Biology subjects

Doyle, L.

Publications and source records attributed to Doyle, L..

7 recordsLinked to original sources

bioRxiv2025

PglZ from Type I BREX phage defence systems is a metal-dependent nuclease that forms a sub-complex with BrxB

BREX (Bacteriophage Exclusion) systems, identified through shared identity with Pgl (Phage Growth Limitation) systems, are a widespread, highly diverse group of phage defence systems found throughout bacteria and archaea. The varied BREX Types harbour multiple protein subunits (between four and eight) and all encode a conserved putative phosphatase (PglZ aka BrxZ) and an equally conserved, putative ATPase (BrxC). Almost all BREX systems also contain a site-specific methyltransferase (PglX aka BrxX). Despite having determined the structure and fundamental biophysical and biochemical behaviours for the PglX methyltransferase, the BrxL effector, the BrxA DNA-binding protein and the BrxR transcriptional regulator, the mechanism by which BREX impedes phage replication remains largely undetermined. In this study, we identify a stable BREX sub-complex of PglZ:BrxB, validate the structure and dynamic behaviour of that sub-complex, and assess the biochemical activity of PglZ, revealing it to be a metal-dependent nuclease. PglZ can cleave cyclic oligonucleotides, linear oligonucleotides, plasmid DNA and both non-modified and modified linear phage genomes. PglZ nuclease activity has no obvious role in BREX-dependent methylation, but does contribute to BREX phage defence. BrxB binding does not impact PglZ nuclease activity. These data contribute to our growing understanding of the BREX phage defence mechanism.

biochemistry↗

bioRxiv2025

Control of stress-activated Cdc42 dynamics by the MAP kinase Sty1-NDR kinase Orb6 regulatory axis

Cdc42 is a Rho-family GTPase that controls cell polarization from yeast to human cells. In fission yeast, under normal growth conditions, Cdc42-GTP oscillates between cell tips to promote polarized growth. However, when exposed to environmental stressors, Cdc42 adopts an "exploratory" pattern of Cdc42 activation along the cell membrane. This pattern also occurs when the NDR kinase Orb6 is downregulated. Here, we describe the molecular mechanism behind the emergence of exploratory Cdc42 dynamics and identify a new substrate of Orb6 kinase, the Cdc42 GAP Rga3. Additionally, we show that MAP kinase Sty1, known for linking stress signals to the Cdc42 polarity module, negatively regulates Orb6 kinase. During nutritional stress, activation of Sty1 and inactivation of Orb6 are associated with chronological lifespan extension. Our findings reveal a novel mechanism controlling cell morphology during stress, with important implications for cell survival.

cell biology↗

bioRxiv2023

Synergistic activity of IL-2 mutein with tolerogenic ImmTOR nanoparticles leads to massive expansion of antigen-specific Tregs and protection against autoimmune disease

Low dose IL-2 therapy and IL-2 molecules engineered to be selective for the high affinity IL-2 receptor have been shown to expand Tregs in vivo, and, in the case of low dose IL-2 therapy, has demonstrated promising therapeutic benefit in autoimmune diseases. One of the potential limitations of IL-2 therapy is the nonselective expansion of pre-existing Treg populations rather than induction of antigen-specific Tregs, as well as potential activation of effector cells. We have recently developed biodegradable nanoparticles encapsulating rapamycin, called ImmTOR, to induce selective immune tolerance to co-administered antigens, such as immunogenic biologic drugs. Unlike Treg-selective IL-2 therapy, ImmTOR alone does not increase total Treg numbers. However, here we demonstrate that the combination of ImmTOR and an engineered Treg-selective IL-2 variant (termed IL-2 mutein) increases the number and durability of total Tregs, as well as inducing a profound synergistic increase in antigen-specific Treg when combined with a target antigen. We demonstrate that the combination of ImmTOR and an IL-2 mutein leads to durable inhibition of antibody responses to co-administered AAV gene therapy capsid, even at sub-optimal doses of ImmTOR, and provides protection in autoimmune models of type 1 diabetes and primary biliary cholangitis. ImmTOR also showed the potential to increase the therapeutic window of engineered IL-2 molecules by mitigating effector T cell expansion typically observed at higher doses of IL-2 and preventing exacerbation of disease in a model of graft-versus-host-disease. At the same time, engineered IL-2 molecules showed potential for dose-sparing of ImmTOR. Overall, these results establish that the combination of ImmTOR and an IL-2 mutein show synergistic benefit on both safety and efficacy to provide durable antigen-specific immune tolerance to mitigate drug immunogenicity and to treat autoimmune diseases.

