Biology subjects

Davies, S.

Publications and source records attributed to Davies, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Therapeutic-induced chromatin remodeling via AP-1/SWI-SNF enhances BK Polyomavirus replication in urothelial cells

Hemorrhagic cystitis (HC) caused by BK polyomavirus (BKPyV) reactivation is a serious complication in immunocompromised patients especially in hematopoietic stem cell transplant recipients, yet the effects of conditioning regimens on viral replication remain undefined. Current therapies for HC are largely supportive, and no specific antiviral drugs are approved for BKPyV reactivation, underscoring an urgent need for new interventions. Here, using a cellular model of HC, we provide the first mechanistic evidence that physiologic concentrations of genotoxic chemotherapy, immune-conditioning, and antiviral exposures commonly enhance BKPyV replication by reprogramming host chromatin remodeling machinery independently of immune suppression. Transcriptomic and epigenomic profiling of urothelial cells revealed that these treatments induce host and virus chromatin remodeling, specifically, the SWI/SNF ATP-dependent remodeling complex is activated and creates a regulatory landscape enriched for AP-1 transcription factor motifs, implicating the AP-1/SWI-SNF axis as a key regulator of viral replication. Functional inhibition of SWI/SNF with AU-15330 and FHD-286 consistently suppressed BKPyV replication across all tested therapeutic conditions. Patient urine samples and cellular experiments demonstrated these effects are independent of viral genomic changes. These findings suggest chromatin remodeling as the mechanistic driver of therapy-associated BKPyV reactivation and propose SWI/SNF inhibition as a translational therapeutic strategy to mitigate hemorrhagic cystitis.

microbiology↗

bioRxiv2026

Neuroendocrine influences on dynamic cerebrovascular function and implications for functional MRI

To fully profile how ovarian hormones interact with cerebrovascular function, it is vital to consider, not just resting physiology, but also dynamic aspects of cerebrovasculature that support neural activity. This study uses hypercapnic cerebrovascular reactivity (CVR) and the visually-evoked haemodynamic response function (HRF) to investigate the influence of menstrual-related changes in oestradiol and progesterone on dynamic aspects of the cerebrovascular system. 20 menstruating females (age mean[SD]=23.01[4.01]years) completed a 3T MRI scanning session during the early follicular, late follicular, and mid-luteal phases of their menstrual cycle. Circulating hormones were measured via blood samples. Simultaneous blood oxygen level dependant (BOLD)-CVR and cerebral blood flow (CBF)-CVR data were collected using a pseudocontinuous arterial spin labelling (pCASL) acquisition using a dual-excitation (DEXI) readout during periods of hypercapnia (5% CO2). The HRF was estimated using a whole brain EPI scan during high-contrast radial checkerboard presentation. Both oestradiol and additional progesterone variance were associated with increased CVR (both BOLD-CVR and CBF-CVR; p<0.001) and altered HRF shape (p<0.005). No statistically significant regional effects were found. A secondary experiment investigated the impact of using either canonical or individually mapped HRF in a standard fMRI processing pipeline; namely, population receptive field (pRF) mapping. Results across phases suggest that neither hormone was associated with pRF size when modelled using a canonical HRF (both p>0.05). However, a significant neuroendocrine influence on pRF sizes was discovered when using individually measured HRFs (p<0.001). This study found evidence that dynamic cerebrovascular functions are sensitive to menstrual-related ovarian hormones, which may be a potential mechanism underlying menstrual symptomatology and has implications for fMRI studies that assume intact neurovascular coupling processes in women, regardless of menstrual staging, to make inferences about neural activity.

neuroscience↗

bioRxiv2026

Seasonal microbiome community dynamics in the massive coral Porites lobata impacted by sedimentation

