Biology subjects

Palmer, D.

Publications and source records attributed to Palmer, D..

At least 19 recordsLinked to original sources

bioRxiv2026

Multi-domain analysis of the fecal microbiome of dairy heifers, beef heifers, bred beef heifers, and adult beef cows in the central United States using paired 16S rRNA and 18S rRNA metabarcoding

The growth and performance of cattle is dependent on efficient feed conversion, facilitated by the gut microbiome, including both prokaryotic and eukaryotic organisms. Extrinsic factors such as management practices and intrinsic factors like age and genetics can shape these communities. To characterize the relative effects of such factors on the prokaryotic and eukaryotic microbiomes, fresh fecal samples from dairy heifers (n = 8), beef heifers (n = 8), bred beef heifers (n = 8), and adult beef cows (n = 8) were subjected to paired 16S rRNA (V4) and a novel 18S rRNA (V4-V5) metabarcoding assay, and 18S rRNA amplicons were annotated using two databases in parallel. Taxonomic resolution of 18S rRNA amplicons was excellent, with SILVA and EUKARYOME databases each providing better resolution of different groups of organisms. While no differences in eukaryotic richness or alpha diversity were detected, beta diversity differed in all pairwise comparisons except between beef heifers and bred beef heifers. Prokaryotic richness was lower in adult beef cows than the other groups, and beta diversity differed in all pairwise comparisons. Adult beef cows were the most distinct, characterized by replacement of fungal organisms with protozoa and loss of thermophilic bacteria in the eukaryotic and prokaryotic compartments, respectively. Among numerous differentially abundant features, dairy heifers harbored greater abundance of Cooperia oncophora while beef heifers contained greater abundance of Buxtonella sulcata and Mucor. Correlation network analysis revealed multiple significant positive and negative associations between bacterial, fungal, and protozoal features during maturation of the fecal microbiome. Collectively, these data highlight the richness and diversity of both the prokaryotic and eukaryotic compartments of the bovine fecal microbiome, and the influence of management practices and age on both communities. From a technical standpoint, these data demonstrate the ability to resolve fungal, protozoal, and metazoan organisms, including potential parasites and pathogens, with a single metabarcoding assay. They also highlight the nuanced differences between databases and the value of parallel analyses using more than one database.

systems biology↗

bioRxiv2026

Rank-based integration identifies convergent disease mechanisms across omics

The rapid growth of omics studies offers new opportunities to uncover disease mechanisms, yet findings from individual studies or single omics may be influenced by cohort-, platform- and layer-specific variation. Integrating evidence across studies and omics layers can reveal robust biological signals that are reproducible across molecular layers, but differences in assay platforms, sample sizes and feature coverage complicate direct combination of summary statistics. Here we present the Omics Rank-Based Integration Tool (ORBIT), a direction-aware framework for prioritizing concordant signals across omics layers using only within-dataset feature ranks and effect directions. ORBIT tests directional rank consistency across omics layers against a closed-form variance-gamma null distribution while accounting for inter-dataset correlation and incomplete feature overlap. Simulations show that ORBIT maintains well-calibrated false-positive rates under inter-omics correlation, increasing numbers of omics layers and missingness, while detecting concordant signals with increasing power as the number of layers grows. We applied ORBIT to tubulointerstitial transcriptomic data from patients with chronic kidney disease in the C-PROBE cohort and proteomic data from the Kidney Precision Medicine Project, identifying a concordant injury programme marked by inflammatory and fibrotic remodeling together with impaired energy metabolism. We also used ORBIT to integrate ten transcriptomic, four proteomic and one translatomic datasets in dilated cardiomyopathy heart tissue, identifying extracellular matrix remodeling and mitochondrial energy failure as the dominant concordant biological programmes. In both diseases, ORBIT prioritized concordant genes and identified pathways that were not significant in any single omics layer alone. These results show that directional rank integration can be used for integrating heterogeneous omics summary data and prioritizing robust molecular mechanisms.

bioinformatics↗

bioRxiv2026

Distinct transcriptional states of draining lymph node T cells following influenza vaccination in individuals with underrepresented ancestries