immunology↗

bioRxiv2023

Interactive Bioacoustic Playback as a Tool for Detecting and Exploring Nonhuman Intelligence: Conversing with an Alaskan Humpback Whale

Here we report on a rare and opportunistic acoustic "conversation" with an adult female humpback whale, known as Twain, in Southeast Alaska. Post hoc acoustic and statistical analyses of a 20-minute acoustic exchange between the broadcast of a recorded contact call, known as a whup/throp, with call responses by Twain revealed an intentional human-whale acoustic (and behavioral) interaction. Our results show that Twain participated both physically and acoustically in three phases of interaction (Phase 1: Engagement, Phase 2: Agitation, Phase 3: Disengagement), independently determined by blind observers reporting on surface behavior and respiratory activity of the interacting whale. A close examination of both changes to the latency between Twains calls and the temporal matching to the latency of the exemplar across phases indicated that Twain was actively engaged in the exchange during Phase 1 (Engagement), less so during Phase 2 (Agitation), and disengaged during Phase 3 (Disengagement). These results, while preliminary, point to several key considerations for effective playback design, namely the importance of salient, dynamic and adaptive playbacks, that should be utilized in experimentation with whales and other intelligent nonhuman species.

animal behavior and cognition↗

bioRxiv2021

Using Conspecific Playbacks to Investigate Contact Calling in Southeast Alaskan Humpback Whales

Humpback whales (Megaptera novaeangliae) produce calls across age and sex class and throughout their migratory range. Despite growing interest in calling behavior, the function of most calls is unknown. Among identified call types, the whup is ubiquitous, and innate, and may serve as a contact call. We conducted an acoustic playback experiment combined with passive acoustic monitoring and visual observations to test the function of the whup on a Southeast Alaskan foraging ground. Using a before-during-after design, we broadcasted either a control sound or a unique whup call sequence. We investigated the change in whup rates (whups/whale/10 minutes) in response to treatment (whup or control) and period (before, during, or after). In 100% of the conspecific trials, whup rates increased during broadcasts, and whup rates were significantly higher than in before or after periods. There was no significant difference in whup rates between before and after periods during conspecific trials. In control trials, there were no significant differences in whup rates between before, during, or after periods. Neither whups nor control playbacks elicited an approach response. Humpback whale vocal responses to whup playbacks suggest that whups function as a contact call, but not necessarily as an aggregation signal.

animal behavior and cognition↗

bioRxiv2019

Parcellation of the cortex using Surface-based Melbourne Children's Regional Infant Brain atlases (M-CRIB-S)

