Biology subjects

Bell, M.

Publications and source records attributed to Bell, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Antimicrobial Resistance Profiling and Phenotypic Characterization of Archived Clinical Bacillus paranthracis Strains

Bacillus paranthracis was formally defined as a species in 2017, after decades of carrying the name "emetic B. cereus" based on cereulide production and clustering within B. cereus sensu lato phylogenetic group III. Commonly associated with foodborne intoxication, reports rarely link B. paranthracis to non-foodborne clinical illness. As such, the new taxonomy and close resemblance of the name to the biothreat pathogen Bacillus anthracis cause confusion in diagnostic and public health settings. To address this issue, B. paranthracis clinical strains (n=20) from the CDC collection were tested with microbiological methods used for identification of B. anthracis and antimicrobial susceptibility testing. Some B. paranthracis phenotypes were similar to B. anthracis, however others were inconsistent across strains. Like B. anthracis: 3 strains tested capsule positive, 5 were non-hemolytic on blood agar, and 9 non-motile. All B. paranthracis strains were resistant to gamma phage lysis, which differentiated them from B. anthracis. Treatment regimens for B. paranthracis infections are not well established, as antimicrobial therapy is not indicated for emetic intoxication caused by B. paranthracis. Notably, six B. paranthracis strains had elevated minimal inhibitory concentrations to anthrax-recommended antibiotics: one for ciprofloxacin, three for doxycycline and tetracycline, and two for clindamycin. Rapid MinION sequencing was assessed for antimicrobial resistance detection prediction but had limited value when using PiMA v.1. These microbiological observations and susceptibility profiles of B. paranthracis expand our understanding of this pathogen, strengthening our ability to differentiate this bacterium from B. anthracis to improve diagnosis and patient outcomes. IMPORTANCEThis study describes in vitro characterization of 20 archived clinical strains of B. paranthracis, an opportunistic pathogen identified more frequently in recent reports. Our findings highlight phenotypic differences and similarities between B. paranthracis and B. anthracis using standard microbiological methods and drug susceptibility profiling. We also assess a rapid B. anthracis specific MinION long read genome sequencing workflow with B. paranthracis. This report highlights the overlapping morphological features shared by B. paranthracis and B. anthracis to improve future laboratory diagnosis and strengthen anthrax preparedness. This article will effectively reach an audience of public health professionals and microbiologists strengthening anthrax preparedness.

microbiology↗

bioRxiv2025

Comparative circadian transcriptome analysis reveals dampened and phase-advanced rhythms in sun-exposed human skin

BackgroundDaily molecular rhythms modulate skin physiology. However, the effects of chronic sun exposure on these rhythms remain unstudied. ObjectivesThis study aimed to identify and compare rhythmic genes and pathways in photoprotected and chronically photoexposed human skin in vivo. MethodsTwenty healthy White women, aged 51-63, with moderate-severe photoageing of the dorsal forearm were recruited. Skin biopsies (3mm) were taken from photoprotected (upper buttock) and photoexposed (dorsal forearm) skin of each individual at noon, 6PM, midnight, and 6AM, across a 24-hour cycle. Skin biopsies were analysed by RNA sequencing. Cosinor analysis identified cycling genes along with their amplitudes and peak expression phases. Nested models were used to identify genes that were differentially rhythmic between the photoprotected and photoexposed sites. Phase set and gene set analyses identified pathways enriched among rhythmic transcripts or altered between the two sites. ResultsIn the photoprotected buttock skin, 1546 genes (12%) met the criteria for cycling. In photoexposed forearm skin, the number was reduced to 959 (8%). As a group, transcripts that cycled in both sites had overall higher amplitude in photoprotected skin (p < 2.2e-16). Peak expression times for these transcripts showed a pronounced bimodal distribution and were clustered in the early morning and mid-afternoon. Distributions of peak times were significantly different between photoexposed and photoprotected skin (p < 0.00025), with peak times advanced in photoexposed skin. We identified 480 genes with significantly different rhythmic properties between the skin sites. Genes involved in DNA repair, MYC targets, E2F and G2M checkpoint pathways were enriched among those that showed higher amplitude oscillations in photoprotected skin. Genes involved in epithelial mesenchymal transition and apical junction pathways showed higher amplitude oscillations in photoexposed skin. ConclusionsTemporal rhythms have a marked influence on skin molecular physiology and are altered in photoaged skin. Temporally advanced cycling patterns and a reduced number of rhythmic genes in photoexposed as compared to photoprotected skin suggest that chronic UV exposure may disrupt and/or reprogram circadian output rhythms to further alter skin physiology.

