bioRxiv Science⌕ Search

Biology subjects

McDonald, R.

Publications and source records attributed to McDonald, R..

8 recordsLinked to original sources

Reversible inhibition of medial septum interneurons abolishes initial acquisition of new place-reward associations and reveals a progressive reduction in dependence on medial septal function

Hippocampal place cells encode spatial information within a theta-organized temporal framework paced by the medial septum (MS). Lesions or inactivation of the MS impair spatial learning and disrupt hippocampal theta rhythmicity, long-term potentiation, and plasticity-related gene expression, while often sparing spatially selective firing of CA1 neurons (but not CA3 neurons). Although many rodent studies argue against classical systems consolidation by showing persistent hippocampal dependence of spatial memories, other work has suggested that training structure, spaced vs. massed trials, can influence this dependence. To investigate this possibility, we used DREADD-based, reversible, inhibition of MS GABAergic neurons, some of which are known to project to hippocampus. DREADD activation reduced hippocampal theta power and spatial information encoded by hippocampal neurons while largely preserving overall neuronal firing. We then examined the effect of inhibition of medial septal GABAergic neurons on learning the correct goal arm in an 8-arm maze when the correct arm was randomly changed each day. On each day, the mice were given two forced-choice trials indicating the correct arm and then 5 free-choice trials (without correction) and were always started from an opaque cylinder in the maze center, in a random orientation, to eliminate possible use of a simple response strategy. When the correct goal arm varied randomly daily, MS cell inhibition severely and repeatedly impaired acquisition. In contrast, when the correct goal arm was subsequently fixed across days, performance was initially impaired but became resistant to DREADD activation over time. Once performance reached asymptote, the goal arm was switched to a new (random) position. In this case, learning was no longer impaired by DREADD activation. This generalization suggests that repeated fixed-goal training in the same environment induces a broader reorganization of the neural systems supporting spatial behaviour. One possibility is that mice develop a septal-independent task-solving strategy that supports both retrieval of established goal locations and acquisition of new ones within a stable environment. This transition could reflect the gradual adoption of a non-spatial strategy such as visual pattern recognition, or the use of a directional cue. Moving the most salient distal cue in the environment (a single room light) produced a substantial change in the visual configurations seen from the arm entry points, and disrupted performance; however, it did not produce a consistent directional shift relative to the cue, suggesting that the light contributed to an integrated visuo-spatial representation rather than serving as the reference frame origin. We conclude that the mice switched from a hippocampus/MS-dependent spatial strategy to a non-hippocampus-dependent visual pattern matching solution.

neuroscience↗

Circadian rhythm disruption alters rhythmic properties of clock and memory gene expression in the hippocampi of rats

Our modern environment - with its artificial lighting, irregular work hours, and frequent travel -- often disrupts our circadian rhythms, which can lead to health problems, particularly in learning and memory. This is especially concerning given the aging population and the rising prevalence of dementia. Yet, the biological mechanisms linking circadian disruption to cognitive impairment remain poorly understood. At the molecular level, genetic techniques have been used to attenuate or abolish expression of key genes involved in circadian rhythms and these manipulations have detrimental effects on memory function. However, whether environmentally induced circadian disruption, impairs memory via changes in overall gene expression levels in the hippocampus or rather via changes in the coordinated rhythmic patterns of circadian expression across groups of genes is less known. Here, we examined how environmental circadian disruption affects the expression of genes involved in the circadian clock and memory in the hippocampus of rats using a forced desynchrony model. Circadian disruption changed the rhythmic properties of gene expression in most genes assessed but had no measurable effect on average expression levels across the day. These findings suggest that the inability to maintain circadian synchrony rather than overall expression may underlie the cognitive deficits observed in circadian-related disorders.

neuroscience↗

Immunomodulatory nanoparticles elicit antifibrotic monocyte activation to resolve murine pulmonary fibrosis

