Biology subjects

Jabbari, S.

Publications and source records attributed to Jabbari, S..

6 recordsLinked to original sources

bioRxiv2026

Mathematical modelling of a novel bioactive glass treatment for bacterial biofilms

Chronic wounds (principally pressure sores, venous leg ulcers and diabetic foot ulcers) are a drain on global health services and remain a major area of unmet clinical need. Chronic wounds are characterised by a bacterial biofilm (densely aggregated colonies of bacteria encased by a matrix of extracellular polymeric substances), which hinders innate immune response and can prevent wound healing. Bioactive glass (BG) fibres doped with antimicrobial metal ions, such as silver, can offer a promising treatment for chronic wound infections, where silver is well known for its antimicrobial activity against a range of pathogens and is commonly used in wound dressings. We first present a system of non-linear partial differential equations to model the treatment of a chronic wound biofilm infection with BG fibres. The BG fibres are assumed to have two mechanisms of action against the biofilm: physical disruption of the top layers of the biofilm by the BG fibres; and release of antimicrobial silver ions from the BG fibres, which then diffuse into the biofilm and can kill the bacteria. Treatment-associated parameters are estimated from in vitro experimental data using a combination of least-squares minimisation and Approximate Bayesian Computation (ABC). Sensitivity investigations are performed on other parameters that cannot currently be calculated experimentally to investigate their influence on treatment efficacy. We thus predict key parameter regimes that should lead to biofilm eradication, crucially informing the future design of metal-doped BG fibres to maximise treatment efficacy.

microbiology↗

bioRxiv2021

Dynamic Boolean modelling reveals the influence of energy supply on bacterial efflux pump expression

Antimicrobial resistance (AMR) is a global health issue. One key factor contributing to AMR is the ability of bacteria to export drugs through efflux pumps, which relies on the ATP-dependent expression and interaction of several controlling genes. Recent studies have shown significant cell-to-cell ATP variability exists within clonal bacterial populations, but the contribution of intrinsic cell-to-cell ATP heterogeneity is generally overlooked in understanding efflux pumps. Here, we consider how ATP variability influences gene regulatory networks controlling expression of efflux pump genes in two bacterial species. We develop and apply a generalisable Boolean modelling framework, developed to incorporate the dependence of gene expression dynamics on available cellular energy supply. Theoretical results show differences in energy availability can cause pronounced downstream heterogeneity in efflux gene expression. Cells with higher energy availability have a superior response to stressors. Further, in the absence of stress, model bacteria develop heterogeneous pulses of efflux pump gene expression which contribute to a sustained sub-population of cells with increased efflux expression activity, potentially conferring a continuous pool of intrinsically resistant bacteria. This modelling approach thus reveals an important source of heterogeneity in cell responses to antimicrobials and sheds light on potentially targetable aspects of efflux pump-related antimicrobial resistance.

systems biology↗

bioRxiv2019

Intracellular Energy Variability Modulates Cellular Decision-Making Capacity

Cells are able to generate phenotypic diversity both during development and in response to stressful and changing environments, aiding survival. The biologically and medically vital process of a cell assuming a functionally important fate from a range of phenotypic possibilities can be thought of as a cell decision. To make these decisions, a cell relies on energy dependent pathways of signalling and expression. However, energy availability is often overlooked as a modulator of cellular decision-making. As cells can vary dramatically in energy availability, this limits our knowledge of how this key biological axis affects cell behaviour. Here, we consider the energy dependence of a highly generalisable decision-making regulatory network, and show that energy variability changes the sets of decisions a cell can make and the ease with which they can be made. Increasing intracellular energy levels can increase the number of stable phenotypes it can generate, corresponding to increased decision-making capacity. For this decision-making architecture, a cell with intracellular energy below a threshold is limited to a singular phenotype, potentially forcing the adoption of a specific cell fate. We suggest that common energetic differences between cells may explain some of the observed variability in cellular decision-making, and demonstrate the importance of considering energy levels in several diverse biological decision-making phenomena.

systems biology↗

bioRxiv2018

Bacterial outer membrane vesicles provide an alternative pathway for trafficking of type III secreted effectors into epithelial cells