Near-shore coral reefs in southern Guam (Mariana Islands) experience severe sedimentation, in particular during the wet season when rainfall and erosion are high. We sampled fragments of the reef-forming coral Porites lobata from opposite ends of a sedimentation gradient in Fouha Bay, southern Guam, during dry and wet seasons. Using DNA metabarcoding, we characterized the diversity and composition of P. lobata-associated Symbiodiniaceae and bacterial microbiome communities. As in many species of Porites, Symbiodiniaceae communities of P. lobata were dominated by variants of Cladocopium C15 with sites showing differences in Symbiodiniaceae communities attributable to variation in these Cladocopium C15 variants. Bacterial microbiomes of P. lobata were dominated by Endozoicomonadaceae, a family of putative coral bacterial endosymbionts involved in nutrient cycling. Site and seasonal differences in bacterial diversity and community composition were apparent. In close proximity to the mouth of the river draining into Fouha Bay, bacterial diversity was highest during the wet season when sedimentation is generally severe. Microbiome reorganization in response to sedimentation may explain this result, but we also found overrepresentation of bacteria associated with terrestrial origin close to the river mouth and/or during the wet season. Together these patterns highlight that coral Symbiodiniaceae and bacterial communities are both spatially and temporally structured in this disturbed system. IMPORTANCEThis study provides a time series dataset of coral-associated microorganisms, including dinoflagellate algae and bacteria, from a tropical bay impacted by sedimentation that results from upstream erosion of disturbed soils. Characterizing temporal patterns of coral-associated microbes provides insights into the dynamic nature of these communities. While microbiome variability across sites and seasons may be a result of acclimatization to different environmental conditions, we identified bacterial groups of putative terrestrial origin in sampled coral microbiomes that may have been exported from eroded soils to the near-shore reef. Considering that disturbed soils act as hotspots for the proliferation of potentially harmful substances, such as antimicrobial resistance genes, understanding microbial community connections at the marine-freshwater-terrestrial interface is an important step toward evaluating environmental impacts across connected ecosystems from ridge to reef.

ecology↗

bioRxiv2025

Plasticity Associated with Adoption of Social Roles in Clown Anemonefish

Central questions of animal behavior are how do individual phenotypes shape and how are individual phenotypes shaped by dominance hierarchies. Using clownfish (Amphiprion percula) as a model system, we investigated how individuals strategically modify their phenotype during hierarchy formation. We tested the overarching hypothesis that interactions among size- and age-matched rivals will lead to the emergence of social roles (dominant, subordinate, solitary), accompanied by divergence in four aspects of individual phenotypes: growth, feeding behavior, agonistic behaviors (aggression, submission), and gene expression. To test this, we created 30 replicates of juvenile clownfish, each comprising a size-matched pair housed together, and a solitary size-matched individual housed separately. Our results show that an individuals social context shapes its growth trajectory through coordinated changes in feeding behavior, agonistic behaviors, and gene expression. Individuals emerging as dominant within pairs grew twice as much compared to those emerging as subordinates, while subordinate and solitary individuals showed comparable growth. Initially, paired individuals consumed more food per capita than solitary individuals, but this difference declined as size hierarchies became established. Agonistic behaviors also decreased over time among paired individuals as size differences emerged. Transcriptomic analyses revealed upregulation of conserved vertebrate growth pathways and ossification related genes, and downregulation of satiety-associated genes, in dominant individuals compared to subordinates and solitaries. Here we identify associations between changes in gene expression, growth, and feeding behavior regulation that reinforce social role differentiation during dominance hierarchy formation in clownfish. Our findings lay the foundation for a broader framework to explore the mechanisms underpinning strategic growth in social vertebrates.

ecology↗

bioRxiv2025

Symbiotic State Affects Microbiome Recovery in a Facultatively Symbiotic Cnidarian