The transcriptional and cell repertoire changes of lymph node (LN) T cells following influenza vaccination have been under-investigated across different ethnicities. Draining (dLN) and non-draining (ndLN) axillary LN cells from 17 participants with genotypically varied African or Asian ancestry (ISRCTN13657999) were collected by fine needle aspiration (FNA) before, 5 days and 42 days after adjuvanted influenza vaccination and analysed by single-cell RNA-sequencing (scRNA-seq). The early dLN transcriptional profile and cellular dynamics were distinct from the ndLN; BACH2 expressing T cells were highly induced, exhibiting stem-like and unique quiescence signatures. Proliferating T follicular helper cells (Tfh) were enriched in dLN and Th1-like Tfh predominated with highly induced transcriptional changes. The BACH2+ T cell state and Th1-like Tfh cells, transcriptionally distinct from germinal centre (GC) T cells, were co-localised with LAMP3+ dendritic cells in the T cell zone of publicly available LN datasets, a region that was also distinct from GC Tfh niches. Together, these findings indicate that the induction of a robust, proliferative, and transcriptionally diverse Tfh response, alongside a discrete subset of BACH2+ T cells, represents a marked feature of the early T cell zone immune response to adjuvanted influenza vaccine in the dLN.

immunology↗

bioRxiv2026

A Patient-Derived Ex Vivo Tissue Model of Cholangiocarcinoma Using Precision-Cut Tissue Slices

Background & Aims: Cholangiocarcinoma (CCA) is an aggressive malignancy with poor five-year survival. Improving outcomes requires preclinical models that faithfully recapitulate the native tumour microenvironment. Precision-Cut Tissue Slices (PCTS) retain in-vivo architecture and represent a promising candidate. We aimed to establish a patient-derived PCTS model of CCA, characterise its response to ex-vivo culture, and assess its use as a platform for therapeutic testing. Methods: PCTS were generated from 25 patients undergoing curative-intent resection for presumed CCA (2022-2024) and cultured for up to 15 days. Viability and histological architecture were assessed serially. Quantitative proteomics (SWATH-DIA) was performed at Days 0, 3, 7 and 15. A subset were treated with staurosporine or clinically relevant chemotherapy (5'-deoxy-5-fluorouridine, gemcitabine {+/-} cisplatin). Results: PCTS viability was maintained to Day 15, with no significant reduction from baseline. PCTS retain tumour architecture, cytokeratin-19-positivity and resident CD3+/CD68+ immune cells during culture. Proteomic profiling quantified 4,578 proteins and identified a staged response, with differentially abundant proteins increasing from 8 (Day 3) to 127 (Day 7) and 180 (Day 15), stabilising thereafter. This comprised of an early loss of inflammatory and stromal proteins, sustained cellular stress responses and metabolic reprogramming. CCA subtype-specific proteomic signatures were preserved throughout culture. Staurosporine produced dose-dependent cytotoxicity whilst chemotherapy responses were variable. Conclusions: Patient-derived CCA PCTS maintain viability, tumour architecture and subtype identity for 15 days while undergoing a defined proteomic response to culture, and retain pharmacological responsiveness,

cancer biology↗

bioRxiv2026

Sequential intra-articular HCAd-NFκB-IL-1Ra delivery improves therapeutic efficacy in post-traumatic osteoarthritis

Osteoarthritis is the most common joint disease for which disease-modifying therapies remain unavailable. Intra-articular gene delivery of interleukin-1 receptor antagonist (IL-1Ra) using high-capacity adenovirus (HCAd) has shown therapeutic promise; however, the duration of therapeutic benefit and the feasibility of repeat dosing under anti-adenoviral immunity remain unresolved. Using the murine anterior cruciate ligament transection model of osteoarthritis, we show that a single intraarticular injection of HCAd5-NF{kappa}B-IL-1Ra provides structural preservation and functional improvement in early-stage osteoarthritis but fails to sustain cartilage protection as disease progresses. However, HCAd5 transduction following repeated treatment is limited due to pre-existing immunity against this serotype. Notably, exchanging serotypes for repeated treatments effectively restores vector transduction and transgene expression in both healthy and osteoarthritic joints. Leveraging this strategy, we demonstrate that sequential intra-articular HCAd-NF{kappa}B-IL-1Ra administration does not further improve pain or motor function compared to the initial treatment, but preserves cartilage as assessed by histopathology and phase-contrast CT, irrespective of serotype. These findings establish HCAd serotype switching as a feasible approach to overcome immune barriers to repeat intra-articular gene therapy. Importantly, sequential HCAd-NF{kappa}B-IL-1Ra administration enhances therapeutic durability in post-traumatic osteoarthritis, providing a translational framework for repeat intra-articular gene delivery strategies aimed at long-term disease modification in osteoarthritis.

