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Biology subjects

Richards, C.

Publications and source records attributed to Richards, C..

At least 19 recordsLinked to original sources

Tripartite toxin-antitoxin system regulates the production and release of pneumolysin by Streptococcus pneumoniae.

The production of toxins is critical to the success of bacteria, with their targets and outcomes varying widely. Pneumolysin (Ply), produced by the major human pathogen Streptococcus pneumoniae, is a cytolytic pore forming toxin that plays many diverse roles including inducing tissue damage and inflammation, evasion of many aspects of the human immune system, invasion of the bacteria into deeper tissue, and transmission to new hosts. Despite its importance, many aspects of the biology of this toxin have to date remained unknown, in particular, what role of the three other genes that form part of the ply operon play in Ply production. Here we demonstrate that these genes encode a complex regulatory system, that includes a putative membrane destabilising protein (PlyA) and a MazEF-like toxin-antitoxin system (PlyB and PlyC), the toxin of which (PlyC) destabilises the Ply transcript. We propose a tripartite model whereby when the operon reaches relatively high levels of expression PlyA destabilises the S. pneumoniae membrane creating a stress that triggers a necessary negative feedback loop which results in the degradation of the PlyB antitoxin, release of the PlyC toxin and degradation of the ply transcript, thereby providing a means by which Ply production can be tightly regulated. Given the importance of Ply to the ability of S. pneumoniae to cause infection, identifying the factors that result in the shutdown of Ply production and release by the bacteria would seem promising target for future therapeutic strategies.

microbiology↗

MEMBRANE PORES ACT AS SELF-RESEALING LIPID SCRAMBLASES

Biological membranes continuously experience leaflet lipid imbalances during growth, lipid synthesis, and vesicle fusion. To alleviate such imbalances and prevent these asymmetries from compromising membrane integrity, cells rely on lipid scramblases - fast and non-specific lipid channel proteins. Here we show that lipid number asymmetry alone is sufficient to drive spontaneous formation of transient hydrophilic pores that function as self-resealing lipid scramblases. Using giant unilamellar vesicles, living cells, and coarse-grained molecular dynamics simulations, we demonstrate that fusion-induced excess lipids in one leaflet lowers membrane edge tension, generating size-selective pores whose size and lifetime scale with the magnitude of asymmetry. Below a critical threshold, these pores reseal spontaneously; above it, membranes collapse. Strikingly, pore opening enables rapid, non-selective lipid translocation between leaflets, dissipating the asymmetry that nucleates the pore and thereby promoting their own closure. Cholesterol buffers moderate imbalances through spontaneous flip flop before pore formation, whereas pore-mediated lipid scrambling relieves the remaining asymmetry and restores cholesterols initial distribution. Our findings identify transient lipid pores as an intrinsic, protein-independent mechanism that couples membrane destabilization to self-repair, providing a universal physical principle for membrane homeostasis during growth, remodelling, and early cellular evolution.

biophysics↗

The Effect of Vaccination on the Evolution of the SARS-CoV-2 B.1.351 Variant

Since the initial distribution of the SARS-CoV-19 vaccine, its widespread use has been hypothesized to act as a selective pressure that drives the COVID-19 virus to mutate. This study aims to investigate the correlation between global vaccination rates and the mutation rate of the SARS-CoV-2 Beta variant (B.1.351). From January to July 2021, nucleotide diversity increased in tandem with vaccination rates, demonstrating that the virus evolved more rapidly in response to selective pressure from mass vaccination. Statistical analysis revealed statistically significant positive correlations between both vaccination rates and vaccine doses administered with nucleotide diversity. Thus, our findings indicate a positive correlation between rising vaccination rates and nucleotide diversity, suggesting that increased vaccination coverage acted as a selective pressure that accelerated viral evolution of SARS CoV2.

molecular biology↗

The effect of the number motor units and their maximum firing rate in a musculoskeletal model of human reaching