The cnidarian holobiont consists of host cells, algal symbionts, and a complex microbiome that resides in and on the host tissue and the algal symbionts. To investigate the interactions between a host cnidarian, its algal symbionts, and its bacterial microbiome, we used antibiotics to deplete the microbiome of the facultatively symbiotic sea anemone Exaiptasia pallida (Aiptasia) in both symbiotic and aposymbiotic states. To understand the dynamics of microbiome reestablishment following disruption, we used 16S gene sequencing of the bacterial microbiome to characterize communities during recovery following antibiotic treatment. We assessed the host molecular response to microbiome depletion and recovery using RNA-seq and Western blotting of the immune transcription factor NF-{kappa}B. 16S results demonstrate that, following depletion, symbiotic Aiptasia can reestablish bacterial communities (based on diversity metrics and community composition) alike to those of controls before microbiome depletion. However, the microbiomes of aposymbiotic Aiptasia fail to reestablish to control conditions even after seven days of recovery. Bacteria in the Family Endozoicomonadaceae reestablish to control levels in symbiotic, but not aposymbiotic, Aiptasia, suggesting an association between Endozoicomonadaceae and algal symbionts. Our molecular analyses show that host immune system gene expression is downregulated during recovery from antibiotic treatment, but that NF-{kappa}B protein levels increase during recovery, suggesting mechanisms for microbiome reestablishment following disruption. This study shows the dynamics of microbiome recovery following depletion and the influence of microbiome community members on host gene expression in a cnidarian model, providing a foundation for future research involving pairwise interactions between microorganisms and cnidarian hosts.

microbiology↗

bioRxiv2025

Synthetic Substitutes as a Conservation Tool: Evaluating Synthetic Leopard Fur for Demand Reduction and Species Recovery

Providing synthetic substitutes is a widely promoted strategy to shift consumer demand away from wildlife products derived from threatened species. Yet, there is little evidence on whether such product substitution interventions effectively prevent illegal or unsustainable harvesting and contribute to the recovery of threatened populations. Drawing on the Furs For Life (FFL) Zambia initiative, which supplied synthetic furs known as "Heritage Furs" to replace leopard skins traditionally worn during Lozi royal ceremonies in Western Zambia, we present an evaluation designed to test both the effects and causal mechanisms of substitution. Guided by the EMMIE framework, commonly used in crime prevention evaluation, we triangulated data from semi-structured questionnaires, law enforcement patrols, court records, camera trap monitoring, and stakeholder interviews conducted between 2018 and 2024. Qualitative analysis using the General Elimination Method was employed to assess plausible alternative explanations for leopard recovery. By 2024, adoption of synthetic furs among leopard fur users exceeded 80 percent, while self-reported ownership of authentic leopard furs declined by 70 percent. At the same time, patrol detections of leopard poaching incidents decreased, and camera trap density estimates increased from an average of 2.7 to 3.8 leopards per 100 square kilometers across the focal landscape. An integrated mechanism of change, derived from stakeholder perspectives, indicates that while substitution reduced demand, concurrent and reinforcing effects of counter-poaching and counter-trafficking operations were critical to leopard recovery. This study provides the first empirical link between a demand reduction initiative based on synthetic substitutes and measurable species population recovery.

ecology↗

bioRxiv2025

Autism-associated oxysterol regulates GABAergic neurogenesis and subtype fates

Distorted GABAergic neurodevelopment is believed to underscore cortical network dysfunction that lies at the heart of neurodevelopmental disorders (NDD) such as autism and schizophrenia. GABAergic neuron diversity is sculptured by cortical environmental cues during protracted postmitotic differentiation. However, the mechanism by which the NDD environment influences GABAergic neuronal development remains largely unknown. Oxysterols are oxidized metabolites of cholesterol that can interact with developmental signaling pathways. Using an iPSC model recapitulating human forebrain GABAergic neuron development and single-cell transcriptomic profiling, we show that 24S, 25-epoxysterol, an NDD-affected oxysterol highly enriched in the fetal brain, promotes neurogenesis, and disturbs the composition of GABAergic neuronal subtypes. Moreover, pharmacological and genetic interrogation identified the liver X receptor as a regulatory pathway mediating the action of 24S, 25-epoxysterol. These findings provide insights into the roles of cholesterol metabolism in neuronal development and a potential mechanism by which dysregulated brain oxysterols contribute to the pathogenesis of NDD.

