Biology subjects

Fisher, M.

Publications and source records attributed to Fisher, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Charting neuroimaging-based head circumference and cranial shape across development

Quantitative assessment of head growth supports early detection of neurological disease, yet current clinical practice relies on manual measurements that are variable, anatomically limited, and difficult to scale. Here we introduce a fully automated imaging-native framework (CranioTrace) that transforms routine neuroimaging into standardized, population-referenced markers of cranial development. By integrating topology-constrained segmentation, contour regularization, and geometry-based quality control for automated slice selection, CranioTrace robustly extracts head circumference and cranial morphology from heterogeneous MRI and CT data without manual intervention. The framework enabled construction of sex-specific population growth models across pediatric development in a dataset comprising 9,685 scans spanning birth to early adulthood across 25 cohorts. Imaging-derived head circumference shows strong agreement with tape measurements across independent datasets, high reproducibility (intraclass correlation up to 0.99), and consistent performance across modalities. Beyond conventional head circumference, CranioTrace quantifies cranial shape and asymmetry, capturing developmental dynamics that are not accessible through conventional measurements. Population modeling reveals rapid early-life expansion followed by nonlinear deceleration and stable sex differences. Application to neurogenetic cohorts identifies disease-consistent shifts in growth trajectories: head circumference was higher in neurofibromatosis type 1 and 16p11.2 deletion and lower in 22q11.2 deletion and 16p11.2 duplication. By converting clinical imaging archives into scalable cranial phenotypes linked to probabilistic reference models, CranioTrace provides a foundation for imaging-based growth charting, integrated skull-brain phenotyping, and precise assessment of neurodevelopment.

neuroscience↗

bioRxiv2026

Siglec-15 is a glyco-immune checkpoint in prostate cancer regulating immune evasion and metastasis

Prostate cancer is a leading cause of cancer-related mortality in men, and effective treatment options are limited for advanced and metastatic disease. The sialoglycan immune checkpoint Siglec-15 has emerged as a key mediator of tumour-associated immune suppression in several malignancies; however, its expression and functional role in prostate cancer remain poorly defined. Here, using dual immunofluorescence and immunohistochemistry, we demonstrate that Siglec-15 is expressed by prostate tumour epithelial cells, immunosuppressive macrophage phenotypes, and bone-resorbing osteoclasts within the tumour microenvironment. Mechanistically, we show that direct Siglec-15 receptor crosslinking, either by antibodies or tumour cell-derived conditioned medium, promotes monocyte-to-macrophage differentiation, generating macrophages with immunosuppressive and pathogenic phenotypes. Using therapeutic antibodies, we show that Siglec-15 blockade suppresses supernatant-induced monocyte to macrophage differentiation, allowing for the recovery of CD8 T-cell activation. Furthermore, we reveal that macrophage colony-stimulating factor (M-CSF) driven monocyte-derived macrophage differentiation is partially dependent on Siglec-15 signalling, with Siglec-15 blockade enhancing CD8 T-cell responses. In addition, anti-Siglec-15 treatment suppressed osteoclast differentiation, highlighting a dual role for Siglec-15 in prostate cancer immune suppression and bone remodelling. Consistent with these in vitro findings, therapeutic Siglec-15 blockade significantly reduced subcutaneous tumour growth in a CD8 T-cell-dependent manner and prolonged survival in a mouse model of prostate cancer metastasis. Together, these findings identify Siglec-15 as a central regulator of the prostate cancer glyco-immune axis, linking tumour-associated macrophage immune suppression with osteoclast-mediated bone remodelling, providing a compelling rationale for the clinical development of Siglec-15-targeted therapies for patients with advanced disease.

cancer biology↗

bioRxiv2026

Evenness and Taylor's law scaling shape biodiversity-stability relationships in subtropical estuarine communities

