Biology subjects

Hamilton, S.

Publications and source records attributed to Hamilton, S..

14 recordsLinked to original sources

bioRxiv2026

Epigenetic and brain age across development: Performance and associations in the MIND consortium

Understanding how biological age measures perform across development lays the groundwork for investigations into lifespan trajectories of healthy aging. We provide the most comprehensive assessment of epigenetic and brain age models across development (birth to 24 years; [≤]20,917 observations across 15 cohorts), evaluating how these models associate with chronological age and with each other, and how these associations change across development. Chronological age-prediction accuracy of epigenetic and brain age models was modest and varied substantially. Accuracy improved with age and stabilized by middle childhood. Few brain and fewer epigenetic clocks performed stably and well across all developmental stages. Performance was better when age range and tissue corresponded between training and testing data. Associations between epigenetic-brain age residuals were small, and changed little across development, tissues or clock generation. Given this developmentally dynamic system of epigenetic-brain age performances and associations, we give key recommendations to improve developmental research in this field.

neuroscience↗

bioRxiv2026

Ketamine attenuates habenula activity in response to aversive outcomes during Pavlovian learning

Ketamine is an NMDA receptor antagonist with rapid-antidepressant properties when administered at a sub-anesthetic dose. Preclinical models indicate that a direct injection of ketamine into lateral habenula (Hb), a small midbrain structure with an evolutionarily preserved role in aversive learning across mammals, can rapidly relieve depression-like behavior. However, there is limited evidence to explain how ketamine acts on the function of the human habenula. In a translational computational neuroscience study, 70 healthy adult volunteers were randomised in a 1:1 ratio to receive ketamine or placebo (NaCl 0.9%). We used an aversive Pavlovian conditioning paradigm combined with 7-Tesla functional neuroimaging to show that ketamine attenuates habenula response during aversive stimuli expectations and outcomes 24 hours post-infusion. We further present preliminary evidence suggesting that when aversive learning occurs after ketamine infusion, reduced habenula activity during the learning process may lead to downstream effects that diminish the aversive impact of negative affective memories. These findings provide translational support for preclinical models of ketamines mechanisms in humans.

neuroscience↗

bioRxiv2025

Friend Request Accepted: Fundamental Features of Social Environments Determine Rate of Social Affiliation

Humans start new friendships and social connections throughout their lives and such relationships foster mental and physical well-being. While friendship initiation may depend on alignment of subtle and complex personal variables, here we investigated whether it also depends on basic features of social environments. This would be analogous to other fundamental behaviours like foraging which depend on basic features of the environment such as the density of opportunities and the likelihood of success. In a pre-registered online study (n=783), we found people were more likely to send friend requests as the density of friendship opportunities decreased and frequency of success increased. Further, we found task-related measures, like overall friend requests, were correlated with personality-related factors like social thriving and anhedonia. Next, in an ultra-high-field fMRI study (n=24), we found that both fundamental features of social environments - opportunity density and frequency of success - affected neural activity across a network of regions linked to foraging including dorsal raphe nucleus, substantia nigra, and anterior insula. Finally, in resting-state fMRI data (n=400), we showed that model predicted estimates of anhedonia were related to functional connectivity between components of the same network. Thus, humans consider the background statistics of an environment while making social decisions and these decisions are linked to activity in ancient subcortical circuits mediating the influence of environmental statistics on other aspects of behaviour. Moreover, individual differences in how environmental features influence social behaviour are associated with variation in personality and psychiatric traits, offering new insights into inter-individual variability in social functioning.

neuroscience↗

bioRxiv2024

Most axonal mitochondria in cortical pyramidal neuronslack mitochondrial DNA and consume ATP