developmental biology↗

bioRxiv2025

Direct pathway bias and altered striatal neurogenesis in human iPSC models of 16p11.2 CNVs: Evidence from single-cell and functional analyses

Striatal medium spiny neurons (MSNs) control motor, cognitive, and social domains via direct (dMSNs) and indirect (iMSNs) basal ganglia pathways. Recent genomic analyses implicate striatal circuit dysfunction in neurodevelopmental disorders (NDDs) and highlight MSNs as a newly recognised cell type affected in schizophrenia, yet much NDD research still focuses on cortical interneurons and glutamatergic neurons, leaving MSN involvement understudied. Here, we use human iPSC-derived MSNs to demonstrate high-fidelity striatal development and explore 16p11.2 copy number variants (CNVs) - mutations predisposing carriers to autism spectrum disorder, schizophrenia, intellectual disability and other NDD conditions featuring basal ganglia deficits. By profiling both 16p11.2 duplication and deletion MSNs, we uncover reciprocal changes in MSN neurogenesis kinetics that converge on a dMSN fate bias. These shifts correspond to altered calcium signalling and enhanced firing upon direct-pathway activation. Our findings reveal a previously unappreciated role for MSN subtype imbalances in NDD pathogenesis and open new avenues for therapeutic intervention.

neuroscience↗

bioRxiv2024

Endocrine modulation of cortical and retinal blood flow across the menstrual cycle

The ovarian hormones, oestrogen and progesterone, have vaso- and neuroprotective effects, likely due to interactions with the cerebrovascular system. This study investigates their neuroendocrine influence on a range of cerebral and retinal vascular functions across a healthy menstrual cycle. Twenty-six healthy, menstruating females completed imaging sessions and assessment of circulating hormone levels during their early follicular, late follicular, and mid-luteal phase (1-4, 10-12 and 20-22 days after menses onset). Cerebral blood flow (CBF), arterial arrival time (AAT), global oxygen extraction fraction (OEF), cerebrovascular metabolic rate of oxygen (CMRO2), carotid artery radius and carotid pulsatility index (PI) were measured using 3T MRI. Retinal vessel density and blood flow resistance were assessed with optical coherence tomography angiography (OCT-A). Assessed with linear models, increased oestradiol was related to increased global CBF ({chi}2(1)=41.682; p=1.074x10-10). An independent progesterone increase was also associated with increased global CBF ({chi}2(1)=14.979; p=0.0001). In the retina, a relationship was found between oestradiol and decreased retinal blood flow resistance ({chi}2(1)=5.28; p=0.0215), which was primarily driven by centrally localised vessels. This study finds that circulating oestrogen increases blood flow in the eye and brain, while progesterone significantly impacts the brain alone. These effects suggest a potential pathway for neuroprotective mechanisms.

neuroscience↗

bioRxiv2024

Molecular characterisation of Streptococcus pyogenes (StrepA) non-invasive isolates during the 2022-23 UK upsurge