Understanding the mechanisms that link biodiversity to ecological stability is crucial for predicting ecosystem responses to global change. Using three decades of standardized monitoring data from eight subtropical estuaries, we analyze diversity components (richness, evenness, dissimilarity, and variance-mean scaling) and interpret stability patterns through synchrony or portfolio mechanisms. Regional {gamma}-diversity increased steadily over time, reflecting sustained gains in fish and invertebrate assemblages. Community stability, defined here as community invariability, was strongly and consistently predicted by Shannon diversity index but not by species richness, underscoring the stabilizing role of evenness. Portfolio effects were robust, with community stability averaging approximately threefold higher than mean population stability, and the strength of this effect more than doubled with each unit increase in Shannon diversity. Structural equation models paired with a null model revealed that shared environmental forcing synchronizes estuarine populations. Shannon diversity generated a large portfolio effect that stabilized the community despite this environmental forcing, whereas richness effects were weak or absent. Taylors law scaling confirmed that abundant, persistent taxa such as blue crab (Callinectes sapidus), brown shrimp (Farfantepenaeus aztecus), and pinfish (Lagodon rhomboides) exhibited higher baseline invariability, contributing to community buffering, while rarer, more variable taxa introduced volatility. In contrast, compositional turnover strongly eroded stability, with high Bray-Curtis dissimilarity predicting reductions in community stability. Together, these results show that long-term estuarine community stability emerges from the interplay of portfolio averaging, demographic variance scaling of dominant species, and the persistence of community composition, highlighting the central role of evenness in biodiversity-stability relationships.

ecology↗

bioRxiv2026

Community reorganization without collapse in a warming world: Habitat-contingent, trait-mediated biodiversity change within a conserved multi-scale structure

Biodiversity change under sustained environmental pressure is increasingly understood as a process of long-term reorganization across spatial scales rather than uniform loss or gain. Estuarine ecosystems, which experience strong environmental gradients and frequent short-term extreme disturbances, provide an ideal context for evaluating how local (), spatial ({beta}), and regional ({gamma}) diversity reorganize across habitat domains and functional guilds through time. Here, we examined four decades of fish and invertebrate community data from a coastwide, ecological monitoring program, spanning multiple estuarine systems along the Texas coast. We asked three main questions: whether habitat context modifies the direction of trait-mediated biodiversity responses across the full -{beta}-{gamma} structure; whether spatial homogenization is detectable through dominance-weighted {beta}-diversity metrics and how they relate to richness-based metrics; and whether the pace of reorganization has intensified over time. Functional traits related to dispersal capacity and thermal affinity structured the magnitude of biodiversity change within habitat domains, but habitat context determined its direction, the same guilds exhibited opposite diversity trajectories across gear-defined habitat domains despite broadly similar functional composition, demonstrating that trait-based forecasting frameworks will mispredict reorganization direction when habitat context is ignored. Spatial homogenization proceeded undetected by richness-based {beta}-diversity metrics but was revealed through dominance-weighted measures, indicating that dominance-weighted homogenization operates through two distinct habitat-dependent mechanisms: convergence on shared warm-adapted dominant taxa in shallow assemblages, and convergence toward impoverished assemblages as dominant taxa declined in deeper habitats, both processes invisible to richness-based metrics. Despite a measurable intensification in the pace of local and regional diversity change after approximately 2000, spatial turnover among bays remained stable and -{beta}-{gamma} scaling relationships were preserved across all diversity orders, demonstrating that rapid reorganization can proceed without destabilizing fundamental metacommunity structure. Across all findings, biodiversity change was persistent, directional, and strongly habitat dependent, following a chronic rather than episodic trajectory consistent with sustained environmental processes as the primary driver.

ecology↗

bioRxiv2026

Identification and SAR optimization of FBXO22-mediated TEAD Targeted Glue degraders

TEAD transcription factors are emerging oncology targets due to their function as key effectors of the Hippo signalling pathway, which is frequently dysregulated in cancer. Here, we report the discovery and development of potent, deep, and rapid-acting TEAD Targeted Glue degraders that leverage an aldehyde-mediated degron mechanism. Our compounds demonstrate exceptional on-pathway selectivity profiles and exhibit the expected Hippo signalling modulation. Mechanistically, we demonstrate that amine-based TEAD degrader scaffolds undergo extracellular conversion to the active aldehyde species, which mediate covalent engagement of FBXO22 C326, triggering TEAD proteasomal degradation. The degraders identified were able to be rationally and systematically optimised for both degradation potency and kinetics, achieving enhanced degradation profiles compared to previously reported FBXO22-targeting approaches, establishing design principles for this degrader class. Our findings highlight strategies for the structure activity relationship (SAR) and rational optimization of aldehyde-mediated degrons to generate novel precision molecular glue degraders against TEAD, a high value oncology target.

