Biology subjects

Brennan, J.

Publications and source records attributed to Brennan, J..

13 recordsLinked to original sources

bioRxiv2026

Extinction order affects community composition under strong competition and asymmetric species interactions

Extinction is a fundamental process impacting how community compositions change though time. Despite this, relatively few studies have examined how the order of species loss in multispecies extinction sequences can differentially impact the composition of the resulting disassembled community, known as an inverse priority effect. Here, we investigate the prevalence and predictors of inverse priority effects across a range of ecological contexts. First, we extend previous theory by deriving all possible cases of inverse priority effects in three-species Lotka-Volterra systems of coexisting competitors with equal intrinsic growth rates. We show that communities with strong, asymmetric competitive interactions are more likely to exhibit inverse priority effects. We then use a random matrix approach to demonstrate that inverse priority effects become more prevalent in more speciose communities and vary with the length of the extinction sequence. Furthermore, in speciose communities, inverse priority effects become increasingly likely with less facilitative or more competitive average interspecific interactions. Together, our results suggest that inverse priority effects are likely common in species-rich communities, particularly those with strong competition and asymmetric species interactions, warranting further theoretical and empirical investigation.

ecology↗

bioRxiv2026

From Lotka-Volterra Dynamics to Community Assembly: Theory, Topography, and Empirical Applications

AO_SCPLOWBSTRACTC_SCPLOWO_LICommunity assembly graphs (CAGs) summarize which species combinations can coexist and how single-species invasions drive transitions between them, encoding the pathways, alternative endpoints, and cycles that make up a communitys assembly history. Constructing CAGs from dynamical models requires methods that are both computationally tractable and faithful to the underlying ecological dynamics. However, existing methods rely on restrictive assumptions, such as global stability, that exclude alternative stable states and non-equilibrium dynamics known to occur in empirical systems. C_LIO_LIWe develop a computational pipeline that constructs CAGs from any generalized Lotka-Volterra model. Building on the invasion graph framework and its connection to permanence, the pipeline verifies that community dynamics are bounded, identifies which subsets of species coexist in the sense of permanence, determines which single-species invasions are dynamically realized, and assigns each community a topographic height equal to the length of the longest assembly path leading to it. We also provide a numerical algorithm to simulate the dynamics of community assembly. C_LIO_LIWe prove several general properties of the resulting graphs, including that a successful invader is never subsequently excluded and that, in the absence of assembly cycles, permanent communities can be reassembled by introducing their species one at a time in the right order. We prove that the CAG faithfully reproduces the compositional shifts seen in the numerically simulated dynamics of assembly. Applying the pipeline to three empirically based models (a New Zealand grassland, a European pasture, and a Puerto Rican ant community), we show how competition strength and mutualistic feedbacks reshape the assembly landscape and how intransitive competition generates assembly cycles. C_LIO_LIOur approach accommodates alternative stable states and non-equilibrium dynamics without requiring global stability, and it turns the long-standing landscape metaphor into a quantitative, mechanistically grounded object by resolving what "height" means. More broadly, it makes the topography of the assembly pathways measurable, providing a way to compare the historical contingency and predictability of the assembly in ecological systems. C_LI

ecology↗

bioRxiv2025

Using Modern Coexistence Theory to understand community disassembly

Community disassembly examines how species extinction alters ecological communities. Sometimes, the extinction of one species can trigger the loss of others, known as secondary extinction. These secondary extinctions often result from complex species interactions, complicating the identification of underlying mechanisms. Here, we leverage Modern Coexistence Theory to identify when and why secondary extinctions occur. To identify when secondary extinctions occur, we introduce the community disassembly graph, that uses invasion growth rates to identify transitions between coexisting communities due to extinction. When a secondary extinction is identified, we decompose the invasion growth rates associated with the secondary extinction to understand why it occurs. We demonstrate the utility of this framework by applying it to models in which different species interactions-competition, facilitation, and predation-contribute significantly to secondary extinctions. Our results show that Modern Coexistence Theory offers a flexible and interpretable approach to understanding when and why secondary extinctions occur.

ecology↗

bioRxiv2025

Evolutionary Genomics Guides Scalable Coral Probiotics for Climate Resilience

A universal bottleneck limiting probiotic efficacy in medicine, aquaculture, agriculture, and wildlife conservation is uncertain long-term colonization, necessitating repeated administration. We present an evolution-guided framework for probiotic identification based on genomic hallmarks of emerging host dependency, including widespread pseudogenization and insertion sequence proliferation driving genomic restructuring. Applied to coral reefs, we screened over 1,200 coral-associated bacterial isolates and identified Ruegeria MC10 as exhibiting these signatures. Its presence was associated with increased thermal tolerance of a model cnidarian. Following nursery application, MC10 persisted in reef corals for an 8-month monitoring period through a natural bleaching event, improving color retention and retaining algal photosynthesis performance. This work establishes a predictive, scalable pipeline for selecting persistent probiotics, directly addressing a central constraint on microbiome-based interventions across host systems.

microbiology↗

bioRxiv2025

Repurposing statins and phenothiazines to treat chemoresistant neuroblastoma.

