Biology subjects

Bruce, M.

Publications and source records attributed to Bruce, M..

7 recordsLinked to original sources

bioRxiv2025

Different data analysis models for detecting miRNAs using nanopores

Nanopore sensors offer exceptional sensitivity for detecting single molecules, making them ideal for early disease diagnostics. In this study, we present a multiplexed nanopore-based assay that combines DNA-barcoded probes with advanced computational analysis to detect microRNAs (miRNAs) with high specificity and quantitative accuracy. Each probe binds selectively to its target biomarker and generates a characteristic delay in the ionic current signal upon translocation through the nanopore, enabling label-free detection. We evaluated three analytical strategies for classifying delayed versus non-delayed events: (1) moving standard deviation (MSD), (2) spectral entropy (SE), and (3) a convolutional neural network (CNN). While MSD and SE rely on manually defined thresholds and exhibit limited sensitivity, the CNN model, trained on image representations of raw current traces, achieved near-perfect classification performance across all metrics. Grad-CAM visualisation confirmed that the CNN focused on biophysically relevant signal regions, enhancing interpretability and generalisability. All methods produced sigmoidal concentration-response curves consistent with expected binding kinetics, and nanopore-derived delay metrics closely matched RT-qPCR validation data. All three methods were capable of distinguishing between signal classes; however, the CNN model demonstrated superior sensitivity and robustness. This work highlights the importance of data interpretation in nanopore sensing and presents a comparative framework for binary event classification. The findings pave the way for the development of machine learning-driven nanopore diagnostics capable of detecting diverse biomarker types at the single-molecule level.

biophysics↗

bioRxiv2024

Use of Stem Cell-Derived Cardiomyocyte and Nasal Epithelium Models to Establish a Multi-Tissue Model Platform to Validate Repurposed Drugs Against SARS-CoV-2 Infection

The novel coronavirus disease (COVID-19) and any future coronavirus outbreaks will require more affordable, effective and safe treatment options to complement current ones such as Paxlovid. Drug repurposing can be a promising approach if we are able to find a rapid, robust and reliable way to down-select and screen candidates using in silico and in vitro approaches. With repurposed drugs, ex vivo models could offer a rigorous route to human clinical trials with less time invested into nonclinical animal (in vivo) studies. We have previously shown the value of commercially available ex vivo/3D airway and alveolar tissue models, and this paper takes this further by developing and validating human nasal epithelial model and embryonic stem cells derived cardiomyocyte model. Five shortlisted candidates (fluvoxamine, everolimus, pyrimethamine, aprepitant and sirolimus) were successfully compared with three control drugs (remdesivir, molnupiravir, nirmatrelvir) when tested against key variants of the SARS-CoV-2 virus including Delta and Omicron, and we were able to reconfirm our earlier finding that fluvoxamine can induce antiviral efficacy in combination with other drugs. Scalability of this high-throughput screening approach has been demonstrated using a liquid handling robotic platform for future Disease-X outbreaks.

microbiology↗

bioRxiv2021

Genomic regions associated with chocolate spot (Botrytis fabae Sard.) resistance in fababean (Vicia faba L.)

Chocolate spot (CS), caused by Botrytis fabae Sard., is an important threat to global faba bean production. Growing resistant faba bean cultivars is, therefore, paramount to preventing yield loss. To date, there have been no reported quantitative trait loci (QTLs) associated with CS resistance in faba bean. The objective of this study was to identify genomic regions associated with CS resistance using a recombinant inbred line (RIL) population derived from resistant accession ILB 938. A total of 165 RILs from the cross Melodie/2 x ILB 938/2 were genotyped and evaluated for CS reactions under replicated controlled climate conditions. QTL analysis identified five loci contributing to CS resistance on faba bean chromosomes 1 and 6, accounting for 5.0-23.4% of the total phenotypic variance. The sequences of SNP markers linked to resistance QTLs on chromosome 1 that have the largest effects encode multiple classes of putative disease and/or defense-related genes. The results of this study not only provide insight into disease-resistance QTLs, but also can be used as potential targets for marker-assisted breeding in faba bean genetic improvement for CS resistance. Key messageQTL mapping identified key genomic regions associated with chocolate spot resistance on faba bean chromosomes 1 and 6, which may serve as novel genetic tools to develop disease-resistant faba bean cultivars.

genomics↗

bioRxiv2021

Partial prevention of glucocorticoid-induced osteocyte deterioration with osteocrin gene therapy