molecular biology↗

bioRxiv2026

Cross-Species Efficacy of Combinatorial Gene Therapy for Osteoarthritis and Correction of Neuro-Inflammatory Pain Mechanisms

Osteoarthritis is a leading cause of chronic pain and disability, which lacks disease-modifying treatment. Given the complex multi-tissue and multifactorial drivers behind disease progression, effective treatments will require simultaneously targeting several mechanisms underlying joint degeneration and pain. Here, we developed and evaluated a combinatorial gene therapy, consisting of a high-capacity adenoviral vector carrying two therapeutic genes to target distinct pathological mechanisms: inflammation (IL-1Ra) and chondrocyte health (PRG4). Intra-articular delivery of this treatment improved functional, structural, and pain outcomes in murine and equine osteoarthritis models. In addition, treatment normalized inflammatory environments in joint tissues, as well as in the dorsal root ganglia (DRG) known to harbor joint-innervating sensory neurons. Moreover, gene therapy reversed OA-induced molecular signatures of neural hyperexcitability, suggesting amelioration of peripheral sensitization. Collectively, these findings support combinatorial gene therapy as a promising treatment for osteoarthritis, while identifying neuroinflammatory signatures for correction of disease progression and pain. One Sentence SummaryA single intra-articular injection of a combinatorial gene therapy slows OA progression and reduces pain in small and large animal models.

systems biology↗

bioRxiv2026

pH-dependent allosteric remodeling of a bacterial riboswitch couples alkaline activation to metal sensing

The widespread yybP-ykoY riboswitches control bacterial manganese (Mn) homeostasis by activating exporter expression in response to intracellular Mn2+ levels. The E. coli alx riboswitch distinctively couples Mn2+ sensing to cytoplasmic alkalinity, but the mechanism is unknown. We show that pH tunes the alx aptamers conformational sampling to modulate Mn2+ sensitivity. Single-molecule FRET reveals that Mn2+ stabilizes a docked three-way-junction conformation, and alkaline pH shifts this equilibrium to sensitize metal-dependent folding. Molecular dynamics simulations identify a loop whose low-pH-induced base pairing perturbs the adjacent helix, predicted to allosterically disrupt the Mn2+-binding state. In vivo reporters indicate that both this loop and the Mn2+-binding core are required for optimal pH-dependent translational activation: replacing the core with the non-pH-responsive mntP sequence abolishes activation. These results define how RNA allosterically integrates orthogonal metal and proton cues to enable combinatorial environmental sensing during alkaline stress.

biochemistry↗

bioRxiv2026

Dual targeting a LIN28B:β-catenin axis in acute myeloid leukaemia

BackgroundWnt/{beta}-catenin signalling is dysregulated in acute myeloid leukaemia (AML), where it lacks effective targeting strategies. Previously, we discovered that {beta}-catenin interacts with several RNA-binding proteins (RBP), indicating post-transcriptional influence which is yet to be therapeutically interrogated in AML. MethodsCo-immunoprecipitation confirmed protein interactions, and TCF/LEF reporters were used to assess Wnt signalling output in leukaemia cells. Regulatory crosstalk was assessed using immunoblotting and RT-qPCR approaches following lentiviral transduction of myeloid cell lines. Targeting of {beta}-catenin and LIN28B was tested through combinations of genetic and pharmacological inhibition in AML cells. ResultsThe most frequent RBP-binding motif amongst {beta}-catenin-bound mRNAs was the GGAG motif targeted by oncofetal miRNA-regulating RBP; LIN28B. {beta}-Catenin:LIN28B interactions were detected in lymphoid and myeloid cell lines, plus primary human CD34 fetal-liver HSCs. LIN28B positively regulated Wnt signalling output through LEF1 regulation involving a post-transcriptional let7 miRNA mechanism. Further miRNA sequencing of {beta}-catenin- and LIN28B-depleted myeloid cells revealed potential cooperative and antagonistic function in miRNA regulation. Finally, dual-targeting both {beta}-catenin and LIN28B through either genetic and/or pharmacological means preferentially reduced AML cell viability. ConclusionThe {beta}-catenin:LIN28B axis could represent a novel synthetically lethal relationship in AML which could be exploited in rare subtypes where LIN28B expression becomes reactivated.

