Genomic and experimental investigations into pneumococcal bacteriocins and their role in competition

Streptococcus pneumoniae ('the pneumococcus') is a frequent asymptomatic coloniser of the nasopharynx, from where it may disseminate to cause life-threatening infections including pneumonia, bacteraemia, and meningitis. Pneumococcal disease remains a leading cause of global mortality despite the use of safe and effective pneumococcal conjugate vaccines (PCVs). Bacteriocins are antimicrobial peptides that are produced by bacteria to target competitor bacteria within the ecological niche. Twenty pneumococcal bacteriocins have been characterised in silico, but their role in competition within the nasopharynx is not yet understood. In the first part of this project, I studied the distribution of bacteriocin genes in two large genomic datasets (>5,000 pneumococcal genomes in total) sampled from Iceland and Kenya. The distribution of some bacteriocins differed by location, between pneumococci recovered from carriage and disease, and between pneumococci recovered before and after the introduction of PCVs. These observations were largely explained by the association of bacteriocins with clonal complexes and suggested that there were different competition dynamics among pneumococci. A functional model of the streptococcin bacteriocins was generated using structural predictions. This informed further genomic studies, which observed genetic heterogeneity in the streptococcins. A dataset of >1,800 genomes from non-pneumococcal streptococci was screened for streptococcins, which were commonly harboured by viridans streptococci. There was evidence that the streptococcin diversification was driven by horizontal exchange between pneumococci and non-pneumococcal streptococci. In the final part of the project, the streptococcins were studied experimentally. A streptococcin toxin was isolated for the first time using a recombinant expression and purification method. The streptococcin was used in susceptibility assays against a panel of pneumococci and non-pneumococcal streptococci. Preliminary results suggested that the streptococcin had activity against some of the test strains. Results presented in this thesis expand our understanding of pneumococcal bacteriocins and will be used to inform further genomic and experimental studies.Open Acces

Persistent neuropsychiatric symptoms after COVID-19: a systematic review and meta-analysis.

The nature and extent of persistent neuropsychiatric symptoms after COVID-19 are not established. To help inform mental health service planning in the pandemic recovery phase, we systematically determined the prevalence of neuropsychiatric symptoms in survivors of COVID-19. For this pre-registered systematic review and meta-analysis (PROSPERO ID CRD42021239750), we searched MEDLINE, EMBASE, CINAHL and PsycINFO to 20 February 2021, plus our own curated database. We included peer-reviewed studies reporting neuropsychiatric symptoms at post-acute or later time-points after COVID-19 infection and in control groups where available. For each study, a minimum of two authors extracted summary data. For each symptom, we calculated a pooled prevalence using generalized linear mixed models. Heterogeneity was measured with I 2. Subgroup analyses were conducted for COVID-19 hospitalization, severity and duration of follow-up. From 2844 unique titles, we included 51 studies (n = 18 917 patients). The mean duration of follow-up after COVID-19 was 77 days (range 14-182 days). Study quality was most commonly moderate. The most prevalent neuropsychiatric symptom was sleep disturbance [pooled prevalence = 27.4% (95% confidence interval 21.4-34.4%)], followed by fatigue [24.4% (17.5-32.9%)], objective cognitive impairment [20.2% (10.3-35.7%)], anxiety [19.1% (13.3-26.8%)] and post-traumatic stress [15.7% (9.9-24.1%)]. Only two studies reported symptoms in control groups, both reporting higher frequencies in COVID-19 survivors versus controls. Between-study heterogeneity was high (I 2 = 79.6-98.6%). There was little or no evidence of differential symptom prevalence based on hospitalization status, severity or follow-up duration. Neuropsychiatric symptoms are common and persistent after recovery from COVID-19. The literature on longer-term consequences is still maturing but indicates a particularly high prevalence of insomnia, fatigue, cognitive impairment and anxiety disorders in the first 6 months after infection

Persistent neuropsychiatric symptoms after COVID-19: a systematic review and meta-analysis.