Organ fibrosis presents a substantial disease burden with few therapeutic options. Innate immunity mediates fibrinogenesis, but also plays a major role in fibrinolysis. Here, we show that immunomodulatory nanoparticles (NPs) can harness this endogenous antifibrotic capacity by catalyzing monocyte activation leading to resolution of bleomycin-induced pulmonary fibrosis in vivo. Cargo-free NPs comprised of the degradable biopolymer poly(lactide-co-glycolide) (PLG) induce a transcriptional shift toward antifibrotic immune activation in profibrotic M2 macrophages (M{Phi}s) in vitro. NPs stimulate M2 M{Phi}s toward a glycolytic, rather than fatty acid oxidative, metabolism; suppress canonical M2 markers like arginase-1 (Arg1) and periostin (Postn); and upregulate collagenases, hyaluronidases and immunoregulatory factors. When delivered intravenously in vivo, NPs reverse established bleomycin-induced pulmonary fibrosis and invert the trajectory of over 1,000 genes from pre- to post-treatment according to bulk RNA-sequencing. NPs also suppress profibrotic signaling and increase expression of repair-associated pathways like peroxisome proliferator-activated receptor gamma (PPAR-{gamma}), nuclear retinoic acid receptor (RAR), vascular endothelial growth factor (VEGF), and sphingolipid signaling in fibrotic lungs. Flow cytometry confirms that NPs induce monocyte recruitment to fibrotic lungs via enhanced integrin expression. Altogether, NPs induce a robust pro-regenerative signature comprised of ECM degradation, inflammation resolution, and tissue repair pathways, concomitant with increased NP+ monocyte recruitment to fibrotic lungs. This work demonstrates that monocytes are not intrinsically profibrotic, but rather, their effects are context-dependent, and they retain a capacity for fibrotic resolution under conditions that can be induced by materials with translational potential. Significance StatementOrgan fibrosis can follow from tissue injury and substantially impairs organ function, but it is incurable and has limited therapeutic options. Myeloid immune cells drive fibrosis onset and progression, but they can also mediate fibrosis resolution. We used polymeric NPs made from clinically translatable biomaterials to harness the antifibrotic capacity of immune cells as a fibrosis therapy. We found that intravenous NPs can reprogram myeloid cells to acquire an antifibrotic phenotype in a mouse model of pulmonary fibrosis. NPs increased myeloid activation and pulmonary recruitment while decreasing fibrosis, showing that directed immune activation, instead of suppression, could be an effective therapeutic strategy for fibrosis.

bioengineering↗

Spatial-temporal dynamics of contact among free-ranging domestic dogs Canis familiaris in rural Africa

1. Transmission of infection is affected by the spatial-temporal dynamics of host contacts. Domestic dogs Canis familiaris share pathogens with humans and wildlife, and managing dog-mediated diseases is a priority for public health and conservation interests. 2. We combined proximity sensors and GPS tracking to analyse spatial-temporal variation in contact among free-ranging dogs in six villages in rural Chad, during both the wet and dry seasons. We investigated dyadic interactions between dogs from different villages, the same village but different households and the same household. We assessed variation in (i) the probability of individuals having had contact, (ii) the hourly frequency of contact and (iii) contact durations. 3. Our results highlight clear seasonal and hourly patterns in contact behaviour. Contacts between dogs from different villages were rare, short in duration, primarily between male-female dyads and predominantly occurred within villages and during the dry season. Contact between dogs in the same village peaked at dawn and dusk. Sex differences were most pronounced in the wet season, where males from different households had the highest hourly contact probabilities, followed by male-female dyads. For all dogs, contact durations were longer in the dry season, but showed little hourly variation. 4. Contact patterns were not equal in space, and the probability of individuals having had contact was less than 5% when dwellings were more than 500m apart. Spatially, the probability of contact was lowest outside the village, but this increased in the dry season and peaked in the morning hours. Contact durations were notably longer outside the village, where they increased in duration for between-household dyads in the dry season. 5. At a coarse temporal scale, variation in dog contacts within and among households, and rarely between villages, may underpin seasonal variation in the incidence of dog-mediated diseases. Variation at finer temporal (hourly) and spatial scales (around households, within and outside villages) highlights the importance of routine behaviours and space use in determining patterns of contact between dogs. Practitioners should consider behavioural heterogeneities, such as those reported here, when using strategic models to support disease management decisions.

animal behavior and cognition↗

A melancholy machine: simulated synapse loss induces depression-like behaviors in deep reinforcement learning

Deep Reinforcement Learning is a branch of artificial intelligence that uses artificial neural networks to model reward-based learning as it occurs in biological agents. Here we modify a Deep Reinforcement Learning approach by imposing a suppressive effect on the connections between neurons in the artificial network - simulating the effect of dendritic spine loss as observed in major depressive disorder (MDD). Surprisingly, this simulated spine loss is sufficient to induce a variety of MDD-like behaviors in the artificially intelligent agent, including anhedonia, increased temporal discounting, avoidance, and an altered exploration/exploitation balance. Furthermore, simulating alternative and longstanding reward-processing-centric conceptions of MDD (dysfunction of the dopamine system, altered reward discounting, context-dependent learning rates, increased exploration) does not produce the same range of MDD-like behaviors. These results support a conceptual model of MDD as a reduction of brain connectivity (and thus information-processing capacity) rather than an imbalance in monoamines - though the computational model suggests a possible explanation for the dysfunction of dopamine systems in MDD. Reversing the spine-loss effect in our computational MDD model can lead to rescue of rewarding behavior under some conditions. This supports the search for treatments that increase plasticity and synaptogenesis, and the model suggests some implications for their effective administration. Significance statementSimulating dendritic spine loss in a deep reinforcement learning agent causes the agent to exhibit a surprising range of depression-like behaviors. Simulating spine restoration allows rewarding behavior to be re-learned. This computational model sees Major Depressive Disorder as a reversible loss of brain capacity, providing some insights on pathology and treatment.