In neurons of the mammalian central nervous system (CNS), axonal mitochondria are thought to be indispensable for supplying ATP during energy-consuming processes such as neurotransmitter release. We have previously shown that glutamatergic excitatory cortical pyramidal neurons (CPNs) are characterized by a striking compartmentalization of mitochondrial structure. Axonal mitochondria are maintained at a small uniform size ([~]1 microns length) by high levels of MFF-dependent fission, whereas dendritic mitochondria form a highly fused network of mitochondria throughout the entire dendritic arbor(1, 2). Here, we tested whether these striking structural differences reflect functional and molecular compartmentalization. Using four independent techniques, we reveal that in CPNs as well as in two subtypes of GABAergic inhibitory cortical interneurons and neuromodulatory dopaminergic neurons of the substantia nigra, the majority of axonal, but not dendritic, mitochondria lack mitochondrial DNA (mtDNA) in vivo. We also show that axonal mitochondria are depleted in both mtDNA-encoded mRNAs and proteins compared to dendritic mitochondria. Timelapse imaging establishes that most mitochondria entering nascent dendritic and axonal processes from the soma are small and lack mtDNA. Using dynamic, optical imaging of genetically encoded sensors for ATP and pH targeted to the mitochondrial matrix, we demonstrate that in axons of CPNs, but not in their dendrites, mitochondrial F1F0-ATP synthase (Complex V) functions in a reverse way, hydrolyzing ATP and extruding H+ out of the matrix to maintain mitochondrial membrane potential. Our results indicate that in neurons of the mammalian CNS, the majority of axonal mitochondria lack mtDNA and likely do not play a major role in ATP generation, despite playing other functions such as regulation of neurotransmission via presynaptic Ca2+ buffering(1, 3-5).

neuroscience↗

bioRxiv2023

An ancient subcortical circuit decides when to orient to threat in humans

Many psychiatric symptoms have been linked to threat-related perception and learning processes. In addition, however, there may also be mechanisms for balancing effectively between threat- and reward-related behaviors and these may also vary between individuals. We investigated neural activity associated with spontaneous switching between foraging for rewards and vigilance for threats with 7T fMRI. In a virtual naturalistic environment, participants freely switched between the two modes of behavior. Switching was driven by estimates of likelihood of threat and reward. Both tracking of threat and switching to vigilance were associated with specific but distributed patterns of activity spanning habenula, dorsal raphe nucleus (DRN), anterior cingulate cortex, and anterior insula cortex. Distinct distributed patterns heralded returns to reward-oriented behavior. Individual variation in DRN activity reflected individual variation in vigilance. All activity patterns were replicated in an initially held-out portion of data.

neuroscience↗

bioRxiv2023

Acquired Cross-resistance in Small Cell Lung Cancer due to Extrachromosomal DNA Amplification of MYC paralogs

Small cell lung cancer (SCLC) presents as a highly chemosensitive malignancy but acquires cross-resistance after relapse. This transformation is nearly inevitable in patients but has been difficult to capture in laboratory models. Here we present a pre-clinical system that recapitulates acquired cross-resistance in SCLC, developed from 51 patient-derived xenografts (PDXs). Each model was tested for in vivo sensitivity to three clinical regimens: cisplatin plus etoposide, olaparib plus temozolomide, and topotecan. These functional profiles captured hallmark clinical features, such as the emergence of treatment-refractory disease after early relapse. Serially derived PDX models from the same patient revealed that cross-resistance was acquired through a MYC amplification on extrachromosomal DNA (ecDNA). Genomic and transcriptional profiles of the full PDX panel revealed that this was not unique to one patient, as MYC paralog amplifications on ecDNAs were recurrent among cross-resistant models derived from patients after relapse. We conclude that ecDNAs with MYC paralogs are recurrent drivers of cross-resistance in SCLC. SIGNIFICANCESCLC is initially chemosensitive, but acquired cross-resistance renders this disease refractory to further treatment and ultimately fatal. The genomic drivers of this transformation are unknown. We use a population of PDX models to discover that amplifications of MYC paralogs on ecDNA are recurrent drivers of acquired cross-resistance in SCLC.

cancer biology↗

bioRxiv2023

RNA-induced allosteric coupling drives viral capsid assembly in bacteriophage MS2

