Biology subjects

Robertson, K.

Publications and source records attributed to Robertson, K..

14 recordsLinked to original sources

bioRxiv2026

Diagnostic Labels and Measurement Timing Drive Systematic Inconsistency in ADNI Neuroimaging Data

The Alzheimer's Disease Neuroimaging Initiative (ADNI) is widely used to train machine learning models for Alzheimer's disease, yet whether it provides consistent ground truth for predictive modeling has not been systematically tested. In this paper, we showed that ADNI contains three interacting sources of bias with direct implications for machine learning: (a) diagnostic label inconsistency, (b) technical measurement drift, and (c) longitudinal survivor bias. A substantial proportion of cases, particularly within intermediate stages, fall outside ADNI's own diagnostic thresholds. MRI field strength and evolving processing pipelines introduce significant technical variability in hippocampal volume, while cohort survivor bias arising from differential retention of participants across phases further distorts longitudinal estimates of disease progression. These findings indicated that ADNI does not provide the stable, internally consistent labels often required in machine learning applications. We proposed a practical framework for diagnostic validation, feature harmonization, and cohort accounting, offering guidance for building more robust and biologically meaningful predictive models from large-scale neuroimaging cohorts.

neuroscience↗

bioRxiv2026

Malnourishment and expanded microbiome maintain superior efficacy of the recombinant tuberculosis vaccine BCG::ESAT-6-PE25SS

Tuberculosis (TB) remains the leading cause of infectious mortality. The limited efficacy of the only TB vaccine, Bacille Calmette-Guerin (BCG) against pulmonary disease necessitates improved vaccines. Host factors such as malnutrition and microbiome composition shape immune responses in humans, though these factors are overlooked in preclinical vaccine evaluation. Here we show that a recombinant BCG strain, BCG::ESAT-6-PE25SS, confers superior protection compared to BCG across murine models of malnutrition, antibiotic-induced dysbiosis and environmentally enriched microbiota. Unexpectedly, malnourished mice displayed reduced Mycobacterium tuberculosis (Mtb) burden, associated with altered host metabolism and immune composition. Microbiome disruption increased TB susceptibility, whereas diversification of microbiota enhanced resistance and immune heterogeneity. Vaccine efficacy correlated with enrichment of known immunomodulatory microbial taxa. These findings suggest diet-microbiome-immunity interactions as potential key determinants of TB pathogenesis and provide evidence for the importance of vaccine candidate evaluation under physiologically relevant co-morbid conditions

microbiology↗

bioRxiv2025

Multiscale Spatial Mapping of Microbial Communities for Biotherapeutic Development

Live biotherapeutic products (LBPs) are emerging as powerful tools to modulate the microbiome using well-defined microbial communities. Yet, designing, manufacturing, and delivering LBPs remains challenging, in part due to a lack of technologies capable of analyzing LBPs as complete, spatially organized consortia. Conventional sequencing-based methods lack sensitivity and specificity and do not provide critical spatial information. To address this, we present high-phylogenetic-resolution spatial mapping platform (HiPR-Map), a state-of-the-art spectral imaging technology that enables precise enumeration and spatial localization of microbial cells at species-level within complex communities. Through these advantages, HiPR-Map provides unique insights for LBP discovery and development. Applying HiPR-Map to an LBP designed to complement immune checkpoint therapy, we profiled over 1.8 million microbial cells engrafted in the murine gut. Our analysis revealed distinctive microbial spatial organization, underscoring the power of imaging-based microbiome profiling to optimize LBP design and characterization. This work highlights the transformative potential of spatial microbiome analysis for next-generation LBP development.

microbiology↗

bioRxiv2024

Gpr37 modulates the severity of inflammation-induced GI dysmotility by regulating enteric reactive gliosis.

The enteric nervous system (ENS) is contained within two layers of the gut wall and is made up of neurons, immune cells, and enteric glia cells (EGCs) that regulate gastrointestinal (GI) function. EGCs in both inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS) change in response to inflammation, referred to as reactive gliosis. Whether EGCs restricted to a specific layer or region within the GI tract alone can influence intestinal immune response is unknown. Using bulk RNA-sequencing and in situ hybridization, we identify G-protein coupled receptor Gpr37, as a gene expressed only in EGCs of the myenteric plexus, one of the two layers of the ENS. We show that Gpr37 contributes to key components of LPS-induced reactive gliosis including activation of NF-kB and IFN-y signaling and response genes, lymphocyte recruitment, and inflammation-induced GI dysmotility. Targeting Gpr37 in EGCs presents a potential avenue for modifying inflammatory processes in the ENS.