cell biology↗

bioRxiv2025

A developmental program of early residency promotes the differentiation of divergent uterine NK cell subsets in humans

Human uterine natural killer cells (uNKs) are a tissue-resident, innate lymphocyte population that have critical roles in supporting pregnancy health. uNKs derive from circulatory cells in the peripheral blood which immigrate into the endometrium and become resident as they reconstitute the uterine lining after menses. How tissue-resident uterine NK cells arise from blood-based precursor cells is unknown. Here, we identify early tissue immigrants, developmental intermediates, and mature effector states in human endometrium. We also uncover a transcriptional program of TGF-{beta} responsive genes that is upregulated in recent tissue immigrants prior to expression of effector molecules. Differences in TGF-{beta} responsiveness of uNK precursors promote differential expression of divergent effector uNK subsets, resulting in either repression or preservation of cytotoxic effector potential. Collectively, these data suggest a molecular mechanism of tissue-resident uNK maturation that links tissue residency with the acquisition of divergent effector functions in human endometrium.

immunology↗

bioRxiv2025

Inhibition of formate production blocks CD8+ T-cell responses and delays disease onset in a mouse model of type 1 diabetes

The one-carbon metabolic pathway is essential for proliferating cells and has recently been identified as an immunomodulatory target in CD4 T cells. However, its role in other immune cell types has not been fully established. We investigated the function of the one-carbon pathway in CD8 T cells, which are the primary effectors responsible for the destruction of pancreatic beta cells that causes type 1 diabetes. Enzymes involved in the one-carbon pathway, as well as levels of formate--a critical intermediate--were upregulated during CD8 T-cell activation. Pharmacological inhibition of MTHFD2, a mitochondrial enzyme involved in one-carbon metabolism, suppressed CD8 T-cell activation, proliferation, and effector function. Mechanistically, this effect was mediated by reduced signaling through KRAS and the mTORC1 downstream targets HIF1, S6, and STAT3. As previously shown in CD4 T cells, formate supplementation reversed the effects of MTHFD2 inhibition on activation, proliferation, and function of CD8+ T cells, and prevented the reduction of the TCF1high CD8 progenitor cell population, which has been shown to drive anti-beta cell autoimmunity. Formate levels were elevated in the immune cells isolated from pancreatic lymph nodes during the insulitis stage in non-obese diabetic mice. Treatment of euglycemic non-obese diabetic mice with an MTHFD2 inhibitor during the insulitis stage delayed CD8 T-cell infiltration into pancreatic islets and postponed the onset of type 1 diabetes. These findings reveal a new paradigm for preventing and delaying the onset of type 1 diabetes.

immunology↗

bioRxiv2025

Denoising 7T Structural MRI with Conditional Generative Diffusion Models

Purpose7T MRI offers ultra-high resolution and improved sensitivity for iron deposition in neurodegenerative disorders, but commonly used acquisitions are long and hence challenging, especially for elderly subjects. Efficiently denoising a short acquisition to achieve the image quality of a longer acquisition would be of translational benefit. Materials and MethodsWe introduce a conditional diffusion model derived from generative AI (a 7T Conditional Diffusion Model, 7TCDM) that was trained on native single-acquisition 2D reconstructions and referenced multi-repetition images to guide the denoising process and improve SNR and contrast. 7TCDM model was tested on 2D T2-weighted gradient-echo imaging from 19 participants, including healthy controls and individuals with mild cognitive impairment or Alzheimers disease (AD). 7TCDMs performance was assessed using Mean Squared Error (MSE), Peak Signal-to-Noise Ratio (PSNR), Structural Similarity Index Measure (SSIM), and comprehensive reader studies. ResultsReferencing the multi-repetition ground truth, 7TCDM improved the single-acquisition original image by 29.1% in MSE, 5.8% in PSNR, and 9.4% in SSIM, and outperformed convolutional neural network-based models in all metrics. Expert rater evaluations confirmed superior image quality, with significantly enhanced detail and contrast preservation in regions such as the hippocampi, white matter lesions, and small cortical veins. The model also demonstrated robust performance in both the concurrently acquired and publicly available 3D multi-echo gradient echo acquisitions, which the model was not trained on. ConclusionsThe 7T Conditional Diffusion Model provides high-quality denoised images from shorter scans, increasing the feasibility of scanning patients in shorter times while preserving essential anatomical and pathological details.