Understanding the mechanisms by which single-stranded RNA viruses regulate capsid assembly around their RNA genomes has become increasingly important for the development of both antiviral treatments and drug delivery systems. Here, we investigate the effects of RNA-induced allostery in a single-stranded RNA virus -- Levivirus bacteriophage MS2 -- using the computational methods of the Dynamic Flexibility Index (DFI) and the Dynamic Coupling Index (DCI). We show that asymmetric binding of RNA to a symmetric MS2 coat protein dimer increases the flexibility of the distant FG-loop and induces a conformational change to an asymmetric dimer that is essential for proper capsid formation. We also show that a point mutation W82R in the FG-loop creates an assembly-deficient dimer in which RNA-binding has no significant effect on FG-loop flexibility. Lastly, we show that the highly flexible disordered FG-loop of the RNA bound asymmetric dimer not only becomes the controller of the rigid FG-loop but enhances its dynamic coupling with all the distal positions in the dimer. This strong dynamic coupling allows highly regulated communication and unidirectional signal transduction that drives the formation of the experimentally observed capsid intermediates. Author summaryThe final stage of an RNA virus life cycle is the assembly of a protein shell encapsulating the viral genome prior to release from the host organism. Despite rapid advancements in both experimental and theoretical biology since the mid-20th century, little is still known about the underlying mechanisms of viral capsid assembly. However, understanding the biophysical principles of viral capsid assembly would bring us one step closer to developing new biotechnologies such as antivirals that inhibit this critical stage of the life cycle or artificial capsids for targeted drug/vaccine delivery. Although we limit the present study to one simple RNA virus that infects bacteria, we propose that the physical implications can extend to other RNA viruses including the human coronavirus SARS-CoV-2. We also propose that the allosteric regulation by specific protein-RNA interactions might be a general mechanism exploited by many other ribonucleoprotein complexes, such as CRISPR-Cas9, spliceosome or ribosome.

biophysics↗

bioRxiv2023

Activity-dependent subcellular compartmentalization of dendritic mitochondria structure in CA1 pyramidal neurons

Neuronal mitochondria play important roles beyond ATP generation, including Ca2+ uptake, and therefore have instructive roles in synaptic function and neuronal response properties. Mitochondrial morphology differs significantly in the axon and dendrites of a given neuronal subtype, but in CA1 pyramidal neurons (PNs) of the hippocampus, mitochondria within the dendritic arbor also display a remarkable degree of subcellular, layer- specific compartmentalization. In the dendrites of these neurons, mitochondria morphology ranges from highly fused and elongated in the apical tuft, to more fragmented in the apical oblique and basal dendritic compartments, and thus occupy a smaller fraction of dendritic volume than in the apical tuft. However, the molecular mechanisms underlying this striking degree of subcellular compartmentalization of mitochondria morphology are unknown, precluding the assessment of its impact on neuronal function. Here, we demonstrate that this compartment-specific morphology of dendritic mitochondria requires activity-dependent, Camkk2- dependent activation of AMPK and its ability to phosphorylate two direct effectors: the pro-fission Drp1 receptor Mff and the recently identified anti-fusion, Opa1-inhibiting protein, Mtfr1l. Our study uncovers a new activity- dependent molecular mechanism underlying the extreme subcellular compartmentalization of mitochondrial morphology in dendrites of neurons in vivo through spatially precise regulation of mitochondria fission/fusion balance.

cell biology↗

bioRxiv2022

Ketones facilitate transcriptional resolution of secondary DNA structures in premature aging

There is currently no established intervention for Cockayne syndrome, a disease characterized by progressive early onset neurodegeneration with features of premature aging. Here, we tested if acetyl-CoA precursors, citrate and beta-hydroxybutyrate, could reduce features of Cockayne syndrome in three model systems. We identified the gene Helicase 89B as a homologue of CSB in drosophila and found that the ketone beta-hydroxybutyrate rescued features of premature aging in Hel89B deficient flies. In mammals, loss of the citrate carrier Indy exacerbated the phenotype of Csbm/m mice which was rescued by a ketogenic diet. The rescue effect appeared to be mediated through ketone stimulated histone acetylation and facilitation of transcriptional readthrough of secondary DNA structures. These findings link a ketogenic diet with transcriptional resolution of secondary structures and DNA repair.

physiology↗

bioRxiv2021

TREM2+ and interstitial macrophages orchestrate airway inflammation in SARS-CoV-2 infection in rhesus macaques