neuroscience↗

bioRxiv2024

Enteric glutamatergic interneurons regulate intestinal motility

The enteric nervous system (ENS) controls digestion autonomously via a complex neural network within the gut wall. Enteric neurons expressing glutamate have been identified by transcriptomic studies as a distinct subpopulation, and glutamate can affect intestinal motility by modulating enteric neuron activity. However, the nature of glutamatergic neurons, their position within the ENS circuit, and their function in regulating gut motility are unknown. Here, we identify glutamatergic neurons as longitudinally projecting descending interneurons in the small intestine and colon, in addition to a novel class of circumferential neurons only in the colon. Both populations make synaptic contact with diverse neuronal subtypes, and signal with a variety of neurotransmitters and neuropeptides in addition to glutamate, including acetylcholine and enkephalin. Knocking out the glutamate transporter VGLUT2 from enkephalin neurons profoundly disrupts gastrointestinal transit, while ex vivo optogenetic stimulation of glutamatergic neurons initiates propulsive motility in the colon. This motility effect is reproduced when stimulating only the descending interneuron class, marked by Calb1 expression. Our results posit glutamatergic neurons as key interneurons that regulate intestinal motility.

neuroscience↗

bioRxiv2023

Thyroid hormone rewires cortical circuits to coordinate body-wide metabolism and exploratory drive

Animals adapt to varying environmental conditions by modifying the function of their internal organs, including the brain. To be adaptive, alterations in behavior must be coordinated with the functional state of organs throughout the body. Here we find that thyroid hormone-- a prominent regulator of metabolism in many peripheral organs-- activates cell-type specific transcriptional programs in anterior regions of cortex of adult mice via direct activation of thyroid hormone receptors. These programs are enriched for axon-guidance genes in glutamatergic projection neurons, synaptic regulators across both astrocytes and neurons, and pro-myelination factors in oligodendrocytes, suggesting widespread remodeling of cortical circuits. Indeed, whole-cell electrophysiology recordings revealed that thyroid hormone induces local transcriptional programs that rewire cortical neural circuits via pre-synaptic mechanisms, resulting in increased excitatory drive with a concomitant sensitization of recruited inhibition. We find that thyroid hormone bidirectionally regulates innate exploratory behaviors and that the transcriptionally mediated circuit changes in anterior cortex causally promote exploratory decision-making. Thus, thyroid hormone acts directly on adult cerebral cortex to coordinate exploratory behaviors with whole-body metabolic state.

neuroscience↗

bioRxiv2023

Loss of ASD-Related Molecule Caspr2 Affects Colonic Motility in Mice

Gastrointestinal (GI) symptoms are highly prevalent among individuals with autism spectrum disorder (ASD), but the molecular link between ASD and GI dysfunction remains poorly understood. The enteric nervous system (ENS) is critical for normal GI motility and has been shown to be altered in mouse models of ASD and other neurological disorders. Contactin-associated protein-like 2 (Cntnap2) is an ASD-related synaptic cell-adhesion molecule important for sensory processing. In this study, we examine the role of Cntnap2 in GI motility by characterizing Cntnap2s expression in the ENS and assessing GI function in Cntnap2 mutant mice. We find Cntnap2 expression predominately in enteric sensory neurons. We further assess in-vivo and ex-vivo GI motility in Cntnap2 mutants and show altered transit time and colonic motility patterns. The overall organization of the ENS appears undisturbed. Our results suggest that Cntnap2 plays a role in GI function and may provide a molecular link between ASD and GI dysfunction.

neuroscience↗

bioRxiv2020

Acute treatment with TrkB agonist LM22A-4 confers neuroprotection and preserves myelin integrity in a mouse model of pediatric traumatic brain injury

