Biology subjects

Pemberton, J.

Publications and source records attributed to Pemberton, J..

8 recordsLinked to original sources

bioRxiv2026

Cell-type-specific cortical feedback coordinates hierarchical credit assignment

Learning is thought to arise from synaptic modifications across brain-wide circuits, yet how these networks coordinate plasticity to support complex behaviour is not known. Inspired by deep learning, we introduce a theory of hierarchical credit assignment in which pathway-specific cortical feedback drives dendrite-dependent burst plasticity across the cortex. We show that this principle enables learning in dynamic settings, complex visual recognition, and goal-directed tasks, mechanistically linking credit assignment to cell-type-specific regulation of dendritic excitation-inhibition balance. Our framework provides a unified account of diverse experimental phenomena -- including cell-type-specific modulation of synaptic plasticity, learning-dependent changes in interneurons, and neuron-specific dendritic error signals. Furthermore, the theory predicts that interneurons constrain the dimensionality of error feedback, offering a functional rationale for cortex-wide gradients in interneuron density. Together, these findings reveal how distinct cortical cell types cooperatively coordinate learning, bridging the gap between synaptic plasticity, circuit-level computation, and behaviour.

neuroscience↗

bioRxiv2026

In Cellulo pharmacological profiling and genomic editing reveals paralog-specific targets for PA generation during PLC signaling

Phosphatidic acid (PA) is an essential intermediate generated during phospholipase C (PLC) signaling, but its regulation is complex. PA can be generated by ten different diacylglycerol kinase paralogs (DGKs) and two different phospholipase D paralogs (PLDs) in mammals. Because these enzymes are activated under diverse conditions and at various membranes, understanding paralog-specific contributions to PA production is critical for therapeutic development of drugs that modulate the PLC pathway. To address this, we aimed to characterize the paralog specificity of the DGK inhibitors R59022 and BMS-502 against individual endogenously-tagged DGK paralogs in live cells. We found that R59022 and BMS-502 both recruited endogenous DGKalpha to the plasma membrane, and inhibited the catalytic fragment of DGKalpha when ectopically localized to the mitochondrial outer membrane. However, at its effective dose, R59022 paradoxically increased PA levels, while BMS-502 functioned as a potent inhibitor. Live-cell imaging experiments using BMS-502 with carbachol stimulation of endogenous muscarinic receptors showed that inhibition of both DGKalpha and the PLDs is needed to substantially reduce PA levels during PLC activation. Our findings both identify paralog-specific druggable targets for modulating PLC signaling events, and establish a new platform for characterizing DGK and PLD activity in living cells.

biochemistry↗

bioRxiv2022

Cerebellar-driven cortical dynamics enable task acquisition, switching and consolidation

To drive behavior, the cortex must bridge sensory cues with future outcomes. However, the principles by which cortical networks learn such sensory-behavioural transformations remain largely elusive. Here, we posit that the cerebellum assumes a crucial role in driving cortical dynamics, thereby enabling rapid and flexible task acquisition. We introduce a computational model of cerebellar networks which learn to drive cortical networks with task-outcome predictions. First, using sensorimotor tasks we show that cerebellar feedback in the presence of minimal cortical plasticity is suffcient for rapid task acquisition and multiple task switching. Next, we demonstrate that, when trained in working memory tasks, the cerebellum can also underlie the maintenance of cognitive-specific dynamics, explaining a range of optogenetic and behavioural observations. Finally, using our model we introduce a systems consolidation theory in which task information is gradually transferred from the cerebellum to the cortex. In summary, our findings suggest that cortico-cerebellar loops play a pivotal role in task acquisition, switching, and consolidation within the brain.

neuroscience↗

bioRxiv2022

Metastatic potential in clonal melanoma cells is driven by a rare, early-invading subpopulation

Metastasis occurs when tumor cells leave the primary tumor site and disseminate to distal organs. Even though most cells remain in the primary tumor, the circumstances by which a small fraction of them disseminate remain unclear. Here, we show that a rare, highly invasive subpopulation of melanoma cells can be detected within clonal cell lines due to non-genetic fluctuations in gene expression. The highly invasive phenotype was intrinsic to the cells, independent of their environment, and was marked by transiently high levels of SEMA3C expression, as revealed by RNA-sequencing analysis. Furthermore, the invasive subpopulation drove the bulk dissemination of tumor cells to distal locations in a mouse model of melanoma. The transcription factor NKX2.2 regulated the proportion of invasive cells in the melanoma 1205Lu cell line. Furthermore, an overall tradeoff between proliferation and invasion in single cells was observed. Our results suggest that phenotypes like metastasis may arise from intrinsic differences stemming from non-genetic fluctuations between single cells.

