured using a commercially available assay. A one-sided 97.5 % upper reference limit for the NT-proBNP concentrations was calculated using non-parametric percentile method. The 97.5 % upper reference limit was 769 pmol/L (90% CI, 547-1214 pmol/L) for the study dogs. This upper reference limit was within the currently established non-breed specific NT-proBNP upper reference limit of 900 pmol/L. No relationship between sex, age, or body weight on plasma levels of NT-proBNP was noted. Results of this study supports the use of currently available non-breed specific NT-proBNP cut-off values for clinical evaluation of healthy Salukis.

physiology↗

bioRxiv2021

Visual evoked feedforward-feedback travelling waves organize neural activity across the cortical hierarchy in mice

Sensory processing is distributed among many brain regions that interact via feedforward and feedback signaling. It has been hypothesized that neuronal oscillations mediating feedforward and feedback interactions organize into travelling waves. However, stimulus evoked travelling waves of sufficient spatial scale have never been demonstrated directly. Here, we show that simple visual stimuli reliably evoke two traveling waves with spatial wavelengths that cover much of the cerebral hemisphere in awake mice. 30-50Hz feedforward waves arise in primary visual cortex (V1) and propagate rostrally, while 3-6Hz feedback waves originate in the association cortex and flow caudally. The phase of the feedback wave modulates the amplitude of the feedforward wave and synchronizes firing between V1 and parietal cortex. Altogether, these results provide direct experimental evidence that visual evoked travelling waves percolate through the cerebral cortex and coordinate neuronal activity across broadly distributed networks mediating visual processing.

neuroscience↗

bioRxiv2018

American Gut: an Open Platform for Citizen-Science Microbiome Research

Although much work has linked the human microbiome to specific phenotypes and lifestyle variables, data from different projects have been challenging to integrate and the extent of microbial and molecular diversity in human stool remains unknown. Using standardized protocols from the Earth Microbiome Project and sample contributions from over 10,000 citizen-scientists, together with an open research network, we compare human microbiome specimens primarily from the USA, UK, and Australia to one another and to environmental samples. Our results show an unexpected range of beta-diversity in human stool microbiomes as compared to environmental samples, demonstrate the utility of procedures for removing the effects of overgrowth during room-temperature shipping for revealing phenotype correlations, uncover new molecules and kinds of molecular communities in the human stool metabolome, and examine emergent associations among the microbiome, metabolome, and the diversity of plants that are consumed (rather than relying on reductive categorical variables such as veganism, which have little or no explanatory power). We also demonstrate the utility of the living data resource and cross-cohort comparison to confirm existing associations between the microbiome and psychiatric illness, and to reveal the extent of microbiome change within one individual during surgery, providing a paradigm for open microbiome research and education.\n\nImportanceWe show that a citizen-science, self-selected cohort shipping samples through the mail at room temperature recaptures many known microbiome results from clinically collected cohorts and reveals new ones. Of particular interest is integrating n=1 study data with the population data, showing that the extent of microbiome change after events such as surgery can exceed differences between distinct environmental biomes, and the effect of diverse plants in the diet which we confirm with untargeted metabolomics on hundreds of samples.

microbiology↗