Outer membrane vesicles (OMVs) are proteo-liposomes universally shed by Gram-negative bacteria. Their secretion is significantly enhanced by the transition into the intra-host milieu and OMVs have been shown to play critical roles during pathogenesis. Enterohemorrhagic Escherichia coli O157 (EHEC), causes diarrheal disease in humans, and soluble toxins including Shiga-like toxins that contribute to disease severity and clinical complications including hemolytic uremic syndrome, have been shown to be OMV associated. In addition to Shiga-like toxins, EHEC produces a type III secretion system (T3SS), and T3SS effectors are associated with colonization and disease severity in vivo. Here, we show that type III secreted substrates including translocators and effectors are incorporated into OMVs independent of type III secretion activity. EHEC strains with non-functional type III secretion systems shed more OMVs and vesicles enter host cells with accelerated kinetics compared to vesicles shed from wild type EHEC. The T3SS effector translocated intimin receptor (Tir) is trafficked from OMVs into host cells and localizes to the membrane. However, its clustering on the host membrane and co-localization with bacterial pedestals is intimin-dependent. We further show that OMV-delivered Tir can cross-complement an effector-deficient EHEC strain, demonstrating that OMV-associated effectors reach the host cell in a biologically intact form. Finally, we observe that the non-LEE encoded E3 ubiquitin ligase effector NleL is also trafficked to host cells via OMVs, where it ubiquitinylates its target kinase JNK. Together, these data demonstrate that trafficking of OMV-associated effectors is a novel and T3SS-independent pathway for the delivery of active effectors to host cells.

microbiology↗

bioRxiv2017

The essential genome of Escherichia coli K-12

Transposon-Directed Insertion-site Sequencing (TraDIS) is a high-throughput method coupling transposon mutagenesis with short-fragment DNA sequencing. It is commonly used to identify essential genes. Single gene deletion libraries are considered the gold standard for identifying essential genes. Currently, the TraDIS method has not been benchmarked against such libraries and therefore it remains unclear whether the two methodologies are comparable. To address this, a high density transposon library was constructed in Escherichia coli K-12. Essential genes predicted from sequencing of this library were compared to existing essential gene databases. To decrease false positive identification of essential gene candidates, statistical data analysis included corrections for both gene length and genome length. Through this analysis new essential genes and genes previously incorrectly designated as essential were identified. We show that manual analysis of TraDIS data reveals novel features that would not have been detected by statistical analysis alone. Examples include short essential regions within genes, orientation-dependent effects and fine resolution identification of genome and protein features. Recognition of these insertion profiles in transposon mutagenesis datasets will assist genome annotation of less well characterized genomes and provides new insights into bacterial physiology and biochemistry.\n\nIMPORTANCEIncentives to define lists of genes that are essential for bacterial survival include the identification of potential targets for antibacterial drug development, genes required for rapid growth for exploitation in biotechnology, and discovery of new biochemical pathways. To identify essential genes in E. coli, we constructed a very high density transposon mutant library. Initial automated analysis of the resulting data revealed many discrepancies when compared to the literature. We now report more extensive statistical analysis supported by both literature searches and detailed inspection of high density TraDIS sequencing data for each putative essential gene for the model laboratory organism, Escherichia coli. This paper is important because it provides a better understanding of the essential genes of E. coli, reveals the limitations of relying on automated analysis alone and a provides new standard for the analysis of TraDIS data.

microbiology↗

bioRxiv2016

Lipopolysaccharide composition determines the preferred route and entry kinetics of bacterial outer membrane vesicles into host cells

Outer membrane vesicles are microvesicles shed by Gram-negative bacteria and play important roles in immune priming and disease pathogenesis. However, our current mechanistic understanding of vesicle - host cell interactions is limited by a lack of methods to study the kinetics of vesicle entry and cargo delivery to host cells in real-time. Here, we describe a highly sensitive method to study the kinetics of vesicle entry into host cells in real-time using a genetically encoded probe targeted to vesicles. We found that route of vesicular uptake, and thus entry kinetics and efficiency of cargo release, are determined by the chemical composition of the bacterial lipopolysaccharide. The presence of O-antigen facilitates receptor-independent entry, which enhances both rate and efficiency of cargo uptake by host cells. Collectively, our findings highlight the chemical composition of the bacterial cell wall as a major determinant of secretion-independent delivery of virulence factors during Gram-negative infections.

microbiology↗