Biology subjects

Awad, M.

Publications and source records attributed to Awad, M..

9 recordsLinked to original sources

bioRxiv2026

Mutations in mfd cause Staphylococcus aureus mucoid hyper-biofilm phenotype in chronic rhinosinusitis

Chronic Rhinosinusitis (CRS) is a common chronic inflammation of the paranasal sinus mucosa. Staphylococcus aureus contributes to its severity through biofilm formation. In this study, we isolated eight sequential methicillin-resistant S. aureus (MRSA) isolates from a patient with severe CRS over a period of 672 days (T1-T8). The isolates were phenotypically and genomically characterised, and the extracellular biofilm proteome analysed. We identified an accumulation of mutations that included the acquisition of an IS21 family insertion sequence inactivating the icaR gene and nucleotide variants in various genes including the transcription repair coupling factor (mfd). The genomic changes were associated with a switch to a mucoid phenotype from T3 onwards (Day 178), with a significant increase in biofilm-forming capacity and the secretion of multiple enterotoxins. Targeted mutagenesis confirmed mfd is a regulator of strain mucoidy with enhanced biofilm and enterotoxin production. These findings support mfd as a target for novel anti-virulence therapies.

microbiology↗

bioRxiv2025

In vivo imaging of reactive oxygen species after myocardial ischemia-reperfusion injury: a large animal multimodal imaging and transcriptomic study

BackgroundReactive oxygen species (ROS) contribute to myocardial ischemia-reperfusion injury (IRI), but in-vivo data on the spatial myocardial distribution and systemic effects of ROS after IRI remain limited. This multimodal CMR and PET/CT study aimed to non-invasively image ROS activity in a clinically-relevant swine model of IRI using [18F]ROStrace, a fluorine-18-labeled analogue of dihydroethidium (DHE), and to investigate regional changes in ROS activity in the infarcted myocardium during the subacute post-IRI phase. MethodsIRI was induced by percutaneous occlusion of the left anterior descending artery for 90 minutes in swine (N=9). CMR and whole-body PET/CT imaging with [18F]ROStrace were performed before myocardial infarction (MI) and 3-5 days post-MI to assess ROS in non-infarct myocardium, lungs, bone marrow, spleen and skeletal muscle. Late gadolinium enhanced CMR was performed to structurally characterize infarct regions. Post-MI, in vivo [18F]ROStrace signal in infarcted myocardium was compared with remote, non-infarcted myocardium and validated via ex vivo DHE fluorescent imaging. Bulk RNA-sequencing (RNA-seq) and Gene Ontology pathway analysis were conducted on biopsies from infarct and remote myocardial tissue to identify differentially expressed genes and pathways connected to oxidative stress. ResultsDuring the subacute phase following MI, [18F]ROStrace fractional uptake rate (FUR; min-1) was significantly increased in skeletal muscle, compared to baseline (0.011{+/-}0.003 vs 0.016{+/-}0.005, p=0.04), with a trend toward increased FUR in bone marrow (0.046{+/-}0.009 vs 0.056{+/-}0.011, p=0.12) and the left ventricular free wall (0.067{+/-}0.007 vs 0.073{+/-}0.010, p=0.15). Within the myocardium, [18F]ROStrace FUR ((min-1)/(mL/min/g)) was significantly higher in infarcted compared to non-infarcted myocardium regions (0.110{+/-}0.034, vs 0.148{+/-}0.035, p=0.0005). DHE staining confirmed elevated ROS levels in the infarcted myocardium. RNA-seq identified 8,707 differentially expressed genes between infarct and remote myocardium, with downregulated pathways in the infarct associated with mitochondrial function, cellular respiration, and metabolic adaptation. ConclusionThis study demonstrated MI ROS imaging using [18F]ROStrace using a whole-body PET/CT scanner and structural assessment with CMR. Systemic and myocardial increases in ROS activity were observed post-MI, accompanied by substantial molecular alterations in infarcted tissue. These findings show potential imaging strategies to evaluate therapeutic targets that can mitigate oxidative stress after MI.

bioengineering↗

bioRxiv2025

Ultraflexible, Biodegradable ECoG Arrays via Rapid Fabrication Enables High-Resolution Cortical Mapping and Seizure Network Classification In Vivo