neuroscience↗

bioRxiv2025

Recapitulating physiologically relevant oxygen levels and extracellular matrix remodeling in patient-derived tumor-immune tunable models reveal targeting opportunities for immunologically cold high-grade serous tumors

High-grade serous tumors are immunologically cold, characterized by limited immune cell infiltration and reduced clinical outcome, primarily due to hypoxia and extensive extracellular matrix remodeling that disrupt tumor-stromal-immune interactions. However, current experimental models fail to fully capture oxygen and matrix microenvironmental features, limiting progress in understanding tumor-immune dynamics and developing effective treatments. Here, we demonstrate that patient-derived tumor-immune tunable models, mimicking physiologically relevant oxygen levels and extracellular matrix remodeling, recapitulate the hypoxia-induced stromal/matrix dysregulation, which causes impaired immune infiltration, and enable dissecting targeted opportunities via TGF-{beta} signaling. The models integrate cancer cells co-cultured with cancer-associated fibroblasts and exposed to immune cells as multi-culture or challenged them to infiltrate into a 3D model bioengineered with autologous plasma from the matching patient or onto decellularized human ovaries. By bioengineering physiologically relevant oxygen levels of hypoxic tumors and physoxic ovaries, we uncovered that intratumoral hypoxia acts as a friend and a foe, causing hypoxia-induced stromal-driven impaired immune infiltration but enhancing the activation and cytotoxicity of CD8+ T cells. We also showed that targeting TGF-{beta} signaling reversed the hypoxia-induced stromal-driven impaired immune infiltration. These human-relevant tunable models may aid the development of targeted therapies to turn immunologically cold tumors into hot ones.

bioengineering↗

bioRxiv2025

First-void urine and cervicovaginal brushes as sampling devices for vaginal microbiome studies: a proof-of-concept study

This proof-of-concept study compares first-void urine (FVU) and cervicovaginal brushes to vaginal swabs for microbiome profiling in ten women. FVU and brushes provided comparable results in most cases, though storage conditions influenced microbial composition, especially for FVU. Despite limitations in sample size and diversity in participants, findings support these methods potential for self-sampling in womens health research, emphasizing the need for optimized techniques to improve vaginal microbiome profiling.

