Biology subjects

Brooks, A. J.

Publications and source records attributed to Brooks, A. J..

4 recordsLinked to original sources

bioRxiv2026

Tracking demographic changes in individual coral colonies through repeated photogrammetric surveys

Understanding the consequences of global change for our ecosystems requires reliable, accurate, and scalable tools for detecting ecological change. To this end, recent efforts have focused on scaling up the quantification of demographic processes from individual organisms (the fundamental ecological unit) to the larger spatial scales they inhabit to yield more precise and informative estimations of ecological change, especially in response to disturbance. Here, we describe a transferable workflow that combines robust underwater photogrammetry techniques with machine-learning-assisted image analysis to quantify demographic changes in coral colonies (growth, stasis, partial mortality, and complete mortality) through time on the reef landscape. We then demonstrate several analytical applications of this workflow that can be broadly applied to sessile and/or clonal organisms in other ecosystems. First, we tracked the fates of 3,162 coral colonies through a marine heatwave that caused substantial mortality. Second, our approach enabled detection of size- and taxon-dependent patterns in demographic changes from before to after the heatwave. Finally, for a subset (425) of these colonies, we further demonstrated how our method can be used to track fates across multiple years, including a year of change before and after the heatwave took place, revealing nuanced patterns of survival and mortality, as well as changes in size structure that occurred before and after the disturbance. Our workflow offers an important advance for increasing the accuracy of change detection on coral reefs and other ecosystems by linking demographic changes in individual organisms with spatially extensive image-based surveys through time.

ecology↗

bioRxiv2026

Heat Waves Promote, but Cyclones Reverse, Coral-to-Seaweed Regime Shifts by Reshaping Reef Resilience

Disturbances alter ecosystem resilience by killing organisms and leaving behind material legacies. We tested how material legacies from marine heat waves and cyclones govern transitions between coral- and seaweed-rich states on tropical reefs. Heat waves kill coral tissue but leave their skeletons to erode gradually, whereas cyclones scour away emergent biota. Field experiments revealed that dead skeletons protect seaweeds from herbivory, catalyzing a transition to a seaweed-rich state that becomes self-sustaining after skeletons disappear. After four years, 73% of skeleton-added (heat wave) plots transitioned to seaweeds compared to 0% of scoured (cyclone) plots that lacked skeletons, while 87% of seaweed-rich plots scoured to simulate a cyclone stayed seaweed-free. Reef trajectories after natural disturbances were similar: four years after heat wave-induced coral mortality, 63% of time-series plots had transitioned to seaweeds with none recovering to coral; four years after a cyclone removed skeletons from a prior disturbance, none had transitioned to seaweeds and 60% had returned to coral. A disturbance not only can displace an ecosystem state, it can rapidly reshape the resilience landscape through the material legacies it creates or removes. Our findings also show that successive disturbances need not have cumulative negative effects: after a reef is driven into a seaweed-rich state, a cyclone can act as a rescue disturbance by removing established seaweeds and, when structural refugia are also removed, shrinking the seaweed stability domain. By reshaping resilience through contrasting material legacies, disturbance type and sequence can be as important as frequency and severity in determining ecosystem trajectories.

ecology↗

bioRxiv2023

Location, Location, Location: Protein kinase nanoclustering for optimized signalling output

Protein kinases (PKs) are proteins at the core of cellular signalling and are thereby responsible for most of the cellular physiological processes and their regulations. As for all cellular proteins, they are subjected to Brownian thermal energy that tends to homogenise their distribution throughout the volume of the cell. To access their substrates and perform their critical functions, PKs localisation is therefore tightly regulated in space and time, relying upon a range of clustering mechanisms. These include post-translational modifications, protein-protein and protein-lipid interactions as well as liquid-liquid phase separation, allowing spatial restriction and ultimately regulating access to their substrates. In this review, we will mainly focus on key mechanisms mediating PK nanoclustering in physiological and pathophysiological processes. We propose that PK nanoclusters act as a cellular unit of signalling output capable of integration and regulation in space and time. We will specifically outline the various super-resolution microscopy approaches currently used to elucidate the mechanisms driving PK nanoscale clustering and explore the pathological consequences of altered kinase clustering in the context of neurodegenerative disorders, inflammation, and cancer.

neuroscience↗

bioRxiv2020

Identification of HIV-Transmitting Sub-Epithelial Mononuclear Phagocytes in Human Anogenital and Colorectal Tissues

Tissue mononuclear phagocytes (MNP) are specialised in pathogen detection and antigen presentation. They are the first cells of the immune system to encounter HIV and play a key role in transmission as they deliver the virus to CD4 T cells, which are the primary HIV target cell in which the virus undergoes replication. Most studies have investigated the role that epithelial MNPs play in HIV transmission but, as mucosal trauma and inflammation are strongly associated with HIV transmission, it is also important to examine the role that sub-epithelial MNPs play. Sub-epithelial MNPs are present in a diverse array of subsets which differ in their function and the pathogens they detect. Understanding how specific subsets interact with HIV and deliver the virus to CD4 T cells is therefore of key importance to vaccine and microbicide development. In this study we have shown that, after topical application, HIV can penetrate to interact with sub-epithelial resident myeloid cells in anogenital explants and defined the full array of MNP subsets that are present in all the human anogenital and colorectal sub-epithelial tissues that HIV may encounter during sexual transmission. In doing so we have identified two subsets that preferentially take up HIV, become infected and transmit the virus to CD4 T cells; CD14+CD1c+CD11c+ monocyte-derived dendritic cells and langerin-expressing dendritic cells 2 (DC2).

immunology↗