The COVID-19 pandemic remains a global health crisis, yet, the immunopathological mechanisms driving the development of severe disease remain poorly defined. Here, we utilize a rhesus macaque (RM) model of SARS-CoV-2 infection to delineate perturbations in the innate immune system during acute infection using an integrated systems analysis. We found that SARS-CoV-2 initiated a rapid infiltration (two days post infection) of plasmacytoid dendritic cells into the lower airway, commensurate with IFNA production, natural killer cell activation, and induction of interferon-stimulated genes. At this early interval, we also observed a significant increase of blood CD14-CD16+ monocytes. To dissect the contribution of lung myeloid subsets to airway inflammation, we generated a novel compendium of RM-specific lung macrophage gene expression using a combination of sc-RNA-Seq data and bulk RNA-Seq of purified populations under steady state conditions. Using these tools, we generated a longitudinal sc-RNA-seq dataset of airway cells in SARS-CoV-2-infected RMs. We identified that SARS-CoV-2 infection elicited a rapid recruitment of two subsets of macrophages into the airway: a C206+MRC1-population resembling murine interstitial macrophages, and a TREM2+ population consistent with CCR2+ infiltrating monocytes, into the alveolar space. These subsets were the predominant source of inflammatory cytokines, accounting for ~75% of IL6 and TNF production, and >90% of IL10 production, whereas the contribution of CD206+MRC+ alveolar macrophages was significantly lower. Treatment of SARS-CoV-2 infected RMs with baricitinib (Olumiant(R)), a novel JAK1/2 inhibitor that recently received Emergency Use Authorization for the treatment of hospitalized COVID-19 patients, was remarkably effective in eliminating the influx of infiltrating, non-alveolar macrophages in the alveolar space, with a concomitant reduction of inflammatory cytokines. This study has delineated the major subsets of lung macrophages driving inflammatory and anti-inflammatory cytokine production within the alveolar space during SARS-CoV-2 infection. One sentence summaryMulti-omic analyses of hyperacute SARS-CoV-2 infection in rhesus macaques identified two population of infiltrating macrophages, as the primary orchestrators of inflammation in the lower airway that can be successfully treated with baricitinib

microbiology↗

bioRxiv2021

The meta-gut: Hippo inputs lead to community coalescence of animal and environmental microbiomes.

All animals carry specialized microbiomes, and their gut microbiotas in particular are continuously released into the environment through excretion of waste. Here we propose the meta-gut as a novel conceptual framework that addresses the ability of the gut microbiome released from an animal to function outside the host and potentially alter ecosystem processes mediated by microbes. An example considered here is the hippopotamus (hippo) and the pools they inhabit. Hippo pool biogeochemistry and fecal and pool water microbial communities were examined through field sampling and an experiment. Sequencing using 16S RNA methods revealed that the active microbial communities in hippo pools that received high inputs of hippo feces are more similar to the hippo gut microbiome than other nearby aquatic environments. The overlap between the microbiomes of the hippo gut and the waters into which they excrete therefore constitutes a meta-gut system with potentially strong influence on the biogeochemistry of pools and downstream waters. We propose that the meta-gut may be present where other species congregate in high densities, particularly in aquatic environments. SignificanceAnimals can have considerable impacts on biogeochemical cycles and ecosystem attributes through the consumption of resources and physical modifications of the environment. Likewise, microbial communities are well known to regulate biogeochemical cycles. This study links those two observations by showing that the gut microbiome in waste excreted by hippos can persist ex-situ in the environment and potentially alter biogeochemical cycles. This "meta-gut" system may be present in other ecosystems where animals congregate, and may have been more widespread in the past before many large animal populations were reduced in range and abundance.

ecology↗

bioRxiv2021

Kawasaki Disease patient stratification and pathway analysis based on host transcriptomic and proteomic profiles

The aetiology of Kawasaki Disease (KD), an acute inflammatory disorder of childhood, remains unknown despite various triggers of KD having been proposed. Host omic profiles offer insights into the host response to infection and inflammation, with the interrogation of multiple omic levels in parallel providing a more comprehensive picture. We used differential abundance analysis, pathway analysis, clustering and classification techniques to explore whether the host response in KD is more similar to the response to bacterial or viral infection at the transcriptomic and proteomic levels through comparison of omic profiles from children with KD to those with bacterial and viral infections. Pathways activated in patients with KD included those involved in anti-viral and anti-bacterial responses. Unsupervised clustering showed that the majority of KD patients clustered with bacterial patients on both omic levels, whilst application of diagnostic signatures specific for bacterial and viral infections revealed that many transcriptomic KD samples had low probabilities of having bacterial or viral infections, suggesting that KD may be triggered by a different process not typical of either common bacterial or viral infections. Clustering based on the transcriptomic and proteomic responses during KD revealed three clusters of KD patients on both omic levels, suggesting heterogeneity within the inflammatory response during KD. The observed heterogeneity may reflect differences in the host response to a common trigger, or variation dependent on different triggers of the condition.