microbiology↗

bioRxiv2025

The role of lipoteichoic acid in Staphylococcus aureus cell wall integrity

In Staphylococcus aureus, lipoteichoic acid (LTA) is crucial for growth, cell division, osmoprotection, and beta-lactam resistance, yet its molecular mechanisms remain unclear. This study reveals that LTA binds to multiple proteins involved in cell wall processes and preserves cell wall integrity by regulating one of the LTA-binding proteins, ScaH. ScaH is a peptidoglycan hydrolase predicted to have N-acetylglucosaminidase and amidase/peptidase activities. LTA inhibits ScaHs enzymatic activities by direct binding and represses scaH transcription by an unknown mechanism. During early growth, LTA is highly expressed and sequesters ScaH at the cell membrane, preventing ScaH activity in the cell wall. However, LTA expression decreases during the late growth phase, leading to ScaH translocation into the cell wall. This reduction in LTA coincides with increased wall teichoic acid (WTA) expression and cleavage of the LTA synthase LtaS. In the LTA-null mutant, ScaH inactivation restored peptidoglycan crosslinking, osmoresistance, and beta-lactam resistance both in vitro and in vivo. These findings suggest that LTA protects the cell wall by suppressing ScaH expression and activity while sequestering it during active growth. Additionally, the reciprocal expression patterns of LTA and WTA indicate an interconnected regulation of teichoic acids in S. aureus, with their roles likely depending on the growth phase. ImportanceStaphylococcus aureus is a significant human pathogen, with LTA playing a crucial role in cell viability, division, and maintaining cell wall integrity. Targeting LTA synthesis holds promise for the development of new therapeutics against S. aureus. Disruption of LTA synthesis leads to phenotypes indicative of compromised cell wall integrity, such as reduced crosslinking, osmosensitivity, and heightened beta-lactam sensitivity, although the precise underlying mechanisms remain unclear. Our research demonstrates that LTA contributes to cell wall integrity by regulating the expression, activity, and translocation of the peptidoglycan hydrolase ScaH. Additionally, LTAs binding to the cell wall synthesis enzymes suggests a role in modulating cell wall integrity through these interactions. These findings significantly advance our understanding of LTAs physiological functions and may serve as a foundation for the development of novel therapeutics targeting S. aureus and other Gram-positive pathogens.

microbiology↗

bioRxiv2024

Acute increase of protein O-GlcNAcylation in mice leads to transcriptome changes in the brain opposite to what is observed in Alzheimer Disease

Enhancing protein O-GlcNAcylation by pharmacological inhibition of the enzyme O-GlcNAcase (OGA) is explored as a strategy to decrease tau and amyloid-beta phosphorylation, aggregation, and pathology in Alzheimers disease (AD). There is still more to be learned about the impact of enhancing global protein O-GlcNAcylation, which is important for understanding the mechanistic path of using OGA inhibition to treat AD. In this study, we investigated the acute effect of pharmacologically increasing O-GlcNAc levels, using OGA inhibitor Thiamet G (TG), on normal mouse brains. We hypothesized that the transcritome signature in respones to TG treatment provides a comprehensive view of the effect of OGA inhibition. We sacrificed the mice and dissected their brains after 3 hours of saline or 50 mg/kg TG treatment, and then performed mRNA sequencing using NovaSeq PE 150 (n=5 each group). We identified 1,234 significant differentially expressed genes with TG versus saline treatment. Functional enrichment analysis of the upregulated genes identified several upregulated pathways, including genes normally down in AD. Among the downregulated pathways were the cell adhesion pathway as well as genes normally up in AD and aging. When comparing acute to chronic TG treatment, protein autophosphorylation and kinase activity pathways were upregulated, whereas cell adhesion and astrocyte markers were downregulated in both datasets. Interestingly, mitochondrial genes and genes normally down in AD were up in acute treatment and down in chronic treatment. Data from this analysis will enable the evaluation of the mechanisms underlying the potential benefits of OGA inhibition in the treatment of AD. In particular, although OGA inhibitors are promising to treat AD, their downstream chronic effects related to bioenergetics may be a limiting factor. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=185 SRC="FIGDIR/small/613769v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@178dcf6org.highwire.dtl.DTLVardef@1f2cc78org.highwire.dtl.DTLVardef@14dfe28org.highwire.dtl.DTLVardef@16918aa_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2024

Inhibition of NFAT promotes loss of tissue resident uterine natural killer cells and attendant pregnancy complications in humans

Uterine natural killer cells (uNKs) are a tissue resident lymphocyte population that are critical for pregnancy success. Although mouse models have demonstrated that NK deficiency results in abnormal placentation and poor pregnancy outcomes, the generalizability of this knowledge to humans remains unclear. Here we identify uterus transplant (UTx) recipients as a human population with reduced uNK cells and altered pregnancy phenotypes. We show that the NK reduction in UTx correlates with impaired transcriptional programming of NK tissue residency arising from the inhibition of NFAT-mediated signaling. Our observations suggest that NFAT-dependent genes modulate multiple molecular tissue residency programs in uNKs. These include early residency programs involving AP-1-family transcription factors and TGF-{beta}-mediated upregulation of surface integrins. Collectively, our data identify a previously undescribed role for NFAT in uterine NK tissue residency and provide novel mechanistic insights into the biologic basis of pregnancy complications due to alteration of tissue resident NK subsets in humans. One Sentence SummaryRole of NFAT in uterine NK cell tissue residency

immunology↗

bioRxiv2024

Sequential Transcriptional Programs of Tissue Residency Drive Human Uterine NK Cell Development