cancer biology↗

bioRxiv2025

An Fc-silent OspA monoclonal antibody passively protects mice from tick and intradermal Borrelia burgdorferi challenge

The monoclonal antibody, LA-2, has played a pivotal role in the development of Outer surface protein A (OspA)-based vaccines for Lyme disease, a multisystem illness caused by the tick-borne spirochete, Borrelia burgdorferi sensu lato. Of particular significance was the demonstration more than three decades ago that LA-2 equivalent antibody titers, defined by a competitive-inhibition ELISA, serve as a reliable correlate of vaccine-induced protection across different species, including humans. In vitro characterization of LA-2 has identified both complement-dependent and -independent activities, although which of these attributes contribute to protection against B. burgdorferi remains unresolved. To address this issue, we generated and characterized an "Fc-silent" version of LA-2 IgG1 carrying so-called LALAPG substitutions (L234A, L235A, P329G). We demonstrate that LA-2 LALAPG retained OspA binding activity but was severely attenuated in in vitro complement deposition and complement-dependent borreliacidal assays. Nonetheless, LA-2 LALAPG was as effective as LA-2 at passively protecting C3H mice against nymphal tick-mediated B. burgdorferi challenge. LA-2 LALAPG was also equivalent to LA-2 in passively protecting BALB/c mice against intradermal B. burgdorferi challenge. In the intradermal challenge model, viable spirochetes were not recoverable 24 h after injection from skin biopsies of mice treated with LA-2 or LA-2 LALAPG, and an influx of pro-inflammatory cytokines and chemokines to the injection site was abrogated. Collectively, these results suggest that LA-2s primary mode of action involves direct physical interactions with the spirochete rather than complement-dependent killing. Elucidating these mechanisms may have implications for understanding the mechanistic correlates of OspA-based vaccine-induced immunity in humans.

immunology↗

bioRxiv2025

TOE1 influences canonical Wnt signalling in myeloid leukaemia cells through LEF-1 modulation and regulates the proliferation of haematopoietic cells through PAK2.

Acute myeloid leukaemia (AML) is an aggressive haematological malignancy characterised by the clonal proliferation of myeloid progenitor cells in the bone marrow and peripheral blood. Dysregulation of the Wnt/{beta}-catenin pathway has been implicated in the establishment and maintenance of leukaemic stem cells in AML, where higher expression of {beta}-catenin promotes clonogenic capacity, drug resistance and inferior survival. The finding that low levels of Wnt signalling are necessary to maintain normal haematopoiesis makes {beta}-catenin an attractive therapeutic target; however, drug design has been hampered by a poor understanding of its molecular interactions in leukaemia cells. To address this, we previously characterised the {beta}-catenin interactome in myeloid cells and identified a plethora of novel interacting proteins. One such interactor was Target of EGR1 (TOE1), a member of the Asp-Glu-Asp-Asp (DEDD) family of deadenylases with previously uncharacterised function in haematopoietic cells. The {beta}-catenin:TOE1 interaction was detected in the nuclear and cytosolic compartments of myeloid cell lines and primary AML samples, and {beta}-catenin depletion was found to promote the cytosolic accumulation of TOE1. Furthermore, TOE1 levels were found to be overexpressed in primary AML blasts versus normal cord-blood derived CD34+ haematopoietic stem and progenitor cells (HSPCs), suggesting that TOE1 levels may be dysregulated in leukaemia. TOE1 depletion abrogated Wnt signalling capacity (TCF/LEF activity), potentially via reduced stability/translatability of the Wnt transcription factor lymphoid enhancing factor 1 (LEF-1). TOE1 depletion further suppressed the proliferation and survival of myeloid leukaemia cell lines (HEL and OCI-AML2) and primary human CD34+ HSPC; however, this could not be fully explained through LEF-1 alone, since OCI-AML2 do not express LEF-1. Using tandem mass tag (TMT)-labelling coupled to mass spectrometry analysis in TOE1 deficient HEL and OCI-AML2 cells, we identified and validated p21 (RAC1) activated kinase 2 (PAK2) as a downregulated target that could reduce the proliferation (but not survival) of AML cell lines. Interestingly, ectopic expression of PAK2 was able to partially rescue the proliferation defect in TOE1 depleted myeloid cell lines and primary human CD34+ HSPC. In summary, these data reveal TOE1 as novel interacting partner for {beta}-catenin in haematological cells capable of modulating Wnt signalling output via LEF-1, and as a novel mediator of growth and survival in human HSPC and AML cells partly through PAK2 regulation.

