Deciphering the metabolic response of Mycobacterium tuberculosis to nitrogen stress.

© 2015 John Wiley & Sons Ltd.A key component to the success of Mycobacterium tuberculosis as a pathogen is the ability to sense and adapt metabolically to the diverse range of conditions encountered in vivo, such as oxygen tension, environmental pH and nutrient availability. Although nitrogen is an essential nutrient for every organism, little is known about the genes and pathways responsible for nitrogen assimilation in M. tuberculosis. In this study we have used transcriptomics and chromatin immunoprecipitation and high-throughput sequencing to address this. In response to nitrogen starvation, a total of 185 genes were significantly differentially expressed (96 up-regulated and 89 down regulated; 5% genome) highlighting several significant areas of metabolic change during nitrogen limitation such as nitrate/nitrite metabolism, aspartate metabolism and changes in cell wall biosynthesis. We identify GlnR as a regulator involved in the nitrogen response, controlling the expression of at least 33 genes in response to nitrogen limitation. We identify a consensus GlnR binding site and relate its location to known transcriptional start sites. We also show that the GlnR response regulator plays a very different role in M. tuberculosis to that in non-pathogenic mycobacteria, controlling genes involved in nitric oxide detoxification and intracellular survival instead of genes involved in nitrogen scavenging

AMBIENT: Active Modules for Bipartite Networks - using high-throughput transcriptomic data to dissect metabolic response

BACKGROUND: With the continued proliferation of high-throughput biological experiments, there is a pressing need for tools to integrate the data produced in ways that produce biologically meaningful conclusions. Many microarray studies have analysed transcriptomic data from a pathway perspective, for instance by testing for KEGG pathway enrichment in sets of upregulated genes. However, the increasing availability of species-specific metabolic models provides the opportunity to analyse these data in a more objective, system-wide manner. RESULTS: Here we introduce ambient (Active Modules for Bipartite Networks), a simulated annealing approach to the discovery of metabolic subnetworks (modules) that are significantly affected by a given genetic or environmental change. The metabolic modules returned by ambient are connected parts of the bipartite network that change coherently between conditions, providing a more detailed view of metabolic changes than standard approaches based on pathway enrichment. CONCLUSIONS: ambient is an effective and flexible tool for the analysis of high-throughput data in a metabolic context. The same approach can be applied to any system in which reactions (or metabolites) can be assigned a score based on some biological observation, without the limitation of predefined pathways. A Python implementation of ambient is available at http://www.theosysbio.bio.ic.ac.uk/ambient

Deciphering the response of Mycobacterium smegmatis to nitrogen stress using bipartite active modules.

Background The ability to adapt to environments with fluctuating nutrient availability is vital for bacterial survival. Although essential for growth, few nitrogen metabolism genes have been identified or fully characterised in mycobacteria and nitrogen stress survival mechanisms are unknown. Results A global transcriptional analysis of the mycobacterial response to nitrogen stress, showed a significant change in the differential expression of 16% of the Mycobacterium smegmatis genome. Gene expression changes were mapped onto the metabolic network using Active Modules for Bipartite Networks (AMBIENT) to identify metabolic pathways showing coordinated transcriptional responses to the stress. AMBIENT revealed several key features of the metabolic response not identified by KEGG enrichment alone. Down regulated reactions were associated with the general reduction in cellular metabolism as a consequence of reduced growth rate. Up-regulated modules highlighted metabolic changes in nitrogen assimilation and scavenging, as well as reactions involved in hydrogen peroxide metabolism, carbon scavenging and energy generation. Conclusions Application of an Active Modules algorithm to transcriptomic data identified key metabolic reactions and pathways altered in response to nitrogen stress, which are central to survival under nitrogen limiting environments

miR-10a is aberrantly overexpressed in Nucleophosmin1 mutated acute myeloid leukaemia and its suppression induces cell death

