50 research outputs found

    A stochastic model of Escherichia coli AI-2 quorum signal circuit reveals alternative synthesis pathways

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    Quorum sensing (QS) is an important determinant of bacterial phenotype. Many cell functions are regulated by intricate and multimodal QS signal transduction processes. The LuxS/AI-2 QS system is highly conserved among Eubacteria and AI-2 is reported as a ‘universal' signal molecule. To understand the hierarchical organization of AI-2 circuitry, a comprehensive approach incorporating stochastic simulations was developed. We investigated the synthesis, uptake, and regulation of AI-2, developed testable hypotheses, and made several discoveries: (1) the mRNA transcript and protein levels of AI-2 synthases, Pfs and LuxS, do not contribute to the dramatically increased level of AI-2 found when cells are grown in the presence of glucose; (2) a concomitant increase in metabolic flux through this synthesis pathway in the presence of glucose only partially accounts for this difference. We predict that ‘high-flux' alternative pathways or additional biological steps are involved in AI-2 synthesis; and (3) experimental results validate this hypothesis. This work demonstrates the utility of linking cell physiology with systems-based stochastic models that can be assembled de novo with partial knowledge of biochemical pathways

    The Antioxidant Protein Peroxiredoxin 4 Is Epigenetically Down Regulated in Acute Promyelocytic Leukemia

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    The antioxidant peroxiredoxin (PRDX) protein family comprises 6 members, which are implicated in a variety of cellular responses, including growth factor signal transduction. PRDX4 resides in the endoplasmic reticulum (ER), where it locally controls oxidative stress by reducing H2O2levels. We recently provided evidence for a regulatory function of PRDX4 in signal transduction from a myeloid growth factor receptor, the granulocyte colony-stimulating factor receptor (G-CSFR). Upon activation, the ligand-induced G-CSFR undergoes endocytosis and routes via the early endosomes where it physically interacts with ER-resident PRDX4. PRDX4 negatively regulates G-CSFR mediated signaling. Here, we investigated whether PRDX4 is affected in acute myeloid leukemia (AML); genomic alterations and expression levels of PRDX4 were investigated. We show that genomic abnormalities involving PRDX4 are rare in AML. However, we find a strong reduction in PRDX4 expression levels in acute promyelocytic leukemia (APL) compared to normal promyelocytes and different molecular subtypes of AML. Subsequently, the possible role of DNA methylation and histone modifications in silencing of PRDX4 in APLs was investigated. We show that the reduced expression is not due to methylation of the CpG island in the promoter region of PRDX4 but correlates with increased trimethylation of histone 3 lysine residue 27 (H3K27me3) and lysine residue 4 (H3K4me3) at the transcriptional start site (TSS) of PRDX4, indicative of a bivalent histone code involved in transcriptional silencing. These findings suggest that the control of G-CSF responses by the antioxidant protein PRDX4 may be perturbed in APL

    The Endoplasmic Reticulum Stress Response in Neuroprogressive Diseases: Emerging Pathophysiological Role and Translational Implications

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    The endoplasmic reticulum (ER) is the main cellular organelle involved in protein synthesis, assembly and secretion. Accumulating evidence shows that across several neurodegenerative and neuroprogressive diseases, ER stress ensues, which is accompanied by over-activation of the unfolded protein response (UPR). Although the UPR could initially serve adaptive purposes in conditions associated with higher cellular demands and after exposure to a range of pathophysiological insults, over time the UPR may become detrimental, thus contributing to neuroprogression. Herein, we propose that immune-inflammatory, neuro-oxidative, neuro-nitrosative, as well as mitochondrial pathways may reciprocally interact with aberrations in UPR pathways. Furthermore, ER stress may contribute to a deregulation in calcium homoeostasis. The common denominator of these pathways is a decrease in neuronal resilience, synaptic dysfunction and even cell death. This review also discusses how mechanisms related to ER stress could be explored as a source for novel therapeutic targets for neurodegenerative and neuroprogressive diseases. The design of randomised controlled trials testing compounds that target aberrant UPR-related pathways within the emerging framework of precision psychiatry is warranted

    The many organisational factors relevant to planning change in emergency care departments:A qualitative study to inform a cluster randomised controlled trial aiming to improve the management of patients with mild traumatic brain injuries

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    BACKGROUND:The Neurotrauma Evidence Translation (NET) Trial aims to design and evaluate the effectiveness of a targeted theory-and evidence-informed intervention to increase the uptake of evidence-based recommended practices for the management of patients who present to an emergency department (ED) with mild head injuries. When designing interventions to bring about change in organisational settings such as the ED, it is important to understand the impact of the context to ensure successful implementation of practice change. Few studies explicitly use organisational theory to study which factors are likely to be most important to address when planning change processes in the ED. Yet, this setting may have a unique set of organisational pressures that need to be taken into account when implementing new clinical practices. This paper aims to provide an in depth analysis of the organisational context in which ED management of mild head injuries and implementation of new practices occurs, drawing upon organisational level theory. METHODS:Semi-structured interviews were conducted with ED staff in Australia. The interviews explored the organisational context in relation to change and organisational factors influencing the management of patients presenting with mild head injuries. Two researchers coded the interview transcripts using thematic content analysis. The "model of diffusion in service organisations" was used to guide analyses and organisation of the results. RESULTS:Nine directors, 20 doctors and 13 nurses of 13 hospitals were interviewed. With regard to characteristics of the innovation (i.e. the recommended practices) the most important factor was whether they were perceived as being in line with values and needs. Tension for change (the degree to which stakeholders perceive the current situation as intolerable or needing change) was relatively low for managing acute mild head injury symptoms, and mixed for managing longer-term symptoms (higher change commitment, but relatively low change efficacy). Regarding implementation processes, the importance of (visible) senior leadership for all professions involved was identified as a critical factor. An unpredictable and hectic environment brings challenges in creating an environment in which team-based and organisational learning can thrive (system antecedents for innovation). In addition, the position of the ED as the entry-point of the hospital points to the relevance of securing buy-in from other units. CONCLUSIONS:We identified several organisational factors relevant to realising change in ED management of patients who present with mild head injuries. These factors will inform the intervention design and process evaluation in a trial evaluating the effectiveness of our implementation intervention
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