At the end of 2022 into early 2023 the UK Health Security Agency reported unusually high levels of scarlet fever and invasive disease caused by Streptococcus pyogenes (StrepA or group A Streptococcus). During this time, we collected and genome sequenced 341 non-invasive throat and skin S. pyogenes isolates identified during routine clinical diagnostic testing in Sheffield, a large UK city. We compared the data with that obtained from a similar collection of 165 isolates from 2016-17. Numbers of throat-associated isolates collected peaked in early December 2022, reflecting the national scarlet fever upsurge, while skin infections peaked later in December. The most common emm-types in 2022-23 were emm1 (28.7%), emm12 (24.9%), and emm22 (7.7%) in throat; and emm1 (22%), emm12 (10%), emm76 (18%), and emm49 (7%) in skin. Whilst all emm1 isolates were the M1UK lineage, comparison with 2016-17 revealed diverse lineages in other emm-types, including emm12, and emergent lineages within other types including a new acapsular emm75 lineage, demonstrating that the upsurge was not completely driven by a single genotype. Analysis of the capsule locus predicted only 51% of throat isolates would produce capsule compared to 78% of skin isolates. 90% of throat isolates were also predicted to have high NADase and Streptolysin O (SLO) expression, based on the promoter sequence, compared to only 56% of skin isolates. Our study has highlighted the value in analysis of non-invasive isolates to characterise tissue tropisms, as well as changing strain diversity and emerging genomic features which may have implications for spillover into invasive disease and future S. pyogenes upsurges. Data summaryAll new genome sequence data is available on the NCBI short read archive under the bioproject PRJNA1062601 and individual accession numbers are listed in Supplementary Table 1 and Table 2. Impact statementThe human bacterial pathogen Streptococcus pyogenes, also known as group A Streptococcus or StrepA, caused a dramatic and sudden upsurge in scarlet fever in the UK at the end of 2022 into early 2023. We present molecular characterisation of this upsurge, through genome sequence analysis of throat, skin and other types of non-severe infection isolates collected by the microbiology diagnostic lab at the Northern General Hospital in Sheffield, England. We found that, whilst two strain types were the predominant cause of infections during the upsurge, other types had emerged or changed when compared to a similar collection from 2016-17. We also identified differences between throat-associated isolates and skin-associated isolates and highlighted important bacterial factors that might influence infection types. Isolates from non-severe throat/skin types of infections are rarely saved and therefore our knowledge of them is limited. However, here we demonstrate that study of such isolates may be key to understanding upsurges of more severe infections.

microbiology↗

bioRxiv2023

Phenotypic screen-based discovery of a small molecule that can increase adult neurogenesis and improve memory

Stem cells and neurogenesis persist in the postnatal and adult brain. Adult brain stem cells can be neuroprotective in disease and augment hippocampal-dependent cognitive function and thus are an important therapeutic target. Although many molecules have been discovered that regulate neurogenesis, few studies have attempted to amplify the process pharmacologically as a therapeutic goal. To address this gap, we used murine neurosphere cultures from the two major stem cell niches: the subventricular zone (SVZ) and the subgranular zone (SGZ). We screened compounds sharing pharmacophores with known inducers of neurogenesis and found several dozen proneurogenic compounds in an in vitro phenotypic screen. One, OXS-N1 was stable, and had acceptable absorption, distribution, metabolism, and excretion profiles in animal studies. OXS-N1 could increase neurogenesis in the SVZ and SGZ in WT mice after both intraperitoneal and oral administration. The number of newborn neurons (BrdU+/NeuN+) was increased; however, the number of activated stem cells (BrdU+/GFAP+) was not, suggesting an effect on neurogenesis independent of stem cell activation. This was supported by OXS-N1 increasing neurosphere differentiation but not proliferation. OXS-N1 also increased neurogenesis and improved performance in a Y maze cognitive task in PDGF-APPSw,Ind mice, a model of Alzheimers disease. RNAseq of SVZ and SGZ neurospheres in turn showed that genes associated with synaptic function were significantly increased by OXS-N1. Our study demonstrates the utility of phenotypic screening for the identification of molecules that increase neurogenesis and might be of therapeutic relevance.

neuroscience↗

bioRxiv2023

Latitudinal scaling of aggregation with abundance and its consequences for coexistence in species rich forests