The nature and extent of persistent neuropsychiatric symptoms after COVID-19 are not established. To help inform mental health service planning in the pandemic recovery phase, we systematically determined the prevalence of neuropsychiatric symptoms in survivors of COVID-19. For this pre-registered systematic review and meta-analysis (PROSPERO ID CRD42021239750), we searched MEDLINE, EMBASE, CINAHL and PsycINFO to 20 February 2021, plus our own curated database. We included peer-reviewed studies reporting neuropsychiatric symptoms at post-acute or later time-points after COVID-19 infection and in control groups where available. For each study, a minimum of two authors extracted summary data. For each symptom, we calculated a pooled prevalence using generalized linear mixed models. Heterogeneity was measured with I 2. Subgroup analyses were conducted for COVID-19 hospitalization, severity and duration of follow-up. From 2844 unique titles, we included 51 studies (n = 18 917 patients). The mean duration of follow-up after COVID-19 was 77 days (range 14-182 days). Study quality was most commonly moderate. The most prevalent neuropsychiatric symptom was sleep disturbance [pooled prevalence = 27.4% (95% confidence interval 21.4-34.4%)], followed by fatigue [24.4% (17.5-32.9%)], objective cognitive impairment [20.2% (10.3-35.7%)], anxiety [19.1% (13.3-26.8%)] and post-traumatic stress [15.7% (9.9-24.1%)]. Only two studies reported symptoms in control groups, both reporting higher frequencies in COVID-19 survivors versus controls. Between-study heterogeneity was high (I 2 = 79.6-98.6%). There was little or no evidence of differential symptom prevalence based on hospitalization status, severity or follow-up duration. Neuropsychiatric symptoms are common and persistent after recovery from COVID-19. The literature on longer-term consequences is still maturing but indicates a particularly high prevalence of insomnia, fatigue, cognitive impairment and anxiety disorders in the first 6 months after infection

Global wealth disparities drive adherence to COVID-safe pathways in head and neck cancer surgery

Peer reviewe

Artificial cell research as a field that connects chemical, biological and philosophical questions

This review article discusses the interdisciplinary nature and implications of artificial cell research. It starts from two historical theories: Gánti's chemoton model and the autopoiesis theory by Maturana and Varela. They both explain the transition from chemical molecules to biological cells. These models exemplify two different ways in which disciplines of chemistry, biology and philosophy can profit from each other. In the chemoton model, conclusions from one disciplinary approach are relevant for the other disciplines. In contrast, the autopoiesis model itself (rather than its conclusions) is transferred from one discipline to the other. The article closes by underpinning the relevance of artificial cell research for philosophy with reference to the on-going philosophical debates on emergence, biological functions and biocentrism

Effect of remote ischaemic conditioning on clinical outcomes in patients with acute myocardial infarction (CONDI-2/ERIC-PPCI): a single-blind randomised controlled trial.

BACKGROUND: Remote ischaemic conditioning with transient ischaemia and reperfusion applied to the arm has been shown to reduce myocardial infarct size in patients with ST-elevation myocardial infarction (STEMI) undergoing primary percutaneous coronary intervention (PPCI). We investigated whether remote ischaemic conditioning could reduce the incidence of cardiac death and hospitalisation for heart failure at 12 months. METHODS: We did an international investigator-initiated, prospective, single-blind, randomised controlled trial (CONDI-2/ERIC-PPCI) at 33 centres across the UK, Denmark, Spain, and Serbia. Patients (age >18 years) with suspected STEMI and who were eligible for PPCI were randomly allocated (1:1, stratified by centre with a permuted block method) to receive standard treatment (including a sham simulated remote ischaemic conditioning intervention at UK sites only) or remote ischaemic conditioning treatment (intermittent ischaemia and reperfusion applied to the arm through four cycles of 5-min inflation and 5-min deflation of an automated cuff device) before PPCI. Investigators responsible for data collection and outcome assessment were masked to treatment allocation. The primary combined endpoint was cardiac death or hospitalisation for heart failure at 12 months in the intention-to-treat population. This trial is registered with ClinicalTrials.gov (NCT02342522) and is completed. FINDINGS: Between Nov 6, 2013, and March 31, 2018, 5401 patients were randomly allocated to either the control group (n=2701) or the remote ischaemic conditioning group (n=2700). After exclusion of patients upon hospital arrival or loss to follow-up, 2569 patients in the control group and 2546 in the intervention group were included in the intention-to-treat analysis. At 12 months post-PPCI, the Kaplan-Meier-estimated frequencies of cardiac death or hospitalisation for heart failure (the primary endpoint) were 220 (8·6%) patients in the control group and 239 (9·4%) in the remote ischaemic conditioning group (hazard ratio 1·10 [95% CI 0·91-1·32], p=0·32 for intervention versus control). No important unexpected adverse events or side effects of remote ischaemic conditioning were observed. INTERPRETATION: Remote ischaemic conditioning does not improve clinical outcomes (cardiac death or hospitalisation for heart failure) at 12 months in patients with STEMI undergoing PPCI. FUNDING: British Heart Foundation, University College London Hospitals/University College London Biomedical Research Centre, Danish Innovation Foundation, Novo Nordisk Foundation, TrygFonden

