Biology subjects

Gibson, T.

Publications and source records attributed to Gibson, T..

7 recordsLinked to original sources

bioRxiv2026

Skuas as sentinels of high pathogenicity avian influenza H5N1 on the Antarctic Peninsula in the 2024/2025 austral summer

Despite Antarcticas geographic isolation, the first incursion of high pathogenicity avian influenza (HPAI) H5N1 was detected in the 2023/24 austral summer. Surveillance for HPAI H5N1 in Antarctica remains patchy due to logistical, financial, and infrastructure challenges, with many suspected cases remaining unconfirmed, and few viral genomes sequences available to date. Through the 2024/25 austral summer we undertook five sampling expeditions to the South Shetland Islands and Antarctic Peninsula facilitated by cruise ships/operators. Across more than 500 faecal environmental samples collected from apparently healthy penguins and marine mammals, we found no detectable evidence of HPAI H5N1. However, HPAI H5N1 was detected in all but one of the skua carcasses sampled, which, in most cases, were found within meters of penguin sub-colonies. All HPAI H5N1 viral genomes sequences from skuas on the Antarctic Peninsula fell within a single lineage, which included those genomes from skuas sampled in the 2024/25 season from the South Shetland Islands. Genomes were in a different clade to those from the Antarctic Peninsula collected in the 2023/24 austral summer. Our results confirm although the prevalence may be low, HPAI H5N1 is established in Antarctica, emphasizing the need for ongoing surveillance to monitor and mitigate threats to wildlife, even in the planets most isolated regions.

microbiology↗

bioRxiv2026

Short linear motifs - Unexplored players driving Toxoplasma gondii infection

Pathogens infect hosts by interacting with host proteins and exploiting their functions to their advantage. Short linear motifs, small functional regions within intrinsically disordered protein regions, are common mediators of host-pathogen protein interactions. While motifs have been more extensively studied in viruses and bacteria, the extent to which eukaryotic unicellular parasites use motifs during infection remains unexplored. Toxoplasma gondii is a widespread intracellular Apicomplexan parasite capable of infecting all warm-blooded animals and invading any of their nucleated cells. Toxoplasmas secreted proteins are key in interacting with host proteins during infection, making them potential sources for motifs. To highlight the role of motifs in Toxoplasma gondii infection, we curated 21 known motif instances in Toxoplasma proteins from the scientific literature. To identify more motifs in Toxoplasma secreted proteins, we developed a computational pipeline that annotates putative motif matches with structural and functional features. Through this approach, we identified a set of 24,291 motif matches in 295 secreted proteins. We highlight strategies for further prioritisation of likely functional motif matches by focusing on integrin motifs, degrons and TRAF6-binding motifs. We subjected four predicted TRAF6-binding motifs to experimental validation, supporting the predicted motifs in the Toxoplasma proteins RON10 and GRA15. Our motif predictions provide a valuable resource for generating hypotheses and designing experiments to study infection mechanisms. The characterisation of motifs in Toxoplasma will be key to understanding the molecular principles underlying its broad host range and more comprehensive Apicomplexan infection strategies. ImportanceToxoplasma gondii is a widely distributed intracellular parasite that achieves a successful infection by interacting with different host cell proteins. Short linear motifs are small functional modules found in unstructured protein regions and recognised by folded protein domains. Given that unstructured protein regions are a common feature of Toxoplasmas proteins, we hypothesise that motifs play important roles during its infection cycle. Here, we highlight the role of motifs during the Toxoplasma host cell invasion cycle through a curated set of motif examples. Through a computational pipeline, we predict thousands of motifs in secreted proteins, outline strategies for working with these predictions and finally experimentally test proteins containing a motif involved in the innate immune response, successfully showing the binding of two motifs. Our work provides a resource for further motif testing in Toxoplasma proteins, aiming at understanding the molecular mechanisms of its infection strategies and its broad host range.

bioinformatics↗

bioRxiv2025

Ovarian development is driven by early spatiotemporal priming of the coelomic epithelium

Ovarian organogenesis relies on the coordinated specification of supporting and steroidogenic lineages from multipotent coelomic epithelium (CE) progenitors. However, it remains unclear how ovarian cellular diversity arises and whether CE progenitors are fate-biased before or after ingression into the gonad. We show that CE cells in fetal mouse and human ovaries are transcriptionally heterogeneous and spatially organized into subdomains already primed toward supporting or steroidogenic identities. CE priming is dynamic, influenced by proximity to the mesonephros, with a transient coexistence of both progenitor types before resolution toward a predominantly supporting-biased CE. In mice, delamination of primed CE cells seeds intragonadal niches that generate pre-granulosa and steroidogenic progenitors. We further demonstrate that fetal steroidogenic progenitors give rise to adult stromal and theca cells, and that granulosa cells have a dual origin from CE-derived and supporting-like cells. Together, these findings reveal a conserved, spatially encoded program of ovarian lineage specification.

developmental biology↗

bioRxiv2022

Structural basis for tunable affinity and specificity of LxCxEdependentprotein interactions with the retinoblastoma protein family