The search for simple principles underlying the complex spatial structure and dynamics of plant communities is a long-standing challenge in ecology1-6. In particular, the relationship between the spatial distribution of plants and species coexistence is challenging to resolve in species-rich communities7-9. Analysing the spatial patterns of tree species in 21 large forest plots, we find that rare species tend to be more spatially aggregated than common species, and a latitudinal gradient in the strength of this negative correlations that increases from tropical to temperate forests. Our analysis suggests that latitudinal gradients in animal seed dispersal10 and mycorrhizal associations11,12,13 may jointly generate this intriguing pattern. To assess the consequences of negative aggregation-abundance correlations for species coexistence, we present here a framework to incorporate the observed spatial patterns into population models8 along with an analytical solution for the local extinction risk14 of species invading from low abundances in dependence of spatial structure, demographic parameters, and immigration. For example, the stabilizing effect of the observed spatial patterns reduced the local extinction risk of species when rare almost by a factor of two. Our approach opens up new avenues for integrating observed spatial patterns into mathematical theory, and our findings demonstrate that spatial patterns, such as species aggregation and segregation, can contribute substantially to coexistence in species-rich communities. This underscores the need to understand the interactions between multiple ecological processes and spatial patterns in greater detail.

ecology↗

bioRxiv2023

Sensing the rainbow: genetic and physiological responses to light quality in Ostreococcus, an ecologically important photosynthetic picoeukaryote

Phytoplankton is exposed to dramatic variations in light quality as it moves up and down the water column or encounters the presence of sediments in the water. We investigated the potential impact on Ostreococcus, a key marine photosynthetic picoeukaryote, by analysing changes in its transcriptome, pigment content and photophysiology after acclimation to monochromatic red, green or blue light. The clade B species RCC809, isolated from the deep Atlantic Ocean, responded to blue light by accelerating cell division at the expense of storage reserves, and by increasing the relative level of blue-light absorbing pigments. In contrast, it responded to red and green light by increasing its potential for photoprotection. In contrast, the clade A species OTTH0595, which originates from a shallow water environment, showed no difference in photosynthetic properties and minor differences in carotenoid contents between light qualities. These results demonstrate that light quality can have a major influence on the physiology of eukaryotic phytoplankton, and suggest that different light quality environments can drive selection for diverse patterns of responsiveness and environmental niche partitioning. HighlightWe characterise the effects of light quality on the transcriptome and photophysiology of Ostreococcus, a photosynthetic picoeukaryote, and show that responses are distinct between two ecotypes originating from different environments.

plant biology↗

bioRxiv2022

Microbial Community Dynamics Provide Evidence for Hypoxia During a Coral Reef Mortality Event

In July 2016, a severe coral reef invertebrate mortality event occurred approximately 200km southeast of Galveston, Texas at the East Flower Garden Bank wherein upwards of 80% of corals in a 0.06 km2 area died. Based on surveys of dead corals and other invertebrates shortly after this mortality event, responders hypothesized that localized hypoxia was the most likely direct cause. However, no dissolved oxygen data were available to test this hypothesis because oxygen is not continuously monitored within the Flower Garden Banks sanctuary. Here we quantify microbial plankton community diversity based on four cruises over two years at the Flower Garden Banks, including a cruise just 5-8 days after the mortality event was first observed. In contrast with observations collected during baseline conditions, microbial plankton communities in the thermocline were differentially enriched with taxa known to be active and abundant in oxygen minimum zones or that have known adaptations to oxygen limitation shortly after the mortality event (e.g. SAR324, Thioglobaceae, Nitrosopelagicus, and Thermoplasmata MGII). Unexpectedly, these enrichments were not localized to the East Bank, but were instead prevalent across the entire study area, suggesting there was a widespread depletion of dissolved oxygen concentrations in the thermocline around the time of the mortality event. Hydrographic analysis revealed the southern East Bank coral reef (where the localized mortality event occurred) was uniquely within the thermocline at this time. Our results demonstrate how temporal monitoring of microbial communities can be a useful tool to address questions related to past environmental events. IMPORTANCEIn the northwestern Gulf of Mexico in July 2016, upwards of 80% of corals in a small area of the East Flower Garden Bank coral reef suddenly died without warning. Oxygen depletion is believed to have been the cause. However, there was considerable uncertainty as no oxygen data is available from the time of the event. Microbes are sensitive to changes in oxygen and can be used as bioindicators of oxygen loss. In this study, we analyze microbial communities in water samples collected over several years at the Flower Garden Banks, including shortly after the mortality event. Our findings indicate that compared to normal conditions, oxygen depletion was widespread in the deep-water layer during the mortality event. Hydrographic analysis of water masses further revealed some of this low oxygen water likely upwelled onto the coral reef.