Neural interfaces are essential tools for diagnosing and managing neurological disorders, yet conventional electrocorticography (ECoG) devices are limited by mechanical mismatch with brain tissue, chronic inflammation, and poor scalability. Here, we introduce a fully inkjet-printed, flexible, and biodegradable ECoG array fabricated on ultrathin polycaprolactone films with gold nanoparticle electrodes. The arrays achieve among the highest electrode densities reported for additive manufacturing (7.44 electrodes/mm{superscript 2}) while maintaining low impedance (10.6 k{Omega} at 1 kHz) and high-fidelity recordings (SNR 28 dB). A rapid, maskless prototyping process relying on photonic sintering enables scalable, cost-effective fabrication. In vivo, the devices conformally mapped cortical seizure propagation and resolved distinct ictal dynamics in a rat model. Histology at 30 days confirmed preserved neuronal density and astrocytic response comparable to controls, indicating minimal chronic inflammation. A convolutional neural network trained on recorded signals classified seizure stages with >95% accuracy, underscoring the translational potential for real-time monitoring and closed-loop neuromodulation. This platform unites rapid prototyping, biodegradability, and high performance, providing a scalable route toward next-generation, patient-specific, and disposable neural interfaces for epilepsy and other neuroengineering applications.

bioengineering↗

bioRxiv2025

LicD-Mediated Cell Wall Decoration Governs Phage Sensitivity in Enterococcus faecalis Clinical Isolates

Enterococcus faecalis has emerged as a prevalent antibiotic-resistant pathogen in clinical settings. Herein, we report the identification of three novel lytic phages targeting vancomycin-resistant E. faecalis. While the isolated phages all belonged to the Kochikohdavirus genus, there were distinctive differences in their tail fibre proteins, affecting their adsorption. The phages showed strong antibacterial activity with wide host range, infecting >90% of the tested E. faecalis clinical and hospital wastewater isolates (n=13) with variable efficiency. The variation in host range was genomically correlated to the presence of the LicD gene in phage sensitive bacteria, which is responsible for phosphorylcholine decoration of the bacterial cell wall. Furthermore, the isolated phages were predicted to harbour genes encoding for depolymerase enzymes, which was confirmed by in vitro testing showing a >80% reduction in biofilm biomass. Phages inhibited bacterial growth for [≥]12 hours, followed by the emergence of bacteriophage insensitive mutants (BIMs) that were 4-fold more sensitive to vancomycin compared to parent strains. In addition, the isolated BIMs showed less capability of evading THP-1 macrophage and produced weaker biofilms. These findings underpin the potential of the isolated phages in combating recalcitrant E. faecalis associated biofilm-mediated infections.

microbiology↗

bioRxiv2024

A Method for Electrical Stimulus Artifact Removal Exploiting Neural Refractoriness: Validation by Contrasting Cathodic and Anodic Stimulation

ObjectiveTo present a novel method for removing stimulus transient that exploits the absolute refractory period of electrically excitable neural tissues. BackgroundElectrical stimulation often generates significant signal artifacts that can obscure important physiological signals. Removal of the artifact and understanding latent information from these signals could provide objective measures of circuit engagement, potentially driving advancements in neuromodulation research and therapies. MethodsWe conducted intracranial physiology studies on five consecutive patients with Parkinsons disease who underwent deep brain stimulation (DBS) surgery as part of their routine care. Monopolar stimuli (either cathodic or anodic) were delivered in pairs through the DBS electrode across a range of inter-stimulus intervals. Recordings from adjacent unused electrode contacts used broadband sampling and precise synchronization to generate a robust template for the stimulus transient during the absolute refractory period. These templates of stimulus transient were then subtracted from recordings at different intervals to extract and analyze the residual neural potentials. ResultsAfter artifact removal, the residual signals exhibited absolute and relative refractory periods with timing indicative of neural activity. Cathodic and anodic DBS pulses generated distinct patterns of local tissue activation, showing phase independence from the prior stimulus. The earliest detectable neural responses occurred at short peak latencies (ranging from 0.19 to 0.38 ms post-stimulus) and were completely or partially obscured by the stimulus artifact prior to removal. Cathodic stimuli produced stronger local tissue responses than anodic stimuli, aligning with clinical observations of lower activation thresholds for cathodic stimulation. However, cathodic and anodic pulses induced artifact patterns that were equivalent but opposite. InterpretationThe proposed artifact removal technique enhances prior approaches by allowing direct measurement of local tissue responses without requirements for stimulus polarity reversal, template scaling, or specialized filters. This approach could be integrated into future neuromodulation systems to visualize stimulus-evoked neural potentials that would otherwise be obscured by stimulus artifacts.