Uterine natural killer cells are critical for pregnancy success, but the origin and development of these cells in humans remain unclear. Here we use various single cell approaches to identify the transcriptional programs governing uterine NK cell development in humans. These analyses suggest a developmental continuum which begins with seeding of the endometrium with blood immature CD56bright precursors, evolves through CD56bright endometrial founder NK cells, and ends with tissue resident decidual NK cells during pregnancy which possess non-cytotoxic functions. Our work identifies a role for sequential programs of tissue residency in the differentiation of these cells, as differentiating endometrial tissue resident NK (trNK) cells acquire early and late transcriptional programs of residency which coincide with acquisition of unique non-cytotoxic effector programs. Notably, we identified early residency programs in human endometrial trNKs by expression of NR4A2, AP-1 transcription factors, and other immediate early response genes that were shared with CD8 tissue resident memory T cells in mice, suggesting conservation of transcriptional programs of early tissue residency programs across species and cell types. Late residency programs were guided by TGF{beta}, which promoted expression of various integrins and trNK subset diversification within the non-pregnant endometrium. Altogether, these data identify the molecular foundations for endometrial trNK heterogeneity and suggest that the uterine NK diversity observed during pregnancy is established before embryo implantation and intimately tied to residency programming.

immunology↗

bioRxiv2023

Phenology across scales: an intercontinental analysis of leaf-out dates in temperate deciduous tree communities

AimTo quantify the intra-community variability of leaf-out (ICVLo) among dominant trees in temperate deciduous forests, assess its links with specific and phylogenetic diversity, identify its environmental drivers, and deduce its ecological consequences with regard to radiation received and exposure to late frost. LocationEastern North America (ENA) and Europe (EUR). Time period2009-2022 Major taxa studiedTemperate deciduous forest trees. MethodsWe developed an approach to quantify ICVLo through the analysis of RGB images taken from phenological cameras. We related ICVLo to species richness, phylogenetic diversity and environmental conditions. We quantified the intra-community variability of the amount of radiation received and of exposure to late frost. ResultsLeaf-out occurred over a longer time interval in ENA than in EUR. The sensitivity of leaf-out to temperature was identical in both regions (-3.4 days per {degrees}C). The distributions of ICVLo were similar in EUR and ENA forests, despite the latter being more species-rich and phylogenetically diverse. In both regions, cooler conditions and an earlier occurrence of leaf-out resulted in higher ICVLo. ICVLo resulted in a ca. 8% difference of radiation absorption over spring among individual trees. Forest communities in ENA had shorter safety margins as regards the exposure to late frosts, and were actually more frequently exposed to late frosts. Main conclusionsWe conducted the first intercontinental analysis of the variability of leaf-out at the scale of tree communities. North American and European forests showed similar ICVLo, in spite of their differences in terms of species richness and phylogenetic diversity, highlighting the relevance of environmental controls on ICVLo. We quantified two ecological implications of ICVLo (difference in terms of radiation absorption and exposure to late frost), which should be explored in the context of ongoing climate change, which affects trees differently according to their phenological niche.

ecology↗

bioRxiv2023

Membrane mechanics dictate axonal morphology and function

Axons are thought to be ultrathin membrane cables of a relatively uniform diameter, designed to conduct electrical signals, or action potentials. Here, we demonstrate that unmyelinated axons are not simple cylindrical tubes. Rather, axons have nanoscopic boutons repeatedly along their length interspersed with a thin cable with a diameter of [~]60 nm like pearls-on-a-string. These boutons are only [~]200 nm in diameter and do not have synaptic contacts or a cluster of synaptic vesicles, hence non-synaptic. Our in silico modeling suggests that axon pearling can be explained by the mechanical properties of the membrane including the bending modulus and tension. Consistent with modeling predictions, treatments that disrupt these parameters like hyper- or hypo-tonic solutions, cholesterol removal, and non-muscle myosin II inhibition all alter the degree of axon pearling, suggesting that axon morphology is indeed determined by the membrane mechanics. Intriguingly, neuronal activity modulates the cholesterol level of plasma membrane, leading to shrinkage of axon pearls. Consequently, the conduction velocity of action potentials becomes slower. These data reveal that biophysical forces dictate axon morphology and function and that modulation of membrane mechanics likely underlies plasticity of unmyelinated axons.

