Biology subjects

Kennedy, B.

Publications and source records attributed to Kennedy, B..

12 recordsLinked to original sources

bioRxiv2025

Mesoscale developmental rivalry in human extrastriate visual cortex

In humans and non-human primates, the extrastriate visual cortex contains fine-scale columns selectively responsive to motion, disparity, and color. However, the developmental interplay between these functional modules remains poorly understood. Using high-resolution fMRI, we compared the mesoscale organization of extrastriate cortex in 16 individuals with normal vision and 15 participants with amblyopia (PwA) caused by strabismus (n=8) or anisometropia (n=7). In controls, the cortical territory occupied by disparity-selective columns exhibited a competitive relationship with that of motion- and color-selective columns. Consistent with this pattern, PwA showed a reduction in disparity-selective responses accompanied by enhanced motion- and color-selective activity, as well as expansion of the cortical territory allocated to them. Our results show that the mesoscale modules of the human visual system are rivals in development allowing intact functions to usurp those that are compromised.

neuroscience↗

bioRxiv2025

Scaffolded hiPSC liver organoids recapitulating bile duct tubulogenesis and periportal architecture.

Recapitulating the liver periportal area in vitro remains a major challenge due to its complex cellular composition and the coordinated development of both ductal and endothelial networks. Most existing bile duct organoid models fail to reproduce tubular extension and multicellular organization. We present a 3D ECM micro-rods system biofunctionalized with grafted growth factors mimicking fetal liver paracrine signaling to initiate and to coordinate the development of bile ducts, parenchymal cells, and vascular structures. Our system recapitulates key developmental stages, from the formation of the ductal plate to the emergence of elongated tubular ducts. The ECM rod alone provides the biophysical cues initiating the elongation of the bile ducts and the spatial structuration of the cellular organization, while the biofunctionalization with growth factors enhance the organization and maturation of the biliary and vascular systems. We further demonstrate that this approach is scalable and amenable to quantitative analysis through label-free Optical Coherence Tomography combined with AI-driven 3D segmentation.

cell biology↗

bioRxiv2025

Antimicrobial stewardship in animal health: experience-based co-design framework to capture progress and accelerate improvement

Antimicrobial stewardship (AMS) is essential for mitigating antimicrobial resistance (AMR) in animal health but implementing national initiatives is challenging due to diverse influencing factors and the need for context-specific approaches. An Animal AMS Practice Group, comprised of individuals with lived experience overseeing AMS in various animal health contexts was engaged, and through an experience-based co-design approach created a comprehensive AMS Framework that captures progress and supports tangible improvements in AMS practices in each context. The Framework supported a cross-sectoral pilot assessment that helped users identify progress, areas for improvement, and contextualise antimicrobial usage and AMR data, while also motivating further AMS efforts. Despite common barriers to sharing sensitive data, participants willingly shared AMS results for benchmarking and publication. The process demonstrated that co-design coupled with peer learning and expert support are essential to ensuring AMS tools are utilised in practice. Several participants incorporated the Framework into routine practice, with some using it to drive sector-level AMS action. The resulting Framework offers an adaptable, scalable entry point for AMS efforts and a platform for setting meaningful improvement goals. It supports broader opportunities for national-level AMS assessments and strategy development. Impact StatementThis research offers a practical, scalable approach to improving AMS in animal health. By embedding behaviour change into the project through an experience-based co-design process, rather than expecting it to occur afterward, veterinarians, animal managers, and other frontline professionals defined what good AMS looks like in their context and identified achievable actions to improve daily practices that aligned across diverse animal health settings. The resulting AMS Framework provides a clear, accessible starting point for those overseeing daily AMS activities to benchmark practices, set meaningful goals, and track progress, while also informing national-level prioritisation and decision-making. This user-led model demonstrates that when AMS tools are co-developed with those who will use them and users are empowered to shape the projects design and outputs, the resulting tools are more likely to be adopted, shared, and sustained.

microbiology↗

bioRxiv2024

Longitudinal evidence for the emergence of multiple intelligences in assistance dog puppies