Young children have a high risk of sustaining a traumatic brain injury (TBI), which can have debilitating life-long consequences. Importantly, the young brain shows particular vulnerability to injury, likely attributed to ongoing maturation of the myelinating nervous system at the time of insult. Here, we examined the effect of acute treatment with partial tropomyosin receptor kinase B (TrkB) agonist, LM22A-4, on the pathological and neurobehavioral outcomes after pediatric TBI, with the hypothesis that targeting TrkB would minimize tissue damage and support functional recovery. We focused on myelinated tracts-- the corpus callosum and external capsules--based on recent evidence that TrkB activation potentiates oligodendrocyte remyelination. Male mice at postnatal day 21 received an experimental TBI or sham surgery. Acutely post-injury, extensive cell death, a robust glial response and disruption of compact myelin were evident in the injured brain. TBI or sham mice then received intranasal saline vehicle or LM22A-4 for 14 days. Behavior testing was performed from 4 weeks post-injury, and brains were collected at 5 weeks for histology. TBI mice showed hyperactivity, reduced anxiety-like behavior, and social memory impairments. LM22A-4 ameliorated the abnormal anxiolytic phenotype but had no effect on social memory deficits. Use of spectral confocal reflectance microscopy detected persistent myelin fragmentation in the external capsule of TBI mice at 5 weeks post-injury, which was accompanied by regionally distinct deficits in oligodendrocyte progenitor cells and postmitotic oligodendrocytes, as well as chronic reactive gliosis and atrophy of the corpus callosum and injured external capsule. LM22A-4 treatment ameliorated myelin deficits in the perilesional external capsule, as well as tissue volume loss and the extent of reactive gliosis. However, there was no effect of this TrkB agonist on oligodendroglial populations detected at 5 weeks post-injury. Collectively, our results demonstrate that targeting TrkB immediately after TBI during early life confers neuroprotection and preserves myelin integrity, and this was associated with some improved neurobehavioral outcomes as the pediatric injured brain matures.

neuroscience↗

bioRxiv2020

Cortical ChAT+ neurons co-transmit acetylcholine and GABA in a target- and brain-region specific manner

The cerebral cortex contains neurons that express choline acetyltransferase (ChAT) and are a potential local source of acetylcholine. However, the neurotransmitters released by cortical ChAT+ neurons and their synaptic connectivity are unknown. We show that the nearly all cortical ChAT+ neurons are specialized VIP+ interneurons that release GABA strongly onto other inhibitory interneurons and acetylcholine sparsely onto layer 1 interneurons and other VIP+/ChAT+ interneurons. This differential transmission of ACh and GABA based on the postsynaptic target neuron is reflected in VIP+/ChAT+ interneuron pre-synaptic terminals, as quantitative molecular analysis shows that only a subset of these are specialized to release acetylcholine. In addition, we identify a separate, sparse population of non-VIP ChAT+ neurons in the medial prefrontal cortex with a distinct developmental origin that robustly release acetylcholine in layer 1. These results demonstrate both cortex-region heterogeneity in cortical ChAT+ interneurons and target-specific co-release of acetylcholine and GABA.

neuroscience↗

bioRxiv2020

Use of unmanned aerial vehicles (UAVs) for mark-resight nesting population estimation of adult female green sea turtles at Raine Island

Nester abundance is a key measure of the performance of the worlds largest green turtle rookery at Raine Island, Australia. Abundance surveys have been undertaken in waters adjacent to Raine Island reef using mark-resight counts by surface observer (SO), underwater video (UWV) and unmanned aerial vehicle (UAV) (since 1984, 2013 and 2016 respectively). UAV and UWV may provide more cost-effective and less biased alternatives, but estimates must be comparable with the historical estimates. Here we compare the three methods. The relative likelihood of resighting a marked turtle was significantly higher by SO than the other methods, which led to lower mark-resight population estimates than by UAV or UWV. Most (96%) variation in resighting probabilities was associated with survey period, with comparatively little variation between consecutive days of sampling or time of day. This resulted in preliminary correction factors of 1.53 and 1.73 from SO-UWV and SO-UAV, respectively. However, the SO and UWV estimates were the most similar when turtle densities were the lowest, suggesting that correction factors need to take into account turtle density and that more data are required. We hypothesise that the UAV and UWV methods improved detection rates of marked turtles because they allowed subsequent review and frame-by-frame analysis, thus reducing observer search error. UAVs were the most efficient in terms of survey time, personnel commitment and weather tolerance compared to the SO and UWV methods. This study indicates that using UAVs for in-water mark-resight turtle abundance estimation is an efficient and accurate method that can provide an accurate adjustment for historical abundance estimates. Underwater video may continue to be useful as a backup alternative to UAV surveys.

ecology↗

bioRxiv2019

Oncogenic and Circadian Effects of Small Molecules Directly and Indirectly Targeting the Core Circadian Clock