Vertebrate muscle has two features which heavily influence its force generation characteristics: rate-coded control and the division of muscles into multiple motor units (MUs). Studying how these features affect functional outcomes is difficult in vivo, but also in silico due to scarcity of modelling frameworks integrating rate-coded MU pool models with musculoskeletal models for functional tasks. We implement a human upper limb reaching model with muscles consisting of multiple rate-coded MUs and demonstrate its ability to generate accurate reaching movements under online control. Using this model, we investigate how reaching performance is influenced by two key features of MU pools, the number of MUs and their maximum firing rates. Our simulations suggest that very small MU pools with low firing rates tend to produce less accurate reaching movements compared to larger pools with higher firing rates. Increasing either the size of the pool or the maximum firing rate generally improves performance, but benefits become negligible beyond about 10-20 MUs and firing rates of 25-50 Hz. This pattern holds for the entire workspace but targets on the distal boundaries appear more sensitive to MU pool properties. Hence, our results indicate that rate coding and MU properties may play a part in determining functional outcomes in a task- and MU pool-dependent manner.

bioengineering↗

Phenotypic plasticity of invasive knotweed across Europe: a distributed common garden experiment

O_LIBiological invasions expose populations of introduced species to strong selection forces in abiotic and biotic factors, which is expected to lead to adaptive differentiation of populations, particularly for large-scale invaders. C_LIO_LITo better understand population differentiation and phenotypic plasticity of invasive Japanese knotweed (Reynoutria japonica) in Europe, we compared the performance of 45 European knotweed populations, collected across a 2000 km latitudinal transect, in three common gardens with contrasting climatic conditions, one at the southern edge, one in the center, and one at the northern edge of the species European distribution. C_LIO_LIThe plants exhibited strong phenotypic plasticity across the three gardens, with a more acquisitive growth strategy in the southern garden, and a more conservative strategy and change of architecture in the climatically unfavorable north. Although we observed phenotypic selection on several leaf traits, and on the plasticity of leaf thickness, with some selection differences between the gardens, there was little evidence of population differentiation, and none for local adaptation. Only for plant architecture (shrubbiness), we detected heritable population variation in trait means and plasticity. However, variation in plasticity was unrelated to climatic variability of origin, and to plant fitness. C_LIO_LISynthesis. Our results suggest that evolutionary processes - local adaptation and evolution of plasticity - did not play a key role in the success of Japanese knotweed in Europe. Instead, its high baseline plasticity appears to be the key factor that makes it such a strong invader across a broad range of environments. C_LI

ecology↗

Visualising joint force-velocity properties in musculoskeletal models

Musculoskeletal modelling opens windows into how muscle properties interact with neural control to govern movement. Though musculoskeletal models produce vast computational data, they lack a visual language which compactly communicates how joint dynamics relate to time-varying muscle activation, force and length change. We developed a novel representation of joint-level force-velocity (joint-FV) properties which shows how agonist and antagonist muscles contribute to overall joint state and its trajectory throughout a movement. Using a model of human goal-directed reaching, we used joint-FV visualisations to discern the salient joint dynamic features across joints and between different reach targets. Regardless of target, we found that the shoulder, elbow and wrist joints traversed a near circular trajectory through joint-FV space when muscle forces were dominant, but trajectories were more complex when joint-interaction forces dominated (i.e. cross-joint forces due to Coriolis, Euler and centrifugal effects). Additionally, we found that co-contraction steepens the instantaneous slope of the instantaneous joint-fv curve causing damping which helps stabilise against small perturbations. We therefore propose that our joint-FV visualisation can be used to explain the intricate features seen in musculoskeletal simulation data to reveal how intrinsic muscle properties govern the behaviour of dynamical systems.

bioengineering↗

Commensal-derived Trehalose Monocorynomycolate Triggers γδ T Cell-driven Protective Ocular Barrier Immunity