cancer biology↗

bioRxiv2025

Siglec-engaging immunosuppressive sialoglycans are upregulated in prostate cancer and are targetable to suppress bone metastasis

Prostate cancer is a leading cause of male cancer-related deaths over the age of 50. New treatment options for prostate cancer are urgently needed, especially for tumours that have spread to bone. Aberrant sialylation holds substantial potential for the discovery of new therapeutic targets but has remained relatively unexplored in the context of prostate cancer, primarily due to the lack of reliable reagents for detecting tumour sialoglycans in clinical tissue. Here, we address this knowledge gap using high-affinity Siglec-based sialoglycan-binding reagents (HYDRAs) to quantify tumour sialoglycans in tissues representing the full clinical heterogeneity of prostate tumours. Using HYDRA immunohistochemistry, we show that sialoglycans that can engage Siglec-3, -7, and -9 are upregulated in primary prostate cancer tissue and sialoglycan ligands for Siglec-7 correlate with prostate cancer bone metastasis and poorer patient prognosis. Analysis of prostate-derived tumours growing in bone reveals Siglec receptors are expressed by immune cells in the bone metastatic tumour microenvironment, suggesting that this axis may play a role in immune cell functions in bone metastatic prostate cancer. Indicating this is clinically actionable, an engineered bisialidase (E-612) can effectively strip Siglec ligands from prostate cancer cells and prolong survival times of mice with bone metastasis. Our findings identify a novel mechanism involving Siglec-engaging sialoglycans in driving the growth of prostate cancer bone metastasis and demonstrate how this axis can be targeted to impede lethal prostate cancer progression.

cancer biology↗

bioRxiv2025

An N4-like Caulobacter phage requires host smooth lipopolysaccharide biosynthesis for infection

Caulobacter species are Alphaproteobacteria that commonly inhabit plant-associated and aquatic microbial communities. Although Caulobacter is widespread and has long served as a model for the study of bacterial cell biology, our understanding of the diversity of viruses that infect Caulobacter species is limited. Here, we describe the discovery and characterization of Circe, a freshwater N4-like podophage belonging to the Schitoviridae family that infects C. crescentus. We isolated two variants, CirceC and CirceH, that differ by a single nucleotide resulting in an F91I substitution in Gp063, an uncharacterized protein found in diverse bacteriophages and bacteria. While both Circe variants adsorb to C. crescentus with similar efficiency, they produce morphologically distinct plaques and display different infection dynamics. Through forward genetic selection and genome-wide transposon fitness profiling, we identified C. crescentus genes involved in cell envelope assembly, membrane sphingolipid biosynthesis, and envelope polysaccharide biosynthesis that influence susceptibility to Circe infection. Loss-of-function mutations in a predicted nucleoside diphosphate sugar epimerase and multiple genes required for smooth lipopolysaccharide (S-LPS) biosynthesis and export conferred strong resistance to infection. These results support a model in which S-LPS functions as a receptor for phage Circe. Our study expands the known repertoire of Caulobacter phages and adds to a growing understanding of the role of envelope polysaccharides in bacterial infection by N4-family phages. IMPORTANCEViruses that infect bacteria and archaea, known as phages, shape microbial community structure and function. Phages initiate infection by binding to specific molecules on the surface of host cells. Yet for many microbes, the identities of infecting phages and their corresponding host receptors remain poorly defined. Caulobacter spp. are ecologically important bacteria that can produce a variety of protein surface structures, including pili, a flagellum, and a surface layer (S-layer), all of which have been identified as phage receptors in this genus. We discovered Caulobacter phage Circe and provide evidence that it relies on host smooth lipopolysaccharide to infect C. crescentus. This study broadens understanding of phage-host interactions in Caulobacter and establishes Circe as a new system to investigate the molecular mechanisms by which phages engage with bacterial cells.