Generative AI technologies applied to ecosystems and the environment: a scoping review

This report provides a scoping review of the literature on the ways that novel generative artificial intelligence (AI) tools are being applied to living things and other elements of ecosystems and the natural environment. The paper outlines several areas where generative AI is being deployed in new research projects and industry applications. These include animal communication and agriculture and plant cultivation, as well as environmental sustainability, biodiversity, climate change and nature conservation initiatives. The paper also details some of the negative environmental costs and ethical issues associated with the manufacture, training and infrastructure that support generative AI and large language models more generally

Risk and protective factors for self-harm in adolescents and young adults: an umbrella review of systematic reviews

We conducted an umbrella review to synthesise the evidence from systematic reviews and meta-analyses that examined the risk and protective factors for self-harm in young people. We searched six different databases and used the AMSTAR-2 checklist for quality assessment. The importance of each risk and protective factor was determined based on (1) the number of times it was identified by general reviews examining any risk or protective factor, and (2) the effect sizes from meta-analyses. There were 61 systematic reviews included in this review. The most frequently identified risk factors for self-harm in young people included childhood abuse, depression/anxiety, bullying, trauma, psychiatric illnesses, substance use/abuse, parental divorce, poor family relationships, lack of friends, and exposure to self-harm behaviour in others. The risk factors with the strongest evidence for an association with self-harm were behavioural disorders, personality disorders and depression or anxiety. There was a dearth of systematic reviews examining protective factors but good family/friend relationships were most frequently identified. There was also evidence to show that non-suicidal and suicidal self-harm shared many of the same risk factors. Clinicians and other professionals who work with young people should be particularly cognisant of the psychiatric and adverse life event risk factors as well as the substance use, education-related and individual-level (e.g. being LGB) risk factors for self-harm. Knowledge of risk factors for self-harm can potentially be used to inform the design and implementation of prevention measures and further research is needed on the protective factors for self-harm.</p

Risk and protective factors for self-harm in adolescents and young adults: an umbrella review of systematic reviews

We conducted an umbrella review to synthesise the evidence from systematic reviews and meta-analyses that examined the risk and protective factors for self-harm in young people. We searched six different databases and used the AMSTAR-2 checklist for quality assessment. The importance of each risk and protective factor was determined based on (1) the number of times it was identified by general reviews examining any risk or protective factor, and (2) the effect sizes from meta-analyses. There were 61 systematic reviews included in this review. The most frequently identified risk factors for self-harm in young people included childhood abuse, depression/anxiety, bullying, trauma, psychiatric illnesses, substance use/abuse, parental divorce, poor family relationships, lack of friends, and exposure to self-harm behaviour in others. The risk factors with the strongest evidence for an association with self-harm were behavioural disorders, personality disorders and depression or anxiety. There was a dearth of systematic reviews examining protective factors but good family/friend relationships were most frequently identified. There was also evidence to show that non-suicidal and suicidal self-harm shared many of the same risk factors. Clinicians and other professionals who work with young people should be particularly cognisant of the psychiatric and adverse life event risk factors as well as the substance use, education-related and individual-level (e.g. being LGB) risk factors for self-harm. Knowledge of risk factors for self-harm can potentially be used to inform the design and implementation of prevention measures and further research is needed on the protective factors for self-harm.</p