Relapse and treatment resistance are common in children with high-risk neuroblastoma, and novel therapies are needed. Conventional drug discovery is slow, expensive, often fails in practice, and consequently falls short in addressing pediatric and rare conditions. In such instances, drug repurposing is a promising strategy. Here, we used two independent in silico prediction tools including machine learning to identify approved drugs for repurposing against neuroblastoma. The combination of statins and phenothiazines showed strong synergistic effects in human neuroblastoma organoids, decreased tumor growth and prolonged survival in MYCN-amplified neuroblastoma patient-derived xenografts. The drug combination altered cholesterol metabolism through a dual-hit mechanism and induced a phenotypic switch towards an adrenergic cell state accompanied by increased sensitivity to chemotherapy. Integration of the drug combination into standard-of-care chemotherapy regressed tumors and prolonged survival in chemoresistant patient-derived xenografts. Thus, a combination of safe and approved medications added to standard-of-care chemotherapy outperforms chemotherapy alone in chemoresistant neuroblastoma. TeaserUsing in silico prediction tools we repurposed statins and phenothiazines as a combination with translational potential in high-risk neuroblastoma.

cancer biology↗

bioRxiv2024

Coexistence of bacteria with a competition-colonization tradeoff on a dynamic coral host

Many macroscopic organisms enter into tightly linked symbiosis with microbial communities. Although experimental work has demonstrated the importance of these symbioses, a theoretical understanding of stable, multi-scale coexistence remains underdeveloped. Here, we explored how the competition-colonization tradeoff, a classic coexistence mechanism, operates when bacterial species compete for a dynamic biological host. Specifically, we introduce a model where corals are colonized by fast-growing mutualists and slow-growing pathogens. We found that the vital rates of the host coral influenced coexistence outcomes between bacterial types. Notably, pathogen-induced host death expanded the region of parameter space where coexistence was stable for all three species and mutualistic bacteria enabled coexistence in systems that would have otherwise collapsed. These findings provide new insights into the interplay between microbial interactions and macroscopic processes. Our work illustrates how host-microbe interactions can shape ecosystem stability, providing a theoretical framework applicable to a wide range of symbiotic systems.

ecology↗

bioRxiv2024

Le Petit Prince Hong Kong (LPPHK): Naturalistic fMRI and EEG data from older Cantonese speakers

Currently, the field of neurobiology of language is based on data from only a few Indo-European languages. The majority of this data comes from younger adults neglecting other age groups. Here we present a multimodal database which consists of task-based and resting state fMRI, structural MRI, and EEG data while participants over 65 years old listened to sections of the story The Little Prince in Cantonese. We also provide data on participants language history, lifetime experiences, linguistic and cognitive skills. Audio and text annotations, including time- aligned speech segmentation and prosodic information, as well as word-by-word predictors such as frequency and part-of-speech tagging derived from natural language processing (NLP) tools are included in this database. Both MRI and EEG data diagnostics revealed that the data has good quality. This multimodal database could advance our understanding of spatiotemporal dynamics of language comprehension in the older population and help us study the effects of healthy aging on the relationship between brain and behaviour.

neuroscience↗

bioRxiv2024

The Updated Mouse Universal Genotyping Array Bioinformatic Pipeline Improves Genetic QC in Laboratory Mice

The MiniMUGA genotyping array is a popular tool for genetic QC of laboratory mice and genotyping of samples from most types of experimental crosses involving laboratory strains, particularly for reduced complexity crosses. The content of the production version of the MiniMUGA array is fixed; however, there is the opportunity to improve arrays performance and the associated reports usefulness by leveraging thousands of samples genotyped since the initial description of MiniMUGA in 2020. Here we report our efforts to update and improve marker annotation, increase the number and the reliability of the consensus genotypes for inbred strains and increase the number of constructs that can reliably be detected with MiniMUGA. In addition, we have implemented key changes in the informatics pipeline to identify and quantify the contribution of specific genetic backgrounds to the makeup of a given sample, remove arbitrary thresholds, include the Y Chromosome and mitochondrial genome in the ideogram, and improve robust detection of the presence of commercially available substrains based on diagnostic alleles. Finally, we have made changes to the layout of the report, to simplify the interpretation and completeness of the analysis and added a table summarizing the ideogram. We believe that these changes will be of general interest to the mouse research community and will be instrumental in our goal of improving the rigor and reproducibility of mouse-based biomedical research.