microbiology↗

bioRxiv2025

Viral adsorption to Moore swabs in passive wastewater sampling

Moore swabs have been used extensively for passive sampling in wastewater surveillance, typically yielding presence/absence information for targets of interest. Quantitative analysis of Moore swab data is only possible if target uptake is well characterized, specifically the relationship between quantity of the target in the liquid sample matrix and the quantity of target sorbing to the Moore swab as a function of time. The mechanism of Moore swab absorption remains unclear and is important to understand toward using them more quantitatively. We conducted viral adsorption and desorption experiments using nonpathogenic SARS-CoV-2 surrogates: {Phi}6, MHV, and BCoV as well as heat-inactivated Zika virus (ZIKV). We fit empirical adsorption data from batch experiments to Langmuir, Freundlich and Redlich-Peterson isotherm models. We observed the adsorption behavior of viral targets onto Moore swabs is best characterized by the Redlich-Peterson isotherm model. Moore swabs retained the highest viral RNA concentrations after exposure durations between 9-12 hours in the presence of target microbes during kinetic viral adsorption experiments. The results inform current and future use of Moore swabs to produce quantitative data during wastewater surveillance, especially in settings where composite sampling remains infeasible. ImportanceThis paper describes the adsorption behavior of viruses and bacteriophages to Moore swabs. Passive sampling via Moore swabs is among the most scalable form of passive wastewater sampling, considered critical to advance wastewater surveillance globally. But key unknowns constrain the utility of Moore swabs and all passive sampling approaches, including the quantitative relationship between targets in wastewater and recovery via Moore swabs. Practical questions such as how long they should be deployed and whether they can be interpreted quantitatively really depend on a characterization of viral target loading behaviors on Moore swab material as a function of time and concentration in the wastewater. Here, we use an approach that is seldom applied to microbial targets to examine adsorption behavior of viruses to Moore swabs, deriving isotherms that describe the relationships between concentration of the viral targets in wastewater and time on attachment to swab material. This is a critical step in advancing the application of Moore swab passive sampling for wastewater surveillance, with potential relevance to other microbial targets of interest.

microbiology↗

bioRxiv2024

Genomic epidemiology of emerging terbinafine-resistant Trichophyton indotineae

Dermatophyte skin infections affect around a quarter of the worlds population and are a growing public health concern due to increasing incidence of novel species causing severe infections that are resistant to antifungal treatments. Trichophyton species cause the greatest burden of dermatophytosis worldwide, with the T. mentagrophytes species complex being particularly associated with the emergence of new aggressive infections. One emerging species, T. indotineae (originally T. mentagrophytes genotype VIII) is notable for the extensive nature of the often inflammatory infection, its clinical resistance to terbinafine antifungal treatment, and its rapid global spread. To better understand the epidemiology of this disease, we sourced isolates from severe cases of dermatophytosis in the United Kingdom, Ireland, France, Canada and India for the period 2018-2023, including the type strain from Japan. We used whole-genome sequencing to confirm 90 isolates were T. indotineae, and antifungal susceptibility testing indicated that over half of these (62%) were resistant to terbinafine (MIC [≥]1 mg/L). Pairwise genetic distances showed very high identity with only 147 (1-414) SNPs separating isolates that were nested within a monophyletic phylogeny, supporting a single evolutionary origin of T. indotineae. That no clear geographic clustering of isolates was observed confirms the rapid transcontinental spread of T. indotineae from its likely centre of diversity in Asia. Genome-wide analyses identified multiple non-synonymous SNPs in SQLE (ERG1), the squalene epoxidase target of terbinafine, that were associated with terbinafine in vitro resistance [≥]1 mg/L. However, five isolates exhibited high MIC values without SQLE mutations, suggesting the presence of alternative resistance mechanisms. Our findings highlight the importance of better genomic surveillance to understand and manage this severe and rapidly emerging terbinafine-resistant dermatophyte.

genomics↗

bioRxiv2024

The Unified Phenotype Ontology (uPheno): A framework for cross-species integrative phenomics