Commensals shape host physiology through molecular crosstalk with host receptors. Identifying specific microbial factors that causally influence host immunity is key to understanding homeostasis at the host-microbe interface and advancing microbial-based therapeutics. Here, we identify trehalose monocorynomycolate (TMCM) from Corynebacterium mastitidis (C. mast) as a potent stimulator of IL-17 production by {gamma}{delta} T cells at the ocular surface. Mechanistically, TMCM-driven IL-17 responses require both IL-1 signals and {gamma}{delta} TCR signaling, which also supports endogenous {gamma}{delta} T cell IL-1R1 expression. Notably, synthetic TMCM alone is sufficient to mimic the effect of C. mast in inducing {gamma}{delta} T cell immunity and protect against pathogenic corneal infection. Our findings establish TMCM as a key mediator of commensal-driven immune defense, highlighting its potential as a {gamma}{delta} T cell adjuvant and a microbiome-informed therapeutic to enhance IL-17-driven protection at barrier sites such as the ocular surface. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/643820v1_ufig1.gif" ALT="Figure 1"> View larger version (68K): org.highwire.dtl.DTLVardef@63139forg.highwire.dtl.DTLVardef@9d6978org.highwire.dtl.DTLVardef@775e37org.highwire.dtl.DTLVardef@ca84b6_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LICorynomycolates enable ocular C. mast colonization and protective IL-17 immunity C_LIO_LITMCM drives IL-17 from {gamma}{delta} T cells through TCR and IL-1R signaling C_LIO_LI{gamma}{delta} TCR signaling maintains the expression of endogenous IL-1R1 C_LIO_LISynthetic TMCM mimics the ability of C. mast to induce {gamma}{delta} T cell immunity in the eye C_LIO_LITMCM protects against P. aeruginosa keratitis, highlighting its therapeutic potential C_LI

immunology↗

Oral dosing of the nucleoside analog obeldesivir is efficacious against RSV infection in African green monkeys

Respiratory syncytial virus (RSV) is a significant cause of morbidity and mortality in high-risk populations. Although prophylactic options are available, there are no effective oral therapeutics for RSV infection. Obeldesivir (ODV) is an orally bioavailable prodrug of the nucleoside analog GS-441524, which is converted intracellularly to its active nucleoside triphosphate and inhibits the RSV RNA polymerase. Here we report the potent antiviral activity of ODV against geographically and temporally diverse RSV A and B clinical isolates (EC50: 0.20-0.66 M). Resistance selection studies with ODV and GS-441524 against RSV identified a single amino acid substitution, I777L, in the L polymerase with reduced susceptibility (3.3-3.8-fold) to ODV and GS-441524, indicating a high barrier for resistance development. In an African green monkey RSV infection model, once-daily oral ODV doses of 30 or 90 mg/kg initiated [~]24 hours post-infection significantly reduced log10 viral RNA copies/mLxday area under the curve by 69-92% in the upper and lower respiratory tracts. Together, these preclinical data support the clinical evaluation of ODV for the treatment of RSV infection.

microbiology↗

A histomorphological atlas of resected mesothelioma from 3446 whole-slide images discovered by self-supervised learning

1Mesothelioma is a highly lethal and poorly biologically understood disease which presents diagnostic challenges due to its morphological complexity. This study uses self-supervised AI (Artificial Intelligence) to map the histomorphological landscape of the disease. The resulting atlas consists of recurrent patterns identified from 3446 Hematoxylin and Eosin (H&E) stained images scanned from resected tumour slides. These patterns generate highly interpretable predictions, achieving state-of-the-art performance with 0.65 concordance index (c-index) for outcomes and 88% AUC in subtyping. Their clinical relevance is endorsed by comprehensive human pathological assessment. Furthermore, we characterise the molecular underpinnings of these diverse, meaningful, predictive patterns. Our approach both improves diagnosis and deepens our understanding of mesothelioma biology, highlighting the power of this self-learning method in clinical applications and scientific discovery.

pathology↗

Matching dynamically varying forces with multi-motor-unit muscle models: A simulation study