<p>Abstract</p> <p>Background</p> <p>Acute myeloid leukaemia (AML) with nucleophosmin-1 (<it>NPM1</it>) mutation is a major subtype of AML. The <it>NPM1 </it>mutation induces a myeloproliferative disorder, but evidence indicates that other insults are necessary for the development of AML. We utilised microRNA microarrays and functional assays to determine if microRNA dysregulation could be involved in the pathogenesis of in <it>NPM1 </it>mutated (<it>NPM1^mut</it>)-AML.</p> <p>Results</p> <p>We used a stringent locked nucleic acid (LNA) based microRNA microarray platform to profile bone marrow samples of patients with normal karyotype AML. A panel of five microRNAs dichotomised AML patients according to their <it>NPM1 </it>mutational status. miR-10a, let-7b and let-7c were significantly over-expressed, while miR-130a and miR-335 were under-expressed in <it>NPM1^mut</it>-AML when compared to <it>NPM1^wildtype</it>-AML. Of these, miR-10a is the most differentially expressed in <it>NPM1^mut</it>-AML versus <it>NPM1^wildtype</it>-AML (> 10 fold higher as confirmed by qRT-PCR). To investigate the functions of miR-10a, the OCI-AML3 cell line was utilised, which is the only commercially available cell line bearing <it>NPM1^mut</it>. OCI-AML3 cells were firstly demonstrated to have a similarly high miR-10a expression to primary <it>NPM1^mut</it>-AML patient samples. Inhibition of miR-10a expression by miRCURY LNA Inhibitors (Exiqon) in these cells resulted in increased cell death as assessed by MTS, cell cycle and Annexin-V assays and reduced clonogenic capacity, indicative of an involvement in leukaemic cell survival. <it>In silico </it>filtering of bioinformatically predicted targets of miR-10a identified a number of potential mRNA targets with annotated functions in haematopoiesis, cell growth and apoptosis. Lucferase reporter assays confirmed a number of these putative tumorogenic genes that are miR-10a suppressible including <it>KLF4 </it>and <it>RB1CC1</it>. This provides a potential mechanism for the pathogenic role of miR-10a in <it>NPM1^mut</it>-AML.</p> <p>Conclusions</p> <p>This study provides, for the first time, <it>in vitro </it>evidence of a pro-survival role of miR-10a in <it>NPM1^mut</it>-AML, that it may contribute to the pathogenesis of <it>NPM1^mut</it>-AML and identifies putative tumorogenic targets.</p

Experiences of Inpatient Bone Marrow Transplantation Nurses and Providers Using Electronic Symptom Reporting

Purpose To investigate the use of electronic patient-reported outcomes (PROs) to assess symptoms and how they can provide opportunities to clinicians to address symptoms in a timely manner to improve clinical care. As part of a larger study to evaluate whether providing standardized symptom reports to the medical team would decrease the time to treatment of reported symptoms in hematopoietic stem-cell transplant recipients, we assessed nurses’ and providers’ perceptions of electronic symptom reporting. Methods Semistructured interviews of RNs, MDs, NPs and PAs were conducted at an academic cancer center in the southeastern United States. Nurses’ and providers’ perceptions of electronic symptom reporting were explored. Interviews were audio-recorded, transcribed, and coded by two investigators to identify major themes. Results Fourteen RNs and seven providers (MDs, PAs, and NPs) participated in the interviews. Three main themes emerged from the interviews: electronic symptom reporting may improve assessment and care, integrating symptom reporting into nurse workflow presents difficulties, and there are barriers for completion of surveys. Conclusion The majority of nurses and providers believed that the inclusion of electronic symptom reporting in bone marrow transplantation inpatient units has the potential to improve care but that barriers to implementation remain

Impact of the COVID-19 pandemic on radiology appointments in a tertiary children's hospital: a retrospective study

In this retrospective observational study, we evaluated the impact of the COVID-19 pandemic in London on paediatric radiology activity, as a surrogate of overall hospital activity. We showed a large reduction in overall outpatient imaging activity: 49 250 records occurred in the 371 days post COVID-19 period compared with an expected 67 806 records pre COVID-19 period, representing 18 556 ‘missed’ records. Governmental restrictions were associated with reductions in activity, with the largest reduction in activity during tiers 3 and 4 restrictions. Rescheduling such missed outpatients’ appointments represents considerable resource planning and the associated clinical impact on paediatric healthcare remains to be determined