Phenotypic data are critical for understanding biological mechanisms and consequences of genomic variation, and are pivotal for clinical use cases such as disease diagnostics and treatment development. For over a century, vast quantities of phenotype data have been collected in many different contexts covering a variety of organisms. The emerging field of phenomics focuses on integrating and interpreting these data to inform biological hypotheses. A major impediment in phenomics is the wide range of distinct and disconnected approaches to recording the observable characteristics of an organism. Phenotype data are collected and curated using free text, single terms or combinations of terms, using multiple vocabularies, terminologies, or ontologies. Integrating these heterogeneous and often siloed data enables the application of biological knowledge both within and across species. Existing integration efforts are typically limited to mappings between pairs of terminologies; a generic knowledge representation that captures the full range of cross-species phenomics data is much needed. We have developed the Unified Phenotype Ontology (uPheno) framework, a community effort to provide an integration layer over domain-specific phenotype ontologies, as a single, unified, logical representation. uPheno comprises (1) a system for consistent computational definition of phenotype terms using ontology design patterns, maintained as a community library; (2) a hierarchical vocabulary of species-neutral phenotype terms under which their species-specific counterparts are grouped; and (3) mapping tables between species-specific ontologies. This harmonized representation supports use cases such as cross-species integration of genotype-phenotype associations from different organisms and cross-species informed variant prioritization.

bioinformatics↗

bioRxiv2024

Targeting of a STING Agonist to Perivascular Macrophages in Prostate Tumors Delays Resistance to Androgen Deprivation Therapy

BackgroundAndrogen deprivation therapy (ADT) is a frontline treatment for prostate cancer but often leads to the development of castration resistant prostate cancer (CRPC). This causes tumors to regrow and metastasize, despite ongoing treatment, and impacts negatively on patient survival. ADT is known to stimulate the accumulation of immunosuppressive cells like protumoral tumor-associated macrophages (TAMs), myeloid-derived suppressor cells and regulatory T cells in prostate tumors, as well as hypofunctional T cells. Protumoral TAMs have been shown to accumulate around tumor blood vessels during chemotherapy and radiotherapy, where they drive tumor relapse. Our aim was to see if such perivascular (PV) TAMs accumulated in ADT-treated prostate tumors prior to CRPC, and, if so, to selectively target these PV cells with a potent immunostimulant, interferon beta (IFN{beta}), an attempt to stimulate anti-tumor immunity and delay CRPC. MethodsWe first used quantitative, multiplex immunofluorescence to assess the effects of ADT on distribution and activation status of TAMs, CD4+ T cells, CD8+ T cells and NK cells in mouse and human prostate tumors. We then used antibody-coated, lipid nanoparticles to selectively target a STING agonist, 2'3'-cGAMP (cGAMP), to PV TAMs in mouse prostate tumors during ADT. ResultsTAMs accumulated at high density around blood vessels in ADT-treated primary mouse and human prostate tumors prior to CRPC, where they expressed markers of a protumoral phenotype, folate receptor beta (FR{beta}), MRC1 (CD206), SIGLEC1 (CD169) and VISTA. Additionally, higher numbers of inactive (PD-1-) CD8+ T cells and reduced numbers of active (CD69+) NK cells were also present in PV tumor areas after ADT. LNPs coated with antibody to FR{beta} selectively delivered cGAMP to PV TAMs in ADT-treated tumors where they activated STING and expression of IFN{beta} by these cells. This resulted in a marked increase in the density of active CD4+ T cells, CD8+T cells and NK cells in PV tumor areas, and significantly delayed in the onset of CRPC. ConclusionTogether, our data indicate that targeting a STING agonist to PV TAMs could be used to extend the treatment window for ADT in prostate cancer. KEY MESSAGESO_ST_ABSWhat is already known about the topicC_ST_ABSAndrogen deprivation therapy (ADT) is a frontline treatment for prostate cancer. However, tumors often develop resistance and start to regrow and metastasize - a condition called castration resistance prostate cancer (CRPC). Prostate cancer is considered to be an immunologically cold tumor type and while ADT stimulates tumor infiltration by cytotoxic (CD8+) T cells, they are largely hypofunctional, possibly due to the immunosuppressive tumor microenvironment. What this study addsThis study is the first to demonstrate that FR{beta}+ macrophages with a immunosuppressive phenotype accumulate around blood vessels in mouse and human prostate tumors during ADT, prior to the onset of CRPC. Lipid nanoparticles coated with an antibody to FR{beta}+ were then used to deliver a STING agonist selectively to these perivascular (PV) cells during ADT. This triggered STING signalling and the release of the potent immunostimulant, interferon beta, by PV macrophages, which then activated tumour-infiltrating CD4+ and CD8+ T cells, and delayed the onset of CRPC. How this study might affect research, practice or policyThe delivery of an immunostimulant specifically to PV regions of tumors represents a new, more targeted form of immunotherapy that ensures the activation of T cells as soon as they cross the vasculature into tumors. This new approach could be used to extend the treatment window for neoadjuvant ADT in men with localised prostate tumors. In doing so, it would delay/circumvent the need for additional treatments like radiotherapy and/or or prostatectomy.