genetics↗

bioRxiv2022

Long-distance linguistic dependencies in Chinese and English brains

Are the brain bases of language comprehension the same across all human languages, or do these bases vary in a way that corresponds to differences in linguistic typology? English and Mandarin Chinese attest such a typological difference in the domain of relative clauses. Using fMRI with English and Chinese participants, who listened to the same translation-equivalent story, we analyzed neuroimages time-aligned to object-extracted relative clauses in both languages. In a GLM analysis of these naturalistic data, comprehension was selectively associated with increased hemodynamic activity in left posterior temporal lobe, angular gyrus, inferior frontal gyrus, precuneus, and posterior cingulate cortex in both languages. This result suggests the processing of object-extracted relative clauses is subserved by a common collection of brain regions, regardless of typology. However, there were also regions that were activated uniquely in our Chinese participants albeit not to a significantly greater degree. These were in the temporal lobe. These Chinese-specific results could reflect structural ambiguity-resolution work that must be done in Chinese but not English ORCs.

neuroscience↗

bioRxiv2021

Open-Source Low-Cost Cardiac Optical Mapping System

Fluorescent imaging with voltage- or calcium-sensitive dyes, i.e. optical mapping, is one of the indispensable modern techniques to study cardiac electrophysiology, unsurpassed by temporal and spatial resolution. High-speed CMOS cameras capable of optical registration of action potential propagation are in general very costly. We present a complete solution priced below US$ 1,000 (including camera and lens) at the moment of publication with an open-source image acquisition and processing software. We demonstrate that the iDS UI-3130CP rev.2 camera we used in this study is capable of 200x200 977 frames per second (FPS) action potential recordings from rodent hearts. The signal-to-noise-ratio of a conditioned signal was 16 {+/-} 10 for rodent hearts. A comparison with a specialized MiCAM Ultimate-L camera has shown that signal-to-noise ratio (SNR) is sufficient for accurate measurements of AP waveform, conduction velocity ({+/-} 0.04 m/s) and action potential duration ({+/-} 7ms) in mouse and rat hearts. We measured the action potential prolongation during 4-aminopyridine administration in mouse heart, showing that proposed system signal quality is adequate for drug studies.

bioengineering↗

bioRxiv2020

Innervation and Neuronal Control of the Mammalian Sinoatrial Node: A Comprehensive Atlas

Cardiac function is under exquisite intrinsic cardiac neural control. Neuroablative techniques to modulate control of cardiac function are currently being studied in patients, albeit with variable and sometimes deleterious results. Recognizing the major gaps in our understanding of cardiac neural control, we sought to evaluate neural regulation of impulse initiation in the sinoatrial node as an initial discovery step. Here, we report an in-depth, multi-scale structural and functional characterization of the innervation of the sinoatrial node (SAN) by the right atrial ganglionated plexus (RAGP) in porcine and human hearts. Combining intersectional strategies including tissue clearing, immunohistochemical and ultrastructural techniques, we have delineated a comprehensive neuroanatomic atlas of the RAGP-SAN complex. The RAGP shows significant phenotypic diversity of neurons while maintaining predominant cholinergic innervation. Cellular and tissue-level electrophysiologic mapping and ablation studies demonstrate interconnected ganglia with synaptic convergence within the RAGP to modulate SAN automaticity, atrioventricular (AV) conduction and left ventricular (LV) contractility. For the first time, we demonstrate that intrinsic cardiac neurons influence the pacemaking site in the heart. This provides an experimental demonstration of a discrete neuronal population controlling a specific geographic region of the heart (SAN) that can serve as a framework for further exploration of other parts of the intrinsic cardiac nervous system (ICNS) in mammalian hearts and for developing targeted therapies.

neuroscience↗

bioRxiv2020

Content and performance of the MiniMUGA genotyping array, a new tool to improve rigor and reproducibility in mouse research