Glucocorticoid (GC)-induced osteoporosis and subsequent bone fragility are preceded by death and dysfunction at the cellular level. In particular, short-term glucocorticoid excess suppresses osteocyte remodeling of the surrounding bone mineral, causes apoptosis of osteoblasts and osteocytes, and disrupts homeostatic bone remodeling. Preventing apoptosis and preserving osteocyte morphology and function could be effective means of preventing bone loss during glucocorticoid excess. We hypothesized that osteocrin, which preserves osteocyte viability and morphology in other models where osteocyte defects exist, could prevent osteocyte death and dysfunction in a GC excess model. We used a liver-targeted adeno-associated virus (AAV8) to induce osteocrin overexpression in mice one week prior to implantation with prednisolone or placebo pellets. After 28 days, tissues were collected for micro-CT and histological analysis. GC excess caused the expected reduction in cortical bone thickness and osteocyte canalicular length in control AAV8-treated mice, and these effects were blunted in mice overexpressing osteocrin. However, GC-induced changes in cortical porosity, trabecular bone mass, and gene expression were not prevented by osteocrin. While the mechanism of osteocrins effects on osteocyte morphology warrants further investigation, this study does not support a role for this model of osteocrin supplementation to combat the full skeletal effects of GC excess.

physiology↗

bioRxiv2021

Control of osteocyte dendrite formation by Sp7 and its target gene osteocrin

Osteocytes use an elaborate network of dendritic connections to control bone remodeling. Some osteoblasts embed within mineralized bone matrix, change shape, and become osteocytes. The molecular circuitry that drives dendrite formation during "osteocytogenesis" is poorly understood. Here we show that deletion of Sp7, a gene linked to rare and common skeletal disease, in mature osteoblasts and osteocytes causes severe defects in osteocyte dendrites. Unbiased profiling of Sp7 target genes and binding sites reveals unexpected repurposing of this transcription factor to drive dendrite formation. Osteocrin is a Sp7 target gene that promotes osteocyte dendrite formation and rescues phenotypic and molecular defects in Sp7-deficient mice. Single-cell RNA-sequencing demonstrates overt defects in osteocyte maturation in vivo in the absence of Sp7. Sp7-dependent gene networks enriched in developing osteocytes are associated with rare and common human skeletal traits. Moreover, humans homozygous for the osteogenesis imperfecta-causing SP7R316C mutation show dramatic defects in osteocyte morphology. Genes that mark osteocytes in vivo and that are regulated by Sp7 in vitro are highly enriched in neurons, highlighting shared features between osteocytic and neuronal connectivity. Taken together, these findings reveal a crucial role for Sp7 and its target gene Osteocrin in osteocytogenesis, demonstrating that pathways that control osteocyte development influence human bone diseases.

molecular biology↗

bioRxiv2020

Treating Porcine Abscesses With Histotripsy: A Pilot Study

Infected abscesses are walled-off collections of pus and bacteria. They are a common sequela of complications in the setting of surgery, trauma, systemic infections, and other disease states. Current treatment is typically limited to antibiotics with long-term catheter drainage, or surgical wash-out when inaccessible to percutaneous drainage or unresponsive to initial care efforts. Antibiotic resistance is also a growing concern. Although bacteria can develop drug resistance, they remain susceptible to thermal and mechanical damage. In particular, short pulses of focused ultrasound (i.e., histotripsy) generate mechanical damage through localized cavitation, representing a potential new paradigm for treating abscesses non-invasively, without the need for long-term catheterization and antibiotics. In this pilot study, boiling and cavitation histotripsy treatments were applied to subcutaneous and intramuscular abscesses developed in a novel porcine model. Ultrasound imaging was used to evaluate abscess maturity, for treatment monitoring and assessment of post-treatment outcomes. Disinfection was quantified by counting bacteria colonies from samples aspirated before and after treatment. Histopathological evaluation of the abscesses was performed to identify changes resulting from histotripsy treatment and potential collateral damage. Cavitation histotripsy was more successful in reducing the bacterial load while having a smaller treatment volume compared with boiling histotripsy. The results of this pilot study suggest focused ultrasound may lead to a technology for in situ treatment of acoustically accessible abscesses.

bioengineering↗

bioRxiv2019

Knowledge, attitudes and practices (KAPs) and risk factors of brucellosis at the human-animal interface in the Nile Delta, Egypt