cancer biology↗

bioRxiv2024

Failed stopping transiently suppresses the electromyogram in task-irrelevant muscles

Selectively stopping individual parts of planned or ongoing movements is an everyday motor skill. For example, while walking in public you may stop yourself from waving at a stranger who you mistook for a friend while continuing to walk. Despite its ubiquity, our ability to selectively stop actions is limited. Canceling one action can delay the execution of other simultaneous actions. This stopping-interference effect on continuing actions during selective stopping may be attributed to a global inhibitory mechanism with widespread effects on the motor system. Previous studies have characterized a transient global reduction in corticomotor excitability by combining brain stimulation with electromyography (EMG). Here, we examined whether global motor inhibition during selective stopping can be measured peripherally and with high temporal resolution using EMG alone. Eighteen participants performed a bimanual anticipatory response inhibition task with their index fingers while maintaining a tonic contraction of the task-irrelevant abductor digiti minimi (ADM) muscles. A time series analysis of the ADM EMG signal revealed transient inhibition during failed stopping compared to go response trials 150 ms to 203 ms following the stop signal. The pattern was observed in both hands during bimanual stop-all trials as well as selective stop-left and stop-right trials of either hand. These results indicate that tonic muscle activity is sensitive to the effects of global motor suppression even when stopping fails. Therefore, EMG can provide a physiological marker of global motor inhibition to probe the time course and extent of stopping processes. Key PointsO_LISuccessfully stopping an initiated response globally suppresses the motor system. C_LIO_LIUsing electromyography of tonic muscle activity, we show inhibition spills over to task-irrelevant muscles during failed stopping. C_LIO_LIThe electromyographic pattern of inhibition is transient, lasting from approximately 150 to 203 ms following a stop signal when stopping fails. C_LIO_LIThe time course of the peripheral suppression of muscle activity may be leveraged to more precisely examine candidate neural mechanisms. C_LIO_LIThis non-invasive measure of motor system inhibition may be useful for tracking inhibitory control deficits in clinical populations. C_LI

neuroscience↗

bioRxiv2024

Corticospinal excitability at rest outside of a task does not differ from task intertrial intervals in healthy adults

Human corticospinal excitability modulates during movement, when muscles are active, but also at rest, when muscles are not active. These changes in resting motor system excitability can be transient or longer lasting. Evidence from transcranial magnetic stimulation (TMS) studies suggests even relatively short periods of motor learning on the order of minutes can have lasting effects on resting corticospinal excitability. Whether individuals are able to return corticospinal excitability to out-of-task resting levels during the intertrial intervals of behavioral tasks that do not include an intended motor learning component is an important question. Here, in twenty-six healthy young adults, we used single-pulse TMS and electromyography (EMG) to measure motor evoked potentials (MEPs) during two different resting contexts: 1) intertrial intervals of a choice-reaction time task, and 2) outside the task. In both contexts, five TMS intensities were used to evaluate possible differences in recruitment of corticospinal output. We hypothesized resting state excitability would be greater during intertrial intervals than out-of-task rest, reflected in larger MEP amplitudes. Contrary to our hypothesis, we observed no significant difference in MEP amplitudes between out-of-task rest and in-task intertrial intervals, and instead found evidence of equivalence, indicating that humans are able to return to a stable motor resting state within seconds after a response. These data support the interpretation that rest is a uniform motor state in the healthy nervous system. In the future, our data may be a useful reference for motor disorder populations with an impaired ability to return to rest.

neuroscience↗

bioRxiv2024

Genomic epidemiology of Candida auris introduction and outbreaks in the United Kingdom

