Biology subjects

Kingston, N.

Publications and source records attributed to Kingston, N..

5 recordsLinked to original sources

bioRxiv2025

Causal necessity of human hippocampus for structure-based inference in learning

When meeting new individuals or encountering known individuals in new circumstances, we intuitively map out their relationships - not merely by direct experience, but by quickly inferring new connections based on prior relational knowledge. Using a novel task, we demonstrated that participants indeed employ knowledge of relational structures to facilitate learning of new relationships in a changing environment. Computational modelling revealed that participants leveraged relational knowledge to support inference, thus facilitating learning. Whole brain neuroimaging identified a uniquely robust representation of relational structure in the hippocampus. Neural networks trained on similar tasks demonstrated the emergence of relational structure representations, resembling those found in hippocampus. Lesioning network units sustaining such representations disrupted structure-based inference and predicted hippocampuss essential role. Transcranial ultrasound stimulation of human hippocampus, transiently modulating its activity without affecting overlying tissue, produced similar disruption effects, empirically confirming the causal necessity of hippocampal representations for structure-based inference in learning.

neuroscience↗

bioRxiv2023

Gut microbiome remains stable following COVID-19 vaccination in healthy and immuno-compromised individuals

The bidirectional interaction between the immune system and the gut microbiota is a key contributor to various host physiological functions. Immune-associated diseases such as cancer and autoimmunity, as well as the efficacy of immunomodulatory therapies, have been linked to microbiome variation. While COVID-19 infection has been shown to cause microbial dysbiosis, it remains understudied whether the inflammatory response associated with vaccination also impacts the microbiota. Here, we investigate the temporal impact of COVID-19 vaccination on the gut microbiome in healthy and immuno-compromised individuals; the latter included patients with primary immunodeficiency and cancer patients on immunomodulating therapies. We find that the gut microbiome remained remarkably stable post-vaccination irrespective of diverse immune status, vaccine response, and microbial composition spanned by the cohort. The stability is evident at all evaluated levels including diversity, phylum, species, and functional capacity. Our results indicate the resilience of the gut microbiome to host immune changes triggered by COVID-19 vaccination and suggest minimal, if any, impact on microbiome-mediated processes. These findings encourage vaccine acceptance, particularly when contrasted with the significant microbiome shifts observed during COVID-19 infection.

microbiology↗

bioRxiv2023

Costimulatory domains direct distinct fates of CAR-driven T cell dysfunction

Chimeric antigen receptor (CAR) engineered T cells often fail to enact effector functions after infusion into patients. Understanding the biological pathways that lead CAR T cells to failure is of critical importance in the design of more effective therapies. We developed and validated an in vitro model that drives T cell dysfunction through chronic CAR activation and interrogated how CAR costimulatory domains contribute to T cell failure. We found that dysfunctional CD28-based CARs targeting CD19 bear hallmarks of classical T cell exhaustion while dysfunctional 41BB-based CARs are phenotypically, transcriptionally and epigenetically distinct. We confirmed activation of this unique transcriptional program in CAR T cells that failed to control clinical disease. Further, we demonstrate that 41BB-dependent activation of the transcription factor FOXO3 is a significant contributor to this dysfunction and disruption of FOXO3 improves CAR T cell function. These findings identify that chronic activation of 41BB leads to novel state of T cell dysfunction that can be alleviated by genetic modification of FOXO3. SummaryChronic stimulation of CARs containing the 41BB costimulatory domain leads to a novel state of T cell dysfunction that is distinct from T cell exhaustion.

immunology↗

bioRxiv2019

Area requirements to safeguard Earth’s marine species

Despite global policy commitments to preserve Earths marine biodiversity, many species are in a state of decline. Using data on 22,885 marine species, we identify 8.5 million km2 of priority areas that complement existing areas of conservation and biodiversity importance. New conservation priorities are found in over half (56%) of all coastal nations, with key priority regions in the northwest Pacific Ocean and Atlantic Ocean. We identify where different conservation actions, ranging from marine protected areas to broader policy approaches, may best overcome anthropogenic threats to these areas. This analysis shows 26-41% of the ocean (depending on targets used for species representation) needs to be effectively conserved through a combination of site-based actions and wider policy responses to achieve global conservation and sustainable development agendas.\n\nOne Sentence SummaryAt least 26% of the ocean needs a combination of site-based conservation and wider policy responses to achieve global conservation goals.

ecology↗

bioRxiv2017

Causal Analyses, Statistical Efficiency And Phenotypic Precision Through Recall-By-Genotype Study Design

Genome-wide association studies have been useful in identifying common genetic variants related to a variety of complex traits and diseases; however, they are often limited in their ability to inform about underlying biology. Whilst bioinformatics analyses, studies of cells, animal models and applied genetic epidemiology have provided some understanding of genetic associations or causal pathways, there is a need for new genetic studies that elucidate causal relationships and mechanisms in a cost-effective, precise and statistically efficient fashion. We discuss the motivation for and the characteristics of the Recall-by-Genotype (RbG) study design, an approach that enables genotype-directed deep-phenotyping and improvement in drawing causal inferences. Specifically, we present RbG designs using single and multiple variants and discuss the inferential properties, analytical approaches and applications of both. We consider the efficiency of the RbG approach, the likely value of RbG studies for the causal investigation of disease aetiology and the practicalities of incorporating genotypic data into population studies in the context of the RbG study design. Finally, we provide a catalogue of the UK-based resources for such studies, an online tool to aid the design of new RbG studies and discuss future developments of this approach.

genetics↗