BackgroundLongitudinal studies of cortical morphology are best facilitated by parcellation schemes that are compatible across all life stages. Until recently, neonatal atlases derived strictly from neonatal data, rather than warping brain labels from an adult atlas, did not exist. The Melbourne Childrens Regional Infant Brain (M-CRIB) and M-CRIB 2.0 atlases now provide voxel-based parcellations of the cerebral cortex within T2-weighted neonatal images. These atlases are compatible with the Desikan-Killiany (DK) and the Desikan-Killiany-Tourville (DKT) cortical labelling schemes commonly used for older children and adults. However, there is still a need for a surface-based approach for parcellating neonatal images using these atlases. AimsWe aimed to introduce surface-based versions of the M-CRIB and M-CRIB 2.0 atlases, termed M-CRIB-S(DK) and M-CRIB-S(DKT), along with a pipeline for automated parcellation with FreeSurfer tools. We also aimed to evaluate the automated parcellation accuracy of our M-CRIB-S atlases using cross-validation with manually labelled data; and to evaluate accuracy of the proposed automated parcellation pipeline for the M-CRIB-S labels against the publicly available surface-based University of North Carolina (UNC) 4D neonatal atlas, which has labels derived from the DK adult atlas. MethodsUsing datasets of 10 M-CRIB or M-CRIB 2.0 manually labelled ground truth images and 48 unlabelled T2-weighted magnetic resonance images (MRI) of healthy neonates, cortical surfaces were extracted using the Deformable module within MIRTK. Cortical regions from the labelled images were encoded into a spherical template space using FreeSurfer tools wherein M-CRIB-S(DK) and M-CRIB-S(DKT) atlases were constructed. Automatic parcellation of the labelled and unlabelled (L+U) images (n=58) using the M-CRIB-S(DK) and M-CRIB-S(DKT) atlases were computed with Bayesian labelling using FreeSurfer tools. Accuracy was assessed by comparison with manually labelled ground truth data (n=10) using Dice coefficients and within a Leave-One-Out (LOO) cross-validation framework. Agreement of the UNC atlas parcellations with manual M-CRIB labelling was also evaluated using Dice coefficients. ResultsWhen comparing automated parcellations from the M-CRIB-S atlases to manual labels, disagreements were mostly closely confined to region boundaries, suggesting high overlap overall. Quantitatively, average regional Dice coefficients were 0.88 (L+U) and 0.83 (LOO) for the M-CRIB 2.0 labels and 0.87 (L+U), 0.80 (LOO) for the M-CRIB labels, and 0.67 for the UNC atlas. ConclusionsThe M-CRIB-S atlases and automatic pipeline described in this paper allow infant cortical surfaces to be accurately parcellated according to the DK or DKT parcellation schemes. This will help facilitate surface-based investigations of brain function at the neonatal time point, and potentially longitudinally across the lifespan. The use of M-CRIB-S outperformed a technique that relies on an adult-derived atlas. The atlases, averaged white, inflated, pial and spherical surfaces, along with customised scripts for segmentation, cortical surface extraction and parcellation, are available for public download.

neuroscience↗

bioRxiv2017

Extracellular Electron Transfer Powers Enterococcus faecalis Biofilm Metabolism

Enterococci are important human commensals and significant opportunistic pathogens associated with endocarditis, urinary tract infections, wound and surgical site infections, and medical device associated infections. These infections often become chronic upon the formation of biofilm. The biofilm matrix establishes properties that distinguish this state from free-living bacterial cells and increase tolerance to antimicrobial interventions. The metabolic versatility of the Enterococci is reflected in the diversity and complexity of environments and communities in which they thrive. Understanding metabolic factors governing colonization and persistence in different host niches can reveal factors influencing the transition from commensal to opportunistic pathogen. Here, we report a new form of iron-dependent metabolism for Enterococcus faecalis where, in the absence of heme, respiration components can be utilised for extracellular electron transfer (EET). Iron augments E. faecalis biofilm growth and generates alterations in biofilm matrix, cell spatial distribution, and biofilm matrix properties. We identify the genes involved in iron-augmented biofilm growth and show that it occurs by promoting EET to iron within biofilm.\n\nSignificanceBacterial metabolic versatility is often key in dictating the outcome of host-pathogen interactions, yet determinants of metabolic shifts are difficult to resolve. The bacterial biofilm matrix provides the structural and functional support that distinguishes this state from free-living bacterial cells. Here, we show that the biofilm matrix provides access to resources necessary for metabolism and growth which are otherwise inaccessible in the planktonic state. Our data shows that in the absence of heme, components of Enterococcus faecalis respiration (l-lactate dehydrogenase and acetaldehyde dehydrogenase) may function as initiators of EET through the cytoplasmic membrane quinone pool and utilize matrix-associated iron to carry out EET. The presence of iron resources within the biofilm matrix leads to enhanced biofilm growth.

microbiology↗