neuroscience↗

Low input capture Hi-C (liCHi-C) identifies promoter-enhancer interactions at high-resolution

Long-range interactions between regulatory elements and promoters are key in gene transcriptional control; however, their study requires large amounts of starting material, which is not compatible with clinical scenarios nor the study of rare cell populations. Here we introduce low input capture Hi-C (liCHi-C) as a cost-effective, flexible method to map and robustly compare promoter interactomes at high resolution. As proof of its broad applicability, we implement liCHi-C to study normal and malignant human hematopoietic hierarchy in clinical samples. We demonstrate that the dynamic promoter architecture identifies developmental trajectories and orchestrates transcriptional transitions during cell-state commitment. Moreover, liCHi-C enables the identification of new disease-relevant cell types, genes and pathways potentially deregulated by non-coding alterations at distal regulatory elements. Finally, we show that liCHi-C can be harnessed to uncover genome-wide structural variants, resolve their breakpoints and infer their pathogenic effects. Collectively, our optimized liCHi-C method expands the study of 3D chromatin organization to unique, low-abundance cell populations, and offers an opportunity to uncover novel factors and regulatory networks involved in disease pathogenesis.

genomics↗

Immunogenicity of convalescent and vaccinated sera against clinical isolates of ancestral SARS-CoV-2, beta, delta, and omicron variants

The omicron variant of concern (VOC) of SARS-CoV-2 was first reported in November 2021 in Botswana and South Africa. Omicron has evolved multiple mutations within the spike protein and the receptor binding domain (RBD), raising concerns of increased antibody evasion. Here, we isolated infectious omicron from a clinical specimen obtained in Canada. The neutralizing activity of sera from 65 coronavirus disease (COVID-19) vaccine recipients and convalescent individuals against clinical isolates of ancestral SARS-CoV-2, beta, delta, and omicron VOCs was assessed. Convalescent sera from unvaccinated individuals infected by the ancestral virus during the first wave of COVID-19 in Canada (July, 2020) demonstrated reduced neutralization against beta and omicron VOCs. Convalescent sera from unvaccinated individuals infected by the delta variant (May-June, 2021) neutralized omicron to significantly lower levels compared to the delta variant. Sera from individuals that received three doses of the Pfizer or Moderna vaccines demonstrated reduced neutralization of the omicron variant relative to ancestral SARS-CoV-2. Sera from individuals that were naturally infected with ancestral SARS-CoV-2 and subsequently received two doses of the Pfizer vaccine induced significantly higher neutralizing antibody levels against ancestral virus and all VOCs. Importantly, infection alone, either with ancestral SARS-CoV-2 or the delta variant was not sufficient to induce high neutralizing antibody titers against omicron. This data will inform current booster vaccination strategies, and we highlight the need for additional studies to identify longevity of immunity against SARS-CoV-2 and optimal neutralizing antibody levels that are necessary to prevent infection and/or severe COVID-19.

immunology↗

Mapping the biogenesis of forward programmed megakaryocytes from induced pluripotent stem cells

Platelet deficiency, known as thrombocytopenia, can cause haemorrhage and is treated with platelet transfusions. We developed a system for the production of platelet precursor cells, megakaryocytes, from pluripotent stem cells. These cultures can be maintained for >100 days, implying culture renewal by megakaryocyte progenitors (MKPs). However, it is unclear whether the MKP state in vitro mirrors the state in vivo, and MKPs cannot be purified using conventional surface markers. We performed single cell RNA sequencing throughout in vitro differentiation and mapped each state to its equivalent in vivo. This enabled the identification of 5 surface markers which reproducibly purify MKPs, allowing us an insight into their transcriptional and epigenetic profiles. Finally, we performed culture optimisation, increasing MKP production. Altogether, this study has mapped parallels between the MKP states in vivo and in vitro and allowed the purification of MKPs, accelerating the progress of in vitro-derived transfusion products towards the clinic.

developmental biology↗