neuroscience↗

bioRxiv2023

Novel in-silico predicted matrikines are differential mediators of in vitro and in vivo cellular metabolism

The exogenous application of small peptides can beneficially affect clinical skin appearance (wrinkles) and architecture (collagen and elastic fibre deposition and epidermal thickness). However, the discovery of new bioactive peptides has not been underpinned by any guiding hypothesis. As endogenous extracellular matrix (ECM)-derived peptides produced during tissue remodelling can act as molecular signals influencing cell metabolism, we hypothesised that protease cleavage site prediction could identify putative novel matrikines with beneficial activities. Here, we present an in silico to in vivo discovery pipeline, which enables the prediction and characterisation of peptide matrikines which differentially influence cellular metabolism in vitro. We use this pipeline to further characterise a combination of two novel ECM peptide mimics (GPKG and LSVD) which act in vitro to enhance the transcription of ECM organisation and cell proliferation genes and in vivo to promote epithelial and dermal remodelling. This pipeline approach can both identify new matrikines and provide insights into the mechanisms underpinning tissue homeostasis and repair.

cell biology↗

bioRxiv2022

Intrinsic Neural Timescales in Autism Spectrum Disorder and Schizophrenia. A Replication and Direct Comparison Study

Intrinsic neural timescales (INT) reflect the duration for which brain areas store information. A posterior - anterior hierarchy of increasingly longer INT has been revealed in both typically developed individuals (TD), as well as patients diagnosed with autism spectrum disorder (ASD) and schizophrenia (SZ), though INT are, overall, shorter in both patient groups. In the present study, we attempted to replicate previously reported group differences by comparing INT of TD to ASD and SZ. We replicated the previously reported result showing reduced INT in the left lateral occipital gyrus and the right post-central gyrus in SZ compared to TD. For the first time, we also directly compared the INT of the two patient groups and found that these same two areas show significantly reduced INT in SZ compared to ASD. In ASD, significant correlations were found between INT and their clinical and phenotypic characteristics. Our results point to the left lateral occipital gyrus and the right post-central gyrus as holding potential for further diagnostic refinement of SZ.

neuroscience↗

bioRxiv2022

Spatiotemporal modeling reveals geometric dependence of AMPAR dynamics on dendritic spine morphology

The modification of neural circuits depends on the strengthening and weakening of synaptic connections. Synaptic strength is often correlated to the density of the ionotropic, glutamateric receptors, AMPAR, (-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor) at the postsynaptic density (PSD). While AMPAR density is known to change based on complex biological signaling cascades, the effect of geometric factors such as dendritic spine shape, size, and curvature remain poorly understood. In this work, we developed a deterministic, spatiotemporal model to study the dynamics of AMPAR during long term potentiation (LTP). This model includes a minimal set of biochemical events that represent the upstream signaling events, trafficking of AMPAR to and from the PSD, lateral diffusion in the plane of the spine membrane, and the presence of an extrasynaptic AMPAR pool. Using idealized and realistic spine geometries, we show that the dynamics and increase of bound AMPAR at the PSD depends on a combination of endo- and exocytosis, membrane diffusion, availability of free AMPAR, and intracellular signaling interactions. We also found non-monotonic relationships between spine volume and change in AMPAR at the PSD, suggesting that spines restrict changes in AMPAR to optimize resources and prevent runaway potentiation. Significance StatementSynaptic plasticity involves dynamic biochemical and physical remodeling of small protrusions called dendritic spines along the dendrites of neurons. Proper synaptic functionality within these spines requires changes in receptor number at the synapse, which has implications for down-stream neural functions, such as learning and memory formation. In addition to being signaling subcompartments, spines also have unique morphological features that can play a role in regulating receptor dynamics on the synaptic surface. We have developed a spatiotemporal model that couples biochemical signaling and receptor trafficking modalities in idealized and realistic spine geometries to investigate the role of biochemical and biophysical factors in synaptic plasticity. Using this model, we highlight the importance of spine size and shape in regulating bound AMPAR dynamics that govern synaptic plasticity, and predict how spine shape might act to reset synaptic plasticity as a built-in resource optimization and regulation tool.