BackgroundCandida auris is a globally emerging fungal pathogen that causes nosocomial invasive infections, particularly in intensive care units (ICU). Four prominent genetic clades originating from distinct geographic regions have been identified: South Asia (Clade I), East Asia (Clade II), Africa (Clade III) and South America (Clade IV) with each clade presenting differing antifungal resistance profiles. We aimed to elucidate the epidemiology of this infection in the United Kingdom (UK) 2014 - 2019 using genomic approaches. MethodsGenome sequences from 24 isolates from six patients in four London hospitals were combined with genome sequences from 183 additional outbreak isolates from nine UK hospitals. These data were used to assess the numbers and timings of C. auris lineage introductions into the UK and to infer subsequent patterns of inter- and intra-hospital transmission. FindingsWe found evidence for at least three introductions of C. auris into the UK, one from Clade I and one from Clade III. The evolutionary rate of C. auris Clade I and Clade III were estimated at 2.764 x 10-4 and 3.186 x 10-4 substitutions per polymorphic site per year, respectively, with entry into the UK as 2013 and 2016 for Clades I and III respectively. We observed temporal and geographical evidence for multiple transmission events between hospitals and identified local within-hospital patient-to-patient transmission events. InterpretationThese data confirm that C. auris is a newly emerged infection in the UK with at least three original introductions into this country. Our analysis shows that hospital outbreaks are linked and confirms that transmission amongst patients has occurred, explaining local hospital outbreaks. Our findings argue that enhanced surveillance of C. auris infection within the UK is necessary in order to protect healthcare and to curtail expansion of this emerging infection. FundingThis work was supported by a Wellcome Trust Institutional Strategic Support Fund Springboard Fellowship, and by the Medical Research Council (MR/R015600/1), the Natural Environment Research Council (NE/P001165/1) and the Wellcome Trust (219551/Z/19/Z). Research in contextSince its first description in 2009, Candida auris has spread across the globe. For this study, authors considered all publications describing whole genome sequences of isolates within the UK up until 2020 to assess the genomic epidemiology of this fungal pathogen. This study adds value to the current understanding of C. auris epidemiology by undertaking the first analysis to assess transmission between and within hospitals using genomic data. We also provide the first in-depth temporal analysis to estimate likely times of introduction into the UK. These results have clinical implications, encouraging hospitals to identify yeast upon admission and to assess multiple isolates from single patients, which may harbour much diversity in terms of genetics and drug resistance.

genomics↗

bioRxiv2023

S1 hydrophobic residues alter the voltage sensing phosphatase enzymatic function and voltage sensing

The voltage sensing domain (VSD) is a four-helix modular protein domain that converts electrical signals into conformational changes, leading to open pores and active enzymes. In most voltage sensing proteins, the VSDs do not interact with one another and the S1-S3 helices are considered mainly as scaffolding. The two exceptions are the voltage sensing phosphatase (VSP) and the proton channel (Hv). VSP is a voltage-regulated enzyme and Hvs are channels that only have VSDs. To investigate the S1 contribution to VSP function, we individually mutated four hydrophobic amino acids in S1 to alanine (F127, I131, I134 and L137). We also combined these mutations to generate quadruple mutation designated S1-Q. Most of these mutations shifted the voltage dependence of activity to higher voltages though interestingly, not all substrate reactions were the same. The kinetics of enzymatic activity were also altered with some mutations significantly slowing down dephosphorylation. The voltage dependence of VSD motions were consistently shifted to lower voltages and indicated a second voltage dependent motion. Co-immunoprecipitation demonstrated that none of the mutations broke the VSP dimer indicating that the S1 impact could stem from intrasubunit and/or intersubunit interactions. Lastly, when the same alanine mutations were introduced into a genetically encoded voltage indicator, they dramatically altered the optical readings, making some of the kinetics faster and shifting the voltage dependence. These results indicate that the S1 helix in VSP plays a critical role in tuning the enzymes conformational response to membrane potential transients and influencing the function of the VSD.

biophysics↗

bioRxiv2023

Architecture of Ca2+ tunneling, a basic Ca2+ signaling modality important for secretion