Circadian rhythms are essential for controlling the cell cycle, cellular proliferation, and apoptosis, and hence, are tightly linked to cell fate. Disruption of circadian rhythms has been shown to trigger various pathological developments, including cancer. Several recent studies have used a variety of small molecules to affect circadian oscillations, however, their concomitant cellular effects were not assessed. Here, we use five molecules, grouped into direct versus indirect effectors of the circadian clock, to modulate periods in a human osteosarcoma cell line (U2OS), and determined their influences on cellular behaviors, including motility and colony formation. Luciferase reporters, whose expression were driven via Bmal1- and Per2-promoters (positive and negative protein components of the core clock), were used to facilitate the visualization and quantitative analysis of circadian oscillations. We show that all molecules significantly increase or decrease the circadian periods of Bmal1 and Per2 in a dose-dependent manner, but period length does not correlate with the extent of cell migration or proliferation. We observed that only molecules that affected circadian oscillations to a greater extent showed significant influence on cell functions (e.g. motility and colony formation). Because it is important to consider the likelihood of biological effects resulting from non-circadian targets, we also provide a thorough discussion of potential modes of action. Future studies should employ additional compounds that directly target circadian proteins and/or have different circadian effects, and evaluation in other cancer models to determine whether results obtained here remain consistent.\n\nFor Table of Contents Only\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=100 SRC=\"FIGDIR/small/645861v1_fig1u.gif\" ALT=\"Figure 1U\">\nView larger version (25K):\norg.highwire.dtl.DTLVardef@ec8881org.highwire.dtl.DTLVardef@f601f1org.highwire.dtl.DTLVardef@f98f5aorg.highwire.dtl.DTLVardef@3278e1_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2019

Killer whale genomes reveal a complex history of recurrent admixture and vicariance

Reconstruction of the demographic and evolutionary history of populations assuming a consensus tree-like relationship can mask more complex scenarios, which are prevalent in nature. An emerging genomic toolset, which has been most comprehensively harnessed in the reconstruction of human evolutionary history, enables molecular ecologists to elucidate complex population histories. Killer whales have limited extrinsic barriers to dispersal and have radiated globally, and are therefore a good candidate model for the application of such tools. Here, we analyse a global dataset of killer whale genomes in a rare attempt to elucidate global population structure in a non-human species. We identify a pattern of genetic homogenisation at lower latitudes and the greatest differentiation at high latitudes, even between currently sympatric lineages. The processes underlying the major axis of structure include high drift at the edge of species range, likely associated with founder effects and allelic surfing during post-glacial range expansion. Divergence between Antarctic and non-Antarctic lineages is further driven by ancestry segments with up to four-fold older coalescence time than the genome-wide average; relicts of a previous vicariance during an earlier glacial cycle. Our study further underpins that episodic gene flow is ubiquitous in natural populations, and can occur across great distances and after substantial periods of isolation between populations. Thus, understanding the evolutionary history of a species requires comprehensive geographic sampling and genome-wide data to sample the variation in ancestry within individuals.

evolutionary biology↗

bioRxiv2018

Target-specific co-transmission of acetylcholine and GABA from a subset of cortical VIP+ interneurons

The modulation of cortex by acetylcholine (ACh) is typically thought to originate from long-range projections arising in the basal forebrain. However, a subset of VIP interneurons express ChAT, the synthetic enzyme for ACh, and are a potential local source of cortical ACh. Which neurotransmitters these VIP/ChAT interneurons (VCINs) release is unclear, and which post-synaptic cell types these transmitters target is not known. Using quantitative molecular analysis of VCIN pre-synaptic terminals, we show expression of the molecular machinery to release both ACh and GABA, with ACh release restricted to a subset of boutons. A systematic survey of potential post-synaptic cell types shows that VCINs release GABA primarily onto other inhibitory interneuron subtypes, while ACh neurotransmission is notably sparse, with most ACh release onto layer 1 interneurons and other VCINs. Therefore, VCINs are an alternative source of cortical ACh signaling that supplement GABA-mediated disinhibition with highly targeted excitation through ACh.

neuroscience↗

bioRxiv2018

Distinct Cortical-Thalamic-Striatal Circuits Through the Parafascicular Nucleus

The thalamic parafascicular nucleus (PF), an excitatory input to the basal ganglia, is targeted with deep-brain-stimulation to alleviate a range of neuropsychiatric symptoms. Furthermore, PF lesions disrupt the execution of correct motor actions in uncertain environments. Nevertheless, the circuitry of the PF and its contribution to action selection are poorly understood. We find that, in mice, PF forms the densest subcortical projection to the striatum. This projection arises from transcriptionally- and physiologically-distinct classes of PF neurons that are also reciprocally connected with functionally-distinct cortical regions, differentially innervate striatum neurons, and are not synaptically connected in PF. Thus, mouse PF contains heterogeneous neurons that are organized into parallel and independent associative, limbic, and motor circuits. Furthermore, these subcircuits share motifs of cortical-PF-cortical and cortical-PF-striatum organization that allow each PF subregion, via its precise connectivity with cortex, to coordinate diverse inputs to striatum.

neuroscience↗