cancer biology↗

bioRxiv2022

Helminth parasites decrease survival probability in young red deer

Helminths are common parasites of wild ungulates that can have substantial costs for growth, mortality, and reproduction. While these costs are relatively well documented for mature animals, knowledge of helminths impacts on juveniles is more limited. Identifying these effects is important because young individuals are often heavily infected, and juvenile mortality is an important process regulating wild populations. Here, we investigated associations between helminth infection and overwinter survival in juvenile wild red deer (Cervus elaphus) on the Isle of Rum, Scotland. We collected faecal samples non-invasively from known individuals and used them to count propagules of three helminth taxa (strongyle nematodes, Fasciola hepatica, and Elaphostrongylus cervi). Using generalised linear models, we investigated associations between parasite counts and overwinter survival for calves and yearlings. Strongyles were associated with reduced survival in both age class, and F. hepatica was associated with reduced survival in yearlings, while E. cervi infection showed no association with survival in either age class. This study provides observational evidence for fitness costs of helminth infection in juveniles of a wild mammal, and suggests that these parasites could play a role in regulating population dynamics.

ecology↗

bioRxiv2022

Cerebro-cerebellar networks facilitate learning through feedback decoupling

Behavioural feedback is critical for learning in the cerebral cortex. However, such feedback is often not readily available. How the cerebral cortex learns efficiently despite the sparse nature of feedback remains unclear. Inspired by recent deep learning algorithms, we introduce a systems-level computational model of cerebro-cerebellar interactions. In this model a cerebral recurrent network receives feedback predictions from a cerebellar network, thereby decoupling learning in cerebral networks from future feedback. When trained in a simple sensorimotor task the model shows faster learning and reduced dysmetria-like behaviours, in line with the widely observed functional impact of the cerebellum. Next, we demonstrate that these results generalise to more complex motor and cognitive tasks. Finally, the model makes several experimentally testable predictions regarding (1) cerebro-cerebellar task-specific representations over learning, (2) task-specific benefits of cerebellar predictions and (3) the differential impact of cerebellar and inferior olive lesions. Overall, our work offers a theoretical framework of cerebro-cerebellar networks as feedback decoupling machines.

neuroscience↗

bioRxiv2021

Associations between MHC class II variation and phenotypic traits in a free-living sheep population

Pathogen-mediated selection (PMS) is thought to maintain the high level of allelic diversity observed in the major histocompatibility complex (MHC) class II genes. A comprehensive way to demonstrate contemporary selection is to examine associations between MHC variation and individual fitness. As individual fitness is hard to measure, many studies examine associations between MHC diversity and phenotypic traits which include direct or indirect measures of adaptive immunity thought to contribute to fitness. Here, we tested associations between MHC class II variation and five representative phenotypic traits measured in August: weight, strongyle faecal egg count, and plasma IgA, IgE and IgG immunoglobulin titres against the gastrointestinal nematode parasite Teladorsagia circumcincta in a free-living population of Soay sheep. We found no association between MHC class II variation and August weight or strongyle faecal egg count. We did however find associations between MHC class II variation and immunoglobulin levels which varied with age, isotype and sex. Our results suggest associations between MHC and phenotypic traits are more likely to be found for traits more closely associated with pathogen defence than integrative traits such as body weight and highlight a useful role of MHC-antibody associations in examining selection on MHC genes.

evolutionary biology↗

bioRxiv2019

The carboxyl-terminal sequence of Bim enables Bax activation and killing of unprimed cells

The Bcl-2 family BH3 protein Bim promotes apoptosis at mitochondria by activating the pore forming proteins Bax and Bak and by inhibiting the anti-apoptotic proteins Bcl-XL, Bcl-2 and Mcl-1. Bim binds to these proteins via its BH3 domain and to the mitochondrial membrane by a carboxyl-terminal sequence (CTS). In cells killed by Bim, the expression of a Bim mutant in which the CTS was deleted (BimL-dCTS) triggered variable amounts of apoptosis that correlated with inhibition of anti-apoptotic proteins being sufficient to permeabilize mitochondria isolated from the same cells. Detailed analysis of the molecular mechanism demonstrated that BimL-dCTS inhibited Bcl-XL but did not activate Bax. Our examination of additional point mutants unexpectedly revealed that the CTS of Bim is required for physiological concentrations of Bim to activate Bax and that different residues in the CTS enable Bax activation and binding to membranes.

biochemistry↗