Ca2+ tunneling is a signaling modality that requires both Store-operated Ca2+ entry (SOCE) and Ca2+ release from the endoplasmic reticulum (ER). Tunneling expands the SOCE microdomain at ER-plasma membrane (PM) contact sites (ERPMCS) through Ca2+ uptake by the sarco/endoplasmic reticulum Ca2+ ATPase (SERCA) into the ER lumen where it diffuses and is released via open inositol trisphosphate (IP3) receptors (IP3Rs). In this study using high resolution imaging, we outline the spatial remodeling of the Ca2+ tunneling machinery (IP3R1; SERCA; PMCA; and Ano1 as an effector) relative to STIM1 in response to store depletion. We show that store depletion leads to redistribution of these Ca2+ signaling modulators to distinct subdomains laterally at the PM and axially within the cortical ER. To functionally define the role of Ca2+ tunneling, we engineered a Ca2+ tunneling attenuator (CaTAr) that blocks tunneling without affecting Ca2+ release or SOCE. CaTAr inhibits Cl- secretion in sweat gland cells. Viral mediated expression of CaTAr in the mouse reduces sweating, showing that Ca2+ tunneling is important physiologically. Collectively our findings outline the architecture of the Ca2+ tunneling machinery and show that it is a fundamental physiological pertinent Ca2+ signaling modality.

cell biology↗

bioRxiv2023

Reversing the decline of threatened koala (Phascolarctos cinereus) populations in New South Wales: Using genomics to define meaningful conservation goals

Genetic management is a critical component of threatened species conservation. Understanding spatial patterns of genetic diversity is essential for evaluating the resilience of fragmented populations to accelerating anthropogenic threats. Nowhere is this more relevant than on the Australian continent, which is experiencing an ongoing loss of biodiversity that exceeds any other developed nation. Using a proprietary genome complexity reduction-based method (DArTSeq), we generated a data set of 3,239 high quality Single Nucleotide Polymorphisms (SNPs) to investigate spatial patterns and indices of genetic diversity in the koala (Phascolarctos cinereus), a highly specialised folivorous marsupial that is experiencing rapid and widespread population declines across much of its former range. Our findings demonstrate that current management divisions across the state of New South Wales (NSW) do not fully represent the distribution of genetic diversity among extant koala populations, and that care must be taken to ensure that translocation paradigms based on these frameworks do not inadvertently restrict gene flow between populations and regions that were historically interconnected. We also recommend that koala populations should be prioritised for conservation action based on the scale and severity of the threatening processes that they are currently faced with, rather than placing too much emphasis on their perceived value (e.g., as reservoirs of potentially adaptive alleles), as our data indicate that existing genetic variation in koalas is primarily partitioned amongst individual animals. As such, the extirpation of koalas from any part of their range represents a potentially critical reduction of genetic diversity for this iconic Australian species.

genomics↗

bioRxiv2023

Invasive European green crab (Carcinus maenas) predation revealed with quantitative DNA metabarcoding

Predation by invasive species can threaten local ecosystems and economies. The European green crab (Carcinus maenas), one of the most widespread marine invasive species, is an effective predator associated with clam and crab population declines outside of its native range. In the U.S. Pacific Northwest, green crab have recently experienced increases in abundance and expanding distributions, generating concern for estuarine ecosystems and associated aquaculture production. However, regionally-specific information on the trophic impacts of invasive green crab is highly limited. We compared the stomach contents of green crabs collected on aquaculture beds versus natural intertidal sloughs in Willapa Bay, Washington, to provide the first in-depth description of European green crab diet at a particularly crucial time for regional management. We first identified putative prey items using DNA metabarcoding. For key prey species, we also applied a quantitative model to calculate the true abundance of each species in stomach content DNA samples. From the stomach contents of 62 green crabs, we identified 56 unique taxa belonging to nine phyla. The stomach contents of crabs collected from aquaculture beds were significantly different from the stomach contents of crabs collected at natural intertidal sloughs. Across all sites, arthropods were the most frequently detected prey, with the native hairy shore crab (Hemigrapsus oregonensis) the single most common prey item. Of the eight species included in the quantitative model, two ecologically-important native species - the sand shrimp (Crangon franciscorum) and the Pacific staghorn sculpin (Leptocottus armatus) - were the most abundant in crab stomach contents, when present. In addition to providing timely information on green crab diet, our research demonstrates the novel application of a recently developed model for quantitative DNA metabarcoding. This represents another step in the ongoing evolution of DNA-based diet analysis towards producing the quantitative data necessary for modeling invasive species impacts.

ecology↗