cancer biology↗

bioRxiv2025

Immunometabolic state modulation of sequential decision making in patch-foraging mice

Animals have evolved sophisticated behavioural and metabolic adaptations to respond to threats to homeostasis, including resource scarcity and infectious pathogens. Energy deficits associated with lack of food availability and sickness-associated anorexia elicit distinctive hypometabolic states, however how such states are integrated with higher-order cognition is largely unknown. Patch-foraging paradigms have proven useful for deciphering evolutionarily conserved and ethologically grounded insights into cost-benefit decision-making as animals continually deliberate between exploiting and exploring their environment. We developed and extensively validated a touchscreen-based patch-foraging task for mice in which food reward dynamically varied across trials, in a dataset comprising over 111,000 sequential decisions from 35 adult male mice. Contrary to predictions that emphasize the impact of inflammation to blunt effortful reward-driven behaviour, our results demonstrate that systemic lipopolysaccharides-induced inflammation promotes hyper-exploitation by attenuating exploratory choice behaviour in animals interacting with complex food environments. Such behaviour can be seen as a bias towards immediate outcomes, with impulsivity as a feature affecting the weighting of temporal factors. Given the ubiquity of systemic inflammation in numerous infectious, metabolic and psychiatric disorders featuring dysfunctional value- and cost-sensitive behaviour, these results provide insight into how immunometabolic states are linked to altered decision-making.

neuroscience↗

bioRxiv2025

Prefrontal parvalbumin neurons as a target for enhancing cognition in non-pathological and 22q11.2 microdeletion syndrome mice

A failure of organized communication in the PFC is thought to contribute to the emergence of cognitive impairments in psychiatric diseases, with attentional deficits occurring as a fundamental symptom across various conditions. The 22q11.2 microdeletion syndrome is a rare genetic condition that confers a high risk for developing psychiatric and neurodevelopmental disorders, and mouse models have been shown to display attention impairments and PFC pathology that are relevant to clinical populations. Abnormalities in prefrontal parvalbumin-expressing neurons (PVNs) are part of the observed pathophysiology, and studies in rodents have shown that the direct manipulation of these cells can induce behavioral deficits that align with the cognitive symptoms observed in psychiatric diseases. In the present study, we expanded on the role of PVNs in supporting cognition by investigating their involvement in multiple aspects of attentional functions using a translationally relevant task of focused visual attention, in both non-pathological mice and a model of the 22q11.2 microdeletion syndrome. We observed that task-evoked prefrontal PVN activity was reduced in mice that exhibited poorer attention and in 22q11.2 mutant mice. While PVN activity was shaped across learning in non-pathological mice, mutant mice exhibited a lack of signal dynamics that coincided with attentional deficits. Importantly, we observed that task performance in both poor performing wild-types and 22q11.2 mutants could be alleviated by gamma frequency stimulation of PVNs. Thus, PVNs appear to be involved in the acquisition of task rules and execution of attention and continue to be a promising therapeutic target for cognitive dysfunction in disease.

neuroscience↗

bioRxiv2025

Intravenous lipid-siRNA conjugate mediates gene silencing at the blood-brain barrier and blood-CSF barrier