neuroscience↗

bioRxiv2021

Crosstalk between biochemical signaling and trafficking determines AMPAR dynamics in synaptic plasticity

Synaptic plasticity involves the modification of both biochemical and structural components of neurons. Many studies have revealed that the change in the number density of the glutamatergic receptor AMPAR at the synapse is proportional to synaptic weight update; increase in AMPAR corresponds to strengthening of synapses while decrease in AMPAR density weakens synaptic connections. The dynamics of AMPAR are thought to be regulated by upstream signaling, primarily the calcium-CaMKII pathway, trafficking to and from the synapse, and influx from extrasynaptic sources. Here, we have developed a set of models using compartmental ordinary differential equations to systematically investigate contributions of signaling and trafficking variations on AMPAR dynamics at the synaptic site. We find that the model properties including network architecture and parameters significantly affect the integration of fast upstream species by slower downstream species. Furthermore, we predict that the model outcome, as determined by bound AMPAR at the synaptic site, depends on (a) the choice of signaling model (bistable CaMKII or monostable CaMKII dynamics), (b) trafficking versus influx contributions, and (c) frequency of stimulus. Therefore, AMPAR dynamics can have unexpected dependencies when upstream signaling dynamics (such as CaMKII and PP1) are coupled with trafficking modalities.

neuroscience↗

bioRxiv2020

Predicting and validating protein degradation in proteomes using deep learning

Age, disease, and exposure to environmental factors can induce tissue remodelling and alterations in protein structure and abundance. In the case of human skin, ultraviolet radiation (UVR)-induced photo-ageing has a profound effect on dermal extracellular matrix (ECM) proteins. We have previously shown that ECM proteins rich in UV-chromophore amino acids are differentially susceptible to UVR. However, this UVR-mediated mechanism alone does not explain the loss of UV-chromophore-poor assemblies such as collagen. Here, we aim to develop novel bioinformatics tools to predict the relative susceptibility of human skin proteins to not only UVR and photodynamically produced ROS but also to endogenous proteases. We test the validity of these protease cleavage site predictions against experimental datasets (both previously published and our own, derived by exposure of either purified ECM proteins or a complex cell-derived proteome, to matrix metalloproteinase [MMP]-9). Our deep Bidirectional Recurrent Neural Network (BRNN) models for cleavage site prediction in nine MMPs, four cathepsins, elastase-2, and granzyme-B perform better than existing models when validated against both simple and complex protein mixtures. We have combined our new BRNN protease cleavage prediction models with predictions of relative UVR/ROS susceptibility (based on amino acid composition) into the Manchester Proteome Susceptibility Calculator (MPSC) webapp http://www.manchesterproteome.manchester.ac.uk/#/MPSC (or http://130.88.96.141/#/MPSC). Application of the MPSC to the dermal proteome suggests that fibrillar collagens and elastic fibres will be preferentially degraded by proteases alone and by UVR/ROS and protease in combination, respectively. We also identify novel targets of oxidative damage and protease activity including dermatopontin (DPT), fibulins (EFEMP-1,-2, FBLN-1,-2,-5), defensins (DEFB1, DEFA3, DEFA1B, DEFB4B), proteases and protease inhibitors themselves (CTSA, CTSB, CTSZ, CTSD, TIMPs-1,-2,-3, SPINK6, CST6, PI3, SERPINF1, SERPINA-1,-3,-12). The MPSC webapp has the potential to identify novel protein biomarkers of tissue damage and to aid the characterisation of protease degradomics leading to improved identification of novel therapeutic targets.

bioinformatics↗