BackgroundBrucellosis is a highly contagious zoonosis affecting human and almost all domestic species. It is a multi-burdens disease leading to severe economic losses due to disability in humans in addition to abortion, infertility and reduced milk production in animals. An Important element for effective prevention and control of brucellosis is to improve knowledge, attitude and practices of the community.\n\nObjective(s)This study aimed to assess the knowledge, attitudes and practices (KAP) related to brucellosis at human-animal interface and to determine the risk factors for human infection in the Nile Delta, Egypt.\n\nMethodsA matched case-control study was conducted at the main fever hospitals located in 6 governorates in the Nile Delta, Egypt between June 2014 and June 2016. Face-to-face interviews with cases and controls was done using a structured questionnaire. Differences in proportions of KAP variables among the cases and controls were evaluated by Pearsons Chi square test and a p value <0.05 was set as a level of significance. A multivariate conditional logistic regression analysis was built to determine the risk factors for Brucella spp. infection among study participants.\n\nResultsA total of 217 cases and 434 controls matched for age, gender and sociodemographic characteristics were enrolled and interviewed. In total, 40.7% of the participants owned animals in their households and lived in shared accommodation with animals [48.8% of cases vs 36.9% of controls; (p= 0.003)]. The majority (78.1%) used to accommodate cows and buffaloes with sheep and goats. Human brucellosis cases experienced more animal abortions comparing to the controls [(23.5% vs 9.7%, respectively), (p= 0.0003)]. The majority of the participants (82.4%) did not notify authorities in case that abortion occurs in their owned animals. Apparently, 67.4% of the participants [(70.0% of the cases vs 66.1% of the controls) (p = 0.315)] had not ever heard about brucellosis. The overall mean practice score regarding animal husbandry, processing and consumption of milk and dairy products was significantly lower among cases comparing to controls (-12.7{+/-}18.1 vs 0.68{+/-}14.2 respectively; p<0.0001). Perceived barrier for notification of animal infection and/or abortion was significantly higher among cases (p= 0.034) and positively correlated with participants education. Results of univariate analysis showed that participants who have animals especially small ruminates were at a higher risk of getting Brucella spp. infection than others. In the proposed multivariate conditional logistic regression model, the predictors of having brucellosis infection were consumption of unpasteurized milk, having consumed dairy products in the last 3 months before the study, consumption of yoghurt or home-made cheeses and involvement in contact with animals [OR (95% CI) = 4.12 (1.62 - 10.75); 2.71 (1.06 - 6.93); 2.51 (1.21 - 5.24); 1.96 (1.17- 3.30), p<0.05; and 4.97 (2.84 - 8.72)], respectively. Participants who take more protective measures against infection were at a significant lower risk of being diseased with brucellosis; [OR (95% CI) = 0.23 (0.10 - 0.58); p<0.001], respectively. A model predicting risk factors for brucellosis among those who own animal showed that frequent abortions per animal increased the chance for brucellosis infection among human cases by 49.33 fold [(95% CI)= (8.79 - 276.91); p= 0.001] whereas the practice protective measures with animals was protective for humans as well [OR (95% CI)= 0.11 (0.03-0.45); p= 0.002].\n\nConclusionConsumption of dairy products stands side by side with the contact with infected animals particularly aborted ones as the major risk factors for Brucella spp. infection among humans in Egypt. On the other hand, there is a poor knowledge, negative attitudes and risky behaviors among villagers which increase the magnitude of the risk of brucellosis transmission at the human-animal interface. This supports the need for integrating health education in the national brucellosis control programs in Egypt with a special emphasis on hygienic animal husbandry, disease notification and benefits of animal vaccination.\n\nAuthor summaryZoonotic brucellosis has a vast global burden and remains neglected in many areas of the world despite notable advances in disease containment strategies. Despite the implementation of a national brucellosis control program in Egypt, the challenges for the disease eradication are intractable and multifaceted. We modeled in the present study the multivariate factors for brucellosis persistence in Egypt which apparently pointed to lack of basic understanding of the nature of brucellosis, traditional practices, beliefs and risky behaviors being undertaken on farms and at households across a wide region of the country. Predominantly, consumption of dairy products from unregulated sources; underreporting animal infection and abortion; underutilization of animal vaccination service; unsanitary disposal of abortus; use of milk of infected/aborted ruminants and lack of protective measure when practicing animal husbandry. Together, these conflict with disease intervention strategies and contribute to disease spread and re-emergence. The proposed model can provide a framework for future containment strategies that should be adopted to support and enhance the adherence to the current national brucellosis control program.

epidemiology↗