Barriers of the central nervous system (CNS), such as the blood-brain barrier (BBB) and blood-cerebrospinal fluid barrier (BCSFB), regulate the two-way exchange of material between the blood and CNS. These barriers pose a considerable challenge for efficacious delivery of intravenously administered therapies into the CNS, motivating exploration of their function and ways to modulate their properties. While the BBB and BCSFB can become dysfunctional in patients with chronic CNS diseases, few studies have focused on strategies for targeting these interfaces. Here, we showed that an intravenously administered albumin-binding lipid-siRNA conjugate was delivered to and silences genes within brain endothelial cells and choroid plexus epithelial cells, which comprise the BBB and BCSFB, respectively. A single intravenous dose of lipid-siRNA conjugate was delivered to [~]100% of brain endothelial cells and major choroid plexus cell types, without any substantial delivery into brain parenchymal tissue. Sustained gene silencing was achieved in both brain endothelial cells (over two weeks) and bulk choroid plexus tissues (up to one month). Moreover, single cell RNA sequencing demonstrated gene knockdown in capillaries, venous endothelial cells, and choroid plexus epithelial cells without silencing genes in parenchymal cell populations. Collectively, this work establishes an effective nonviral framework to mediate gene inhibition in the brain barriers. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=156 SRC="FIGDIR/small/642142v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@b00a52org.highwire.dtl.DTLVardef@175a363org.highwire.dtl.DTLVardef@39be75org.highwire.dtl.DTLVardef@1072093_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2024

Structurally distinct manganese-sensing riboswitch aptamers regulate diverse expression platform architectures

Manganese (Mn)-sensing riboswitches protect bacteria from Mn toxicity by upregulating expression of Mn exporters. The Mn aptamers share key features but diverge in other important elements, including within the metal-binding core. Although X-ray crystal structures of isolated aptamers exist, these structural snapshots lack crucial details about how the aptamer communicates the presence or absence of ligand to the expression platform. In this work, we investigated the Mn-sensing translational riboswitches in E. coli (mntP and alx), which differ in aptamer secondary structure, nucleotide sequence, and pH-dependence of Mn response. We performed co-transcriptional RNA chemical probing, allowing us to visualize RNA folding intermediates that form and resolve en route to the final folded riboswitch. For the first time, we report that sampling of metal ions by the RNA begins before the aptamer synthesis and folding are complete. At a single-nucleotide resolution, we pinpoint the transcription window where "riboswitching" occurs in response to Mn binding and uncover key differences in how the alx and mntP riboswitches fold. Finally, we describe riboswitch-specific effects of pH, providing insights into how two members of the same riboswitch family differentially sense two distinct environmental cues: concentration of Mn and pH. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=147 SRC="FIGDIR/small/628514v5_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@1319d00org.highwire.dtl.DTLVardef@3a9bd3org.highwire.dtl.DTLVardef@1cc5368org.highwire.dtl.DTLVardef@177e43b_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2024

Dissociable patterns of dopamine dynamics and causal contributions to stimulus-response behaviors across striatal subregions.

Rationale: Midbrain dopamine (DA) neurons project principally towards the striatum, serving as key regulators of movement, motivation, and cognition. Different striatal dopaminergic (DA) pathways may regulate different aspects of cognition. Objectives: We investigated how different striatal DA pathways contribute to a known function of the striatum, visuomotor conditional learning. Methods: Using fiber photometry, we recorded DA transients in these regions as mice learned the touchscreen Visuo-Motor Conditional Learning task. Results: DA transients in all regions dynamically tracked task events, but differed in the timing of peak responses and ramp-like activity preceding a choice, indicating region-specific temporal dynamics across learning. Manipulations of reward probability revealed DA transients in all regions during reward delivery and omission that are consistent with an interpretation in terms of reward prediction error. Thus, DA dynamics in all regions could indicate involvement in visuomotor conditional learning. Therefore, to determine whether nigrostriatal or mesolimbic DA is necessary for learning, we chemogenetically inhibited DA striatal afferents, revealing that only DLS-projecting nigrostriatal DA, and not NAc-projecting mesolimbic striatal DA, was necessary for learning the task. Conclusion: These findings demonstrate functional heterogeneity of aspects of striatal DA signaling, and selective causal roles in the learning of visuomotor conditional learning.