Cognitive test batteries suggest that adult dogs have different types of cognitive abilities that vary independently. In the current study, we tested puppies repeatedly over a crucial period of development to explore the timing and rate at which these different cognitive skills develop. Service dog puppies (n = 113), raised using two different socialization strategies, were either tested longitudinally (n =91) or at a single time point (n = 22). Subjects tested longitudinally participated in the battery every two weeks during and just beyond their final period of rapid brain growth (from approximately 8-20 weeks of age). Control puppies only participated in the test battery once, which allowed us to evaluate the impact of repeated testing. In support of the multiple intelligences hypothesis (MIH), cognitive skills emerged at different points across the testing period, not simultaneously. Maturational patterns also varied between cognitive skills, with puppies showing adult-like performance on some tasks only weeks after a skill emerged, while never achieving adult performance in others. Differences in rearing strategy did not lead to differences in developmental patterns while, in some cases, repeated testing did. Overall, our findings provide strong support for the MIH by demonstrating differentiated development across the cognitive abilities tested.

animal behavior and cognition↗

bioRxiv2024

Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes

While rapid demographic changes in Asia are driving the incidence of chronic diseases related to aging, the limited availability of high-quality in vivo data hampers our ability to understand complex multi-factorial contributions, including gut microbial, to healthy aging. Leveraging the availability of a well-phenotyped cohort of community-living octogenarians in Singapore, we used deep shotgun metagenomic sequencing to do high-resolution taxonomic and functional characterization of their gut microbiomes (n=234). Joint species-level analysis with other Asian cohorts identified a distinct age-associated shift in Asian gut metagenomes, characterized by a reduction in microbial richness, and enrichment of specific Alistipes and Bacteroides species (e.g. Alistipes shahii and Bacteroides xylanisolvens). Functional pathway analysis confirmed that these changes correspond to a metabolic potential expansion in aging towards alternate pathways that synthesize and utilize amino-acid precursors, relative to the dominant microbial guilds that typically produce butyrate in the gut from pyruvate (e.g. Faecalibacterium prausnitzii, Roseburia inulinivorans). Extending these observations to key clinical markers helped identify >10 robust gut microbial associations to inflammation, cardiometabolic and liver health, including potential probiotic species such as Parabacteroides goldsteinii and pathobionts such as Klebsiella pneumoniae, highlighting the role of the microbiome as biomarkers and potential intervention targets for promoting healthy aging.

genomics↗

bioRxiv2024

A metabolic atlas of mouse aging

Humans are living longer, but this is accompanied by an increased incidence of age-related chronic diseases. Many of these diseases are influenced by age-associated metabolic dysregulation, but how metabolism changes in multiple organs during aging in males and females is not known. Answering this could reveal new mechanisms of aging and age-targeted therapeutics. In this study, we describe how metabolism changes in 12 organs in male and female mice at 5 different ages. Organs show distinct patterns of metabolic aging that are affected by sex differently. Hydroxyproline shows the most consistent change across the dataset, decreasing with age in 11 out of 12 organs investigated. We also developed a metabolic aging clock that predicts biological age and identified alpha-ketoglutarate, previously shown to extend lifespan in mice, as a key predictor of age. Our results reveal fundamental insights into the aging process and identify new therapeutic targets to maintain organ health.

molecular biology↗

bioRxiv2024

Using high-resolution functional MRI to differentiate impacts of strabismic and anisometropic amblyopia on evoked ocular dominance activity in humans