Human muscles exhibit great versatility, not only generating forces for demanding athleticism, but also for fine motor tasks. While standard musculoskeletal models may reproduce this versatility, they often lack multiple motor units (MUs) and rate-coded control. To investigate how these features affect a muscles ability to generate desired force profiles, we performed simulations with nine alternative MU pool models for two cases: 1) a tibialis anterior muscle generating an isometric trapezoidal force profile, and 2) a generic shoulder muscle generating force for a reaching movement whilst undergoing predetermined length changes. We implemented two control strategies, pure feedforward and combined feedforward-feedback, each parameterised using elementary tasks. The results suggest that the characteristics of MU pools have relatively little impact on the pools overall ability to match forces across all tasks, although performances for individual tasks varied. Feedback improved performance for nearly all MU pools and tasks, but the physiologically more relevant MU pool types were more responsive to feedback particularly during reaching. While all MU pool models performed well in the conditions tested, we highlight the need to consider the functional characteristics of the control of rate-coded MU pools given the vast repertoire of dynamic tasks performed by muscles.

physiology↗

The impact of paediatric epilepsy and co-occurring neurodevelopmental disorders on functional brain networks in wake and sleep

Epilepsy is one of the most common neurological disorders in children. Diagnosing epilepsy in children can be very challenging, especially as it often coexists with neurodevelopmental conditions like autism and ADHD. Functional brain networks obtained from neuroimaging and electrophysiological data in wakefulness and sleep have been shown to contain signatures of neurological disorders, and can potentially support the diagnosis and management of co-occurring neurodevelopmental conditions. In this work, we use electroencephalography (EEG) recordings from children, in restful wakefulness and sleep, to extract functional connectivity networks in different frequency bands. We explore the relationship of these networks with epilepsy diagnosis and with measures of neurodevelopmental traits, obtained from questionnaires used as screening tools for autism and ADHD. We explore differences in network markers between children with and without epilepsy in wake and sleep, and quantify the correlation between such markers and measures of neurodevelopmental traits. Our findings highlight the importance of considering the interplay between epilepsy and neurodevelopmental traits when exploring network markers of epilepsy.

neuroscience↗

Evolution of a fatty acyl-CoA elongase underlies desert adaptation in Drosophila

To survive in extreme environments such as hot-arid deserts, desert-dwelling species have evolved physiological traits to withstand the high temperatures and low aridity beyond the physiologically tolerable ranges of most species. Such traits which include reducing water loss have independently evolved in multiple taxa. However, the genetic and evolutionary mechanisms underlying these traits have thus far not been elucidated. Here we show that Drosophila mojavensis, a fruitfly species endemic to the Sonoran and Mojave deserts, had evolved extremely high desiccation resistance, by producing very long chained methylbranched cuticular hydrocarbons (mbCHCs) that contributes to a cuticular waterproofing lipid layer reducing water loss. We show that the ability to synthesize these longer mbCHCs is due to evolutionary changes in a fatty acyl-CoA elongase (mElo). CRISPR/Cas9 knockout of mElo in D. mojavensis led to loss of longer mbCHC production and significant reduction of desiccation resistance at high temperatures but did not affect mortality at high temperatures or desiccating conditions individually, indicating that this gene is crucial for desert adaptation. Phylogenetic analysis showed that mElo is a Drosophila specific gene with no clear ortholog outside Diptera. This suggests that while the physiological mechanisms underlying desert adaptation are general, the genetic mechanisms may be lineage-specific.

evolutionary biology↗

Individual variability in neural event segmentation reflects stimulus content and interpretation