bioinformatics↗

bioRxiv2020

Macrophages drive the inflammatory phase in experimental osteoarthritis

Macrophages fulfill critical functions in maintaining tissue homeostasis in steady-state, as well as in inflammation and immune response. Inflammation is not considered a major driver of osteoarthritis (OA), but macrophages have been implicated in its pathogenesis. Here, we use two mouse models of experiment OA - collagenase-induced osteoarthritis (CIOA) and destabilization of the medial meniscus (DMM) - to quantify the immune cell infiltration into the knee joint during the early stages of disease. We find that the peak of inflammation occurs at day 3 in CIOA and is characterized by a transitory increase in neutrophils and monocytes and a longer-lived expansion of synovial macrophages. Macrophage sub-populations are disproportionally expanded with CX3CR1+ cells accounting for a larger proportion of the macrophage compartment. Transcriptional profiling demonstrates that synovial macrophages up-regulate inflammatory genes coinciding with peak inflammation and down-regulate genes associated with homeostasis and tissue-residence. Female mice exhibit a similar expansion of macrophages post-CIOA indicating that the inflammatory phase is not sex-specific. Finally, we find day 7 post-DMM is also characterized by increases in neutrophil, monocyte, and macrophage sub-population numbers. These results support a role for macrophages in early stages of OA through driving the inflammatory phase. Further investigation may elucidate potential targets for the prevention or attenuation of OA-associated cartilage damage.

immunology↗

bioRxiv2018

Robust and sensitive GFP-based cGMP sensor for real time imaging in intact Caenorhabditis elegans

cGMP is a ubiquitous second messenger that plays a role in sensory signaling and plasticity through its regulation of ion channels and kinases. Previous studies that primarily used genetic and biochemical tools suggest that cGMP is spatiotemporally regulated in multiple sensory modalities, including light, heat, gases, salt and odor. FRET- and GFP-based cGMP sensors were developed to visualize cGMP in primary cell culture and Caenorhabditis elegans to corroborate these findings. While a FRET-based sensor has been used in an intact animal to visualize cGMP, the requirement of a multiple emission system limits its ability to be used on its own as well as with other sensors and fluorescent markers. Here, we demonstrate that WincG2, a codon-optimized version of the cpEGFP-based cGMP sensor FlincG3, can be used in C. elegans to visualize rapidly changing cGMP levels in living, behaving animals using a single fluorophore. We coexpressed the sensor with the blue light-activated guanylyl cyclases BeCyclOp and bPGC in body wall muscles and found that the rate of WincG2 fluorescence correlated with the rate of cGMP production by each cyclase. Furthermore, we show that WincG2 responds linearly upon NaCl concentration changes and SDS presentation in the cell bodies of the gustatory neuron ASER and the nociceptive phasmid neuron PHB, respectively. Intriguingly, WincG2 fluorescence in the ASER cell body decreased in response to a NaCl concentration downstep and either stopped decreasing or increased in response to a NaCl concentration upstep, which is opposite in sign to previously published calcium recordings. These results illustrate that WincG2 can be used to report rapidly changing cGMP levels in an intact animal and that the reporter can potentially reveal unexpected spatiotemporal landscapes of cGMP in response to stimuli.\n\nAuthor SummarycGMP is a second messenger that plays an important role in sensory signaling and neural plasticity. Previous genetic and biochemical studies indirectly suggest that cGMP is spatiotemporally regulated in neurons to modulate neural activity. While a FRET-based sensor for cGMP has been used in intact Caenorhabditis elegans to examine its spatiotemporal regulation in neurobiological processes, its use has been limited due to the complicated setup required to image this type of sensor. Here, we describe a GFP-based cGMP sensor that has been codon optimized for use in C. elegans and demonstrate that it responds robustly and reliably to endogenously changing cGMP levels. We show that the sensor responds to cGMP production by coexpressing it with blue light-activated guanylyl cyclases, and we show that it responds to NaCl and sodium dodecyl sulfate when expressed in a gustatory and nociceptive neuron, respectively. We think that this sensor can be used to investigate the spatiotemporal regulation of cGMP in neurons and its relationship to neural activity.

neuroscience↗