The retinoblastoma protein (Rb) and its homologs p107 and p130 are critical regulators of gene expression during the cell cycle. Functional inactivation of Rb family proteins leads to loss of cell-cycle control and promotes genome instability and proliferation, which are hallmarks of cancer. Rb proteins share a structural domain, known as the "pocket domain", which mediates association with a large number of cellular proteins. A cleft in the pocket domain binds an LxCxE sequence motif in these proteins, many of which function with Rb proteins to co-regulate transcription during quiescence and G1. Proteins from oncogenic DNA viruses also bind this cleft to inactivate Rb family proteins, and the E7 protein from the human papillomavirus has been used as the primary model for understanding LxCxE motif interactions. Evidence presented previously and here demonstrates that the E7 sequence binds tighter and competes with cellular proteins for the LxCxE site, but the molecular basis for the relatively weak affinities of the cellular proteins has been poorly understood. Here, we present binding data and a series of crystal structures of the p107 pocket domain in complex with LxCxE peptides derived from the transcriptional co-repressor proteins HDAC1, ARI4DA, and EID1. The structures reveal determinants of protein binding beyond the L-C-E core that include the N and C-terminal sides of the LxCxE motif and the x (wild card) residues. Our results explain how differences in these interactions outside the L-C-E core result in weaker affinities of pocket protein for cellular LxCxE proteins compared to E7 and result in differences in Rb and p107 affinities for some LxCxE-containing sequences. Our study provides new insights into how Rb proteins bind their myriad of cell partners and lays the foundation for structure-based design of peptides that inhibit oncogenic viral protein interactions.

biochemistry↗

bioRxiv2021

Theta activity during encoding interacts with NREM sleep oscillations to predict memory generalization

Relatively little is known regarding the interaction between encoding-related neural activity and sleep-based memory consolidation. One suggestion is that a function of encoding-related theta power may be to tag memories for subsequent processing during sleep. This study aimed to extend previous work on the relationships between sleep spindles, slow oscillation-spindle coupling and task-related theta activity with a combined Deese-Roediger-McDermott (DRM) and nap paradigm. This allowed us to examine the influence of task- and sleep-related oscillatory activity on the recognition of both encoded list words and associative theme words. Thirty-three participants (29 females, mean age = 23.2 years) learned and recognised DRM lists separated by either a 2hr wake or sleep period. Mixed-effects modelling revealed the sleep condition endorsed more associative theme words and fewer list words in comparison to the wake group. Encoding-related theta power was also found to influence sleep spindle density, and this interaction was predictive of memory outcomes. The influence of encoding-related theta was specific to sleep spindle density, and did not appear to influence the strength of slow oscillation-spindle coupling as it relates to memory outcomes. The finding of interactions between wakeful and sleep oscillatory-related activity in promoting memory and learning has important implications for theoretical models of sleep-based memory consolidation.

neuroscience↗

bioRxiv2020

Divergent evolution of a protein-protein interaction revealed through ancestral sequence reconstruction and resurrection

The postsynaptic density extends across the postsynaptic dendritic spine with Discs large (DLG) as the most abundant scaffolding protein. DLG dynamically alters the structure of the postsynaptic density, thus controlling the function and distribution of specific receptors at the synapse. PDZ domains make up one of the most abundant protein interaction domain families in animals. One important interaction governing postsynaptic architecture is that between the PDZ3 domain from DLG and cysteine-rich interactor of PDZ3 (CRIPT). However, little is know regarding functional evolution of the PDZ3:CRIPT interaction. Here, we subjected PDZ3 and CRIPT to ancestral sequence reconstruction, resurrection and biophysical experiments. We show that the PDZ3:CRIPT interaction is an ancient interaction, which was present in the last common ancestor of Eukaryotes, and that high affinity is maintained in most extant animal phyla. However, affinity is low in nematodes and insects, raising questions about the physiological function of the interaction in species from these animal groups. Our findings demonstrate how an apparently established protein-protein interaction involved in cellular scaffolding in bilaterians can suddenly be subject to dynamic evolution including possible loss of function.

molecular biology↗

bioRxiv2018

Inducible Cooperation in a Synthetic Gut Bacterial Consortium Introduces Population Balance and Stability

In nature, microbes interact antagonistically, neutrally or beneficially. To shed light on the effects of positive interactions in microbial consortia we introduced metabolic dependencies and metabolite overproduction into four bacterial species. While antagonistic interactions govern the wildtype consortium behavior, the genetic modifications alleviated antagonistic interactions and resulted in beneficial interactions. Engineered cross-feeding increased population evenness, a component of ecological diversity, in different environments including in a more complex gnotobiotic mouse gut environment. Our findings suggest that metabolite cross-feeding could be used as a tool for intentionally shaping microbial consortia in complex environments.\n\nImportanceMicrobial communities are ubiquitous in nature. Bacterial consortia live in and on our body and in our environment and more recently, biotechnology is applying microbial consortia for bioproduction. As part of our body, bacterial consortia influence us in health and disease. Microbial consortia function is determined by its composition, which in turn is driven by the interactions between species. Further understanding of microbial interactions will help us deciphering how consortia function in complex environments and may enable us to modify microbial consortia for health and environmental benefits.

synthetic biology↗