We employed high-resolution functional MRI (fMRI) to distinguish the impacts of anisometropia and strabismus (the two most frequent causes of amblyopia) on the evoked ocular dominance (OD) response. Sixteen amblyopic participants (8 females), comprising 8 individuals with strabismus, 7 with anisometropia, 1 with deprivational amblyopia, along with 8 individuals with normal visual acuity (1 female), participated in this study for whom, we measured the difference between the response to stimulation of the two eyes, across early visual areas (V1-V4). In controls, as expected from the organization of OD columns, the evoked OD response formed a striped pattern that was mostly confined to V1. Compared to controls, the OD response in amblyopic participants formed larger fused patches that extended into downstream visual areas. Moreover, both anisometropic and strabismic participants showed stronger OD responses in V1, as well as in downstream visual areas V2-V4. Although this increase was most pronounced in V1, the correlation between the OD response level and the interocular visual acuity difference (measured behaviorally) was stronger in higher-level visual areas (V2-V4). Beyond these common effects, and despite similar densities of amblyopia between the anisometropic and strabismic participants, we found a greater increase in the size of V1 portion that responded preferentially to fellow eye stimulation in anisometropic compared to strabismic individuals. We also found a greater difference between the amplitudes of the response to binocular stimulation, in those regions that responded preferentially to the fellow vs. amblyopic eye, in anisometropic compared to strabismic subjects. In contrast, strabismic subjects demonstrated increased correlation between the OD responses evoked within V1 superficial and deep cortical depths, whereas anisometropic subjects did not. These results provide some of the first direct functional evidence for distinct impacts of strabismus and anisometropia on the mesoscale functional organization of the human visual system, thus extending what was inferred previously about amblyopia from animal models.

neuroscience↗

bioRxiv2022

Two interdigitated fine-scale channels for encoding motion and stereopsis within the human magnocellular stream

In humans and non-human primates (NHPs), motion and stereopsis are processed within fine-scale cortical sites, including V2 thick stripes and their extensions into areas V3 and V3A that are believed to be under the influence of magnocellular stream. However, in both species, the functional organization (overlapping vs. interdigitated) of these sites remains unclear. Using high-resolution functional MRI (fMRI), we found evidence for two interdigitated channels within human extrastriate areas that contribute to processing motion and stereopsis. Across multiple experiments that included different stimuli (random dots, gratings, and natural scenes), the functional selectivity of these channels for motion vs. stereopsis remained consistent. Furthermore, an analysis of resting state functional connectivity revealed stronger functional connectivity within the two channels rather than between them. This finding provides a new perspective toward the mesoscale organization of the magnocellular stream within the human extrastriate visual cortex, beyond our previous understanding based on animal models.

neuroscience↗

bioRxiv2021

Metabolite discovery through global annotation of untargeted metabolomics data

Liquid chromatography-high resolution mass spectrometry (LC-MS)-based metabolomics aims to identify and quantitate all metabolites, but most LC-MS peaks remain unidentified. Here, we present a global network optimization approach, NetID, to annotate untargeted LC-MS metabolomics data. The approach aims to generate, for all experimentally observed ion peaks, annotations that match the measured masses, retention times, and (when available) MS/MS fragmentation patterns. Peaks are connected based on mass differences reflecting adducting, fragmentation, isotopes, or feasible biochemical transformations. Global optimization generates a single network linking most observed ion peaks, enhances peak assignment accuracy, and produces chemically-informative peak-peak relationships, including for peaks lacking MS/MS spectra. Applying this approach to yeast and mouse data, we identified five novel metabolites (thiamine derivatives and N-glucosyl-taurine). Isotope tracer studies indicate active flux through these metabolites. Thus, NetID applies existing metabolomic knowledge and global optimization to annotate untargeted metabolomics data, revealing novel metabolites.

bioinformatics↗

bioRxiv2020

Control of mammalian brain aging by the unfolded protein response (UPR)

Aging is the major risk factor for the development of dementia and neurodegenerative disorders, and the aging brain manifests severe deficits in buffering capacity by the proteostasis network. Accordingly, we investigated the significance of the unfolded protein response (UPR), a major signaling pathway that copes with endoplasmic reticulum (ER) stress, to normal mammalian brain aging. Genetic disruption of ER stress sensor IRE1 accelerated cognitive and motor dysfunction during aging. Exogenous bolstering of the UPR by overexpressing an active form of the transcription factor XBP1 restored synaptic and cognitive function in addition to reducing cell senescence. Remarkably, proteomic profiling of hippocampal tissue indicated that XBP1s expression corrected age-related alterations in synaptic function. Collectively, our data demonstrate that strategies to manipulate the UPR sustain healthy brain aging. One Sentence SummaryThe IRE1/XBP1 pathway dictates when and how brain function declines during aging.