microbiology↗

bioRxiv2020

Loss of RNF43/ZNRF3 predisposes to Hepatocellular carcinoma by impairing liver regeneration and altering liver fat metabolism

The homologous E3 ubiquitin ligases RNF43/ZNRF3 negatively regulate WNT signalling activation. Recently, both genes have been found mutated in several types of cancers. Specifically, loss-of-function mutations result in adenoma formation in mouse small intestine. However, their role in liver cancer has not been explored yet. Here we describe that hepatocyte-specific deletion of both Rnf43/Znrf3 results in altered lipid metabolism and a non-alcoholic steatohepatitis (NASH) phenotype in mouse, in the absence of exogenous fat supplementation. The effect is cell-autonomous, as evidenced by the intracellular lipid accumulation detected in mutant liver organoids. Upon chronic liver damage, Rnf43/Znrf3 deletion results in impaired hepatocyte regeneration, subsequent to an imbalance between hepatocyte differentiation and proliferation, which leads to hepatocellular carcinoma. Remarkably, hepatocellular carcinoma patients with mutations in ZNRF3 also present altered lipid metabolism and poorer survival. Our findings imply that Wnt activation through the RNF43/ZNRF3 module predisposes to liver cancer by altering the liver lipid metabolic ground-state and impairing liver regeneration, which combined, facilitate the progression towards malignancy. Our results highlight the requirement for personalized therapeutic or dietary interventions for those RNF43/ZNRF3 mutated individuals at risk of developing steatosis, NASH and/or liver cancer.

cancer biology↗

bioRxiv2020

Detection of Prenatal Alcohol Exposure Using Machine Learning Classification of Resting-State Functional Network Connectivity Data

IntroductionPrevious work utilizing resting state fMRI to measure functional network connectivity in rodents with moderate prenatal alcohol exposure (PAE) revealed several sex- and region-dependent alterations in FNC implicating FNC as potential biomarker for PAE. Given that FNC is sensitive to neurological and psychiatric conditions in humans, here, we explore the use of previously acquired FNC data and machine learning methods to detect PAE among a sample of rodents exposed to moderate PAE and controls exposed to a saccharin solution. Materials & MethodsWe utilized previously acquired fMRI data from 48 adult rats 24 PAE (12 male 12 female) and 24 saccharin exposed (SAC) controls (12 male and 12 female) for classification. The entire data sample was utilized to perform binary classification (SAC or PAE) of FNC data with multiple support vector machine (SVM) kernels and out-of-sample cross-validation to evaluate classification performance. ResultsResults revealed accuracy rates of 62.5% for all samples, 58.3% for males, and 79.2% for females using a quadratic SVM kernel to classify moderate PAE from FNC data. In addition, brain networks localized to hippocampal and cortical regions contributed strongly to QSVM classifications. ConclusionOur results suggest overall modest classification performance of a QSVM to detect moderate PAE from FNC data gathered from adult rats, yet good performance among females. Further developments and refinement of the technique hold promise for the detection of PAE in earlier developmental time periods that potentially offer additional tools for the non-invasive detection of PAE from FNC data. IMPACT STATEMENTThe diagnosis of fetal alcohol spectrum disorders (FASDs) can be challenging in individuals who lack the hallmark facial dysmorphologies associated with heavy prenatal alcohol exposure (PAE). The absence of a diagnosis prevents individuals with PAE from receiving the treatment and services that improves quality of life outcomes. This research explores the use of preclinical functional network connectivity data and machine learning techniques as a novel and non-invasive means of detecting PAE. Our aim is to contribute basic science towards improving diagnostic strategies that can lead to securing timely and appropriate support for individuals with FASD and their caregivers.