Investigation of the obscuring circumnuclear torus in the active galaxy Mrk231

Here we report on observations of powerful hydroxyl (OH) line emissions that trace the obscuring material within the circumnuclear environment of the galaxy Markarian 231. The hydroxyl (mega)-maser emission shows the characteristics of a rotating, dusty, molecular torus (or thick disk) located between 30 and 100 pc from the central engine. We now have a clear view of the physical conditions, the kinematics and the spatial structure of this material on intermediate size scales, confirming the main tenets of unification models.Comment: 10 pages, including 3 Figures, published in Nature Vol 421 2003; the published pdf--file and higher quality images are available at http://www.astro.rug.nl/~hrkloeck/np/pubmrk231.htm

Coronavirus (COVID-19) infection in children at a specialist centre: outcome and implications of underlying ‘high-risk’ comorbidities in a paediatric population

Background: There is evolving evidence of significant differences in severity and outcomes of coronavirus disease 2019 (COVID-19) in children compared to adults. Underlying medical conditions associated with increased risk of severe disease are based on adult data, but have been applied across all ages resulting in large numbers of families undertaking social ‘shielding’ (vulnerable group). We conducted a retrospective analysis of children with suspected COVID-19 at a Specialist Children’s Hospital to determine outcomes based on COVID-19 testing status and underlying health vulnerabilities. Methods: Routine clinical data were extracted retrospectively from the Institution’s Electronic Health Record system and Digital Research Environment for patients with suspected and confirmed COVID-19 diagnoses. Data were compared between Sars-CoV-2 positive and negative patients (CoVPos / CoVNeg respectively), and in relation to presence of underlying health vulnerabilities based on Public Health England guidance. Findings Between 1st March and 15th May 2020, 166 children (<18 years of age) presented to a specialist children’s hospital with clinical features of possible COVID-19 infection. 65 patients (39.2%) tested positive for SARS-CoV-2 virus. CoVPos patients were older (median 9 [0.9 - 14] years vs median 1 [0.1 - 5.7.5] years respectively, p<0.001). There was a significantly reduced proportion of vulnerable cases (47.7% vs 72.3%, p=0.002), but no difference in proportion of vulnerable patients requiring ventilation (61% vs 64.3%, p = 0.84) between CoVPos and CoVNeg groups. However, a significantly lower proportion of CoVPos patients required mechanical ventilation support compared to CoVNeg patients (27.7 vs 57.4%, p<0.001). Mortality was not significantly different between CoVPos and CoVNeg groups (1.5 vs 4% respectively, p=0.67) although there were no direct COVID-19 related deaths in this highly preselected paediatric population. Interpretation COVID-19 infection may be associated with severe disease in childhood presenting to a specialist hospital, but does not appear significantly different in severity to other causes of similar clinical presentations. In children presenting with pre-existing ‘COVID-19 vulnerable’ medical conditions at a specialist centre, there does not appear to be significantly increased risk of either contracting COVID-19 or severe complications, apart from those undergoing chemotherapy, who are over-represented. Competing Interest Statement The authors have declared no competing interest. Funding Statement: Funding RI is funded by a British Heart Foundation Research Fellowship Grant. HH is funded by NIHR UCLH BRC and HDRUK, NJS is funded by GOSHCC and HDRUK. Role of the funding source The study sponsor / funders had no role or influence in study design, in the collection, analysis, and interpretation of data, in the writing of the report or in the decision to submit the paper for publicatio

Introducing EMMIE: An evidence rating scale to encourage mixed-method crime prevention synthesis reviews

Objectives This short report describes the need for, and the development of, a coding system to distil the quality and coverage of systematic reviews of the evidence relating to crime prevention interventions. The starting point for the coding system concerns the evidence needs of policymakers and practitioners. Methods The coding scheme (EMMIE) proposed builds on previous scales that have been developed to assess the probity, coverage and utility of evidence both in health and criminal justice. It also draws on the principles of realist synthesis and review. Results The proposed EMMIE scale identifies five dimensions to which systematic reviews intended to inform crime prevention should speak. These are the Effect of intervention, the identification of the causal Mechanism(s) through which interventions are intended to work, the factors that Moderate their impact, the articulation of practical Implementation issues, and the Economic costs of intervention