animal behavior and cognition↗

bioRxiv2023

Ventral pallidum projections to the ventral tegmental area reinforce but do not invigorate reward-seeking behavior

Reward-predictive cues acquire motivating and reinforcing properties that contribute to the escalation and relapse of drug use in addiction. The ventral pallidum (VP) and ventral tegmental area (VTA) are two key nodes in brain reward circuitry implicated in addiction and necessary for the performance of cue-driven behavior. Evidence suggests that VP neurons projecting to the VTA (VP[->]VTA) promote cue-induced reinstatement of drug-seeking, but the mechanisms by which these neurons do so are undefined. In addition, the role of these neurons in the pursuit of non-drug reward is not known. In the current study, we used in vivo fiber photometry and optogenetics to record from and manipulate VP[->]VTA in rats performing a discriminative stimulus task (DS task) with sucrose reward to determine the fundamental role these neurons play in invigoration and reinforcement by reward and associated discriminative cues. We find that VP[->]VTA neurons are selectively active during reward consumption, that optogenetic stimulation of these neurons paired with reward consumption biases choice, and that VP[->]VTA optogenetic stimulation is reinforcing. Critically, we found no significant encoding of cue-elicited reward-seeking vigor and acute optogenetic stimulation of these neurons paired with cue onset did not enhance the probability or vigor of reward-seeking. Our results suggest that VP[->]VTA neurons are active during the consumption of natural reward and that this activity reinforces seeking behavior.

neuroscience↗

bioRxiv2023

Epigenetic fidelity in complex biological systems and implications for ageing

The study of age is plagued by a lack of delineation between the causes and effects within the ageing phenotype. This has made it difficult to fully explain the biological ageing process from first principles with a single definition. Lacking a clear description of the underlying root cause of biological age confounds clarity in this critical field. In this paper, we demonstrate that the epigenetic system has a built-in, unavoidable fidelity limitation and consequently demonstrate that there is a distinct class of DNA methylation loci that increases in variance in a manner tightly correlated with chronological age. We demonstrate the existence of epigenetic activation functions and that topological features beyond these activation functions represent deregulation. We show that the measurement of epigenetic fidelity is an accurate predictor of cross-species age and present a deep-learning model that predicts chronological age exclusively from knowledge of variance. We find that the classes of epigenetic loci in which variation correlates with chronological age control genes that regulate transcription and suggest that the inevitable consequence of this is a feedback cycle of system-wide deregulation causing a progressive collapse into the phenotype of age. This paper represents a novel theory of biological systemic ageing with arguments as to why, how and when epigenetic ageing is inevitable.

genomics↗

bioRxiv2022

Ventral pallidal GABAergic neuron calcium activity encodes cue-driven reward-seeking and persists in the absence of reward delivery

Reward-seeking behavior is often initiated by environmental cues that signal reward availability. This is a necessary behavioral response; however, cue reactivity and reward-seeking behavior can become maladaptive. To better understand how cue elicited reward-seeking becomes maladaptive, it is important to understand the neural circuits involved in assigning appetitive value to rewarding cues and actions. Ventral pallidum (VP) neurons are known to contribute to cue elicited reward-seeking behavior and have heterogeneous responses in a discriminative stimulus (DS) task. The VP neuronal subtypes and output pathways that encode distinct aspects of the DS task remain unknown. Here, we used an intersectional viral approach with fiber photometry to record bulk calcium activity in VP GABAergic (VP GABA) neurons in male and female rats as they learned and performed the DS task. We found that VP GABA neurons are excited by reward-predictive cues but not neutral cues, and that this response develops over time. We also found that this cue-evoked response predicts reward-seeking behavior. Additionally, we found increased VP GABA calcium activity at the time of expected reward delivery, which occurred even on trials when reward was omitted. Together, these findings suggest that VP GABA neurons encode reward expectation and calcium activity in these neurons is predictive of the vigor of cue-elicited reward-seeking.

neuroscience↗