neuroscience↗

bioRxiv2019

Isometric exercise facilitates attention to salient events in women via the noradrenergic system

The locus coeruleus (LC) plays a critical role in regulating attention via the release of norepinephrine (NE), with levels of tonic LC activity constraining the intensity of phasic LC responses. However, the effects of manipulating tonic LC-NE activity on phasic activity have yet to be demonstrated in humans. In the current fMRI study, we used isometric handgrip to modulate tonic LC-NE activity in the time period immediately afterwards. During this post-handgrip time, an oddball detection task was used to probe how changes in tonic arousal influenced functional coordination between the LC and a right frontoparietal network that supports attentional selectivity. As expected, the frontoparietal network responded more to infrequent target and novel sounds than to frequent sounds. Across participants, greater LC-frontoparietal functional connectivity, pupil dilation, and faster oddball detection were all positively associated with LC MRI contrast from a neuromelanin-sensitive structural scan. Thus, LC structural integrity was related to LC functional dynamics and attentional performance during the oddball task. We also found that handgrip led to larger phasic pupil responses to oddball sounds, faster oddball detection speed, and greater frontoparietal network activation, suggesting that something that induces strong LC activity benefits attentional performance for at least the next few minutes. In addition, older women showed a similar benefit of handgrip on frontoparietal network activation as younger women, despite showing lower frontoparietal network activation overall. Together these findings suggest that a simple exercise may improve selective attention in healthy aging, at least for several minutes afterwards.\n\nHighlightsO_LIWe examined how handgrip affects arousal-attention dynamics during an oddball task\nC_LIO_LISalient stimuli enhanced pupil dilation and were detected faster post-handgrip\nC_LIO_LIA decrease in tonic pupil size after handgrip suggests norepinephrine depletion\nC_LIO_LIMRI-assessed LC integrity was related to oddball detection and pupil dilation\nC_LIO_LILC integrity also associated with LC-frontoparietal network functional connectivity\nC_LI

neuroscience↗

bioRxiv2019

Calcitriol and Non-Calcemic Vitamin D Analogue, 22 Oxacalcitriol, Attenuate Developmental and Pathological Ocular Angiogenesis Ex Vivo and In Vivo

Aberrant ocular blood vessel growth can underpin vision loss in leading causes of blindness, including neovascular age-related macular degeneration, retinopathy of prematurity and proliferative diabetic retinopathy. Current pharmacological interventions require repeated invasive administrations, lack efficacy in some patients and are associated with poor patient compliance and tachyphylaxis. Small molecule vitamin D has de novo pro-differentiative, anti-proliferative, immunomodulatory, pro-apoptotic and anti-angiogenic properties. Here, our aim was to validate the anti-angiogenic activity of the biologically active form of vitamin D, calcitriol, and a selected vitamin D analogue, 22-oxacalcitriol, across a range of ocular angiogenesis models.\n\nFirst, we validated the anti-angiogenic activity of calcitriol, showing calcitriol to significantly inhibit choroidal sprouting in an ex vivo mouse choroidal fragment sprouting assay. Viability studies in human RPE cell line, ARPE-19, suggested non-calcemic vitamin D analogues have the least off-target anti-proliferative activity compared to calcitriol and additional analogues. Thereafter, the ocular anti-angiogenic activity of non-calcemic vitamin D analogue, 22-oxacalcitriol, was demonstrated in the ex vivo mouse choroidal fragment sprouting assay. In zebrafish larvae, 22-oxacalcitriol was anti-angiogenic, inducing a dose-dependent reduction in choriocapillary angiogenesis. Inhibition of mouse retinal vasculature development was not induced by systemically delivered calcitriol. However, both calcitriol and 22-oxacalcitriol administered intraperitoneally significantly attenuate choroidal neovascularisation lesion volume in the laser-induced CNV mouse model. 22-oxacalcitriol presented with a more favourable safety profile than calcitriol.\n\nIn summary, calcitriol and 22-oxacalcitriol attenuate ex vivo and in vivo choroidal vasculature angiogenesis. Vitamin D has potential as a preventative or interventional treatment for ophthalmic neovascular indications.

pharmacology and toxicology↗