Event segmentation is a spontaneous part of perception, important for processing continuous information and organizing it into memory. While neural and behavioral event segmentation show a degree of inter-subject consistency, meaningful individual variability exists atop these shared patterns. Here we characterized individual differences in the location of neural event boundaries across four short movies that evoked variable interpretations. Event boundary alignment across subjects followed a posterior-to-anterior gradient that was tightly correlated with the rate of segmentation: slower-segmenting regions that integrate information over longer time periods showed more individual variability in boundary locations. This relationship held irrespective of the stimulus, but the degree to which boundaries in particular regions were shared versus idiosyncratic depended on certain aspects of movie content. Furthermore, this variability was behaviorally significant in that similarity of neural boundary locations during movie-watching predicted similarity in how the movie was ultimately remembered and appraised. In particular, we identified a subset of regions in which neural boundary locations are both aligned with behavioral boundaries during encoding and predictive of stimulus interpretation, suggesting that event segmentation may be a mechanism by which narratives generate variable memories and appraisals of stimuli.

neuroscience↗

Desiccation resistance differences in Drosophila species can be largely explained by variations in cuticular hydrocarbons

Maintaining water balance is a universal challenge for organisms living in terrestrial environments, especially for insects, which have essential roles in our ecosystem. Although the high surface area to volume ratio in insects makes them vulnerable to water loss, insects have evolved different levels of desiccation resistance to adapt to diverse environments. To withstand desiccation, insects use a lipid layer called cuticular hydrocarbons (CHCs) to reduce water evaporation from the body surface. It has long been hypothesized that the waterproofing capability of this CHC layer, which can confer different levels of desiccation resistance, depends on its chemical composition. However, it is unknown which CHC components are important contributors to desiccation resistance and how these components can determine differences in desiccation resistance. In this study, we used machine learning algorithms, correlation analyses, and synthetic CHCs to investigate how different CHC components affect desiccation resistance in 50 Drosophila and related species. We showed that desiccation resistance differences across these species can be largely explained by variation in cuticular hydrocarbons. In particular, length variation in a subset of CHCs, the methyl-branched CHCs (mbCHCs), is a key determinant of desiccation resistance. We also showed a significant correlation between the evolution of longer mbCHCs and higher desiccation resistance. Given the ubiquitous presence of mbCHCs in insects, the evolution of mbCHCs may be a general mechanism of how insects evolve desiccation resistance and adapt to diverse and changing environments. SignificanceAs our planet is becoming more arid due to global warming, preventing dehydration is key to the survival of insects, an essential part of our ecosystem. However, factors that determine how insects may evolve resistance to desiccation are relatively unknown. Using Drosophila species from diverse habitats, we showed that variations in the composition of cuticular hydrocarbons (CHCs), a hydrophobic layer found on insects to prevent evaporative water loss, can largely explain desiccation resistance differences. In addition, the evolution of longer methyl-branched CHCs (mbCHCs), underlies the evolution of higher desiccation resistance in this genus. As mbCHCs are ubiquitously present in most insects, we suggest that evolutionary changes in mbCHCs may be a general determinant of desiccation resistance across insect species.

evolutionary biology↗

Response to nitrogen and salinity in Rhizophora mangle propagules varies by maternal family and population of origin

Many coastal foundation plant species thrive across a range of environmental conditions, often displaying dramatic phenotypic variation in response to environmental variation. We characterized the response of propagules from six populations of the foundation species Rhizophora mangle L. to full factorial combinations of two levels of salt (15 ppt and 45 ppt) reflecting the range of salinity measured in the field populations, and two levels of nitrogen (N; no addition and amended at approximately 3 mg N per pot each week) equivalent to comparing ambient N to a rate of addition of 75 kg per hectare per year. The response to increasing salt included significant plasticity in succulence. Propagules also showed plasticity in maximum photosynthetic rate in response to N amendment, but the responses depended on the level of salt and varied by population of origin. Generally, survival was lower in high salt and high N, but the impact varied among populations. Overall, this study revealed significant phenotypic plasticity in response to salt and N level. Propagules from different populations differed in all traits measured. Variation in phenotypic plasticity and propagule survival in R. mangle may contribute to adaptation to a complex mosaic of environmental conditions and response to climate change.

ecology↗

Purinoreceptors and ectonucleotidases control ATP-induced calcium waveforms and calcium-dependent responses in microglia