bioengineering↗

bioRxiv2024

Polyploid genome assembly of Cardamine chenopodiifolia

BackgroundCardamine chenopodiifolia is an amphicarpic plant that develops two fruit morphs, one above and the other below ground. Above-ground fruit disperse their seeds by explosive coiling of the fruit valves, while below-ground fruit are non-explosive. Amphicarpy is a rare trait that is associated with polyploidy in C. chenopodiifolia. Studies into the development and evolution of this trait are currently limited by the absence of genomic data for C. chenopodiifolia. ResultsWe produced a chromosome-scale assembly of the octoploid C. chenopodiifolia genome using high-fidelity long read sequencing with the Pacific Biosciences platform. We successfully assembled 32 chromosomes and two organelle genomes with a total length of 597.2 Mbp and an N50 of 18.8 kbp (estimated genome size from flow cytometry: 626 Mbp). We assessed the quality of this assembly using genome-wide chromosome conformation capture (Omni-C) and BUSCO analysis (97.1% genome completeness). Additionally, we conducted synteny analysis to infer that C. chenopodiifolia likely originated via allo-rather than auto-polyploidy and phased one of the four sub-genomes. ConclusionsThis study provides a draft genome assembly for C. chenopodiifolia, which is a polyploid, amphicarpic species within the Brassicaceae family. This genome offers a valuable resource to investigate the under-studied trait of amphicarpy and the origin of new traits by allopolyploidy.

plant biology↗

bioRxiv2024

Testosterone-Induced Metabolic Changes in Seminal Vesicle Epithelial cells Alter Plasma Components to Enhance Sperm Fertility

Male factors account for almost half of the causes of infertility. In rodents and humans, most of the components of semen are supplied by the seminal vesicles, and they support male reproductive ability, but there are many unknown details. In this study, the metabolic changes in the seminal vesicle epithelial cells were focused on, and the mechanisms by which testosterone affected the seminal plasma composition were investigated. A factor improving the linear motility of sperm was secreted from the seminal vesicles, and it was produced in an androgen-dependent manner. Bioassays, gene expression, and flux analysis studies demonstrated that testosterone promotes glucose uptake in seminal vesicle epithelial cells via GLUT4, resulting in fatty acid synthesis. ACLY was a critical factor in this metabolic change, which produced fatty acid, especially oleic acid. In conclusion, the critical role of testosterone-induced metabolic changes in the seminal vesicles is to ensure the synthesis of fatty acid. These findings suggest that testosterone-dependent lipid remodeling may contribute to sperm straight-line motility, and further functional verification is required. One Sentence Summary Testosterone promotes the conversion of glucose to fatty acid by increasing the expression of ACLY in seminal vesicle epithelial cells, thereby regulating the seminal plasma components.

cell biology↗

bioRxiv2022

O-GlcNAc glycosylation orchestrates fate decision and niche function of bone marrow stromal progenitors

In mammals, interactions between the bone marrow (BM) stroma and hematopoietic progenitors contribute to bone-BM homeostasis. Perinatal bone growth and ossification provide a microenvironment for the transition to definitive hematopoiesis; however, mechanisms and interactions orchestrating the development of skeletal and hematopoietic systems remain largely unknown. Here, we establish intracellular O-linked {beta}-N-acetylglucosamine (O-GlcNAc) modification as a posttranslational switch that dictates the differentiation fate and niche function of early BM stromal cells (BMSCs). By modifying and activating RUNX2, O-GlcNAcylation promotes osteogenic differentiation of BMSCs and stromal IL-7 expression to support lymphopoiesis. In contrast, C/EBP{beta}-dependent marrow adipogenesis and expression of myelopoietic stem cell factor (SCF) is inhibited by O-GlcNAcylation. Ablating O-GlcNAc transferase (OGT) in BMSCs leads to impaired bone formation, increased marrow adiposity, as well as defective B-cell lymphopoiesis and myeloid overproduction in mice. Thus, the balance of osteogenic and adipogenic differentiation of BMSCs is determined by reciprocal O-GlcNAc regulation of transcription factors, which simultaneously shapes the hematopoietic niche.

physiology↗

bioRxiv2020

GALA: gap-free chromosome-scale assembly with long reads

High-quality genome assembly has wide applications in genetics and medical studies. However, it is still very challenging to achieve gap-free chromosome-scale assemblies using current workflows for long-read platforms. Here we propose GALA (Gap-free long-read assembler), a chromosome-by-chromosome assembly method implemented through a multi-layer computer graph that identifies mis-assemblies within preliminary assemblies or chimeric raw reads and partitions the data into chromosome-scale linkage groups. The subsequent independent assembly of each linkage group generates a gap-free assembly free from the mis-assembly errors which usually hamper existing workflows. This flexible framework also allows us to integrate data from various technologies, such as Hi-C, genetic maps, a reference genome and even motif analyses, to generate gap-free chromosome-scale assemblies. We de novo assembled the C. elegans and A. thaliana genomes using combined Pacbio and Nanopore sequencing data from publicly available datasets. We also demonstrated the new methods applicability with a gap-free assembly of a human genome with the help a reference genome. In addition, GALA showed promising performance for Pacbio high-fidelity long reads. Thus, our method enables straightforward assembly of genomes with multiple data sources and overcomes barriers that at present restrict the application of de novo genome assembly technology.

bioinformatics↗