The laboratory mouse is the most widely used animal model for biomedical research, due in part to its well annotated genome, wealth of genetic resources and the ability to precisely manipulate its genome. Despite the importance of genetics for mouse research, genetic quality control (QC) is not standardized, in part due to the lack of cost effective, informative and robust platforms. Genotyping arrays are standard tools for mouse research and remain an attractive alternative even in the era of high-throughput whole genome sequencing. Here we describe the content and performance of a new Mouse Universal Genotyping Array (MUGA). MiniMUGA, an array-based genetic QC platform with over 11,000 probes. In addition to robust discrimination between most classical and wild-derived laboratory strains, MiniMUGA was designed to contain features not available in other platforms: 1) chromosomal sex determination, 2) discrimination between substrains from multiple commercial vendors, 3) diagnostic SNPs for popular laboratory strains, 4) detection of constructs used in genetically engineered mice, and 5) an easy to interpret report summarizing these results. In-depth annotation of all probes should facilitate custom analyses by individual researchers. To determine the performance of MiniMUGA we genotyped 6,899 samples from a wide variety of genetic backgrounds. The performance of MiniMUGA compares favorably with three previous iterations of the MUGA family of arrays both in discrimination capabilities and robustness. We have generated publicly available consensus genotypes for 241 inbred strains including classical, wild-derived and recombinant inbred lines. Here we also report the detection of a substantial number of XO and XXY individuals across a variety of sample types, the extension of the utility of reduced complexity crosses to genetic backgrounds other than C57BL/6, and the robust detection of 17 genetic constructs. There is preliminary but striking evidence that the array can be used to identify both partial sex chromosome duplication and mosaicism, and that diagnostic SNPs can be used to determine how long inbred mice have been bred independently from the main stock for a significant action of the genotyped inbred samples. We conclude that MiniMUGA is a valuable platform for genetic QC and important new tool to the increase rigor and reproducibility of mouse research.

genetics↗

bioRxiv2018

Sudden heart rate reduction upon optogenetic release of acetylcholine from cardiac parasympathetic neurons in perfused hearts

The balance of sympathetic and parasympathetic tone provides exquisite control of heart rate and contractility and has also been shown to modulate coronary flow and inflammation. Understanding how autonomic balance is altered by cardiac disease is an active area of research and developing new ways to control this balance is providing insights into disease therapies. However, achieving acute neuron-specific stimulation of autonomic neurons can be difficult in experiments that measure the acute effects of nerve stimulation on the heart. Conventional electrical and pharmacological approaches can be spatially and temporally non-selective. Cell-specific expression of light-activated channels (channelrhodopsin, ChR2) is a powerful approach that enables control of the timing and distribution of cellular stimulation using light. We present such an optogenetic approach where parasympathetic cardiac neurons are selectively photoactivated at high temporal precision to initiate cholinergic-mediated slowing of heart rate.\n\nMice were crossbred to express ChR2 in peripheral cholinergic neurons using Cre-Lox recombination driven by a choline acetyltransferase (ChAT) promoter. Hearts from adult mice were excised, perfused, and the epicardium was illuminated (peak 460-465nm) to photoactivate ChR2. In one set of studies, hearts were illuminated using a large-field LED light source. In other studies, a micro LED was placed on the right atrium to selectively illuminate the junction of the superior vena cava and right atrium. The ECG was acquired before, during, and after tissue illumination to measure changes in heart rate. Upon illumination, hearts exhibited sudden and dramatic reductions in heart rate with restoration of normal heart rate after cessation of illumination. Delays in atrioventricular conduction were also observed. Heart rate reductions at the highest irradiance levels were similar to heart rate reductions caused by application of bethanechol (10{micro}M) or acetylcholine (800{micro}M). Atropine (50nM) completely blocked the effect of ChR2 photoactivation, confirming cholinergic mediation.\n\nOptogenetic activation of intrinsic parasympathetic neurons reduced heart rate in an immediate, dose-dependent fashion, resembling the slowing of sinus rate in response to acetylcholine. Our results demonstrate a new approach for controlling parasympathetic modulation of cardiac function by selectively activating the endogenous release of acetylcholine from intrinsic cardiac cholinergic neurons.\n\nKey MessageOptogenetic photoactivation of intrinsic cardiac neurons provides immediate, tissuespecific stimulation with minimal cross-reactivity. Our results demonstrate that selective expression of channelrhodopsin within cardiac cholinergic neurons enables photoactivated release of acetylcholine, thereby instantaneously slowing sinus rate and altering atrioventricular conduction. This provides for indepth examination of the endogenous interplay between cardiac autonomic neurons and the functional outcomes of downstream post-synaptic receptor activation.

physiology↗