neuroscience↗

bioRxiv2020

Structure of human endo-α-1,2-mannosidase (MANEA), an antiviral host-glycosylation target

Mammalian protein N-linked glycosylation is critical for glycoprotein folding, quality control, trafficking, recognition and function. N-linked glycans are synthesized from Glc3Man9GlcNAc2 precursors that are trimmed and modified in the endoplasmic reticulum (ER) and Golgi apparatus by glycoside hydrolases and glycosyltransferases. Endo--1,2-mannosidase (MANEA) is the sole endo-acting glycoside hydrolase involved in N-glycan trimming and unusually is located within the Golgi, where it allows ER escaped glycoproteins to bypass the classical N-glycosylation trimming pathway involving ER glucosidases I and II. There is considerable interest in the use of small molecules that disrupt N-linked glycosylation as therapeutic agents for diseases such as cancer and viral infection. Here we report the structure of the catalytic domain of human MANEA and complexes with substrate-derived inhibitors, which provide insight into dynamic loop movements that occur upon substrate binding. We reveal structural features of the human enzyme that explain its substrate preference and the mechanistic basis for catalysis. The structures inspired the development of new inhibitors that disrupted host protein N-glycan processing of viral glycans and reduced infectivity of bovine viral diarrhea and dengue viruses in cellular models. These results may contribute to efforts of developing broad-spectrum antiviral agents and bring about a more detailed view of the biology of mammalian glycosylation. SIGNIFICANCE STATEMENTThe glycosylation of proteins is a major protein modification that occurs extensively in eukaryotes. Glycosidases in the secretory pathway that trim N-linked glycans play a key role in protein quality control and in the specific modifications leading to mature glycoproteins. Inhibition of glucosidases in the secretory pathway is a proven therapeutic strategy, and one with great promise in the treatment of viral disease. The enzyme endo--1,2-mannosidase, MANEA, provides an alternative processing pathway to evade glucosidase inhibitors. We report the 3D structure of human MANEA and complexes with enzyme inhibitors that we show act as antivirals for bovine viral diarrhea and human dengue viruses. The structure of MANEA will support inhibitor optimization and the development of more potent antivirals.

biochemistry↗

bioRxiv2020

Stability of extemporaneously compounded amiloride nasal spray

Anxiety disorders (AD) are the most common mental illnesses affecting an estimated 40 million adults in the United States. Amiloride, a diuretic agent, has shown efficacy in treating AD in preclinical models by inhibiting the acid-sensing ion channels (ASIC). By delivering amiloride via nasal route, rapid onset of action can be achieved due to direct "nose-to-brain" access. Therefore, this study reports the formulation, physical, chemical, and microbiological stability of an extemporaneously prepared amiloride 2 mg/mL nasal spray. The amiloride nasal spray was prepared by adding 100 mg of amiloride hydrochloride to 50 mL of sterile water for injection in a sterile reagent bottle. A stability-indicating high-performance liquid chromatography (HPLC) method was developed and validated. Forced-degradation studies were performed to confirm the ability of the HPLC method to identify the degradation products from amiloride distinctively. The physical stability of the amiloride nasal spray was assessed by pH, clarity, and viscosity assessments. For chemical stability studies, samples of nasal sprays stored at room temperature were collected at time-points 0, 3 hr., 24 hr., and 7 days and were assayed in triplicate using the stability-indicating HPLC method. Microbiological stability of the nasal spray solution was evaluated for up to 7 days based on the sterility test outlined in United States Pharmacopoeia (USP) chapter 71. The stability-indicting HPLC method identified the degradation products of amiloride without interference from amiloride. All tested solutions retained over 90% of the initial amiloride concentration for the 7-day study period. There were no changes in color, pH, and viscosity in any sample. The nasal spray solutions were sterile for up to 7 days in all samples tested. An extemporaneously prepared nasal spray solution of amiloride hydrochloride (2 mg/mL) was physically, chemically, and microbiologically stable for 7 days when stored at room temperature.

pharmacology and toxicology↗