1Adenosine triphosphate (ATP) drives microglia motility and cytokine production by activating P2X- and P2Y- class purinergic receptors with extracellular ATP and its metabolites. Purinergic receptor activation gives rise to diverse intracellular Ca2+ signals, or waveforms, that differ in amplitude, duration, and frequency. Whether and how these diverse waveforms influence microglia function is not well established. We developed a computational model trained with published primary murine microglia studies. We simulate how purinoreceptors influence Ca2+ signaling and migration and how purinoreceptor expression modifies these processes. Our simulation confirmed that P2 receptors encode the amplitude and duration of the ATP-induced calcium waveforms. Our simulations also implicate CD39, an ectonucleotidase that rapidly degrades ATP, as a regulator of purinergic receptor-induced Ca2+ responses. We, therefore, next evaluated how purinoreceptors and ectonucleotidase work in tandem. Our modeling results indicate that small transients are sufficient to promote motility, while large and sustained transients are needed for cytokine responses. Lastly, we predict how these phenotypical responses vary in a BV2 microglia cell line using published P2 receptor mRNA data to illustrate how our computer model can be extrapolated to diverse microglia subtypes. These findings provide important insights into how differences in purinergic receptor expression influence the microglias responses to ATP.

physiology↗

Species' traits and exposure as a future lens for quantifying seabird bycatch vulnerability in global fisheries

Fisheries bycatch, the incidental mortality of non-target species, is a global threat to seabirds and a major driver of their declines worldwide. Identifying the most vulnerable species is core to developing sustainable fisheries management strategies that aim to improve conservation outcomes. To advance this goal, we present a preliminary vulnerability framework that integrates dimensions of species exposure, sensitivity, and adaptive capacity to fisheries bycatch to classify species into five vulnerability classes. The framework combines species traits and distribution ranges for 341 seabirds, along with a spatially resolved fishing effort dataset. Overall, we find most species have high vulnerability scores for the sensitivity and adaptive capacity dimensions. By contrast, exposure is more variable across species, and thus the median scores calculated within seabird families is low. We further find 46 species have high exposure to fishing activities, but are not identified as vulnerable to bycatch, whilst 133 species have lower exposure, but are vulnerable to bycatch. Thus, the framework has been valuable for revealing patterns between and within the vulnerability dimensions. Still, further methodological development, additional traits, and greater availability of threat data are required to advance the framework and provide a new lens for quantifying seabird bycatch vulnerability that complements existing efforts, such as the International Union for Conservation of Nature (IUCN) Red List.

ecology↗

Bycatch mitigation could prevent strong changes in the ecological strategies of seabird communities across the globe

Fisheries bycatch, the incidental mortality of non-target species, is a major threat to seabirds worldwide. Mitigating bycatch is an important factor to reduce seabird population declines and consequent changes in ocean trophic dynamics and ecosystem functioning. However, it remains an open question how and where mitigating bycatch at a global scale may conserve seabird traits and the ecological strategies that traits represent. Here we combine a dataset of species traits and distribution ranges for 341 seabirds with spatially resolved fishing effort data for gillnet, longline, trawl, and purse seine gears to: (1) understand spatial variation in seabird community traits; and (2) test whether mitigating fisheries bycatch may prevent shifts in traits of seabird communities and loss of ecological strategies. We find distinct spatial variation in the community weighted mean of five seabird traits (clutch size, body mass, generation length, foraging guild, and diet guild). Furthermore, our analysis suggests that successful bycatch mitigation could prevent strong shifts in the traits of seabird communities across the globe particularly in the North Atlantic and Southern Oceans. Specifically, changes in dominant foraging and diet guilds, and shifts towards communities with faster reproductive speeds (larger clutch sizes and shorter generation lengths) and smaller body masses could be avoided. Therefore, bycatch mitigation may have important indirect benefits for sustaining ecosystem functioning, as mediated by species traits. Incorporating species traits into management actions will provide valuable tools for marine spatial planning and when evaluating the success of conservation initiatives.

ecology↗